resources: - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.internationalgenome.org/ - contact_type: email value: info@1000genomes.org id: ebi label: International Genome Sample Resource (EMBL-EBI) creation_date: '2025-09-04T00:00:00Z' description: The International Genome Sample Resource (IGSR) maintains and shares the open human genetic variation resources built by the 1000 Genomes Project, updates them to current reference assemblies (e.g., GRCh38), and incorporates new data sets and populations. IGSR provides a searchable data portal, bulk download methods, and guidance for proper reuse and citation. domains: - genomics homepage_url: https://www.internationalgenome.org/ id: 1000genomes last_modified_date: '2025-09-09T00:00:00Z' layout: resource_detail license: id: https://www.internationalgenome.org/IGSR_disclaimer label: IGSR Data Disclaimer / Terms of Use name: 1000 Genomes Project (IGSR) products: - category: GraphicalInterface description: Main IGSR website with links to data portal, help, and announcements format: http id: 1000genomes.portal name: IGSR Portal product_url: https://www.internationalgenome.org/ - category: GraphicalInterface description: Interactive data portal to browse IGSR/1000 Genomes data by sample, population, technology, data type, and collection format: http id: 1000genomes.data-portal name: IGSR Data Portal product_url: https://www.internationalgenome.org/data-portal - category: Product description: Primary FTP site hosting IGSR and 1000 Genomes Project data collections and releases format: http id: 1000genomes.ftp name: IGSR FTP Site product_url: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/ - category: DocumentationProduct description: Instructions for accessing IGSR data via Globus or Aspera (recommended for bulk transfers) format: http id: 1000genomes.globus-docs name: Globus Access Instructions product_url: https://www.internationalgenome.org/faq/what-tools-can-i-use-to-download-igsr-data - category: Product description: Mirror of original 1000 Genomes Project data at NCBI format: http id: 1000genomes.ncbi-mirror name: NCBI Mirror product_url: https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/ - category: Product description: The EPA has developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Since its inception, the AOP-DB has been developed with the aim of integrating AOP molecular target information with other publicly available datasets to facilitate computational analyses of AOP information. id: aop-db.data name: AOP-DB Data original_source: - aop-wiki - ctd - toxcast - disgenet - ncbigene - string - 1000genomes - ensembl - gwascatalog product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 secondary_source: - aop-db taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: support@4dnucleome.org - contact_type: url value: https://data.4dnucleome.org/help/about/contact-us label: 4D Nucleome Network Data Coordination and Integration Center (DCIC) creation_date: '2025-06-10T00:00:00Z' curators: - category: Individual contact_details: - contact_type: github value: caufieldjh label: Harry Caufield description: The 4D Nucleome (4DN) Network aims to understand the principles underlying nuclear organization in space and time (the 4th dimension). The 4DN Data Portal provides a platform to search, visualize, and download nucleomics data generated by the 4DN Network and other reference datasets. domains: - genomics - biological systems - biomedical - medical imaging homepage_url: https://data.4dnucleome.org/ id: 4dn last_modified_date: '2025-06-12T20:16:27Z' layout: resource_detail license: id: https://data.4dnucleome.org/help/user-guide/faq#downloading-and-using-data-from-the-4dn-data-portal label: Varies name: 4D Nucleome Data Portal products: - category: DataProduct description: A comprehensive collection of Hi-C datasets generated by the 4DN Network and other reference datasets, available for search, visualization, and download. format: tsv id: 4dn.hic name: 4DN Hi-C Datasets product_url: https://data.4dnucleome.org/hic-data-overview - category: DataProduct description: A collection of microscopy datasets, including super-resolution microscopy and chromatin tracing data, for visualizing nuclear organization. format: tsv id: 4dn.microscopy name: 4DN Microscopy Datasets product_url: https://data.4dnucleome.org/microscopy-data-overview - category: DataProduct description: A specialized collection of chromatin tracing datasets that provide insights into the 3D organization of chromatin in the nucleus. format: tsv id: 4dn.chromatin_tracing name: 4DN Chromatin Tracing Datasets product_url: https://data.4dnucleome.org/resources/data-collections/chromatin-tracing-datasets - category: GraphicalInterface description: A web-based visualization tool for exploring and comparing genomic data, particularly suited for Hi-C and other 4DN datasets. id: 4dn.higlass name: HiGlass product_url: https://data.4dnucleome.org/tools/visualization - category: ProcessProduct description: A cloud-based Jupyter environment for analyzing 4DN data without downloading it, including example notebooks for data exploration. id: 4dn.jupyterhub name: 4DN JupyterHub product_url: https://data.4dnucleome.org/tools/jupyterhub - category: ProcessProduct description: A tool for entering and accessing microscope metadata with standardized formats. id: 4dn.micrometa name: Micro Meta App product_url: https://data.4dnucleome.org/tools/micro-meta-app - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg publications: - authors: - Dekker J - Belmont AS - Guttman M - Leshyk VO - Lis JT - Lomvardas S - Mirny LA - et al. doi: doi:10.1038/nature23884 id: https://doi.org/10.1038/nature23884 journal: Nature preferred: true title: The 4D Nucleome Project year: '2017' - authors: - Reiff SB - Schroeder AJ - Kirli K - Cosolo A - Bakken TE - Hodge RD - Cortés-Ciriano I - et al. doi: doi:10.1038/s41467-022-29697-4 id: https://doi.org/10.1038/s41467-022-29697-4 journal: Nature Communications title: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data year: '2022' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: 5SRNAdb (5S rRNA Database) is a curated repository of unique full-length 5S ribosomal RNA sequences and genes across Bacteria, Archaea, and Eukaryota (cytoplasmic and organellar), providing alignments, secondary structure diagrams, taxonomic browsing, and downloadable custom or global alignments for comparative and structural studies. domains: - genomics - biological systems homepage_url: http://www.combio.pl/5srnadb/ id: 5srrnadb last_modified_date: '2025-09-10T00:00:00Z' layout: resource_detail name: 5SRNAdb products: - category: GraphicalInterface description: Web portal with search, taxonomic browser, interactive alignments, and secondary structure visualizations format: fasta id: 5srrnadb.portal name: 5SRNAdb Portal product_url: http://www.combio.pl/5srnadb/ - category: Product description: Archaea 5S rRNA sequences (non-structural alignment) in FASTA format format: fasta id: 5srrnadb.downloads.archaea.sequences name: Archaea Sequences FASTA product_file_size: 49552 product_url: http://www.combio.pl/rrna/static/download/Archaea.fasta - category: Product description: Archaea 5S rRNA structural alignment (FASTA with secondary structure annotation) format: fasta id: 5srrnadb.downloads.archaea.structural name: Archaea Structural Alignment FASTA product_file_size: 56822 product_url: http://www.combio.pl/rrna/static/download/Archaea.ss.fasta - category: Product description: Bacteria 5S rRNA sequences (non-structural alignment) in FASTA format format: fasta id: 5srrnadb.downloads.bacteria.sequences name: Bacteria Sequences FASTA product_file_size: 1109201 product_url: http://www.combio.pl/rrna/static/download/Bacteria.fasta - category: Product description: Bacteria 5S rRNA structural alignment (FASTA with secondary structure annotation) format: fasta id: 5srrnadb.downloads.bacteria.structural name: Bacteria Structural Alignment FASTA product_file_size: 1483731 product_url: http://www.combio.pl/rrna/static/download/Bacteria.ss.fasta - category: Product description: Eukaryota 5S rRNA sequences (non-structural alignment) in FASTA format format: fasta id: 5srrnadb.downloads.eukaryota.sequences name: Eukaryota Sequences FASTA product_file_size: 431005 product_url: http://www.combio.pl/rrna/static/download/Eukaryota.fasta - category: Product description: Eukaryota 5S rRNA structural alignment (FASTA with secondary structure annotation) format: fasta id: 5srrnadb.downloads.eukaryota.structural name: Eukaryota Structural Alignment FASTA product_file_size: 497661 product_url: http://www.combio.pl/rrna/static/download/Eukaryota.ss.fasta - category: Product description: Plastids 5S rRNA sequences (non-structural alignment) in FASTA format format: fasta id: 5srrnadb.downloads.plastids.sequences name: Plastids Sequences FASTA product_file_size: 127316 product_url: http://www.combio.pl/rrna/static/download/Plastids.fasta - category: Product description: Plastids 5S rRNA structural alignment (FASTA with secondary structure annotation) format: fasta id: 5srrnadb.downloads.plastids.structural name: Plastids Structural Alignment FASTA product_file_size: 153189 product_url: http://www.combio.pl/rrna/static/download/Plastids.ss.fasta - category: Product description: Mitochondria 5S rRNA sequences (non-structural alignment) in FASTA format format: fasta id: 5srrnadb.downloads.mitochondria.sequences name: Mitochondria Sequences FASTA product_file_size: 16156 product_url: http://www.combio.pl/rrna/static/download/Mitochondria.fasta - category: Product description: Mitochondria 5S rRNA structural alignment (FASTA with secondary structure annotation) format: fasta id: 5srrnadb.downloads.mitochondria.structural name: Mitochondria Structural Alignment FASTA product_file_size: 18634 product_url: http://www.combio.pl/rrna/static/download/Mitochondria.ss.fasta - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - doi: 10.1093/nar/gkv1081 id: doi:10.1093/nar/gkv1081 journal: Nucleic Acids Research preferred: true title: '5SRNAdb: an information resource for 5S ribosomal RNAs' year: '2016' taxon: - NCBITaxon:2 - NCBITaxon:2157 - NCBITaxon:2759 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://aact.ctti-clinicaltrials.org/contactus label: Clinical Trials Transformation Initiative (CTTI) creation_date: '2025-10-30T00:00:00Z' description: AACT is a publicly available relational PostgreSQL database that contains all protocol and result data elements from every study registered in ClinicalTrials.gov, refreshed daily from the ClinicalTrials.gov registry. domains: - clinical - public health - translational homepage_url: https://aact.ctti-clinicaltrials.org/ id: aact infores_id: aact last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail name: Aggregate Analysis of ClinicalTrials.gov (AACT) Database products: - category: GraphicalInterface description: Web-based SQL query playground for running queries on AACT data directly from the browser format: http id: aact.playground name: AACT Playground original_source: - aact product_url: https://aact.ctti-clinicaltrials.org/playground - category: Product description: Cloud-based PostgreSQL database with daily refreshed clinical trial data, accessible via standard PostgreSQL clients format: postgres id: aact.database name: AACT Cloud Database original_source: - clinicaltrialsgov product_url: https://aact.ctti-clinicaltrials.org/connect - category: Product description: Static downloadable copies of the complete AACT database format: postgres id: aact.downloads name: AACT Database Downloads original_source: - clinicaltrialsgov product_url: https://aact.ctti-clinicaltrials.org/downloads - category: DocumentationProduct description: Complete database schema documentation showing table structure and relationships id: aact.schema name: AACT Database Schema original_source: - aact product_url: https://aact.ctti-clinicaltrials.org/schema - category: DocumentationProduct description: Data dictionary with detailed information about all AACT data elements and their relationship to ClinicalTrials.gov definitions id: aact.dictionary name: AACT Data Dictionary original_source: - aact product_url: https://aact.ctti-clinicaltrials.org/data_dictionary repository: https://github.com/ctti-clinicaltrials/aact synonyms: - AACT - Aggregate Analysis of ClinicalTrial.gov taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: achilles@broadinstitute.org - contact_type: url value: https://depmap.org/portal/achilles/ id: broad label: Project Achilles, Broad Institute creation_date: '2025-07-08T00:00:00Z' curators: - category: Organization contact_details: - contact_type: url value: https://depmap.org/ label: DepMap description: Project Achilles is a systematic effort aimed at identifying and cataloging gene essentiality across hundreds of genomically characterized cancer cell lines. Achilles uses genome-scale RNAi and CRISPR-Cas9 genetic perturbation reagents to silence or knockout individual genes and identify those genes that affect cell survival. domains: - biomedical - genomics - health homepage_url: https://depmap.org/portal/achilles/ id: achilles last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://depmap.org/portal/terms/ label: DepMap Terms of Use name: Project Achilles products: - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - authors: - Tsherniak A - Vazquez F - Montgomery PG - Weir BA - Kryukov G - Cowley GS doi: 10.1016/j.cell.2017.06.010 id: doi:10.1016/j.cell.2017.06.010 journal: Cell title: Defining a Cancer Dependency Map year: '2017' taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: alpha.tom.kodamullil@scai.fraunhofer.de - contact_type: github value: akodamullil label: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 creation_date: '2025-09-29T00:00:00Z' description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining. domains: - biomedical homepage_url: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO id: ado last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Alzheimer's Disease Ontology products: - category: OntologyProduct description: Alzheimer's Disease Ontology in OWL format format: owl id: ado.owl name: ado.owl product_file_size: 1166665 product_url: http://purl.obolibrary.org/obo/ado.owl repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO - activity_status: active category: DataSource contacts: - category: Individual label: Juan M. Banda - category: Individual label: Lee Evans - category: Individual label: Rami S. Vanguri - category: Individual label: Nicholas P. Tatonetti - category: Individual label: Patrick B. Ryan creation_date: '2025-10-30T00:00:00Z' description: AEOLUS (Adverse Event Open Learning through Universal Standardization) is a curated and standardized version of the FDA Adverse Event Reporting System (FAERS) that removes duplicate case records and applies standardized vocabularies, with drug names mapped to RxNorm concepts and outcomes mapped to SNOMED-CT concepts, providing pre-computed summary statistics about drug-outcome relationships. domains: - clinical - pharmacology - drug discovery - health - biomedical homepage_url: https://datadryad.org/stash/dataset/doi:10.5061/dryad.8q0s4 id: aeolus infores_id: aeolus last_modified_date: '2025-11-22T00:00:00Z' layout: resource_detail name: Adverse Event Open Learning through Universal Standardization (AEOLUS) products: - category: Product description: Standardized and deduplicated version of FDA FAERS data with drug names mapped to RxNorm and adverse event outcomes mapped to SNOMED-CT, including pre-computed summary statistics for drug-outcome relationships. id: aeolus.standardized_data name: AEOLUS Standardized FAERS Data original_source: - faers - aeolus product_url: https://datadryad.org/stash/dataset/doi:10.5061/dryad.8q0s4 publications: - authors: - Banda JM - Evans L - Vanguri RS - Tatonetti NP - Ryan PB doi: 10.1038/sdata.2016.26 id: doi:10.1038/sdata.2016.26 journal: Scientific Data title: A curated and standardized adverse drug event resource to accelerate drug safety research year: '2016' synonyms: - AEOLUS taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mcmelek@msn.com - contact_type: github value: Melek-C label: Melek Chaouch orcid: 0000-0001-5868-4204 creation_date: '2025-09-29T00:00:00Z' description: AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms. domains: - biological systems homepage_url: https://github.com/h3abionet/afpo id: afpo last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: African Population Ontology products: - category: OntologyProduct description: The main ontology in OWL. Contains all MP terms and links to other OBO ontologies format: owl id: afpo.owl name: AfPO (OWL edition) product_file_size: 96804 product_url: http://purl.obolibrary.org/obo/afpo.owl - category: OntologyProduct description: A direct translation of the AfPO (OWL edition) into OBO format format: obo id: afpo.obo name: AfPO (OBO edition) product_url: http://purl.obolibrary.org/obo/afpo.obo warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: A direct translation of the AfPO (OWL edition) into OBOGraph JSON format format: json id: afpo.json name: AfPO (obographs JSON edition) product_url: http://purl.obolibrary.org/obo/afpo.json warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/h3abionet/afpo - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: m.a.laporte@cgiar.org - contact_type: github value: marieALaporte label: Marie-Ang lique Laporte orcid: 0000-0002-8461-9745 creation_date: '2025-09-29T00:00:00Z' description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments domains: - agriculture homepage_url: https://github.com/AgriculturalSemantics/agro id: agro last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Agronomy Ontology products: - category: OntologyProduct description: Contains all AgrO terms and links to other relevant ontologies. format: owl id: agro.owl name: AgrO product_file_size: 463598 product_url: http://purl.obolibrary.org/obo/agro.owl repository: https://github.com/AgriculturalSemantics/agro - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: entiminae@gmail.com - contact_type: github value: JCGiron label: Jennifer C. Gir n orcid: 0000-0002-0851-6883 creation_date: '2025-09-29T00:00:00Z' description: The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. 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activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.alliancegenome.org/contact-us label: Alliance of Genome Resources creation_date: '2025-08-13T00:00:00Z' description: The Alliance of Genome Resources (Alliance) is a collaborative platform integrating model organism knowledge (FlyBase, MGD, RGD, SGD, WormBase, Xenbase, ZFIN) and Gene Ontology Consortium annotations to provide harmonized comparative genomics, gene function, phenotype, disease association, expression, orthology, and variant data for cross-species research and translation. domains: - genomics homepage_url: https://www.alliancegenome.org/ id: alliance last_modified_date: '2025-09-03T00:00:00Z' layout: resource_detail license: id: https://www.alliancegenome.org/privacy-warranty-licensing label: Alliance Data Licensing & Privacy name: Alliance of Genome Resources products: - category: GraphicalInterface description: Primary web portal for integrated cross-species search and exploration of genes, phenotypes, disease models, expression, variants, and orthology summaries format: http id: alliance.portal name: Alliance Web Portal original_source: - 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kg-monarch - category: GraphProduct description: KGX graph package for Alliance of Genome Resources (build alliance_8.2.0_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.alliance.graph name: Translator Alliance KGX Graph original_source: - alliance product_url: https://stars.renci.org/var/translator/releases/alliance/2025_12_15/ secondary_source: - translator taxon: - NCBITaxon:6239 - NCBITaxon:7227 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: EpistasisLab - contact_type: url value: https://alzkb.ai/ label: Joseph D Romano creation_date: '2025-06-24T00:00:00Z' curators: - category: Individual contact_details: - contact_type: github value: caufieldjh label: Harry Caufield description: A knowledge base for AI research in Alzheimer Disease, based on graph databases. domains: - neuroscience - biomedical - health - drug discovery - genomics evaluation_page: resource/alzkb/alzkb_eval_automated.html homepage_url: https://alzkb.ai/Home id: alzkb last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: Alzheimer's Knowledge Base products: - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet publications: - authors: - Joseph D Romano - Van Truong - Rachit Kumar - Mythreye Venkatesan - Britney E Graham - Yun Hao - Nick Matsumoto - Xi Li - Zhiping Wang - Marylyn D Ritchie - Li Shen - Jason H Moore doi: doi:10.2196/46777 id: https://doi.org/10.2196/46777 journal: Journal of Medical Internet Research preferred: true title: 'The Alzheimer''s Knowledge Base: A Knowledge Graph for Alzheimer Disease Research' year: '2024' repository: https://github.com/EpistasisLab/AlzKB taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: hescriva@obs-banyuls.fr - contact_type: github value: hescriva label: Hector Escriva orcid: 0000-0001-7577-5028 creation_date: '2025-09-29T00:00:00Z' description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). domains: - anatomy and development homepage_url: https://github.com/EBISPOT/amphx_ontology id: amphx last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: The Amphioxus Development and Anatomy Ontology products: - category: OntologyProduct description: The Amphioxus Development and Anatomy Ontology in OWL format format: owl id: amphx.owl name: amphx.owl product_file_size: 13761 product_url: http://purl.obolibrary.org/obo/amphx.owl - category: OntologyProduct description: The Amphioxus Development and Anatomy Ontology in OBO format format: obo id: amphx.obo name: amphx.obo product_file_size: 8608 product_url: http://purl.obolibrary.org/obo/amphx.obo repository: https://github.com/EBISPOT/amphx_ontology - activity_status: active category: Aggregator collection: - aop contacts: - category: Organization contact_details: - contact_type: url value: https://www.epa.gov/ label: U.S. Environmental Protection Agency (EPA) creation_date: '2025-06-24T00:00:00Z' description: The Adverse Outcome Pathway Database (AOP-DB) is an EPA-developed integrative knowledgebase that connects chemicals and stressors to molecular initiating events, key events across biological organization levels, and adverse outcomes relevant to human health and ecological risk assessment. It harmonizes data from toxicology, high‑throughput screening, pathway, gene/protein, and phenotype resources to enable computational toxicology, mode-of-action analysis, and predictive risk prioritization. domains: [] homepage_url: https://www.epa.gov/healthresearch/adverse-outcome-pathway-database-aop-db id: aop-db last_modified_date: '2025-09-04T00:00:00Z' layout: resource_detail license: id: https://www.epa.gov/healthresearch/adverse-outcome-pathway-database-aop-db label: EPA AOP-DB Use & Access name: AOP-DB products: - category: GraphicalInterface description: Public information portal describing the AOP-DB scope, data integration approach, and access points format: http id: aop-db.portal name: AOP-DB Information Portal original_source: - aop-db product_url: https://www.epa.gov/healthresearch/adverse-outcome-pathway-database-aop-db - category: Product description: The EPA has developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Since its inception, the AOP-DB has been developed with the aim of integrating AOP molecular target information with other publicly available datasets to facilitate computational analyses of AOP information. id: aop-db.data name: AOP-DB Data original_source: - aop-wiki - ctd - toxcast - disgenet - ncbigene - string - 1000genomes - ensembl - gwascatalog product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 secondary_source: - aop-db - category: DocumentationProduct description: The EPA Adverse Outcome Pathway Database (Aop-DB) Application User Manual format: pdf id: aop-db.manual name: Manual original_source: - aop-db product_url: https://ordspub.epa.gov/ords/eims/eimscomm.getfile?p_download_id=543383 warnings: - File was not able to be retrieved when checked on 2025-12-07_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-05_ No Content-Length header found - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ HTTPSConnectionPool(host='ordspub.epa.gov', port=443)_ Max retries exceeded with url_ /ords/eims/eimscomm.getfile?p_download_id=543383 (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 101] Network is unreachable')) - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ HTTPSConnectionPool(host='ordspub.epa.gov', port=443)_ Max retries exceeded with url_ /ords/eims/eimscomm.getfile?p_download_id=543383 (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 101] Network is unreachable')) - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ HTTPSConnectionPool(host='ordspub.epa.gov', port=443)_ Max retries exceeded with url_ /ords/eims/eimscomm.getfile?p_download_id=543383 (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 101] Network is unreachable')) - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ HTTPSConnectionPool(host='ordspub.epa.gov', port=443)_ Max retries exceeded with url_ /ords/eims/eimscomm.getfile?p_download_id=543383 (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 101] Network is unreachable')) - File was not able to be retrieved when checked on 2025-10-28_ Error connecting to URL_ HTTPSConnectionPool(host='ordspub.epa.gov', port=443)_ Max retries exceeded with url_ /ords/eims/eimscomm.getfile?p_download_id=543383 (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 101] Network is unreachable')) - File was not able to be retrieved when checked on 2025-10-27_ Error connecting to URL_ HTTPSConnectionPool(host='ordspub.epa.gov', port=443)_ Max retries exceeded with url_ /ords/eims/eimscomm.getfile?p_download_id=543383 (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 101] Network is unreachable')) - File was not able to be retrieved when checked on 2025-10-08_ Error connecting to URL_ HTTPSConnectionPool(host='ordspub.epa.gov', port=443)_ Max retries exceeded with url_ /ords/eims/eimscomm.getfile?p_download_id=543383 (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 101] Network is unreachable')) - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet taxon: - NCBITaxon:9606 - activity_status: active category: DataSource collection: - aop contacts: - category: Organization contact_details: - contact_type: url value: https://aopwiki.org/info_pages/10 label: AOP-Wiki Coordination Group creation_date: '2025-09-04T00:00:00Z' description: The AOP-Wiki is the primary collaborative authoring and curation interface for the Adverse Outcome Pathway Knowledge Base (AOP-KB). It enables the community to develop, review, browse, and export Adverse Outcome Pathways (AOPs) linking molecular initiating events through key events to adverse outcomes relevant to human and ecological risk assessment. Structured exports (XML and tabular subsets) support computational toxicology, ontology mapping, and integration into predictive assessment workflows. domains: [] homepage_url: https://aopwiki.org/ id: aop-wiki last_modified_date: '2025-09-04T00:00:00Z' layout: resource_detail license: id: https://aopwiki.org/ label: Varies name: AOP-Wiki products: - category: GraphicalInterface description: Web portal for browsing, authoring, and reviewing AOPs, key events (KEs), key event relationships (KERs), stressors, and supporting documentation format: http id: aop-wiki.portal name: AOP-Wiki Portal original_source: - aop-wiki product_url: https://aopwiki.org/ - category: Product description: Quarterly permanent XML snapshot (versioned) of AOP-Wiki content suitable for citation and archival use format: xml id: aop-wiki.quarterly-xml name: AOP-Wiki Quarterly XML Snapshot original_source: - aop-wiki product_url: https://aopwiki.org/downloads warnings: - File was not able to be retrieved when checked on 2026-02-13_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-04_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - category: Product description: Nightly XML export (rolling) containing latest AOP-Wiki content (overwritten daily) format: xml id: aop-wiki.nightly-xml name: AOP-Wiki Nightly XML Export original_source: - aop-wiki product_file_size: 9933339 product_url: https://aopwiki.org/downloads/aop-wiki-xml.gz warnings: - File was not able to be retrieved when checked on 2026-02-13_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads/aop-wiki-xml.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads/aop-wiki-xml.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - category: Product description: Tab-delimited subset listing AOP to Key Event (including MIE, intermediate KE, and Adverse Outcome) associations format: tsv id: aop-wiki.ke-overview name: AOP-Wiki Key Events TSV original_source: - aop-wiki product_file_size: 238066 product_url: https://aopwiki.org/downloads/aop_ke_mie_ao.tsv warnings: - File was not able to be retrieved when checked on 2026-02-13_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads/aop_ke_mie_ao.tsv (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads/aop_ke_mie_ao.tsv (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - category: Product description: Tab-delimited subset listing Key Event Relationships (KERs) with evidence and quantitative understanding indicators format: tsv id: aop-wiki.ker name: AOP-Wiki Key Event Relationships TSV original_source: - aop-wiki product_file_size: 189389 product_url: https://aopwiki.org/downloads/aop_ke_ker.tsv warnings: - File was not able to be retrieved when checked on 2026-02-13_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads/aop_ke_ker.tsv (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads/aop_ke_ker.tsv (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - category: Product description: Tab-delimited subset of Key Event Components (actions, biological objects/processes with ontology references) format: tsv id: aop-wiki.ke-components name: AOP-Wiki Key Event Components TSV original_source: - aop-wiki product_file_size: 291132 product_url: https://aopwiki.org/downloads/aop_ke_ec.tsv warnings: - File was not able to be retrieved when checked on 2026-02-13_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads/aop_ke_ec.tsv (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /downloads/aop_ke_ec.tsv (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - category: Product description: Per-AOP dynamic XML feed accessible via each AOP page (XML button) for up-to-minute content retrieval format: xml id: aop-wiki.dynamic-aop-xml name: AOP-Wiki Dynamic AOP XML Feed original_source: - aop-wiki product_url: https://aopwiki.org/aops warnings: - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-02-13_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /aops (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /aops (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - category: DocumentationProduct description: This document is the AOP Developers' Handbook supplement to the Guidance Document for developing and assessing Adverse Outcome Pathways (AOPs). The Guidance Document provides a historical background for the AOP development programme, and outlines the elements required to construct an AOP as well as the principles of the AOP framework. format: http id: aop-wiki.devhandbook name: AOP Developers' Handbook product_url: https://aopwiki.org/handbooks/4 warnings: - File was not able to be retrieved when checked on 2026-02-13_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /handbooks/4 (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-04_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /handbooks/4 (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='aopwiki.org', port=443)_ Max retries exceeded with url_ /handbooks/4 (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - category: Product description: The EPA has developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Since its inception, the AOP-DB has been developed with the aim of integrating AOP molecular target information with other publicly available datasets to facilitate computational analyses of AOP information. id: aop-db.data name: AOP-DB Data original_source: - aop-wiki - ctd - toxcast - disgenet - ncbigene - string - 1000genomes - ensembl - gwascatalog product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 secondary_source: - aop-db taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: stacia@stanford.edu - contact_type: github value: srengel label: Stacia R Engel orcid: 0000-0001-5472-917X creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi domains: - biological systems homepage_url: http://www.yeastgenome.org/ id: apo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ascomycete phenotype ontology products: - category: OntologyProduct description: Ascomycete phenotype ontology in OWL format format: owl id: apo.owl name: apo.owl product_file_size: 32488 product_url: http://purl.obolibrary.org/obo/apo.owl - category: OntologyProduct description: Ascomycete phenotype ontology in OBO format format: obo id: apo.obo name: apo.obo product_file_size: 16796 product_url: http://purl.obolibrary.org/obo/apo.obo repository: https://github.com/obophenotype/ascomycete-phenotype-ontology taxon: - NCBITaxon:4890 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: hoganwr@gmail.com - contact_type: github value: hoganwr label: William Hogan orcid: 0000-0002-9881-1017 creation_date: '2025-09-29T00:00:00Z' description: An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. domains: - biomedical homepage_url: https://github.com/ApolloDev/apollo-sv id: apollo_sv last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Apollo Structured Vocabulary products: - category: OntologyProduct description: Apollo Structured Vocabulary in OWL format format: owl id: apollo_sv.owl name: apollo_sv.owl product_file_size: 266319 product_url: http://purl.obolibrary.org/obo/apollo_sv.owl repository: https://github.com/ApolloDev/apollo-sv - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://github.com/NCATSTranslator/Translator-All/wiki/ARAGORN label: NCATS Translator creation_date: '2025-11-05T00:00:00Z' description: ARAGORN (Autonomous Relay Agent for Generation Of Ranked Networks) is an NCATS Translator Autonomous Relay Agent (ARA) that performs query operations by compiling and ranking data from multiple ARAGORN-affiliated knowledge provider services. ARAGORN acts as an intermediary between user queries and underlying knowledge providers, aggregating results, performing inference, and ranking answers based on evidence and confidence scores. It implements the Translator Reasoner API (TRAPI) standard for biomedical question-answering. domains: - biomedical - translational - information technology homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/ARAGORN id: aragorn infores_id: aragorn last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: ARAGORN products: - category: ProgrammingInterface description: TRAPI-compliant API for biomedical question answering format: http id: aragorn.api name: ARAGORN API original_source: - aragorn product_url: https://aragorn.renci.org/ - category: GraphicalInterface description: Web interface for querying ARAGORN format: http id: aragorn.ui name: ARAGORN User Interface original_source: - aragorn product_url: https://ui.transltr.io/ repository: https://github.com/ranking-agent/aragorn synonyms: - ARAGORN - Autonomous Relay Agent for Generation Of Ranked Networks tags: - translator - activity_status: active category: Aggregator collection: - translator contacts: - category: Organization contact_details: - contact_type: email value: expander.agent@gmail.com label: Expander Agent Team - category: Individual contact_details: - contact_type: email value: stephen.ramsey@oregonstate.edu label: Stephen Ramsey - category: Individual contact_details: - contact_type: email value: edeutsch@systemsbiology.org label: Eric Deutsch - category: Individual contact_details: - contact_type: email value: dmk333@psu.edu label: David Koslicki creation_date: '2025-10-31T00:00:00Z' description: ARAX (Expander Agent) is a graph-based modular reasoning tool for translational biomedicine developed as part of the NCATS Biomedical Data Translator program. It provides a web browser user interface and TRAPI-compliant API for encoding translational biomedical questions and integrating knowledge across multiple sources. ARAX features ARAXi, an intuitive domain-specific language for specifying knowledge graph analysis workflows. The system accesses around 40 Knowledge Providers covering over 100 underlying knowledge sources and provides versatile methods for scoring and ranking result subgraphs. ARAX uses RTX-KG2 as its primary knowledge graph and supports query planning, knowledge gathering, overlay of contextual information, filtering, and result ranking through five core modules (Expander, Overlay, Filter, Resultify, and Ranker). domains: - biomedical - precision medicine - health - translational homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/Expander-Agent id: arax infores_id: arax last_modified_date: '2025-11-21T00:00:00Z' layout: resource_detail name: ARAX Translator Reasoner products: - category: ProgrammingInterface description: TRAPI-compliant API endpoint for programmatic access to ARAX reasoning capabilities. Supports v1.3+ of the Translator Reasoner API standard. Provides /query, /asyncquery, and /entity endpoints. id: arax.api name: ARAX TRAPI API original_source: - arax product_url: https://arax.ncats.io/api/arax/v1.4/ui/ - category: GraphicalInterface description: Web browser interface for querying ARAX and exploring answers. Provides interactive visual query graph builder, TRAPI operations input, TRAPI JSON input, and ARAXi workflow language input methods. format: http id: arax.ui name: ARAX Web UI original_source: - arax product_url: https://arax.ncats.io/ - category: DocumentationProduct description: ARAXi domain-specific language documentation for expressing knowledge graph analysis workflows. id: arax.araxi.docs name: ARAXi Documentation original_source: - arax product_file_size: 12191 product_url: https://github.com/RTXteam/RTX/blob/master/code/ARAX/Documentation/DSL_Documentation.md - category: ProgrammingInterface description: Source code repository for ARAX and the RTX system including ARAX-specific modules and RTX-KG2 knowledge graph. id: arax.github name: RTX GitHub Repository original_source: - arax product_url: https://github.com/RTXteam/RTX - category: DocumentationProduct description: Example queries and workflows demonstrating ARAX capabilities for various translational biomedicine use cases. id: arax.examples name: ARAX Examples original_source: - arax product_url: https://github.com/RTXteam/RTX/tree/master/code/ARAX/Examples publications: - doi: 10.1093/bioinformatics/btad082 id: btad082 journal: Bioinformatics title: 'ARAX: a graph-based modular reasoning tool for translational biomedicine' year: '2023' synonyms: - ARAX - Expander Agent tags: - translator - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mcarthua@mcmaster.ca - contact_type: github value: agmcarthur label: Andrew G. McArthur orcid: 0000-0002-1142-3063 creation_date: '2025-09-29T00:00:00Z' description: Antibiotic resistance genes and mutations domains: - biological systems homepage_url: https://github.com/arpcard/aro id: aro last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Antibiotic Resistance Ontology products: - category: OntologyProduct description: Antibiotic Resistance Ontology in OWL format format: owl id: aro.owl name: aro.owl product_file_size: 687021 product_url: http://purl.obolibrary.org/obo/aro.owl repository: https://github.com/arpcard/aro - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://ncats.nih.gov/translator label: NCATS Biomedical Data Translator creation_date: '2025-10-30T00:00:00Z' description: The Autonomous Relay System (ARS) is the primary interface and query routing service for the NCATS Biomedical Data Translator, orchestrating queries across multiple knowledge providers and reasoning agents. domains: - biomedical homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/Autonomous-Relay-System-(ARS) id: ars infores_id: ars last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Autonomous Relay System products: - category: GraphicalInterface description: Primary web entry point for submitting and tracking Translator ARS queries. format: http id: ars.portal name: ARS Production Portal original_source: - ars product_url: https://ars-prod.transltr.io/ - category: ProgrammingInterface connection_url: https://ars-prod.transltr.io/ars/api description: TRAPI-compatible ARS endpoint for asynchronous query submission. format: http id: ars.api is_public: true name: ARS API original_source: - ars product_url: https://ars-prod.transltr.io/ars/api/submit synonyms: - ARS - Translator ARS - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.ohdsi.org/ label: OHDSI creation_date: '2025-11-05T00:00:00Z' description: Athena is the OHDSI (Observational Health Data Sciences and Informatics) standardized vocabulary repository that provides access to standardized terminologies and vocabularies for observational healthcare data. It includes SNOMED CT, RxNorm, LOINC, ICD codes, and many other standard vocabularies, along with mappings between them. Athena enables the transformation of healthcare data into the OMOP Common Data Model format for federated research across multiple healthcare systems. domains: - clinical - biomedical - health - information technology homepage_url: https://athena.ohdsi.org/ id: athena infores_id: athena last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: Athena products: - category: GraphicalInterface description: Web interface for searching and browsing standardized vocabularies format: http id: athena.web name: Athena Vocabulary Browser original_source: - athena product_url: https://athena.ohdsi.org/search-terms/start - category: Product description: Downloadable standardized vocabulary bundles for OMOP CDM format: csv id: athena.vocabularies name: Athena Vocabulary Downloads original_source: - athena product_url: https://athena.ohdsi.org/vocabulary/list warnings: - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ Exceeded 30 redirects. - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ Exceeded 30 redirects. - category: MappingProduct description: Concept mappings between different terminology systems format: csv id: athena.mappings name: Athena Concept Mappings original_source: - snomedct - icd10 - icd10cm - mesh - loinc - cdiscvocab - ciel product_url: https://athena.ohdsi.org/search-terms/start secondary_source: - athena warnings: - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ Exceeded 30 redirects. - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ Exceeded 30 redirects. synonyms: - Athena - OHDSI Athena taxon: - NCBITaxon:9606 - activity_status: active category: Aggregator collection: - translator contacts: - category: Individual contact_details: - contact_type: email value: kebedey@renci.org - contact_type: github value: YaphetKG label: Yaphet Kebede orcid: 0000-0002-5046-0246 creation_date: '2025-03-09T00:00:00Z' description: A Translator Knowledge Provider offering multiple sub-graphs in KGX format. domains: - health homepage_url: https://robokop.renci.org/api-docs/docs/category/automat id: automat last_modified_date: '2025-10-29T00:00:00Z' layout: resource_detail license: id: https://biopragmatics.github.io/obo-db-ingest/ label: Varies name: Automat products: - category: GraphProduct description: Robokop KG (Automat) format: kgx-jsonl id: automat.robokopkg name: robokopkg original_source: - robokop product_url: https://stars.renci.org/var/plater/bl-4.2.1/RobokopKG/4901b2bc764444ea/ secondary_source: - automat - category: GraphProduct description: Robokop Plus format: kgx-jsonl id: automat.robokopplus name: robokopplus original_source: - robokop product_url: https://stars.renci.org/var/plater/bl-3.1.2/RobokopPlus/ad8cb4d0a7ccc923/kgx_files/ secondary_source: - automat - category: GraphProduct description: Biolink Automat format: kgx-jsonl id: automat.biolink name: biolink_automat original_source: - biolink product_url: https://stars.renci.org/var/plater/bl-3.1.2/Biolink_Automat/329f8c92051c18d4/ secondary_source: - automat - category: GraphProduct description: CTD Automat format: kgx-jsonl id: automat.ctd infores_id: automat-ctd name: ctd_automat original_source: - ctd product_url: https://stars.renci.org/var/plater/bl-4.2.1/CTD_Automat/f92c663160ec5e36/ secondary_source: - automat - category: GraphProduct description: DrugCentral Automat format: kgx-jsonl id: automat.drugcentral infores_id: automat-drug-central name: drugcentral_automat original_source: - drugcentral product_url: https://stars.renci.org/var/plater/bl-4.2.1/DrugCentral_Automat/dec0617490b49c7a/ secondary_source: - automat - category: GraphProduct description: GTEx Automat format: kgx-jsonl id: automat.gtex infores_id: automat-gtex name: gtex_automat original_source: - gtex product_url: https://stars.renci.org/var/plater/bl-4.2.1/GTEx_Automat/a6448b9092bb81a1/ secondary_source: - automat - category: GraphProduct description: GtoPdb Automat format: kgx-jsonl id: automat.gtopdb infores_id: automat-gtopdb name: gtopdb_automat original_source: - gtopdb product_url: https://stars.renci.org/var/plater/bl-4.2.1/GtoPdb_Automat/0ea6074c824c2236/ secondary_source: - automat - category: GraphProduct description: GWASCatalog Automat format: kgx-jsonl id: automat.gwascatalog infores_id: automat-gwas-catalog name: gwascatalog_automat original_source: - gwascatalog product_url: https://stars.renci.org/var/plater/bl-4.2.1/GWASCatalog_Automat/e30aceb322a33462/ secondary_source: - automat - category: GraphProduct description: Hetio Automat format: kgx-jsonl id: automat.hetio name: hetio_automat original_source: - hetionet product_url: https://stars.renci.org/var/plater/bl-4.2.1/Hetio_Automat/85a5f53e63150e1e/ secondary_source: - automat - category: GraphProduct description: HGNC Automat format: kgx-jsonl id: automat.hgnc infores_id: automat-hgnc name: hgnc_automat original_source: - hgnc product_url: https://stars.renci.org/var/plater/bl-4.2.1/HGNC_Automat/dee31cfce74e5944/ secondary_source: - automat - category: GraphProduct description: HMDB Automat format: kgx-jsonl id: automat.hmdb infores_id: automat-hmdb name: hmdb_automat original_source: - hmdb product_url: https://stars.renci.org/var/plater/bl-4.2.1/HMDB_Automat/6715124699b6dbf0/ secondary_source: - automat - category: GraphProduct description: HumanGOA Automat format: kgx-jsonl id: automat.humangoa infores_id: automat-human-goa name: humangoa_automat original_source: - goa product_url: https://stars.renci.org/var/plater/bl-4.2.1/HumanGOA_Automat/06f107a4e9e8e547/ secondary_source: - automat - category: GraphProduct description: IntAct Automat format: kgx-jsonl id: automat.intact infores_id: automat-intact name: intact_automat original_source: - intact product_url: https://stars.renci.org/var/plater/bl-4.2.1/IntAct_Automat/e5b936f966a02c2c/ secondary_source: - automat - category: GraphProduct description: PANTHER Automat format: kgx-jsonl id: automat.panther infores_id: automat-panther name: panther_automat original_source: - panther product_url: https://stars.renci.org/var/plater/bl-4.2.1/PANTHER_Automat/c0189f14ba41da6c/ secondary_source: - automat - category: GraphProduct description: PHAROS Automat format: kgx-jsonl id: automat.pharos infores_id: automat-pharos name: pharos_automat original_source: - pharos product_url: https://stars.renci.org/var/plater/bl-4.2.1/PHAROS_Automat/d3068b509bf17ff3/ secondary_source: - automat - category: GraphProduct description: STRING-DB Automat format: kgx-jsonl id: automat.stringdb name: stringdb_automat original_source: - string product_url: https://stars.renci.org/var/plater/bl-4.2.1/STRING-DB_Automat/4ca5a0ce557e2c18/ secondary_source: - automat - category: GraphProduct description: UberGraph Automat format: kgx-jsonl id: automat.ubergraph name: ubergraph_automat original_source: - ubergraph product_url: https://stars.renci.org/var/plater/bl-4.2.1/UbergraphRedundant_Automat/e6b3204fd3a04413/ secondary_source: - automat repository: https://github.com/RobokopU24/ - activity_status: active category: DataSource creation_date: '2025-11-25T00:00:00Z' description: BacDive (Bacterial Diversity Metadatabase) is the world's largest database for standardized bacterial information, containing strain-level data on morphology, physiology, growth conditions, and isolation sources for over 99,000 bacterial strains. It integrates research data from diverse sources and provides freely accessible, standardized information with Digital Object Identifiers for each strain. domains: - microbiology - biological systems homepage_url: https://bacdive.dsmz.de/ id: bacdive last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: BacDive products: - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe - category: Product description: Trait data table listing all 140+ harmonized traits available in metaTraits, mapped to standardized ontologies. id: metatraits.traits name: metaTraits Trait List original_source: - bacdive - bv-brc - goldterms - progenomes product_url: https://metatraits.embl.de/traits taxon: - NCBITaxon:2 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.univ-lorraine.fr/ id: univ-lorraine label: Université de Lorraine creation_date: '2025-11-25T00:00:00Z' description: A comprehensive database of bacterial phenotypic traits including morphology, physiology, ecology, and growth characteristics for thousands of bacterial species. BactoTraits provides standardized trait annotations for comparative microbiology and systems biology applications. domains: - microbiology - biological systems - systems biology homepage_url: https://ordar.otelo.univ-lorraine.fr/record?id=10.24396/ORDAR-53 id: bactotraits last_modified_date: '2026-01-05T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: BactoTraits products: - category: Product description: BactoTraits database with downloadable trait datasets format: http id: bactotraits.database is_public: true name: BactoTraits Database and Downloads product_url: https://ordar.otelo.univ-lorraine.fr/record?id=10.24396/ORDAR-53 - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe synonyms: - BactoTraits - Bacterial Traits Database taxon: - NCBITaxon:2 - activity_status: active category: DataSource creation_date: '2026-02-18T00:00:00Z' description: BATMAN-TCM is a web resource for predicting potential targets and molecular mechanisms of traditional Chinese medicine ingredients and formulas. domains: - pharmacology - drug discovery - pathways homepage_url: http://bionet.ncpsb.org.cn/batman-tcm/ id: batman last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail name: BATMAN-TCM products: - category: GraphicalInterface description: Interactive BATMAN-TCM web interface for querying compounds, targets, and enriched pathways. format: http id: batman.web name: BATMAN-TCM Web Interface original_source: - batman product_url: http://bionet.ncpsb.org.cn/batman-tcm/ - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv synonyms: - BATMAN - BATMAN-TCM - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: rlwalls2008@gmail.com - contact_type: github value: ramonawalls label: Ramona Walls orcid: 0000-0001-8815-0078 creation_date: '2025-09-29T00:00:00Z' description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. domains: - biological systems homepage_url: https://github.com/BiodiversityOntologies/bco id: bco last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Biological Collections Ontology products: - category: OntologyProduct description: Biological Collections Ontology in OWL format format: owl id: bco.owl name: bco.owl product_file_size: 108849 product_url: http://purl.obolibrary.org/obo/bco.owl repository: https://github.com/BiodiversityOntologies/bco - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: phismith@buffalo.edu - contact_type: github value: phismith label: Barry Smith orcid: 0000-0003-1384-116X creation_date: '2025-06-25T00:00:00Z' description: The upper level ontology upon which OBO Foundry ontologies are built. domains: - biological systems homepage_url: http://ifomis.org/bfo/ id: bfo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Basic Formal Ontology products: - category: OntologyProduct description: Basic Formal Ontology in OWL format format: owl id: bfo.owl name: bfo.owl product_file_size: 20902 product_url: http://purl.obolibrary.org/obo/bfo.owl - 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bgee product_url: https://stars.renci.org/var/translator/releases/bgee/2025_12_15/ secondary_source: - translator publications: - authors: - Bastian FB - Brandulas Cammarata A - Carsanaro S - Detering H - Huang W-T - Joye S - Niknejad A - Nyamari M - Mendes de Farias T - Moretti S - Tzivanopoulou M - Wollbrett J - Robinson-Rechavi M doi: doi:10.1093/nar/gkae1118 id: doi:10.1093/nar/gkae1118 preferred: true title: Bgee in 2024 - focus on curated single-cell RNA-seq datasets, and query tools year: '2025' - authors: - Bastian FB - Roux J - Niknejad A - Comte A - Fonseca Costa SS - de Farias TM - Moretti S - Parmentier G - de Laval VR - Rosikiewicz M - Wollbrett J - Echchiki A - Escoriza A - Gharib WH - Gonzales-Porta M - Jarosz Y - Laurenczy B - Moret P - Person E - Roelli P - Sanjeev K - Seppey M - Robinson-Rechavi M doi: doi:10.1093/nar/gkaa793 id: doi:10.1093/nar/gkaa793 title: The Bgee suite - integrated curated expression atlas and comparative transcriptomics in animals year: '2021' repository: https://github.com/BgeeDB/bgee_apps taxon: - NCBITaxon:9606 - NCBITaxon:10090 - NCBITaxon:10116 - NCBITaxon:9615 - NCBITaxon:9685 - NCBITaxon:9796 - NCBITaxon:9823 - NCBITaxon:9913 - NCBITaxon:9925 - NCBITaxon:9940 - NCBITaxon:9986 - NCBITaxon:10141 - NCBITaxon:9031 - NCBITaxon:9103 - NCBITaxon:9258 - NCBITaxon:9483 - NCBITaxon:9531 - NCBITaxon:9541 - NCBITaxon:7227 - NCBITaxon:7955 - NCBITaxon:6239 - NCBITaxon:8355 - NCBITaxon:8364 - NCBITaxon:4932 - NCBITaxon:3702 - activity_status: active category: DataSource collection: - ber contacts: - category: Organization label: Systems Biology Research Group at the University of California, San Diego creation_date: '2025-03-09T00:00:00Z' description: BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. domains: - biological systems - systems biology - pathways - simulation homepage_url: http://bigg.ucsd.edu/ id: bigg last_modified_date: '2025-09-27T00:00:00Z' layout: resource_detail license: id: http://bigg.ucsd.edu/license#license label: Custom name: BiGG Models products: - 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bigg product_file_size: 1151 product_url: https://w3id.org/biopragmatics/resources/bigg.model/bigg.model.tsv secondary_source: - obo-db-ingest - category: Product description: bigg.reaction Nodes TSV format: tsv id: obo-db-ingest.bigg.reaction.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.reaction Nodes TSV original_source: - bigg product_file_size: 593163 product_url: https://w3id.org/biopragmatics/resources/bigg.reaction/bigg.reaction.tsv secondary_source: - obo-db-ingest publications: - authors: - King ZA - Lu JS - Dräger A - Miller PC - Federowicz S - Lerman JA - Ebrahim A - Palsson BO - Lewis NE doi: doi:10.1093/nar/gkv1049 id: doi:10.1093/nar/gkv1049 preferred: true title: 'BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models' year: '2016' repository: https://github.com/SBRG/bigg_models - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: bindingdb@gmail.com - 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category: Product compression: zip description: COVID-19 related binding data in tab-separated values format format: tsv id: bindingdb.covid19_tsv name: BindingDB COVID-19 Data (TSV) product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_Covid-19_202507_tsv.zip warnings: [] - category: Product description: FASTA format protein sequences of all protein targets in BindingDB format: fasta id: bindingdb.target_sequences name: BindingDB Target Sequences product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/BindingDBTargetSequences.fasta warnings: [] - category: MappingProduct description: Mapping of BindingDB monomer (compound) IDs to PubChem CIDs id: bindingdb.cid_mapping name: BindingDB-PubChem CID Mapping product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/BindingDB_CID.txt warnings: [] - category: MappingProduct description: Mapping of BindingDB monomer (compound) IDs to PubChem SIDs id: bindingdb.sid_mapping name: BindingDB-PubChem SID Mapping product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/BindingDB_SID.txt warnings: [] - category: MappingProduct description: Mapping of BindingDB monomer (compound) IDs to ChEBI IDs id: bindingdb.chebi_mapping name: BindingDB-ChEBI Mapping product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/BindingDB_CHEBI_ID.txt warnings: [] - category: MappingProduct description: Mapping of BindingDB monomer (compound) IDs to DrugBank IDs id: bindingdb.drugbank_mapping name: BindingDB-DrugBank Mapping product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/BindingDB_DrugBankID.txt warnings: [] - category: MappingProduct description: Mapping of BindingDB polymer (single protein) IDs to UniProt IDs id: bindingdb.uniprot_mapping name: BindingDB-UniProt Mapping product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/BindingDB_UniProt.txt warnings: [] - category: ProgrammingInterface description: RESTful web services for programmatic access to BindingDB data id: bindingdb.api name: BindingDB RESTful API product_url: https://www.bindingdb.org/rwd/bind/BindingDBRESTfulAPI.jsp - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - authors: - Tiqing Liu - Linda Hwang - Stephen K Burley - Carmen I Nitsche - Christopher Southan - W Patrick Walters - Michael K Gilson doi: 10.1093/nar/gkae1075 id: doi:10.1093/nar/gkae1075 journal: Nucleic Acids Research title: 'BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data' year: '2025' - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: tom@insilica.co label: Tom Luechtefeld creation_date: '2025-12-08T00:00:00Z' description: BioBricks AOP-Wiki is an open knowledge graph for Adverse Outcome Pathways from the AOP-Wiki. It provides structured data about biological pathways linking chemical exposures to adverse health effects. domains: - toxicology - biological systems evaluation_page: resource/biobricks-aopwiki/biobricks-aopwiki_eval_automated.html homepage_url: https://github.com/biobricks-ai/aopwikirdf-kg id: biobricks-aopwiki last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: BioBricks AOP-Wiki products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks AOP-Wiki id: biobricks-aopwiki.sparql name: BioBricks AOP-Wiki SPARQL original_source: - biobricks-aopwiki product_url: https://frink.apps.renci.org/biobricks-aopwiki/sparql repository: https://github.com/biobricks-ai/aopwikirdf-kg - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: tom@insilica.co label: Tom Luechtefeld creation_date: '2025-12-08T00:00:00Z' description: BioBricks ICE (Integrated Chemical Environment) is an open knowledge graph for cheminformatics and chemical safety data from EPA's CompTox database. domains: - chemistry and biochemistry - toxicology evaluation_page: resource/biobricks-ice/biobricks-ice_eval_automated.html homepage_url: https://github.com/biobricks-ai/biobricks-okg id: biobricks-ice last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: BioBricks ICE products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks ICE id: biobricks-ice.sparql name: BioBricks ICE SPARQL original_source: - biobricks-ice product_url: https://frink.apps.renci.org/biobricks-ice/sparql repository: https://github.com/biobricks-ai/biobricks-okg - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: tom@insilica.co label: Tom Luechtefeld creation_date: '2025-12-08T00:00:00Z' description: BioBricks MeSH is an open knowledge graph of Medical Subject Headings (MeSH) biomedical vocabulary, providing structured access to the NLM's controlled vocabulary thesaurus. domains: - biomedical - health evaluation_page: resource/biobricks-mesh/biobricks-mesh_eval_automated.html homepage_url: https://github.com/biobricks-ai/mesh-kg id: biobricks-mesh last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: BioBricks MeSH products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks MeSH id: biobricks-mesh.sparql name: BioBricks MeSH SPARQL original_source: - biobricks-mesh product_url: https://frink.apps.renci.org/biobricks-mesh/sparql repository: https://github.com/biobricks-ai/mesh-kg - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: tom@insilica.co label: Tom Luechtefeld creation_date: '2025-12-08T00:00:00Z' description: BioBricks PubChem Annotations is an open knowledge graph of chemical annotations from PubChem, providing structured access to chemical compound data and annotations. domains: - chemistry and biochemistry evaluation_page: resource/biobricks-pubchem-annotations/biobricks-pubchem-annotations_eval_automated.html homepage_url: https://github.com/biobricks-ai/pubchem-annotations-kg id: biobricks-pubchem-annotations last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: BioBricks PubChem Annotations products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks PubChem Annotations id: biobricks-pubchem-annotations.sparql name: BioBricks PubChem Annotations SPARQL original_source: - biobricks-pubchem-annotations product_url: https://frink.apps.renci.org/biobricks-pubchem-annotations/sparql repository: https://github.com/biobricks-ai/pubchem-annotations-kg - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: tom@insilica.co label: Tom Luechtefeld creation_date: '2025-12-08T00:00:00Z' description: BioBricks Tox21 is an open knowledge graph for Tox21 toxicology screening data, providing structured access to high-throughput toxicity testing results. domains: - toxicology evaluation_page: resource/biobricks-tox21/biobricks-tox21_eval_automated.html homepage_url: https://github.com/biobricks-ai/biobricks-okg id: biobricks-tox21 last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: BioBricks Tox21 products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks Tox21 id: biobricks-tox21.sparql name: BioBricks Tox21 SPARQL original_source: - biobricks-tox21 product_url: https://frink.apps.renci.org/biobricks-tox21/sparql repository: https://github.com/biobricks-ai/biobricks-okg - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: tom@insilica.co label: Tom Luechtefeld creation_date: '2025-12-08T00:00:00Z' description: BioBricks ToxCast is an open knowledge graph for EPA ToxCast high-throughput screening data, providing structured access to chemical toxicity testing results. domains: - toxicology evaluation_page: resource/biobricks-toxcast/biobricks-toxcast_eval_automated.html homepage_url: https://github.com/biobricks-ai/biobricks-okg id: biobricks-toxcast last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: BioBricks ToxCast products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks ToxCast id: biobricks-toxcast.sparql name: BioBricks ToxCast SPARQL original_source: - biobricks-toxcast product_url: https://frink.apps.renci.org/biobricks-toxcast/sparql repository: https://github.com/biobricks-ai/biobricks-okg - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: email value: biocyc-support@sri.com label: BioCyc creation_date: '2025-03-18T00:00:00Z' description: BioCyc is a collection of 20,070 Pathway/Genome Databases (PGDBs) for model eukaryotes and for thousands of microbes, plus software tools for exploring them. BioCyc is an encyclopedic reference that contains curated data from 146,000 publications. domains: - biological systems homepage_url: https://biocyc.org/ id: biocyc last_modified_date: '2026-01-30T00:00:00Z' layout: resource_detail license: id: https://biocyc.org/download.shtml label: Varies name: BioCyc products: - category: MappingProduct description: bigg.metabolite SSSOM format: sssom id: obo-db-ingest.bigg.metabolite.sssom.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.metabolite SSSOM original_source: - chebi - bigg - biocyc - kegg - reactome product_file_size: 400516 product_url: https://w3id.org/biopragmatics/resources/bigg.metabolite/bigg.metabolite.sssom.tsv secondary_source: - obo-db-ingest - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - 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interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - 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category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz taxon: - NCBITaxon:2759 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: http://biogps.org/about/ label: BioGPS / The Scripps Research Institute creation_date: '2025-08-12T00:00:00Z' description: BioGPS is an extensible and customizable gene annotation portal that aggregates gene-centric data (expression profiles, functional annotations, pathways, interactions, ontologies) from numerous external resources using a community-driven plugin system. It enables interactive expression visualization across tissues/cell types and provides programmatic and bulk access to underlying annotation tables. domains: - genomics - biomedical - biological systems homepage_url: http://biogps.org/ id: biogps last_modified_date: '2025-09-10T00:00:00Z' layout: resource_detail name: BioGPS products: - category: GraphicalInterface description: Main BioGPS web portal with searchable gene pages, expression charts, and plugin system aggregating external annotations format: http id: biogps.portal name: BioGPS Portal product_url: http://biogps.org/ - category: ProgrammingInterface description: REST-style API for retrieving gene annotations and expression data (JSON/TSV responses) format: http id: biogps.api name: BioGPS API product_url: http://biogps.org/api/ - category: Product description: Bulk annotation and expression data downloads (gene expression compendia, annotation tables) format: http id: biogps.downloads name: BioGPS Downloads product_url: http://biogps.org/downloads/ - category: DocumentationProduct description: FAQ and usage guidance including plugin system overview and data interpretation notes format: http id: biogps.faq name: BioGPS FAQ / Help product_url: http://biogps.org/faq/ - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg - category: Product description: Gene expression data aggregated from GTEx, BioGPS, Bgee and other expression databases format: http id: genecards.expression.data name: GeneCards Expression Data original_source: - gtex - biogps - bgee product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' publications: - authors: - Wu C - Orozco C - Boyer J - Leglise M - Goodale J - Batalov S - Hodge CL - Haase J - Janes J - Huss JW 3rd - Su AI doi: 10.1186/gb-2009-10-11-r130 id: doi:10.1186/gb-2009-10-11-r130 journal: Genome Biology title: 'BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources' year: '2009' - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: email value: support@thebiogrid.org - contact_type: url value: https://thebiogrid.org/ label: BioGRID creation_date: '2025-08-13T00:00:00Z' description: The Biological General Repository for Interaction Datasets (BioGRID) is an open, curated database of genetic, protein, and chemical interaction data, post-translational modifications (PTMs), CRISPR screen results (ORCS), and themed curation project datasets spanning model organisms and human, freely available under the MIT License. domains: - biomedical - proteomics - genomics - systems biology homepage_url: https://thebiogrid.org/ id: biogrid infores_id: biogrid last_modified_date: '2025-12-22T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: BioGRID products: - category: GraphicalInterface description: Web interface for browsing, searching, and visualizing BioGRID interaction and project data format: http id: biogrid.web name: BioGRID Website original_source: - biogrid product_url: https://thebiogrid.org/ - category: ProgrammingInterface description: REST-based web service for programmatic access to BioGRID interaction, chemical association, PTM, and CRISPR (ORCS) data format: http id: biogrid.api is_public: true name: BioGRID REST API original_source: - biogrid product_url: https://wiki.thebiogrid.org/doku.php/biogridrest - category: GraphProduct compression: zip description: Latest complete BioGRID interaction dataset in PSI-MI MITAB format (non-redundant and raw interactions combined) format: psi_mi_mitab id: biogrid.interactions.mitab latest_version: 5.0.252 name: BIOGRID-ALL-LATEST.mitab.zip product_url: https://downloads.thebiogrid.org/BioGRID/Latest-Release/BIOGRID-ALL-LATEST.mitab.zip secondary_source: - 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unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz publications: - id: https://doi.org/10.1002/pro.3978 journal: Protein Science preferred: true title: The BioGRID database – a comprehensive biomedical resource of curated protein, genetic, and chemical interactions year: '2020' - id: https://doi.org/10.1093/nar/gky1079 journal: Nucleic Acids Research title: 'The BioGRID interaction database: 2019 update' year: '2019' - id: https://doi.org/10.1093/nar/gkj109 journal: Nucleic Acids Research title: 'BioGRID: a general repository for interaction datasets' year: '2006' taxon: - NCBITaxon:9606 - NCBITaxon:4932 - NCBITaxon:4896 - NCBITaxon:3702 - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: aidong@virginia.edu label: Aidong Zhang creation_date: '2025-12-08T00:00:00Z' description: Bio-Health KG is a dynamically-updated open knowledge network for health, integrating biomedical insights with social determinants of health. domains: - health - biomedical - social determinants evaluation_page: resource/biohealth/biohealth_eval_automated.html homepage_url: https://frink.apps.renci.org/biohealth/sparql id: biohealth last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: Bio-Health KG products: - category: ProgrammingInterface description: SPARQL endpoint for Bio-Health KG id: biohealth.sparql name: Bio-Health KG SPARQL original_source: - biohealth product_url: https://frink.apps.renci.org/biohealth/sparql - activity_status: active category: DataModel contacts: - category: Individual contact_details: - contact_type: email value: smoxon@lbl.gov - contact_type: github value: sierra-moxon label: Sierra Taylor Moxon orcid: 0000-0002-8719-7760 creation_date: '2025-03-09T00:00:00Z' description: Entity and association taxonomy and datamodel for life-sciences data domains: - upper homepage_url: https://biolink.github.io/biolink-model/ id: biolink last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Biolink-Model products: - category: DocumentationProduct description: Biolink Model Documentation format: http id: biolink.docs name: Biolink Model Documentation original_source: - biolink product_url: https://biolink.github.io/biolink-model/ secondary_source: - biolink - category: DocumentationProduct description: Information Resource Registry Model documentation, including descriptions of the information resource (infores) registry itself. format: http id: biolink.infores.docs name: Information Resource Registry Model Documentation original_source: - biolink product_url: https://biolink.github.io/information-resource-registry/ secondary_source: - biolink - category: DataModelProduct compatibility: - standard: biolink version: v4.2.5 description: OWL release of Biolink Model format: owl id: biolink.model.owl latest_version: v4.2.6-rc5 name: Biolink Model OWL release original_source: - biolink product_file_size: 717005 product_url: https://w3id.org/biolink/biolink-model.owl.ttl secondary_source: - biolink versions: - v4.2.6-rc5 - v4.2.6-rc4 - v4.2.6-rc3 - v4.2.6-rc2 - v4.2.6-rc1 - v4.2.5 - v4.2.5-rc2 - v4.2.5-rc1 - v4.2.4 - v4.2.3 - v4.2.2 - v4.2.1 - v4.2.0 - v4.2.0-rc.2 - v4.2.0-rc.1 - v4.1.6 - v4.1.5 - v4.1.4 - v4.1.3 - v4.1.2 - v4.1.1 - v4.1.0 - v4.0.0 - v3.6.0 - v3.5.4 - v3.5.3 - v3.5.2 - v3.5.1 - v3.5.0 - v3.4.3 - category: DataModelProduct compatibility: - standard: biolink version: v4.2.5 description: JSON schema release of Biolink Model format: json id: biolink.model.json latest_version: v4.2.6-rc5 name: Biolink Model JSON release original_source: - biolink product_file_size: 138288 product_url: https://w3id.org/biolink/biolink-model.json secondary_source: - biolink versions: - v4.2.6-rc5 - v4.2.6-rc4 - v4.2.6-rc3 - v4.2.6-rc2 - v4.2.6-rc1 - v4.2.5 - v4.2.5-rc2 - v4.2.5-rc1 - v4.2.4 - v4.2.3 - v4.2.2 - v4.2.1 - v4.2.0 - v4.2.0-rc.2 - v4.2.0-rc.1 - v4.1.6 - v4.1.5 - v4.1.4 - v4.1.3 - v4.1.2 - v4.1.1 - v4.1.0 - v4.0.0 - v3.6.0 - v3.5.4 - v3.5.3 - v3.5.2 - v3.5.1 - v3.5.0 - v3.4.3 - category: DataModelProduct compatibility: - standard: biolink version: v4.2.5 description: GraphQL release of Biolink Model format: graphql id: biolink.model.graphql latest_version: v4.2.6-rc5 name: Biolink Model GraphQL release original_source: - biolink product_file_size: 9599 product_url: https://w3id.org/biolink/biolink-model.graphql secondary_source: - biolink versions: - v4.2.6-rc5 - v4.2.6-rc4 - v4.2.6-rc3 - v4.2.6-rc2 - v4.2.6-rc1 - v4.2.5 - v4.2.5-rc2 - v4.2.5-rc1 - v4.2.4 - v4.2.3 - v4.2.2 - v4.2.1 - v4.2.0 - v4.2.0-rc.2 - v4.2.0-rc.1 - v4.1.6 - v4.1.5 - v4.1.4 - v4.1.3 - v4.1.2 - v4.1.1 - v4.1.0 - v4.0.0 - v3.6.0 - v3.5.4 - v3.5.3 - v3.5.2 - v3.5.1 - v3.5.0 - v3.4.3 - category: DataModelProduct compatibility: - standard: biolink version: v4.2.5 description: Protobuf release of Biolink Model format: protobuf id: biolink.model.proto latest_version: v4.2.6-rc5 name: Biolink Model Protobuf release original_source: - biolink product_file_size: 18600 product_url: https://raw.githubusercontent.com/biolink/biolink-model/refs/heads/master/project/protobuf/biolink_model.proto secondary_source: - biolink versions: - v4.2.6-rc5 - v4.2.6-rc4 - v4.2.6-rc3 - v4.2.6-rc2 - v4.2.6-rc1 - v4.2.5 - v4.2.5-rc2 - v4.2.5-rc1 - v4.2.4 - v4.2.3 - v4.2.2 - v4.2.1 - v4.2.0 - v4.2.0-rc.2 - v4.2.0-rc.1 - v4.1.6 - v4.1.5 - v4.1.4 - v4.1.3 - v4.1.2 - v4.1.1 - v4.1.0 - v4.0.0 - v3.6.0 - v3.5.4 - v3.5.3 - v3.5.2 - v3.5.1 - v3.5.0 - v3.4.3 - category: DataModelProduct compatibility: - standard: biolink version: v4.2.5 description: SHACL release of Biolink Model format: shacl id: biolink.model.shacl latest_version: v4.2.6-rc5 name: Biolink Model SHACL release original_source: - biolink product_file_size: 161190 product_url: https://raw.githubusercontent.com/biolink/biolink-model/refs/heads/master/project/shacl/biolink_model.shacl.ttl secondary_source: - biolink versions: - v4.2.6-rc5 - v4.2.6-rc4 - v4.2.6-rc3 - v4.2.6-rc2 - v4.2.6-rc1 - v4.2.5 - v4.2.5-rc2 - v4.2.5-rc1 - v4.2.4 - v4.2.3 - v4.2.2 - v4.2.1 - v4.2.0 - v4.2.0-rc.2 - v4.2.0-rc.1 - v4.1.6 - v4.1.5 - v4.1.4 - v4.1.3 - v4.1.2 - v4.1.1 - v4.1.0 - v4.0.0 - v3.6.0 - v3.5.4 - v3.5.3 - v3.5.2 - v3.5.1 - v3.5.0 - v3.4.3 - category: DataModelProduct compatibility: - standard: biolink version: v4.2.5 description: ShEx release of Biolink Model format: shex id: biolink.model.shex latest_version: v4.2.6-rc5 name: Biolink Model ShEx release original_source: - biolink product_file_size: 17816 product_url: https://raw.githubusercontent.com/biolink/biolink-model/refs/heads/master/project/shex/biolink_model.shex secondary_source: - biolink versions: - v4.2.6-rc5 - v4.2.6-rc4 - v4.2.6-rc3 - v4.2.6-rc2 - v4.2.6-rc1 - v4.2.5 - v4.2.5-rc2 - v4.2.5-rc1 - v4.2.4 - v4.2.3 - v4.2.2 - v4.2.1 - v4.2.0 - v4.2.0-rc.2 - v4.2.0-rc.1 - v4.1.6 - v4.1.5 - v4.1.4 - v4.1.3 - v4.1.2 - v4.1.1 - v4.1.0 - v4.0.0 - v3.6.0 - v3.5.4 - v3.5.3 - v3.5.2 - v3.5.1 - v3.5.0 - v3.4.3 - category: GraphProduct description: Biolink Automat format: kgx-jsonl id: automat.biolink name: biolink_automat original_source: - biolink product_url: https://stars.renci.org/var/plater/bl-3.1.2/Biolink_Automat/329f8c92051c18d4/ secondary_source: - automat - category: ProcessProduct description: This repository is a code reference for the C-Path Knowledge Graph project, to increase discoverability of rare disease datasets through integration with the Monarch Knowlege Graph. Note that this is only a reference to scripts and queries associated with this project and is not provided as a runnable project because these workflows depend on an internal data catalog. format: python id: cpathkg.code name: C-Path Knowledge Graph Integration original_source: - biolink - kg-monarch product_url: https://gitlab.c-path.org/c-pathontology/c-path-knowledge-graph-integration secondary_source: - cpathkg - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg publications: - authors: - Unni DR - Moxon SAT - Bada M - Brush M - Bruskiewich R - Caufield JH - Clemons PA - Dancik V - Dumontier M - Fecho K - Glusman G - Hadlock JJ - Harris NL - Joshi A - Putman T - Qin G - Ramsey SA - Shefchek KA - Solbrig H - Soman K - Thessen AE - Haendel MA - Bizon C - Mungall CJ - The Biomedical Data Translator Consortium doi: doi:10.1111/cts.13302 id: doi:10.1111/cts.13302 preferred: true title: '''Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science''' year: '2022' repository: https://github.com/biolink/biolink-model/ - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://glygen.ccrc.uga.edu/frontend/contact label: BiomarkerKB Team creation_date: '2025-05-29T00:00:00Z' description: BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that organizes and integrates biomarker data from different public sources, providing researchers with comprehensive, integrated access to biomarker information. domains: - health - biological systems - biomedical evaluation_page: resource/biomarker/biomarker_eval_automated.html homepage_url: https://glygen.ccrc.uga.edu/frontend/home/ id: biomarker last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: BiomarkerKB products: - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: avi.maayan@mssm.edu label: MaayanLab creation_date: '2025-05-04T00:00:00Z' description: Biomarker Knowledge Graph (BKG) is a comprehensive resource for biomarker data that integrates multiple biomedical resources to connect biomarkers with anatomical structures, compounds, conditions, roles, and variants. domains: - health - biological systems evaluation_page: resource/biomarkerkg/biomarkerkg_eval_automated.html homepage_url: https://bkg.dev.maayanlab.cloud/ id: biomarkerkg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: Biomarker Knowledge Graph products: - category: GraphicalInterface description: Web interface to explore and query the Biomarker Knowledge Graph id: biomarkerkg.site name: BKG Explorer original_source: - biomarkerkg product_url: https://bkg.dev.maayanlab.cloud/ secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Nodes from Uber-Anatomy Ontology format: csv id: biomarkerkg.nodes.anatomy name: BKG Anatomy Nodes original_source: - uberon product_file_size: 332 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Anatomy.nodes.zip secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Nodes from GlyGen Biomarker Database format: csv id: biomarkerkg.nodes.biomarker name: BKG Biomarker Nodes original_source: - glygen product_file_size: 1252064 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Biomarker.nodes.zip secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Nodes from PubChem Database format: csv id: biomarkerkg.nodes.compound name: BKG Compound Nodes original_source: - pubchem product_file_size: 871 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Compound.nodes.zip secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Nodes from Human Disease Ontology format: csv id: biomarkerkg.nodes.condition name: BKG Condition Nodes original_source: - doid product_file_size: 5501 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Condition.nodes.zip secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Nodes from OBCI format: csv id: biomarkerkg.nodes.role name: BKG Role Nodes original_source: - biomarkerkg product_file_size: 276 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Role.nodes.zip secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Nodes from dbSNP format: csv id: biomarkerkg.nodes.variant name: BKG Variant Nodes original_source: - dbsnp product_file_size: 782975 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Variant.nodes.zip secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Biomarker to Anatomy relationships (determined_using_sample_from) format: csv id: biomarkerkg.edges.anatomy name: BKG Anatomy Edges original_source: - biomarkerkg product_file_size: 1229 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Anatomy.edges.zip secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Biomarker to Compound relationships (indicated_by_above_normal_level_of, indicated_by_below_normal_level_of) format: csv id: biomarkerkg.edges.compound name: BKG Compound Edges original_source: - biomarkerkg product_file_size: 1333 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Compound.edges.zip secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Biomarker to Condition relationships (diagnostic_for, indicates_risk_of_developing, prognostic_for) format: csv id: biomarkerkg.edges.condition name: BKG Condition Edges original_source: - biomarkerkg product_file_size: 1204603 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Condition.edges.zip secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Biomarker to Role relationships (has_best_classification) format: csv id: biomarkerkg.edges.role name: BKG Role Edges original_source: - biomarkerkg product_file_size: 355306 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Role.edges.zip secondary_source: - biomarkerkg - category: GraphProduct compression: zip description: Biomarker to Variant relationships (indicated_by_presence_of) format: csv id: biomarkerkg.edges.variant name: BKG Variant Edges original_source: - biomarkerkg product_file_size: 1067491 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Variant.edges.zip secondary_source: - biomarkerkg repository: https://github.com/MaayanLab/BiomarkerKG - activity_status: active category: DataSource creation_date: '2025-10-30T00:00:00Z' description: The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogues all pathways, their healthy and disease state annotations, and targets within and relationships among them. domains: - pathways - toxicology homepage_url: https://tripod.nih.gov/bioplanet/ id: bioplanet infores_id: bioplanet last_modified_date: '2025-11-25T00:00:00Z' layout: resource_detail name: BioPlanet products: - category: Product description: Comprehensive integrated pathway resource that incorporates 1,658 distinct human pathways. id: bioplanet.data name: BioPlanet Pathway Data original_source: - bioplanet publications: - authors: - Huang R - Grishagin I - Wang Y - Zhao T - Greene J - Obenauer JC - Ngan D - Nguyen D-T - Guha R - Jadhav A - Southall N - Simeonov A - Austin CP doi: 10.3389/fphar.2019.00445 id: doi:10.3389/fphar.2019.00445 journal: Front Pharmacol title: The NCATS BioPlanet – An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics year: '2019' - activity_status: active category: Aggregator creation_date: '2025-08-20T00:00:00Z' description: BioPortal is a comprehensive open repository and portal for biomedical ontologies and terminologies, providing search, browsing, mappings, versioned downloads, REST APIs, widgets, and analytics to support data integration, annotation, and semantic interoperability in the life and health sciences. domains: - biomedical - clinical - information technology - upper id: bioportal infores_id: bioportal last_modified_date: '2025-09-16T00:00:00Z' layout: resource_detail license: id: https://www.bioontology.org/terms/ label: BioPortal Terms of Use (includes attribution & reuse conditions) name: BioPortal products: - category: GraphicalInterface description: Web portal for searching, browsing, and visualizing biomedical ontologies and mappings format: http id: bioportal.portal name: BioPortal Portal product_url: https://bioportal.bioontology.org/ - category: ProgrammingInterface description: REST API for ontology concepts, search, mappings, metrics, and downloads format: http id: bioportal.api name: BioPortal REST API product_url: http://data.bioontology.org/ - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build publications: - doi: 10.1093/nar/gkaf402 id: doi:10.1093/nar/gkaf402 journal: Nucleic Acids Research title: 'BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies' year: '2025' taxon: - NCBITaxon:9606 warnings: - Some ontologies have distinct licenses; review individual ontology license metadata before reuse. - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: patrick.aloy@irbbarcelona.org label: Patrick Aloy orcid: 0000-0002-3557-0236 - category: Organization contact_details: - contact_type: url value: http://sbnb.irbbarcelona.org/ label: Structural Bioinformatics and Network Biology Group, Institute for Research in Biomedicine (IRB Barcelona) creation_date: '2025-03-09T00:00:00Z' description: A knowledge graph of biological entities and their associations that integrates and formats biomedical data as pre-calculated knowledge graph embeddings domains: - health evaluation_page: resource/bioteque/bioteque_eval.html homepage_url: https://bioteque.irbbarcelona.org/ id: bioteque last_modified_date: '2025-09-10T00:00:00Z' layout: resource_detail name: Bioteque products: - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: ProcessProduct description: Scripts used to preprocess and accommodate biomedical datasets into the knowledge database behind the Bioteque repository id: bioteque.code license: id: https://opensource.org/licenses/MIT label: MIT License name: Bioteque code original_source: - bioteque product_url: https://gitlabsbnb.irbbarcelona.org/bioteque/bioteque secondary_source: - bioteque - category: ProcessProduct description: BQsupports is a tool to uncover biomedical evidence behind experimental paired data. id: bioteque.bqsupports name: BQsupports original_source: - bioteque product_url: https://bioteque.irbbarcelona.org/bqsupports secondary_source: - bioteque publications: - authors: - Fernández-Torras A - Duran-Frigola M - Bertoni M - Locatelli M - Aloy P doi: doi:10.1038/s41467-022-33026-0 id: doi:10.1038/s41467-022-33026-0 title: Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque year: '2022' repository: https://gitlabsbnb.irbbarcelona.org/bioteque/bioteque - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: alpha.tom.kodamullil@scai.fraunhofer.de - contact_type: github value: akodamullil label: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 creation_date: '2025-09-29T00:00:00Z' description: An application ontology that represents comprehensive knowledge involving a variety of fields of medical and biological aspects. domains: - biomedical homepage_url: https://github.com/SCAI-BIO/BiomarkerOntology id: bmont last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Biomarker Ontology products: - category: OntologyProduct description: Includes axioms linking to other ontologies, but no imports of those ontologies format: owl id: bmont.BMONT.owl name: bmont.BMONT.owl product_file_size: 167585 product_url: http://purl.obolibrary.org/obo/BMONT.owl repository: https://github.com/SCAI-BIO/BiomarkerOntology - activity_status: active category: DataSource creation_date: '2025-11-19T00:00:00Z' description: BRENDA (BRaunschweig ENzyme DAtabase) is the main collection of enzyme functional data available to the scientific community. It provides comprehensive information on enzyme nomenclature, reaction mechanisms, specificity, functional parameters, and enzyme-related disease information. BRENDA integrates biochemical and molecular information from primary literature, patents, and data collections to support enzyme research and applications in biotechnology, medicine, and metabolic engineering. The database is curated at the Leibniz Institute DSMZ and is part of ELIXIR Core Data Resources and the German Network for Bioinformatics Infrastructure (de.NBI). domains: - chemistry and biochemistry - pathways - biomedical homepage_url: https://www.brenda-enzymes.org/ id: brenda last_modified_date: '2025-11-19T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: BRENDA products: - category: GraphicalInterface description: Web-based search and browsing interface for enzyme data with advanced query capabilities including EC number classification, organism taxonomy, metabolic pathways, enzyme structures, and functional parameters format: http id: brenda.web name: BRENDA Web Portal original_source: - brenda product_url: https://www.brenda-enzymes.org/ - category: ProgrammingInterface description: SOAP web service API providing programmatic access to enzyme data with methods for querying kinetic parameters, substrates, products, organisms, sequences, and other enzyme properties format: http id: brenda.soap name: BRENDA SOAP API original_source: - brenda product_url: https://www.brenda-enzymes.org/soap.php - category: ProgrammingInterface description: SPARQL endpoint for querying BRENDA knowledge graph with semantic web technologies format: http id: brenda.sparql name: BRENDA SPARQL Endpoint original_source: - brenda product_url: https://sparql.dsmz.de/brenda - category: Product description: Downloadable text files containing complete BRENDA enzyme data in structured format format: mixed id: brenda.textfile name: BRENDA Textfile Download original_source: - brenda product_url: https://www.brenda-enzymes.org/download.php - category: Product description: Downloadable JSON files containing complete BRENDA enzyme data with schema documentation format: json id: brenda.json name: BRENDA JSON Download original_source: - brenda product_url: https://www.brenda-enzymes.org/download.php - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi publications: - authors: - Hauenstein, J. - Jeske, L. - Jäde, A. - Krull, M. - Dümmer, K. - Koblitz, J. - Tietz, A. - Jahn, D. - Reimer, L. C. - Bunk, B. doi: 10.1093/nar/gkaf1113 id: PMID:41206471 journal: Nucleic Acids Research title: 'BRENDA in 2026: a Global Core Biodata Resource for functional enzyme and metabolic data within the DSMZ Digital Diversity' year: '2025' - authors: - Chang, A. - Jeske, L. - Ulbrich, S. - Hofmann, J. - Koblitz, J. - Schomburg, I. - Neumann-Schaal, M. - Jahn, D. - Schomburg, D. doi: 10.1093/nar/gkaa1025 id: PMID:33211880 journal: Nucleic Acids Research title: 'BRENDA, the ELIXIR core data resource in 2021: new developments and updates' year: '2021' taxon: - NCBITaxon:131567 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-09-29T00:00:00Z' description: An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces domains: - anatomy and development homepage_url: https://github.com/obophenotype/biological-spatial-ontology id: bspo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Biological Spatial Ontology products: - category: OntologyProduct description: Biological Spatial Ontology in OWL format format: owl id: bspo.owl name: bspo.owl product_file_size: 45961 product_url: http://purl.obolibrary.org/obo/bspo.owl - category: OntologyProduct description: Biological Spatial Ontology in OBO format format: obo id: bspo.obo name: bspo.obo product_file_size: 27154 product_url: http://purl.obolibrary.org/obo/bspo.obo repository: https://github.com/obophenotype/biological-spatial-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: c.dudek@tu-braunschweig.de - contact_type: github value: chdudek label: Christian-Alexander Dudek orcid: 0000-0001-9117-7909 creation_date: '2025-06-25T00:00:00Z' description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. domains: - anatomy and development homepage_url: http://www.brenda-enzymes.org id: bto last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: BRENDA tissue / enzyme source products: - category: OntologyProduct description: BRENDA tissue / enzyme source in OWL format format: owl id: bto.owl name: bto.owl product_file_size: 722362 product_url: http://purl.obolibrary.org/obo/bto.owl - category: OntologyProduct description: BRENDA tissue / enzyme source in OBO format format: obo id: bto.obo name: bto.obo product_file_size: 479657 product_url: http://purl.obolibrary.org/obo/bto.obo - category: OntologyProduct description: BRENDA tissue / enzyme source in JSON format format: json id: bto.json name: bto.json product_file_size: 595708 product_url: http://purl.obolibrary.org/obo/bto.json - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/BRENDA-Enzymes/BTO - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.bv-brc.org/ label: Bacterial and Viral Bioinformatics Resource Center - category: Organization contact_details: - contact_type: email value: help@bv-brc.org label: BV-BRC Help Desk creation_date: '2025-05-28T00:00:00Z' description: The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is a comprehensive resource for bacterial and viral infectious disease research that combines the data, technology, and extensive user communities from two long-running centers - PATRIC (the bacterial system) and IRD/ViPR (the viral systems). BV-BRC provides integrated data, advanced bioinformatics tools, and workflows to support the scientific community in understanding and combating infectious diseases. domains: - microbiology - genomics - health - biomedical homepage_url: https://www.bv-brc.org/ id: bv-brc last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://www.bv-brc.org/about label: Custom name: Bacterial and Viral Bioinformatics Resource Center products: - category: GraphicalInterface description: Web-based interface providing access to BV-BRC data, tools, and services format: http id: bv-brc.site name: BV-BRC Web Interface product_url: https://www.bv-brc.org/ - category: ProgrammingInterface description: Application Programming Interface for programmatic access to BV-BRC data format: http id: bv-brc.api is_public: true name: BV-BRC Data API product_url: https://www.bv-brc.org/api/doc/ - category: ProcessProduct description: Command Line Interface for batch access to BV-BRC data and services format: http id: bv-brc.cli name: BV-BRC CLI product_url: https://www.bv-brc.org/docs/cli_tutorial/index.html - category: Product description: FTP server providing direct access to BV-BRC data files format: http id: bv-brc.ftp name: BV-BRC FTP product_url: https://www.bv-brc.org/docs/quick_references/ftp.html - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: Product description: Trait data table listing all 140+ harmonized traits available in metaTraits, mapped to standardized ontologies. id: metatraits.traits name: metaTraits Trait List original_source: - bacdive - bv-brc - goldterms - progenomes product_url: https://metatraits.embl.de/traits publications: - authors: - Olson RD - Assaf R - Brettin T - Conrad N - Cucinell C - Davis JJ - Dempsey DM - Dickerman A - Dietrich EM - Kenyon RW - Kuscuoglu M - Lefkowitz EJ - Lu J - Machi D - Macken C - Mao C - Niewiadomska A - Nguyen M - Olsen GJ - Overbeek JC - Parrello B - Parrello V - Porter JS - Pusch GD - Shukla M - Singh I - Stewart L - Tan G - Thomas C - VanOeffelen M - Vonstein V - Wallace ZS - Warren AS - Wattam AR - Xia F - Yoo H - Zhang Y - Zmasek CM - Scheuermann RH - Stevens RL doi: doi:10.1093/nar/gkac1003 id: https://pubmed.ncbi.nlm.nih.gov/36350631/ journal: Nucleic Acids Research preferred: true title: 'Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR' year: '2022' repository: https://github.com/BV-BRC taxon: - NCBITaxon:2 - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-08-12T00:00:00Z' description: Cancer Genome Interpreter (CGI) is a resource that annotates tumor genomic alterations to identify likely oncogenic events and interpret their potential therapeutic, prognostic, and diagnostic relevance using curated knowledge bases, machine learning (BoostDM, OncodriveMUT), and clinical evidence levels. domains: - biomedical - clinical - precision medicine - drug discovery id: cancer-genome-interpreter last_modified_date: '2025-09-16T00:00:00Z' layout: resource_detail license: id: https://www.cancergenomeinterpreter.org/conditions#license label: Cancer Genome Interpreter License and Terms name: Cancer Genome Interpreter products: - category: GraphicalInterface description: Web portal for submitting variant lists, interpreting oncogenicity, and exploring biomarkers format: http id: cancer-genome-interpreter.portal name: Cancer Genome Interpreter Portal product_url: https://www.cancergenomeinterpreter.org/ - category: ProgrammingInterface description: REST API for programmatic access to annotation and interpretation endpoints format: http id: cancer-genome-interpreter.api name: Cancer Genome Interpreter REST API product_url: https://www.cancergenomeinterpreter.org/rest_api - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph creation_date: '2025-11-22T00:00:00Z' description: A semantic web-based knowledge graph integrating cancer registry data from multiple U.S. state registries with external datasets to enable advanced analytics, complex queries, hypothesis generation, and visualization for cancer surveillance and research domains: - clinical - biomedical - health - translational evaluation_page: resource/cancer-registry-kg/cancer-registry-kg_eval_automated.html homepage_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC8324069/ id: cancer-registry-kg last_modified_date: '2025-11-22T00:00:00Z' layout: resource_detail license: id: https://www.hhs.gov/open/public-access-guiding-principles/index.html label: NIHMS Public Access name: Cancer Registry Knowledge Graph products: - category: GraphProduct description: RDF-based knowledge graph containing 374,682 unique tumor records from Louisiana Tumor Registry (2000-2016) with 240 columns of NAACCR-standardized cancer data including demographics, tumor characteristics, treatment, and outcomes. Contains 90,673,527 triples stored in Virtuoso triplestore with SPARQL endpoint access. id: cancer-registry-kg.ltr name: Louisiana Tumor Registry Knowledge Graph original_source: - cancer-registry-kg product_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC8324069/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 405 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 405 error when accessing file - File was not able to be retrieved when checked on 2026-02-15_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 405 error when accessing file' - category: GraphProduct description: RDF-based knowledge graph containing 207,766 unique tumor records from Kentucky Cancer Registry (2010-2016) with 232 columns of cancer data. Contains 48,409,945 triples demonstrating the framework's ability to dynamically integrate multiple registry datasets without code changes. id: cancer-registry-kg.kcr name: Kentucky Cancer Registry Knowledge Graph original_source: - cancer-registry-kg product_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC8324069/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 405 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 405 error when accessing file - File was not able to be retrieved when checked on 2026-02-15_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 405 error when accessing file' - category: Product description: Linked neighborhood concentrated disadvantage index (CDI) dataset for Louisiana and Kentucky census tracts, enabling socioeconomic analysis of cancer incidence patterns and disparities. Demonstrates knowledge graph capability for third-party data integration to explain variation in cancer outcomes. id: cancer-registry-kg.cdi name: Concentrated Disadvantage Index Integration original_source: - cancer-registry-kg product_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC8324069/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 405 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 405 error when accessing file - File was not able to be retrieved when checked on 2026-02-15_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 405 error when accessing file' - category: ProgrammingInterface description: Python-based API using RDFLib for parameterized SPARQL query execution against cancer registry knowledge graph. Provides template-based queries for hypothesis generation, treatment sequence analysis, and multi-dataset integration without requiring users to write SPARQL directly. id: cancer-registry-kg.api name: Cancer Registry Query API original_source: - cancer-registry-kg product_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC8324069/ - category: GraphicalInterface description: Interactive graph visualization service using Gephi with Semantic Web Importer plugin to query Virtuoso SPARQL endpoint. Provides high-level and low-level visualizations with graph algorithms (PageRank, connected components, modularity) for pattern discovery and anomaly detection. id: cancer-registry-kg.visualization name: Gephi-Based KG Visualization original_source: - cancer-registry-kg product_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC8324069/ publications: - authors: - S.M. Shamimul Hasan - Donna Rivera - Xiao-Cheng Wu - Eric B. Durbin - J. Blair Christian - Georgia Tourassi doi: 10.1109/JBHI.2020.2990797 id: PMID:32386166 journal: IEEE Journal of Biomedical and Health Informatics title: Knowledge Graph-Enabled Cancer Data Analytics year: '2020' taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://www.naturalis.nl/ id: naturalis label: Naturalis Biodiversity Center - category: Organization contact_details: - contact_type: url value: https://www.inhs.illinois.edu/ id: inhs label: Illinois Natural History Survey - category: Organization contact_details: - contact_type: url value: https://www.gbif.org/ id: gbif label: Global Biodiversity Information Facility (GBIF) creation_date: '2025-12-20T00:00:00Z' description: Catalogue of Life is the most comprehensive global taxonomic resource providing an authoritative checklist of all known species on Earth. It aggregates 2.2+ million living species and 153,000 extinct species from 165 peer-reviewed taxonomic databases representing 500+ expert taxonomists. It serves as the foundational taxonomic backbone for biodiversity research, conservation policy, and species identification worldwide, with both static annual releases and dynamic monthly updates. domains: [] evaluation_page: resource/catalogue-of-life/catalogue-of-life_eval_automated.html homepage_url: https://www.catalogueoflife.org/ id: catalogue-of-life infores_id: catalogue-of-life last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY 4.0 (transitioning to CC-0) logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Catalogue of Life products: - category: GraphicalInterface description: Interactive web portal for browsing hierarchical taxonomy from kingdom level through infraspecific ranks with expandable taxonomy tree and full-text search for species names and synonyms format: http id: catalogue-of-life.web is_public: true name: Catalogue of Life Web Portal product_url: https://www.catalogueoflife.org/ - category: ProgrammingInterface description: RESTful JSON API providing programmatic access to species information, taxonomic names, classification hierarchies, and species identifiers with multiple endpoints format: http id: catalogue-of-life.api is_public: true name: Catalogue of Life API product_url: https://api.catalogueoflife.org/ - category: Product description: Annual comprehensive Catalogue of Life releases (Base Release with expert curation and Extended Release with broader source integration) with permanent archiving and DOI assignment id: catalogue-of-life.annual-releases name: Annual Releases product_url: https://www.catalogueoflife.org/ - category: Product description: Downloadable Catalogue of Life datasets in multiple standardized formats including Catalogue of Life Data Package (ColDP), Darwin Core Archive, ACEF, TextTree, and MySQL dumps id: catalogue-of-life.downloads name: Data Downloads product_url: https://www.catalogueoflife.org/data/download - category: Product description: ChecklistBank repository infrastructure for publishing, discovery, and management of taxonomic datasets with data standardization to ColDP format and quality control workflows id: catalogue-of-life.checklistbank name: ChecklistBank Repository product_url: https://checklistbank.org/ - category: DocumentationProduct description: Comprehensive documentation including API specifications, data format standards (ColDP, DwC-A), usage guides, citation guidelines, and taxonomic contribution workflows format: http id: catalogue-of-life.documentation is_public: true name: Catalogue of Life Documentation product_url: https://api.catalogueoflife.org/ publications: - authors: - Bisby F - Roskov Y - Culham A doi: 10.1186/1471-2105-12-447 id: doi:10.1186/1471-2105-12-447 journal: BMC Bioinformatics title: Catalogue of Life — Relational Database Design and Implementation year: '2011' - authors: - Rueda M - Hawkins BA - Moreno-Salas L - et al. doi: 10.1371/journal.pbio.2005053 id: doi:10.1371/journal.pbio.2005053 journal: PLOS Biology title: Species richness matches productivity in grassland and forest plots across the Americas year: '2017' repository: https://github.com/CatalogueOfLife synonyms: - Catalogue of Life - CoL - Species 2000/ITIS - Catalogue of Life Checklist taxon: - NCBITaxon:1 - activity_status: active category: DataSource contacts: - category: Organization label: CCLE creation_date: '2025-03-18T00:00:00Z' description: CCLE is the Cancer Cell Line Encyclopedia, a collaboration between the Broad Institute and the Novartis Institutes for Biomedical Research. domains: - health homepage_url: https://sites.broadinstitute.org/ccle/ id: ccle last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail name: CCLE products: - category: Product description: ccle OBO format: obo id: obo-db-ingest.ccle.obo license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: ccle OBO original_source: - ccle product_file_size: 19324 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.obo secondary_source: - obo-db-ingest - category: Product description: ccle OWL format: owl id: obo-db-ingest.ccle.owl license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: ccle OWL original_source: - ccle product_file_size: 29770 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.owl secondary_source: - obo-db-ingest - category: Product description: ccle OBO Graph JSON format: json id: obo-db-ingest.ccle.json license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: ccle OBO Graph JSON original_source: - ccle product_file_size: 23282 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.json secondary_source: - obo-db-ingest - category: MappingProduct description: ccle SSSOM format: sssom id: obo-db-ingest.ccle.sssom.tsv license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: ccle SSSOM original_source: - ccle product_file_size: 14414 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra - category: Product description: ccle Nodes TSV format: tsv id: obo-db-ingest.ccle.tsv license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: ccle Nodes TSV original_source: - ccle product_file_size: 12188 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.tsv secondary_source: - obo-db-ingest taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: balhoff@renci.org - contact_type: github value: balhoff label: Jim Balhoff orcid: 0000-0002-8688-6599 creation_date: '2025-09-29T00:00:00Z' description: a formalization of concepts and relations relevant to evolutionary comparative analysis domains: - biological systems homepage_url: https://github.com/evoinfo/cdao id: cdao last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Comparative Data Analysis Ontology products: - category: OntologyProduct description: Comparative Data Analysis Ontology in OWL format format: owl id: cdao.owl name: cdao.owl product_file_size: 10952 product_url: http://purl.obolibrary.org/obo/cdao.owl repository: https://github.com/evoinfo/cdao - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.cdisc.org/contact label: Clinical Data Interchange Standards Consortium (CDISC) - category: Organization contact_details: - contact_type: url value: https://evs.nci.nih.gov/ label: NCI Enterprise Vocabulary Services (EVS) creation_date: '2025-11-05T00:00:00Z' description: CDISC Controlled Terminology provides standardized codelists and valid values for clinical research data collection, tabulation, analysis, and submission to regulatory agencies including FDA and PMDA. Maintained as part of NCI Thesaurus and distributed by NCI EVS in multiple formats. domains: - clinical - biomedical - health - information technology homepage_url: https://www.cdisc.org/standards/terminology/controlled-terminology id: cdiscvocab last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: CDISC Controlled Terminology products: - category: Product description: Study Data Tabulation Model controlled terminology for clinical research data tabulation and FDA/PMDA regulatory submissions. Includes CDISC questionnaires, ratings, and scales terminology. format: mixed id: cdiscvocab.sdtm name: SDTM Controlled Terminology original_source: - cdiscvocab product_url: https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ warnings: - File was not able to be retrieved when checked on 2025-11-21_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2025-11-19_ HTTP 403 error when accessing file - category: Product description: Clinical Data Acquisition Standards Harmonization controlled terminology for consistent data collection across research studies. A subset of SDTM terminology. format: mixed id: cdiscvocab.cdash name: CDASH Controlled Terminology original_source: - cdiscvocab product_url: https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ warnings: - File was not able to be retrieved when checked on 2025-11-21_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2025-11-19_ HTTP 403 error when accessing file - category: Product description: Analysis Data Model controlled terminology for efficient generation, replication, review, and submission of analysis results from clinical trial data. format: mixed id: cdiscvocab.adam name: ADaM Controlled Terminology original_source: - cdiscvocab product_url: https://evs.nci.nih.gov/ftp1/CDISC/ADaM/ warnings: - File was not able to be retrieved when checked on 2025-11-21_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2025-11-19_ HTTP 403 error when accessing file - category: Product description: Standard for Exchange of Nonclinical Data controlled terminology for preclinical study data interchange and regulatory submissions to FDA. format: mixed id: cdiscvocab.send name: SEND Controlled Terminology original_source: - cdiscvocab product_url: https://evs.nci.nih.gov/ftp1/CDISC/SEND/ warnings: - File was not able to be retrieved when checked on 2025-11-21_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2025-11-19_ HTTP 403 error when accessing file - category: Product description: Define-XML controlled terminology providing enumeration values for the CDISC Define-XML data exchange standard. format: mixed id: cdiscvocab.definexml name: Define-XML Controlled Terminology original_source: - cdiscvocab product_url: https://evs.nci.nih.gov/ftp1/CDISC/Define-XML/ warnings: - File was not able to be retrieved when checked on 2025-11-21_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2025-11-19_ HTTP 403 error when accessing file - category: Product description: Protocol Representation Model controlled terminology for commonly used words and phrases in clinical research protocols, supporting PRM and CTR-XML standards. format: mixed id: cdiscvocab.protocol name: Protocol Controlled Terminology original_source: - cdiscvocab product_url: https://evs.nci.nih.gov/ftp1/CDISC/Protocol/ warnings: - File was not able to be retrieved when checked on 2025-11-21_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2025-11-19_ HTTP 403 error when accessing file - category: Product description: CDISC Glossary controlled terminology harmonizing definitions, acronyms, abbreviations, and initials across CDISC-managed standards initiatives. format: mixed id: cdiscvocab.glossary name: CDISC Glossary Terminology original_source: - cdiscvocab product_url: https://evs.nci.nih.gov/ftp1/CDISC/Glossary/ warnings: - File was not able to be retrieved when checked on 2025-11-21_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2025-11-19_ HTTP 403 error when accessing file - category: Product description: Digital Data Flow controlled terminology for study definition reference architecture and standardized study definitions repository development. format: mixed id: cdiscvocab.ddf name: DDF Controlled Terminology original_source: - cdiscvocab product_url: https://evs.nci.nih.gov/ftp1/CDISC/DDF/ warnings: - File was not able to be retrieved when checked on 2025-11-21_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2025-11-19_ HTTP 403 error when accessing file - category: Product description: Trial Master File controlled terminology for standardized structure, nomenclature, and metadata for electronic trial master file content. format: mixed id: cdiscvocab.tmf name: TMF Controlled Terminology original_source: - cdiscvocab product_url: https://evs.nci.nih.gov/ftp1/CDISC/TMF/ warnings: - File was not able to be retrieved when checked on 2025-11-21_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2025-11-19_ HTTP 403 error when accessing file - category: Product description: MRCT Center Clinical Research Glossary controlled terminology with plain language definitions for enhancing health literacy and participant communications. format: mixed id: cdiscvocab.mrct name: MRCT Glossary Terminology original_source: - cdiscvocab product_url: https://evs.nci.nih.gov/ftp1/CDISC/MRCT%20Center%20Clinical%20Research%20Glossary/ warnings: - File was not able to be retrieved when checked on 2025-11-21_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2025-11-19_ HTTP 403 error when accessing file - category: GraphicalInterface description: NCI Enterprise Vocabulary Services browser for exploring and searching CDISC Controlled Terminology concepts within NCI Thesaurus. format: http id: cdiscvocab.browser name: NCI EVS CDISC Terminology Browser original_source: - cdiscvocab product_url: https://evsexplore.semantics.cancer.gov/ - category: MappingProduct description: Concept mappings between different terminology systems format: csv id: athena.mappings name: Athena Concept Mappings original_source: - snomedct - icd10 - icd10cm - mesh - loinc - cdiscvocab - ciel product_url: https://athena.ohdsi.org/search-terms/start secondary_source: - athena warnings: - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ Exceeded 30 redirects. - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ Exceeded 30 redirects. synonyms: - CDISC Controlled Terminology - CDISC CT taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: landreshdz@gmail.com - contact_type: github value: LilyAndres label: Liliana Andres Hernandez orcid: 0000-0002-7696-731X creation_date: '2025-09-29T00:00:00Z' description: CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. domains: - chemistry and biochemistry homepage_url: https://cdno.info/ id: cdno last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Compositional Dietary Nutrition Ontology products: - category: OntologyProduct description: Compositional Dietary Nutrition Ontology in OWL format format: owl id: cdno.owl name: cdno.owl product_file_size: 590900 product_url: http://purl.obolibrary.org/obo/cdno.owl - category: OntologyProduct description: Compositional Dietary Nutrition Ontology in OBO format format: obo id: cdno.obo name: cdno.obo product_file_size: 331277 product_url: http://purl.obolibrary.org/obo/cdno.obo repository: https://github.com/CompositionalDietaryNutritionOntology/cdno - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://manticore.niehs.nih.gov/cebssearch/ label: NIEHS creation_date: '2025-11-05T00:00:00Z' description: Chemical Effects in Biological Systems (CEBS) is a public, web-accessible, manually curated repository of toxicology study data from the National Toxicology Program (NTP) and other research programs. CEBS contains individual-level and summarized study data from carcinogenicity studies, short-term toxicity studies, genetic toxicity assays, and other toxicological investigations. The database integrates chemical structure information, study designs, experimental conditions, and biological effects to support toxicology research and risk assessment. domains: - toxicology - biomedical - health - public health homepage_url: https://manticore.niehs.nih.gov/cebssearch/ id: cebs infores_id: cebs last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: CEBS products: - category: GraphicalInterface description: Web interface for searching and browsing CEBS toxicology data format: http id: cebs.web name: CEBS Search Interface original_source: - cebs product_url: https://manticore.niehs.nih.gov/cebssearch/ - category: Product description: Toxicology study data from NTP and other programs format: mixed id: cebs.data name: CEBS Study Data original_source: - cebs product_url: https://manticore.niehs.nih.gov/cebssearch/ - category: ProgrammingInterface description: API access to CEBS data format: http id: cebs.api name: CEBS API original_source: - cebs product_url: https://manticore.niehs.nih.gov/cebssearch/ synonyms: - CEBS - Chemical Effects in Biological Systems - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: xiaoyun@ems.hrbmu.edu.cn label: Yun Xiao creation_date: '2025-07-20T00:00:00Z' description: CellMarker is a comprehensive and accurate resource of cell markers for various cell types in tissues of human and mouse. By manually curating over 100,000 published papers, the database contains 13,605 cell markers of 467 cell types in 158 human tissues/sub-tissues and 9,148 cell makers of 389 cell types in 81 mouse tissues/sub-tissues. domains: - biomedical - genomics - biological systems - organisms homepage_url: http://xteam.xbio.top/ id: cellmarker infores_id: cellmarker last_modified_date: '2025-07-20T00:00:00Z' layout: resource_detail name: CellMarker products: - category: Product description: Cell markers of different cell types from different tissues in human id: cellmarker.human name: Human Cell Markers product_url: http://xteam.xbio.top/download/Human_cell_markers.txt warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-24_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Cell markers of different cell types from different tissues in mouse id: cellmarker.mouse name: Mouse Cell Markers product_url: http://xteam.xbio.top/download/Mouse_cell_markers.txt warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-24_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Cell markers derived from single-cell sequencing researches in human and mouse id: cellmarker.singlecell name: Single Cell Markers product_url: http://xteam.xbio.top/download/Single_cell_markers.txt warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-24_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: All cell markers of different cell types from different tissues in human and mouse id: cellmarker.all name: All Cell Markers product_url: http://xteam.xbio.top/download/all_cell_markers.txt warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-24_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphicalInterface description: ACT is a tool that makes cell type annotation easier by integrating the CellMarker resource. id: cellmarker.act name: ACT (Annotation of Cell Types) product_url: http://xteam.xbio.top/ACT/ - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra publications: - authors: - Zhang X - Lan Y - Xu J - Quan F - Zhao E - Deng C - Luo T - Xu L - Liao G - Yan M - Ping Y - Li F - Shi A - Bai J - Zhao T - Li X - Xiao Y doi: 10.1093/nar/gky900 id: doi:10.1093/nar/gky900 journal: Nucleic Acids Research preferred: true title: CellMarker - a manually curated resource of cell markers in human and mouse year: '2018' taxon: - NCBITaxon:9606 - NCBITaxon:10090 - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: amos.bairoch@sib.swiss label: Amos Bairoch orcid: 0000-0002-2261-7130 - category: Organization contact_details: - contact_type: url value: https://web.expasy.org/groups/calipho/ - contact_type: email value: cellosaurus@sib.swiss id: sib label: CALIPHO Group - SIB Swiss Institute of Bioinformatics creation_date: '2025-05-07T00:00:00Z' description: Cellosaurus is a knowledge resource on cell lines providing information on cell lines from vertebrates, invertebrates, and plants, including standardized nomenclature, cross-references to other databases, and information on problematic cell lines. domains: - biological systems - health homepage_url: https://www.cellosaurus.org/ id: cellosaurus last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Cellosaurus products: - category: GraphicalInterface description: Web interface for searching and exploring Cellosaurus data format: http id: cellosaurus.site is_public: true name: Cellosaurus Web Interface original_source: - cellosaurus product_url: https://www.cellosaurus.org/ secondary_source: - cellosaurus - category: Product description: Complete Cellosaurus data in flat text format format: tsv id: cellosaurus.txt name: Cellosaurus Text original_source: - cellosaurus product_file_size: 117036445 product_url: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt secondary_source: - cellosaurus - category: Product description: Cellosaurus data in XML format format: xml id: cellosaurus.xml name: Cellosaurus XML original_source: - cellosaurus product_file_size: 634465764 product_url: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.xml secondary_source: - cellosaurus - category: MappingProduct description: Cellosaurus cross-references in tab-delimited format format: tsv id: cellosaurus.xrefs name: Cellosaurus Cross-references original_source: - cellosaurus product_url: https://ftp.expasy.org/databases/cellosaurus/cellosaurus_xrefs.tsv secondary_source: - cellosaurus warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Complete Cellosaurus data in RDF format using the Turtle syntax format: ttl id: cellosaurus.rdf name: Cellosaurus RDF original_source: - cellosaurus product_url: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.ttl secondary_source: - cellosaurus warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: ProgrammingInterface description: RESTful API for programmatic access to Cellosaurus data id: cellosaurus.api.rest is_public: true name: Cellosaurus API original_source: - cellosaurus product_url: https://api.cellosaurus.org/ secondary_source: - cellosaurus - category: ProgrammingInterface description: SPARQL endpoint for querying Cellosaurus RDF data id: cellosaurus.api.sparql is_public: true name: Cellosaurus SPARQL Endpoint original_source: - cellosaurus product_url: https://api.cellosaurus.org/sparql-editor secondary_source: - cellosaurus - category: ProcessProduct description: CLASTR tool for STR similarity search across cell lines format: javascript id: cellosaurus.clastr name: CLASTR STR Similarity Search original_source: - cellosaurus product_url: https://www.cellosaurus.org/str-search/ secondary_source: - cellosaurus - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - authors: - Bairoch A doi: doi:10.7171/jbt.18-2902-002 id: doi:10.7171/jbt.18-2902-002 preferred: true title: The Cellosaurus, a cell-line knowledge resource year: '2018' repository: https://github.com/calipho-sib/cellosaurus taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: jeevangelista label: John Erol Evangelista creation_date: '2025-03-09T00:00:00Z' description: The Common Fund Data Ecosystem (CFDE) aims to facilitate better integration, and reuse of Common Fund data to accelerate discoveries in biomedical research.The Data Distillery project aims to integrate summarized (“distilled”) Common Fund data within a knowledge graph. The purpose of the Data Distillery Knowledge Graph (DDKG) is to link multiple sources of expertly curated data, thus providing data integration across multiple Common Fund data coordinating centers (DCCs). domains: - health evaluation_page: resource/cfde-ddkg/cfde-ddkg_eval_automated.html homepage_url: https://dd-kg-ui.cfde.cloud/about id: cfde-ddkg last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Data Distillery Knowledge Graph (DDKG) products: - category: GraphicalInterface description: Interactive web interface for browsing and querying Data Distillery Knowledge Graph resources. format: http id: cfde-ddkg.portal name: DDKG Web Interface original_source: - cfde-ddkg product_url: https://dd-kg-ui.cfde.cloud/ - category: Product description: JSON manifest listing downloadable DDKG resources and files. format: json id: cfde-ddkg.downloads name: DDKG Downloads Manifest original_source: - cfde-ddkg product_file_size: 5216 product_url: https://s3.amazonaws.com/maayan-kg/dd-kg/minio/downloads.json repository: https://github.com/MaayanLab/datadistillery-kg - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: cfde-support@nih-cfde.org - contact_type: url value: https://cfde.cloud/ label: Common Fund Data Ecosystem - category: Organization contact_details: - contact_type: email value: avi.maayan@mssm.edu - contact_type: url value: https://labs.icahn.mssm.edu/maayanlab/ label: Ma'ayan Laboratory creation_date: '2025-09-23T00:00:00Z' description: Common Fund Data Ecosystem Gene Set Enrichment (CFDE-GSE) is a knowledge graph that integrates gene set collections from multiple Common Fund programs to enable cross-program gene set enrichment analysis, functional annotation, and systems-level understanding of biological processes across diverse biomedical research domains. domains: - biomedical - genomics - systems biology - biological systems evaluation_page: resource/cfde-gse/cfde-gse_eval_automated.html homepage_url: https://cfde.cloud/gse/ id: cfde-gse last_modified_date: '2025-09-23T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Common Fund Data Ecosystem Gene Set Enrichment (CFDE-GSE) products: - category: GraphicalInterface description: Interactive web interface for cross-program gene set enrichment analysis across Common Fund datasets format: http id: cfde-gse.portal name: CFDE Gene Set Enrichment Portal product_url: https://cfde.cloud/gse/ - category: ProgrammingInterface description: RESTful API for programmatic access to Common Fund gene set collections and enrichment analysis format: http id: cfde-gse.api name: CFDE-GSE API product_url: https://cfde.cloud/gse/api/ - category: GraphProduct description: Neo4j knowledge graph containing integrated gene sets from multiple Common Fund programs with cross-references dump_format: neo4j format: neo4j id: cfde-gse.graph name: CFDE-GSE Knowledge Graph - category: Product description: Standardized gene set collections from Common Fund programs in GMT format id: cfde-gse.genesets name: CFDE Gene Set Collections product_url: https://cfde.cloud/gse/downloads/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' publications: - authors: - Clarke DJB - Jeon M - Stein DJ - Moiseyev N - Kropiwnicki E - Ben-Moshe NB - Barupal DK - Ma'ayan A id: doi:10.1038/s41467-2022-28631-3 journal: Nature Communications preferred: true title: Cross-program analysis of the CFDE gene sets reveals common biological themes year: '2022' repository: https://github.com/nih-cfde/cfde-gse - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: agbase@email.arizona.edu label: CGNC creation_date: '2025-03-24T00:00:00Z' description: CGNC is the Chicken Gene Nomenclature Consortium. It is an international group of researchers interested in providing standardized gene nomenclature for chicken genes. domains: - organisms homepage_url: http://birdgenenames.org/cgnc/ id: cgnc last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: CGNC products: - category: Product description: All CGNC public data, including CGNC ID, Entrez Gene ID, Ensembl Gene ID, gene symbol, gene name, gene synonym, curation status and last edit date. format: tsv id: cgnc.genes name: CGNC Genes original_source: - cgnc product_url: http://birdgenenames.org/cgnc/downloads.jsp?file=standard secondary_source: - cgnc warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: cgnc OBO format: obo id: obo-db-ingest.cgnc.obo license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: cgnc OBO original_source: - cgnc product_file_size: 683991 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.obo secondary_source: - obo-db-ingest - category: Product description: cgnc OWL format: owl id: obo-db-ingest.cgnc.owl license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: cgnc OWL original_source: - cgnc product_file_size: 911421 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.owl secondary_source: - obo-db-ingest - category: Product description: cgnc OBO Graph JSON format: json id: obo-db-ingest.cgnc.json license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: cgnc OBO Graph JSON original_source: - cgnc product_file_size: 861880 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.json secondary_source: - obo-db-ingest - category: MappingProduct description: cgnc SSSOM format: sssom id: obo-db-ingest.cgnc.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: cgnc SSSOM original_source: - cgnc product_file_size: 258292 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: cgnc Nodes TSV format: tsv id: obo-db-ingest.cgnc.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: cgnc Nodes TSV original_source: - cgnc product_file_size: 406670 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.tsv secondary_source: - obo-db-ingest publications: - authors: - Burt DW - CarrÎ W - Fell M - Law AS - Antin PB - Maglott DR - Weber JA - Schmidt CJ - Burgess SC - McCarthy FM doi: 10.1186/1471-2164-10-S2-S5 id: doi:10.1186/1471-2164-10-S2-S5 title: The Chicken Gene Nomenclature Committee report year: '2009' - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: avi.maayan@mssm.edu - contact_type: url value: https://labs.icahn.mssm.edu/maayanlab/ label: Ma'ayan Laboratory creation_date: '2025-09-23T00:00:00Z' description: ChEA-KG is a knowledge graph built around the ChEA (ChIP Enrichment Analysis) database that integrates chromatin immunoprecipitation sequencing data with transcription factor binding sites, gene regulatory networks, and functional annotations to provide comprehensive insights into transcriptional regulation across cell types and conditions. domains: - biomedical - genomics - systems biology evaluation_page: resource/chea-kg/chea-kg_eval_automated.html homepage_url: https://maayanlab.cloud/chea-kg/ id: chea-kg last_modified_date: '2025-09-23T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: ChEA-KG products: - category: GraphicalInterface description: Interactive web interface for exploring transcription factor-target gene relationships with regulatory network visualization format: http id: chea-kg.portal name: ChEA-KG Explorer product_url: https://maayanlab.cloud/chea-kg/ - category: ProgrammingInterface description: RESTful API for programmatic access to ChIP-seq derived transcription factor binding data format: http id: chea-kg.api name: ChEA-KG API product_url: https://maayanlab.cloud/chea-kg/api/ - category: GraphProduct description: Neo4j database containing transcription factors, target genes, and regulatory relationships from ChIP-seq studies dump_format: neo4j format: neo4j id: chea-kg.graph name: ChEA-KG Database - category: Product description: Processed ChIP-seq datasets with transcription factor binding sites and target gene annotations id: chea-kg.chipseq name: ChEA ChIP-seq Data product_url: https://maayanlab.cloud/chea3/index.html#content4-13 publications: - authors: - Keenan AB - Torre D - Lachmann A - Leong AK - Wojtkiewicz ML - Utti V - Jagodnik KM - Kropiwnicki E - Wang Z - Ma'ayan A id: doi:10.1093/nar/gkz446 journal: Nucleic Acids Research preferred: true title: 'ChEA3: transcription factor enrichment analysis by orthogonal omics integration' year: '2019' repository: https://github.com/MaayanLab/chea-kg - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: amalik@ebi.ac.uk - contact_type: github value: amalik01 label: Adnan Malik orcid: 0000-0001-8123-5351 creation_date: '2025-03-18T00:00:00Z' description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. domains: - chemistry and biochemistry homepage_url: http://www.ebi.ac.uk/chebi id: chebi last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Chemical Entities of Biological Interest products: - category: OntologyProduct description: Chemical Entities of Biological Interest in OWL format format: owl id: chebi.owl name: chebi.owl product_url: http://purl.obolibrary.org/obo/chebi.owl - category: OntologyProduct description: Chemical Entities of Biological Interest in OBO format format: obo id: chebi.obo name: chebi.obo product_url: http://purl.obolibrary.org/obo/chebi.obo - category: OntologyProduct description: Chemical Entities of Biological Interest in JSON format format: json id: chebi.json name: chebi.json product_file_size: 506385117 product_url: http://purl.obolibrary.org/obo/chebi.json - category: OntologyProduct description: chebi, compressed owl format: owl id: chebi.owl.gz name: chebi, compressed owl product_file_size: 62935653 product_url: http://purl.obolibrary.org/obo/chebi.owl.gz - category: OntologyProduct description: chebi_lite, no syns or xrefs format: obo id: chebi.chebi_lite.obo name: chebi_lite, no syns or xrefs product_url: http://purl.obolibrary.org/obo/chebi/chebi_lite.obo - category: OntologyProduct description: chebi_core, no xrefs format: obo id: chebi.chebi_core.obo name: chebi_core, no xrefs product_url: http://purl.obolibrary.org/obo/chebi/chebi_core.obo - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - category: MappingProduct description: bigg.metabolite SSSOM format: sssom id: obo-db-ingest.bigg.metabolite.sssom.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.metabolite SSSOM original_source: - chebi - bigg - biocyc - kegg - reactome product_file_size: 400516 product_url: https://w3id.org/biopragmatics/resources/bigg.metabolite/bigg.metabolite.sssom.tsv secondary_source: - obo-db-ingest - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: GraphProduct description: KGX distribution of the ICEES Exposures KP in Knowledge Graph Exchange (KGX) format, containing integrated clinical and environmental exposures data as a knowledge graph with 226 nodes and 14,342 edges format: kgx-jsonl id: icees-kg.graph name: KGX distribution of the ICEES Exposures KP original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/ secondary_source: - icees-kg - category: ProgrammingInterface description: Translator Reasoner API (TRAPI) endpoint for querying ICEES KG using standardized Translator protocols format: http id: icees-kg.trapi name: ICEES KG TRAPI API original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg-trapi secondary_source: - icees-kg - category: Product description: Meta knowledge graph and metadata describing the data sources, node types, edge types, and predicates available in ICEES KG format: json id: icees-kg.metadata name: ICEES KG Metadata original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/metadata-metadata-get-icees-kg secondary_source: - icees-kg - category: GraphProduct description: Downloadable knowledge graph dump in TAR/GZ format containing complete FORUM data id: forum.graph.dump name: FORUM Knowledge Graph Dump original_source: - mesh - chebi - cito - fabio - dc - cheminf - skos - chemont - pubchem - pubmed product_url: ftp://forum:Forum2021Cov!@ftp.semantic-metabolomics.org/dumps/2021/share.tar.gz secondary_source: - forum warnings: - File was not able to be retrieved when checked on 2026-03-08_ FTP error_ timed out - File was not able to be retrieved when checked on 2026-02-26_ FTP error_ timed out - 'File was not able to be retrieved when checked on 2026-03-11: FTP error: timed out' - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct description: Nodes for the Drug Approvals KP, v0.3.9 format: kgx id: drug-approvals-kp.graph.nodes name: Drug Approvals KP Graph Nodes original_source: - chebi - doid - hp - mondo product_file_size: 701451 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_nodes_v0.3.9.tsv secondary_source: - drug-approvals-kp - category: GraphProduct description: Edges for the Drug Approvals KP, v0.3.9 format: kgx id: drug-approvals-kp.graph.edges name: Drug Approvals KP Graph Edges original_source: - chebi - doid - hp - mondo product_file_size: 31052966 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_edges_v0.3.9.tsv secondary_source: - drug-approvals-kp - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' - category: GraphProduct description: RDF dump of the Open Research Knowledge Graph distributed in N-Triples format. format: ntriples id: orkg.dump name: ORKG RDF Dump original_source: - orkg - wikidata - geonames - ncit - chebi - ncbitaxon - go - clo - omit - iao - uo - stato - obi product_file_size: 642902930 product_url: https://orkg.org/api/rdf/dump secondary_source: - orkg repository: https://github.com/ebi-chebi/ChEBI - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: chembl-help@ebi.ac.uk id: ebi label: ChEMBL creation_date: '2025-03-09T00:00:00Z' description: ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. domains: - chemistry and biochemistry homepage_url: https://www.ebi.ac.uk/chembl/ id: chembl infores_id: chembl last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 logo: https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png name: ChEMBL products: - category: GraphicalInterface description: Web interface for searching and exploring ChEMBL data id: chembl.site is_public: true name: ChEMBL Web Interface original_source: - chembl product_url: https://www.ebi.ac.uk/chembl/ secondary_source: - chembl - category: ProgrammingInterface description: RESTful API for accessing ChEMBL data programmatically id: chembl.api is_public: true name: ChEMBL API original_source: - chembl product_url: https://www.ebi.ac.uk/chembl/api/data/docs secondary_source: - chembl - category: Product compression: gzip description: PostgreSQL database dump of the complete ChEMBL database format: postgres id: chembl.postgres name: ChEMBL PostgreSQL original_source: - chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ secondary_source: - chembl - category: Product compression: gzip description: MySQL database dump of the complete ChEMBL database format: mysql id: chembl.mysql name: ChEMBL MySQL original_source: - chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ secondary_source: - chembl - category: Product compression: gzip description: SQLite database file containing the complete ChEMBL database format: sqlite id: chembl.sqlite name: ChEMBL SQLite original_source: - chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ secondary_source: - chembl - category: Product compression: gzip description: Structure data files for all chemical compounds in ChEMBL format: sdf id: chembl.sdf name: ChEMBL SDF original_source: - chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ secondary_source: - chembl - category: Product compression: gzip description: RDF version of the ChEMBL database format: ttl id: chembl.rdf name: ChEMBL RDF original_source: - chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/latest/ secondary_source: - chembl - category: ProgrammingInterface description: SPARQL endpoint for the ChEMBL RDF data id: chembl.sparql is_public: true name: ChEMBL SPARQL original_source: - chembl product_url: https://www.ebi.ac.uk/rdf/services/sparql secondary_source: - chembl - category: MappingProduct description: Mapping between chembl_35 target chembl_ids and UniProt accessions id: chembl.map_to_uniprot is_public: true name: ChEMBL map to UniProt original_source: - chembl - uniprot product_file_size: 1012901 product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_uniprot_mapping.txt secondary_source: - chembl - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra - category: GraphProduct description: KGX distribution of the ICEES Exposures KP in Knowledge Graph Exchange (KGX) format, containing integrated clinical and environmental exposures data as a knowledge graph with 226 nodes and 14,342 edges format: kgx-jsonl id: icees-kg.graph name: KGX distribution of the ICEES Exposures KP original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/ secondary_source: - icees-kg - category: ProgrammingInterface description: Translator Reasoner API (TRAPI) endpoint for querying ICEES KG using standardized Translator protocols format: http id: icees-kg.trapi name: ICEES KG TRAPI API original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg-trapi secondary_source: - icees-kg - category: Product description: Meta knowledge graph and metadata describing the data sources, node types, edge types, and predicates available in ICEES KG format: json id: icees-kg.metadata name: ICEES KG Metadata original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/metadata-metadata-get-icees-kg secondary_source: - icees-kg - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - category: GraphProduct description: KGX graph package for ChEMBL (build chembl_36_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.chembl.graph name: Translator ChEMBL KGX Graph original_source: - chembl product_url: https://stars.renci.org/var/translator/releases/chembl/2025_12_15/ secondary_source: - translator - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv - category: Product description: chembl.compound Nodes TSV format: tsv id: obo-db-ingest.chembl.compound.tsv license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.compound Nodes TSV original_source: - chembl product_file_size: 411222 product_url: https://w3id.org/biopragmatics/resources/chembl.compound/chembl.compound.tsv secondary_source: - obo-db-ingest - category: Product description: chembl.target Nodes TSV format: tsv id: obo-db-ingest.chembl.target.tsv license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.target Nodes TSV original_source: - chembl product_file_size: 260194 product_url: https://w3id.org/biopragmatics/resources/chembl.target/chembl.target.tsv secondary_source: - obo-db-ingest publications: - authors: - Zdrazil B - Felix E - Hunter F - Manners EJM - Blackshaw J - Corbett S - de Veij M - Ioannidis H - Mendez Lopez DM - Mosquera JF - Magarinos MP - Bosc N - Arcila R - Kizilören T - Gaulton A - Bento AP - Adasme MF - Monecke PM - Landrum GA - Leach AR doi: doi:10.1093/nar/gkad1004 id: doi:10.1093/nar/gkad1004 preferred: true title: 'The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods' year: '2023' repository: https://github.com/chembl taxon: - NCBITaxon:9606 - NCBITaxon:10090 - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: miquel.duran@irbbarcelona.org label: Miquel Duran - category: Individual contact_details: - contact_type: email value: patrick.aloy@irbbarcelona.org label: Patrick Aloy creation_date: '2025-07-08T00:00:00Z' description: The Chemical Checker (CC) is a data-driven resource of small molecule bioactivity data, organized into five levels of increasing complexity, ranging from chemical properties to clinical outcomes. It is designed to support computational drug discovery tasks. domains: - drug discovery homepage_url: http://packages.sbnb-pages.irbbarcelona.org/chemical_checker/ id: chemicalchecker last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail name: Chemical Checker products: - category: Product description: Precomputed signatures for small molecules, suitable for machine learning. format: hdf5 id: chemicalchecker.signatures name: Chemical Checker Signatures product_url: http://packages.sbnb-pages.irbbarcelona.org/chemical_checker/signaturization.html - category: ProcessProduct description: Software tool for producing bioactivity signature vectors. format: python id: chemicalchecker.signaturizer name: Signaturizer product_url: https://github.com/sbnb-irb/signaturizer - category: ProgrammingInterface description: Programmatic interface for Chemical Checker data. id: chemicalchecker.api name: Chemical Checker RESTful API product_url: https://chemicalchecker.com/api/db/getSignature/ - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque repository: https://github.com/sbnb-irb/chemical-checker taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: egon.willighagen@gmail.com - contact_type: github value: egonw label: Egon Willighagen orcid: 0000-0001-7542-0286 creation_date: '2025-09-29T00:00:00Z' description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. domains: - chemistry and biochemistry homepage_url: https://github.com/semanticchemistry/semanticchemistry id: cheminf last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Chemical Information Ontology products: - category: OntologyProduct description: Chemical Information Ontology in OWL format format: owl id: cheminf.owl name: cheminf.owl product_file_size: 22830 product_url: http://purl.obolibrary.org/obo/cheminf.owl - category: GraphProduct description: Downloadable knowledge graph dump in TAR/GZ format containing complete FORUM data id: forum.graph.dump name: FORUM Knowledge Graph Dump original_source: - mesh - chebi - cito - fabio - dc - cheminf - skos - chemont - pubchem - pubmed product_url: ftp://forum:Forum2021Cov!@ftp.semantic-metabolomics.org/dumps/2021/share.tar.gz secondary_source: - forum warnings: - File was not able to be retrieved when checked on 2026-03-08_ FTP error_ timed out - File was not able to be retrieved when checked on 2026-02-26_ FTP error_ timed out - 'File was not able to be retrieved when checked on 2026-03-11: FTP error: timed out' repository: https://github.com/semanticchemistry/semanticchemistry - activity_status: active category: Ontology creation_date: '2025-12-11T00:00:00Z' description: ChemOnt (Chemical Ontology) is a comprehensive chemical ontology that provides a hierarchical classification of chemical entities. It is designed to support chemical informatics applications and enable semantic integration of chemical data across biomedical systems. ChemOnt is developed and maintained by the Wishart Lab and integrates chemical structures with ontological classifications. domains: - chemistry and biochemistry homepage_url: http://classyfire.wishartlab.com/ id: chemont last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: ChemOnt products: - category: GraphicalInterface description: ClassyFire web interface for chemical classification and ontology exploration id: chemont.classyfire name: ClassyFire Web Interface product_url: http://classyfire.wishartlab.com/ - category: OntologyProduct description: ChemOnt OBO format ontology file (version 2.1) format: obo id: chemont.obo name: ChemOnt OBO Ontology product_file_size: 307900 product_url: http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip - category: GraphProduct description: Downloadable knowledge graph dump in TAR/GZ format containing complete FORUM data id: forum.graph.dump name: FORUM Knowledge Graph Dump original_source: - mesh - chebi - cito - fabio - dc - cheminf - skos - chemont - pubchem - pubmed product_url: ftp://forum:Forum2021Cov!@ftp.semantic-metabolomics.org/dumps/2021/share.tar.gz secondary_source: - forum warnings: - File was not able to be retrieved when checked on 2026-03-08_ FTP error_ timed out - File was not able to be retrieved when checked on 2026-02-26_ FTP error_ timed out - 'File was not able to be retrieved when checked on 2026-03-11: FTP error: timed out' repository: https://github.com/wishartlab/chemontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: vasilevs@ohsu.edu - contact_type: github value: nicolevasilevsky label: Nicole Vasilevsky orcid: 0000-0001-5208-3432 creation_date: '2025-09-29T00:00:00Z' description: CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. domains: - chemistry and biochemistry homepage_url: https://github.com/obophenotype/chiro id: chiro last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: CHEBI Integrated Role Ontology products: - category: OntologyProduct description: CHEBI Integrated Role Ontology in OWL format format: owl id: chiro.owl name: chiro.owl product_file_size: 7043 product_url: http://purl.obolibrary.org/obo/chiro.owl - category: OntologyProduct description: CHEBI Integrated Role Ontology in OBO format format: obo id: chiro.obo name: chiro.obo product_file_size: 3337 product_url: http://purl.obolibrary.org/obo/chiro.obo repository: https://github.com/obophenotype/chiro - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: batchelorc@rsc.org - contact_type: github value: batchelorc label: Colin Batchelor orcid: 0000-0001-5985-7429 creation_date: '2025-09-29T00:00:00Z' description: CHMO, the chemical methods ontology, describes methods used to domains: - biomedical homepage_url: https://github.com/rsc-ontologies/rsc-cmo id: chmo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Chemical Methods Ontology products: - category: OntologyProduct description: Chemical Methods Ontology in OWL format format: owl id: chmo.owl name: chmo.owl product_file_size: 460248 product_url: http://purl.obolibrary.org/obo/chmo.owl repository: https://github.com/rsc-ontologies/rsc-cmo - activity_status: active category: Ontology contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Christopher J. Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-03-09T00:00:00Z' description: Monochrom, also known as Chromo or CHR, is an automatic translation of UCSC chromosome bands to OWL classes. Each chromosome and chromosomal region is represented as an OWL class. domains: - chemistry and biochemistry homepage_url: https://monarch-initiative.github.io/monochrom/ id: chr last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Monochrom Ontology products: - category: OntologyProduct description: OWL release of Monochrom Ontology format: owl id: chr.model.owl name: Monochrom Ontology OWL release original_source: - ro - go - ncbitaxon - iao - geno - skos - gff product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl secondary_source: - chr repository: https://github.com/monarch-initiative/monochrom/ - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: yongqunh@med.umich.edu - contact_type: github value: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 creation_date: '2025-09-29T00:00:00Z' description: The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. domains: - biomedical homepage_url: https://github.com/cido-ontology/cido id: cido last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Coronavirus Infectious Disease Ontology products: - category: OntologyProduct description: Coronavirus Infectious Disease Ontology in OWL format format: owl id: cido.owl name: cido.owl product_file_size: 2511321 product_url: http://purl.obolibrary.org/obo/cido.owl repository: https://github.com/cido-ontology/cido - activity_status: active category: Aggregator contacts: - category: Individual contact_details: - contact_type: email value: ask2164@cumc.columbia.edu label: Andrew S. Kanter, MD MPH - category: Organization contact_details: - contact_type: url value: https://www.dbmi.columbia.edu/ label: Columbia University Department of Biomedical Informatics creation_date: '2025-11-05T00:00:00Z' description: The Columbia International eHealth Laboratory (CIEL) dictionary is a shared open concept dictionary that provides comprehensive terminology services to OpenMRS and other health information systems. Based at Columbia University's Department of Biomedical Informatics, CIEL contains over 55,000 medical concepts mapped to standardized code systems including ICD, SNOMED CT, LOINC, RxNorm, and many others. CIEL supports open source health initiatives globally and has been recognized as both a Digital Public Good by the Digital Public Goods Alliance and a Content Public Good by Digital Square. domains: - clinical - health - biomedical - information technology homepage_url: https://openconceptlab.org/project/ciel/ id: ciel last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: CIEL products: - category: GraphicalInterface description: Web interface for browsing CIEL concept dictionary via Open Concept Lab format: http id: ciel.ocl name: CIEL on OCL Online original_source: - ciel product_url: https://app.openconceptlab.org/#/orgs/CIEL/sources/CIEL/ - category: Product description: CIEL concept dictionary with over 55,000 medical concepts format: mixed id: ciel.dictionary name: CIEL Concept Dictionary original_source: - ciel product_url: https://app.openconceptlab.org/#/orgs/CIEL/sources/CIEL/ - category: Product description: COVID-19 concept starter set for rapid implementation format: mixed id: ciel.covid19 name: CIEL COVID-19 Starter Set original_source: - ciel product_url: https://app.openconceptlab.org/#/orgs/CIEL/collections/COVID-19-Starter-Set/ - category: Product description: Monkeypox (mpox) concept starter set format: mixed id: ciel.mpx name: CIEL Monkeypox Starter Set original_source: - ciel product_url: https://app.openconceptlab.org/#/orgs/CIEL/collections/MPX/ - category: MappingProduct description: Concept mappings between different terminology systems format: csv id: athena.mappings name: Athena Concept Mappings original_source: - snomedct - icd10 - icd10cm - mesh - loinc - cdiscvocab - ciel product_url: https://athena.ohdsi.org/search-terms/start secondary_source: - athena warnings: - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ Exceeded 30 redirects. - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ Exceeded 30 redirects. synonyms: - CIEL - Columbia International eHealth Laboratory - CIEL Concept Dictionary taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: frederic.bastian@unil.ch - contact_type: github value: fbastian label: Fr d ric Bastian orcid: 0000-0002-9415-5104 creation_date: '2025-09-29T00:00:00Z' description: An ontology to capture confidence information about annotations. domains: - biomedical homepage_url: https://github.com/BgeeDB/confidence-information-ontology id: cio last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Confidence Information Ontology products: - category: OntologyProduct description: Confidence Information Ontology in OWL format format: owl id: cio.owl name: cio.owl product_file_size: 6187 product_url: http://purl.obolibrary.org/obo/cio.owl - category: OntologyProduct description: Confidence Information Ontology in OBO format format: obo id: cio.obo name: cio.obo product_file_size: 3960 product_url: http://purl.obolibrary.org/obo/cio.obo repository: https://github.com/BgeeDB/confidence-information-ontology - activity_status: active category: Aggregator creation_date: '2025-08-25T00:00:00Z' description: circBase is a database and exploration portal for circular RNAs (circRNAs), aggregating published circRNA detection datasets across multiple species, tissues, and experimental conditions, and providing search, genomic context, expression summaries, and downloadable data plus scripts for circRNA discovery. domains: - genomics - biological systems - organisms id: circbase last_modified_date: '2025-09-16T00:00:00Z' layout: resource_detail license: id: http://www.circbase.org/ label: circBase site terms (dataset-specific; cite original studies) name: circBase products: - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphicalInterface description: Web interface for searching and browsing circular RNA annotations across species. id: circbase.portal name: circBase Portal product_url: https://www.circbase.org/ - category: Product description: Bulk data downloads (BED/GFF and sequence files) for circular RNAs provided via the downloads CGI page. id: circbase.downloads name: circBase Bulk Downloads product_url: https://www.circbase.org/cgi-bin/downloads.cgi - category: DocumentationProduct description: Help and documentation describing circBase data sources, identifiers, and usage notes. id: circbase.docs name: circBase Documentation product_url: https://www.circbase.org/doc/help_mod.html - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg publications: - id: doi:10.1261/rna.043687.113 journal: RNA preferred: true title: 'circBase: a database for circular RNAs' year: '2014' - activity_status: active category: Ontology creation_date: '2025-12-11T00:00:00Z' description: CiTO (Citation Typing Ontology) is a formal ontology that provides a machine-readable vocabulary for describing the nature and type of citations within bibliographic references. It enables the semantic representation of the relationships between citing and cited scholarly works, supporting the analysis of citation networks and the characterization of how one publication cites another. domains: - literature - general homepage_url: https://sparontologies.github.io/cito/current/cito.html id: cito last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: CiTO products: - category: OntologyProduct description: CiTO ontology in Turtle RDF format format: ttl id: cito.ttl name: CiTO Turtle File product_file_size: 53618 product_url: http://purl.org/spar/cito.ttl - category: DocumentationProduct description: CiTO documentation and specification id: cito.documentation name: CiTO Documentation product_url: https://sparontologies.github.io/cito/current/cito.html - category: GraphProduct description: Downloadable knowledge graph dump in TAR/GZ format containing complete FORUM data id: forum.graph.dump name: FORUM Knowledge Graph Dump original_source: - mesh - chebi - cito - fabio - dc - cheminf - skos - chemont - pubchem - pubmed product_url: ftp://forum:Forum2021Cov!@ftp.semantic-metabolomics.org/dumps/2021/share.tar.gz secondary_source: - forum warnings: - File was not able to be retrieved when checked on 2026-03-08_ FTP error_ timed out - File was not able to be retrieved when checked on 2026-02-26_ FTP error_ timed out - 'File was not able to be retrieved when checked on 2026-03-11: FTP error: timed out' repository: https://github.com/sparontologies/cito - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: help@civicdb.org label: CIViC Support - category: Organization label: The McDonnell Genome Institute at Washington University School of Medicine creation_date: '2025-05-29T00:00:00Z' description: The Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase is a free and open resource for public use that enables the interpretation of variants in cancer by providing community-curated information about the clinical significance of genomic variants. domains: - biomedical - health - genomics - clinical - precision medicine homepage_url: https://civicdb.org/ id: civic infores_id: civic last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: CIViC products: - category: GraphicalInterface description: Web interface that allows searching, browsing, and curating content in the CIViC database. id: civic.site name: CIViC Web Interface product_url: https://civicdb.org/ - category: ProgrammingInterface description: GraphQL API for programmatic access to the CIViC database. id: civic.api.v2 is_public: true name: CIViC GraphQL API (V2) product_url: https://civicdb.org/api/graphiql - category: ProgrammingInterface description: REST API for programmatic access to the CIViC database (deprecated but still accessible). id: civic.api.v1 is_public: true name: CIViC REST API (V1 - Deprecated) product_url: https://v1.civicdb.org/api - category: Product description: CIViC Feature summaries, nightly version format: tsv id: civic.data.features name: CIViC Features (Nightly) product_file_size: 171302 product_url: https://civicdb.org/downloads/nightly/nightly-FeatureSummaries.tsv - category: Product description: CIViC Variant summaries, nightly version format: tsv id: civic.data.variants name: CIViC Variants (Nightly) product_file_size: 533165 product_url: https://civicdb.org/downloads/nightly/nightly-VariantSummaries.tsv - category: Product description: CIViC Molecular Profile summaries, nightly version format: tsv id: civic.data.molecularprofile name: CIViC Molecular Profiles (Nightly) product_file_size: 621001 product_url: https://civicdb.org/downloads/nightly/nightly-MolecularProfileSummaries.tsv - category: Product description: CIViC Clinical Evidence summaries, nightly version format: tsv id: civic.data.evidence name: CIViC Clinical Evidence (Nightly) product_file_size: 3711846 product_url: https://civicdb.org/downloads/nightly/nightly-ClinicalEvidenceSummaries.tsv - 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category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: Product description: civic.gid Nodes TSV format: tsv id: obo-db-ingest.civic.gid.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: civic.gid Nodes TSV original_source: - civic product_file_size: 34804 product_url: https://w3id.org/biopragmatics/resources/civic.gid/civic.gid.tsv secondary_source: - obo-db-ingest publications: - authors: - Griffith M - Spies NC - Krysiak K - McMichael JF - Coffman AC - Danos AM - Ainscough BJ - Ramirez CA - Rieke DT - Kujan L - Barnell EK - Wagner AH - Skidmore ZL - Wollam A - Liu CJ - Jones MR - Bilski RL - Lesurf R - Feng YY - Shah NM - Bonakdar M - Trani L - Matlock M - Ramu A - Campbell KM - Spies GC - Graubert AP - Gangavarapu K - Eldred JM - Larson DE - Walker JR - Good BM - Wu C - Su AI - Dienstmann R - Margolin AA - Tamborero D - Lopez-Bigas N - Jones SJ - Bose R - Spencer DH - Wartman LD - Wilson RK - Mardis ER - Griffith OL doi: doi:10.1038/ng.3774 id: https://doi.org/10.1038/ng.3774 journal: Nature Genetics title: CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer year: '2017' - authors: - Danos AM - Ritter DI - Wagner AH - Krysiak K - Sonkin D - Micheel C - McCoy M - Rao S - Raca G - Boca SM - Roy A - Barnell EK - McMichael JF - Kiwala S - Coffman AC - Kujan L - Kulkarni S - Griffith M - Madhavan S - Griffith OL doi: doi:10.1186/s13073-019-0687-x id: https://doi.org/10.1186/s13073-019-0687-x journal: Genome Medicine title: Standard operating procedure for curation and clinical interpretation of variants in cancer year: '2019' taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: do12@sanger.ac.uk - contact_type: github value: dosumis label: David Osumi-Sutherland orcid: 0000-0002-7073-9172 creation_date: '2025-06-04T00:00:00Z' description: The Cell Ontology is a structured controlled vocabulary for cell types in animals. domains: - anatomy and development homepage_url: https://obophenotype.github.io/cell-ontology/ id: cl last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Cell Ontology products: - category: OntologyProduct description: Complete ontology, plus inter-ontology axioms, and imports modules format: owl id: cl.owl name: Main CL OWL edition product_file_size: 66753027 product_url: http://purl.obolibrary.org/obo/cl.owl - category: OntologyProduct description: Complete ontology, plus inter-ontology axioms, and imports modules merged in format: obo id: cl.obo name: CL obo format edition product_file_size: 17349355 product_url: http://purl.obolibrary.org/obo/cl.obo - category: OntologyProduct description: Complete ontology, plus inter-ontology axioms, and imports modules merged in format: json id: cl.json name: CL OBOGraph-JSON format edition product_file_size: 38790011 product_url: http://purl.obolibrary.org/obo/cl.json - category: OntologyProduct description: Basic version, no inter-ontology axioms format: owl id: cl.cl-basic.owl name: Basic CL product_file_size: 8979957 product_url: http://purl.obolibrary.org/obo/cl/cl-basic.owl - category: OntologyProduct description: Basic version, no inter-ontology axioms format: obo id: cl.cl-basic.obo name: Basic CL (OBO version) product_file_size: 3112081 product_url: http://purl.obolibrary.org/obo/cl/cl-basic.obo - category: OntologyProduct description: Basic version, no inter-ontology axioms format: json id: cl.cl-basic.json name: Basic CL (OBOGraph-JSON version) product_file_size: 5189872 product_url: http://purl.obolibrary.org/obo/cl/cl-basic.json - category: OntologyProduct description: complete CL but with no imports or external axioms format: owl id: cl.cl-base.owl name: CL base module product_file_size: 12017204 product_url: http://purl.obolibrary.org/obo/cl/cl-base.owl - 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Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' repository: https://github.com/obophenotype/cell-ontology taxon: - NCBITaxon:33208 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: ubyndr label: Ugur Bayindir orcid: 0000-0002-6012-3729 creation_date: '2025-03-09T00:00:00Z' description: CL-KG is a knowledge graph integrating the cell ontology and linked ontologies with hierarchical annotations of single cell transcriptomics data from CellXGene. domains: - biological systems evaluation_page: resource/cl-kg/cl-kg_eval_automated.html homepage_url: https://cellular-semantics.github.io/CL_KG/ id: cl-kg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: Cell Ontology Knowledge Graph (CL-KG) products: - category: ProgrammingInterface connection_url: cl-kg-neo4j-db.cellgeni.sanger.ac.uk:443 description: Publicly available Neo4j instance for CL-KG. id: cl-kg.api.neo4j is_neo4j: true is_public: true name: CL-KG Neo4j graph instance original_source: - cl-kg product_url: https://cellular-semantics.sanger.ac.uk/browser/ secondary_source: - cl-kg repository: https://github.com/Cellular-Semantics/CL_KG - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: lagonzalezmo@unal.edu.co - contact_type: github value: luis-gonzalez-m label: Luis Gonz lez-Monta a orcid: 0000-0002-9136-9932 creation_date: '2025-09-29T00:00:00Z' description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' domains: - anatomy and development homepage_url: https://github.com/luis-gonzalez-m/Collembola id: clao last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Collembola Anatomy Ontology products: - category: OntologyProduct description: Collembola Anatomy Ontology in OWL format format: owl id: clao.owl name: clao.owl product_file_size: 112550 product_url: http://purl.obolibrary.org/obo/clao.owl - category: OntologyProduct description: Collembola Anatomy Ontology in OBO format format: obo id: clao.obo name: clao.obo product_file_size: 74344 product_url: http://purl.obolibrary.org/obo/clao.obo repository: https://github.com/luis-gonzalez-m/Collembola - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: mustapha.adamu@temple.edu label: Mustapha Adamu creation_date: '2025-12-08T00:00:00Z' description: Climate Models KG is a knowledge graph to support evaluation and development of climate models, providing structured access to climate modeling data and relationships. domains: - environment - simulation evaluation_page: resource/climatemodelskg/climatemodelskg_eval_automated.html homepage_url: https://frink.apps.renci.org/climatemodelskg/sparql id: climatemodelskg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: Climate Models KG products: - category: ProgrammingInterface description: SPARQL endpoint for Climate Models KG id: climatemodelskg.sparql name: Climate Models KG SPARQL original_source: - climatemodelskg product_url: https://frink.apps.renci.org/climatemodelskg/sparql - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: support@clinicalgenome.org - contact_type: url value: https://clinicalgenome.org/about/contact-clingen/ label: ClinGen creation_date: '2025-06-04T00:00:00Z' description: The Clinical Genome Resource (ClinGen) is a National Institutes of Health (NIH)-funded resource dedicated to building a central resource that defines the clinical relevance of genes and variants for use in precision medicine and research. ClinGen brings together clinical and research experts to develop standard approaches for interpreting genomic variants, curate evidence for gene-disease relationships, and share this knowledge through freely accessible databases. domains: - genomics - biomedical - clinical - health homepage_url: https://clinicalgenome.org/ id: clingen infores_id: clingen last_modified_date: '2026-01-23T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: ClinGen products: - category: Product description: ClinGen Gene-Disease Validity curations assess the strength of evidence supporting or refuting a gene's role in a given disease. 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These curations score the actionability of gene-disease pairs based on severity, likelihood of disease, efficacy of interventions, and knowledge base. format: tsv id: clingen.actionability name: Clinical Actionability Curations product_url: https://search.clinicalgenome.org/kb/actionability - category: Product description: ClinGen Variant Pathogenicity curations assess the clinical significance of genetic variants based on ACMG/AMP guidelines. Expert panels classify variants as Pathogenic, Likely Pathogenic, Uncertain Significance, Likely Benign, or Benign. format: csv id: clingen.variant name: Variant Pathogenicity Curations product_url: https://search.clinicalgenome.org/kb/variant-pathogenicity/all - category: ProgrammingInterface description: REST API providing access to ClinGen's Evidence Repository for variant pathogenicity assessments. Allows programmatic retrieval of structured evidence used to evaluate the clinical significance of genetic variants. id: clingen.evrepo.api name: ClinGen Evidence Repository API product_url: https://erepo.clinicalgenome.org/evrepo/api/ - category: GraphicalInterface description: Web-based interface for accessing ClinGen's curated data. Allows users to search and browse curated gene-disease pairs, variant interpretations, and other ClinGen resources. id: clingen.web.interface name: ClinGen Search Interface product_url: https://search.clinicalgenome.org/ - category: ProcessProduct description: Framework for standardized interpretation of genetic variants, including disease-specific modifications to the ACMG/AMP guidelines. These frameworks guide variant classification by expert panels and clinical laboratories. id: clingen.variant.frameworks name: Variant Interpretation Frameworks product_url: https://www.clinicalgenome.org/working-groups/sequence-variant-interpretation/ - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. 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kg-monarch publications: - authors: - Rehm HL - Berg JS - Brooks LD - Bustamante CD - Evans JP - Landrum MJ - Ledbetter DH - et al. doi: doi:10.1056/NEJMsr1406261 id: https://doi.org/10.1056/NEJMsr1406261 journal: New England Journal of Medicine preferred: true title: ClinGen — The Clinical Genome Resource year: '2015' - authors: - ClinGen Consortium doi: doi:10.1016/j.gim.2024.101228 id: https://doi.org/10.1016/j.gim.2024.101228 journal: Genetics in Medicine title: 'The Clinical Genome Resource (ClinGen): Advancing genomic knowledge through global curation' year: '2024' taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual contact_details: - contact_type: email value: ct2865@columbia.edu label: Casey Ta - category: Individual label: Vincent Emonet - category: Individual contact_details: - contact_type: email value: michel.dumontier@maastrichtuniversity.nl label: Michel Dumontier creation_date: '2025-03-09T00:00:00Z' description: A Translator Knowledge Provider integrating clinical data. domains: - health - clinical - digital health - medical imaging evaluation_page: resource/clinical-data-kp/clinical-data-kp_eval_automated.html homepage_url: https://ncats.nih.gov/research/research-activities/translator/projects id: clinical-data-kp last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Clinical Data KP products: - category: GraphicalInterface description: Translator project portal describing clinical data provider activities. format: http id: clinical-data-kp.portal name: Clinical Data KP Portal original_source: - clinical-data-kp product_url: https://ncats.nih.gov/research/research-activities/translator/projects - category: DocumentationProduct description: Team and tooling documentation for the Clinical Data Provider. format: http id: clinical-data-kp.docs name: Clinical Data KP Documentation original_source: - clinical-data-kp product_url: https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Data-Provider taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://github.com/MannLabs label: Mann Labs creation_date: '2025-08-12T00:00:00Z' description: The Clinical Knowledge Graph (CKG) is an open-source platform that integrates proteomics and clinical data with knowledge from diverse biomedical databases and literature to support precision medicine. The CKG has reported scale of ~16 million nodes and ~220 million relationships and provides tooling for analysis, reporting, and knowledge discovery. domains: - clinical - proteomics - biomedical - health evaluation_page: resource/clinicalkg/clinicalkg_eval.html homepage_url: https://ckg.readthedocs.io/ id: clinicalkg last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: Clinical Knowledge Graph (CKG) products: - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 publications: - authors: - Alberto Santos - Ana R. Colaço - Annelaura B. Nielsen - Matthias Mann doi: 10.1101/2020.05.09.084897 id: doi:10.1101/2020.05.09.084897 journal: bioRxiv title: Clinical Knowledge Graph Integrates Proteomics Data into Clinical Decision-Making year: '2020' repository: https://github.com/MannLabs/CKG taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for clinicaltrials. This page was automatically generated because it was referenced by other resources. domains: - stub id: clinicaltrials last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Clinicaltrials products: - category: Product description: clinicaltrials Nodes TSV format: tsv id: obo-db-ingest.clinicaltrials.tsv license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials Nodes TSV original_source: - clinicaltrials product_file_size: 19140027 product_url: https://w3id.org/biopragmatics/resources/clinicaltrials/clinicaltrials.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: ClinicalTrials.gov@nih.gov - contact_type: url value: https://clinicaltrials.gov/about-site/contact id: ncbi label: National Library of Medicine Clinical Trials Team - category: Organization contact_details: - contact_type: email value: register@clinicaltrials.gov label: ClinicalTrials.gov Help Desk creation_date: '2025-05-28T00:00:00Z' description: ClinicalTrials.gov is a database of privately and publicly funded clinical studies conducted around the world, maintained by the National Library of Medicine (NLM) at the National Institutes of Health (NIH). The registry contains information on over 400,000 studies covering a wide range of diseases and conditions, providing details about study design, locations, eligibility criteria, interventions, outcomes, and results. ClinicalTrials.gov serves as the primary registry for clinical trials required by the FDA Amendments Act and WHO International Clinical Trials Registry Platform (ICTRP). domains: - clinical - health - public health - drug discovery - precision medicine - biomedical - translational fairsharing_id: FAIRsharing.mewhad homepage_url: https://clinicaltrials.gov/ id: clinicaltrialsgov infores_id: clinicaltrials last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://clinicaltrials.gov/about-site/terms-conditions label: Public Domain name: ClinicalTrials.gov products: - category: GraphicalInterface description: Web-based interface for searching and browsing clinical trials with advanced filtering and export capabilities format: http id: clinicaltrialsgov.search name: ClinicalTrials.gov Search Portal original_source: - clinicaltrialsgov product_url: https://clinicaltrials.gov/search - category: ProgrammingInterface description: RESTful API providing programmatic access to all clinical trial records with JSON and CSV output formats format: http id: clinicaltrialsgov.api is_public: true name: ClinicalTrials.gov API original_source: - clinicaltrialsgov product_url: https://clinicaltrials.gov/data-api/api - category: Product description: Bulk downloads of all clinical trial records in multiple formats including XML, JSON, and CSV format: mixed id: clinicaltrialsgov.downloads name: ClinicalTrials.gov Data Downloads original_source: - clinicaltrialsgov product_url: https://clinicaltrials.gov/data-about-studies/download-clinical-trial-data - category: Product description: Aggregate Analysis of ClinicalTrials.gov (AACT) - A relational PostgreSQL database containing all clinical trial data, updated daily format: postgres id: clinicaltrialsgov.aact name: AACT Database original_source: - clinicaltrialsgov product_url: https://aact.ctti-clinicaltrials.org/ - category: DocumentationProduct description: Comprehensive documentation covering data structure, data element definitions, and API usage format: http id: clinicaltrialsgov.docs name: ClinicalTrials.gov Documentation original_source: - clinicaltrialsgov product_url: https://clinicaltrials.gov/about-site - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra - category: Product description: Complete RepoDB dataset containing drug repositioning successes and failures, with approved drugs, indications, and clinical trial outcomes format: csv id: repodb.full_dataset name: RepoDB Full Dataset original_source: - drugcentral - clinicaltrialsgov product_url: https://unmtid-shinyapps.net/shiny/repodb/session/98046b0f66cea75c432b5576c1ba2840/download/downloadFull?w= warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-10-27_ HTTP 500 error when accessing file - File was not able to be retrieved when checked on 2025-08-07_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Clinical trial information from ClinicalTrials.gov format: http id: genecards.clinical.trials name: GeneCards Clinical Trials original_source: - clinicaltrialsgov product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Cloud-based PostgreSQL database with daily refreshed clinical trial data, accessible via standard PostgreSQL clients format: postgres id: aact.database name: AACT Cloud Database original_source: - clinicaltrialsgov product_url: https://aact.ctti-clinicaltrials.org/connect - category: Product description: Static downloadable copies of the complete AACT database format: postgres id: aact.downloads name: AACT Database Downloads original_source: - clinicaltrialsgov product_url: https://aact.ctti-clinicaltrials.org/downloads publications: - authors: - Zarin DA - Tse T - Williams RJ - Califf RM - Ide NC doi: doi:10.1056/NEJMsa1012065 id: https://pubmed.ncbi.nlm.nih.gov/21366476/ journal: The New England Journal of Medicine preferred: true title: The ClinicalTrials.gov results database--update and key issues year: '2011' repository: https://github.com/ctti-clinicaltrials/aact taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: clinvar@ncbi.nlm.nih.gov id: ncbi label: ClinVar Team, National Center for Biotechnology Information (NCBI) creation_date: '2025-06-04T00:00:00Z' description: ClinVar is a freely accessible, public archive of reports of human genetic variations and their relationships to human health. It collects and presents data on variants found in patient samples, classifications for diseases and drug responses, and supporting evidence. ClinVar enables access to and communication about the clinical significance of genetic variants, providing healthcare professionals, researchers, and the public with vital information for interpreting genetic test results. domains: - biomedical - genomics - clinical - precision medicine - health - translational homepage_url: https://www.ncbi.nlm.nih.gov/clinvar/ id: clinvar infores_id: clinvar last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://www.ncbi.nlm.nih.gov/home/about/policies/ label: NCBI and NLM Data Usage Policies and Disclaimers name: ClinVar products: - category: Product description: Complete public data set in XML format containing comprehensive variant information, clinical significance classifications, and supporting evidence. format: xml id: clinvar.xml name: ClinVar XML product_url: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ - category: Product description: ClinVar data in VCF format for GRCh37 human genome assembly, containing variant information and clinical significance. format: vcf id: clinvar.vcf.grch37 name: ClinVar VCF (GRCh37) product_url: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/ - category: Product description: ClinVar data in VCF format for GRCh38 human genome assembly, containing variant information and clinical significance. format: vcf id: clinvar.vcf.grch38 name: ClinVar VCF (GRCh38) product_url: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/ - category: Product description: Tab-delimited files summarizing variant data, gene-condition relationships, and other aspects of ClinVar data. format: tsv id: clinvar.tab name: ClinVar Tab-Delimited Files product_url: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/ - category: ProgrammingInterface description: API access to ClinVar data through NCBI's E-utilities, supporting programmatic queries and data retrieval. format: http id: clinvar.api name: ClinVar API (E-utilities) product_url: https://www.ncbi.nlm.nih.gov/clinvar/docs/maintenance_use/ - category: GraphicalInterface description: Web interface for searching and browsing ClinVar data, with detailed variant information and evidence. format: http id: clinvar.web name: ClinVar Web Interface product_url: https://www.ncbi.nlm.nih.gov/clinvar/ - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: GraphProduct description: KGX Distribution of KG-Monarch edge_count: 15356321 format: kgx id: kg-monarch.graph name: KGX Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 230877741 product_url: http://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz secondary_source: - kg-monarch - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch edge_count: 15356321 format: kgx-jsonl id: kg-monarch.graph.jsonl name: KGX JSON-L Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - 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kg-monarch - category: GraphProduct description: RDF Distribution of KG-Monarch edge_count: 15356321 format: rdfxml id: kg-monarch.graph.rdf name: RDF Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 879238775 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.nt.gz secondary_source: - kg-monarch - category: GraphProduct description: Neo4j Dump of KG-Monarch dump_format: neo4j edge_count: 15356321 id: kg-monarch.graph.neo4j name: Neo4j Dump of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 1438250397 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.neo4j.dump secondary_source: - kg-monarch warnings: [] - category: GraphProduct description: DuckDB database of KG-Monarch edge_count: 15356321 id: kg-monarch.graph.duckdb name: DuckDB database of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - 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omim - malacards - clinvar - orphanet - disgenet product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Genetic variant data from ClinVar, dbSNP, GWAS Catalog and other variant databases format: http id: genecards.variant.data name: GeneCards Variant Data original_source: - clinvar - dbsnp - gwascatalog product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' publications: - authors: - Landrum MJ - Chitipiralla S - Kaur K - Brown G - Chen C - Hart J - Hoffman D - Jang W - Liu C - Maddipatla Z - Maiti R - Mitchell J - Rezaie T - Riley G - Song G - Yang J - Ziyabari L - Russette A - Kattman BL doi: 10.1093/nar/gkae1090 id: doi:10.1093/nar/gkae1090 journal: Nucleic Acids Research preferred: true title: 'ClinVar: updates to support classifications of both germline and somatic variants' year: '2024' - authors: - Landrum MJ - Lee JM - Benson M - Brown GR - Chao C - Chitipiralla S - Gu B - Hart J - Hoffman D - Jang W - Karapetyan K - Katz K - Liu C - Maddipatla Z - Malheiro A - McDaniel K - Ovetsky M - Riley G - Zhou G - Holmes JB - Kattman BL - Maglott DR doi: 10.1093/nar/gkx1153 id: doi:10.1093/nar/gkx1153 journal: Nucleic Acids Research title: ClinVar - improving access to variant interpretations and supporting evidence year: '2018' taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: zhengj2007@gmail.com - contact_type: github value: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 creation_date: '2025-06-25T00:00:00Z' description: An ontology to standardize and integrate cell line information and to support computer-assisted reasoning. domains: - anatomy and development homepage_url: https://github.com/CLO-Ontology/CLO id: clo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Cell Line Ontology products: - category: OntologyProduct description: Cell Line Ontology in OWL format format: owl id: clo.owl name: clo.owl product_file_size: 2121232 product_url: http://purl.obolibrary.org/obo/clo.owl - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - 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category: Organization contact_details: - contact_type: url value: https://clue.io/about id: broad label: Broad Institute of MIT and Harvard creation_date: '2025-08-12T00:00:00Z' description: CLUE (formerly known as the Connectivity Map or CMap 2.0) is a comprehensive resource for connecting drugs, genes, and diseases through large-scale perturbational data. Built and maintained by the Broad Institute, CLUE provides access to over 1.3 million gene expression profiles from the LINCS L1000 assay, covering more than 42,000 perturbagens (drugs, genetic reagents, and other compounds) tested across multiple cell lines. The platform enables researchers to discover connections between diseases, drugs, and biological mechanisms through gene expression signatures. domains: - drug discovery - genomics - biomedical - systems biology homepage_url: https://clue.io/ id: clue last_modified_date: '2025-10-07T00:00:00Z' layout: resource_detail name: CLUE products: - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque repository: https://github.com/cmap taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: lucas.leclere@obs-banyuls.fr - contact_type: github value: Leclere-L label: Lucas Leclere orcid: 0000-0002-7440-0467 creation_date: '2025-09-29T00:00:00Z' description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle. domains: - anatomy and development homepage_url: https://github.com/EBISPOT/clyh_ontology id: clyh last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Clytia hemisphaerica Development and Anatomy Ontology products: - category: OntologyProduct description: Clytia hemisphaerica Development and Anatomy Ontology in OWL format format: owl id: clyh.owl name: clyh.owl product_file_size: 13404 product_url: http://purl.obolibrary.org/obo/clyh.owl - category: OntologyProduct description: Clytia hemisphaerica Development and Anatomy Ontology in OBO format format: obo id: clyh.obo name: clyh.obo product_file_size: 9651 product_url: http://purl.obolibrary.org/obo/clyh.obo repository: https://github.com/EBISPOT/clyh_ontology - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://cm4ai.org/ label: Bridge2AI CM4AI creation_date: '2025-07-16T00:00:00Z' description: A knowledge graph containing connections between researchers, projects, and publications centering on members of the Bridge2AI Consortium and the Cell Maps for AI (CM4AI) project. domains: - literature evaluation_page: resource/cm4ai_talent_kg/cm4ai_talent_kg_eval_automated.html homepage_url: https://cm4aikg.vercel.app/ id: cm4ai_talent_kg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: CM4AI Talent KG products: - category: GraphicalInterface description: Web-based interface for browsing and exploring the CM4AI Talent Knowledge Graph format: http id: cm4ai_talent_kg.web_interface name: CM4AI Talent KG Web Interface original_source: - cm4ai_talent_kg product_url: https://cm4aikg.vercel.app/ - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: cmap@broadinstitute.org - contact_type: url value: https://www.broadinstitute.org/connectivity-map-cmap id: broad label: Broad Institute creation_date: '2025-01-10T00:00:00Z' description: The Connectivity Map (CMap) is a groundbreaking genome-scale perturbation resource containing over 3 million gene expression profiles cataloging transcriptional responses to chemical, genetic, and disease perturbations across multiple cancer cell types. Developed by the Broad Institute as part of the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program, CMap addresses fundamental challenges in understanding protein function and small molecule mechanisms of action by creating a comprehensive catalog of cellular signatures representing systematic perturbation. The database employs the L1000 high-throughput gene expression assay, which directly measures ~978 landmark genes and computationally infers expression of ~11,350 additional genes using inference algorithms, providing a cost-effective reduced representation of the transcriptome. CMap contains signatures from approximately 5,000 small-molecule compounds, 3,000 genetic reagents including shRNAs, CRISPR knockdowns, and overexpression constructs, tested primarily across nine core cancer cell lines that include A375, A549, HA1E, HCC515, HT29, HEPG2, MCF7, PC3, and VCAP. The resource enables researchers to query with their own gene expression signatures to identify perturbagens that induce similar or opposing transcriptional responses, thereby discovering unexpected connections between diseases, drug mechanisms, and protein functions. CMap data is accessible through CLUE, a cloud-based unified environment providing user-friendly web applications including query tools, data browsers, metadata search, and visualization apps for exploring perturbation-driven gene expression patterns. The database supports diverse research applications including drug repurposing by identifying compounds with similar mechanisms, target identification by finding small molecules that mimic genetic perturbations, disease mechanism understanding by connecting disease signatures to perturbagen responses, and biomarker discovery through systematic analysis of transcriptional responses. While personalized support ended in July 2022, all data, tools, and extensive documentation through Connectopedia remain fully accessible, with over 1.5 million replicate-collapsed signatures and 3 million profiles available for download and programmatic access via Python libraries and APIs. domains: - genomics - drug discovery - pharmacology homepage_url: https://clue.io/ id: cmap infores_id: cmap last_modified_date: '2025-01-10T00:00:00Z' layout: resource_detail license: id: https://clue.io/connectopedia/terms label: CLUE Terms of Use name: Connectivity Map products: - category: GraphicalInterface description: Cloud-based user interface providing suite of apps for querying gene expression signatures, browsing perturbagen data, searching metadata, and visualizing connectivity results id: cmap.clue name: CLUE Platform original_source: - cmap product_url: https://clue.io/ - category: ProgrammingInterface description: Python library cmapBQ for programmatic access to CMap data through Google BigQuery with query capabilities for signatures and metadata id: cmap.python_api is_public: true name: cmapBQ Python Library original_source: - cmap product_url: https://cmapbq.readthedocs.io/ - category: GraphicalInterface description: Query app enabling users to search CMap database with custom gene expression signatures to find perturbagens with similar or opposing transcriptional effects id: cmap.query_app name: CLUE Query App original_source: - cmap product_url: https://clue.io/query - category: Product description: Data releases containing replicate-collapsed signatures and gene expression profiles in GCTx matrix format available for download format: hdf5 id: cmap.data_downloads name: CMap Data Downloads original_source: - cmap product_url: https://clue.io/releases/data-dashboard - category: DocumentationProduct description: Comprehensive knowledge base containing glossary, tutorials, analytical methods, experimental protocols, and detailed documentation format: http id: cmap.connectopedia name: Connectopedia original_source: - cmap product_url: https://clue.io/connectopedia publications: - id: https://doi.org/10.1016/j.cell.2017.10.049 title: 'A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles' repository: https://github.com/cmap synonyms: - CMap - Connectivity Map - LINCS L1000 taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jrsmith@mcw.edu - contact_type: github value: jrsjrs label: Jennifer Smith orcid: 0000-0002-6443-9376 creation_date: '2025-09-29T00:00:00Z' description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. domains: - biomedical homepage_url: http://rgd.mcw.edu/rgdweb/ontology/search.html id: cmo last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Clinical measurement ontology products: - category: OntologyProduct description: Clinical measurement ontology in OWL format format: owl id: cmo.owl name: cmo.owl product_file_size: 9404365 product_url: http://purl.obolibrary.org/obo/cmo.owl - 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category: OntologyProduct description: Core Ontology for Biology and Biomedicine, main ontology format: owl id: cob.owl name: COB product_file_size: 7601 product_url: http://purl.obolibrary.org/obo/cob.owl - category: OntologyProduct description: base module for COB format: owl id: cob.cob-base.owl name: COB base module product_file_size: 2994 product_url: http://purl.obolibrary.org/obo/cob/cob-base.owl - category: OntologyProduct description: COB with native IDs preserved rather than rewired to OBO IDs format: owl id: cob.cob-native.owl name: COB native module product_file_size: 6472 product_url: http://purl.obolibrary.org/obo/cob/cob-native.owl - category: OntologyProduct description: COB to external format: owl id: cob.cob-to-external.owl name: COB to external product_url: http://purl.obolibrary.org/obo/cob/cob-to-external.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: demo of COB including subsets of other ontologies (Experimental, for demo purposes only) format: owl id: cob.products.demo-cob.owl name: COB demo ontology (experimental) product_file_size: 447985 product_url: http://purl.obolibrary.org/obo/cob/products/demo-cob.owl - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/OBOFoundry/COB - activity_status: active category: DataSource creation_date: '2026-01-30T00:00:00Z' description: A resource for orthology-based functional classification of proteins into clusters of orthologous groups (COGs) across complete genomes. domains: - genomics - microbiology - biological systems homepage_url: https://www.ncbi.nlm.nih.gov/research/cog-project/ id: cog last_modified_date: '2026-02-15T00:00:00Z' layout: resource_detail name: COG products: - category: GraphicalInterface description: NCBI web interface for exploring the 2024 COG update and project resources. format: http id: cog.portal name: COG Project Portal product_url: https://www.ncbi.nlm.nih.gov/research/cog - category: Product description: COG 2024 functional assignment table in CSV format. format: csv id: cog.download.cog-24-csv name: COG 2024 Functional Assignments product_file_size: 637440210 product_url: https://ftp.ncbi.nlm.nih.gov/pub/COG/COG2024/data/cog-24.cog.csv - category: Product compression: gzip description: Protein FASTA set for the COG 2024 release. format: fasta id: cog.download.cogorg24-fasta name: COG 2024 Protein FASTA product_file_size: 1629401512 product_url: https://ftp.ncbi.nlm.nih.gov/pub/COG/COG2024/data/COGorg24.faa.gz - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz synonyms: - COG - Clusters of Orthologous Groups - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: http://people.dbmi.columbia.edu/~chw7007/ label: Columbia University Department of Biomedical Informatics - Weng Lab creation_date: '2025-11-04T00:00:00Z' description: The Columbia Open Health Data (COHD) API provides access to observed clinical frequencies and co-occurrence frequencies from electronic health records at Columbia University Medical Center. The database contains counts and frequencies of conditions, procedures, drug exposures, and patient demographics from the OHDSI common data model, along with statistical associations between clinical concepts. To protect patient privacy, all concepts where count ≤10 were excluded and counts were randomized using Poisson distribution. COHD offers multiple datasets including 5-year (2013-2017) and lifetime data, both in hierarchical and non-hierarchical forms, plus beta temporal co-occurrence data. domains: - clinical - health - public health - precision medicine homepage_url: https://cohd.io/ id: cohd infores_id: cohd last_modified_date: '2025-11-04T00:00:00Z' layout: resource_detail name: Columbia Open Health Data (COHD) products: - category: ProgrammingInterface description: RESTful API providing programmatic access to clinical concept frequencies, co-occurrences, and associations with JSON output format: http id: cohd.api name: COHD API original_source: - cohd product_url: https://cohd.io/api - category: GraphicalInterface description: Interactive web interface for exploring clinical concept frequencies and associations format: http id: cohd.portal name: COHD Web Interface original_source: - cohd product_url: https://cohd.io/ - category: ProcessProduct description: Python Jupyter notebooks demonstrating COHD API usage and analysis workflows format: http id: cohd.notebooks name: COHD API Examples original_source: - cohd product_file_size: 2834847 product_url: https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb - category: DocumentationProduct description: API documentation covering endpoint descriptions, data structure, and usage examples format: http id: cohd.docs name: COHD Documentation original_source: - cohd product_url: https://cohd.io/api warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 502 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 502 error when accessing file' - category: GraphProduct description: KGX graph package for Columbia Open Health Data (build cohd_2024-11-25_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.cohd.graph name: Translator COHD KGX Graph original_source: - cohd product_url: https://stars.renci.org/var/translator/releases/cohd/2025_12_15/ secondary_source: - translator repository: https://github.com/WengLab-InformaticsResearch/cohd_api taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: entiminae@gmail.com - contact_type: github value: JCGiron label: Jennifer C. Giron orcid: 0000-0002-0851-6883 creation_date: '2025-09-29T00:00:00Z' description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone. domains: - anatomy and development homepage_url: https://github.com/insect-morphology/colao id: colao last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Coleoptera Anatomy Ontology (COLAO) products: - category: OntologyProduct description: Coleoptera Anatomy Ontology (COLAO) in OWL format format: owl id: colao.owl name: colao.owl product_file_size: 164547 product_url: http://purl.obolibrary.org/obo/colao.owl - category: OntologyProduct description: Coleoptera Anatomy Ontology (COLAO) in OBO format format: obo id: colao.obo name: colao.obo product_file_size: 83585 product_url: http://purl.obolibrary.org/obo/colao.obo repository: https://github.com/insect-morphology/colao - activity_status: active category: DataSource creation_date: '2025-07-08T00:00:00Z' description: COMPARTMENTS is an evidence-weighted subcellular localization knowledge resource that integrates experimental data, manual curation, high-throughput localization screens, automatic text mining, and sequence-based predictions to assign proteins to cellular compartments with confidence scores. domains: - proteomics - systems biology - biological systems id: compartments last_modified_date: '2026-01-30T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: COMPARTMENTS products: - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphicalInterface description: Web interface for exploring protein subcellular localization evidence across integrated sources. id: compartments.portal name: COMPARTMENTS Portal product_url: https://compartments.jensenlab.org/ - category: Product description: Bulk data downloads of localization scores and evidence files. id: compartments.downloads name: COMPARTMENTS Bulk Downloads product_url: https://compartments.jensenlab.org/Downloads warnings: - File was not able to be retrieved when checked on 2025-09-23_ No Content-Length header found - File was not able to be retrieved when checked on 2025-09-16_ No Content-Length header found - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz - activity_status: active category: DataSource creation_date: '2026-01-28T00:00:00Z' description: A pathway mapping and harmonization framework for integrating and comparing pathway knowledge across multiple pathway databases. domains: - pathways - biological systems homepage_url: https://compath.scai.fraunhofer.de/ id: compath last_modified_date: '2026-02-15T00:00:00Z' layout: resource_detail name: ComPath products: - category: GraphicalInterface description: Main ComPath portal for pathway database harmonization and analysis. format: http id: compath.portal name: ComPath Portal product_url: https://compath.scai.fraunhofer.de/ - category: GraphicalInterface description: Overview interface for pathway databases integrated in ComPath. format: http id: compath.overview name: ComPath Overview product_url: https://compath.scai.fraunhofer.de/overview - category: GraphicalInterface description: Interface for pathway similarity comparisons. format: http id: compath.similarity name: ComPath Similarity Explorer product_url: https://compath.scai.fraunhofer.de/similarity - category: GraphicalInterface description: Catalog interface for browsing curated pathway mappings. format: http id: compath.catalog name: ComPath Catalog product_url: https://compath.scai.fraunhofer.de/catalog - category: DocumentationProduct description: Curation protocol and methodology documentation for ComPath mappings. format: http id: compath.curation-protocol name: ComPath Curation Protocol product_url: https://compath.scai.fraunhofer.de/curation_protocol - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv synonyms: - ComPath - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: intact-help@ebi.ac.uk - contact_type: url value: https://www.ebi.ac.uk/about/contact/support/complexportal id: ebi label: EMBL-EBI creation_date: '2025-07-17T00:00:00Z' description: The Complex Portal is an encyclopaedic resource of macromolecular complexes from model organisms, providing manually curated and high-confidence machine-learning predicted protein complexes with comprehensive structural and functional annotation. domains: - proteomics - systems biology funding: - EMBL-EBI homepage_url: https://www.ebi.ac.uk/complexportal/ id: complexportal infores_id: complexportal last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Complex Portal products: - category: GraphicalInterface description: Web portal for searching, browsing, and visualizing macromolecular complexes with detailed annotations and structural information format: http id: complexportal.portal name: Complex Portal Web Interface original_source: - complexportal product_url: https://www.ebi.ac.uk/complexportal/ - category: Product description: Complete Complex Portal dataset in PSI-MI XML 2.5 format, organized by species format: psi_mi_xml id: complexportal.psi25 name: Complex Portal PSI-MI XML 2.5 original_source: - complexportal product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/ - category: Product description: Complete Complex Portal dataset in PSI-MI XML 3.0 format, organized by species format: psi_mi_xml id: complexportal.psi30 name: Complex Portal PSI-MI XML 3.0 original_source: - complexportal product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi30/ - category: Product description: Complex Portal data in ComplexTAB flat-file format for easy parsing and Excel compatibility, organized by species format: tsv id: complexportal.complextab name: Complex Portal ComplexTAB original_source: - complexportal product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/ - category: Product compression: zip description: Human complexes dataset from Complex Portal in PSI-MI XML 2.5 format format: psi_mi_xml id: complexportal.human.psi25 name: Complex Portal Human PSI-MI XML 2.5 original_source: - complexportal product_file_size: 27080450 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/Homo_sapiens.zip - category: Product compression: zip description: Human complexes dataset from Complex Portal in PSI-MI XML 3.0 format format: psi_mi_xml id: complexportal.human.psi30 name: Complex Portal Human PSI-MI XML 3.0 original_source: - complexportal product_file_size: 23735308 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi30/human.zip - category: Product compression: zip description: Human predicted complexes dataset from Complex Portal in PSI-MI XML 2.5 format format: psi_mi_xml id: complexportal.human.predicted.psi25 name: Complex Portal Human Predicted PSI-MI XML 2.5 original_source: - complexportal product_file_size: 152994603 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/Homo_sapiens_predicted.zip - category: Product compression: zip description: Human predicted complexes dataset from Complex Portal in PSI-MI XML 3.0 format format: psi_mi_xml id: complexportal.human.predicted.psi30 name: Complex Portal Human Predicted PSI-MI XML 3.0 original_source: - complexportal product_file_size: 120346920 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi30/human_predicted.zip - category: Product description: Human complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.human.complextab name: Complex Portal Human ComplexTAB original_source: - complexportal product_file_size: 5056483 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/9606.tsv - category: Product description: Human predicted complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.human.predicted.complextab name: Complex Portal Human Predicted ComplexTAB original_source: - complexportal product_file_size: 5194064 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/9606_predicted.tsv - category: Product compression: zip description: Mouse complexes dataset from Complex Portal in PSI-MI XML 2.5 format format: psi_mi_xml id: complexportal.mouse.psi25 name: Complex Portal Mouse PSI-MI XML 2.5 original_source: - complexportal product_file_size: 6265397 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/Mus_musculus.zip - category: Product compression: zip description: Mouse complexes dataset from Complex Portal in PSI-MI XML 3.0 format format: psi_mi_xml id: complexportal.mouse.psi30 name: Complex Portal Mouse PSI-MI XML 3.0 original_source: - complexportal product_file_size: 5335441 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi30/mouse.zip - category: Product description: Mouse complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.mouse.complextab name: Complex Portal Mouse ComplexTAB original_source: - complexportal product_file_size: 1451848 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/10090.tsv - category: Product compression: zip description: Yeast complexes dataset from Complex Portal in PSI-MI XML 2.5 format format: psi_mi_xml id: complexportal.yeast.psi25 name: Complex Portal Yeast PSI-MI XML 2.5 original_source: - complexportal product_file_size: 4635082 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi25/Saccharomyces_cerevisiae.zip - category: Product compression: zip description: Yeast complexes dataset from Complex Portal in PSI-MI XML 3.0 format format: psi_mi_xml id: complexportal.yeast.psi30 name: Complex Portal Yeast PSI-MI XML 3.0 original_source: - complexportal product_file_size: 4038669 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/psi30/yeast.zip - category: Product description: Budding yeast (S288c) complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.yeast.s288c.complextab name: Complex Portal Yeast S288c ComplexTAB original_source: - complexportal product_file_size: 892741 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/559292.tsv - category: Product description: Fruit fly complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.fruitfly.complextab name: Complex Portal Fruit Fly ComplexTAB product_file_size: 331098 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/7227.tsv - category: Product description: Worm complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.worm.complextab name: Complex Portal Worm ComplexTAB product_file_size: 179822 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/6239.tsv - category: Product description: E. coli complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.ecoli.complextab name: Complex Portal E. coli ComplexTAB product_file_size: 545353 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/83333.tsv - category: Product description: Bacillus subtilis complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.bsubtilis.complextab name: Complex Portal Bacillus subtilis ComplexTAB product_file_size: 4539 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/562.tsv - category: Product description: Arabidopsis thaliana complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.arabidopsis.complextab name: Complex Portal Arabidopsis thaliana ComplexTAB product_file_size: 426981 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/3702.tsv - category: Product description: Lamprey complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.lamprey.complextab name: Complex Portal Lamprey ComplexTAB product_file_size: 2639 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/6523.tsv - category: Product description: Pufferfish (Tetraodon nigroviridis) complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.pufferfish.tetraodon.complextab name: Complex Portal Pufferfish (Tetraodon) ComplexTAB product_file_size: 2753 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/7787.tsv - category: Product description: Pufferfish (Takifugu rubripes) complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.pufferfish.takifugu.complextab name: Complex Portal Pufferfish (Takifugu) ComplexTAB product_file_size: 2900 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/7788.tsv - category: Product description: Zebrafish complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.zebrafish.complextab name: Complex Portal Zebrafish ComplexTAB product_file_size: 10758 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/7955.tsv - category: Product description: African clawed frog complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.xenopus.complextab name: Complex Portal African Clawed Frog ComplexTAB product_file_size: 9146 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/8355.tsv - category: Product description: Sea urchin complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.seaurchin.complextab name: Complex Portal Sea Urchin ComplexTAB product_file_size: 25445 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/8732.tsv - category: Product description: Chicken complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.chicken.complextab name: Complex Portal Chicken ComplexTAB product_file_size: 59744 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/9031.tsv - category: Product description: Dog complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.dog.complextab name: Complex Portal Dog ComplexTAB product_file_size: 5945 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/9615.tsv - category: Product description: Pig complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.pig.complextab name: Complex Portal Pig ComplexTAB product_file_size: 11171 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/9823.tsv - category: Product description: Cattle complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.cattle.complextab name: Complex Portal Cattle ComplexTAB product_file_size: 32682 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/9913.tsv - category: Product description: Sheep complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.sheep.complextab name: Complex Portal Sheep ComplexTAB product_file_size: 1339 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/9940.tsv - category: Product description: Rabbit complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.rabbit.complextab name: Complex Portal Rabbit ComplexTAB product_file_size: 13180 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/9986.tsv - category: Product description: Rat complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.rat.complextab name: Complex Portal Rat ComplexTAB product_file_size: 267755 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/10116.tsv - category: Product description: Helicobacter pylori complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.hpylori.complextab name: Complex Portal Helicobacter pylori ComplexTAB product_file_size: 2243 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/208964.tsv - category: Product description: Pseudomonas aeruginosa complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.paeru.complextab name: Complex Portal Pseudomonas aeruginosa ComplexTAB product_file_size: 2105 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/243277.tsv - category: Product description: Fission yeast complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.fissionyeast.complextab name: Complex Portal Fission Yeast ComplexTAB product_file_size: 172403 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/284812.tsv - category: Product description: Dictyostelium discoideum complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.dictyostelium.complextab name: Complex Portal Dictyostelium discoideum ComplexTAB product_file_size: 33082 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/694009.tsv - category: Product description: Leishmania major complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.leishmania.complextab name: Complex Portal Leishmania major ComplexTAB product_file_size: 9412 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/1235996.tsv - category: Product description: Toxoplasma gondii complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.toxoplasma.complextab name: Complex Portal Toxoplasma gondii ComplexTAB product_file_size: 24961 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/1263720.tsv - category: Product description: SARS-CoV-2 complexes dataset from Complex Portal in ComplexTAB format format: tsv id: complexportal.sarscov2.complextab name: Complex Portal SARS-CoV-2 ComplexTAB product_file_size: 73071 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/2697049.tsv - category: Product description: Tab-delimited list of complexes released in the current Complex Portal FTP release format: txt id: complexportal.released-complexes name: Complex Portal Released Complexes original_source: - complexportal product_file_size: 265768 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/released_complexes.txt - category: MappingProduct description: Cross-references exported from Complex Portal to external databases format: tsv id: complexportal.db-crossrefs name: Complex Portal Database Cross-References original_source: - complexportal product_file_size: 1258425 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/various/complex_portal_dr_export.tsv - category: MappingProduct description: Translation table between stable Complex Portal IDs and IntAct accession identifiers format: txt id: complexportal.id-translation name: Complex Portal ID Translation Table original_source: - complexportal product_file_size: 69895 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/complex/current/various/cpx_ebi_ac_translation.txt - category: ProgrammingInterface description: RESTful web service API for programmatic access to Complex Portal data format: http id: complexportal.webservice name: Complex Portal Web Service original_source: - complexportal product_url: https://www.ebi.ac.uk/complexportal/webservice - category: DocumentationProduct description: Comprehensive documentation covering data formats, API usage, and complex annotation guidelines format: http id: complexportal.documentation name: Complex Portal Documentation original_source: - complexportal product_url: https://www.ebi.ac.uk/complexportal/documentation - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: Product description: complexportal Nodes TSV format: tsv id: obo-db-ingest.complexportal.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: complexportal Nodes TSV original_source: - complexportal product_file_size: 654220 product_url: https://w3id.org/biopragmatics/resources/complexportal/complexportal.tsv secondary_source: - obo-db-ingest publications: - authors: - Birgit H M Meldal - Hema Bye-A-Jee - Lukáš Gajdoš - Zuzana Hammerová - Aneta Horáčková - Filip Melicher - Livia Perfetto - Daniel Pokorný - Milagros Rodriguez Lopez - Alžběta Türková - Edith D Wong - Zengyan Xie - Elisabeth Barrera Casanova - Noemi del-Toro - Maximilian Koch - Pablo Porras - Henning Hermjakob - Sandra Orchard doi: 10.1093/nar/gky1001 id: doi:10.1093/nar/gky1001 journal: Nucleic Acids Research preferred: true title: 'Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes' year: '2019' - authors: - Birgit H M Meldal - Sandra Orchard doi: 10.1093/nar/gku975 id: doi:10.1093/nar/gku975 journal: Nucleic Acids Research title: The complex portal–an encyclopaedia of macromolecular complexes year: '2015' repository: https://github.com/EBI-IntAct/intact-data-exchange taxon: - NCBITaxon:562 - NCBITaxon:3702 - NCBITaxon:6239 - NCBITaxon:6523 - NCBITaxon:7227 - NCBITaxon:7787 - NCBITaxon:7788 - NCBITaxon:7955 - NCBITaxon:8355 - NCBITaxon:8732 - NCBITaxon:9031 - NCBITaxon:9606 - NCBITaxon:9615 - NCBITaxon:9823 - NCBITaxon:9913 - NCBITaxon:9940 - NCBITaxon:9986 - NCBITaxon:10090 - NCBITaxon:10116 - NCBITaxon:83333 - NCBITaxon:208964 - NCBITaxon:243277 - NCBITaxon:284812 - NCBITaxon:559292 - NCBITaxon:694009 - NCBITaxon:1235996 - NCBITaxon:1263720 - NCBITaxon:2697049 - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual label: Gregory Hyde creation_date: '2025-03-09T00:00:00Z' description: A Translator Knowledge Provider exploring connections hypotheses. domains: - health evaluation_page: resource/connections-hypothesis-kp/connections-hypothesis-kp_eval_automated.html homepage_url: https://github.com/di2ag/chp_api id: connections-hypothesis-kp last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Connections Hypothesis KP products: - category: ProcessProduct description: Source code for the Connections Hypothesis Provider API implementation. format: http id: connections-hypothesis-kp.code name: Connections Hypothesis KP Source Code original_source: - connections-hypothesis-kp product_url: https://github.com/di2ag/chp_api/tree/production - category: DocumentationProduct description: SmartAPI registry listing for CHP service metadata and interface documentation. format: http id: connections-hypothesis-kp.smartapi name: Connections Hypothesis KP SmartAPI Entry original_source: - connections-hypothesis-kp product_url: https://smart-api.info/registry?q=412af63e15b73e5a30778aac84ce313f - activity_status: active category: DataSource creation_date: '2025-11-05T00:00:00Z' description: CoralKinome is a comprehensive resource for coral kinase sequences and annotations, providing phylogenetic and functional information about protein kinases in coral species to support coral biology research and conservation efforts. domains: - genomics - systems biology homepage_url: https://www.coralkinome.org/ id: coralkinome last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: CoralKinome products: - category: GraphicalInterface description: Interactive web interface for exploring and visualizing kinase-substrate interactions format: http id: kinace.portal name: KinAce Web Portal original_source: - phosphositeplus - iptmnet - uniprot - epsd - kinhub - coralkinome - darkkinasekb - hgnc - kegg - interpro product_url: https://kinace.kinametrix.com/ secondary_source: - kinace synonyms: - CoralKinome - Coral Kinome Database - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.helmholtz-munich.de/ - contact_type: email value: corum@helmholtz-muenchen.de label: Helmholtz Zentrum München creation_date: '2025-07-22T00:00:00Z' description: CORUM (Comprehensive Resource of Mammalian Protein Complexes) is a curated database of experimentally characterized protein complexes from mammalian organisms, particularly human, mouse, and rat, with a focus on manually annotated information from scientific literature. domains: - proteomics - biomedical - chemistry and biochemistry homepage_url: https://mips.helmholtz-muenchen.de/corum/ id: corum last_modified_date: '2025-09-05T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC BY-NC 4.0 name: CORUM products: - category: Product description: Complete dataset of all curated protein complexes in CORUM in tab-delimited format format: tsv id: corum.all_complexes license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC BY-NC 4.0 name: CORUM All Complexes product_url: https://mips.helmholtz-muenchen.de/corum/download/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-02-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''mips.helmholtz-muenchen.de'', port=443): Max retries exceeded with url: /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Core dataset of manually curated, non-redundant protein complexes in CORUM in tab-delimited format format: tsv id: corum.core_complexes license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC BY-NC 4.0 name: CORUM Core Complexes product_url: https://mips.helmholtz-muenchen.de/corum/download/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-02-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''mips.helmholtz-muenchen.de'', port=443): Max retries exceeded with url: /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Dataset of all CORUM protein complexes in PSI-MI XML format (Proteomics Standards Initiative) format: psi_mi_xml id: corum.psi_mi license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC BY-NC 4.0 name: CORUM PSI-MI product_url: https://mips.helmholtz-muenchen.de/corum/download/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-02-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''mips.helmholtz-muenchen.de'', port=443): Max retries exceeded with url: /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Dataset of all CORUM protein complexes in PSI-MI MITAB 2.5 format format: psi_mi_mitab id: corum.mitab license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC BY-NC 4.0 name: CORUM MITAB product_url: https://mips.helmholtz-muenchen.de/corum/download/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-02-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='mips.helmholtz-muenchen.de', port=443)_ Max retries exceeded with url_ /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''mips.helmholtz-muenchen.de'', port=443): Max retries exceeded with url: /corum/download/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 publications: - authors: - Stefanie Gößler - Gisela Fobo - Barbara Wankerl - Christopher J. Mann - Hans-Werner Mewes - Andreas Ruepp doi: 10.1093/nar/gkac1015 id: doi:10.1093/nar/gkac1015 journal: Nucleic Acids Research preferred: true title: 'CORUM: the comprehensive resource of mammalian protein complexes—2023' year: '2023' - authors: - Andreas Giurgiu - Julian Reinhard - Barbara Brauner - Irmtraud Dunger-Kaltenbach - Gisela Fobo - Goar Frishman - Corinna Montrone - Andreas Ruepp doi: 10.1093/nar/gky973 id: doi:10.1093/nar/gky973 journal: Nucleic Acids Research title: 'CORUM: the comprehensive resource of mammalian protein complexes—2019' year: '2019' - authors: - Andreas Ruepp - Barbara Brauner - Irmtraud Dunger-Kaltenbach - Goar Frishman - Corinna Montrone - Michael Stransky - Brigitte Waegele - Thorsten Schmidt - Octave Noubibou Doudieu - Volker Stümpflen - Hans-Werner Mewes doi: 10.1093/nar/gkp914 id: doi:10.1093/nar/gkp914 journal: Nucleic Acids Research title: 'CORUM: the comprehensive resource of mammalian protein complexes—2009' year: '2010' repository: https://mips.helmholtz-muenchen.de/corum/download taxon: - NCBITaxon:40674 - NCBITaxon:10090 - NCBITaxon:10116 - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://cancer.sanger.ac.uk/cosmic/about label: COSMIC Team (Wellcome Sanger Institute) creation_date: '2025-07-08T00:00:00Z' description: COSMIC (Catalogue Of Somatic Mutations In Cancer) is a comprehensive resource for somatic mutations in human cancer. It curates, standardizes, and integrates mutation data across genes, cancer types, and samples, and provides access via a web portal and licensed downloads. domains: - genomics - biomedical homepage_url: https://cancer.sanger.ac.uk/cosmic id: cosmic infores_id: cosmic last_modified_date: '2025-09-09T00:00:00Z' layout: resource_detail license: id: https://cancer.sanger.ac.uk/cosmic/license label: COSMIC License name: COSMIC products: - category: GraphicalInterface description: Web portal for exploring somatic mutations, gene pages, cancer types, and curated annotations format: http id: cosmic.portal name: COSMIC Portal original_source: - cosmic product_url: https://cancer.sanger.ac.uk/cosmic - category: Product description: Top-level downloads page with links to COSMIC release files (registration/license required) format: http id: cosmic.downloads name: COSMIC Downloads original_source: - cosmic product_url: https://cancer.sanger.ac.uk/cosmic/download/cosmic - category: DocumentationProduct description: COSMIC Knowledgebase overview and documentation pages format: http id: cosmic.kb.overview name: COSMIC-KB Portal overview original_source: - cosmic product_url: https://www.cosmickb.org/about/ - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg taxon: - NCBITaxon:9606 warnings: - COSMIC data downloads for commercial users are provided by Qiagen. - activity_status: active category: KnowledgeGraph contacts: - category: Organization label: Critical Path Institute - category: Individual contact_details: - contact_type: email value: ibraun@c-path.org - contact_type: other contact_type_name: Critical Path Institute GitLab contact_type_url: https://gitlab.c-path.org/ value: ibraun label: Ian Braun creation_date: '2025-04-11T00:00:00Z' description: The C-Path Knowledge Graph project is intended to increase discoverability of rare disease datasets through integration with the Monarch Knowlege Graph. domains: - health evaluation_page: resource/cpathkg/cpathkg_eval_automated.html id: cpathkg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: C-Path Knowledge Graph products: - category: ProcessProduct description: This repository is a code reference for the C-Path Knowledge Graph project, to increase discoverability of rare disease datasets through integration with the Monarch Knowlege Graph. Note that this is only a reference to scripts and queries associated with this project and is not provided as a runnable project because these workflows depend on an internal data catalog. format: python id: cpathkg.code name: C-Path Knowledge Graph Integration original_source: - biolink - kg-monarch product_url: https://gitlab.c-path.org/c-pathontology/c-path-knowledge-graph-integration secondary_source: - cpathkg publications: - authors: - Braun I - Hartley E - Olson D - Matentzoglu N - Schaper K - Walls R - Vasilevsky N doi: 10.1093/jamiaopen/ooaf001 id: doi:10.1093/jamiaopen/ooaf001 title: Increased discoverability of rare disease datasets through knowledge graph integration year: '2025' - activity_status: active category: Resource contacts: - category: Organization contact_details: - contact_type: url value: https://cpicpgx.org/contact/ - contact_type: email value: contact@cpicpgx.org label: Clinical Pharmacogenetics Implementation Consortium (CPIC) creation_date: '2025-09-03T00:00:00Z' description: The Clinical Pharmacogenetics Implementation Consortium (CPIC) creates, curates, and disseminates freely available, peer-reviewed, evidence-based, and updatable clinical practice guidelines that translate patient pharmacogenetic test results into actionable prescribing decisions. CPIC also publishes structured gene–drug annotations, allele function data, standardized terminology resources, and implementation tools (database, API, SOPs, educational materials) to accelerate pharmacogenomics in clinical care. domains: - biomedical - health - clinical - drug discovery homepage_url: https://cpicpgx.org/ id: cpic last_modified_date: '2025-09-03T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: CPIC products: - category: GraphicalInterface description: Main CPIC website portal providing access to guidelines, genes-drugs tables, alleles, publications, resources, and implementation information format: http id: cpic.portal name: CPIC Website Portal original_source: - cpic product_url: https://cpicpgx.org/ - category: DocumentationProduct description: Peer-reviewed, evidence-based, updatable pharmacogenetic clinical practice guidelines translating genotype into prescribing recommendations id: cpic.guidelines is_public: true name: CPIC Clinical Practice Guidelines original_source: - cpic product_url: https://cpicpgx.org/guidelines/ - category: DataProduct description: Curated gene–drug pair tables linking pharmacogenes with affected medications and guideline recommendations id: cpic.genes_drugs is_public: true name: CPIC Genes-Drugs Tables original_source: - cpic product_url: https://cpicpgx.org/genes-drugs/ - category: DataProduct description: Allele function and diplotype-to-phenotype tables standardized for clinical pharmacogenetic test result interpretation id: cpic.alleles is_public: true name: CPIC Allele & Diplotype Function Tables original_source: - cpic product_url: https://cpicpgx.org/alleles/ - category: ProgrammingInterface description: Structured data (database and API) for CPIC guideline-derived gene–drug relationships, allele function, and standardized terms id: cpic.api is_public: true name: CPIC Database & API original_source: - cpic product_url: https://github.com/cpicpgx/cpic-data/wiki - category: DocumentationProduct description: Standard operating procedure PDF for assigning allele function and translating diplotypes to phenotypes format: pdf id: cpic.sop name: CPIC Pharmacogene Curation SOP original_source: - cpic product_file_size: 812796 product_url: https://github.com/cpicpgx/cpic-sop/raw/main/CPIC%20Pharmacogene%20Curation%20SOP.pdf - category: DocumentationProduct description: Overview slide deck describing CPIC assumptions, development process, and implementation guidance (PowerPoint) id: cpic.overview.slides name: CPIC Overview Presentation Slides original_source: - cpic product_file_size: 8552272 product_url: https://files.cpicpgx.org/resources/CPIC-overview-updates-02.2025.pptx - category: DocumentationProduct description: One-page summary document providing concise overview of CPIC mission and guideline process (DOCX) format: docx id: cpic.onepager name: CPIC One-Page Summary original_source: - cpic product_file_size: 160131 product_url: https://cpicpgx.org/wp-content/uploads/2025/07/CPIC-One-Page-CLEAN.docx - category: DocumentationProduct description: Term standardization project resources for clinical pharmacogenetic test result terminology id: cpic.term_standardization name: CPIC Term Standardization Project original_source: - cpic product_url: https://cpicpgx.org/resources/term-standardization - category: DocumentationProduct description: CYP2D6 genotype to phenotype translation project resources id: cpic.cyp2d6_translation name: CPIC CYP2D6 Genotype to Phenotype Project original_source: - cpic product_url: https://cpicpgx.org/resources/cyp2d6-genotype-to-phenotype-standardization-project/ - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for cpt. This page was automatically generated because it was referenced by other resources. domains: - stub id: cpt last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Cpt products: - category: Product description: cpt Nodes TSV format: tsv id: obo-db-ingest.cpt.tsv name: cpt Nodes TSV original_source: - cpt product_file_size: 4342 product_url: https://w3id.org/biopragmatics/resources/cpt/cpt.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://ncats.nih.gov/translator label: NCATS Biomedical Data Translator creation_date: '2025-10-30T00:00:00Z' description: The Translator Curated Query Service (CQS) is an SRI service providing ARA-like reasoning capabilities through customizable inference rules captured as templates, generating predicted edges with provenance metadata and scoring. domains: - biomedical homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/Translator-Curated-Query-Service id: cqs infores_id: cqs last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Translator Curated Query Service products: - category: DocumentationProduct description: Service overview and usage guidance for CQS in the Translator wiki. format: http id: cqs.docs name: CQS Documentation original_source: - cqs product_url: https://github.com/NCATSTranslator/Translator-All/wiki/Translator-Curated-Query-Service - category: ProcessProduct description: Source code and templates implementing Curated Query Service inference logic. format: http id: cqs.code name: CQS Source Repository original_source: - cqs product_url: https://github.com/TranslatorSRI/CQS synonyms: - CQS - Curated Query Service - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for credit. 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Since its inception, the AOP-DB has been developed with the aim of integrating AOP molecular target information with other publicly available datasets to facilitate computational analyses of AOP information. id: aop-db.data name: AOP-DB Data original_source: - aop-wiki - ctd - toxcast - disgenet - ncbigene - string - 1000genomes - ensembl - gwascatalog product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 secondary_source: - aop-db - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe - category: Product description: Chemical-gene interaction models and toxicological pathways derived from the Comparative Toxicogenomics Database (CTD) covering 17,700+ chemicals and 55,400 genes id: cam-kp.ctd-interactions name: CTD Chemical-Gene Models original_source: - ctd - category: GraphProduct description: KGX graph package for Comparative Toxicogenomics Database (build ctd_November_2025_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.ctd.graph name: Translator CTD KGX Graph original_source: - ctd product_url: https://stars.renci.org/var/translator/releases/ctd/2025_12_15/ secondary_source: - translator warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-09-29T00:00:00Z' description: An anatomical and developmental ontology for ctenophores (Comb Jellies) domains: - anatomy and development homepage_url: https://github.com/obophenotype/ctenophore-ontology id: cteno last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ctenophore Ontology products: - category: OntologyProduct description: Ctenophore Ontology in OWL format format: owl id: cteno.owl name: cteno.owl product_file_size: 15458 product_url: http://purl.obolibrary.org/obo/cteno.owl repository: https://github.com/obophenotype/ctenophore-ontology taxon: - NCBITaxon:10197 - activity_status: active category: KnowledgeGraph collection: - translator creation_date: '2026-02-18T00:00:00Z' description: Clinical Trials Knowledge Provider (CTKP) is a Translator knowledge provider maintained by the Multiomics Provider that exposes clinical trial-derived associations from ClinicalTrials.gov (via AACT), including trial interventions, conditions, and related biomedical entities. domains: - clinical - health - translational homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Trials-KP id: ctkp last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail name: Clinical Trials KP products: - category: GraphProduct description: KGX graph package for Clinical Trials Knowledge Provider (build ctkp_3.1.23_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.ctkp.graph name: Translator CTKP KGX Graph original_source: - ctkp product_url: https://stars.renci.org/var/translator/releases/ctkp/2025_12_15/ secondary_source: - translator - category: DocumentationProduct description: Translator wiki documentation for Clinical Trials KP, including source and access details. format: http id: ctkp.docs name: Clinical Trials KP Documentation original_source: - ctkp product_url: https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Trials-KP repository: https://github.com/multiomicsKP/clinical_trials_kp tags: - translator - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: alpha.tom.kodamullil@scai.fraunhofer.de - contact_type: github value: akodamullil label: Dr. Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 creation_date: '2025-09-29T00:00:00Z' description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. domains: - biomedical homepage_url: https://github.com/ClinicalTrialOntology/CTO/ id: cto last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: 'CTO: Core Ontology of Clinical Trials' products: - category: OntologyProduct description: 'CTO: Core Ontology of Clinical Trials in OWL format' format: owl id: cto.owl name: cto.owl product_file_size: 96492 product_url: http://purl.obolibrary.org/obo/cto.owl repository: https://github.com/ClinicalTrialOntology/CTO - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.broadinstitute.org/scientific-community/science/programs/csoft/center-science-therapeutics id: broad label: Broad Institute Center for the Science of Therapeutics - category: Individual contact_details: - contact_type: url value: https://www.broadinstitute.org/bios/stuart-l-schreiber label: Stuart L. Schreiber creation_date: '2025-11-10T00:00:00Z' description: The Cancer Therapeutics Response Portal (CTRP) is a comprehensive cancer cell line profiling resource that links genetic, lineage, and other cellular features of cancer cell lines to small-molecule sensitivity with the goal of accelerating discovery of patient-matched cancer therapeutics. Developed by researchers at the Broad Institute Center for the Science of Therapeutics as part of the NCI Cancer Target Discovery and Development (CTD2) Network, CTRP measured the sensitivity of 860 deeply characterized human cancer cell lines encompassing 25 lineages to an Informer Set of 481 small-molecule probes and drugs that selectively target distinct nodes in cell circuitry. The resource provides correlations between small-molecule sensitivity patterns and basal gene expression profiles from the Cancer Cell Line Encyclopedia (CCLE) across approximately 19,000 transcripts, enabling identification of mechanisms of action, cellular targets, metabolic processing pathways, and drug resistance mechanisms. CTRP measurements were performed over 16-point concentration ranges in duplicate using automated high-throughput workflows, with cellular ATP levels assessed 72 hours after compound treatment as a surrogate for viability. The portal provides interactive tools for exploring clustering by small molecule and cell line, enrichment analyses for annotations, correlations to copy-number and gene-expression data, on-the-fly correlation analysis, box-whisker visualizations, drill-down to scatter plots and concentration-response curves, and filtering by lineage, subtype, or growth mode. CTRP enables correlation of chemical sensitivity with basal gene expression to reveal direct target connections, target pathway relationships, metabolic activation mechanisms, small-molecule import and export mechanisms, and novel therapeutic targets, supporting the identification of predictive biomarkers for patient-matched therapeutics and the systematic characterization of small-molecule mechanisms of action. domains: - pharmacology - drug discovery homepage_url: https://portals.broadinstitute.org/ctrp/ id: ctrp infores_id: ctrp last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: Cancer Therapeutics Response Portal products: - category: GraphicalInterface description: Interactive web portal (version 2) for exploring 481 compounds tested against 860 cancer cell lines with clustering, enrichments, and correlations id: ctrp.portal name: CTRP v2 Portal product_url: https://portals.broadinstitute.org/ctrp/ - category: Product description: Raw sensitivity data, enrichment data, and supporting information available through the NCI CTD2 Data Portal format: csv id: ctrp.data name: CTRP Data Downloads product_url: https://ocg.cancer.gov/programs/ctd2/data-portal/ publications: - id: https://doi.org/10.1038/nchembio.1986 title: Correlating chemical sensitivity and basal gene expression reveals mechanism of action - id: https://doi.org/10.1158/2159-8290.CD-15-0235 title: Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset - id: https://doi.org/10.1016/j.cell.2013.08.003 title: An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules synonyms: - CTRP - Cancer Therapeutics Response Portal taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: paul.fabry@usherbrooke.ca - contact_type: github value: pfabry label: Paul Fabry orcid: 0000-0002-3336-2476 creation_date: '2025-09-29T00:00:00Z' description: An ontology to describe entities related to cardiovascular diseases domains: - biomedical homepage_url: https://github.com/OpenLHS/CVDO id: cvdo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Cardiovascular Disease Ontology products: - category: OntologyProduct description: Cardiovascular Disease Ontology in OWL format format: owl id: cvdo.owl name: cvdo.owl product_file_size: 105498 product_url: http://purl.obolibrary.org/obo/cvdo.owl repository: https://github.com/OpenLHS/CVDO - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for cvx. This page was automatically generated because it was referenced by other resources. domains: - stub id: cvx last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Cvx products: - category: Product description: cvx Nodes TSV format: tsv id: obo-db-ingest.cvx.tsv name: cvx Nodes TSV original_source: - cvx product_file_size: 6401 product_url: https://w3id.org/biopragmatics/resources/cvx/cvx.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://support.nlm.nih.gov/support/create-case/ id: ncbi label: National Library of Medicine creation_date: '2025-11-08T00:00:00Z' description: DailyMed is the National Library of Medicine's official provider of FDA drug label information, offering a searchable database of the most recent labeling submitted to the Food and Drug Administration by pharmaceutical companies and currently in use. As a comprehensive public resource providing over 154,000 drug labels, DailyMed contains labeling for prescription and nonprescription drugs for both human and animal use, as well as additional products including medical gases, devices, cosmetics, dietary supplements, and medical foods. All labeling information is formatted in Structured Product Labeling (SPL), an HL7 standard that provides a standardized, machine-readable format for drug product information enabling interoperability between healthcare systems. DailyMed serves as the authoritative source for current package inserts, medication guides, patient information sheets, and prescribing information directly as submitted by manufacturers to the FDA. The database is updated daily as new labeling is submitted and approved, ensuring users have access to the most current drug safety and efficacy information available. DailyMed provides detailed information including indications and usage, dosage and administration, contraindications, warnings and precautions, adverse reactions, drug interactions, use in specific populations, clinical pharmacology, and how the drug is supplied. domains: - health homepage_url: https://dailymed.nlm.nih.gov/dailymed/ id: dailymed infores_id: dailymed last_modified_date: '2025-11-08T00:00:00Z' layout: resource_detail name: DailyMed products: - category: GraphicalInterface description: Interactive web interface providing searchable access to over 154,000 FDA-approved drug labels with advanced search, browsing by therapeutic class, and pill image viewing format: http id: dailymed.website name: DailyMed Website product_url: https://dailymed.nlm.nih.gov/dailymed/ - category: ProgrammingInterface description: RESTful web services enabling programmatic access to DailyMed drug labeling data in Structured Product Labeling (SPL) format format: xml id: dailymed.web_services name: DailyMed Web Services product_url: https://dailymed.nlm.nih.gov/dailymed/app-support-web-services.cfm - category: Product description: Downloadable SPL files for all drug labels in the DailyMed database, updated daily format: xml id: dailymed.spl_files name: DailyMed SPL Data Files product_url: https://dailymed.nlm.nih.gov/dailymed/spl-resources-all-drug-labels.cfm - category: Product description: Mapping files linking DailyMed drug labels to RxNorm codes, UNII identifiers, and NDC codes for interoperability format: http id: dailymed.mapping_files name: DailyMed Mapping Files product_url: https://dailymed.nlm.nih.gov/dailymed/app-support-mapping-files.cfm - category: Product description: RSS feeds providing notifications of new and updated drug labels published on DailyMed format: http id: dailymed.rss_feeds name: DailyMed RSS Feeds product_url: https://dailymed.nlm.nih.gov/dailymed/rss-updates.cfm taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-11-13T00:00:00Z' description: The Dark Kinase Knowledgebase (DKK) is a comprehensive resource focused on providing data and reagents for 162 poorly studied or 'dark' kinases to the broader research community. Supported through NIH's Illuminating the Druggable Genome (IDG) Program, the DKK collects and disseminates experimental and computational data that provides functional context for understudied kinases, including parallel reaction monitoring peptides, protein interactions, NanoBRET reagents, kinase-specific compounds, tissue expression profiles, and functional relationships. domains: - genomics - proteomics homepage_url: https://darkkinome.org id: darkkinasekb infores_id: darkkinasekb last_modified_date: '2025-11-13T00:00:00Z' layout: resource_detail name: Dark Kinase Knowledgebase products: - category: Portal description: Main web portal for Dark Kinase Knowledgebase providing comprehensive data on 162 understudied kinases including tool compounds, PRM peptides, protein interactions, and expression profiles format: http id: darkkinasekb.portal name: DKK Main Portal original_source: - darkkinasekb product_url: https://darkkinome.org - category: Browser description: Interactive expression browser showing tissue-specific expression of dark kinases using GTEx RNA-seq and Human Proteome Map data with kinome-wide comparisons format: http id: darkkinasekb.expression name: DKK Expression Browser original_source: - darkkinasekb product_url: http://expression.darkkinome.org/ - category: Dataset description: Parallel reaction monitoring (PRM) peptides for quantitative mass spectrometry of dark kinases with standard curves and detection limits format: http id: darkkinasekb.prm name: DKK PRM Peptides original_source: - darkkinasekb product_url: https://darkkinome.org/PRM_params - category: Dataset description: Tool compounds for dark kinases with kinome-wide selectivity profiles and NanoBRET validation format: http id: darkkinasekb.compounds name: DKK Tool Compounds original_source: - darkkinasekb product_url: https://darkkinome.org/compounds - category: Dataset description: Protein interaction networks for dark kinases from affinity purification mass spectrometry and proximity labeling experiments format: http id: darkkinasekb.interactions name: DKK Protein Interactions original_source: - darkkinasekb product_url: https://darkkinome.org - category: Repository description: GitHub repository containing source code for Dark Kinase Knowledgebase website format: http id: darkkinasekb.github name: DKK GitHub Repository original_source: - darkkinasekb product_url: https://github.com/IDG-Kinase/darkkinasekb - category: Dataset description: Bulk datasets and resources distributed through Synapse platform format: http id: darkkinasekb.synapse name: DKK Synapse Data Repository original_source: - darkkinasekb product_url: https://www.synapse.org/#!Synapse:syn18360482/files/ - category: GraphicalInterface description: Interactive web interface for exploring and visualizing kinase-substrate interactions format: http id: kinace.portal name: KinAce Web Portal original_source: - phosphositeplus - iptmnet - uniprot - epsd - kinhub - coralkinome - darkkinasekb - hgnc - kegg - interpro product_url: https://kinace.kinametrix.com/ secondary_source: - kinace publications: - id: PMID:33079988 synonyms: - DKK - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://www.dbpedia.org/about/ label: DBpedia Association creation_date: '2026-03-11T00:00:00Z' description: DBpedia is a community knowledge graph published as RDF and built from structured content extracted from Wikipedia and related Wikimedia data. It is accessible through linked data URIs, a public SPARQL endpoint, and continuously updated releases distributed through the DBpedia Databus. domains: - general homepage_url: https://www.dbpedia.org/ id: dbpedia last_modified_date: '2026-03-11T00:00:00Z' layout: resource_detail name: DBpedia products: - category: GraphicalInterface description: Main DBpedia website with documentation, service links, and access points for DBpedia datasets and tooling. format: http id: dbpedia.portal name: DBpedia Web Portal original_source: - dbpedia product_url: https://www.dbpedia.org/ - category: ProgrammingInterface description: Public SPARQL endpoint for querying the DBpedia knowledge graph. format: http id: dbpedia.sparql is_public: true name: DBpedia SPARQL Endpoint original_source: - dbpedia product_url: http://dbpedia.org/sparql - category: Product description: Databus collection for the latest core DBpedia release used by the main SPARQL endpoint and linked data interface. format: http id: dbpedia.latest-core name: DBpedia Latest Core Collection original_source: - dbpedia - wikipedia - wikidata product_file_size: 18605 product_url: https://databus.dbpedia.org/dbpedia/collections/latest-core secondary_source: - dbpedia synonyms: - DBpedia - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: info@ncbi.nlm.nih.gov - contact_type: url value: https://www.ncbi.nlm.nih.gov/home/about/contact/ id: ncbi label: National Center for Biotechnology Information (NCBI) creation_date: '2025-05-04T00:00:00Z' description: dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations. domains: - biological systems - health homepage_url: https://www.ncbi.nlm.nih.gov/snp/ id: dbsnp infores_id: dbsnp last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://www.ncbi.nlm.nih.gov/home/about/policies/ label: Public Domain name: dbSNP products: - category: GraphicalInterface description: Web interface for searching and exploring dbSNP data id: dbsnp.site is_public: true name: dbSNP Web Interface original_source: - dbsnp product_url: https://www.ncbi.nlm.nih.gov/snp/ secondary_source: - dbsnp - category: ProgrammingInterface description: Programmatic access to dbSNP data via the NCBI E-utilities API id: dbsnp.api is_public: true name: dbSNP E-utilities API original_source: - dbsnp product_url: https://www.ncbi.nlm.nih.gov/books/NBK25500/ secondary_source: - dbsnp - category: Product compression: gzip description: JSON format files with dbSNP RefSNP data format: json id: dbsnp.json name: dbSNP JSON Files original_source: - dbsnp product_url: https://ftp.ncbi.nih.gov/snp/latest_release/JSON/ secondary_source: - dbsnp - category: ProgrammingInterface description: NCBI Variation Services API for accessing and manipulating variant data id: dbsnp.variation.api is_public: true name: NCBI Variation Services API original_source: - dbsnp product_url: https://api.ncbi.nlm.nih.gov/variation/v0/ secondary_source: - dbsnp - category: GraphProduct compression: zip description: Nodes from dbSNP format: csv id: biomarkerkg.nodes.variant name: BKG Variant Nodes original_source: - dbsnp product_file_size: 782975 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Variant.nodes.zip secondary_source: - biomarkerkg - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg - category: Product description: Genetic variant data from ClinVar, dbSNP, GWAS Catalog and other variant databases format: http id: genecards.variant.data name: GeneCards Variant Data original_source: - clinvar - dbsnp - gwascatalog product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' publications: - authors: - Sherry ST - Ward MH - Kholodov M - Baker J - Phan L - Smigielski EM - Sirotkin K doi: doi:10.1093/nar/29.1.308 id: doi:10.1093/nar/29.1.308 title: dbSNP - Database for Single Nucleotide Polymorphisms and Other Classes of Minor Genetic Variation year: '2001' - authors: - Kitts A - Phan L - Ward M - Holmes JB doi: doi:10.1093/nar/gkad1045 id: doi:10.1093/nar/gkad1045 preferred: true title: The evolution of dbSNP - 25 years of impact in genomic research year: '2023' repository: https://github.com/ncbi/dbsnp taxon: - NCBITaxon:9606 - activity_status: active category: DataModel creation_date: '2025-06-25T00:00:00Z' description: Dublin Core Metadata Initiative (DCMI) Metadata Terms is an authoritative specification of metadata terms for resource description. It includes the fifteen elements of the Dublin Core Metadata Element Set plus several dozen properties, classes, datatypes, and vocabulary encoding schemes. The terms are intended for use in combination with metadata terms from other vocabularies in application profiles. DCMI metadata terms are expressed in RDF vocabularies for use in Linked Data and are published as ISO standards (ISO 15836-1:2017 for the original 15 elements, ISO 15836-2:2019 for extended terms). domains: - information technology - literature homepage_url: https://www.dublincore.org/ id: dc last_modified_date: '2025-10-21T00:00:00Z' layout: resource_detail name: Dublin Core Metadata Terms products: - category: DocumentationProduct description: The DCMI Metadata Terms specification document, providing comprehensive documentation of all properties in the /terms/ namespace including abstract, accessRights, contributor, coverage, creator, date, description, format, identifier, language, publisher, relation, rights, subject, title, type, and many others. format: http id: dc.terms_spec name: DCMI Metadata Terms Specification product_url: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ - category: DocumentationProduct description: Documentation for the fifteen core Dublin Core elements in the /elements/1.1/ namespace (contributor, coverage, creator, date, description, format, identifier, language, publisher, relation, rights, source, subject, title, type). format: http id: dc.elements_spec name: Dublin Core Elements 1.1 Specification product_url: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3 - category: DataModelProduct description: RDF schema for Dublin Core terms in the /terms/ namespace. format: rdfxml id: dc.terms_rdf name: Dublin Core Terms RDF Schema product_url: http://purl.org/dc/terms/ - category: DataModelProduct description: RDF schema for Dublin Core elements in the /elements/1.1/ namespace. format: rdfxml id: dc.elements_rdf name: Dublin Core Elements RDF Schema product_url: http://purl.org/dc/elements/1.1/ - category: DataModelProduct description: RDF schema for the DCMI Type Vocabulary, defining classes for basic types (Collection, Dataset, Event, Image, InteractiveResource, MovingImage, PhysicalObject, Service, Software, Sound, StillImage, Text). format: rdfxml id: dc.dcmitype_rdf name: DCMI Type Vocabulary RDF Schema product_url: http://purl.org/dc/dcmitype/ - category: DocumentationProduct description: Documentation for vocabulary encoding schemes (DCMIType, DDC, IMT, LCC, LCSH, MESH, NLM, TGN, UDC) and syntax encoding schemes (Box, ISO3166, ISO639-2, ISO639-3, Period, Point, RFC standards, URI, W3CDTF). format: http id: dc.encoding_schemes name: Dublin Core Encoding Schemes product_url: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-4 - category: DocumentationProduct description: Documentation for Dublin Core classes including Agent, BibliographicResource, FileFormat, Frequency, Jurisdiction, LicenseDocument, LinguisticSystem, Location, MediaType, and others. format: http id: dc.classes name: Dublin Core Classes product_url: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-6 - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: OntologyProduct description: EDAM OWL release format: owl id: edam.owl name: EDAM OWL original_source: - edam - dc - skos product_file_size: 3373041 product_url: http://edamontology.org/EDAM.owl secondary_source: - edam - category: OntologyProduct description: EDAM TSV export format: tsv id: edam.tsv name: EDAM TSV original_source: - edam - dc - skos product_file_size: 1977072 product_url: https://edamontology.org/EDAM.tsv secondary_source: - edam - category: OntologyProduct description: EDAM CSV export format: csv id: edam.csv name: EDAM CSV original_source: - edam - dc - skos product_file_size: 1977072 product_url: https://edamontology.org/EDAM.csv secondary_source: - edam - category: GraphProduct description: Downloadable knowledge graph dump in TAR/GZ format containing complete FORUM data id: forum.graph.dump name: FORUM Knowledge Graph Dump original_source: - mesh - chebi - cito - fabio - dc - cheminf - skos - chemont - pubchem - pubmed product_url: ftp://forum:Forum2021Cov!@ftp.semantic-metabolomics.org/dumps/2021/share.tar.gz secondary_source: - forum warnings: - File was not able to be retrieved when checked on 2026-03-08_ FTP error_ timed out - File was not able to be retrieved when checked on 2026-02-26_ FTP error_ timed out - 'File was not able to be retrieved when checked on 2026-03-11: FTP error: timed out' publications: - id: https://www.iso.org/standard/71339.html preferred: true title: 'ISO 15836-1:2017 Information and documentation — The Dublin Core metadata element set — Part 1: Core elements' year: '2017' - id: https://www.iso.org/standard/71341.html title: 'ISO 15836-2:2019 Information and documentation — The Dublin Core metadata element set — Part 2: DCMI Properties and classes' year: '2019' repository: https://github.com/dcmi/ - activity_status: active category: Ontology creation_date: '2025-06-04T00:00:00Z' description: Dublin Core Metadata Terms (DCT) is a vocabulary of standardized metadata elements for describing resources, providing interoperable metadata standards for resource discovery across digital libraries and information systems. domains: [] homepage_url: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ id: dct last_modified_date: '2025-11-25T00:00:00Z' layout: resource_detail name: Dublin Core Terms products: - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg synonyms: - DCT - DCMI Terms - Dublin Core - Dublin Core Metadata Initiative warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: pfey@northwestern.edu - contact_type: github value: pfey03 label: Petra Fey orcid: 0000-0002-4532-2703 creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum domains: - anatomy and development homepage_url: http://dictybase.org/ id: ddanat last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Dictyostelium discoideum anatomy products: - category: OntologyProduct description: Dictyostelium discoideum anatomy in OWL format format: owl id: ddanat.owl name: ddanat.owl product_file_size: 15269 product_url: http://purl.obolibrary.org/obo/ddanat.owl - category: OntologyProduct description: Dictyostelium discoideum anatomy in OBO format format: obo id: ddanat.obo name: ddanat.obo product_file_size: 8493 product_url: http://purl.obolibrary.org/obo/ddanat.obo repository: https://github.com/dictyBase/migration-data taxon: - NCBITaxon:44689 - activity_status: active category: DataSource creation_date: '2025-10-30T00:00:00Z' description: DDInter is an open-access database specific to drug-drug interactions (DDIs) with comprehensive annotations including mechanism descriptions, risk levels, management strategies, and alternative medications to improve clinical decision-making and patient safety. domains: - pharmacology - clinical - drug discovery - biomedical - health homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/ddinter id: ddinter infores_id: ddinter last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: DDinter products: - category: DataProduct description: Comprehensive drug-drug interaction annotations with mechanism descriptions, risk levels, management strategies, and alternative medication recommendations for clinical decision support. id: ddinter.ddi_annotations name: DDInter Drug-Drug Interaction Annotations original_source: - ddinter product_url: https://github.com/NCATSTranslator/Translator-All/wiki/ddinter synonyms: - DDInter taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: pfey@northwestern.edu - contact_type: github value: pfey03 label: Petra Fey orcid: 0000-0002-4532-2703 creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. domains: - anatomy and development homepage_url: http://dictybase.org/ id: ddpheno last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Dictyostelium discoideum phenotype ontology products: - category: OntologyProduct description: Dictyostelium discoideum phenotype ontology in OWL format format: owl id: ddpheno.owl name: ddpheno.owl product_file_size: 72832 product_url: http://purl.obolibrary.org/obo/ddpheno.owl - category: OntologyProduct description: Dictyostelium discoideum phenotype ontology in OBO format format: obo id: ddpheno.obo name: ddpheno.obo product_file_size: 41003 product_url: http://purl.obolibrary.org/obo/ddpheno.obo repository: https://github.com/obophenotype/dicty-phenotype-ontology taxon: - NCBITaxon:44689 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: depmap@broadinstitute.org - contact_type: url value: https://depmap.org/portal/ id: broad label: DepMap Team, Broad Institute creation_date: '2025-10-09T00:00:00Z' description: The Cancer Dependency Map (DepMap) is a genome-wide pooled CRISPR-Cas9 knockout and small molecule screen of cancer cell lines. The goal of DepMap is to systematically identify cancer dependencies and the biomarkers that predict them. DepMap provides open access to key cancer dependencies, analytical tools, and visualization resources for the research community. domains: - biomedical - genomics - health - drug discovery - precision medicine homepage_url: https://depmap.org/portal/ id: depmap infores_id: depmap last_modified_date: '2025-10-09T00:00:00Z' layout: resource_detail license: id: https://depmap.org/portal/terms/ label: DepMap Terms of Use name: DepMap products: - category: GraphicalInterface description: Web portal for exploring cancer dependencies, cell line data, and biomarkers format: http id: depmap.portal name: DepMap Portal product_url: https://depmap.org/portal/ - category: GraphicalInterface description: Interactive tool for exploring relationships across DepMap datasets and cell lines format: http id: depmap.data_explorer name: DepMap Data Explorer product_url: https://depmap.org/portal/interactive/ - category: GraphicalInterface description: Tool for exploring and selecting cancer cell lines based on various criteria format: http id: depmap.cell_line_selector name: DepMap Cell Line Selector product_url: https://depmap.org/portal/cell_line_selector/ - category: GraphicalInterface description: Context Explorer tool for exploring enriched genetic dependencies and compound sensitivities across lineage and subtype contexts format: http id: depmap.context_explorer name: DepMap Context Explorer product_url: https://depmap.org/portal/context/ - category: GraphicalInterface description: Target Discovery App for identifying selective and predictable gene dependencies format: http id: depmap.target_discovery name: DepMap Target Discovery product_url: https://depmap.org/portal/tda/ - category: Product description: Complete collection of DepMap datasets available for download including CRISPR screens, drug screens, and omics data format: mixed id: depmap.downloads name: DepMap Data Downloads product_url: https://depmap.org/portal/data_page/ - category: Product description: CRISPR-Cas9 knockout screening data processed with Chronos algorithm to identify gene dependencies format: csv id: depmap.crispr_gene_effects name: DepMap CRISPR Gene Effects (Chronos) product_url: https://depmap.org/portal/data_page/ - category: Product description: Drug screening data from various platforms including GDSC, PRISM, and CTD2 format: csv id: depmap.drug_sensitivity name: DepMap Drug Sensitivity Data product_url: https://depmap.org/portal/data_page/ - category: Product description: Gene expression data (RNA-seq) for DepMap cell lines format: csv id: depmap.expression_data name: DepMap Expression Data product_url: https://depmap.org/portal/data_page/ - category: Product description: Copy number variation data for DepMap cell lines format: csv id: depmap.copy_number name: DepMap Copy Number Data product_url: https://depmap.org/portal/data_page/ - category: Product description: Mutation data for DepMap cell lines format: csv id: depmap.mutations name: DepMap Mutation Data product_url: https://depmap.org/portal/data_page/ - category: Product description: Proteomics data for DepMap cell lines format: csv id: depmap.proteomics name: DepMap Proteomics Data product_url: https://depmap.org/portal/data_page/ - category: Product description: Metabolomics data for DepMap cell lines format: csv id: depmap.metabolomics name: DepMap Metabolomics Data product_url: https://depmap.org/portal/data_page/ - 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category: GraphProduct description: KGX graph package for DGIdb drug–gene interactions (build dgidb_2024_12_06_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.dgidb.graph name: Translator DGIdb KGX Graph original_source: - dgidb product_url: https://stars.renci.org/var/translator/releases/dgidb/2025_12_15/ secondary_source: - translator publications: - authors: - Cotto KC - Wagner AH - Feng YY - Kiwala S - Coffman AC - Spies G - Wollam A - Spies NC - Griffith OL - Griffith M doi: doi:10.1093/nar/gkx1143 id: https://doi.org/10.1093/nar/gkx1143 journal: Nucleic Acids Research preferred: true title: 'DGIdb 3.0: a redesign and expansion of the drug-gene interaction database' year: '2018' - authors: - Wagner AH - Coffman AC - Ainscough BJ - Spies NC - Skidmore ZL - Campbell KM - Krysiak K - Pan D - McMichael JF - Eldred JM - Walker JR - Wilson RK - Mardis ER - Griffith M - Griffith OL doi: doi:10.1093/nar/gkv1165 id: https://doi.org/10.1093/nar/gkv1165 journal: Nucleic Acids Research title: 'DGIdb 2.0: mining clinically relevant drug-gene interactions' year: '2016' - authors: - Griffith M - Griffith OL - Coffman AC - Weible JV - McMichael JF - Spies NC - Koval J - Das I - Callaway MB - Eldred JM - Miller CA - Subramanian J - Govindan R - Kumar RD - Bose R - Ding L - Walker JR - Larson DE - Dooling DJ - Smith SM - Ley TJ - Mardis ER - Wilson RK doi: doi:10.1038/nmeth.2689 id: https://doi.org/10.1038/nmeth.2689 journal: Nature Methods title: DGIdb - mining the druggable genome year: '2013' repository: https://github.com/griffithlab/dgi-db - activity_status: active category: DataSource creation_date: '2025-08-13T00:00:00Z' description: dictyBase is a comprehensive genomic database for the social amoeba Dictyostelium discoideum and related species. 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dictybase product_file_size: 197677 product_url: https://w3id.org/biopragmatics/resources/dictybase.gene/dictybase.gene.tsv secondary_source: - obo-db-ingest repository: https://github.com/dictybase taxon: - NCBITaxon:44689 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mbrochhausen@gmail.com - contact_type: github value: mbrochhausen label: Mathias Brochhausen orcid: 0000-0003-1834-3856 creation_date: '2025-09-29T00:00:00Z' description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology domains: - chemistry and biochemistry homepage_url: https://github.com/DIDEO/DIDEO id: dideo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology products: - category: OntologyProduct description: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology in OWL format format: owl id: dideo.owl name: dideo.owl product_file_size: 88427 product_url: http://purl.obolibrary.org/obo/dideo.owl repository: https://github.com/DIDEO/DIDEO - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://dip.doe-mbi.ucla.edu/ - contact_type: email value: dip@mbi.ucla.edu label: UCLA-DOE Institute for Genomics and Proteomics - category: Individual contact_details: - contact_type: url value: https://www.chem.ucla.edu/~eisenberg/ label: David Eisenberg creation_date: '2025-11-10T00:00:00Z' description: The Database of Interacting Proteins (DIP) is a curated biological database that catalogs experimentally determined interactions between proteins, developed and maintained by the research group of David Eisenberg at the University of California Los Angeles (UCLA). Established in 2002, DIP combines information from diverse sources to create a unified, consistent set of protein-protein interactions with both manual expert curation and automated computational approaches that leverage knowledge extracted from the most reliable core subset of the data. DIP serves as a member of the International Molecular Exchange (IMEx) Consortium, an international collaboration of major public providers of protein interaction data including IntAct, MINT, BioGRID, and others that work together to avoid duplication of curation efforts by collecting data from non-overlapping sources and sharing curated interaction data. The database enables searches through its web interface based on multiple criteria including interactions described in specific journal articles, interactions supported by particular types of experimental evidence, and protein identifiers or sequences. DIP data have been curated using both manual approaches by expert biologists and automated computational methods that utilize machine learning and network analysis of the high-confidence core interaction data. The IMEx consortium developed the HUPO Proteomics Standards Initiative Molecular Interaction (HUPO-PSI-MI) XML format, which has become widely implemented for standardizing molecular interaction data representation. All information within DIP is freely available under a Creative Commons Attribution-NoDerivatives 3.0 license. DIP provides downloads of complete datasets and specialized subsets, supporting integration with other protein interaction databases and serving as a foundational resource for systems biology, network analysis, and protein function prediction studies. domains: - biological systems homepage_url: https://dip.doe-mbi.ucla.edu/ id: dip infores_id: dip last_modified_date: '2025-11-10T00:00:00Z' layout: resource_detail name: Database of Interacting Proteins products: - category: GraphicalInterface description: Web-based search interface for exploring protein-protein interactions by journal article, experimental evidence, or protein identifiers id: dip.search name: DIP Search Interface product_url: https://dip.doe-mbi.ucla.edu/dip/Search.cgi - category: Product description: Complete DIP dataset and specialized subsets available for download in PSI-MI formats (registration required) format: psi_mi_mitab id: dip.downloads name: DIP Data Downloads product_url: https://dip.doe-mbi.ucla.edu/dip/Download.cgi warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='dip.doe-mbi.ucla.edu', port=443)_ Max retries exceeded with url_ /dip/Download.cgi (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='dip.doe-mbi.ucla.edu', port=443)_ Max retries exceeded with url_ /dip/Download.cgi (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='dip.doe-mbi.ucla.edu', port=443)_ Max retries exceeded with url_ /dip/Download.cgi (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='dip.doe-mbi.ucla.edu', port=443)_ Max retries exceeded with url_ /dip/Download.cgi (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''dip.doe-mbi.ucla.edu'', port=443): Max retries exceeded with url: /dip/Download.cgi (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Historical consolidated protein interaction index in PSI-MITAB 2.5 format aggregating data from BIND, BioGrid, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID format: psi_mi_mitab id: irefindex.database name: iRefIndex Database original_source: - bind - biogrid - dip - hprd - intact - mint - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - 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biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz publications: - id: https://doi.org/10.1093/nar/30.1.303 title: 'DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions' - id: https://doi.org/10.1093/nar/gkh086 title: 'The Database of Interacting Proteins: 2004 update' - id: https://doi.org/10.1038/nmeth.1931 title: 'Protein interaction data curation: The International Molecular Exchange (IMEx) consortium' synonyms: - DIP - Database of Interacting Proteins - activity_status: active category: DataSource creation_date: '2025-11-25T00:00:00Z' description: Database of microbiome-disease associations, cataloging relationships between microbial taxa and human diseases based on experimental and clinical evidence. domains: - microbiology - biomedical - clinical - health homepage_url: https://disbiome.ugent.be/ id: disbiome last_modified_date: '2025-11-25T00:00:00Z' layout: resource_detail name: Disbiome products: - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe synonyms: - Disbiome - Disbiome Database taxon: - NCBITaxon:9606 - NCBITaxon:2 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: lynn.schriml@gmail.com - contact_type: github value: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 creation_date: '2025-09-29T00:00:00Z' description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI. domains: - biomedical homepage_url: https://disease-ontology.org/ id: disdriv last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Disease Drivers Ontology products: - category: OntologyProduct description: Disease Drivers Ontology in OWL format format: owl id: disdriv.owl name: disdriv.owl product_file_size: 13794 product_url: http://purl.obolibrary.org/obo/disdriv.owl repository: https://github.com/DiseaseOntology/DiseaseDriversOntology taxon: - NCBITaxon:9606 - activity_status: active category: Aggregator contacts: - category: Individual contact_details: - contact_type: email value: qingyao.huang@uzh.ch label: Qingyao Huang - category: Organization contact_details: - contact_type: url value: https://jensenlab.org/ label: JensenLab creation_date: '2025-06-04T00:00:00Z' description: DISEASES is a weekly updated database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It provides confidence scores to facilitate comparison of different types and sources of evidence. domains: - health - genomics - biomedical - literature homepage_url: https://diseases.jensenlab.org/ id: diseases infores_id: diseases last_modified_date: '2026-01-30T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: DISEASES products: - category: GraphicalInterface description: Web search interface for querying human genes and diseases to view integrated evidence from multiple channels format: http id: diseases.portal name: DISEASES Web Search original_source: - diseases product_url: https://diseases.jensenlab.org/ - category: Product description: Disease-gene associations from text mining channel with z-scores and confidence scores (full dataset) format: tsv id: diseases.textmining-full name: Text Mining Channel (Full) product_file_size: 1920661253 product_url: https://download.jensenlab.org/human_disease_textmining_full.tsv - category: Product description: Disease-gene associations from text mining channel with z-scores and confidence scores (filtered non-redundant) format: tsv id: diseases.textmining-filtered name: Text Mining Channel (Filtered) product_file_size: 48652618 product_url: https://download.jensenlab.org/human_disease_textmining_filtered.tsv - category: Product description: Disease-gene associations from manually curated knowledge channel with evidence types and confidence scores (full dataset) format: tsv id: diseases.knowledge-full name: Knowledge Channel (Full) product_file_size: 6883980 product_url: https://download.jensenlab.org/human_disease_knowledge_full.tsv - category: Product description: Disease-gene associations from manually curated knowledge channel with evidence types and confidence scores (filtered non-redundant) format: tsv id: diseases.knowledge-filtered name: Knowledge Channel (Filtered) product_file_size: 602129 product_url: https://download.jensenlab.org/human_disease_knowledge_filtered.tsv - category: Product description: Disease-gene associations from experimental data channel including cancer mutations and GWAS with source scores and confidence scores (full dataset) format: tsv id: diseases.experiments-full name: Experiments Channel (Full) product_file_size: 26901903 product_url: https://download.jensenlab.org/human_disease_experiments_full.tsv - category: Product description: Disease-gene associations from experimental data channel including cancer mutations and GWAS with source scores and confidence scores (filtered non-redundant) format: tsv id: diseases.experiments-filtered name: Experiments Channel (Filtered) product_file_size: 2567625 product_url: https://download.jensenlab.org/human_disease_experiments_filtered.tsv - category: Product description: Experimental integrated channel combining evidence from all sources (full dataset) format: tsv id: diseases.integrated-full name: Integrated Channel (Full) product_file_size: 648296693 product_url: https://download.jensenlab.org/human_disease_integrated_full.tsv - category: Product compression: targz description: Dictionary of human gene and disease names for the DISEASES tagger id: diseases.dictionary name: DISEASES Dictionary product_file_size: 15984342 product_url: https://download.jensenlab.org/diseases_dictionary.tar.gz - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: Product description: Manually curated disease-gene associations and annotations for amyloidoses and amyloid deposition-related diseases extracted from biomedical literature. id: amyco.annotations name: AmyCo Curated Annotations original_source: - pubmed - amyco secondary_source: - diseases - category: GraphProduct description: KGX graph package for DISEASES text-mined associations (build diseases_2025_12_07_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.diseases.graph name: Translator DISEASES KGX Graph original_source: - diseases product_url: https://stars.renci.org/var/translator/releases/diseases/2025_12_15/ secondary_source: - translator - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz publications: - id: PMID:35348650 preferred: true - id: PMID:25484339 synonyms: - DISEASES Database - JensenLab DISEASES taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: info@disgenet.com label: MedBioinformatics Solutions SL creation_date: '2025-06-04T00:00:00Z' description: DisGeNET is the world's largest and most extensive gene-disease association (GDA) network, integrating data from expert-curated repositories, GWAS catalogs, animal models, and scientific literature. It contains gene-disease associations, variant-disease associations, and disease-disease associations with extensive evidence supporting each connection. domains: - biomedical - genomics - clinical - precision medicine - translational - drug discovery homepage_url: https://www.disgenet.com/ id: disgenet infores_id: disgenet last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://www.disgenet.com/Legal label: DisGeNET License name: DisGeNET products: - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: ProgrammingInterface description: API access to DisGeNET data (requires registration and subscription). format: http id: disgenet.api name: DisGeNET API original_source: - disgenet product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: GraphicalInterface description: Browser for DisGeNET data (requires registration and subscription). format: http id: disgenet.browser name: DisGeNET Browser original_source: - disgenet product_url: https://www.disgenet.com/search?view=ALL&idents=ALL&source=ALL&tab=GDA secondary_source: - disgenet - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: Product description: The EPA has developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Since its inception, the AOP-DB has been developed with the aim of integrating AOP molecular target information with other publicly available datasets to facilitate computational analyses of AOP information. id: aop-db.data name: AOP-DB Data original_source: - aop-wiki - ctd - toxcast - disgenet - ncbigene - string - 1000genomes - ensembl - gwascatalog product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 secondary_source: - aop-db - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: Product description: Disease association data integrated from OMIM, MalaCards, ClinVar, Orphanet, DisGeNET and other disease databases format: http id: genecards.disease.associations name: GeneCards Disease Associations original_source: - omim - malacards - clinvar - orphanet - disgenet product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' publications: - authors: - Janet Piñero - Juan Manuel Ramírez-Anguita - Josep Saüch-Pitarch - Francesco Ronzano - Emilio Centeno - Ferran Sanz - Laura I. Furlong doi: 10.1093/nar/gkz1021 id: doi:10.1093/nar/gkz1021 journal: Nucleic Acids Research preferred: true title: The DisGeNET knowledge platform for disease genomics - 2019 update year: '2020' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: info@disprot.org label: DisProt Team - category: Individual contact_details: - contact_type: email value: biocomp@bio.unipd.it label: Damiano Piovesan creation_date: '2025-10-30T00:00:00Z' description: DisProt is a manually curated database of experimentally validated intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs), providing annotations for structural disorder and functional aspects of protein disorder. domains: - proteomics - biological systems homepage_url: https://www.disprot.org id: disprot infores_id: disprot last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: Creative Commons Attribution 4.0 International (CC BY 4.0) logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: DisProt products: - category: GraphicalInterface description: Web interface for browsing and searching intrinsically disordered protein annotations with search filters and organism browsing format: http id: disprot.browser name: DisProt Browser original_source: - disprot product_url: https://www.disprot.org/browse - category: Product description: Bulk download of DisProt data in multiple formats including JSON, TSV, FASTA, and GAF format: json id: disprot.downloads name: DisProt Downloads original_source: - disprot product_url: https://www.disprot.org/download - category: ProgrammingInterface description: RESTful API for programmatic access to DisProt data format: http id: disprot.api is_public: true name: DisProt API original_source: - disprot product_url: https://www.disprot.org/api - category: GraphicalInterface description: Deposition system for submitting experimental data on intrinsically disordered proteins id: disprot.deposition name: DisProt Deposition System original_source: - disprot product_url: https://deposition.disprot.org/ - category: OntologyProduct description: IDP Ontology (IDPO) for representing functional aspects of intrinsically disordered proteins format: owl id: disprot.idpo name: IDP Ontology (IDPO) original_source: - disprot product_file_size: 50945 product_url: https://www.disprot.org/assets/data/IDPO_v0.3.0.owl publications: - category: Publication id: PMID:37904585 preferred: true - category: Publication id: PMID:34850135 - category: Publication id: PMID:31713636 - activity_status: active category: Ontology contacts: - category: Organization contact_details: - contact_type: url value: http://www.sparontologies.net/ id: spar label: SPAR (Semantic Publishing and Referencing) Ontologies creation_date: '2025-12-17T00:00:00Z' description: DOCO (Document Components Ontology) is an OWL ontology for describing the structural and rhetorical components of documents. It is part of the SPAR (Semantic Publishing and Referencing) Ontologies suite and provides a vocabulary for semantic annotation of document structure. domains: - literature homepage_url: https://github.com/SPAROntologies/doco id: doco last_modified_date: '2026-01-05T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Document Components Ontology (DOCO) products: - category: OntologyProduct description: DOCO ontology in OWL/RDF format format: owl id: doco.owl is_public: true name: DOCO Ontology (OWL) product_file_size: 67374 product_url: https://svn.code.sf.net/p/sempublishing/code/DoCO/2015-07-03_doco-1_3.owl - category: OntologyProduct description: OpenBioDiv-O, the OpenBiodiv Ontology format: ttl id: openbiodiv.ontology.ttl is_public: true name: OpenBioDiv-O original_source: - skos - proton - fabio - doco - openbiodiv product_file_size: 8176 product_url: https://raw.githubusercontent.com/pensoft/OpenBiodiv/refs/heads/master/ontology/openbiodiv-ontology-latest.ttl secondary_source: - openbiodiv repository: https://github.com/SPAROntologies/doco - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: lynn.schriml@gmail.com - contact_type: github value: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 creation_date: '2025-09-29T00:00:00Z' description: An ontology for describing the classification of human diseases organized by etiology. domains: - biomedical homepage_url: https://disease-ontology.org id: doid last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Human Disease Ontology products: - category: OntologyProduct description: Disease Ontology, OWL format. This file contains DO's is_a asserted hierarchy plus equivalent axioms to other OBO Foundry ontologies. format: owl id: doid.owl name: Disease Ontology, OWL format. This file contains DO's is_a asserted hierarchy plus equivalent axioms to other OBO Foundry ontologies. product_file_size: 2105834 product_url: http://purl.obolibrary.org/obo/doid.owl - category: OntologyProduct description: Disease Ontology, OBO format. This file omits the equivalent axioms. format: obo id: doid.obo name: Disease Ontology, OBO format. This file omits the equivalent axioms. product_file_size: 1368474 product_url: http://purl.obolibrary.org/obo/doid.obo - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: GraphProduct compression: zip description: Nodes from Human Disease Ontology format: csv id: biomarkerkg.nodes.condition name: BKG Condition Nodes original_source: - doid product_file_size: 5501 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Condition.nodes.zip secondary_source: - biomarkerkg - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct description: Nodes for the Drug Approvals KP, v0.3.9 format: kgx id: drug-approvals-kp.graph.nodes name: Drug Approvals KP Graph Nodes original_source: - chebi - doid - hp - mondo product_file_size: 701451 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_nodes_v0.3.9.tsv secondary_source: - drug-approvals-kp - category: GraphProduct description: Edges for the Drug Approvals KP, v0.3.9 format: kgx id: drug-approvals-kp.graph.edges name: Drug Approvals KP Graph Edges original_source: - chebi - doid - hp - mondo product_file_size: 31052966 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_edges_v0.3.9.tsv secondary_source: - drug-approvals-kp - category: MappingProduct description: MONDO SSSOM. Mappings from MONDO identifiers to other namespaces. format: sssom id: mondo.sssom name: MONDO SSSOM original_source: - doid - hp - hgnc product_file_size: 1437457 product_url: https://raw.githubusercontent.com/monarch-initiative/mondo/refs/heads/master/src/ontology/mappings/mondo.sssom.tsv secondary_source: - mondo repository: https://github.com/DiseaseOntology/HumanDiseaseOntology taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph creation_date: '2025-09-11T00:00:00Z' description: DoRothEA is a curated resource of transcription factor (TF) – target gene (regulon) interactions with confidence scoring, enabling inference of TF activity from gene expression data. It integrates literature-curated interactions and various experimental evidence (e.g. ChIP-seq, TF binding motifs, perturbation data) to build context-agnostic and confidence-stratified regulons for multiple species. Frequently used with PROGENy to estimate pathway and TF activities. domains: - genomics - biological systems - biomedical evaluation_page: resource/dorothea/dorothea_eval_automated.html homepage_url: https://saezlab.github.io/dorothea/ id: dorothea last_modified_date: '2025-09-11T00:00:00Z' layout: resource_detail name: DoRothEA products: - category: GraphProduct description: Core TF–target regulon knowledge graph (multi-species) with confidence levels (A–E) id: dorothea.graph name: DoRothEA Regulon Graph product_url: https://github.com/saezlab/dorothea/releases/tag/v1.0.0 - category: ProcessProduct description: R package containing regulon data and helper functions for TF activity inference format: http id: dorothea.r-package name: DoRothEA R Package product_url: https://github.com/saezlab/dorothea/ - category: DocumentationProduct description: Project documentation, usage examples, and methodological notes format: http id: dorothea.docs name: DoRothEA Documentation product_url: https://saezlab.github.io/dorothea/articles/dorothea.html - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - doi: 10.1101/gr.240663.118 id: doi:10.1101/gr.240663.118 journal: Genome Research title: Benchmark and integration of resources for the estimation of human transcription factor activities year: '2019' - doi: 10.1101/2023.03.30.534849 id: doi:10.1101/2023.03.30.534849 journal: bioRxiv title: Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities year: '2023' - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cp390@cam.ac.uk - contact_type: github value: Clare72 label: Clare Pilgrim orcid: 0000-0002-1373-1705 creation_date: '2025-09-29T00:00:00Z' description: An ontology of commonly encountered and/or high level Drosophila phenotypes. domains: - biological systems homepage_url: http://purl.obolibrary.org/obo/fbcv id: dpo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Drosophila Phenotype Ontology products: - category: OntologyProduct description: Drosophila Phenotype Ontology in OWL format format: owl id: dpo.owl name: dpo.owl product_file_size: 4002750 product_url: http://purl.obolibrary.org/obo/dpo.owl - category: OntologyProduct description: Drosophila Phenotype Ontology in OBO format format: obo id: dpo.obo name: dpo.obo product_file_size: 133576 product_url: http://purl.obolibrary.org/obo/dpo.obo - category: OntologyProduct description: Drosophila Phenotype Ontology in JSON format format: json id: dpo.json name: dpo.json product_file_size: 2021460 product_url: http://purl.obolibrary.org/obo/dpo.json repository: https://github.com/FlyBase/drosophila-phenotype-ontology taxon: - NCBITaxon:7227 - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: yuzhou.chen@temple.edu label: Yuzhou Chen creation_date: '2025-12-08T00:00:00Z' description: DREAM-KG (Develop Dynamic, REsponsive, Adaptive, and Multifaceted Knowledge Graphs) is a knowledge graph designed to address homelessness with explainable AI, integrating data across social services and community resources. domains: - social determinants - health evaluation_page: resource/dreamkg/dreamkg_eval_automated.html homepage_url: https://dreamkg.com/ id: dreamkg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: DREAM-KG products: - category: ProgrammingInterface description: SPARQL endpoint for DREAM-KG id: dreamkg.sparql name: DREAM-KG SPARQL original_source: - dreamkg product_url: https://frink.apps.renci.org/dreamkg/sparql - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: https://github.com/bioannidis label: Vassilis N. Ioannidis orcid: 0000-0002-8367-0733 creation_date: '2025-03-09T00:00:00Z' description: Drug Repurposing Knowledge Graph (DRKG) is a comprehensive biological knowledge graph relating genes, compounds, diseases, biological processes, side effects and symptoms. domains: - health evaluation_page: resource/drkg/drkg_eval_automated.html homepage_url: https://github.com/gnn4dr/DRKG id: drkg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: Drug Repurposing Knowledge Graph products: - category: GraphProduct compression: targz description: DRKG graph files, including a TSV of triples, embeddings, ID mappings, and a glossary of relation types. id: drkg.graph name: DRKG graph original_source: - drkg product_file_size: 216650245 product_url: https://dgl-data.s3-us-west-2.amazonaws.com/dataset/DRKG/drkg.tar.gz secondary_source: - drkg - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi repository: https://github.com/gnn4dr/DRKG - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: hoganwr@gmail.com - contact_type: github value: hoganwr label: William Hogan orcid: 0000-0002-9881-1017 creation_date: '2025-09-29T00:00:00Z' description: An ontology to support comparative effectiveness researchers studying claims data. domains: - biomedical homepage_url: https://github.com/ufbmi/dron id: dron last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: The Drug Ontology products: - category: OntologyProduct description: The Drug Ontology in OWL format format: owl id: dron.owl name: dron.owl product_file_size: 701717829 product_url: http://purl.obolibrary.org/obo/dron.owl repository: https://github.com/ufbmi/dron - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual contact_details: - contact_type: email value: gglusman@isbscience.org - contact_type: github value: gglusman label: Gwênlyn Glusman creation_date: '2025-04-22T00:00:00Z' description: A Translator knowledge provider focused on drug approval status and other drug-related metadata. domains: - health - pharmacology - drug discovery - biomedical evaluation_page: resource/drug-approvals-kp/drug-approvals-kp_eval_automated.html id: drug-approvals-kp last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: Drug Approvals KP products: - category: GraphProduct description: Nodes for the Drug Approvals KP, v0.3.9 format: kgx id: drug-approvals-kp.graph.nodes name: Drug Approvals KP Graph Nodes original_source: - chebi - doid - hp - mondo product_file_size: 701451 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_nodes_v0.3.9.tsv secondary_source: - drug-approvals-kp - category: GraphProduct description: Edges for the Drug Approvals KP, v0.3.9 format: kgx id: drug-approvals-kp.graph.edges name: Drug Approvals KP Graph Edges original_source: - chebi - doid - hp - mondo product_file_size: 31052966 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_edges_v0.3.9.tsv secondary_source: - drug-approvals-kp - category: ProcessProduct description: Code for the Drug Approvals KP id: drug-approvals-kp.code name: Drug Approvals KP code original_source: - drug-approvals-kp product_url: https://github.com/multiomicsKP/drug_approvals_kp secondary_source: - drug-approvals-kp repository: https://github.com/multiomicsKP/drug_approvals_kp - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: info@drugbank.com - contact_type: url value: https://www.drugbank.com/contact label: DrugBank creation_date: '2025-03-09T00:00:00Z' description: DrugBank Online is a comprehensive, publicly accessible database containing detailed information on drugs and drug targets, combining chemical, pharmacological, pharmaceutical data with drug target information including sequence, structure, and pathway details. domains: - health - chemistry and biochemistry - pharmacology - genomics - proteomics homepage_url: https://www.drugbank.com/ id: drugbank infores_id: drugbank last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://go.drugbank.com/legal/terms_of_use label: Custom (free for academic research with license) name: DrugBank products: - category: GraphicalInterface description: Web interface for browsing and searching the DrugBank database format: http id: drugbank.web name: DrugBank Online original_source: - drugbank product_url: https://go.drugbank.com/ - category: DataModelProduct description: Academic access to DrugBank database dumps in XML and other formats format: xml id: drugbank.academic license: id: https://go.drugbank.com/legal/terms_of_use label: Academic License name: DrugBank Academic Downloads original_source: - drugbank product_url: https://go.drugbank.com/releases/latest - category: ProgrammingInterface connection_url: https://www.drugbank.com/clinical description: Clinical API for integrating DrugBank data into healthcare applications id: drugbank.clinical.api is_public: true name: DrugBank Clinical API original_source: - drugbank product_url: https://www.drugbank.com/clinical - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: Product description: Pharmacogenomics data from PharmGKB, DrugBank and other pharmacogenomics sources format: http id: genecards.pharmacogenomics name: GeneCards Pharmacogenomics Data original_source: - pharmgkb - drugbank product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - id: https://doi.org/10.1093/nar/gkad976 journal: Nucleic Acids Research preferred: true title: DrugBank 6.0 - The DrugBank Knowledgebase for 2024 year: '2024' - id: https://doi.org/10.1093/nar/gkx1037 journal: Nucleic Acids Research title: DrugBank 5.0 - A major update to the DrugBank database for 2018 year: '2018' repository: https://go.drugbank.com/releases/latest tags: - core - biopragmatics taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization label: DrugCentral creation_date: '2025-03-09T00:00:00Z' description: DrugCentral is online drug information resource created and maintained by Division of Translational Informatics at University of New Mexico. domains: - health homepage_url: https://drugcentral.org/ id: drugcentral infores_id: drugcentral last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: DrugCentral products: - category: GraphProduct description: DrugCentral Automat format: kgx-jsonl id: automat.drugcentral infores_id: automat-drug-central name: drugcentral_automat original_source: - drugcentral product_url: https://stars.renci.org/var/plater/bl-4.2.1/DrugCentral_Automat/dec0617490b49c7a/ secondary_source: - automat - category: Product compression: gzip description: PostgreSQL (v14.5) database dump of all information in DrugCentral. format: postgres id: drugcentral.data name: DrugCentral Database dump original_source: - drugcentral product_file_size: 1400714190 product_url: https://unmtid-dbs.net/download/drugcentral.dump.11012023.sql.gz secondary_source: - drugcentral - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: Training data for the MIND knowledge graph containing 9,651,040 edges format: tsv id: mind.train license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: MIND Training Data original_source: - drugcentral - mechreponet product_url: https://zenodo.org/records/8117748/files/train.txt secondary_source: - mind warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-22_ HTTP 429 error when accessing file - File was not able to be retrieved when checked on 2025-12-18_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: Test data for the MIND knowledge graph containing DrugCentral indications format: tsv id: mind.test license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: MIND Test Data original_source: - drugcentral - mechreponet product_url: https://zenodo.org/records/8117748/files/test.txt secondary_source: - mind warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-18_ HTTP 429 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: Validation data for the MIND knowledge graph containing DrugCentral indications format: tsv id: mind.valid license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: MIND Validation Data original_source: - drugcentral - mechreponet product_url: https://zenodo.org/records/8117748/files/valid.txt secondary_source: - mind warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-22_ HTTP 429 error when accessing file - File was not able to be retrieved when checked on 2025-10-30_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Dictionary of entities in the MIND knowledge graph format: tsv id: mind.entities license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: MIND Entities Dictionary original_source: - drugcentral - mechreponet product_file_size: 5629618 product_url: https://zenodo.org/records/8117748/files/entities.dict secondary_source: - mind - category: Product description: Dictionary of relations in the MIND knowledge graph format: tsv id: mind.relations license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: MIND Relations Dictionary original_source: - drugcentral - mechreponet product_file_size: 1648 product_url: https://zenodo.org/records/8117748/files/relations.dict secondary_source: - mind - category: Product description: Complete RepoDB dataset containing drug repositioning successes and failures, with approved drugs, indications, and clinical trial outcomes format: csv id: repodb.full_dataset name: RepoDB Full Dataset original_source: - drugcentral - clinicaltrialsgov product_url: https://unmtid-shinyapps.net/shiny/repodb/session/98046b0f66cea75c432b5576c1ba2840/download/downloadFull?w= warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-10-27_ HTTP 500 error when accessing file - File was not able to be retrieved when checked on 2025-08-07_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphProduct description: KGX graph package for DrugCentral Annotation KP (build dakp_0.4.3_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.dakp.graph name: Translator DAKP KGX Graph original_source: - drugcentral product_url: https://stars.renci.org/var/translator/releases/dakp/2025_12_15/ secondary_source: - translator - category: Product description: drugcentral Nodes TSV format: tsv id: obo-db-ingest.drugcentral.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: drugcentral Nodes TSV original_source: - drugcentral product_file_size: 407590 product_url: https://w3id.org/biopragmatics/resources/drugcentral/drugcentral.tsv secondary_source: - obo-db-ingest publications: - authors: - Ursu O - Holmes J - Knockel J - Bologa CG - Yang JJ - Mathias SL - Nelson SJ - Oprea TI doi: doi:10.1093/nar/gkw993 id: doi:10.1093/nar/gkw993 title: 'DrugCentral: online drug compendium' year: '2017' - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://sulab.org/ label: Su Lab creation_date: '2025-08-12T00:00:00Z' description: DrugMechDB is a curated database that captures mechanistic paths from a drug to a disease within a given indication. Expert curators normalize concepts and relationships to standard biomedical identifiers and represent each indication as a directed path through a biological knowledge graph, suitable for computational analysis and benchmarking. domains: - biomedical - pharmacology - drug discovery - literature evaluation_page: resource/drugmechdb/drugmechdb_eval.html homepage_url: https://sulab.github.io/DrugMechDB/ id: drugmechdb infores_id: drugmechdb last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 Universal logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: DrugMechDB products: - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' - category: GraphicalInterface description: Web interface for exploring curated DrugMechDB paths by drug and disease. format: http id: drugmechdb.web name: DrugMechDB Website product_url: https://sulab.github.io/DrugMechDB/ publications: - doi: 10.1038/s41597-023-02534-z id: doi:10.1038/s41597-023-02534-z journal: Scientific Data title: DrugMechDB — a curated database of drug mechanisms year: '2023' repository: https://github.com/SuLab/DrugMechDB taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.broadinstitute.org/center-development-therapeutics-cdot id: broad-cdot label: Broad Institute Center for the Development of Therapeutics (CDoT) - category: Organization contact_details: - contact_type: url value: https://www.broadinstitute.org/ id: broad-institute label: Broad Institute creation_date: '2026-01-22T00:00:00Z' description: Curated collection of approved, clinical, and pre-clinical compounds with detailed annotations and sample metadata to support drug repurposing screens and analyses. domains: - drug discovery - pharmacology - biomedical homepage_url: https://repo-hub.broadinstitute.org/repurposing id: drugrephub last_modified_date: '2026-01-22T00:00:00Z' layout: resource_detail name: Drug Repurposing Hub products: - category: Product description: Latest drug-level annotations including compound names, clinical phase, mechanism of action, and protein targets (listed as version 2025-08-19 on the site). format: tsv id: drugrephub.drug-info.tsv name: Drug Repurposing Hub Drug Information TSV product_url: https://repo-hub.broadinstitute.org/public/data/repo-drug-annotation-20200324.txt warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /public/data/repo-drug-annotation-20200324.txt (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /public/data/repo-drug-annotation-20200324.txt (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /public/data/repo-drug-annotation-20200324.txt (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /public/data/repo-drug-annotation-20200324.txt (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Latest physical sample-level metadata including Broad sample IDs, vendor catalog numbers, SMILES, InChIKey, and PubChem IDs (listed as version 2025-08-19 on the site). format: tsv id: drugrephub.sample-info.tsv name: Drug Repurposing Hub Sample Information TSV product_url: https://repo-hub.broadinstitute.org/public/data/repo-sample-annotation-20240610.txt warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /public/data/repo-sample-annotation-20240610.txt (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /public/data/repo-sample-annotation-20240610.txt (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /public/data/repo-sample-annotation-20240610.txt (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /public/data/repo-sample-annotation-20240610.txt (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: GraphProduct description: KGX graph package for Drug Repurposing Hub (build drug_rep_hub_2025-08-19_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.drug_rep_hub.graph name: Translator Drug Repurposing Hub KGX Graph original_source: - drugrephub product_url: https://stars.renci.org/var/translator/releases/drug_rep_hub/2025_12_15/ secondary_source: - translator - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: email value: EPA_ComptoxTools@epa.gov label: EPA CCTE creation_date: '2025-06-24T00:00:00Z' description: EPA's Distributed Structure-Searchable Toxicity (DSSTox) Database contains curated chemical substances mapped to data including chemical identifiers and structure representations, providing the chemical underpinning for EPA's computational toxicology tools. domains: - biomedical - chemistry and biochemistry - environment - health homepage_url: https://www.epa.gov/comptox-tools/distributed-structure-searchable-toxicity-dsstox-database id: dsstox last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: DSSTox products: - category: Product description: The complete DSSTox database containing over 1.2 million chemical substances with identifiers and structures format: csv id: dsstox.complete name: DSSTox Complete Database product_url: https://doi.org/10.23645/epacomptox.5588566 warnings: [] - category: GraphicalInterface description: The CompTox Chemicals Dashboard provides access to the DSSTox database through a web interface format: http id: dsstox.dashboard name: CompTox Chemicals Dashboard product_url: https://comptox.epa.gov/dashboard - category: ProgrammingInterface description: Public API for programmatic access to DSSTox data id: dsstox.api is_public: true name: CompTox API product_url: https://api-ccte.epa.gov/docs/index.html - category: DocumentationProduct description: Documentation for the DSSTox database format: docx id: dsstox.description name: DSSToxDB Description product_url: https://clowder.edap-cluster.com/files/6616d945e4b063812d70fcb5?dataset=61147fefe4b0856fdc65639b&space=&folder=6616d85ce4b063812d70fc8f warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet publications: - authors: - Williams AJ - Grulke CM - Edwards J - McEachran AD - Mansouri K - Baker NC - Patlewicz G - Shah I - Wambaugh JF - Judson RS - Richard AM doi: 10.1186/s13321-017-0247-6 id: doi:10.1186/s13321-017-0247-6 journal: Journal of Cheminformatics preferred: true title: 'The CompTox Chemistry Dashboard: a community data resource for environmental chemistry' year: '2017' - activity_status: active category: DataSource creation_date: '2025-11-19T00:00:00Z' description: EPA's Distributed Structure-Searchable Toxicity (DSSTox) database provides high-quality chemical and chemistry data underpinning several publicly available computational toxicology applications. DSSTox contains curated chemical substances mapped to chemical identifiers including CAS Registry Numbers, IUPAC names, SMILES, and InChIKeys. The database currently exceeds 1.2 million substances which includes chemical lists of interest to EPA, other federal agencies, states, tribes, industry and stakeholder groups. DSSTox provides accurate linkages of chemical structures to source substance identifiers, allowing high-quality association of chemicals to existing toxicity data, bioactivity data, experimental chemical property data and enabling structure-based predictive modeling. The database supports the CompTox Chemicals Dashboard, EcoTox Knowledgebase, Chemical Exposure Knowledgebase, and other EPA tools. domains: - toxicology - chemistry and biochemistry - environment homepage_url: https://www.epa.gov/chemical-research/distributed-structure-searchable-toxicity-dsstox-database id: dsstoxdb infores_id: dsstoxdb last_modified_date: '2025-11-19T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Distributed Structure-Searchable Toxicity (DSSTox) Database products: - category: GraphicalInterface description: Web-based interface for searching over 1.2 million chemicals with integrated toxicity, bioactivity, and exposure data format: http id: dsstoxdb.dashboard name: CompTox Chemicals Dashboard original_source: - dsstoxdb product_url: https://comptox.epa.gov/dashboard/ - category: MappingProduct description: Downloadable Excel and CSV files containing DSSTox identifiers mapped to CAS numbers, InChIKeys, SMILES, molecular formulas, and other chemical identifiers for over 1.2 million substances format: mixed id: dsstoxdb.downloads name: DSSTox Data Downloads original_source: - dsstoxdb product_url: https://epa.figshare.com/articles/dataset/Chemistry_Dashboard_Data_DSSTox_Identifiers_Mapped_to_CAS_Numbers_and_Names/5588566 - category: ProgrammingInterface description: Public API providing programmatic access to DSSTox chemical data and computational toxicology information format: http id: dsstoxdb.api name: EPA CompTox API original_source: - dsstoxdb product_url: https://api-ccte.epa.gov/docs/index.html - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mcourtot@gmail.com - contact_type: github value: mcourtot label: Melanie Courtot orcid: 0000-0002-9551-6370 creation_date: '2025-09-29T00:00:00Z' description: DUO is an ontology which represent data use conditions. domains: - biomedical homepage_url: https://github.com/EBISPOT/DUO id: duo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Data Use Ontology products: - category: OntologyProduct description: Data Use Ontology in OWL format format: owl id: duo.owl name: duo.owl product_file_size: 8062 product_url: http://purl.obolibrary.org/obo/duo.owl repository: https://github.com/EBISPOT/DUO - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: kg@ebrains.eu label: EBRAINS team creation_date: '2025-05-01T00:00:00Z' description: A knowledge graph for the EBRAINS project, an infrastructure for data, tools and computing facilities for brain-related research. domains: - health - neuroscience - biomedical evaluation_page: resource/ebrains/ebrains_eval_automated.html homepage_url: https://docs.kg.ebrains.eu/ id: ebrains last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: EBRAINS Knowledge Graph products: - category: GraphicalInterface description: A visualization of the contents of the EBRAINS knowledge graph. format: http id: ebrains.stats name: KG Statistics original_source: - ebrains product_url: https://stats.kg.ebrains.eu/ secondary_source: - ebrains - category: ProgrammingInterface description: Interface for accessing the EBRAINS KG (also known as the MarmotGraph API) format: http id: ebrains.api.core name: EBRAINS KG Core API original_source: - ebrains product_url: https://core.kg.ebrains.eu/swagger-ui/index.html secondary_source: - ebrains repository: https://github.com/HumanBrainProject/kg-core - activity_status: active category: Ontology contacts: - category: Organization contact_details: - contact_type: url value: https://www.iubmb.org/ id: iubmb label: International Union of Biochemistry and Molecular Biology creation_date: '2025-11-25T00:00:00Z' description: The Enzyme Commission classification system provides a hierarchical numbering scheme for enzymes based on the chemical reactions they catalyze, maintained by the IUBMB. domains: - systems biology - biological systems homepage_url: https://www.enzyme-database.org/ id: ec last_modified_date: '2026-01-05T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Enzyme Commission products: - category: GraphicalInterface description: Official Enzyme Commission nomenclature and EC number database format: http id: ec.database is_public: true name: Enzyme Commission Official Database product_url: https://www.enzyme-database.org/ - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe - category: Product description: ec Nodes TSV format: tsv id: obo-db-ingest.ec.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: ec Nodes TSV original_source: - ec product_file_size: 283274 product_url: https://w3id.org/biopragmatics/resources/ec/ec.tsv secondary_source: - obo-db-ingest synonyms: - EC - EC Numbers - Enzyme Commission Numbers - IUBMB Enzyme Nomenclature warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: ettensohn@cmu.edu - contact_type: github value: ettensohn label: Charles Ettensohn orcid: 0000-0002-3625-0955 creation_date: '2025-09-29T00:00:00Z' description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586). domains: - anatomy and development homepage_url: https://github.com/echinoderm-ontology/ecao_ontology id: ecao last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: The Echinoderm Anatomy and Development Ontology products: - category: OntologyProduct description: The Echinoderm Anatomy and Development Ontology in OWL format format: owl id: ecao.owl name: ecao.owl product_file_size: 1546949 product_url: http://purl.obolibrary.org/obo/ecao.owl - category: OntologyProduct description: The Echinoderm Anatomy and Development Ontology in OBO format format: obo id: ecao.obo name: ecao.obo product_file_size: 1002010 product_url: http://purl.obolibrary.org/obo/ecao.obo repository: https://github.com/echinoderm-ontology/ecao_ontology - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: url value: https://www.ecidbase.org/contact label: Integrated Data Science Laboratory for Metabolomics and Exposomics (IDSL-ME) - category: Individual contact_details: - contact_type: email value: dinesh.barupal@mssm.edu label: Dinesh Kumar Barupal creation_date: '2025-05-12T00:00:00Z' description: ECID is a biomedical knowledgebase of curated inter-chemical correlations from the core chemical datasets in exposomics. These datasets are prioritized from human biomonitoring studies using targeted and untargeted assays. ECID has applications in characterizing and understanding the effects of exposome chemicals on the human health. domains: - environment - health - chemistry and biochemistry - public health - social determinants - biomedical homepage_url: https://www.ecidbase.org/ id: ecid last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail name: ECID products: - category: GraphicalInterface description: Interface for the Chemical Correlation Database for exploring curated inter-chemical correlations id: ecid.ccdb.site is_public: true name: CCDB original_source: - ecid product_url: https://ccdb.ecidbase.org/ secondary_source: - ecid - category: GraphicalInterface description: Interface for Exposome Data Interpretation Resource for interpreting inter-chemical correlations id: ecid.edir.site is_public: true name: EDIR original_source: - ecid product_url: https://edir.ecidbase.org/ secondary_source: - ecid - category: Product description: Compound lists from 73 untargeted datasets with 3,329 unique 2D structures. id: ecid.compound.lists is_public: true name: ECID Compound Lists original_source: - ecid product_url: https://zenodo.org/records/15204234 secondary_source: - ecid - category: Product description: Analytes measured by targeted assays for the NIEHS HHEAR program. id: ecid.hhear.analyte.list is_public: true name: HHEAR Analyte List original_source: - ecid product_url: https://zenodo.org/records/15127651 secondary_source: - ecid - category: Product description: Chemical analytes reported for the ECHO cohort measured by targeted assays. id: ecid.echo.analyte.list is_public: true name: ECHO Analyte List original_source: - ecid product_url: https://zenodo.org/records/15127650 secondary_source: - ecid - category: Product description: Selected datasets (n=289) for computing and curating inter-chemical correlations. id: ecid.dataset.list is_public: true name: ECID Dataset List original_source: - ecid product_url: https://zenodo.org/records/15122961 secondary_source: - ecid - category: Product description: Chemical analytes reported by the NHANES biomonitoring survey. id: ecid.nhanes.analyte.list is_public: true name: NHANES Analyte List original_source: - ecid product_url: https://zenodo.org/records/11528668 secondary_source: - ecid - category: Product description: Metabolite and chemical names reported by Metabolon Inc. in PMC articles. id: ecid.metabolomics.data.dictionary is_public: true name: Metabolomics Data Dictionary original_source: - ecid product_url: https://zenodo.org/records/10974865 secondary_source: - ecid - category: Product description: mwTAB files processed to yield curated compound names and identifiers. id: ecid.metabolomics.workbench.dictionary is_public: true name: Metabolomics WorkBench Compound Dictionary original_source: - ecid product_url: https://zenodo.org/records/10963201 secondary_source: - ecid - category: Product description: Catalogues chemicals expected and detected in human blood specimens. format: csv id: ecid.bloodexposome.data is_public: true name: Blood Exposome Database original_source: - ecid product_url: https://zenodo.org/records/8146024 secondary_source: - ecid publications: - authors: - Barupal DK - Mahajan P - Fakouri-Baygi S - Wright RO - Arora M - Teitelbaum SL doi: doi:10.1016/j.envint.2022.107240 id: doi:10.1016/j.envint.2022.107240 title: 'CCDB: A database for exploring inter-chemical correlations in metabolomics and exposomics datasets' year: '2022' repository: https://github.com/idslme/ecid taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mgiglio@som.umaryland.edu - contact_type: github value: mgiglio99 label: Michelle Giglio orcid: 0000-0001-7628-5565 creation_date: '2025-09-29T00:00:00Z' description: An ontology for experimental and other evidence statements. domains: - biomedical homepage_url: https://www.evidenceontology.org id: eco last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Evidence and Conclusion Ontology products: - 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category: Organization contact_details: - contact_type: url value: https://kghub.org - contact_type: github value: Knowledge Graph Hub label: Knowledge Graph Hub creation_date: '2025-03-09T00:00:00Z' description: A knowledge graph of plant traits starting with Planteome and EOL TraitBank. domains: - organisms - environment - biological systems evaluation_page: resource/eco-kg/eco-kg_eval_automated.html homepage_url: https://kghub.org/eco-kg/index.html id: eco-kg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: eco-KG products: - category: GraphProduct compression: tar description: Knowledge graph containing plant traits data from Planteome and EOL TraitBank format: kgx id: eco-kg.graph name: eco-KG Graph original_source: - eco-kg product_url: https://kg-hub.berkeleybop.io/eco-kg/ - category: ProgrammingInterface connection_url: https://kghub.org/eco-kg/api description: API for accessing eco-KG data id: eco-kg.api is_public: true name: eco-KG API original_source: - eco-kg product_url: https://kghub.org/eco-kg/api repository: https://github.com/Knowledge-Graph-Hub/eco-kg tags: - core taxon: - NCBITaxon:33090 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: p.buttigieg@gmail.com - contact_type: github value: pbuttigieg label: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 creation_date: '2025-09-29T00:00:00Z' description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. domains: - environment homepage_url: https://github.com/EcologicalSemantics/ecocore id: ecocore last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: An ontology of core ecological entities products: - category: OntologyProduct description: An ontology of core ecological entities in OWL format format: owl id: ecocore.owl name: ecocore.owl product_file_size: 1287569 product_url: http://purl.obolibrary.org/obo/ecocore.owl - category: OntologyProduct description: An ontology of core ecological entities in OBO format format: obo id: ecocore.obo name: ecocore.obo product_file_size: 834439 product_url: http://purl.obolibrary.org/obo/ecocore.obo repository: https://github.com/EcologicalSemantics/ecocore - activity_status: active category: DataSource collection: - translator - ber contacts: - category: Organization contact_details: - contact_type: email value: biocyc-support@sri.com - contact_type: url value: https://ecocyc.org/contact.shtml label: EcoCyc creation_date: '2025-03-17T00:00:00Z' description: EcoCyc captures information from 44,000 publications for Escherichia coli K-12 substr. MG1655. Use EcoCyc to search for knowledge on E. coli genes, regulation, and metabolism; analyze transcriptomics data; perform comparative analyses; and run a metabolic model. domains: - microbiology - genomics - biological systems - pathways homepage_url: https://ecocyc.org/ id: ecocyc last_modified_date: '2025-09-27T00:00:00Z' layout: resource_detail license: id: https://ecocyc.org/download.shtml label: Varies name: EcoCyc products: - category: MappingProduct description: rhea SSSOM format: sssom id: obo-db-ingest.rhea.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rhea SSSOM original_source: - rhea - reactome - kegg - metacyc - m-csa - ecocyc product_file_size: 154171 product_url: https://w3id.org/biopragmatics/resources/rhea/rhea.sssom.tsv secondary_source: - obo-db-ingest - category: GraphicalInterface description: Web interface for EcoCyc database id: ecocyc.web name: EcoCyc Web Interface original_source: - ecocyc product_url: https://ecocyc.org/ - category: ProgrammingInterface connection_url: https://ecocyc.org/web-services.shtml description: Web services and APIs for programmatic access to EcoCyc data id: ecocyc.api is_public: true name: EcoCyc Web Services original_source: - ecocyc product_url: https://ecocyc.org/web-services.shtml - category: ProcessProduct description: Metabolic model for E. coli K-12 derived from EcoCyc id: ecocyc.metabolic_model name: EcoCyc Metabolic Model original_source: - ecocyc product_url: http://www.biomedcentral.com/1752-0509/8/79 repository: https://biocyc.org/download.shtml - activity_status: active category: Resource collection: - ber contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Christopher J. Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-03-09T00:00:00Z' description: Ontology rendering of the EcoSIM Land System Model domains: - environment homepage_url: http://purl.obolibrary.org/obo/ecosim.owl id: ecosim last_modified_date: '2025-09-27T00:00:00Z' layout: resource_detail name: ecosim products: - category: Product description: OWL release of ecosim format: owl id: ecosim.model.owl name: ecosim OWL release original_source: - ecosim secondary_source: - ecosim repository: http://purl.obolibrary.org/obo/ecosim.owl - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: annethessen@gmail.com - contact_type: github value: diatomsRcool label: Anne Thessen orcid: 0000-0002-2908-3327 creation_date: '2025-06-25T00:00:00Z' description: ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). domains: - environment homepage_url: https://github.com/EnvironmentOntology/environmental-exposure-ontology id: ecto last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Environmental conditions, treatments and exposures ontology products: - category: OntologyProduct description: Environmental conditions, treatments and exposures ontology in OWL format format: owl id: ecto.owl name: ecto.owl product_file_size: 2277332 product_url: http://purl.obolibrary.org/obo/ecto.owl - category: OntologyProduct description: Environmental conditions, treatments and exposures ontology in OBO format format: obo id: ecto.obo name: ecto.obo product_file_size: 1509031 product_url: http://purl.obolibrary.org/obo/ecto.obo - category: OntologyProduct description: Environmental conditions, treatments and exposures ontology in JSON format format: json id: ecto.json name: ecto.json product_file_size: 1646990 product_url: http://purl.obolibrary.org/obo/ecto.json - category: OntologyProduct description: Environmental conditions, treatments and exposures ontology in OWL format format: owl id: ecto.ecto-base.owl name: ecto.ecto-base.owl product_file_size: 160667 product_url: http://purl.obolibrary.org/obo/ecto/ecto-base.owl - category: OntologyProduct description: Environmental conditions, treatments and exposures ontology in OBO format format: obo id: ecto.ecto-base.obo name: ecto.ecto-base.obo product_file_size: 97093 product_url: http://purl.obolibrary.org/obo/ecto/ecto-base.obo - category: OntologyProduct description: Environmental conditions, treatments and exposures ontology in JSON format format: json id: ecto.ecto-base.json name: ecto.ecto-base.json product_file_size: 141984 product_url: http://purl.obolibrary.org/obo/ecto/ecto-base.json - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology - activity_status: active category: Ontology contacts: - category: Individual contact_details: - contact_type: github value: joncison label: Jon Ison - category: Individual contact_details: - contact_type: github value: matuskalas label: Matúš Kalaš - category: Individual contact_details: - contact_type: github value: hmenager label: Hervé Ménager creation_date: '2025-06-04T00:00:00Z' description: EDAM is an ontology of bioscientific data analysis and data management, covering topics, operations, data, identifiers, and formats. It supports semantic annotation of tools, workflows, training, and provenance metadata across life sciences. domains: - information technology - biological systems homepage_url: https://edamontology.org/ id: edam last_modified_date: '2025-10-15T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 logo: https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png name: EDAM Ontology products: - category: OntologyProduct description: EDAM OWL release format: owl id: edam.owl name: EDAM OWL original_source: - edam - dc - skos product_file_size: 3373041 product_url: http://edamontology.org/EDAM.owl secondary_source: - edam - category: OntologyProduct description: EDAM TSV export format: tsv id: edam.tsv name: EDAM TSV original_source: - edam - dc - skos product_file_size: 1977072 product_url: https://edamontology.org/EDAM.tsv secondary_source: - edam - category: OntologyProduct description: EDAM CSV export format: csv id: edam.csv name: EDAM CSV original_source: - edam - dc - skos product_file_size: 1977072 product_url: https://edamontology.org/EDAM.csv secondary_source: - edam - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg publications: - authors: - Ison J - Kalaš M - Jonassen I - Bolser D - Uludag M - et al. doi: 10.1093/bioinformatics/btt113 id: doi:10.1093/bioinformatics/btt113 journal: Bioinformatics preferred: true title: 'EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats' year: '2013' repository: https://github.com/edamontology/edamontology - activity_status: active category: Ontology contacts: - category: Organization contact_details: - contact_type: email value: efo-users@ebi.ac.uk - contact_type: url value: https://www.ebi.ac.uk/spot/ontology/ id: ebi label: EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT) creation_date: '2025-06-04T00:00:00Z' description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. domains: - biological systems - biomedical - health - phenotype homepage_url: https://www.ebi.ac.uk/efo/ id: efo infores_id: efo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache 2.0 name: Experimental Factor Ontology products: - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphicalInterface description: Browse EFO with EBI's Ontology Lookup Service (OLS) format: http id: efo.ols name: EFO in OLS original_source: - efo product_url: https://www.ebi.ac.uk/ols/ontologies/efo secondary_source: - efo - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: OntologyProduct description: Cell Line Ontology in OWL format format: owl id: clo.owl name: clo.owl product_file_size: 2121232 product_url: http://purl.obolibrary.org/obo/clo.owl - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 publications: - authors: - James Malone - Ele Holloway - Tomasz Adamusiak - Misha Kapushesky - Jie Zheng - Nikolay Kolesnikov - Anna Zhukova - Alvis Brazma - Helen Parkinson doi: doi:10.1093/bioinformatics/btq099 id: https://doi.org/10.1093/bioinformatics/btq099 journal: Bioinformatics preferred: true title: Modeling Sample Variables with an Experimental Factor Ontology year: '2010' repository: https://github.com/EBISPOT/efo - activity_status: active category: DataSource creation_date: '2026-01-30T00:00:00Z' description: A database of orthologous groups and functional annotations derived from comparative genomics, supporting cross-species gene function inference. domains: - genomics - biological systems homepage_url: https://eggnogdb.org/ id: eggnog last_modified_date: '2026-02-15T00:00:00Z' layout: resource_detail name: eggNOG products: - category: GraphicalInterface description: Main web interface for browsing orthologous groups and functional annotations. format: http id: eggnog.portal name: eggNOG Portal product_url: https://eggnogdb.org/ - category: Product description: Download interface for eggNOG annotation and orthology data releases. format: http id: eggnog.download name: eggNOG Downloads product_url: https://eggnogdb.org/downloads/ - category: Product compression: gzip description: All protein sequences covered in eggNOG 7. format: fasta id: eggnog.download.e7.proteins name: eggNOG 7 Proteins product_file_size: 12753324465 product_url: https://eggnogdb.org/public/eggnog7/e7.proteins.fa.gz - category: Product description: Tar archive containing orthologous group FASTA sequence files. format: mixed id: eggnog.download.e7.og-fasta-sequences name: eggNOG 7 OG FASTA Sequences product_file_size: 28479795200 product_url: https://eggnogdb.org/public/eggnog7/e7.og_fasta_sequences.tar - category: Product compression: gzip description: Orthologous group information table including KEGG and GO annotations. format: tsv id: eggnog.download.e7.og-info-kegg-go name: eggNOG 7 OG Info (KEGG/GO) product_file_size: 967458606 product_url: https://eggnogdb.org/public/eggnog7/e7.og_info_kegg_go.tsv.gz - category: Product compression: gzip description: Protein family information table. format: tsv id: eggnog.download.e7.protein-families name: eggNOG 7 Protein Families product_file_size: 807966782 product_url: https://eggnogdb.org/public/eggnog7/e7.protein_families.tsv.gz - category: Product compression: gzip description: Table listing orthologous groups per protein family. format: tsv id: eggnog.download.e7.clu2ogs name: eggNOG 7 Protein Family to OGs product_file_size: 15838901 product_url: https://eggnogdb.org/public/eggnog7/e7.clu2ogs.tsv.gz - category: Product compression: gzip description: Taxonomic information table for genomes included in eggNOG 7. format: tsv id: eggnog.download.e7.taxid-info name: eggNOG 7 Taxonomic Information product_file_size: 1270490 product_url: https://eggnogdb.org/public/eggnog7/e7.taxid_info.tsv.gz - category: Product compression: gzip description: Protein family phylogenetic trees table. format: tsv id: eggnog.download.e7.trees name: eggNOG 7 Protein Family Trees product_file_size: 2753498624 product_url: https://eggnogdb.org/public/eggnog7/e7.trees.tsv.gz - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - 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It provides a structured representation of metabolomic data within a semantic framework. domains: - biological systems - chemistry and biochemistry evaluation_page: resource/emikg/emikg_eval_automated.html homepage_url: https://github.com/digital-botanical-gardens-initiative/earth_metabolome_ontology id: emikg last_modified_date: '2026-01-15T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: EMI KG products: - category: GraphProduct description: Graph version of the Earth Metabolome Initiative Ontology format: kgx id: emikg.kg name: EMI Knowledge Graph original_source: - emi - pf1600 - globi - try product_url: https://doi.org/10.5281/zenodo.17079767 repository: https://github.com/earth-metabolome-initiative/metrin-kg warnings: - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - category: ProgrammingInterface description: SPARQL endpoint for programmatic access to the EMI Knowledge Graph format: http id: emikg.sparql name: EMI KG SPARQL Endpoint original_source: - emi - pf1600 - globi - try product_url: https://qlever.earthmetabolome.org/api/metrin-kg - category: GraphicalInterface description: Web-based SPARQL query editor for the EMI Knowledge Graph id: emikg.web name: EMI KG SPARQL Query Editor original_source: - emi - pf1600 - globi - try product_url: https://sib-swiss.github.io/sparql-editor/emi - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: The European Nucleotide Archive (ENA) is a comprehensive database providing free and open access to nucleotide sequence data, functional genomics data, and associated metadata. It is operated by EMBL-EBI and serves as an ELIXIR Core Data Resource and a Global Core Biodata Resource. domains: - genomics - biological systems id: ena last_modified_date: '2025-10-10T00:00:00Z' layout: resource_detail name: European Nucleotide Archive (ENA) products: - category: GraphicalInterface description: Web portal for searching, browsing, and viewing nucleotide sequence data and metadata. format: http id: ena.browser name: ENA Browser product_url: https://www.ebi.ac.uk/ena/browser/home - category: ProgrammingInterface description: REST API for programmatic access to ENA data, including sequence retrieval and metadata queries. format: http id: ena.api name: ENA REST API product_url: https://www.ebi.ac.uk/ena/browser/api - category: Product description: FTP archive with nucleotide sequences, assemblies, and associated data files. format: http id: ena.ftp name: ENA FTP Archive product_url: ftp://ftp.ebi.ac.uk/pub/databases/ena warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/ena' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/ena' - category: GraphicalInterface description: Interface for setting up and managing pre-release and public Data Hubs for pathogen and other sequence data. format: http id: ena.datahubs name: ENA Data Hubs Portal product_url: https://www.ebi.ac.uk/ena/browser/data-hubs - category: DocumentationProduct description: Documentation and help resources for ENA, including submission guidelines and API documentation. format: http id: ena.docs name: ENA Documentation product_url: https://www.ebi.ac.uk/ena/browser/support - category: DocumentationProduct description: Training resources for ENA users, including tutorials and webinars. format: http id: ena.training name: ENA Training product_url: https://www.ebi.ac.uk/training/services/ena - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: avi.maayan@mssm.edu - contact_type: url value: https://labs.icahn.mssm.edu/maayanlab/ label: Ma'ayan Laboratory creation_date: '2025-09-23T00:00:00Z' description: Enrichr-KG is a comprehensive knowledge graph that integrates gene set enrichment analysis libraries from Enrichr, connecting genes to biological terms, pathways, diseases, drugs, and other functional annotations across multiple domains and species to enable multi-layered biological discovery and hypothesis generation. domains: - biomedical - genomics - systems biology - drug discovery - biological systems evaluation_page: resource/enrichr-kg/enrichr-kg_eval_automated.html homepage_url: https://maayanlab.cloud/enrichr-kg/ id: enrichr-kg last_modified_date: '2025-09-23T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Enrichr-KG products: - category: GraphicalInterface description: Interactive web interface for exploring the Enrichr-KG knowledge graph with single and two-term search capabilities format: http id: enrichr-kg.portal name: Enrichr-KG Explorer product_url: https://maayanlab.cloud/enrichr-kg/ - category: ProgrammingInterface description: API endpoints for programmatic access to Enrichr-KG graph data and enrichment analysis format: http id: enrichr-kg.api name: Enrichr-KG API product_url: https://maayanlab.cloud/enrichr-kg/api/ - category: GraphProduct description: Neo4j graph database containing integrated gene set enrichment libraries with genes, terms, pathways, and functional annotations dump_format: neo4j format: neo4j id: enrichr-kg.graph name: Enrichr-KG Neo4j Database publications: - authors: - Evangelista JE - Xie Z - Marino GB - Nguyen N - Clarke DJB - Ma'ayan A id: doi:10.1093/nar/gkad393 journal: Nucleic Acids Research preferred: true title: 'Enrichr-KG: bridging enrichment analysis across multiple libraries' year: '2023' repository: https://github.com/MaayanLab/enrichr-kg taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: helpdesk@ensembl.org id: ebi label: Ensembl Help Desk creation_date: '2025-05-30T00:00:00Z' description: A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation, and transcriptional regulation domains: - genomics homepage_url: https://www.ensembl.org id: ensembl infores_id: ensembl-gene last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: http://www.apache.org/licenses/LICENSE-2.0 label: Apache License, Version 2.0 name: Ensembl products: - category: GraphicalInterface description: A web-based platform for browsing and analyzing vertebrate genomes, including gene annotations, comparative genomics, and variation data. id: ensembl.browser name: Ensembl Genome Browser product_url: https://www.ensembl.org - 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category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - 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category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb - category: Product description: The EPA has developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. 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biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz publications: - authors: - Dyer SC - Austine-Orimoloye O - Azov AG - Barba M - Barnes I - Barrera-Enriquez VP - Becker A - Bennett R - Beracochea M - Berry A - Ensembl team doi: doi:10.1093/nar/gkae1071 id: https://doi.org/10.1093/nar/gkae1071 journal: Nucleic Acids Research preferred: true title: Ensembl 2025 year: '2025' repository: https://github.com/Ensembl/ taxon: - NCBITaxon:10116 - NCBITaxon:9606 - NCBITaxon:10090 - NCBITaxon:7227 - NCBITaxon:7955 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.ncbi.nlm.nih.gov/home/about/contact/ id: ncbi label: NCBI creation_date: '2025-11-05T00:00:00Z' description: Entrez is NCBI's primary text search and retrieval system that integrates multiple biological databases including PubMed, GenBank, Gene, Protein, and many others. It provides a unified query interface and retrieval mechanism across NCBI's vast collection of biomedical and genomic data resources, enabling researchers to search and access information from disparate databases using a single query system. domains: - biomedical - literature homepage_url: https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html id: entrez infores_id: entrez last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: Entrez products: - category: ProgrammingInterface description: E-utilities API for programmatic access to Entrez databases format: http id: entrez.eutils name: Entrez E-utilities original_source: - entrez product_url: https://www.ncbi.nlm.nih.gov/books/NBK25501/ - category: GraphicalInterface description: Web-based search interface for Entrez databases format: http id: entrez.web name: Entrez Web Interface original_source: - entrez product_url: https://www.ncbi.nlm.nih.gov/sites/gquery - category: ProgrammingInterface description: Entrez Direct command-line tools for Unix systems format: mixed id: entrez.edirect name: Entrez Direct (EDirect) original_source: - entrez product_url: https://www.ncbi.nlm.nih.gov/books/NBK179288/ repository: https://github.com/ncbi/entrez-direct synonyms: - Entrez - NCBIGene - NCBI Entrez taxon: - NCBITaxon:1 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: pier.buttigieg@awi.de - contact_type: github value: pbuttigieg label: Pier Luigi Buttigieg orcid: 0000-0002-4366-3088 creation_date: '2025-07-10T00:00:00Z' description: An ontology of environmental systems, components, and processes. domains: - environment homepage_url: http://environmentontology.org/ id: envo last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Environment Ontology products: - category: OntologyProduct description: main ENVO OWL release format: owl id: envo.owl name: main ENVO OWL release product_file_size: 819909 product_url: http://purl.obolibrary.org/obo/envo.owl - category: OntologyProduct description: ENVO in obographs JSON format format: json id: envo.json name: ENVO in obographs JSON format product_file_size: 653600 product_url: http://purl.obolibrary.org/obo/envo.json - category: OntologyProduct description: ENVO in OBO Format. May be lossy format: obo id: envo.obo name: ENVO in OBO Format. May be lossy product_file_size: 595276 product_url: http://purl.obolibrary.org/obo/envo.obo - category: OntologyProduct description: OBO-Basic edition of ENVO format: obo id: envo.subsets.envo-basic.obo name: OBO-Basic edition of ENVO product_file_size: 422465 product_url: http://purl.obolibrary.org/obo/envo/subsets/envo-basic.obo - category: OntologyProduct description: Earth Microbiome Project subset format: owl id: envo.subsets.envoEmpo.owl name: Earth Microbiome Project subset product_file_size: 19016 product_url: http://purl.obolibrary.org/obo/envo/subsets/envoEmpo.owl - category: OntologyProduct description: GSC Lite subset of ENVO format: obo id: envo.subsets.EnvO-Lite-GSC.obo name: GSC Lite subset of ENVO product_file_size: 12912 product_url: http://purl.obolibrary.org/obo/envo/subsets/EnvO-Lite-GSC.obo - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe repository: https://github.com/EnvironmentOntology/envo - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://naturalhistory.si.edu/research/eol id: smithsonian-nmnh label: Smithsonian Institution's National Museum of Natural History creation_date: '2025-12-17T00:00:00Z' description: Encyclopedia of Life (EOL) TraitBank is a searchable, comprehensive, open digital repository for organism traits, measurements, interactions, and other attributes aggregated from 50+ data sources. It covers 1.7 million taxa across the entire tree of life with 11 million+ trait records organized using semantic web standards and Darwin Core terminology. domains: [] homepage_url: https://eol.org/pages/traitbank id: eol-traitbank infores_id: eol-traitbank last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Encyclopedia of Life (EOL) TraitBank products: - category: GraphicalInterface description: Interactive web interface for searching, browsing, and discovering organism trait data across all taxa with filtering by taxonomic group and attribute type format: http id: eol-traitbank.web name: TraitBank Web Portal product_url: https://eol.org/pages/traitbank - category: ProgrammingInterface description: Neo4j Cypher query interface providing programmatic access to structured trait data, requiring authentication via EOL account format: http id: eol-traitbank.cypher is_public: true name: TraitBank Cypher Query Interface product_url: https://eol.org/services/authenticate - category: ProgrammingInterface description: RESTful API endpoints for taxonomy, media, and text data access from Encyclopedia of Life format: http id: eol-traitbank.api is_public: true name: EOL API product_url: https://api.eol.org/ - category: ProgrammingInterface description: EOL Reconciliation Service API for resolving taxon names to EOL taxon IDs using OpenRefine-compatible reconciliation protocol format: http id: eol-traitbank.reconciliation is_public: true name: EOL Reconciliation API product_url: https://eol.org/api/reconciliation - category: Product compression: zip description: Complete TraitBank bulk data export containing all 11 million+ trait records in CSV format with measurement details and source attribution format: csv id: eol-traitbank.bulk-csv name: TraitBank Bulk Data Export product_file_size: 592310894 product_url: https://editors.eol.org/other_files/SDR/traits_all.zip warnings: - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='editors.eol.org', port=443)_ Max retries exceeded with url_ /other_files/SDR/traits_all.zip (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='editors.eol.org', port=443)_ Max retries exceeded with url_ /other_files/SDR/traits_all.zip (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-28_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='editors.eol.org', port=443)_ Max retries exceeded with url_ /other_files/SDR/traits_all.zip (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - category: DocumentationProduct description: Comprehensive documentation covering TraitBank data structure, API usage, authentication methods, and data formats format: http id: eol-traitbank.docs name: TraitBank Documentation product_url: https://eol.org/docs/what-is-eol/data-services warnings: - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='eol.org', port=443)_ Max retries exceeded with url_ /docs/what-is-eol/data-services (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-25_ Error connecting to URL_ HTTPSConnectionPool(host='eol.org', port=443)_ Max retries exceeded with url_ /docs/what-is-eol/data-services (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='eol.org', port=443)_ Max retries exceeded with url_ /docs/what-is-eol/data-services (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-02-15_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='eol.org', port=443)_ Max retries exceeded with url_ /docs/what-is-eol/data-services (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) publications: - authors: - Adams B - Franz N - König-Ries B - McGuinness D - Schildhauer M - Parr CS - Schulz KS - Hammock J - Wilson N - Leary P - Rice J - Corrigan RJ doi: 10.3233/SW-150190 id: doi:10.3233/SW-150190 journal: Semantic Web Journal preferred: true title: 'TraitBank: Practical semantics for organism attribute data' year: '2016' - authors: - Parr CS - Wilson N - Leary P - Struzan GS - Ved P - Lans KA - Loyacano J - Brest M - Corrigan RJ - Hancher C - Helgen KM - Herrick J - Hammock J - Kataoka C - Lara MJ - Maney D - Martínez-Meyer E - Measey J - Rapp C - Sarkar I - Schulz KS - Seubert E - Wee B - Wyckoff M doi: 10.1371/journal.pone.0089965 id: doi:10.1371/journal.pone.0089965 journal: PLoS ONE title: 'The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth' year: '2014' repository: https://github.com/EOL taxon: - NCBITaxon:1 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: feedback@epigraphdb.org - contact_type: url value: https://docs.epigraphdb.org/ - contact_type: github value: https://github.com/MRCIEU/epigraphdb label: EpiGraphDB Team (MRC Integrative Epidemiology Unit, University of Bristol) creation_date: '2025-09-03T00:00:00Z' description: EpiGraphDB is an analytical platform and graph database for health data science that integrates Mendelian randomization causal estimates across a wide range of phenotypes with diverse bioinformatic and epidemiological resources. It supports systematic causal inference, data mining, and exploration through a web application, API, R package, and curated graph knowledge base. domains: - health - biomedical - genomics - investigations evaluation_page: resource/epigraphdb/epigraphdb_eval_automated.html homepage_url: https://epigraphdb.org/ id: epigraphdb last_modified_date: '2025-09-03T00:00:00Z' layout: resource_detail license: id: https://github.com/MRCIEU/epigraphdb label: Mixed name: EpiGraphDB products: - category: GraphicalInterface description: Web application for interactive exploration of EpiGraphDB including search, causal estimates, pathways, literature evidence, ontology, and visualization gallery format: http id: epigraphdb.web name: EpiGraphDB Web UI original_source: - epigraphdb product_url: https://epigraphdb.org/ - category: ProgrammingInterface description: Public REST API for programmatic access to EpiGraphDB graph entities, relationships, causal estimates, and metadata id: epigraphdb.api is_public: true name: EpiGraphDB REST API original_source: - epigraphdb product_url: https://api.epigraphdb.org/ - category: ProgrammingInterface description: R client package providing higher-level access to EpiGraphDB API endpoints and analysis workflows id: epigraphdb.rpackage is_public: true name: epigraphdb R Package original_source: - epigraphdb product_url: https://mrcieu.github.io/epigraphdb-r/ secondary_source: - epigraphdb - category: DocumentationProduct description: Example notebooks demonstrating EpiGraphDB use cases, including causal inference, pleiotropy assessment, drug target identification, literature triangulation, and metadata queries id: epigraphdb.examples name: EpiGraphDB Example Notebooks original_source: - epigraphdb product_url: https://github.com/MRCIEU/epigraphdb/tree/master/paper-case-studies - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb - category: DocumentationProduct description: Documentation hub containing conceptual overviews, API endpoint references, data integration details, metrics, and research study links format: http id: epigraphdb.docs name: EpiGraphDB Documentation original_source: - epigraphdb product_url: https://docs.epigraphdb.org/ - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: alpha.tom.kodamullil@scai.fraunhofer.de - contact_type: github value: akodamullil label: Alpha Tom Kodamullil orcid: 0000-0001-9896-3531 creation_date: '2025-09-29T00:00:00Z' description: A application driven Epilepsy Ontology with official terms from the ILAE. domains: - biomedical homepage_url: https://github.com/SCAI-BIO/EpilepsyOntology id: epio last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Epilepsy Ontology products: - category: OntologyProduct description: Epilepsy Ontology in OWL format format: owl id: epio.owl name: epio.owl product_file_size: 415175 product_url: http://purl.obolibrary.org/obo/epio.owl - category: OntologyProduct description: Epilepsy Ontology in OWL format format: owl id: epio.EPIO_merged.owl name: epio.EPIO_merged.owl product_url: http://purl.obolibrary.org/obo/EPIO_merged.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/SCAI-BIO/EpilepsyOntology - activity_status: active category: DataSource creation_date: '2025-11-13T00:00:00Z' description: EPSD (Eukaryotic Phosphorylation Site Database) is a comprehensive database that curates and annotates experimentally identified protein phosphorylation sites across eukaryotic species. Version 2.0 contains 2,769,163 phosphorylation sites in 362,707 phosphoproteins from 223 eukaryotic species (95 animals, 20 protists, 61 plants, 48 fungi). The database integrates data from high-throughput phosphoproteomic studies and 10 public databases, providing detailed annotations including phosphopeptide sequences, localization probability scores, cell/tissue sources, and primary references. EPSD 2.0 features 88,074 functional annotations for 32,762 phosphorylation sites, covering 58 types of downstream effects on phosphoproteins and 107 regulatory impacts on biological processes. For eight model organisms (human, mouse, rat, Drosophila, C. elegans, Arabidopsis, S. pombe, S. cerevisiae), phosphoproteins are meticulously annotated with information from 100 external resources across 15 aspects including kinase/phosphatase regulators, 3D structures, physicochemical characteristics, genomic variations, functional descriptions, protein domains, molecular interactions, drug-target associations, disease data, orthologs, transcript expression, proteomics, subcellular localization, and regulatory pathways. EPSD 2.0 represents a 2.5-fold increase in data volume compared to version 1.0 and provides intrinsic disorder propensity and surface accessibility calculations for phosphorylation sites. The database supports advanced search options including substrate search, peptide search, batch search, BLAST search, and browse by species functionality. domains: - genomics - proteomics homepage_url: https://epsd.biocuckoo.cn id: epsd infores_id: epsd last_modified_date: '2025-11-13T00:00:00Z' layout: resource_detail name: Eukaryotic Phosphorylation Site Database 2.0 products: - category: Portal description: Main web portal for EPSD 2.0 providing search, browse, and visualization of protein phosphorylation sites across 223 eukaryotic species with functional annotations format: http id: epsd.portal name: EPSD 2.0 Portal original_source: - epsd product_url: https://epsd.biocuckoo.cn warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ certificate has expired (_ssl.c_1017)'))) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-11-25_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ certificate has expired (_ssl.c_1000)'))) - category: Browser description: Browse phosphorylation sites by species across 223 eukaryotes including 95 animals, 20 protists, 61 plants, and 48 fungi format: http id: epsd.browse name: EPSD Browse by Species original_source: - epsd product_url: https://epsd.biocuckoo.cn warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ certificate has expired (_ssl.c_1017)'))) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-11-25_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ certificate has expired (_ssl.c_1000)'))) - category: Search description: Advanced search interface supporting substrate search, peptide search, batch search, BLAST search, and multi-condition queries format: http id: epsd.search name: EPSD Advanced Search original_source: - epsd product_url: https://epsd.biocuckoo.cn warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ certificate has expired (_ssl.c_1017)'))) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-11-25_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ / (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ certificate has expired (_ssl.c_1000)'))) - category: Download description: Download page for complete phosphorylation site datasets and annotation data from EPSD 2.0 format: http id: epsd.download name: EPSD Data Download original_source: - epsd product_url: https://epsd.biocuckoo.cn/Download.php secondary_source: [] warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ /Download.php (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ certificate has expired (_ssl.c_1017)'))) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ /Download.php (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ /Download.php (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-11-25_ Error connecting to URL_ HTTPSConnectionPool(host='epsd.biocuckoo.cn', port=443)_ Max retries exceeded with url_ /Download.php (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ certificate has expired (_ssl.c_1000)'))) - category: GraphicalInterface description: Interactive web interface for exploring and visualizing kinase-substrate interactions format: http id: kinace.portal name: KinAce Web Portal original_source: - phosphositeplus - iptmnet - uniprot - epsd - kinhub - coralkinome - darkkinasekb - hgnc - kegg - interpro product_url: https://kinace.kinametrix.com/ secondary_source: - kinace publications: - id: PMID:40581078 - id: PMID:32008039 synonyms: - EPSD - Eukaryotic phosphorylation site database - EPSD 2.0 taxon: - NCBITaxon:3702 - NCBITaxon:10090 - NCBITaxon:10116 - NCBITaxon:7227 - NCBITaxon:6239 - NCBITaxon:4932 - NCBITaxon:2759 - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-09-03T00:00:00Z' description: The eQTLGen Consortium conducts large-scale meta-analyses of expression quantitative trait loci (eQTLs) in blood samples to investigate the genetic architecture of gene expression and understand the genetic underpinnings of complex traits. Phase I analyzed 31,684 blood and PBMC samples from 37 cohorts, identifying thousands of cis-eQTLs, trans-eQTLs, and expression quantitative trait score (eQTS) associations. The consortium also includes a single-cell eQTLGen project. Phase II is expanding to genome-wide eQTL meta-analysis across even more blood-based cohorts. The resulting summary statistics provide a valuable resource for interpreting genome-wide association studies (GWAS), developing novel methods, and understanding molecular mechanisms of complex traits. domains: - genomics - biological systems homepage_url: https://www.eqtlgen.org/ id: eqtlgen last_modified_date: '2025-10-21T00:00:00Z' layout: resource_detail name: eQTLGen Consortium products: - category: Product description: Significant cis-eQTL associations from Phase I meta-analysis (FDR < 0.05, tested in at least 2 cohorts), including Bonferroni-adjusted p-values. format: tsv id: eqtlgen.cis_eqtl_significant name: Significant cis-eQTLs product_file_size: 322775879 product_url: https://molgenis26.gcc.rug.nl/downloads/eqtlgen/cis-eqtl/2019-12-11-cis-eQTLsFDR0.05-ProbeLevel-CohortInfoRemoved-BonferroniAdded.txt.gz - category: Product description: Full cis-eQTL summary statistics from Phase I meta-analysis at the probe level, with cohort information removed and Bonferroni-adjusted p-values added. format: tsv id: eqtlgen.cis_eqtl_full name: Full cis-eQTL Summary Statistics product_file_size: 3880187026 product_url: https://molgenis26.gcc.rug.nl/downloads/eqtlgen/cis-eqtl/2019-12-11-cis-eQTLsFDR-ProbeLevel-CohortInfoRemoved-BonferroniAdded.txt.gz - category: Product description: Significant trans-eQTL associations from Phase I meta-analysis for ~10,000 known genetic risk variants (FDR < 0.05), including Bonferroni-adjusted p-values. format: tsv id: eqtlgen.trans_eqtl_significant name: Significant trans-eQTLs product_file_size: 1839918 product_url: https://molgenis26.gcc.rug.nl/downloads/eqtlgen/trans-eqtl/2018-09-04-trans-eQTLsFDR0.05-CohortInfoRemoved-BonferroniAdded.txt.gz - category: Product description: Full trans-eQTL summary statistics from Phase I meta-analysis for ~10,000 known genetic risk variants, with cohort information removed and Bonferroni-adjusted p-values added. format: tsv id: eqtlgen.trans_eqtl_full name: Full trans-eQTL Summary Statistics product_file_size: 6090297103 product_url: https://molgenis26.gcc.rug.nl/downloads/eqtlgen/trans-eqtl/2018-09-04-trans-eQTLsFDR-CohortInfoRemoved-BonferroniAdded.txt.gz - category: Product compression: targz description: cis-eQTL results formatted for Summary-data-based Mendelian Randomization (SMR) analysis, enabling inference of putatively causal genes. format: txt id: eqtlgen.cis_eqtl_smr name: SMR-formatted cis-eQTLs product_file_size: 1372512049 product_url: https://molgenis26.gcc.rug.nl/downloads/eqtlgen/cis-eqtl/SMR_formatted/cis-eQTL-SMR_20191212.tar.gz - category: Product description: Allele frequencies for all tested SNPs based on 26,609 eQTLGen samples (excluding FHS), including combined allele counts and minor allele frequencies. format: tsv id: eqtlgen.allele_frequencies name: Allele Frequencies product_file_size: 240045342 product_url: https://molgenis26.gcc.rug.nl/downloads/eqtlgen/cis-eqtl/2018-07-18_SNP_AF_for_AlleleB_combined_allele_counts_and_MAF_pos_added.txt.gz - category: GraphicalInterface description: Web interface for browsing significant cis-eQTL, trans-eQTL, and eQTS results from Phase I, with SMR-prioritised gene lists for various traits. format: http id: eqtlgen.phase1_browser name: eQTLGen Phase I Browser product_url: https://www.eqtlgen.org/phase1.html - category: DocumentationProduct description: Analysis cookbook and documentation for eQTLGen Phase II genome-wide eQTL meta-analysis in blood. format: http id: eqtlgen.phase2_cookbook name: eQTLGen Phase II Cookbook product_url: https://eqtlgen.github.io/eqtlgen-web-site/eQTLGen-p2-cookbook.html - category: GraphicalInterface description: Website for the single-cell eQTLGen project, providing resources and publications for single-cell eQTL analysis. format: http id: eqtlgen.sc_website name: Single-cell eQTLGen Website product_url: https://www.eqtlgen.org/sc - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb publications: - authors: - Võsa U - Claringbould A - Westra HJ - Bonder MJ - Deelen P - Zeng B - Franke L id: https://doi.org/10.1038/s41588-021-00913-z journal: Nature Genetics preferred: true title: Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression year: '2021' repository: https://github.com/eqtlgen - activity_status: active category: DataSource creation_date: '2025-11-19T00:00:00Z' description: The encyclopedia of Rare disease Annotation for Precision Medicine (eRAM) is a standardized system providing computational annotations for rare diseases to support precision medicine. eRAM provides annotations for approximately 16,000 rare diseases, including detailed information on clinical phenotypes, symptoms, genes, and genotypes. The database contains over 6,100 human disease-related phenotype terms, 31,600 mammalian phenotype terms, 10,200 symptoms from UMLS, 18,800 genes and 92,500 genotypes. eRAM organizes diseases in a tree structure to systematically display relationships between diseases with similar pathogenesis, close anatomical sites, the same clinical symptoms or subtypes, facilitating both research into rare disease mechanisms and clinical diagnosis and treatment decisions. domains: - clinical - health - phenotype - precision medicine homepage_url: http://119.3.41.228/eram/ id: eram infores_id: eram last_modified_date: '2025-11-19T00:00:00Z' layout: resource_detail name: 'eRAM: encyclopedia of rare disease annotations for precision medicine' products: - category: GraphicalInterface description: Web-based interface for browsing and querying rare disease annotations including phenotypes, symptoms, genes, and genotypes with tree-structured disease organization format: http id: eram.web name: eRAM Web Interface original_source: - eram product_url: http://119.3.41.228/eram/ - category: Product description: Downloadable data files containing rare disease annotations, phenotypes, symptoms, genes, and genotypes format: mixed id: eram.downloads name: eRAM Data Downloads original_source: - eram product_url: http://119.3.41.228/eram/download.php publications: - authors: - Jia J - An Z - Ming Y - Guo Y - Li W - Liang Y - Guo D - Li X - Tai J - Chen G - Jin Y - Liu Z - Ni X - Shi T doi: 10.1093/nar/gkx1062 id: PMID:29106618 journal: Nucleic Acids Research title: 'eRAM: encyclopedia of rare disease annotations for precision medicine' year: '2018' synonyms: - eRAM taxon: - NCBITaxon:9606 - NCBITaxon:40674 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: info@exrna.org label: Extracellular RNA Communication Consortium creation_date: '2025-06-04T00:00:00Z' description: ERCC RNA Binding Protein dataset (ERCCRBP) is a collection of data focused on RNA binding proteins involved in extracellular RNA functions as part of the NIH Common Fund's Extracellular RNA Communication Consortium (ERCC) program. This dataset provides insights into the protein-RNA interactions important for exRNA stability, transport, and signaling. domains: - biomedical - genomics - chemistry and biochemistry homepage_url: https://exrna.org/ id: erccrbp last_modified_date: '2025-10-15T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: ERCC RNA Binding Protein Dataset products: - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: info@exrna.org label: Extracellular RNA Communication Consortium creation_date: '2025-06-04T00:00:00Z' description: ERCC Regulatory Element dataset (erccreg) is a collection of data related to regulatory elements of extracellular RNA as part of the NIH Common Fund's Extracellular RNA Communication Consortium (ERCC) program. This dataset focuses on RNA-based regulatory mechanisms involved in extracellular communication. domains: - biomedical - genomics - chemistry and biochemistry homepage_url: https://exrna.org/ id: erccreg last_modified_date: '2025-10-15T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: ERCC Regulatory Element Dataset products: - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - activity_status: active category: DataSource creation_date: '2025-08-30T00:00:00Z' description: The Eukaryotic Pathogen Database (EuPathDB) is an integrated genomics database covering numerous eukaryotic pathogens including Plasmodium, Trypanosoma, and other parasites. It provides functional genomics resources integrating data from human and veterinary parasites, now known as VEuPathDB (Vectorbase and EuPathDB). domains: - genomics - biological systems - organisms id: eupathdb last_modified_date: '2025-10-10T00:00:00Z' layout: resource_detail name: Eukaryotic Pathogen Database (EuPathDB) products: - category: GraphicalInterface description: Web portal for searching, browsing, and analyzing eukaryotic pathogen genomic data including gene searches, genome browsers, and pathway analysis. format: http id: eupathdb.portal name: VEuPathDB Web Portal product_url: https://veupathdb.org/veupathdb/app - category: ProgrammingInterface description: Web services API for programmatic access to EuPathDB data and analyses. format: http id: eupathdb.api name: VEuPathDB Web Services API product_url: https://veupathdb.org/veupathdb/service - category: Product description: FTP and download access to genome sequences, annotations, and analysis results for component databases. format: http id: eupathdb.downloads name: VEuPathDB Data Downloads product_url: https://veupathdb.org/veupathdb/app/downloads - category: GraphicalInterface description: Real-time collaborative genome annotation and curation platform for structural and functional annotation. format: http id: eupathdb.apollo name: Apollo Genome Annotation product_url: https://veupathdb.org/veupathdb/app/workspace/strategies - category: GraphicalInterface description: Map-based visualization tool for field-collected data including insecticide resistance, population abundance, and pathogen infection status. format: http id: eupathdb.mapveu name: MapVEu product_url: https://mapveu.org - category: DocumentationProduct description: Comprehensive documentation including tutorials, exercises, and user guides for VEuPathDB tools and features. format: http id: eupathdb.docs name: VEuPathDB Documentation and Tutorials product_url: https://veupathdb.org/veupathdb/app/static-content/landing.html - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg publications: - authors: - Aurrecoechea C - Barreto A - Brestelli J - Brunk BP - Cade S - Doherty R - Fischer S - Gajria B - Gao X - Gingle A id: https://doi.org/10.1093/nar/gks1113 journal: Nucleic Acids Research preferred: true title: 'EuPathDB: the eukaryotic pathogen database' year: '2013' taxon: - NCBITaxon:9606 - NCBITaxon:2759 warnings: - EuPathDB is an active data source providing integrated genomics resources for eukaryotic pathogens. The project is now known as VEuPathDB. - activity_status: active category: DataSource creation_date: '2018-01-05T00:00:00Z' description: EVLncRNAs is a comprehensive database of experimentally validated functional long non-coding RNAs (lncRNAs) curated manually from low-throughput experimental studies. The database covers functional lncRNAs from 162 species, including disease associations, biological functions, interaction partners, structures, circular RNAs, exosomal lncRNAs, peptide-coding lncRNAs, and resistant lncRNAs. EVLncRNAs provides functional classifications based on Gene Ontology categories (biological processes, cellular components, molecular functions, and clinical applications), detailed interaction pathways, and integration with homologous lncRNAs, subcellular localization, phase separation, COVID-19, and organoid-related data. domains: - genomics - biological systems homepage_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/ id: evlncrnas last_modified_date: '2025-10-21T00:00:00Z' layout: resource_detail name: EVLncRNAs products: - category: GraphicalInterface description: Web portal for browsing and searching experimentally validated functional lncRNAs format: http id: evlncrnas.portal name: EVLncRNAs Web Portal product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/ - category: GraphicalInterface description: Browse functional lncRNAs by species with sortable entries format: http id: evlncrnas.species name: Species Browser product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/species - category: GraphicalInterface description: Browse lncRNAs by associated diseases including cancers and other pathologies format: http id: evlncrnas.diseases name: Disease Browser product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/diseases - category: GraphicalInterface description: Interactive network visualization of lncRNA interactions with proteins, RNAs, and DNAs format: http id: evlncrnas.interactions name: Interaction Network Viewer product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/interactions - category: GraphicalInterface description: Browse lncRNA structural information from experimental studies format: http id: evlncrnas.structures name: Structure Browser product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/structures - category: GraphicalInterface description: Browse peptide-coding lncRNAs validated by experiments format: http id: evlncrnas.peptide name: Peptide-Coding lncRNA Browser product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/peptide-coding - category: GraphicalInterface description: Browse circular RNA (circRNA) entries with functional validation format: http id: evlncrnas.circrnas name: CircRNA Browser product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/circrnas - category: GraphicalInterface description: Browse exosomal lncRNAs from extracellular vesicles format: http id: evlncrnas.exosomal name: Exosomal lncRNA Browser product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/exosomal - category: GraphicalInterface description: Browse resistant lncRNAs including drug resistance-associated entries format: http id: evlncrnas.resistant name: Resistant lncRNA Browser product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/resistant - category: DocumentationProduct description: Help documentation and usage instructions for EVLncRNAs database format: http id: evlncrnas.help name: Help Documentation product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/help - category: Product description: Download page for bulk data access to EVLncRNAs database content format: http id: evlncrnas.download name: Download Data product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/download - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Bailing Zhou - Baohua Ji - Congcong Shen - Xia Zhang - Xue Yu - Pingping Huang - Ru Yu - Hongmei Zhang - Xianghua Dou - Qingshuai Chen - Gang Hu - Keren Wang - Fengcui Qian - Fengxia Chen - Xiaojuan Zhi - Chunqing Wang - Jian Ren - Yan Wang id: https://doi.org/10.1093/nar/gkad1057 journal: Nucleic Acids Research preferred: true title: 'EVLncRNAs 3.0: an updated comprehensive database for manually curated functional long non-coding RNAs validated by low-throughput experiments' year: '2024' taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: xyz19940216@163.com - contact_type: github value: DarkKnight0-0 label: Xingyun Liu orcid: 0000-0002-9295-2767 creation_date: '2025-09-29T00:00:00Z' description: A core reference ontology built upon BFO about exercise medicine and it contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise. domains: - biomedical homepage_url: https://github.com/Exercise-Medicine-Ontology/EXMO id: exmo last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Exercise Medicine Ontology products: - category: OntologyProduct description: Exercise Medicine Ontology in OWL format format: owl id: exmo.owl name: exmo.owl product_url: http://purl.obolibrary.org/obo/exmo.owl repository: https://github.com/Exercise-Medicine-Ontology/EXMO - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: annethessen@gmail.com - contact_type: github value: diatomsRcool label: Anne Thessen orcid: 0000-0002-2908-3327 creation_date: '2025-09-29T00:00:00Z' description: Vocabularies for describing exposure data to inform understanding of environmental health. domains: - biomedical homepage_url: https://github.com/CTDbase/exposure-ontology id: exo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Exposure ontology products: - category: OntologyProduct description: Exposure ontology in OWL format format: owl id: exo.owl name: exo.owl product_file_size: 17786 product_url: http://purl.obolibrary.org/obo/exo.owl - category: OntologyProduct description: Exposure ontology in OBO format format: obo id: exo.obo name: exo.obo product_file_size: 12690 product_url: http://purl.obolibrary.org/obo/exo.obo repository: https://github.com/CTDbase/exposure-ontology - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.ebi.ac.uk/about/contact - contact_type: email value: atlas-help@ebi.ac.uk id: ebi label: European Bioinformatics Institute (EMBL-EBI) - category: Individual contact_details: - contact_type: other value: Lead, Gene Expression Team, EMBL-EBI label: Irene Papatheodorou creation_date: '2025-09-09T00:00:00Z' description: Expression Atlas is EMBL-EBI's open science resource that provides information about gene and protein expression across species and biological conditions. It aggregates, processes, and visualizes gene expression data from thousands of manually curated experiments spanning multiple species, tissue types, developmental stages, diseases, and experimental perturbations. Both bulk RNA-sequencing and single-cell RNA-sequencing datasets are supported, offering baseline expression profiles and differential gene expression analysis results through standardized processing pipelines. domains: - genomics - biological systems - organisms homepage_url: https://www.ebi.ac.uk/gxa/home id: expressionatlas last_modified_date: '2025-11-10T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Expression Atlas products: - category: GraphicalInterface description: Main web portal for searching and exploring gene expression data across species, tissues, and experimental conditions with interactive heatmaps and visualizations format: http id: expressionatlas.portal name: Expression Atlas Portal product_url: https://www.ebi.ac.uk/gxa/home - category: GraphicalInterface description: Single Cell Expression Atlas portal for exploring single-cell RNA-seq data with interactive t-SNE/UMAP plots, cell type annotations, and marker gene analysis format: http id: expressionatlas.single-cell name: Single Cell Expression Atlas product_url: https://www.ebi.ac.uk/gxa/sc - category: ProgrammingInterface description: REST API for programmatic access to expression data, experiment metadata, and differential expression results format: http id: expressionatlas.api name: Expression Atlas REST API product_url: https://www.ebi.ac.uk/gxa/help/api.html - category: Product description: FTP archive containing processed expression data files, experiment metadata, and analysis results for bulk RNA-seq experiments format: http id: expressionatlas.ftp-bulk name: Expression Atlas FTP (Bulk Data) product_url: https://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/ - category: Product description: Individual experiment data downloads in TSV format containing expression matrices and statistical results format: tsv id: expressionatlas.experiment-downloads name: Expression Atlas Experiment Downloads product_url: https://www.ebi.ac.uk/gxa/download - category: Product description: Normalized gene expression data and raw count matrices in R data object format for computational analysis format: mixed id: expressionatlas.r-objects name: Expression Atlas R Data Objects product_url: https://www.ebi.ac.uk/gxa/help/r-data-objects.html warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 500 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 500 error when accessing file' - category: Product description: Baseline expression summary data across human tissues and cell types from GTEx, Human Protein Atlas and other major studies format: tsv id: expressionatlas.baseline-summary name: Expression Atlas Baseline Summary product_url: https://www.ebi.ac.uk/gxa/baseline/experiments - category: Product description: Differential gene expression results across diseases, perturbations, and comparative studies with statistical significance metrics format: tsv id: expressionatlas.differential-results name: Expression Atlas Differential Results product_url: https://www.ebi.ac.uk/gxa/experiments?experimentType=differential - category: DocumentationProduct description: Comprehensive help documentation covering data access, analysis methods, API usage, and interpretation guidelines format: http id: expressionatlas.documentation name: Expression Atlas Help Documentation product_url: https://www.ebi.ac.uk/gxa/help/index.html - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Nancy George - Silvie Fexova - Alfonso Munoz Fuentes - Pedro Madrigal - Yalan Bi - Haider Iqbal - Upendra Kumbham - Nadja Francesca Nolte - Lingyun Zhao - Anil S Thanki - Iris D Yu - Jose C Marugan Calles - Karoly Erdos - Liora Vilmovsky - Sandeep R Kurri - Anna Vathrakokoili-Pournara - David Osumi-Sutherland - Ananth Prakash - Shengbo Wang - Marcela K Tello-Ruiz - Sunita Kumari - Doreen Ware - Damien Goutte-Gattat - Yanhui Hu - Nick Brown - Norbert Perrimon - Juan Antonio Vizcaíno - Tony Burdett - Sarah Teichmann - Alvis Brazma - Irene Papatheodorou doi: 10.1093/nar/gkad1021 id: https://doi.org/10.1093/nar/gkad1021 journal: Nucleic Acids Research preferred: true title: 'Expression Atlas update: insights from sequencing data at both bulk and single cell level' year: '2024' - authors: - Irene Papatheodorou - Nancy George - Silvie Fexova - Alfonso Munoz-Fuentes - Pedro Madrigal - Haider Iqbal - Upendra Kumbham - Nadja F Nolte - Lingyun Zhao - Anil S Thanki - David Osumi-Sutherland - Ananth Prakash - Shengbo Wang - Marcela K Tello-Ruiz - Sunita Kumari - Doreen Ware - Juan Antonio Vizcaíno - Tony Burdett - Sarah A Teichmann - Alvis Brazma doi: 10.1093/nar/gkz947 id: https://doi.org/10.1093/nar/gkz947 journal: Nucleic Acids Research title: 'Expression Atlas update: from tissues to single cells' year: '2020' repository: https://github.com/ebi-gene-expression-group - activity_status: active category: Ontology creation_date: '2025-12-11T00:00:00Z' description: FABIO (Functional Requirements for Bibliographic Records Object) is a comprehensive ontology for describing bibliographic resources and their properties. It extends the FRBR (Functional Requirements for Bibliographic Records) model into a machine-readable ontology format, enabling semantic representation of bibliographic entities, relationships, and metadata. FABIO supports the organization and discovery of scholarly works and publication resources across knowledge systems. domains: - literature - general homepage_url: https://sparontologies.github.io/fabio/current/fabio.html id: fabio last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: FABIO products: - category: OntologyProduct description: FABIO ontology in Turtle RDF format format: ttl id: fabio.ttl name: FABIO Turtle File product_file_size: 140152 product_url: http://purl.org/spar/fabio.ttl - category: DocumentationProduct description: FABIO ontology documentation, specification, and usage guidelines id: fabio.documentation name: FABIO Documentation product_url: https://sparontologies.github.io/fabio/current/fabio.html - category: GraphProduct description: Downloadable knowledge graph dump in TAR/GZ format containing complete FORUM data id: forum.graph.dump name: FORUM Knowledge Graph Dump original_source: - mesh - chebi - cito - fabio - dc - cheminf - skos - chemont - pubchem - pubmed product_url: ftp://forum:Forum2021Cov!@ftp.semantic-metabolomics.org/dumps/2021/share.tar.gz secondary_source: - forum warnings: - File was not able to be retrieved when checked on 2026-03-08_ FTP error_ timed out - File was not able to be retrieved when checked on 2026-02-26_ FTP error_ timed out - 'File was not able to be retrieved when checked on 2026-03-11: FTP error: timed out' - category: OntologyProduct description: OpenBioDiv-O, the OpenBiodiv Ontology format: ttl id: openbiodiv.ontology.ttl is_public: true name: OpenBioDiv-O original_source: - skos - proton - fabio - doco - openbiodiv product_file_size: 8176 product_url: https://raw.githubusercontent.com/pensoft/OpenBiodiv/refs/heads/master/ontology/openbiodiv-ontology-latest.ttl secondary_source: - openbiodiv repository: https://github.com/SPAROntologies/fabio - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: FDA-SRS@fda.hhs.gov id: fda label: FDA Center for Drug Evaluation and Research creation_date: '2025-11-04T00:00:00Z' description: The FDA Adverse Event Reporting System (FAERS) is a database that contains adverse event reports, medication error reports, and product quality complaints resulting in adverse events submitted to the FDA. FAERS supports the FDA's post-marketing safety surveillance program for drug and therapeutic biologic products. The database adheres to ICH E2B international safety reporting guidance, and adverse events are coded using MedDRA (Medical Dictionary for Regulatory Activities) terminology. FAERS provides quarterly data files in ASCII and XML formats dating back to 2012, with archives available for earlier data. domains: - pharmacology - drug discovery - clinical - public health homepage_url: https://www.fda.gov/drugs/surveillance/fdas-adverse-event-reporting-system-faers id: faers infores_id: faers last_modified_date: '2025-11-04T00:00:00Z' layout: resource_detail name: FDA Adverse Event Reporting System products: - category: GraphicalInterface description: Interactive dashboard for exploring FAERS data with visualizations and search capabilities format: http id: faers.public_dashboard name: FAERS Public Dashboard original_source: - faers product_url: https://fis.fda.gov/sense/app/95239e26-e0be-42d9-a960-9a5f7f1c25ee/sheet/7a47a261-d58b-4203-a8aa-6d3021737452/state/analysis - category: Product description: Quarterly data extracts in ASCII format containing demographic, drug, reaction, outcome, and source information for reported adverse events format: txt id: faers.quarterly_data_ascii name: FAERS Quarterly Data Files (ASCII) original_source: - faers product_url: https://fis.fda.gov/extensions/FPD-QDE-FAERS/FPD-QDE-FAERS.html - category: Product description: Quarterly data extracts in XML format adhering to ICH E2B standards for international safety reporting format: xml id: faers.quarterly_data_xml name: FAERS Quarterly Data Files (XML) original_source: - faers product_url: https://fis.fda.gov/extensions/FPD-QDE-FAERS/FPD-QDE-FAERS.html - category: DocumentationProduct description: Frequently asked questions about FAERS data structure, reporting requirements, and data usage format: http id: faers.faq name: FAERS FAQ original_source: - faers product_url: https://fis.fda.gov/extensions/FPD-FAQ/FPD-FAQ.html - category: GraphicalInterface description: Portal for submitting adverse event reports electronically to the FDA format: http id: faers.electronic_submissions name: FAERS Electronic Submissions Portal original_source: - faers product_url: https://www.fda.gov/drugs/questions-and-answers-fdas-adverse-event-reporting-system-faers/fda-adverse-event-reporting-system-faers-electronic-submissions - category: Product description: Standardized and deduplicated version of FDA FAERS data with drug names mapped to RxNorm and adverse event outcomes mapped to SNOMED-CT, including pre-computed summary statistics for drug-outcome relationships. id: aeolus.standardized_data name: AEOLUS Standardized FAERS Data original_source: - faers - aeolus product_url: https://datadryad.org/stash/dataset/doi:10.5061/dryad.8q0s4 taxon: - NCBITaxon:9606 - activity_status: active category: Ontology contacts: - category: Organization contact_details: - contact_type: url value: https://groups.google.com/forum/#!forum/faldo label: FALDO Google Group creation_date: '2025-06-04T00:00:00Z' description: FALDO (Feature Annotation Location Description Ontology) is an ontology for describing sequence feature locations using RDF/OWL. It provides a standardized way to represent genomic and protein sequence positions, regions, and strands in Semantic Web formats. domains: - genomics - biological systems - information technology homepage_url: http://biohackathon.org/resource/faldo id: faldo last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: FALDO products: - category: OntologyProduct description: FALDO ontology in Turtle/RDF format for describing feature locations on sequences format: ttl id: faldo.ttl name: FALDO Ontology (Turtle) original_source: - faldo product_file_size: 13615 product_url: http://biohackathon.org/resource/faldo.ttl - category: OntologyProduct description: FALDO ontology in RDF/XML format format: rdfxml id: faldo.rdf name: FALDO Ontology (RDF/XML) original_source: - faldo product_file_size: 25812 product_url: http://biohackathon.org/resource/faldo.rdf - category: DocumentationProduct description: Interactive ontology browser with class and property descriptions format: http id: faldo.browser name: FALDO Ontology Browser original_source: - faldo product_url: http://biohackathon.org/resource/faldo - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg repository: https://github.com/OBioFoundry/FALDO synonyms: - Feature Annotation Location Description Ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: vw253@cam.ac.uk - contact_type: github value: ValWood label: Val Wood orcid: 0000-0001-6330-7526 creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary for the anatomy of fungi. domains: - anatomy and development homepage_url: https://github.com/obophenotype/fungal-anatomy-ontology/ id: fao last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Fungal gross anatomy products: - category: OntologyProduct description: Fungal gross anatomy in OWL format format: owl id: fao.owl name: fao.owl product_file_size: 14367 product_url: http://purl.obolibrary.org/obo/fao.owl - category: OntologyProduct description: Fungal gross anatomy in OBO format format: obo id: fao.obo name: fao.obo product_file_size: 9190 product_url: http://purl.obolibrary.org/obo/fao.obo repository: https://github.com/obophenotype/fungal-anatomy-ontology taxon: - NCBITaxon:4751 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cp390@cam.ac.uk - contact_type: github value: Clare72 label: Clare Pilgrim orcid: 0000-0002-1373-1705 creation_date: '2025-06-25T00:00:00Z' description: An ontology representing the gross anatomy of Drosophila melanogaster. domains: - anatomy and development homepage_url: http://purl.obolibrary.org/obo/fbbt id: fbbt last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Drosophila gross anatomy products: - category: OntologyProduct description: Drosophila gross anatomy in OWL format format: owl id: fbbt.owl name: fbbt.owl product_file_size: 119307478 product_url: http://purl.obolibrary.org/obo/fbbt.owl - category: OntologyProduct description: Drosophila gross anatomy in OBO format format: obo id: fbbt.obo name: fbbt.obo product_file_size: 38424787 product_url: http://purl.obolibrary.org/obo/fbbt.obo - category: OntologyProduct description: Drosophila gross anatomy in JSON format format: json id: fbbt.json name: fbbt.json product_file_size: 77689601 product_url: http://purl.obolibrary.org/obo/fbbt.json - category: OntologyProduct description: Drosophila gross anatomy in OWL format format: owl id: fbbt.fbbt-simple.owl name: fbbt.fbbt-simple.owl product_file_size: 111168511 product_url: http://purl.obolibrary.org/obo/fbbt/fbbt-simple.owl - category: OntologyProduct description: Drosophila gross anatomy in OBO format format: obo id: fbbt.fbbt-simple.obo name: fbbt.fbbt-simple.obo product_file_size: 38424811 product_url: http://purl.obolibrary.org/obo/fbbt/fbbt-simple.obo - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology taxon: - NCBITaxon:7227 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cp390@cam.ac.uk - contact_type: github value: Clare72 label: Clare Pilgrim orcid: 0000-0002-1373-1705 creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary used for various aspects of annotation by FlyBase. domains: - biological systems homepage_url: http://purl.obolibrary.org/obo/fbcv id: fbcv last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: FlyBase Controlled Vocabulary products: - category: OntologyProduct description: FlyBase Controlled Vocabulary in OWL format format: owl id: fbcv.owl name: fbcv.owl product_file_size: 4275897 product_url: http://purl.obolibrary.org/obo/fbcv.owl - category: OntologyProduct description: FlyBase Controlled Vocabulary in OBO format format: obo id: fbcv.obo name: fbcv.obo product_file_size: 568316 product_url: http://purl.obolibrary.org/obo/fbcv.obo - category: OntologyProduct description: FlyBase Controlled Vocabulary in JSON format format: json id: fbcv.json name: fbcv.json product_file_size: 2731574 product_url: http://purl.obolibrary.org/obo/fbcv.json repository: https://github.com/FlyBase/flybase-controlled-vocabulary - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cp390@cam.ac.uk - contact_type: github value: Clare72 label: Clare Pilgrim orcid: 0000-0002-1373-1705 creation_date: '2025-06-25T00:00:00Z' description: A structured controlled vocabulary of the development of Drosophila melanogaster. domains: - anatomy and development homepage_url: http://purl.obolibrary.org/obo/fbdv id: fbdv last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Drosophila development products: - category: OntologyProduct description: Drosophila development in OWL format format: owl id: fbdv.owl name: fbdv.owl product_file_size: 523797 product_url: http://purl.obolibrary.org/obo/fbdv.owl - category: OntologyProduct description: Drosophila development in OBO format format: obo id: fbdv.obo name: fbdv.obo product_file_size: 118696 product_url: http://purl.obolibrary.org/obo/fbdv.obo - category: OntologyProduct description: Drosophila development in JSON format format: json id: fbdv.json name: fbdv.json product_file_size: 358729 product_url: http://purl.obolibrary.org/obo/fbdv.json - category: OntologyProduct description: Drosophila development in OWL format format: owl id: fbdv.fbdv-simple.owl name: fbdv.fbdv-simple.owl product_file_size: 442797 product_url: http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl - category: OntologyProduct description: Drosophila development in OBO format format: obo id: fbdv.fbdv-simple.obo name: fbdv.fbdv-simple.obo product_file_size: 118720 product_url: http://purl.obolibrary.org/obo/fbdv/fbdv-simple.obo - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/FlyBase/drosophila-developmental-ontology taxon: - NCBITaxon:7227 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: georgeta.bordea@u-bordeaux.fr - contact_type: github value: getbordea label: Georgeta Bordea orcid: 0000-0001-9921-8234 creation_date: '2025-09-29T00:00:00Z' description: Food-Drug interactions automatically extracted from scientific literature domains: - chemistry and biochemistry homepage_url: https://gitub.u-bordeaux.fr/erias/fideo id: fideo last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Food Interactions with Drugs Evidence Ontology products: - category: OntologyProduct description: Food Interactions with Drugs Evidence Ontology in OWL format format: owl id: fideo.owl name: fideo.owl product_url: http://purl.obolibrary.org/obo/fideo.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' repository: https://gitub.u-bordeaux.fr/erias/fideo - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: finngen-info@helsinki.fi label: FinnGen creation_date: '2025-06-27T00:00:00Z' description: FinnGen is a large-scale genomics research project aimed at improving human health through genetic insights from the genetically unique Finnish population, combining genome information with digital health record data from 500,000 Finnish biobank participants. domains: - genomics - biomedical - health - precision medicine - clinical homepage_url: https://www.finngen.fi/en id: finngen last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: FinnGen products: - category: Product description: Summary statistics from genome-wide association studies of various disease phenotypes conducted on Finnish population data, with the most recent release being Data Freeze 13. id: finngen.summary_stats name: FinnGen GWAS Summary Statistics product_url: https://www.finngen.fi/en/access_results - category: GraphicalInterface description: A web service for browsing disease endpoints in FinnGen, including statistics, definitions, and relationships between diseases. id: finngen.risteys name: Risteys product_url: https://risteys.finngen.fi/ - category: Product description: Results from meta-analysis of FinnGen data with other major biobanks, allowing for more powerful detection of genetic associations. id: finngen.meta_analysis name: FinnGen Meta-Analysis Results product_url: https://www.finngen.fi/en/access_results - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: Product description: Clinical endpoint definitions and control groups for FinnGen data releases, including detailed documentation for each data freeze. id: finngen.endpoints name: FinnGen Clinical Endpoints product_url: https://www.finngen.fi/en/researchers/clinical-endpoints publications: - doi: 10.1038/s41588-024-01975-5 id: doi:10.1038/s41588-024-01975-5 title: Genome-wide association study reveals mechanisms underlying dilated cardiomyopathy and myocardial resilience year: '2024' - doi: 10.1038/s41588-025-02100-w id: doi:10.1038/s41588-025-02100-w title: Genome-wide association study of long COVID year: '2025' taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: torsten.hahmann@maine.edu label: Torsten Hahmann creation_date: '2025-12-08T00:00:00Z' description: The FIO KG is part of the SAWGraph (Safe Agricultural Products and Water Graph) project, providing structured data about food industry operations and their environmental impacts. domains: - environment - agriculture evaluation_page: resource/fiokg/fiokg_eval_automated.html homepage_url: https://sawgraph.github.io/ id: fiokg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SAWGraph FIO KG products: - category: ProgrammingInterface description: SPARQL endpoint for SAWGraph FIO KG id: fiokg.sparql name: SAWGraph FIO KG SPARQL original_source: - fiokg product_url: https://frink.apps.renci.org/fiokg/sparql - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: robert.hoehndorf@kaust.edu.sa - contact_type: github value: leechuck label: Robert Hoehndorf orcid: 0000-0001-8149-5890 creation_date: '2025-09-29T00:00:00Z' description: Traits and phenotypes of flowering plants occurring in digitized Floras domains: - biological systems homepage_url: https://github.com/flora-phenotype-ontology/flopoontology id: flopo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Flora Phenotype Ontology products: - category: OntologyProduct description: Flora Phenotype Ontology in OWL format format: owl id: flopo.owl name: flopo.owl product_file_size: 767285 product_url: http://purl.obolibrary.org/obo/flopo.owl repository: https://github.com/flora-phenotype-ontology/flopoontology taxon: - NCBITaxon:33090 - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: FlyBase is a comprehensive database of genomic and genetic data for Drosophila melanogaster (fruit fly) and related species. It provides curated information on genes, genomes, phenotypes, genetic variants, stocks, and experimental tools for the Drosophila research community. The database integrates sequence data, genome annotations, functional characterizations, expression patterns, genetic interactions, disease models, and orthology relationships. FlyBase serves as the primary reference for Drosophila gene nomenclature and provides extensive tools for querying and analyzing genomic data across multiple Drosophila species. domains: - genomics - organisms - biological systems homepage_url: https://flybase.org/ id: flybase infores_id: flybase last_modified_date: '2025-10-08T00:00:00Z' layout: resource_detail name: FlyBase products: - category: Product description: Genome annotation files for Drosophila melanogaster in GFF3 format, including gene models, transcripts, exons, and functional elements format: gff id: flybase.genome.annotations.gff name: FlyBase Genome Annotations original_source: - flybase product_url: https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview - category: Product description: Complete genome sequences for Drosophila species in FASTA format, including chromosome assemblies and scaffolds format: fasta id: flybase.genome.sequences.fasta name: FlyBase Genome Sequences original_source: - flybase product_url: https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview - category: Product description: Gene, transcript, and protein sequence data for Drosophila in FASTA format, including CDS, UTRs, and polypeptide sequences format: fasta id: flybase.gene.sequences.fasta name: FlyBase Gene Sequences original_source: - flybase product_url: https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview - category: Product description: Bulk data files containing gene annotations, phenotypes, interactions, expression data, stocks, and orthology information in tab-separated format format: tsv id: flybase.bulk.data name: FlyBase Bulk Data Files original_source: - flybase product_url: https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview - category: GraphicalInterface description: Interactive genome browser for visualizing Drosophila genomes, gene models, expression data, and genomic features using JBrowse technology id: flybase.jbrowse name: FlyBase JBrowse Genome Browser original_source: - flybase product_url: https://flybase.org/ - category: GraphicalInterface description: Web-based search and query interface for accessing FlyBase data, including gene information, phenotypes, stocks, and literature id: flybase.web.interface name: FlyBase Web Interface original_source: - flybase product_url: https://flybase.org/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database - category: Product description: Model organism data from FlyBase, SGD, ZFIN and other model organism databases format: http id: genecards.model.organisms name: GeneCards Model Organism Data original_source: - flybase - sgd - zfin product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - 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hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz - category: Product description: flybase Nodes TSV format: tsv id: obo-db-ingest.flybase.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: flybase Nodes TSV original_source: - flybase product_file_size: 2007373 product_url: https://w3id.org/biopragmatics/resources/flybase/flybase.tsv secondary_source: - obo-db-ingest repository: https://github.com/FlyBase taxon: - NCBITaxon:7227 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: polcaes@gmail.com - contact_type: github value: pcastellanoescuder label: Pol Castellano Escuder orcid: 0000-0001-6466-877X creation_date: '2025-09-29T00:00:00Z' description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data domains: - chemistry and biochemistry homepage_url: https://github.com/pcastellanoescuder/FoodBiomarkerOntology id: fobi last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Food-Biomarker Ontology products: - category: OntologyProduct description: FOBI is an ontology to represent food intake data and associate it with metabolomic data format: owl id: fobi.owl name: FOBI is an ontology to represent food intake data and associate it with metabolomic data product_file_size: 118923 product_url: http://purl.obolibrary.org/obo/fobi.owl repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: shhan@ualberta.ca label: Scott Han - category: Organization label: The Metabolomics Innovation Centre (TMIC) creation_date: '2025-05-29T00:00:00Z' description: The Food Database (FooDB) is the world's largest and most comprehensive resource on food constituents, chemistry, and biology. It provides detailed information about the chemical constituents found in food, designed for applications in nutrition, food science, dietary planning, and general education. domains: - biomedical - food science - nutrition - health homepage_url: https://foodb.ca/ id: foodb infores_id: foodb last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC-BY-NC-4.0 name: FooDB products: - category: GraphicalInterface description: Web interface that allows searching, browsing, and exploring food compounds and their properties. id: foodb.web name: FooDB Web Interface product_url: https://foodb.ca/ - category: Product compression: targz description: Complete FooDB database in CSV format format: csv id: foodb.data.csv name: FooDB CSV Data product_url: https://foodb.ca/public/system/downloads/foodb_2020_4_7_csv.tar.gz warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-05_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: targz description: Complete FooDB database in XML format format: xml id: foodb.data.xml name: FooDB XML Data product_url: https://foodb.ca/public/system/downloads/foodb_2020_4_7_xml.tar.gz warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: zip description: Complete FooDB database in JSON format format: json id: foodb.data.json name: FooDB JSON Data product_url: https://foodb.ca/public/system/downloads/foodb_2020_04_07_json.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: targz description: Complete FooDB database as MySQL dump id: foodb.data.mysql name: FooDB MySQL Dump product_url: https://foodb.ca/public/system/downloads/foodb_2020_4_7_mysql.tar.gz warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: zip description: Experimental C-MS Spectra data from FooDB id: foodb.data.experimental_cms name: FooDB Experimental C-MS Spectra product_url: https://foodb.ca/public/system/downloads/foodb_experimental_cms_spectra.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-05_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: zip description: Predicted C-MS Spectra data from FooDB id: foodb.data.predicted_cms name: FooDB Predicted C-MS Spectra product_url: https://foodb.ca/public/system/downloads/foodb_predicted_cms_spectra.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-05_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: zip description: Experimental MS-MS Spectra data from FooDB id: foodb.data.experimental_msms name: FooDB Experimental MS-MS Spectra product_url: https://foodb.ca/public/system/downloads/foodb_experimental_msms_spectra.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: zip description: Predicted MS-MS Spectra data from FooDB id: foodb.data.predicted_msms name: FooDB Predicted MS-MS Spectra product_url: https://foodb.ca/public/system/downloads/foodb_predicted_msms_spectra.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: zip description: NMR Spectra data from FooDB id: foodb.data.nmr name: FooDB NMR Spectra product_url: https://foodb.ca/public/system/downloads/foodb_nmr_spectra.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: zip description: Free Induction Decay (FID) files from FooDB id: foodb.data.fid name: FooDB FID Files product_url: https://foodb.ca/public/system/downloads/foodb_fid_files.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product compression: zip description: Image files of compounds, foods, and chemical structures id: foodb.data.images name: FooDB Image Files product_url: https://foodb.ca/public/system/downloads/foodb_image_files.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-11_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-11-26_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-08-07_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - authors: - Wishart DS - Knox C - Guo AC - Eisner R - Young N - Gautam B - Hau DD - Psychogios N - Dong E - Bouatra S - Mandal R - Sinelnikov I - Xia J - Jia L - Cruz JA - Lim E - Sobsey CA - Shrivastava S - Huang P - Liu P - Fang L - Peng J - Fradette R - Cheng D - Tzur D - Clements M - Lewis A - De Souza A - Zuniga A - Dawe M - Xiong Y - Clive D - Greiner R - Nazyrova A - Shaykhutdinov R - Li L - Vogel HJ - Forsythe I doi: doi:10.1093/nar/gkn810 id: https://doi.org/10.1093/nar/gkn810 journal: Nucleic Acids Research preferred: true title: HMDB - a knowledgebase for the human metabolome year: '2009' - authors: - Wishart DS - Feunang YD - Marcu A - Guo AC - Liang K - Vázquez-Fresno R - Sajed T - Johnson D - Li C - Karu N - Sayeeda Z - Lo E - Assempour N - Berjanskii M - Singhal S - Arndt D - Liang Y - Badran H - Grant J - Serra-Cayuela A - Liu Y - Mandal R - Neveu V - Pon A - Knox C - Wilson M - Manach C - Scalbert A id: https://doi.org/10.1093/nar/gkx1089 journal: Nucleic Acids Research title: HMDB 4.0 - The Human Metabolome Database for 2018 year: '2018' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://foodb.ca/ - contact_type: email value: david.wishart@ualberta.ca id: wishart-lab label: Wishart Lab (University of Alberta) creation_date: '2025-10-30T00:00:00Z' description: FooDB (The Food Database) is the world's largest and most comprehensive freely accessible resource on food constituents, chemistry, and biology, providing detailed information about chemical constituents found in food with over 100 data fields per compound covering nomenclature, structure, chemical properties, food sources, sensory properties, and health effects. domains: - nutrition - biomedical homepage_url: https://foodb.ca/ id: fooddb infores_id: fooddb last_modified_date: '2026-01-15T00:00:00Z' layout: resource_detail name: FooDB products: - category: GraphicalInterface description: Interactive web interface for browsing and searching food composition data format: http id: fooddb.portal is_public: true name: FooDB Web Portal original_source: - fooddb product_url: https://foodb.ca/ - category: Product description: FooDB complete dataset in CSV format (TAR/GZ compressed, 952.52 MB) format: csv id: fooddb.csv is_public: true name: FooDB CSV File original_source: - fooddb product_file_size: 998314299 product_url: https://foodb.ca/public/system/downloads/foodb_2020_4_7_csv.tar.gz - category: Product description: FooDB complete dataset in XML format (TAR/GZ compressed, 6438.08 MB) format: xml id: fooddb.xml is_public: true name: FooDB XML File original_source: - fooddb product_file_size: 6731854848 product_url: https://foodb.ca/public/system/downloads/foodb_2020_4_7_xml.tar.gz - category: Product description: FooDB complete dataset in JSON format (ZIP compressed, 86.66 MB) format: json id: fooddb.json is_public: true name: FooDB JSON File original_source: - fooddb product_file_size: 90852659 product_url: https://foodb.ca/public/system/downloads/foodb_2020_04_07_json.zip - category: Product description: FooDB complete dataset as MySQL database dump (TAR/GZ compressed, 172.73 MB) format: mysql id: fooddb.mysql is_public: true name: FooDB MySQL Dump File original_source: - fooddb product_file_size: 180900659 product_url: https://foodb.ca/public/system/downloads/foodb_2020_4_7_mysql.tar.gz publications: - category: Publication id: PMID:29140464 preferred: true synonyms: - FooDB - The Food Database - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: damion_dooley@sfu.ca - contact_type: github value: ddooley label: Damion Dooley orcid: 0000-0002-8844-9165 creation_date: '2025-09-29T00:00:00Z' description: A broadly scoped ontology representing entities which bear a food role . It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research domains: - chemistry and biochemistry homepage_url: https://foodon.org/ id: foodon last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Food Ontology products: - category: OntologyProduct description: FoodOn ontology with import file references and over 9,000 food products format: owl id: foodon.owl name: FoodOn ontology with import file references and over 9,000 food products product_file_size: 2852449 product_url: http://purl.obolibrary.org/obo/foodon.owl - category: OntologyProduct description: FoodOn core ontology (currently the same as foodon.owl) format: owl id: foodon_core.owl name: FoodOn core ontology (currently the same as foodon.owl) product_url: http://purl.obolibrary.org/obo/foodon_core.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/FoodOntology/foodon - activity_status: active category: KnowledgeGraph creation_date: '2025-12-11T00:00:00Z' description: FORUM is a Knowledge Graph providing a semantic representation of relations between chemicals and biomedical concepts. It is built from a federation of life science databases and scientific literature repositories. FORUM supports metabolomics studies by enabling the identification of biomarkers and classification of individuals through comprehensive chemical-concept associations. domains: - chemistry and biochemistry - biomedical evaluation_page: resource/forum/forum_eval_automated.html homepage_url: https://forum-webapp.semantic-metabolomics.fr/ id: forum last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: FORUM products: - category: GraphicalInterface description: FORUM web application interface for semantic metabolomics exploration id: forum.webapp name: FORUM Web Application product_url: https://forum-webapp.semantic-metabolomics.fr/ - category: ProgrammingInterface description: FORUM REST API for programmatic access to chemical-disease associations id: forum.api name: FORUM API product_url: https://forum-webapp.semantic-metabolomics.fr/#/openapi-documentation - category: DocumentationProduct description: FORUM VoID (Vocabulary of Interlinked Datasets) metadata describing the knowledge graph structure id: forum.void name: FORUM VoID Metadata product_file_size: 96461 product_url: https://forum.semantic-metabolomics.fr/.well-known/void - category: GraphProduct description: Downloadable knowledge graph dump in TAR/GZ format containing complete FORUM data id: forum.graph.dump name: FORUM Knowledge Graph Dump original_source: - mesh - chebi - cito - fabio - dc - cheminf - skos - chemont - pubchem - pubmed product_url: ftp://forum:Forum2021Cov!@ftp.semantic-metabolomics.org/dumps/2021/share.tar.gz secondary_source: - forum warnings: - File was not able to be retrieved when checked on 2026-03-08_ FTP error_ timed out - File was not able to be retrieved when checked on 2026-02-26_ FTP error_ timed out - 'File was not able to be retrieved when checked on 2026-03-11: FTP error: timed out' publications: - authors: - Delmas M - Filangi O - Paulhe N - Vinson F - Duperier C - Garrier W - Saunier PE - Pitarch Y - Jourdan F - Giacomoni F - Frainay C doi: 10.1093/bioinformatics/btab627 id: doi:10.1093/bioinformatics/btab627 journal: Bioinformatics preferred: true title: 'FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases' year: '2021' repository: https://github.com/eMetaboHUB/Forum-DiseasesChem - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: meghan.balk@gmail.com - contact_type: github value: megbalk label: Meghan Balk orcid: 0000-0003-2699-3066 creation_date: '2025-09-29T00:00:00Z' description: FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA). domains: - biological systems homepage_url: https://github.com/futres/fovt id: fovt last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: FuTRES Ontology of Vertebrate Traits products: - category: OntologyProduct description: FuTRES Ontology of Vertebrate Traits in OWL format format: owl id: fovt.owl name: fovt.owl product_file_size: 2417022 product_url: http://purl.obolibrary.org/obo/fovt.owl - category: OntologyProduct description: FuTRES Ontology of Vertebrate Traits in OBO format format: obo id: fovt.obo name: fovt.obo product_file_size: 1539512 product_url: http://purl.obolibrary.org/obo/fovt.obo - category: OntologyProduct description: FuTRES Ontology of Vertebrate Traits in OWL format format: owl id: fovt.fovt-base.owl name: fovt.fovt-base.owl product_file_size: 76581 product_url: http://purl.obolibrary.org/obo/fovt/fovt-base.owl - category: OntologyProduct description: FuTRES Ontology of Vertebrate Traits in OBO format format: obo id: fovt.fovt-base.obo name: fovt.fovt-base.obo product_file_size: 33174 product_url: http://purl.obolibrary.org/obo/fovt/fovt-base.obo repository: https://github.com/futres/fovt - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: vw253@cam.ac.uk - contact_type: github value: ValWood label: Val Wood orcid: 0000-0001-6330-7526 creation_date: '2025-09-29T00:00:00Z' description: FYPO is a formal ontology of phenotypes observed in fission yeast. domains: - biological systems homepage_url: https://github.com/pombase/fypo id: fypo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Fission Yeast Phenotype Ontology products: - category: OntologyProduct description: Fission Yeast Phenotype Ontology in OWL format format: owl id: fypo.owl name: fypo.owl product_file_size: 45154688 product_url: http://purl.obolibrary.org/obo/fypo.owl - category: OntologyProduct description: Fission Yeast Phenotype Ontology in OBO format format: obo id: fypo.obo name: fypo.obo product_file_size: 7094161 product_url: http://purl.obolibrary.org/obo/fypo.obo repository: https://github.com/pombase/fypo taxon: - NCBITaxon:4896 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: adeans@psu.edu - contact_type: github value: adeans label: Andy Deans orcid: 0000-0002-2119-4663 creation_date: '2025-09-29T00:00:00Z' description: Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls. domains: - biological systems homepage_url: https://adeans.github.io/gallont/ id: gallont last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Plant Gall Ontology products: - category: OntologyProduct description: Plant Gall Ontology in OWL format format: owl id: gallont.owl name: gallont.owl product_file_size: 91521 product_url: http://purl.obolibrary.org/obo/gallont.owl - category: OntologyProduct description: Plant Gall Ontology in JSON format format: json id: gallont.json name: gallont.json product_url: http://purl.obolibrary.org/obo/gallont.json warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: Plant Gall Ontology in OBO format format: obo id: gallont.obo name: gallont.obo product_file_size: 60631 product_url: http://purl.obolibrary.org/obo/gallont.obo repository: https://github.com/adeans/gallont - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for gard. This page was automatically generated because it was referenced by other resources. domains: - stub id: gard last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Gard products: - category: Product description: gard Nodes TSV format: tsv id: obo-db-ingest.gard.tsv name: gard Nodes TSV original_source: - gard product_file_size: 314439 product_url: https://w3id.org/biopragmatics/resources/gard/gard.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: lschriml@som.umaryland.edu - contact_type: github value: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 creation_date: '2025-09-29T00:00:00Z' description: A gazetteer constructed on ontological principles. The countries are actively maintained. domains: - environment homepage_url: http://environmentontology.github.io/gaz/ id: gaz last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Gazetteer products: - category: OntologyProduct description: Gazetteer in OWL format format: owl id: gaz.owl name: gaz.owl product_file_size: 1308877129 product_url: http://purl.obolibrary.org/obo/gaz.owl - category: OntologyProduct description: Gazetteer in OBO format format: obo id: gaz.obo name: gaz.obo product_file_size: 189228723 product_url: http://purl.obolibrary.org/obo/gaz.obo - category: OntologyProduct description: A country specific subset of the GAZ. format: owl id: gaz.gaz-countries.owl name: GAZ countries product_file_size: 42847 product_url: http://purl.obolibrary.org/obo/gaz/gaz-countries.owl repository: https://github.com/EnvironmentOntology/gaz - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.gbif.org/ - contact_type: email value: info@gbif.org id: gbif-secretariat label: GBIF Secretariat creation_date: '2025-12-17T00:00:00Z' description: Global Biodiversity Information Facility (GBIF) is an international network and data infrastructure providing open access to over 3.1 billion species occurrence records from 81,000+ datasets contributed by 2,500+ publishing institutions worldwide. GBIF aggregates species distribution and biodiversity data using Darwin Core standards. domains: [] homepage_url: https://www.gbif.org/ id: gbif infores_id: gbif last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 and CC BY (mixed) logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Global Biodiversity Information Facility (GBIF) products: - category: GraphicalInterface description: Web portal for searching, filtering, and discovering occurrence records, species information, datasets, and organizations with interactive mapping and download capabilities format: http id: gbif.portal name: GBIF.org Portal product_url: https://www.gbif.org/ - category: ProgrammingInterface description: RESTful API providing programmatic access to registry, species, occurrence, and map data with JSON responses and support for complex queries format: http id: gbif.api is_public: true name: GBIF REST API product_url: https://api.gbif.org/v1/ - category: ProgrammingInterface description: Raster tile maps API providing global occurrence distribution maps in PNG and Mapbox Vector Tile (MVT) formats format: http id: gbif.maps-api is_public: true name: GBIF Maps API product_url: https://api.gbif.org/maps/ - category: Product compression: zip description: Darwin Core Archive format occurrence downloads from 81,000+ datasets with interpreted and verbatim data, metadata, and multimedia information id: gbif.dwc-archive name: GBIF Darwin Core Archive Downloads product_url: https://www.gbif.org/occurrence/download warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product compression: zip description: Simple CSV format occurrence downloads with interpreted data and commonly used columns, suitable for spreadsheet and programming analysis id: gbif.csv-download name: GBIF Simple CSV Downloads product_url: https://www.gbif.org/occurrence/download warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: DocumentationProduct description: Comprehensive technical documentation, API reference, developer guides, and data formats documentation format: http id: gbif.documentation is_public: true name: GBIF Technical Documentation product_url: https://techdocs.gbif.org/ - category: Product description: Integrated Publishing Toolkit (IPT) - free, open-source Java software for publishing Darwin Core formatted biodiversity datasets with web interface and automated data management capabilities id: gbif.ipt name: GBIF Integrated Publishing Toolkit (IPT) product_url: https://www.gbif.org/ipt warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' publications: - authors: - Robertson T - Döring M - Guralnick R - Bloom D - Wieczorek J - Braak K - Otegui J - Russell L - Desmet P doi: 10.1371/journal.pone.0102623 id: doi:10.1371/journal.pone.0102623 journal: PLOS ONE title: 'The GBIF Integrated Publishing Toolkit: Facilitating the Efficient Publishing of Biodiversity Data on the Internet' year: '2014' repository: https://github.com/gbif taxon: - NCBITaxon:1 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.cancer.gov/ - contact_type: url value: https://gdc.cancer.gov/ label: National Cancer Institute creation_date: '2025-10-30T00:00:00Z' description: The NCI Genomic Data Commons (GDC) is a data sharing platform promoting precision medicine in oncology by providing unified access to harmonized cancer genomic and clinical data from major cancer research programs including TCGA and TARGET, processed with standardized bioinformatics pipelines to enable direct comparison and integrated analysis. domains: - genomics - precision medicine - clinical - biomedical homepage_url: https://portal.gdc.cancer.gov id: gdc infores_id: gdc last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: National Cancer Institute Genomic Data Commons Data Portal products: - category: GraphicalInterface description: Main GDC web portal for interactive exploration of projects, cohorts, and files. format: http id: gdc.portal name: GDC Data Portal original_source: - gdc product_url: https://portal.gdc.cancer.gov/ - category: ProgrammingInterface connection_url: https://api.gdc.cancer.gov/ description: REST API documentation and endpoint for programmatic access to GDC metadata and files. format: http id: gdc.api is_public: true name: GDC API original_source: - gdc product_url: https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/ - category: DocumentationProduct description: Documentation and download links for the GDC Data Transfer Tool used for bulk file download. format: http id: gdc.data-transfer-tool name: GDC Data Transfer Tool original_source: - gdc product_url: https://gdc.cancer.gov/access-data/gdc-data-transfer-tool publications: - doi: 10.1182/blood-2017-03-735654 id: doi:10.1182/blood-2017-03-735654 journal: Blood preferred: true title: The NCI Genomic Data Commons as an engine for precision medicine year: '2017' synonyms: - GDC - Genomic Data Commons taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.cancerrxgene.org/ label: Genomics of Drug Sensitivity in Cancer Project - category: Organization contact_details: - contact_type: url value: https://www.sanger.ac.uk/ label: Wellcome Sanger Institute - category: Organization contact_details: - contact_type: url value: http://www.massgeneral.org/cancer/ label: Massachusetts General Hospital Cancer Center creation_date: '2025-05-28T00:00:00Z' description: The Genomics of Drug Sensitivity in Cancer (GDSC) is a database and resource that characterizes cancer cell lines and their responses to anti-cancer drugs. It contains drug screening data for over 1000 cancer cell lines with hundreds of compounds, as well as genomic feature data such as mutations, copy number variations, methylation, and gene expression. The aim is to identify molecular features of cancers that predict response to anti-cancer drugs. domains: - biomedical - health - drug discovery - genomics - pharmacology homepage_url: https://www.cancerrxgene.org/ id: gdsc infores_id: gdsc last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://www.cancerrxgene.org/legal label: Custom (non-commercial research use) name: Genomics of Drug Sensitivity in Cancer products: - category: GraphicalInterface description: Web interface for searching and browsing GDSC data including cell lines, compounds, and genomic features format: http id: gdsc.site name: GDSC Web Interface original_source: - gdsc product_url: https://www.cancerrxgene.org/ - category: Product description: Drug sensitivity data including IC50 values for cancer cell lines format: csv id: gdsc.drug_data name: GDSC Drug Sensitivity Data original_source: - gdsc product_url: https://www.cancerrxgene.org/downloads/drug_data - category: Product description: ANOVA analysis results of associations between drug sensitivity and genomic features format: csv id: gdsc.anova name: GDSC ANOVA Results original_source: - gdsc product_url: https://www.cancerrxgene.org/downloads/anova - category: Product description: Genetic feature data including mutations, copy number variations, gene expression, and methylation format: csv id: gdsc.genetic_features name: GDSC Genetic Features original_source: - gdsc product_url: https://www.cancerrxgene.org/downloads/genetic_features - category: Product description: FTP repository with all GDSC data releases and archives format: csv id: gdsc.ftp name: GDSC FTP Data Repository original_source: - gdsc product_url: https://ftp.sanger.ac.uk/project/cancerrxgene/releases/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - authors: - Yang W - Soares J - Greninger P - Edelman EJ - Lightfoot H - Forbes S - Bindal N - Beare D - Smith JA - Thompson IR - Ramaswamy S - Futreal PA - Haber DA - Stratton MR - Benes C - McDermott U - Garnett MJ doi: doi:10.1093/nar/gks1111 id: http://doi.org/10.1093/nar/gks1111 journal: Nucleic Acids Research preferred: true title: 'Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells' year: '2013' - authors: - Iorio F - Knijnenburg TA - Vis DJ - Bignell GR - Menden MP - Schubert M - Aben N - Gonçalves E - Barthorpe S - Lightfoot H - Cokelaer T - Greninger P - van Dyk E - Chang H - de Silva H - Heyn H - Deng X - Egan RK - Liu Q - Mironenko T - Mitropoulos X - Richardson L - Wang J - Zhang T - Moran S - Sayols S - Soleimani M - Tamborero D - Lopez-Bigas N - Ross-Macdonald P - Esteller M - Gray NS - Haber DA - Stratton MR - Benes CH - Wessels LFA - Saez-Rodriguez J - McDermott U - Garnett MJ id: https://doi.org/10.1016/j.cell.2016.06.017 journal: Cell title: A landscape of pharmacogenomic interactions in cancer year: '2016' - authors: - Garnett MJ - Edelman EJ - Heidorn SJ - Greenman CD - Dastur A - Lau KW - Greninger P - Thompson IR - Luo X - Soares J - Liu Q - Iorio F - Surdez D - Chen L - Milano RJ - Bignell GR - Tam AT - Davies H - Stevenson JA - Barthorpe S - Lutz SR - Kogera F - Lawrence K - McLaren-Douglas A - Mitropoulos X - Mironenko T - Thi H - Richardson L - Zhou W - Jewitt F - Zhang T - O'Brien P - Boisvert JL - Price S - Hur W - Yang W - Deng X - Butler A - Choi HG - Chang JW - Baselga J - Stamenkovic I - Engelman JA - Sharma SV - Delattre O - Saez-Rodriguez J - Gray NS - Settleman J - Futreal PA - Haber DA - Stratton MR - Ramaswamy S - McDermott U - Benes CH id: https://doi.org/10.1038/nature11005 journal: Nature title: Systematic identification of genomic markers of drug sensitivity in cancer cells year: '2012' repository: https://github.com/CancerRxGene taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: rbca.jackson@gmail.com - contact_type: github value: beckyjackson label: Rebecca Jackson orcid: 0000-0003-4871-5569 creation_date: '2025-09-29T00:00:00Z' description: An ontology to represent genomics cohort attributes domains: - biological systems homepage_url: https://github.com/IHCC-cohorts/GECKO id: gecko last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Genomics Cohorts Knowledge Ontology products: - category: OntologyProduct description: Genomics Cohorts Knowledge Ontology in OWL format format: owl id: gecko.owl name: gecko.owl product_file_size: 18443 product_url: http://purl.obolibrary.org/obo/gecko.owl repository: https://github.com/IHCC-cohorts/GECKO - activity_status: active category: DataSource creation_date: '2025-10-30T00:00:00Z' description: Gene-List Network Enrichment Analysis (GeLiNEA) is a computational tool that evaluates the significance of connections between a gene list (e.g., from screening experiments) and curated gene sets (e.g., MSigDB) within protein-protein association networks (e.g., STRING). It uses a null model of degree-preserving random gene lists to assess statistical significance of network connections, supporting pathway enrichment analysis and functional interpretation of experimental gene lists. domains: - genomics - systems biology - biomedical homepage_url: https://github.com/broadinstitute/GeLiNEA id: gelinea infores_id: gelinea last_modified_date: '2025-11-17T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: GeLiNEA products: - category: Product description: Command-line tool for performing gene-list network enrichment analysis using degree-preserving random gene list null models format: python id: gelinea.tool name: GeLiNEA Tool original_source: - gelinea product_url: https://github.com/broadinstitute/GeLiNEA publications: - authors: - Yilong Zou - Whitney S Henry - Emily L Ricq - Emily T Graham - Vasant V Phadnis - Peter Maretich - Sanchari Paradkar - Natalie Boehnke - Amy A Deik - Frederik Reinhardt - Jennifer K Eaton - Brittany Ferguson - Wan Wang - Jocelyn Fairman - Hillary R Keys - Vlado Dančík - Clary B Clish - Paul A Clemons - Paula T Hammond - Laurie A Boyer - Robert A Weinberg - Stuart L Schreiber doi: 10.1038/s41586-020-2732-8 id: PMID:32939090 journal: Nature title: Plasticity of ether lipids promotes ferroptosis susceptibility and evasion year: '2020' repository: https://github.com/broadinstitute/GeLiNEA synonyms: - GeLiNEA - Gene-List Network Enrichment Analysis - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: jp@senescence.info label: Genomics of Ageing and Rejuvenation Lab creation_date: '2025-10-30T00:00:00Z' description: GenAge is a curated database of genes related to ageing and longevity, part of the Human Ageing Genomic Resources (HAGR). It includes genes directly related to human ageing plus candidate genes from model organisms (yeast, worms, flies, mice), manually curated by experts to ensure high-quality content. domains: - genomics - health homepage_url: http://genomics.senescence.info/genes/ id: genage infores_id: genage last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail name: GenAge Database of Ageing-Related Genes products: - category: Product compression: zip description: Tab-delimited file containing all human ageing-related genes with extensive annotations format: tsv id: genage.human name: GenAge Human Genes Dataset original_source: - genage product_file_size: 9465 product_url: https://genomics.senescence.info/genes/human_genes.zip - category: Product compression: zip description: Tab-delimited file containing genes associated with longevity and ageing in model organisms (yeast, worms, flies, mice) format: tsv id: genage.models name: GenAge Model Organisms Dataset original_source: - genage product_file_size: 48796 product_url: https://genomics.senescence.info/genes/models_genes.zip - category: GraphicalInterface description: Web interface for searching and browsing human ageing-related genes format: http id: genage.human.search name: GenAge Human Genes Search original_source: - genage product_url: https://genomics.senescence.info/genes/human.html - category: GraphicalInterface description: Web interface for searching and browsing model organism ageing genes format: http id: genage.models.search name: GenAge Model Organisms Search original_source: - genage product_url: https://genomics.senescence.info/genes/models.html publications: - authors: - de Magalhaes JP - et al doi: 10.1093/nar/gkad927 id: doi:10.1093/nar/gkad927 journal: Nucleic Acids Research preferred: true title: 'Human Ageing Genomic Resources: updates on key databases in ageing research' year: '2024' - authors: - de Magalhaes JP - Toussaint O doi: 10.1016/j.febslet.2004.06.080 id: doi:10.1016/j.febslet.2004.06.080 journal: FEBS Letters title: 'GenAge: a genomic and proteomic network map of human ageing' year: '2004' - authors: - Fernandes M - et al doi: 10.1093/hmg/ddw307 id: doi:10.1093/hmg/ddw307 journal: Human Molecular Genetics title: Systematic analysis of the gerontome reveals links between aging and age-related diseases year: '2016' synonyms: - GenAge - The Aging Gene Database taxon: - NCBITaxon:9606 - NCBITaxon:4932 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: gencc@thegencc.org - contact_type: url value: https://thegencc.org/ label: GenCC Team creation_date: '2025-11-08T00:00:00Z' description: The Gene Curation Coalition (GenCC) is a global collaborative effort to harmonize gene-disease validity curation across multiple expert organizations and clinical testing laboratories. GenCC brings together leading resources including ClinGen, OMIM, Orphanet, DECIPHER, Genomics England PanelApp, and multiple clinical diagnostic laboratories to standardize terminology and share gene-disease validity assertions publicly. The coalition was formed in 2018 to address the lack of universal standards and terminologies for defining gene-disease relationships used in genomic medicine and research. Through a modified Delphi survey involving the international genetics community, GenCC established consensus terminology for grading gene-disease validity, including standardized terms such as Definitive, Strong, Moderate, Limited, Disputed Evidence, Refuted Evidence, No Known Disease Relationship, and Animal Model Only. The GenCC database provides curated gene-disease validity assertions with a focus on monogenic Mendelian diseases, including information on mode of inheritance, classification confidence level, supporting evidence, and links to detailed curations from member organizations. domains: - genomics homepage_url: https://thegencc.org/ id: gencc infores_id: gencc last_modified_date: '2025-11-08T00:00:00Z' layout: resource_detail name: The Gene Curation Coalition (GenCC) products: - category: Product description: The GenCC database containing over 15,000 curated gene-disease validity assertions on 4,500+ unique genes from 12 international submitters, with standardized classifications and evidence links format: http id: gencc.database name: GenCC Database product_url: https://search.thegencc.org/ - category: GraphicalInterface description: Interactive web-based search and browse interface at search.thegencc.org allowing users to filter gene-disease assertions by gene symbol, disease, submitter, and validity classification format: http id: gencc.search_interface name: GenCC Search Interface product_url: https://search.thegencc.org/ - category: Product description: Freely available downloadable datasets in multiple formats (XLSX, XLS, TSV, CSV) containing all GenCC gene-disease assertions with comprehensive metadata under CC0 1.0 Public Domain Dedication format: http id: gencc.downloads name: GenCC Data Downloads product_url: https://search.thegencc.org/download publications: - authors: - Marina T. DiStefano - Scott Goehringer - Heidi L. Rehm doi: 10.1016/j.gim.2022.04.017 id: doi:10.1016/j.gim.2022.04.017 journal: Genetics in Medicine preferred: true title: 'The Gene Curation Coalition: A global effort to harmonize gene–disease evidence resources' year: '2022' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-11-26T00:00:00Z' description: GENCODE is a comprehensive and high-quality reference annotation of the human and mouse genomes, providing evidence-based gene annotations including protein-coding genes, long non-coding RNAs, small RNAs, pseudogenes, and other genomic features based on manual curation and computational analysis. domains: - genomics homepage_url: https://www.gencodegenes.org/ id: gencode last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: GENCODE products: - category: Product description: Comprehensive gene annotations for human genome in GTF format format: gff id: gencode.human.gtf name: GENCODE Human Annotations GTF original_source: - gencode product_url: https://www.gencodegenes.org/human/ - category: Product description: Comprehensive gene annotations for mouse genome in GTF format format: gff id: gencode.mouse.gtf name: GENCODE Mouse Annotations GTF original_source: - gencode product_url: https://www.gencodegenes.org/mouse/ - category: Product description: GENCODE Primary transcript set capturing minimal transcripts at protein coding genes format: gff id: gencode.primary name: GENCODE Primary Transcripts original_source: - gencode product_url: https://www.gencodegenes.org/pages/gencode_primary/ - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg synonyms: - GENCODE - Encyclopedia of genes and gene variants taxon: - NCBITaxon:9606 - NCBITaxon:10090 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: http://genomics.senescence.info/help.html label: Human Ageing Genomic Resources creation_date: '2025-11-05T00:00:00Z' description: GenDR (Database of Dietary Restriction-Related Genes) is a curated database of genes associated with dietary restriction (DR) and its effects on longevity and aging. Part of the Human Ageing Genomic Resources (HAGR), GenDR compiles experimental data on genes whose expression or function is altered by dietary restriction regimens across multiple model organisms. The database includes information on gene function, expression changes, and links to aging-related phenotypes. domains: - genomics - health - nutrition - biological systems homepage_url: http://genomics.senescence.info/diet/ id: gendr infores_id: gendr last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: GenDR Database of Dietary Restriction-Related Genes products: - category: GraphicalInterface description: Web-based search and browsing interface for GenDR format: http id: gendr.web name: GenDR Web Interface original_source: - gendr product_url: http://genomics.senescence.info/diet/ - category: Product description: Downloadable dataset of dietary restriction-related genes format: csv id: gendr.data name: GenDR Data Download original_source: - gendr product_file_size: 8209 product_url: http://genomics.senescence.info/diet/dataset.zip - category: ProgrammingInterface description: Programmatic access to GenDR data format: http id: gendr.api name: GenDR API original_source: - gendr product_url: http://genomics.senescence.info/diet/help.html#api publications: - id: https://doi.org/10.1093/nar/gkp1108 synonyms: - GenDR - gendr taxon: - NCBITaxon:2759 - activity_status: active category: Ontology contacts: - category: Organization contact_details: - contact_type: url value: https://geneontology.org/ id: gene-ontology-consortium label: Gene Ontology Consortium creation_date: '2025-12-18T00:00:00Z' description: The Gene Ontology (GO) is a major bioinformatics initiative to standardize the representation of gene and gene product attributes across species, databases, and data types. It provides controlled vocabularies (ontologies) for describing molecular functions, cellular components, and biological processes associated with gene products. domains: - biomedical - biological systems homepage_url: https://geneontology.org/ id: gene-ontology last_modified_date: '2026-03-07T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Gene Ontology (GO) products: - category: OntologyProduct description: The main ontology in OWL. This is self contained and does not have connections to other OBO ontologies format: owl id: go.owl name: GO (OWL edition) product_file_size: 129057533 product_url: http://purl.obolibrary.org/obo/go.owl - category: OntologyProduct description: Equivalent to go.owl, in obo format format: obo id: go.obo name: GO (OBO Format edition) product_file_size: 36289217 product_url: http://purl.obolibrary.org/obo/go.obo - category: GraphicalInterface description: Gene Ontology web browser and search interface format: http id: gene-ontology.amigo is_public: true name: AmiGO 2 product_url: https://amigo.geneontology.org/amigo - category: ProgrammingInterface description: Gene Ontology API for programmatic access format: http id: gene-ontology.api is_public: true name: Gene Ontology API product_url: https://api.geneontology.org/ - category: Product description: Gene Ontology Causal Activity Model (GO-CAM) annotations manually curated by Gene Ontology biocurators linking genes, proteins, and biological processes id: cam-kp.go-cams name: Gene Ontology CAMs original_source: - gene-ontology repository: https://github.com/geneontology synonyms: - GO taxon: - NCBITaxon:all - activity_status: active category: DataSource creation_date: '2026-01-23T00:00:00Z' description: A curated gene-disease evidence resource linking genes, variant mechanisms, and clinical phenotypes to support rare disease interpretation. domains: - genomics - phenotype - health homepage_url: https://www.ebi.ac.uk/gene2phenotype/ id: gene2phenotype last_modified_date: '2026-02-15T00:00:00Z' layout: resource_detail name: Gene2Phenotype products: - category: GraphicalInterface description: Main interface for searching curated gene-disease evidence and panels. format: http id: gene2phenotype.portal name: Gene2Phenotype Portal product_url: https://www.ebi.ac.uk/gene2phenotype/ - category: ProgrammingInterface description: API documentation interface for programmatic access to G2P records. format: http id: gene2phenotype.api name: Gene2Phenotype API product_url: https://www.ebi.ac.uk/gene2phenotype/api/ - category: ProgrammingInterface description: OpenAPI schema endpoint for the Gene2Phenotype API. format: http id: gene2phenotype.api.schema name: Gene2Phenotype API Schema product_url: https://www.ebi.ac.uk/gene2phenotype/api/schema/ - category: GraphProduct description: KGX graph package for Gene2Phenotype (build gene2phenotype_2025_12_15_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.gene2phenotype.graph name: Translator Gene2Phenotype KGX Graph original_source: - gene2phenotype product_url: https://stars.renci.org/var/translator/releases/gene2phenotype/2025_12_15/ secondary_source: - translator repository: https://github.com/EBI-G2P/gene2phenotype_api synonyms: - G2P - Gene2Phenotype - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.ukbiobank.ac.uk/ label: UK Biobank creation_date: '2025-10-30T00:00:00Z' description: Genebass is a comprehensive resource of exome-based gene-level and single-variant association statistics from 281,852 UK Biobank participants across 3,817 phenotypes, enabling large-scale genotype-phenotype association studies. domains: - genomics - biomedical homepage_url: https://genebass.org/ id: genebass infores_id: genebass last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: 'Genebass: Gene-based association summary statistics' products: - category: GraphicalInterface description: Interactive web interface for searching and browsing Genebass gene-based and variant-level association results. format: http id: genebass.portal name: Genebass Portal original_source: - genebass product_url: https://app.genebass.org/ publications: - doi: 10.1016/j.xgen.2022.100168 id: doi:10.1016/j.xgen.2022.100168 journal: Cell Genomics preferred: true title: Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes year: '2022' synonyms: - Genebass - Gene-based association summary statistics - activity_status: active category: Aggregator creation_date: '2025-09-09T00:00:00Z' description: GeneCards is a comprehensive, integrative database that aggregates gene-centric information from over 200 web sources. It provides searchable access to genomic, transcriptomic, proteomic, genetic, clinical and functional information for all annotated and predicted human genes. GeneCards automatically integrates data on gene function, pathways, diseases, variants, expression patterns, protein interactions, and more. The database includes over 443,000 gene entries with rich annotations from sources including HGNC, OMIM, Ensembl, UniProt, NCBI Gene, GTEx, PubMed, and many other major biomedical databases. GeneCards serves as a central hub for human gene information, making it accessible to researchers worldwide. domains: - genomics - biomedical - health - clinical - proteomics - pathways homepage_url: https://www.genecards.org/ id: genecards last_modified_date: '2025-10-08T00:00:00Z' layout: resource_detail name: GeneCards products: - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources id: genecards.web.interface name: GeneCards Web Interface original_source: - genecards product_url: https://www.genecards.org/ - category: Product description: Integrated gene annotation data aggregated from HGNC, OMIM, Ensembl, NCBI Gene, UniProt and other genomic databases format: http id: genecards.gene.annotations name: GeneCards Gene Annotations original_source: - hgnc - omim - ensembl - ncbigene - uniprot - refseq product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Disease association data integrated from OMIM, MalaCards, ClinVar, Orphanet, DisGeNET and other disease databases format: http id: genecards.disease.associations name: GeneCards Disease Associations original_source: - omim - malacards - clinvar - orphanet - disgenet product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Gene expression data aggregated from GTEx, BioGPS, Bgee and other expression databases format: http id: genecards.expression.data name: GeneCards Expression Data original_source: - gtex - biogps - bgee product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Pathway information integrated from Reactome, WikiPathways and other pathway databases format: http id: genecards.pathway.data name: GeneCards Pathway Data original_source: - reactome - wikipathways product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Protein interaction data aggregated from IntAct, STRING, BioGRID and other interaction databases format: http id: genecards.protein.interactions name: GeneCards Protein Interactions original_source: - intact - string - biogrid product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Genetic variant data from ClinVar, dbSNP, GWAS Catalog and other variant databases format: http id: genecards.variant.data name: GeneCards Variant Data original_source: - clinvar - dbsnp - gwascatalog product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Literature references from PubMed automatically associated with genes format: http id: genecards.literature name: GeneCards Literature References original_source: - pubmed product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Gene ontology annotations from the Gene Ontology Consortium format: http id: genecards.gene.ontology name: GeneCards Gene Ontology Annotations original_source: - go product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Pharmacogenomics data from PharmGKB, DrugBank and other pharmacogenomics sources format: http id: genecards.pharmacogenomics name: GeneCards Pharmacogenomics Data original_source: - pharmgkb - drugbank product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Model organism data from FlyBase, SGD, ZFIN and other model organism databases format: http id: genecards.model.organisms name: GeneCards Model Organism Data original_source: - flybase - sgd - zfin product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Protein structure data from PDB Europe and other structural databases format: http id: genecards.protein.structures name: GeneCards Protein Structure Data original_source: - pdbe product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Clinical trial information from ClinicalTrials.gov format: http id: genecards.clinical.trials name: GeneCards Clinical Trials original_source: - clinicaltrialsgov product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database repository: null taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-08-20T00:00:00Z' description: GeneMANIA is a gene function prediction resource that integrates many types of functional association networks (co-expression, protein and genetic interactions, pathways, co-localization, and shared protein domains) and uses adaptive network weighting with label propagation to prioritize related genes and expand gene lists. domains: - genomics - biomedical - proteomics homepage_url: https://genemania.org/ id: genemania last_modified_date: '2025-08-20T00:00:00Z' layout: resource_detail name: GeneMANIA products: - category: GraphicalInterface description: Web interface for searching, visualizing, and analyzing functional association networks id: genemania.web name: GeneMANIA Web Interface product_url: https://genemania.org/ - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build publications: - authors: - Warde-Farley D - Donaldson SL - Comes O - Zuberi K - Badrawi R - et al. doi: 10.1093/nar/gkq537 id: doi:10.1093/nar/gkq537 journal: Nucleic Acids Research preferred: true title: 'The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function' year: '2010' usages: - description: The PheKnowLator knowledge graph ingests GeneMANIA functional association networks to construct gene-to-gene associations (e.g., co-expression and interaction edges) during its build. id: pheknowlator-gene-gene-edges label: PheKnowLator gene–gene edges type: actual url: https://github.com/callahantiff/PheKnowLator/wiki - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: damion_dooley@sfu.ca - contact_type: github value: ddooley label: Damion Dooley orcid: 0000-0002-8844-9165 creation_date: '2025-09-29T00:00:00Z' description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. domains: - biomedical homepage_url: http://genepio.org/ id: genepio last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Genomic Epidemiology Ontology products: - category: OntologyProduct description: Genomic Epidemiology Ontology in OWL format format: owl id: genepio.owl name: genepio.owl product_file_size: 732830 product_url: http://purl.obolibrary.org/obo/genepio.owl repository: https://github.com/GenEpiO/genepio - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual label: Jason Flannick creation_date: '2025-03-09T00:00:00Z' description: A Translator Knowledge Provider focusing on genetic data. domains: - health evaluation_page: resource/genetics-kp/genetics-kp_eval_automated.html id: genetics-kp last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Genetics KP products: - category: DocumentationProduct description: Team overview and data source documentation for the Genetics Knowledge Provider. format: http id: genetics-kp.docs name: Genetics KP Documentation original_source: - genetics-kp product_url: https://github.com/NCATSTranslator/Translator-All/wiki/Genetics-Knowledge-Provider - category: ProcessProduct description: Source code repository for the Genetics Knowledge Provider implementation. format: http id: genetics-kp.code name: Genetics KP Source Code original_source: - genetics-kp product_url: https://github.com/broadinstitute/genetics-kp-dev - activity_status: active category: KnowledgeGraph collection: - translator creation_date: '2026-02-18T00:00:00Z' description: Genetics KP is a Translator knowledge provider focused on integrating genetic association evidence (including GWAS-derived signals) into a unified framework for gene-disease relationship analysis. domains: - genomics - health - translational homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/Genetics-Knowledge-Provider id: geneticskp last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail name: Genetics KP products: - category: GraphProduct description: KGX graph package for Genetics KP (build geneticskp_2025-12-15_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.geneticskp.graph name: Translator Genetics KP KGX Graph original_source: - geneticskp product_url: https://stars.renci.org/var/translator/releases/geneticskp/2025_12_15/ secondary_source: - translator - category: ProgrammingInterface description: Translator Reasoner API endpoint for Genetics KP. format: http id: geneticskp.trapi name: Genetics KP TRAPI Endpoint original_source: - geneticskp product_url: https://genetics-kp.transltr.io/genetics_provider/trapi/v1.4/ repository: https://github.com/broadinstitute/genetics-kp-dev tags: - translator - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mhb120@gmail.com - contact_type: github value: mbrush label: Matthew Brush orcid: 0000-0002-1048-5019 creation_date: '2025-09-04T00:00:00Z' description: An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases. domains: - biological systems homepage_url: https://github.com/monarch-initiative/GENO-ontology/ id: geno last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Genotype Ontology products: - category: OntologyProduct description: GENO format: owl id: geno.owl name: GENO product_file_size: 172287 product_url: http://purl.obolibrary.org/obo/geno.owl - category: OntologyProduct description: OWL release of Monochrom Ontology format: owl id: chr.model.owl name: Monochrom Ontology OWL release original_source: - ro - go - ncbitaxon - iao - geno - skos - gff product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl secondary_source: - chr repository: https://github.com/monarch-initiative/GENO-ontology - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: wyq@umich.edu label: Yiqun Wang - category: Individual contact_details: - contact_type: email value: drjieliu@umich.edu label: Jie Liu creation_date: '2025-03-20T00:00:00Z' description: Genomic Knowledgebase (GenomicKB) is a database that uses a knowledge graph to consolidate genomic datasets and annotations. GenomicKB integrates data from more than 30 consortia, in which the genomic entities and relationships are represented as diverse nodes and edges with properties. domains: - biological systems - genomics - biomedical evaluation_page: resource/genomickb/genomickb_eval.html homepage_url: https://gkb.dcmb.med.umich.edu/ id: genomickb last_modified_date: '2025-08-12T00:00:00Z' layout: resource_detail license: id: https://available-inventions.umich.edu/product/genomickb-a-knowledgebase-for-the-human-genome#modal-licence-preview label: PolyForm Noncommercial License 1.0.0 name: GenomicKB products: - category: GraphicalInterface description: Graphical interface for GenomicKB id: genomickb.site name: GenomicKB Site original_source: - genomickb product_url: https://gkb.dcmb.med.umich.edu/search secondary_source: - genomickb - category: GraphProduct description: GenomicKB 1.0 Neo4j Database Dump (Requires license) dump_format: neo4j id: genomickb.graph name: GenomicKB Graph Dump original_source: - genomickb product_url: https://available-inventions.umich.edu/product/genomickb-a-knowledgebase-for-the-human-genome secondary_source: - genomickb - activity_status: active category: KnowledgeGraph creation_date: '2025-11-22T00:00:00Z' description: A knowledge graph integrating plant genomics, phenomics, and environmental data to predict gene expression patterns across multiple species under different environmental conditions, particularly drought stress domains: - genomics - environment - phenotype - systems biology - biological systems - biomedical evaluation_page: resource/genophenoenvo-kg/genophenoenvo-kg_eval_automated.html homepage_url: https://github.com/genophenoenvo/knowledge-graph id: genophenoenvo-kg last_modified_date: '2025-11-22T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/BSD-3-Clause label: BSD-3-Clause name: GenoPhenoEnvo Knowledge Graph products: - category: GraphProduct description: Merged knowledge graph data files containing over 400,000 nodes and 5,000,000 edges integrating gene expression, molecular interactions, functions, pathways, homology-based annotations, and environmental exposures from Planteome, EMBL-EBI Expression Atlas, and other sources. Available as tab-separated value files in KGX format with nodes and edges following the Biolink model. id: genophenoenvo-kg.data name: GenoPhenoEnvo KG Data original_source: - genophenoenvo-kg product_url: https://datacommons.cyverse.org/browse/iplant/home/shared/genophenoenvo - category: GraphicalInterface description: Interactive graph database visualization and query interface using Neo4j for exploring plant gene expression patterns, homologous genes, and environmental responses across multiple plant species including Arabidopsis thaliana, Populus trichocarpa, Zea mays, Sorghum bicolor, and Oryza sativa. id: genophenoenvo-kg.neo4j name: GenoPhenoEnvo KG Neo4j Visualization original_source: - genophenoenvo-kg product_url: https://github.com/genophenoenvo/knowledge-graph - category: ProcessProduct description: Python-based pipeline for downloading, transforming, and merging plant genomics and phenomics data into a standardized knowledge graph using KG-Hub tools, custom transformation scripts, and Biolink model annotations. Includes Cypher query utilities for graph exploration. id: genophenoenvo-kg.code name: GenoPhenoEnvo KG Construction Pipeline original_source: - genophenoenvo-kg product_url: https://github.com/genophenoenvo/knowledge-graph publications: - authors: - Anne E. Thessen - Laurel Cooper - Tyson L. Swetnam - Harshad Hegde - Justin Reese - Justin Elser - Pankaj Jaiswal doi: 10.3389/frai.2023.1201002 id: PMID:37384147 journal: Frontiers in Artificial Intelligence title: Using knowledge graphs to infer gene expression in plants year: '2023' taxon: - NCBITaxon:33090 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: hoganwr@gmail.com - contact_type: github value: hoganwr label: Bill Hogan orcid: 0000-0002-9881-1017 creation_date: '2025-09-29T00:00:00Z' description: An ontology of geographical entities domains: - environment homepage_url: https://github.com/ufbmi/geographical-entity-ontology/wiki id: geo last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Geographical Entity Ontology products: - category: OntologyProduct description: Geographical Entity Ontology in OWL format format: owl id: geo.owl name: geo.owl product_file_size: 17397 product_url: http://purl.obolibrary.org/obo/geo.owl - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz repository: https://github.com/ufbmi/geographical-entity-ontology - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: apadilla@lincolninst.edu label: Andrew Padilla creation_date: '2025-12-08T00:00:00Z' description: Geoconnex is an open, community-driven knowledge graph linking U.S. hydrologic features to enable seamless water data discovery, access, and collaborative monitoring. domains: - environment evaluation_page: resource/geoconnex/geoconnex_eval_automated.html homepage_url: https://docs.geoconnex.us/about/intro id: geoconnex last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: GEOCONNEX products: - category: ProgrammingInterface description: SPARQL endpoint for GEOCONNEX id: geoconnex.sparql name: GEOCONNEX SPARQL original_source: - geoconnex product_url: https://frink.apps.renci.org/geoconnex/sparql - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for geonames. This page was automatically generated because it was referenced by other resources. domains: - stub id: geonames last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Geonames products: - category: DataModelProduct description: Automatically generated stub product. Please update with accurate information. id: feature name: Feature (Stub) - category: Product description: geonames Nodes TSV format: tsv id: obo-db-ingest.geonames.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: geonames Nodes TSV original_source: - geonames product_file_size: 549884 product_url: https://w3id.org/biopragmatics/resources/geonames/geonames.tsv secondary_source: - obo-db-ingest - category: GraphProduct description: RDF dump of the Open Research Knowledge Graph distributed in N-Triples format. format: ntriples id: orkg.dump name: ORKG RDF Dump original_source: - orkg - wikidata - geonames - ncit - chebi - ncbitaxon - go - clo - omit - iao - uo - stato - obi product_file_size: 642902930 product_url: https://orkg.org/api/rdf/dump secondary_source: - orkg warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: DataModel contacts: - category: Organization contact_details: - contact_type: url value: http://www.sequenceontology.org/ id: sequence-ontology label: Sequence Ontology Consortium creation_date: '2025-09-04T00:00:00Z' description: GFF (General Feature Format) is a standard file format for describing genomic features including genes, transcripts, exons, and other sequence annotations, widely used in genome annotation and bioinformatics. domains: - genomics homepage_url: http://www.sequenceontology.org/gff3.shtml id: gff last_modified_date: '2026-01-05T00:00:00Z' layout: resource_detail name: GFF products: - category: DocumentationProduct description: GFF3 specification and documentation from Sequence Ontology format: http id: gff.specification is_public: true name: GFF3 Specification product_url: http://www.sequenceontology.org/gff3.shtml - category: OntologyProduct description: OWL release of Monochrom Ontology format: owl id: chr.model.owl name: Monochrom Ontology OWL release original_source: - ro - go - ncbitaxon - iao - geno - skos - gff product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl secondary_source: - chr synonyms: - GFF - General Feature Format - GFF3 - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: drjieliu@umich.edu label: Jie Liu creation_date: '2025-03-20T00:00:00Z' description: The Genomic Literature Knowledge Base (GLKB) is a comprehensive and powerful resource that integrates over 263 million biomedical terms and more than 14.6 million biomedical relationships. This collection is curated from 33 million PubMed abstracts and nine well-established biomedical repositories, offering an unparalleled wealth of knowledge for researchers and practitioners in the field. domains: - biological systems homepage_url: https://glkb.dcmb.med.umich.edu/ id: glkb last_modified_date: '2025-04-11T00:00:00Z' layout: resource_detail name: GLKB products: - category: GraphicalInterface description: Graphical interface for GLKB format: http id: glkb.site name: GLKB Site original_source: - glkb product_url: https://glkb.dcmb.med.umich.edu/ secondary_source: - glkb publications: - authors: - Huang Y - Han Z - Luo X - Luo X - Gao Y - Zhao M - Tang F - Wang Y - Chen J - Li C - Lu X - Jiao T - Qiu J - Deng F - Guan L - Shang H - Feng F - Vu THH - Bate T - Xue D - Cartailler J-P - Stitzel M - Chen S - Brissova M - Parker S - Liu J doi: 10.1101/2024.09.22.614323 id: doi:10.1101/2024.09.22.614323 title: Building a literature knowledge base towards transparent biomedical AI year: '2025' - activity_status: active category: KnowledgeGraph collection: - ber creation_date: '2025-09-14T00:00:00Z' description: Global Biotic Interactions (GloBI) integrates and normalizes species interaction datasets (e.g., predation, pollination, parasitism, mutualism, host-pathogen) from many primary sources to provide open, queryable access to organism-to-organism interaction records with taxonomic resolution and provenance. domains: - environment - biological systems - public health evaluation_page: resource/globi/globi_eval_automated.html homepage_url: https://www.globalbioticinteractions.org/ id: globi last_modified_date: '2025-12-15T17:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 (data) logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Global Biotic Interactions (GloBI) products: - category: GraphicalInterface description: Search and browse interface for interaction queries across integrated datasets format: http id: globi.portal name: GloBI Portal product_url: https://www.globalbioticinteractions.org/ - category: ProgrammingInterface description: REST-style API endpoints for programmatic species interaction queries (JSON/CSV) format: http id: globi.api name: GloBI API product_url: https://www.globalbioticinteractions.org/how-to - category: Product description: Bulk data export and dataset listing (downloads and dataset metadata) format: http id: globi.datasets name: GloBI Datasets product_url: https://www.globalbioticinteractions.org/datasets - category: Product compression: gzip description: Tab-separated integrated species interaction pairs (interpreted names) format: tsv id: globi.interactions.tsv name: GloBI interpreted interactions (TSV) product_file_size: 3044531169 product_url: https://zenodo.org/record/14640564/files/interactions.tsv.gz - category: Product compression: gzip description: Comma-separated integrated species interaction pairs (interpreted names) format: csv id: globi.interactions.csv name: GloBI interpreted interactions (CSV) product_url: https://zenodo.org/record/14640564/files/interactions.csv.gz warnings: - 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File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-01-06_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-12-22_ HTTP 429 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: gzip description: Tab-separated refuted species interaction pairs (interpreted names) format: tsv id: globi.refuted_interactions.tsv name: GloBI refuted interactions (TSV) product_file_size: 17546643 product_url: https://zenodo.org/record/14640564/files/refuted-interactions.tsv.gz - category: Product compression: gzip description: Comma-separated refuted species interaction pairs (interpreted names) format: csv id: globi.refuted_interactions.csv name: GloBI refuted interactions (CSV) product_url: https://zenodo.org/record/14640564/files/refuted-interactions.csv.gz warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-01-06_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-12-22_ HTTP 429 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: gzip description: Comma-separated refuted verbatim species interaction pairs (original names) format: csv id: globi.refuted_verbatim_interactions.csv name: GloBI refuted verbatim interactions (CSV) product_url: https://zenodo.org/record/14640564/files/refuted-verbatim-interactions.csv.gz warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-01-15_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-02_ HTTP 429 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: gzip description: RDF N-Quads representation of interaction data format: nquads id: globi.interactions.nq name: GloBI interactions RDF (N-Quads) product_file_size: 13113796760 product_url: https://zenodo.org/record/14640564/files/interactions.nq.gz - category: Product compression: zip description: Neo4j graph database backup (v3.5.x) of interaction graph format: neo4j id: globi.neo4j.graphdb name: GloBI Neo4j graph database snapshot product_file_size: 9059233137 product_url: https://zenodo.org/record/14640564/files/neo4j-graphdb.zip - category: Product compression: gzip description: Tab-separated dataset namespace index format: tsv id: globi.datasets.tsv name: GloBI datasets index (TSV) product_file_size: 4373 product_url: https://zenodo.org/record/14640564/files/datasets.tsv.gz - category: Product compression: gzip description: Comma-separated dataset namespace index format: csv id: globi.datasets.csv name: GloBI datasets index (CSV) product_url: https://zenodo.org/record/14640564/files/datasets.csv.gz warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-12-22_ HTTP 429 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: gzip description: Tab-separated taxonomic name mapping file format: tsv id: globi.taxon_map.tsv name: GloBI taxonomic name map product_file_size: 111241785 product_url: https://zenodo.org/record/14640564/files/taxonMap.tsv.gz - category: Product compression: gzip description: Tab-separated taxonomic hierarchy and identifier cache format: tsv id: globi.taxon_cache.tsv name: GloBI taxonomic hierarchy cache product_file_size: 310167049 product_url: https://zenodo.org/record/14640564/files/taxonCache.tsv.gz - category: Product compression: gzip description: Tab-separated data citations format: tsv id: globi.citations.tsv name: GloBI data citations (TSV) product_file_size: 40815688 product_url: https://zenodo.org/record/14640564/files/citations.tsv.gz - category: Product compression: gzip description: Comma-separated data citations format: csv id: globi.citations.csv name: GloBI data citations (CSV) product_url: https://zenodo.org/record/14640564/files/citations.csv.gz warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-02_ HTTP 429 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product compression: gzip description: Tab-separated refuted species interactions (original unresolved names) format: tsv id: globi.refuted_verbatim_interactions.tsv name: GloBI refuted verbatim interactions (TSV) product_file_size: 2467674 product_url: https://zenodo.org/record/14640564/files/refuted-verbatim-interactions.tsv.gz - category: Product description: Field (column) definitions JSON endpoint format: json id: globi.fields.json name: interactionFields.json product_url: https://api.globalbioticinteractions.org/interactionFields?type=json warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Field (column) definitions CSV endpoint format: csv id: globi.fields.csv name: interactionFields.csv product_file_size: 15860 product_url: https://api.globalbioticinteractions.org/interactionFields?type=csv - category: DocumentationProduct description: About and methodological documentation, contribution guidelines, and references format: http id: globi.docs name: GloBI Documentation product_url: https://www.globalbioticinteractions.org/about - category: Product description: Zenodo DOI badge pointing to latest archived release snapshot of integrated datasets format: http id: globi.release name: GloBI Archived Release (Zenodo) product_url: https://zenodo.org/badge/latestdoi/2478263 - category: Product compression: gzip description: Bee interaction data extracted from Global Biotic Interactions (September 2021 snapshot), including flower visitation, parasitic interactions, and other bee-related interactions from natural history collections, community science, and scientific literature format: tsv id: globi.bee.interactions name: Bee Interaction Data from Global Biotic Interactions product_url: https://zenodo.org/records/7753956 - category: GraphProduct description: Graph version of the Earth Metabolome Initiative Ontology format: kgx id: emikg.kg name: EMI Knowledge Graph original_source: - emi - pf1600 - globi - try product_url: https://doi.org/10.5281/zenodo.17079767 repository: https://github.com/earth-metabolome-initiative/metrin-kg warnings: - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - category: ProgrammingInterface description: SPARQL endpoint for programmatic access to the EMI Knowledge Graph format: http id: emikg.sparql name: EMI KG SPARQL Endpoint original_source: - emi - pf1600 - globi - try product_url: https://qlever.earthmetabolome.org/api/metrin-kg - category: GraphicalInterface description: Web-based SPARQL query editor for the EMI Knowledge Graph id: emikg.web name: EMI KG SPARQL Query Editor original_source: - emi - pf1600 - globi - try product_url: https://sib-swiss.github.io/sparql-editor/emi publications: - doi: 10.1016/j.ecoinf.2014.08.005 id: doi:10.1016/j.ecoinf.2014.08.005 journal: Ecological Informatics title: 'Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets' year: '2014' taxon: - NCBITaxon:2759 - NCBITaxon:33208 - activity_status: active category: Ontology contacts: - category: Individual contact_details: - contact_type: github value: yamadaissaku - contact_type: email value: issaku@noguchi.or.jp label: Issaku Yamada - category: Individual contact_details: - contact_type: email value: m.campbell@griffith.edu.au label: Matthew P Campbell - category: Individual contact_details: - contact_type: email value: kkiyoko@soka.ac.jp label: Kiyoko F Aoki-Kinoshita creation_date: '2025-10-29T00:00:00Z' description: The Glycoconjugate Ontology (GlycoCoO) is a standard semantic framework for describing and representing glycoproteomics and glycolipidomics data in RDF format. It provides a formal representation of glycoconjugate structures (glycoproteins and glycolipids), their associated metadata including publication information, biological source data, experimental evidence, and abundance ratios. GlycoCoO extends GlycoRDF by creating subclasses of ReferencedCompound including ReferencedGlycoconjugate, ReferencedProtein, and ReferencedLipid, enabling comprehensive annotation of glycan structures attached to proteins and lipids with contextual information such as glycosylation sites, disease associations, tissue and cell line sources, and analytical methods. The ontology supports both complete structural information and compositional data, can represent single glycans or glycoform mixtures at specific sites, and accommodates partially missing site information when no mapping is performed. It has been adopted by major glycoproteomics databases including UniCarbKB, GlyConnect, and GlycoNAVI, enabling federated queries across resources to retrieve integrated information about glycoconjugates from multiple publications and experimental contexts. domains: - chemistry and biochemistry - biological systems - biomedical homepage_url: https://github.com/glycoinfo/GlycoCoO id: glycocoo last_modified_date: '2025-10-29T00:00:00Z' layout: resource_detail name: GlycoConjugate Ontology (GlycoCoO) products: - category: OntologyProduct description: The GlycoCoO OWL ontology file defining classes and predicates for glycoconjugate structures and their metadata format: owl id: glycocoo.ontology name: GlycoCoO OWL Ontology product_file_size: 5642 product_url: https://github.com/glycoinfo/GlycoCoO/blob/master/ontology/glycocoo.owl - category: DocumentationProduct description: GitHub Wiki with developer information, database providers, and prefix documentation format: http id: glycocoo.wiki name: GlycoCoO Wiki Documentation product_url: https://github.com/glycoinfo/GlycoCoO/wiki - category: Product description: Sample RDF data files demonstrating GlycoCoO usage with examples from UniCarbKB, GlyConnect, and GlycoNAVI format: http id: glycocoo.rdf-samples name: GlycoCoO RDF Sample Data product_url: https://github.com/glycoinfo/GlycoCoO/tree/master/RDF_Sample - category: Product description: Example SPARQL queries for querying glycoconjugate data across federated endpoints format: http id: glycocoo.sparql-examples name: GlycoCoO SPARQL Query Examples product_file_size: 2467 product_url: https://github.com/glycoinfo/GlycoCoO/blob/master/SPARQL_Query.md - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg publications: - authors: - Issaku Yamada - Matthew P Campbell - Nathan Edwards - Leyla Jael Castro - Frederique Lisacek - Julien Mariethoz - Tamiko Ono - Rene Ranzinger - Daisuke Shinmachi - Kiyoko F Aoki-Kinoshita category: Publication id: https://doi.org/10.1093/glycob/cwab013 journal: Glycobiology preferred: true title: The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application year: '2021' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: glyconnect@sib.swiss - contact_type: url value: https://glyconnect.expasy.org/ id: sib label: GlyConnect Team - SIB Swiss Institute of Bioinformatics creation_date: '2025-05-07T00:00:00Z' description: GlyConnect is a knowledgebase of glycoproteins spanning protein, glycosite and glycan information, with data on various species, tissues, and disease associations. domains: - biological systems - chemistry and biochemistry homepage_url: https://glyconnect.expasy.org/ id: glyconnect last_modified_date: '2025-12-07T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: GlyConnect products: - category: GraphicalInterface description: Web interface for exploring GlyConnect data id: glyconnect.site is_public: true name: GlyConnect Web Interface original_source: - glyconnect product_url: https://glyconnect.expasy.org/ secondary_source: - glyconnect - category: ProgrammingInterface description: RESTful API for accessing GlyConnect data id: glyconnect.api.rest is_public: true name: GlyConnect RESTful API original_source: - glyconnect product_url: https://glyconnect.expasy.org/api secondary_source: - glyconnect - category: ProgrammingInterface description: SPARQL endpoint for querying GlyConnect RDF data id: glyconnect.api.sparql is_public: true name: GlyConnect SPARQL Endpoint original_source: - glyconnect product_url: https://glyconnect.expasy.org/rdf secondary_source: - glyconnect - category: Product description: Compositions dataset containing glycan compositions format: csv id: glyconnect.compositions name: GlyConnect Glycan Compositions original_source: - glyconnect product_url: https://glyconnect.expasy.org/downloads/compositions/ secondary_source: - glyconnect - category: Product description: Immunoglobulins dataset containing glycans commonly found on immunoglobulins format: csv id: glyconnect.immunoglobulins name: GlyConnect Immunoglobulins Dataset original_source: - glyconnect product_url: https://glyconnect.expasy.org/downloads/Immunoglobulins/ secondary_source: - glyconnect publications: - authors: - Alocci D - Mariethoz J - Gastaldello A - Gasteiger E - Karlsson NG - Kolarich D - Packer NH - Lisacek F doi: doi:10.1021/acs.jproteome.8b00766 id: doi:10.1021/acs.jproteome.8b00766 title: 'GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical' year: '2019' - activity_status: active category: Ontology contacts: - category: Individual contact_details: - contact_type: email value: rene@ccrc.uga.edu label: Rene Ranzinger - category: Individual contact_details: - contact_type: email value: kkiyoko@soka.ac.jp label: Kiyoko F. Aoki-Kinoshita creation_date: '2025-10-29T00:00:00Z' curators: - category: Individual contact_details: - contact_type: github value: ReneRanzinger label: Rene Ranzinger - category: Individual contact_details: - contact_type: email value: kkiyoko@soka.ac.jp label: Kiyoko F. Aoki-Kinoshita description: 'GlycoRDF is a standardized ontology for representing glycomics data in Resource Description Framework (RDF) format. It provides a common machine-readable interface for glycomics databases, enabling integration and cross-referencing of glycan structures, biological source information, publications, and experimental data. Developed by an international consortium of glycomics bioinformatics experts, GlycoRDF defines classes and predicates for diverse glycomics data types including glycan sequences, monosaccharide compositions, biological sources, literature references, NMR data, mass spectrometry data, and liquid chromatography-mass spectrometry data. The ontology reuses concepts from established ontologies including UniProt Core, Bibliographic Ontology, Dublin Core Metadata Initiative, and HUPO-PSI Mass Spectrometry Ontology. GlycoRDF has been adopted by major glycomics database providers including CSDB, MonosaccharideDB, GlycomeDB, UniCarbKB, GlycoEpitope, GlycoNAVI, and GlycoProtDB, facilitating semantic web applications and SPARQL queries across heterogeneous glycomics data sources. ' domains: - chemistry and biochemistry - biological systems - biomedical homepage_url: http://www.glycoinfo.org/GlycoRDF/ id: glycordf last_modified_date: '2025-10-29T00:00:00Z' layout: resource_detail name: 'GlycoRDF: An Ontology to Standardize Glycomics Data in RDF' products: - category: OntologyProduct description: OWL ontology file defining the GlycoRDF standard for representing glycomics data in RDF format format: owl id: glycordf.ontology name: GlycoRDF Ontology (OWL) product_file_size: 32914 product_url: https://github.com/ReneRanzinger/GlycoRDF/blob/master/ontology/glycan.owl - category: GraphicalInterface description: NCBO BioPortal entry for browsing and exploring the GlycoRDF ontology format: http id: glycordf.bioportal name: GlycoRDF BioPortal Entry product_url: https://bioportal.bioontology.org/ontologies/GLYCORDF - category: DocumentationProduct description: Comprehensive documentation of the GlycoRDF ontology classes, predicates, and usage examples format: doc id: glycordf.documentation name: GlycoRDF Documentation product_file_size: 62492 product_url: https://github.com/ReneRanzinger/GlycoRDF/blob/master/ontology/documentation.docx - category: GraphicalInterface description: Official project homepage with overview, documentation, and links to database implementations format: http id: glycordf.homepage name: GlycoRDF Project Homepage product_url: http://www.glycoinfo.org/GlycoRDF/ - category: GraphicalInterface description: GitHub repository containing ontology files, documentation, and source code for RDF generation format: http id: glycordf.github name: GlycoRDF GitHub Repository product_url: https://github.com/glycoinfo/GlycoRDF - category: DocumentationProduct description: Wiki with developer information, database provider documentation, and implementation guidelines format: http id: glycordf.wiki name: GlycoRDF Wiki product_url: https://github.com/ReneRanzinger/GlycoRDF/wiki - category: ProcessProduct description: Java source code for generating GlycoRDF data from glycomics databases format: java id: glycordf.java-source name: GlycoRDF Java Source Code repository: https://github.com/glycoinfo/GlycoRDF - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg publications: - authors: - Rene Ranzinger - Kiyoko F. Aoki-Kinoshita - Matthew P. Campbell - Shin Kawano - Thomas Lütteke - Shujiro Okuda - Daisuke Shinmachi - Toshihide Shikanai - Hiromichi Sawaki - Philip Toukach category: Publication id: https://doi.org/10.1093/bioinformatics/btu732 journal: Bioinformatics preferred: true title: 'GlycoRDF: an ontology to standardize glycomics data in RDF' year: '2015' - authors: - Kiyoko F. Aoki-Kinoshita category: Publication id: https://doi.org/10.1186/2041-1480-4-39 journal: Journal of Biomedical Semantics preferred: false title: Introducing glycomics data into the Semantic Web year: '2013' repository: https://github.com/glycoinfo/GlycoRDF tags: - biopragmatics - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://glygen.org/contact-us/ label: GlyGen Team creation_date: '2025-05-04T00:00:00Z' description: GlyGen is an integrated, data-driven resource for glycoproteins, glycans, and carbohydrate-active enzymes, providing researchers with comprehensive, high-quality data on glycobiology. domains: - chemistry and biochemistry - biological systems homepage_url: https://glygen.org/ id: glygen last_modified_date: '2025-08-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: GlyGen products: - category: GraphicalInterface description: Web interface for exploring GlyGen data id: glygen.site is_public: true name: GlyGen Website original_source: - glygen product_url: https://glygen.org/ secondary_source: - glygen - category: ProgrammingInterface description: RESTful API for accessing GlyGen data id: glygen.api is_public: true name: GlyGen API original_source: - glygen product_url: https://api.glygen.org/ secondary_source: - glygen - category: GraphicalInterface description: Interface for searching GlyGen protein and glycan data format: csv id: glygen.data.site name: GlyGen Data Downloads original_source: - glygen product_url: https://data.glygen.org/ secondary_source: - glygen - category: GraphProduct compression: zip description: Nodes from GlyGen Biomarker Database format: csv id: biomarkerkg.nodes.biomarker name: BKG Biomarker Nodes original_source: - glygen product_file_size: 1252064 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Biomarker.nodes.zip secondary_source: - biomarkerkg publications: - authors: - Kahsay R - Vora J - Navelkar R - Mousavi R - Bittremieux W - Bakker H - Moremen K - Ten F - Abrahams D - Campbell M - Glushka J - Ranzinger R - York W - Haslam S - Dell A - Packer N - Bourne P - Azadi P - Aoki-Kinoshita K - Lisacek F - Tiemeyer M - Neelamegham S doi: doi:10.1093/glycob/cwaa085 id: doi:10.1093/glycob/cwaa085 preferred: true title: GlyGen - Computational and informatics resources for glycoscience year: '2020' repository: https://github.com/glygener/glygen-backend-api - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: github value: jakelever - contact_type: url value: https://github.com/jakelever/GNBR label: GNBR creation_date: '2025-08-12T00:00:00Z' description: The Global Network of Biomedical Relationships (GNBR) is a large-scale biomedical knowledge graph derived from literature. GNBR uses text mining of PubMed abstracts to extract typed relationships between genes, diseases and drugs/chemicals, organizing them into semantic themes suitable for link prediction and downstream applications such as drug repurposing. GNBR has been widely used as a text-derived KG resource and is available via GitHub and Zenodo. domains: - biomedical - literature - health evaluation_page: resource/gnbr/gnbr_eval.html homepage_url: https://github.com/jakelever/GNBR id: gnbr infores_id: gnbr last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail name: GNBR products: - category: GraphProduct description: Text-mined biomedical knowledge graph of gene–disease–drug relationships (semantic themes) id: gnbr.graph name: GNBR graph original_source: - pubtator product_url: https://zenodo.org/records/3459420 secondary_source: - gnbr - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg publications: - authors: - Percha B - Altman RB doi: 10.1093/bioinformatics/bty114 id: doi:10.1093/bioinformatics/bty114 journal: Bioinformatics title: A global network of biomedical relationships derived from text year: '2018' repository: https://github.com/jakelever/GNBR taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: nje5@georgetown.edu - contact_type: github value: edwardsnj label: Nathan Edwards orcid: 0000-0001-5168-3196 creation_date: '2025-09-29T00:00:00Z' description: GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels. domains: - chemistry and biochemistry homepage_url: https://gnome.glyomics.org/ id: gno last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Glycan Naming and Subsumption Ontology (GNOme) products: - category: OntologyProduct description: Glycan Naming and Subsumption Ontology, OWL format (primary) format: owl id: gno.owl name: gno.owl product_file_size: 214324748 product_url: http://purl.obolibrary.org/obo/gno.owl - category: OntologyProduct description: Glycan Naming and Subsumption Ontology, OBO format (automated conversion from OWL) format: obo id: gno.obo name: gno.obo product_file_size: 135112461 product_url: http://purl.obolibrary.org/obo/gno.obo - category: OntologyProduct description: Glycan Naming and Subsumption Ontology, JSON format (automated conversion from OWL) format: json id: gno.json name: gno.json product_file_size: 358051529 product_url: http://purl.obolibrary.org/obo/gno.json repository: https://github.com/glygen-glycan-data/GNOme - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: suzia@stanford.edu - contact_type: github value: suzialeksander label: Suzi Aleksander orcid: 0000-0001-6787-2901 creation_date: '2025-03-16T00:00:00Z' description: An ontology for describing the function of genes and gene products domains: - biological systems homepage_url: http://geneontology.org/ id: go last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Gene Ontology products: - category: OntologyProduct description: The main ontology in OWL. This is self contained and does not have connections to other OBO ontologies format: owl id: go.owl name: GO (OWL edition) product_file_size: 129057533 product_url: http://purl.obolibrary.org/obo/go.owl - category: OntologyProduct description: Equivalent to go.owl, in obo format format: obo id: go.obo name: GO (OBO Format edition) product_file_size: 36289217 product_url: http://purl.obolibrary.org/obo/go.obo - category: OntologyProduct description: Equivalent to go.owl, in obograph json format format: json id: go.json name: GO (JSON edition) product_url: http://purl.obolibrary.org/obo/go.json warnings: - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: OntologyProduct description: The main ontology plus axioms connecting to select external ontologies, with subsets of those ontologies format: owl id: go.extensions.go-plus.owl name: GO-Plus product_file_size: 235714202 product_url: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl - category: OntologyProduct description: The main ontology plus axioms connecting to select external ontologies, excluding the external ontologies themselves format: owl id: go.go-base.owl name: GO Base Module product_file_size: 160299649 product_url: http://purl.obolibrary.org/obo/go/go-base.owl - category: OntologyProduct description: As go-plus.owl, in obographs json format format: json id: go.extensions.go-plus.json name: GO-Plus product_url: http://purl.obolibrary.org/obo/go/extensions/go-plus.json warnings: - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: OntologyProduct description: Basic version of the GO, filtered such that the graph is guaranteed to be acyclic and annotations can be propagated up the graph. The relations included are is a, part of, regulates, negatively regulates and positively regulates. This version excludes relationships that cross the 3 GO hierarchies. format: obo id: go.go-basic.obo name: GO-Basic, Filtered, for use with legacy tools product_file_size: 31933366 product_url: http://purl.obolibrary.org/obo/go/go-basic.obo - category: OntologyProduct description: As go-basic.obo, in json format format: json id: go.go-basic.json name: GO-Basic, Filtered, for use with legacy tools (JSON) product_url: http://purl.obolibrary.org/obo/go/go-basic.json warnings: - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: OntologyProduct description: Classes added to ncbitaxon for groupings such as prokaryotes format: owl id: go.extensions.go-taxon-groupings.owl name: GO Taxon Groupings product_url: http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: OntologyProduct description: Equivalent to go.owl, but released daily. Note the snapshot release is not archived. format: owl id: go.snapshot.go.owl name: GO (OWL edition), daily snapshot release product_file_size: 129414878 product_url: http://purl.obolibrary.org/obo/go/snapshot/go.owl - category: OntologyProduct description: Equivalent to go.owl, but released daily. Note the snapshot release is not archived. format: obo id: go.snapshot.go.obo name: GO (OBO Format edition), daily snapshot release product_file_size: 36415389 product_url: http://purl.obolibrary.org/obo/go/snapshot/go.obo - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: KGX Distribution of KG-Monarch edge_count: 15356321 format: kgx id: kg-monarch.graph name: KGX Distribution of KG-Monarch node_categories: - 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biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - 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biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - 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chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - 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intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - 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category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: OntologyProduct description: OWL release of Monochrom Ontology format: owl id: chr.model.owl name: Monochrom Ontology OWL release original_source: - ro - go - ncbitaxon - iao - geno - skos - gff product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl secondary_source: - chr - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' - category: Product description: Gene ontology annotations from the Gene Ontology Consortium format: http id: genecards.gene.ontology name: GeneCards Gene Ontology Annotations original_source: - go product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphicalInterface description: Browser for searching and viewing Gene Ontology terms and GOA annotations format: http id: goa.quickgo name: QuickGO Browser original_source: - go product_url: https://www.ebi.ac.uk/QuickGO/ - category: Product description: FTP site containing current and archived GOA annotation files for all species format: http id: goa.ftp name: GOA FTP Site original_source: - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/' - category: Product description: GO annotations for all UniProtKB entries format: txt id: goa.uniprot name: UniProt GOA Annotations original_source: - uniprot - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/' - category: Product description: GO annotations for human proteins format: txt id: goa.human name: Human GOA Annotations original_source: - uniprot - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/' - category: Product description: GO annotations for mouse proteins format: txt id: goa.mouse name: Mouse GOA Annotations original_source: - uniprot - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/' - File was not able to be retrieved when checked on 2025-12-04_ FTP error_ [Errno 104] Connection reset by peer - category: MappingProduct description: Files containing transitive assignments of InterPro matches, UniProtKB keywords, subcellular locations, EC numbers, or HAMAP matches to manually-selected GO terms format: txt id: goa.mapping-files name: GO Mapping Files original_source: - interpro - uniprot - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/' - category: Product description: GO annotations for PDB entries format: txt id: goa.pdb name: PDB GOA Annotations original_source: - pdbe - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/' - category: Product description: GO annotations organized by proteomes format: txt id: goa.proteomes name: Proteomes GOA Annotations original_source: - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/' - File was not able to be retrieved when checked on 2025-12-04_ FTP error_ [Errno 104] Connection reset by peer - category: GraphProduct description: ProteomeHD data files id: proteomehd.data name: ProteomeHD Data original_source: - proteomehd - uniprot - reactome - intact - go - goa product_url: https://github.com/Rappsilber-Laboratory/ProteomeHD/tree/master/Data - category: MappingProduct description: Mappings between InterPro entries and Gene Ontology (GO) terms format: tsv id: interpro.interpro2go name: InterPro to GO Mappings original_source: - go - interpro product_file_size: 3088718 product_url: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro2go secondary_source: - interpro - category: MappingProduct compression: gzip description: Gene to Gene Ontology mapping data providing functional annotations for genes format: tsv id: ncbigene.gene2go name: Gene to GO Mapping original_source: - go - ncbigene product_file_size: 1223833668 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz - category: GraphProduct description: RDF dump of the Open Research Knowledge Graph distributed in N-Triples format. format: ntriples id: orkg.dump name: ORKG RDF Dump original_source: - orkg - wikidata - geonames - ncit - chebi - ncbitaxon - go - clo - omit - iao - uo - stato - obi product_file_size: 642902930 product_url: https://orkg.org/api/rdf/dump secondary_source: - orkg - category: Product description: TSV export of SwissLipids links to Gene Ontology terms with taxon context. format: tsv id: swisslipid.go name: SwissLipids GO Annotations original_source: - swisslipid - go product_file_size: 48388 product_url: https://www.swisslipids.org/api/file.php?cas=download_files&file=go.tsv - category: GraphProduct description: UniBioMap Gene Ontology entity descriptions. format: json id: unibiomap.go_desc name: UniBioMap GO Descriptions original_source: - go product_url: https://aideepmed.com/UniBioMap/database/unibiomap/go_desc.json secondary_source: - unibiomap warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' repository: https://github.com/geneontology/go-ontology taxon: - NCBITaxon:1 - activity_status: active category: DataModel contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Christopher J. Mungall orcid: 0000-0002-6601-2165 - category: Organization contact_details: - contact_type: url value: http://geneontology.org/ - contact_type: email value: go-helpdesk@geneontology.org label: Gene Ontology Consortium creation_date: '2025-03-09T00:00:00Z' description: A structured framework for integrating Gene Ontology annotations into computable models of biological functions. domains: - biological systems - genomics - pathways - proteomics homepage_url: http://geneontology.org/go-cam/docs id: go-cam infores_id: go-cam last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Gene Ontology Causal Activity Modeling (GO-CAM) products: - category: GraphicalInterface description: Web-based tool for collaborative editing of Gene Ontology Causal Activity Models (GO-CAMs) format: http id: go-cam.noctua name: Noctua original_source: - go-cam product_url: https://noctua.geneontology.org/ - category: GraphicalInterface description: Web interface for browsing, searching, and exploring GO-CAM models format: http id: go-cam.browser name: GO-CAM Browser original_source: - go-cam product_url: http://geneontology.org/go-cam - category: DataModelProduct description: RDF-based format for representing causal activity models in Gene Ontology format: rdfxml id: go-cam.model name: GO-CAM Model Format original_source: - go-cam product_url: https://github.com/geneontology/go-cam warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: ProgrammingInterface connection_url: http://api.geneontology.org/api/ description: Programmatic access to GO-CAM models through the Gene Ontology API id: go-cam.api is_public: true name: GO-CAM API original_source: - go-cam product_url: http://api.geneontology.org/api/ - category: ProcessProduct description: Server-side component for storing, validating, and reasoning over GO-CAM models id: go-cam.minerva name: Minerva original_source: - go-cam product_url: https://github.com/geneontology/minerva - category: GraphProduct description: KGX graph package for GO-CAM models (build go_cam_2025-10-10_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.go_cam.graph name: Translator GO-CAM KGX Graph original_source: - go-cam product_url: https://stars.renci.org/var/translator/releases/go_cam/2025_12_15/ secondary_source: - translator publications: - authors: - Paul D Thomas - David P Hill - Huaiyu Mi - David Osumi-Sutherland - Kimberly Van Auken - Seth Carbon - James P Balhoff - Laurent-Philippe Albou - Benjamin Good - Pascale Gaudet - Suzanna E Lewis - Christopher J Mungall doi: 10.1038/s41588-019-0500-1 id: doi:10.1038/s41588-019-0500-1 preferred: true title: Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems year: '2019' repository: https://github.com/geneontology/noctua - activity_status: active category: DataModel collection: - translator - ber contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-03-09T00:00:00Z' description: Translation of JGI GOLD (Genomes OnLine Database) ecosystem classification paths to OWL, plus mappings to MIxS and environment ontologies like ENVO. domains: - environment - microbiology - genomics - biological systems homepage_url: https://gold.jgi.doe.gov/ id: goldterms last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://github.com/cmungall/gold-ontology/blob/main/LICENSE label: BSD 3-Clause License name: GOLD Environmental Paths products: - category: DataModelProduct format: owl id: goldterms.data.owl name: Main GOLDTERMS OWL release original_source: - goldterms product_url: https://w3id.org/goldterms/goldterms.owl secondary_source: - goldterms warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-09-11_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphicalInterface format: owl id: goldterms.bioportal name: GOLDTERMS on BioPortal original_source: - goldterms product_url: https://bioportal.bioontology.org/ontologies/GOLDTERMS secondary_source: - goldterms - category: DataModelProduct format: yaml id: goldterms.definitions.yaml name: GOLD definitions in YAML format original_source: - goldterms product_file_size: 27808 product_url: https://github.com/cmungall/gold-ontology/blob/main/gold_definitions.yaml secondary_source: - goldterms - category: Product description: Trait data table listing all 140+ harmonized traits available in metaTraits, mapped to standardized ontologies. id: metatraits.traits name: metaTraits Trait List original_source: - bacdive - bv-brc - goldterms - progenomes product_url: https://metatraits.embl.de/traits repository: https://github.com/cmungall/gold-ontology tags: - biopragmatics - core - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: rxx@case.edu label: Rong Xu creation_date: '2025-03-09T00:00:00Z' description: A knowledge graph for drug repurposing domains: - health evaluation_page: resource/gp-kg/gp-kg_eval_automated.html homepage_url: http://nlp.case.edu/public/data/GPKG-Predict/ id: gp-kg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: GP-KG products: - category: GraphProduct description: GP_KG.txt edge_count: 1246726 id: gp-kg.graph name: GP-KG node_count: 61146 original_source: - gp-kg product_file_size: 48397035 product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt secondary_source: - gp-kg - category: ProcessProduct description: A computational framework for drug repurposing, used with GP-KG id: gp-kg.process.kg-predict name: KG-Predict original_source: - gp-kg product_url: http://nlp.case.edu/public/data/GPKG-Predict/code/ secondary_source: - gp-kg publications: - authors: - Gao Z - Ding P - Xu R doi: doi:10.1016/j.jbi.2022.104133 id: doi:10.1016/j.jbi.2022.104133 title: 'KG-Predict: A knowledge graph computational framework for drug repurposing' year: '2022' repository: http://nlp.case.edu/public/data/GPKG-Predict/ - activity_status: active category: DataSource collection: - ber contacts: - category: Individual contact_details: - contact_type: email value: damcdonald@ucsd.edu label: Daniel McDonald - category: Organization contact_details: - contact_type: url value: https://greengenes2.ucsd.edu/ label: University of California San Diego creation_date: '2025-09-09T00:00:00Z' description: Greengenes2 is a comprehensive reference database and phylogenetic tree for 16S rRNA gene sequences that unifies microbial data from multiple sources into a single coherent framework. It provides standardized taxonomic assignments and phylogenetic placement for microbiome research and enables consistent analysis across different studies and sequencing platforms. domains: - biomedical - microbiome - microbiology - organisms homepage_url: https://greengenes2.ucsd.edu/ id: greengenes last_modified_date: '2025-09-24T00:00:00Z' layout: resource_detail name: Greengenes2 products: - category: GraphicalInterface description: Web-based search interface for querying Greengenes2 database by species, ASV sequences, or clade names format: http id: greengenes.portal name: Greengenes2 Web Portal product_url: https://greengenes2.ucsd.edu/ - category: Product description: FTP archive containing Greengenes2 database files including phylogenetic trees, taxonomy, and sequence data format: http id: greengenes.ftp name: Greengenes2 FTP Archive product_url: http://ftp.microbio.me/greengenes_release/current/ - category: Product description: Reference phylogenetic tree in Newick format containing unified microbial phylogeny format: txt id: greengenes.phylogeny name: Greengenes2 Phylogenetic Tree product_url: http://ftp.microbio.me/greengenes_release/current/ - category: Product description: 16S rRNA gene sequences in FASTA format for all organisms in the database format: fasta id: greengenes.sequences name: Greengenes2 Sequences product_url: http://ftp.microbio.me/greengenes_release/current/ - category: Product description: Taxonomic assignments and metadata for all sequences in the database format: tsv id: greengenes.taxonomy name: Greengenes2 Taxonomy product_url: http://ftp.microbio.me/greengenes_release/current/ - category: ProcessProduct description: QIIME 2 plugin for integrating Greengenes2 data into microbiome analysis workflows format: python id: greengenes.qiime2-plugin name: q2-greengenes2 Plugin product_url: https://github.com/biocore/q2-greengenes2/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - McDonald D - Jiang Y - Balaban M - Cantrell K - Zhu Q - Gonzalez A - Morton JT - Nicolaou G - Parks DH - Karst SM - Albertsen M - Hugenholtz P - Keller A - Knight R id: doi:10.1038/s41587-023-01845-1 journal: Nature Biotechnology preferred: true title: Greengenes2 unifies microbial data in a single reference tree year: '2024' repository: https://github.com/biocore/greengenes2/ taxon: - NCBITaxon:2 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: kronkcj@mail.uc.edu - contact_type: github value: Superraptor label: Clair Kronk orcid: 0000-0001-8397-8810 creation_date: '2025-09-29T00:00:00Z' description: The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences. domains: - biological systems homepage_url: https://gsso.research.cchmc.org/ id: gsso last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://www.apache.org/licenses/LICENSE-2.0 label: Apache 2.0 License name: Gender, Sex, and Sexual Orientation (GSSO) ontology products: - category: OntologyProduct description: Gender, Sex, and Sexual Orientation (GSSO) ontology in OWL format format: owl id: gsso.owl name: gsso.owl product_file_size: 2201424 product_url: http://purl.obolibrary.org/obo/gsso.owl - category: OntologyProduct description: Gender, Sex, and Sexual Orientation (GSSO) ontology in OBO format format: obo id: gsso.obo name: gsso.obo product_file_size: 969731 product_url: http://purl.obolibrary.org/obo/gsso.obo - category: OntologyProduct description: Gender, Sex, and Sexual Orientation (GSSO) ontology in JSON format format: json id: gsso.json name: gsso.json product_file_size: 1894658 product_url: http://purl.obolibrary.org/obo/gsso.json repository: https://github.com/Superraptor/GSSO - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for gtdb. This page was automatically generated because it was referenced by other resources. domains: - stub id: gtdb last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Gtdb products: - category: Product compression: gzip description: gtdb Nodes TSV format: tsv id: obo-db-ingest.gtdb.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: gtdb Nodes TSV original_source: - gtdb product_file_size: 2918783 product_url: https://w3id.org/biopragmatics/resources/gtdb/gtdb.tsv.gz secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: gtex-help@broadinstitute.org - contact_type: url value: https://www.gtexportal.org/home/contact label: GTEx Consortium creation_date: '2025-06-04T00:00:00Z' description: The Genotype-Tissue Expression (GTEx) project provides a comprehensive resource to study tissue-specific gene expression and regulation. Samples were collected from 54 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. domains: - genomics - biomedical - anatomy and development homepage_url: https://www.gtexportal.org/home/ id: gtex infores_id: gtex last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: GTEx products: - category: GraphicalInterface description: GTEx Portal web interface for exploring tissue-specific gene expression data, eQTLs, and other genomic analyses format: http id: gtex.portal name: GTEx Portal original_source: - gtex product_url: https://www.gtexportal.org/home/ - category: Product description: Complete GTEx v8 data including gene expression, transcript expression, exon expression, and junction data across tissues format: tsv id: gtex.bulk-data name: GTEx Bulk Data Downloads original_source: - gtex product_url: https://www.gtexportal.org/home/downloads/adult-gtex - category: Product description: eQTL (expression quantitative trait loci) data linking genetic variants to gene expression across tissues format: tsv id: gtex.eqtl-data name: GTEx eQTL Data original_source: - gtex product_url: https://www.gtexportal.org/home/downloads/adult-gtex/qtl - category: ProgrammingInterface description: GTEx REST API for programmatic access to gene expression and eQTL data format: json id: gtex.api name: GTEx REST API original_source: - gtex product_url: https://gtexportal.org/rest/ - category: Product description: Individual-level genotype and phenotype data available through dbGaP format: vcf id: gtex.dbgap-data name: GTEx dbGaP Data original_source: - gtex product_url: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000424 - category: GraphProduct description: GTEx Automat format: kgx-jsonl id: automat.gtex infores_id: automat-gtex name: gtex_automat original_source: - gtex product_url: https://stars.renci.org/var/plater/bl-4.2.1/GTEx_Automat/a6448b9092bb81a1/ secondary_source: - automat - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb - category: Product description: Gene expression data aggregated from GTEx, BioGPS, Bgee and other expression databases format: http id: genecards.expression.data name: GeneCards Expression Data original_source: - gtex - biogps - bgee product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' publications: - authors: - GTEx Consortium doi: 10.1126/science.aaz1776 id: doi:10.1126/science.aaz1776 title: The GTEx Consortium atlas of genetic regulatory effects across human tissues year: '2020' - authors: - GTEx Consortium doi: 10.1126/science.1262110 id: doi:10.1126/science.1262110 title: 'The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans' year: '2015' repository: https://github.com/broadinstitute/gtex-pipeline taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: enquiries@guidetopharmacology.org label: Guide to Pharmacology Help Desk - category: Individual contact_details: - contact_type: email value: jamie.davies@ed.ac.uk label: Jamie Davies creation_date: '2025-05-30T00:00:00Z' description: The IUPHAR/BPS Guide to PHARMACOLOGY is an expert-curated resource providing quantitative information on drug targets and the substances that act on them, including approved drugs and experimental therapeutics domains: - pharmacology - health - biomedical - drug discovery - translational homepage_url: https://www.guidetopharmacology.org id: gtopdb infores_id: gtopdb last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 logo: https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png name: Guide to Pharmacology products: - category: GraphicalInterface description: A web-based interface for accessing and browsing drug target data, ligand information, and pharmacological interactions id: gtopdb.web name: Guide to Pharmacology Web Interface product_url: https://www.guidetopharmacology.org - category: ProgrammingInterface description: RESTful web services enabling computational access to most of the GtoPdb data in JSON format id: gtopdb.api.rest name: Guide to Pharmacology REST API product_url: https://www.guidetopharmacology.org/webServices.jsp - category: Product description: Complete list of drug targets and their families with detailed information format: csv id: gtopdb.targets.csv name: GtoPdb Targets and Families product_url: https://www.guidetopharmacology.org/DATA/targets_and_families.csv warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-08-14_ HTTP 503 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Complete list of ligands including drugs, small molecules, and other bioactive compounds format: csv id: gtopdb.ligands.csv name: GtoPdb Ligands Dataset product_url: https://www.guidetopharmacology.org/DATA/ligands.csv warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-08-14_ HTTP 503 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Comprehensive dataset of all interactions between ligands and targets format: csv id: gtopdb.interactions.csv name: GtoPdb Interactions Dataset product_url: https://www.guidetopharmacology.org/DATA/interactions.csv warnings: - 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category: Product description: SDF file containing chemical structures with SMILES for all ligands in the database format: sdf id: gtopdb.download.sdf name: GtoPdb Ligand SDF File product_url: https://www.guidetopharmacology.org/DATA/all_ligands.sdf warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-08-14_ HTTP 503 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: RDF/linked data format of the GtoPdb data (target-ligand interactions with supporting information) format: rdfxml id: gtopdb.download.rdf name: GtoPdb RDF Dataset product_url: https://www.guidetopharmacology.org/DATA/rdf/2025.1/gtp-rdf.n3 warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-08-14_ HTTP 503 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Complete PostgreSQL database dump of the current Guide to Pharmacology database id: gtopdb.database name: GtoPdb Full Database product_url: https://www.guidetopharmacology.org/DATA/public_iuphardb_v2025.1.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-08-14_ HTTP 503 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphicalInterface description: An extension of the Guide to PHARMACOLOGY database providing immunological access-point to GtoPdb data id: gtopdb.immunopharmacology name: Guide to IMMUNOPHARMACOLOGY product_url: https://www.guidetopharmacology.org/immuno/index.jsp - category: GraphicalInterface description: A specialized portal providing optimized access for the malaria research community id: gtopdb.malaria name: Guide to MALARIA PHARMACOLOGY product_url: https://www.guidetopharmacology.org/malaria/index.jsp - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: GraphProduct description: GtoPdb Automat format: kgx-jsonl id: automat.gtopdb infores_id: automat-gtopdb name: gtopdb_automat original_source: - gtopdb product_url: https://stars.renci.org/var/plater/bl-4.2.1/GtoPdb_Automat/0ea6074c824c2236/ secondary_source: - automat - category: GraphProduct description: KGX graph package for Guide to Pharmacology (build gtopdb_20251215_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.gtopdb.graph name: Translator GToPdb KGX Graph original_source: - gtopdb product_url: https://stars.renci.org/var/translator/releases/gtopdb/2025_12_15/ secondary_source: - translator publications: - authors: - Harding SD - Armstrong JF - Faccenda E - Southan C - Alexander SPH - Davenport AP - Spedding M - Davies JA doi: doi:10.1093/nar/gkad944 id: https://doi.org/10.1093/nar/gkad944 journal: Nucleic Acids Research preferred: true title: The IUPHAR/BPS Guide to PHARMACOLOGY in 2024 year: '2024' repository: https://www.guidetopharmacology.org/download.jsp - activity_status: active category: DataSource creation_date: '2009-01-05T00:00:00Z' description: The Genomic tRNA Database (GtRNAdb) is a comprehensive repository of transfer RNA (tRNA) gene predictions identified by tRNAscan-SE in complete and draft genomes across all domains of life. The database contains over 431,000 tRNA gene predictions from 4,867 genomes (609 eukaryotes, 220 archaea, and 4,038 bacteria) as of Data Release 22 (September 2024). GtRNAdb provides detailed annotations including tRNA sequences, predicted secondary structures, isotype-specific scoring, genomic context via UCSC Genome Browser integration, and functional data such as RNA modifications from MODOMICS, tRNA fragment expression profiles, genomic variants from dbSNP, epigenetic information from ENCODE, and evolutionary conservation across species. The database enables comparative analysis through search capabilities by phylogenetic domain, species, amino acid isotypes, anticodons, tRNA scores, structural features, and sequence similarity via BLAST. domains: - genomics - biological systems homepage_url: https://gtrnadb.org/ id: gtrnadb last_modified_date: '2025-10-21T00:00:00Z' layout: resource_detail name: GtRNAdb products: - category: GraphicalInterface description: Web portal for browsing tRNA gene predictions organized by phylogenetic domain and species format: http id: gtrnadb.portal name: GtRNAdb Web Portal product_url: https://gtrnadb.org/ - category: GraphicalInterface description: Browse tRNA predictions organized by phylogenetic taxonomy (Eukaryota, Archaea, Bacteria) format: http id: gtrnadb.browse name: Browse by Phylogeny product_url: https://gtrnadb.org/browse.html - category: GraphicalInterface description: Search tRNAs by species, amino acid isotype, anticodon, intron count, tRNA score, and structural features format: http id: gtrnadb.sifter name: tRNA Sifter product_url: https://gtrnadb.org/search.html - category: GraphicalInterface description: BLAST search interface for sequence similarity searches against all tRNAs in the database format: http id: gtrnadb.blast name: Search by Sequence (BLAST) product_url: https://gtrnadb.org/blast.html - category: DocumentationProduct description: Frequently asked questions about GtRNAdb and tRNA gene predictions format: http id: gtrnadb.faq name: FAQ product_url: https://gtrnadb.org/faq.html - category: DocumentationProduct description: Comprehensive user guide for GtRNAdb features and search capabilities format: http id: gtrnadb.docs name: User Guide product_url: https://gtrnadb.org/docs/ - category: Product description: Archive of previous GtRNAdb data releases with change logs format: http id: gtrnadb.archives name: Previous Releases Archive product_url: https://gtrnadb.org/archives.html - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Patricia P. Chan - Todd M. Lowe id: https://doi.org/10.1093/nar/gkv1309 journal: Nucleic Acids Research preferred: true title: 'GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes' year: '2016' - authors: - Patricia P. Chan - Todd M. Lowe id: https://doi.org/10.1093/nar/gkn787 journal: Nucleic Acids Research title: 'GtRNAdb: A database of transfer RNA genes detected in genomic sequence' year: '2009' taxon: - NCBITaxon:2 - NCBITaxon:2157 - NCBITaxon:2759 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://github.com/NCATSTranslator/Translator-All/wiki/gtrx label: NCATS Translator creation_date: '2025-11-05T00:00:00Z' description: Genome-to-Treatment (gTRx) is a NCATS Translator knowledge provider that integrates genomic, pharmacological, and clinical data to support precision medicine applications. It connects genetic variants with drug treatments and clinical outcomes, enabling researchers to explore relationships between genomic profiles and therapeutic options. The resource aggregates data from multiple sources to provide evidence-based connections between genes, variants, drugs, and diseases. domains: - genomics - pharmacology - precision medicine - translational - biomedical homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/gtrx id: gtrx infores_id: gtrx last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: Genome-to-Treatment products: - category: ProgrammingInterface description: TRAPI-compliant API for querying genomic-treatment relationships format: http id: gtrx.api name: gTRx API original_source: - gtrx product_url: https://github.com/NCATSTranslator/Translator-All/wiki/gtrx - category: Product description: Integrated genomic-treatment data for precision medicine format: mixed id: gtrx.data name: gTRx Data original_source: - gtrx product_url: https://github.com/NCATSTranslator/Translator-All/wiki/gtrx synonyms: - gTRx - Genome-to-Treatment tags: - translator taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: liangcheng@hrbmu.edu.cn label: Liang Cheng - category: Individual contact_details: - contact_type: email value: xuezhang@hrbmu.edu.cn label: Xue Zhang creation_date: '2025-04-13T00:00:00Z' description: A manually curated database of target genes of gut microbes and microbial metabolites in humans and mice. domains: - biological systems - microbiology homepage_url: http://bio-computing.hrbmu.edu.cn/gutmgene id: gutmgene last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail name: GutMGene products: - category: GraphicalInterface description: GutMGene data and interface id: gutmgene.site name: GutMGene site original_source: - gutmgene product_url: http://bio-computing.hrbmu.edu.cn/gutmgene secondary_source: - gutmgene - category: ProcessProduct description: Code for generating MGMLink id: mgmlink.code name: MGMLink code original_source: - gutmgene - pheknowlator product_url: https://github.com/bsantan/MGMLink secondary_source: - mgmlink publications: - authors: - Cheng L - Qi C - Yang H - Lu M - Cai Y - Fu T - Ren J - Jin Q - Zhang X doi: 10.1093/nar/gkab786 id: doi:10.1093/nar/gkab786 title: '''gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites''' year: '2021' - authors: - Qi C - He G - Qian K - Guan S - Li Z - Liang S - Liu J - Ke X - Zhang S - Lu M - Cheng L - Zhang X doi: 10.1093/nar/gkae1002 id: doi:10.1093/nar/gkae1002 title: '''gutMGene v2.0: an updated comprehensive database fortarget genes of gut microbes and microbial metabolites''' year: '2025' taxon: - NCBITaxon:2 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: gwas-info@ebi.ac.uk - contact_type: url value: https://www.ebi.ac.uk/gwas/ id: ebi label: NHGRI-EBI GWAS Catalog Team creation_date: '2025-07-20T00:00:00Z' description: The NHGRI-EBI GWAS Catalog is a curated, searchable, and freely available database of SNP-trait associations from published and submitted genome-wide association studies. Expert curators extract reported traits, significant variant-trait associations, and study metadata, providing an integrated resource updated on a weekly cycle and accessible via web interfaces, bulk downloads, summary statistics, and a REST API. domains: - genomics - health - biomedical - investigations homepage_url: https://www.ebi.ac.uk/gwas/ id: gwascatalog infores_id: gwas-catalog last_modified_date: '2025-09-02T00:00:00Z' layout: resource_detail license: id: https://www.ebi.ac.uk/about/terms-of-use label: EMBL-EBI Terms of Use (summary statistics CC0 unless otherwise stated) name: GWAS Catalog products: - category: GraphicalInterface description: Web interface for searching, browsing, and visualizing curated GWAS variant-trait associations and study metadata format: http id: gwascatalog.web name: GWAS Catalog Web Portal original_source: - gwascatalog product_url: https://www.ebi.ac.uk/gwas/ - category: ProgrammingInterface description: REST API providing programmatic access to GWAS Catalog studies, associations, variants, traits, and summary statistics metadata id: gwascatalog.api is_public: true name: GWAS Catalog REST API v2 original_source: - gwascatalog product_url: https://www.ebi.ac.uk/gwas/docs/api - category: Product description: Full data dump of GWAS Catalog associations in tab-delimited format (SNP-trait association data) format: tsv id: gwascatalog.associations.tsv name: GWAS Catalog Associations TSV original_source: - gwascatalog product_file_size: 482336061 product_url: https://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-associations.tsv - category: Product description: Full data dump of GWAS Catalog associations in JSON format format: json id: gwascatalog.associations.json name: GWAS Catalog Associations JSON original_source: - gwascatalog product_url: https://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-associations.json warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Study metadata file containing per-study information for GWAS Catalog entries format: tsv id: gwascatalog.studies.tsv name: GWAS Catalog Studies TSV original_source: - gwascatalog product_file_size: 48604130 product_url: https://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-studies.tsv - category: Product description: Variant metadata file containing per-variant information (e.g., rsIDs) present in the GWAS Catalog format: tsv id: gwascatalog.variants.tsv name: GWAS Catalog Variants TSV original_source: - gwascatalog product_url: https://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-variants.tsv warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: EFO trait mapping file linking GWAS Catalog reported traits to Experimental Factor Ontology terms format: tsv id: gwascatalog.traits_efo.tsv name: GWAS Catalog Trait EFO Mappings TSV original_source: - gwascatalog product_url: https://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-traits-efo.tsv warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: RDF/OWL representation of GWAS Catalog associations enabling semantic integration format: owl id: gwascatalog.associations.owl name: GWAS Catalog Associations OWL original_source: - gwascatalog product_url: https://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-associations.owl.gz warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: DocumentationProduct description: Compressed GWAS Catalog diagram (karyotype visualization) in SVG format (current release) format: svg id: gwascatalog.diagram.current name: GWAS Catalog Diagram (Current SVG) original_source: - gwascatalog product_url: https://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-diagram.svg warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: DocumentationProduct description: Archive of previous GWAS Catalog diagram versions (SVG format) format: svg id: gwascatalog.diagram.archive name: GWAS Catalog Diagram Archive original_source: - gwascatalog product_url: https://ftp.ebi.ac.uk/pub/databases/gwas/releases/latest/gwas-catalog-diagram-archive.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: DocumentationProduct description: Harmonised summary statistics landing page (FTP directory containing per-study summary statistics under CC0 where available) id: gwascatalog.summary_statistics.ftp name: GWAS Catalog Summary Statistics FTP original_source: - gwascatalog product_url: ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/' - category: GraphProduct description: GWASCatalog Automat format: kgx-jsonl id: automat.gwascatalog infores_id: automat-gwas-catalog name: gwascatalog_automat original_source: - gwascatalog product_url: https://stars.renci.org/var/plater/bl-4.2.1/GWASCatalog_Automat/e30aceb322a33462/ secondary_source: - automat - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: Product description: The EPA has developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Since its inception, the AOP-DB has been developed with the aim of integrating AOP molecular target information with other publicly available datasets to facilitate computational analyses of AOP information. id: aop-db.data name: AOP-DB Data original_source: - aop-wiki - ctd - toxcast - disgenet - ncbigene - string - 1000genomes - ensembl - gwascatalog product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 secondary_source: - aop-db - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: Product description: Genetic variant data from ClinVar, dbSNP, GWAS Catalog and other variant databases format: http id: genecards.variant.data name: GeneCards Variant Data original_source: - clinvar - dbsnp - gwascatalog product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: dwelter.ontologist@gmail.com - contact_type: github value: daniwelter label: Danielle Welter orcid: 0000-0003-1058-2668 creation_date: '2025-06-25T00:00:00Z' description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. domains: - biological systems homepage_url: https://ebispot.github.io/hancestro/ id: hancestro last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Human Ancestry Ontology products: - category: OntologyProduct description: The full version of HANCESTRO in OWL format, with BFO upper hierarchy for easier integration with other ontologies format: owl id: hancestro.owl name: HANCESTRO product_file_size: 145675 product_url: http://purl.obolibrary.org/obo/hancestro.owl - category: OntologyProduct description: Base version of HANCESTRO format: owl id: hancestro-base.owl name: HANCESTRO Base product_url: http://purl.obolibrary.org/obo/hancestro-base.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/EBISPOT/hancestro - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: diapriid@gmail.com - contact_type: github value: mjy label: Matt Yoder orcid: 0000-0002-5640-5491 creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) domains: - anatomy and development homepage_url: http://hymao.org id: hao last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Hymenoptera Anatomy Ontology products: - category: OntologyProduct description: Hymenoptera Anatomy Ontology in OWL format format: owl id: hao.owl name: hao.owl product_file_size: 287954 product_url: http://purl.obolibrary.org/obo/hao.owl - category: OntologyProduct description: Hymenoptera Anatomy Ontology in OBO format format: obo id: hao.obo name: hao.obo product_file_size: 129805 product_url: http://purl.obolibrary.org/obo/hao.obo - category: OntologyProduct description: Hymenoptera Anatomy Ontology in OWL format format: owl id: hao.depictions.owl name: hao.depictions.owl product_file_size: 33370 product_url: http://purl.obolibrary.org/obo/hao/depictions.owl repository: https://github.com/hymao/hao taxon: - NCBITaxon:7399 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: avi.maayan@mssm.edu - contact_type: url value: https://labs.icahn.mssm.edu/maayanlab/ label: Ma'ayan Laboratory creation_date: '2025-09-23T00:00:00Z' description: Harmonizome-KG is a comprehensive knowledge graph derived from the Harmonizome database, integrating functional genomics data across multiple biological domains to connect genes with their functional annotations, regulatory relationships, protein interactions, and phenotypic associations in a unified graph structure. domains: - biomedical - genomics - systems biology - biological systems evaluation_page: resource/harmonizome-kg/harmonizome-kg_eval_automated.html homepage_url: https://maayanlab.cloud/harmonizome-kg/ id: harmonizome-kg last_modified_date: '2025-09-23T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Harmonizome-KG products: - category: GraphicalInterface description: Interactive web interface for exploring the Harmonizome knowledge graph with gene-centric network visualization format: http id: harmonizome-kg.portal name: Harmonizome-KG Explorer product_url: https://maayanlab.cloud/harmonizome-kg/ - category: ProgrammingInterface description: RESTful API for programmatic access to Harmonizome functional genomics knowledge graph format: http id: harmonizome-kg.api name: Harmonizome-KG API product_url: https://maayanlab.cloud/harmonizome-kg/api/ - category: GraphProduct description: Neo4j database containing integrated functional genomics data with genes, proteins, pathways, diseases, and regulatory relationships dump_format: neo4j format: neo4j id: harmonizome-kg.graph name: Harmonizome-KG Neo4j Database publications: - authors: - Rouillard AD - Gundersen GW - Fernandez NF - Wang Z - Monteiro CD - McDermott MG - Ma'ayan A id: doi:10.1093/database/baw100 journal: Database preferred: true title: 'The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins' year: '2016' repository: https://github.com/MaayanLab/harmonizome-kg tags: - translator - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: daniel.himmelstein@gmail.com - contact_type: github value: dhimmel label: Daniel Himmelstein creation_date: '2025-06-24T00:00:00Z' description: Hetionet is an integrative network of biomedical knowledge assembled from 29 different databases of genes, compounds, diseases, and more. It combines over 50 years of biomedical information into a single resource. domains: - biomedical - drug discovery - genomics - health - biological systems evaluation_page: resource/hetionet/hetionet_eval.html homepage_url: https://het.io/ id: hetionet infores_id: hetionet last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Hetionet products: - category: GraphicalInterface description: Browser for complete Hetionet v1.0 graph database in Neo4j format: http id: hetionet.neo4j name: Hetionet v1.0 Neo4j Database product_url: https://neo4j.het.io/browser/ - category: GraphProduct description: Hetionet v1.0 in JSON format format: json id: hetionet.data.json name: Hetionet v1.0 JSON product_file_size: 131 product_url: https://github.com/hetio/hetionet/blob/master/hetnet/json/hetionet-v1.0.json.bz2 - category: GraphProduct description: Hetionet v1.0 as a Neo4j database id: hetionet.data.neo4j name: Hetionet v1.0 Neo4j product_file_size: 132 product_url: https://github.com/hetio/hetionet/blob/master/hetnet/neo4j/hetionet-v1.0.db.tar.bz2 - category: GraphProduct description: Hetionet v1.0 as SIF edges format: sif id: hetionet.data.edges name: Hetionet v1.0 edges (SIF) product_file_size: 131 product_url: https://github.com/hetio/hetionet/blob/main/hetnet/tsv/hetionet-v1.0-edges.sif.gz - category: GraphProduct description: Hetionet v1.0 as TSV nodes format: tsv id: hetionet.data.nodes name: Hetionet v1.0 nodes (TSV) product_file_size: 427128 product_url: https://github.com/hetio/hetionet/blob/main/hetnet/tsv/hetionet-v1.0-nodes.tsv - category: ProcessProduct description: Python package for creating, querying, and operating on hetnets (heterogeneous networks) id: hetnetpy name: hetnetpy product_url: https://github.com/hetio/hetnetpy - category: GraphicalInterface description: Web application to search and explore connectivity between nodes in Hetionet format: http id: hetionet.search name: Hetnet Connectivity Search product_url: https://het.io/search - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: GraphProduct description: Hetio Automat format: kgx-jsonl id: automat.hetio name: hetio_automat original_source: - hetionet product_url: https://stars.renci.org/var/plater/bl-4.2.1/Hetio_Automat/85a5f53e63150e1e/ secondary_source: - automat publications: - authors: - Daniel S Himmelstein - Michael Zietz - Vincent Rubinetti - Kyle Kloster - Benjamin J Heil - Faisal Alquaddoomi - Dongbo Hu - David N Nicholson - Yun Hao - Blair D Sullivan - Michael W Nagle - Casey S Greene doi: doi:10.1093/gigascience/giad047 id: https://doi.org/10.1093/gigascience/giad047 journal: GigaScience title: Hetnet connectivity search provides rapid insights into how biomedical entities are related year: '2023' repository: https://github.com/hetio/hetionet taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: hgnc@genenames.org label: HUGO Gene Nomenclature Committee creation_date: '2025-03-09T00:00:00Z' description: HGNC is the HUGO Gene Nomenclature Committee. It is a resource for approved human gene names. domains: - biological systems fairsharing_id: FAIRsharing.amcv1e homepage_url: https://www.genenames.org/ id: hgnc infores_id: hgnc last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: HGNC products: - category: Product description: hgnc OBO format: obo id: obo-db-ingest.hgnc.obo license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: hgnc OBO original_source: - hgnc product_file_size: 4253807 product_url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.obo secondary_source: - obo-db-ingest - category: Product compression: gzip description: hgnc OWL format: owl id: obo-db-ingest.hgnc.owl license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: hgnc OWL original_source: - hgnc product_file_size: 6489789 product_url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.owl.gz secondary_source: - obo-db-ingest - category: Product compression: gzip description: hgnc OBO Graph JSON format: json id: obo-db-ingest.hgnc.json license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: hgnc OBO Graph JSON original_source: - hgnc product_file_size: 4855839 product_url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.json.gz secondary_source: - obo-db-ingest - category: MappingProduct description: hgnc SSSOM format: sssom id: obo-db-ingest.hgnc.sssom.tsv license: id: https://creativecommons.org.publicdomain/zero/1.0/ label: CC0-1.0 name: hgnc SSSOM original_source: - hgnc product_file_size: 1816550 product_url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: hgnc.genegroup OBO format: obo id: obo-db-ingest.hgnc.genegroup.obo license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: hgnc.genegroup OBO original_source: - hgnc product_file_size: 185057 product_url: https://w3id.org/biopragmatics/resources/hgnc.genegroup/hgnc.genegroup.obo secondary_source: - obo-db-ingest - category: Product description: hgnc.genegroup OWL format: owl id: obo-db-ingest.hgnc.genegroup.owl license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: hgnc.genegroup OWL original_source: - hgnc product_file_size: 231939 product_url: https://w3id.org/biopragmatics/resources/hgnc.genegroup/hgnc.genegroup.owl secondary_source: - obo-db-ingest - category: Product description: hgnc.genegroup OBO Graph JSON format: json id: obo-db-ingest.hgnc.genegroup.json license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: hgnc.genegroup OBO Graph JSON original_source: - hgnc product_file_size: 207059 product_url: https://w3id.org/biopragmatics/resources/hgnc.genegroup/hgnc.genegroup.json secondary_source: - obo-db-ingest - category: Product compression: zip description: This HGNC OWL file is generated from the data at https://www.genenames.org/. It contains all genes in HGNC organised in a shallow hierarchy, classified by their locus type and gene group. Gene groups are also derived from HGNC. The ontology contains approved gene symbol, approved gene name, previous names and symbols and mappings to external databases. format: owl id: scibite.hgnc license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: SciBite HGNC original_source: - hgnc product_url: https://github.com/elsevier-health/scibite-ontology/blob/main/hgnc_2025_02_04.owl.zip repository: https://github.com/elsevier-health/scibite-ontology secondary_source: - scibite warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: MappingProduct description: MONDO SSSOM. Mappings from MONDO identifiers to other namespaces. format: sssom id: mondo.sssom name: MONDO SSSOM original_source: - doid - hp - hgnc product_file_size: 1437457 product_url: https://raw.githubusercontent.com/monarch-initiative/mondo/refs/heads/master/src/ontology/mappings/mondo.sssom.tsv secondary_source: - mondo - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: HGNC Automat format: kgx-jsonl id: automat.hgnc infores_id: automat-hgnc name: hgnc_automat original_source: - hgnc product_url: https://stars.renci.org/var/plater/bl-4.2.1/HGNC_Automat/dee31cfce74e5944/ secondary_source: - automat - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: MappingProduct description: Public mapping of MIM numbers to NCBI Gene IDs, Ensembl Gene IDs, and HGNC symbols format: tsv id: omim.mim2gene name: OMIM mim2gene.txt original_source: - omim - ncbigene - ensembl - hgnc product_file_size: 974440 product_url: https://www.omim.org/static/omim/data/mim2gene.txt - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: Product description: Integrated gene annotation data aggregated from HGNC, OMIM, Ensembl, NCBI Gene, UniProt and other genomic databases format: http id: genecards.gene.annotations name: GeneCards Gene Annotations original_source: - hgnc - omim - ensembl - ncbigene - uniprot - refseq product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphicalInterface description: Interactive web interface for exploring and visualizing kinase-substrate interactions format: http id: kinace.portal name: KinAce Web Portal original_source: - phosphositeplus - iptmnet - uniprot - epsd - kinhub - coralkinome - darkkinasekb - hgnc - kegg - interpro product_url: https://kinace.kinametrix.com/ secondary_source: - kinace - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - category: MappingProduct compression: zip description: A single delimited text file format containing a list of mappings between different identifiers stored in BioGRID and the identifiers used in downloads. format: tsv id: biogrid.identifiers latest_version: 5.0.252 name: BIOGRID-IDENTIFIERS-LATEST.tab.zip original_source: - biogrid - uniprot - ncbigene - zfin - xenbase - hgnc product_url: https://downloads.thebiogrid.org/File/BioGRID/Latest-Release/BIOGRID-IDENTIFIERS-LATEST.tab.zip secondary_source: - biogrid - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz - category: Product description: hgnc Nodes TSV format: tsv id: obo-db-ingest.hgnc.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: hgnc Nodes TSV original_source: - hgnc product_file_size: 1234512 product_url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.tsv secondary_source: - obo-db-ingest - category: Product description: hgnc.genegroup Nodes TSV format: tsv id: obo-db-ingest.hgnc.genegroup.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: hgnc.genegroup Nodes TSV original_source: - hgnc product_file_size: 190009 product_url: https://w3id.org/biopragmatics/resources/hgnc.genegroup/hgnc.genegroup.tsv secondary_source: - obo-db-ingest repository: https://github.com/HGNC taxon: - NCBITaxon:9606 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.hmdb.ca/w/contact label: Human Metabolome Database (HMDB) creation_date: '2025-08-12T00:00:00Z' description: The Human Metabolome Database (HMDB) is a comprehensive curated knowledgebase of small molecule metabolites found in the human body, integrating chemical, clinical, biochemical, spectral, and physiological data along with associated enzyme, transporter, and disease information to support metabolomics, biomarker discovery, systems biology, and precision medicine research. domains: [] homepage_url: https://www.hmdb.ca/ id: hmdb infores_id: hmdb last_modified_date: '2025-09-03T00:00:00Z' layout: resource_detail license: id: https://www.hmdb.ca/downloads label: HMDB Data Use (non-commercial without permission) name: Human Metabolome Database products: - category: GraphicalInterface description: Web portal providing integrated search, metabolite pages (MetaboCards), spectra, pathways, and download access format: http id: hmdb.portal name: HMDB Web Portal original_source: - hmdb product_url: https://www.hmdb.ca/ - category: Product description: All metabolite metabolizing enzyme protein sequences (FASTA) format: fasta id: hmdb.fasta.enzymes name: HMDB Enzyme Protein Sequences (FASTA) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#protein-gene-sequences warnings: - File was not able to be retrieved when checked on 2025-09-04_ Timeout connecting to URL - category: Product description: All metabolite metabolizing enzyme gene sequences (FASTA) format: fasta id: hmdb.fasta.genes name: HMDB Gene Sequences (FASTA) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#protein-gene-sequences - category: Product description: All metabolite structures (SDF) format: sdf id: hmdb.structures.sdf name: HMDB Metabolite Structures (SDF) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#structures warnings: - File was not able to be retrieved when checked on 2025-09-04_ Timeout connecting to URL - category: Product description: All metabolites dataset (XML) format: xml id: hmdb.xml.metabolites name: HMDB All Metabolites (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#metabolite-protein-xml - category: Product description: All proteins dataset (XML) format: xml id: hmdb.xml.proteins name: HMDB All Proteins (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#metabolite-protein-xml - category: Product description: Urine metabolites subset (XML) format: xml id: hmdb.xml.metabolites.urine name: HMDB Urine Metabolites (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#metabolite-protein-xml - category: Product description: Serum metabolites subset (XML) format: xml id: hmdb.xml.metabolites.serum name: HMDB Serum Metabolites (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#metabolite-protein-xml - category: Product description: Cerebrospinal fluid (CSF) metabolites subset (XML) format: xml id: hmdb.xml.metabolites.csf name: HMDB CSF Metabolites (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#metabolite-protein-xml - category: Product description: Saliva metabolites subset (XML) format: xml id: hmdb.xml.metabolites.saliva name: HMDB Saliva Metabolites (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#metabolite-protein-xml - category: Product description: Feces metabolites subset (XML) format: xml id: hmdb.xml.metabolites.feces name: HMDB Feces Metabolites (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#metabolite-protein-xml - category: Product description: Sweat metabolites subset (XML) format: xml id: hmdb.xml.metabolites.sweat name: HMDB Sweat Metabolites (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#metabolite-protein-xml - category: Product compression: zip description: Mass spectra image files archive id: hmdb.spectra.mass.images name: HMDB Mass Spectra Images original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product compression: zip description: NMR spectra FID files archive id: hmdb.spectra.nmr.fid name: HMDB NMR Spectra FID Files original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: Raw NMR peaklist text files archive format: txt id: hmdb.spectra.nmr.peaklist name: HMDB NMR Peaklists (TXT) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: Predicted GC-MS spectra peaklist text files archive format: txt id: hmdb.spectra.gc.predicted.txt name: HMDB GC-MS Predicted Peaklists (TXT) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: Predicted MS-MS spectra peaklist text files archive format: txt id: hmdb.spectra.msms.predicted.txt name: HMDB MS-MS Predicted Peaklists (TXT) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: Experimental MS-MS spectra peaklist text files archive format: txt id: hmdb.spectra.msms.experimental.txt name: HMDB MS-MS Experimental Peaklists (TXT) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: All raw spectra peaklists (aggregated TXT archive) format: txt id: hmdb.spectra.all.peaklists name: HMDB All Raw Spectra Peaklists (TXT) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: NMR spectra collection (XML) format: xml id: hmdb.spectra.nmr.xml name: HMDB NMR Spectra (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: Predicted GC-MS spectra collection (XML) format: xml id: hmdb.spectra.gc.predicted.xml name: HMDB GC-MS Predicted Spectra (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: Experimental GC-MS spectra collection (XML) format: xml id: hmdb.spectra.gc.experimental.xml name: HMDB GC-MS Experimental Spectra (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: Predicted MS-MS spectra collection (XML) format: xml id: hmdb.spectra.msms.predicted.xml name: HMDB MS-MS Predicted Spectra (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: Experimental MS-MS spectra collection (XML) format: xml id: hmdb.spectra.msms.experimental.xml name: HMDB MS-MS Experimental Spectra (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: Product description: All spectra files aggregate (XML) format: xml id: hmdb.spectra.all.xml name: HMDB All Spectra (XML) original_source: - hmdb product_url: https://www.hmdb.ca/downloads#spectra - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: HMDB Automat format: kgx-jsonl id: automat.hmdb infores_id: automat-hmdb name: hmdb_automat original_source: - hmdb product_url: https://stars.renci.org/var/plater/bl-4.2.1/HMDB_Automat/6715124699b6dbf0/ secondary_source: - automat - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: KGX distribution of the ICEES Exposures KP in Knowledge Graph Exchange (KGX) format, containing integrated clinical and environmental exposures data as a knowledge graph with 226 nodes and 14,342 edges format: kgx-jsonl id: icees-kg.graph name: KGX distribution of the ICEES Exposures KP original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/ secondary_source: - icees-kg - category: ProgrammingInterface description: Translator Reasoner API (TRAPI) endpoint for querying ICEES KG using standardized Translator protocols format: http id: icees-kg.trapi name: ICEES KG TRAPI API original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg-trapi secondary_source: - icees-kg - category: Product description: Meta knowledge graph and metadata describing the data sources, node types, edge types, and predicates available in ICEES KG format: json id: icees-kg.metadata name: ICEES KG Metadata original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/metadata-metadata-get-icees-kg secondary_source: - icees-kg - category: DatabaseProduct description: Multi-sourced relational database integrating metabolomic pathway information, biochemical reactions, ontologies, and chemical descriptors for genes, proteins, and metabolites with query and enrichment analysis capabilities. id: rampdb.database is_public: true name: RaMP-DB Integrated Database original_source: - kegg - reactome - hmdb - wikipathways - rampdb product_url: https://rampdb.nih.gov/ - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: bgee@sib.swiss - contact_type: github value: fbastian label: Frederic Bastian orcid: 0000-0002-9415-5104 creation_date: '2025-09-29T00:00:00Z' description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. domains: - anatomy and development homepage_url: https://github.com/BgeeDB/homology-ontology id: hom last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Homology Ontology products: - category: OntologyProduct description: Homology Ontology in OWL format format: owl id: hom.owl name: hom.owl product_url: http://purl.obolibrary.org/obo/hom.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' repository: https://github.com/BgeeDB/homology-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: dr.sebastian.koehler@gmail.com - contact_type: github value: drseb label: Sebastian Koehler orcid: 0000-0002-5316-1399 creation_date: '2025-04-22T00:00:00Z' description: The Human Phenotype Ontology (HPO) is a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. domains: - biological systems homepage_url: http://www.human-phenotype-ontology.org/ id: hp last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://hpo.jax.org/app/license label: hpo name: Human Phenotype Ontology (HPO) products: - category: OntologyProduct description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in obographs JSON format. format: json id: hp.json name: Official HPO release in obographs JSON format product_file_size: 22063007 product_url: http://purl.obolibrary.org/obo/hp.json - category: OntologyProduct description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in OBO file format. format: obo id: hp.obo name: Official HPO release in OBO format product_file_size: 10703106 product_url: http://purl.obolibrary.org/obo/hp.obo - category: OntologyProduct description: Manually classified version of the ontology without the use of a reasoner, with imported terms, in OWL format (RDF/XML). format: owl id: hp.owl name: Official HPO release in OWL product_file_size: 76165285 product_url: http://purl.obolibrary.org/obo/hp.owl - category: OntologyProduct description: Manually curated version of the ontology without the use of a reasoner, with references to imported terms, in obographs JSON file format. format: obo id: hp.hp-base.json name: HPO base release in obographs JSON format product_file_size: 22264343 product_url: http://purl.obolibrary.org/obo/hp/hp-base.json - category: OntologyProduct description: Manually curated version of the ontology without the use of a reasoner, with references to imported terms, in OBO file format. format: obo id: hp.hp-base.obo name: HPO base release in OBO format product_file_size: 11259310 product_url: http://purl.obolibrary.org/obo/hp/hp-base.obo - category: OntologyProduct description: Manually curated version of the ontology without the use of a reasoner, with references to imported terms, in OWL (RDF/XML) file format. format: owl id: hp.hp-base.owl name: HPO base release in OWL format product_file_size: 48376110 product_url: http://purl.obolibrary.org/obo/hp/hp-base.owl - category: OntologyProduct description: Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in obographs JSON file format. format: json id: hp.hp-full.json name: HPO full release in obographs JSON format product_file_size: 42991056 product_url: http://purl.obolibrary.org/obo/hp/hp-full.json - category: OntologyProduct description: Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in OBO file format. format: obo id: hp.hp-full.obo name: HPO full release in OBO format product_file_size: 19203487 product_url: http://purl.obolibrary.org/obo/hp/hp-full.obo - category: OntologyProduct description: Version of the ontology automatically classified with the use of a reasoner, including all imported terms, in OWL (RDF/XML) file format. format: owl id: hp.hp-full.owl name: HPO full release in OWL format product_file_size: 85256414 product_url: http://purl.obolibrary.org/obo/hp/hp-full.owl - category: OntologyProduct description: Version of the ontology corresponding to the primary release (hp.owl), with translated labels, synonyms, and definitions, in obographs JSON file format. format: json id: hp.hp-international.json name: HPO International Edition in obographs JSON format product_file_size: 49246551 product_url: http://purl.obolibrary.org/obo/hp/hp-international.json - category: OntologyProduct description: Version of the ontology corresponding to the primary release (hp.owl), with translated labels, synonyms, and definitions, in OBO file format. format: obo id: hp.hp-international.obo name: HPO International Edition in OBO format product_file_size: 22152711 product_url: http://purl.obolibrary.org/obo/hp/hp-international.obo - category: OntologyProduct description: Version of the ontology corresponding to the primary release (hp.owl), with translated labels, synonyms, and definitions, in OWL (RDF/XML) file format. format: owl id: hp.hp-international.owl name: HPO International Edition in OWL format product_file_size: 208345468 product_url: http://purl.obolibrary.org/obo/hp/hp-international.owl - category: OntologyProduct description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in obographs JSON file format. format: json id: hp.hp-simple-non-classified.json name: HPO simple, manually classified, without imports in obographs JSON format product_file_size: 22063054 product_url: http://purl.obolibrary.org/obo/hp/hp-simple-non-classified.json - category: OntologyProduct description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in OBO file format. format: obo id: hp.hp-simple-non-classified.obo name: HPO simple, manually classified, without imports in OBO format product_file_size: 10703156 product_url: http://purl.obolibrary.org/obo/hp/hp-simple-non-classified.obo - category: OntologyProduct description: Simple, manually curated version of the ontology without the use of a reasoner, and without any imported terms, in OWL (RDF/XML) file format. format: owl id: hp.hp-simple-non-classified.owl name: HPO simple, manually classified, without imports in OWL format product_file_size: 29893603 product_url: http://purl.obolibrary.org/obo/hp/hp-simple-non-classified.owl - category: OntologyProduct description: https://hpo.jax.org/app/data/annotations format: tsv id: hp.phenotype.hpoa name: HPO Annotations (Phenotype to Disease) product_file_size: 35261380 product_url: http://purl.obolibrary.org/obo/hp/phenotype.hpoa - category: OntologyProduct description: https://hpo.jax.org/app/data/annotations format: tsv id: hp.phenotype_to_genes.txt name: HPO phenotype to gene annotations product_file_size: 65852754 product_url: http://purl.obolibrary.org/obo/hp/phenotype_to_genes.txt - category: OntologyProduct description: https://hpo.jax.org/app/data/annotations format: tsv id: hp.genes_to_phenotype.txt name: HPO gene to phenotype annotations product_file_size: 20533481 product_url: http://purl.obolibrary.org/obo/hp/genes_to_phenotype.txt - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: KGX Distribution of KG-Monarch edge_count: 15356321 format: kgx id: kg-monarch.graph name: KGX Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - 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chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: GraphProduct description: KGX distribution of the ICEES Exposures KP in Knowledge Graph Exchange (KGX) format, containing integrated clinical and environmental exposures data as a knowledge graph with 226 nodes and 14,342 edges format: kgx-jsonl id: icees-kg.graph name: KGX distribution of the ICEES Exposures KP original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/ secondary_source: - icees-kg - category: ProgrammingInterface description: Translator Reasoner API (TRAPI) endpoint for querying ICEES KG using standardized Translator protocols format: http id: icees-kg.trapi name: ICEES KG TRAPI API original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg-trapi secondary_source: - icees-kg - category: Product description: Meta knowledge graph and metadata describing the data sources, node types, edge types, and predicates available in ICEES KG format: json id: icees-kg.metadata name: ICEES KG Metadata original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/metadata-metadata-get-icees-kg secondary_source: - icees-kg - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct description: Nodes for the Drug Approvals KP, v0.3.9 format: kgx id: drug-approvals-kp.graph.nodes name: Drug Approvals KP Graph Nodes original_source: - chebi - doid - hp - mondo product_file_size: 701451 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_nodes_v0.3.9.tsv secondary_source: - drug-approvals-kp - category: GraphProduct description: Edges for the Drug Approvals KP, v0.3.9 format: kgx id: drug-approvals-kp.graph.edges name: Drug Approvals KP Graph Edges original_source: - chebi - doid - hp - mondo product_file_size: 31052966 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_edges_v0.3.9.tsv secondary_source: - drug-approvals-kp - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' - category: MappingProduct description: MONDO SSSOM. Mappings from MONDO identifiers to other namespaces. format: sssom id: mondo.sssom name: MONDO SSSOM original_source: - doid - hp - hgnc product_file_size: 1437457 product_url: https://raw.githubusercontent.com/monarch-initiative/mondo/refs/heads/master/src/ontology/mappings/mondo.sssom.tsv secondary_source: - mondo - category: MappingProduct compression: gzip description: Mappings between MedGen and Human Phenotype Ontology terms with gzip compression format: txt id: medgen.hpo-mapping name: MedGen HPO Mapping original_source: - medgen - hp product_file_size: 389609 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGen_HPO_Mapping.txt.gz - category: MappingProduct compression: gzip description: Combined mappings between MedGen, HPO, and OMIM with gzip compression format: txt id: medgen.hpo-omim-mapping name: MedGen HPO OMIM Mapping original_source: - medgen - hp - omim product_file_size: 4125863 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGen_HPO_OMIM_Mapping.txt.gz - category: Product description: History file tracking changes to HPO term mappings to CUIs format: txt id: medgen.hpo-history name: HPO CUI History original_source: - medgen - hp product_file_size: 1299018 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/HPO_CUI_history.txt - category: GraphProduct description: KGX graph package for Human Phenotype Ontology annotations (build hpoa_2025-11-24_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.hpoa.graph name: Translator HPOA KGX Graph original_source: - hp product_url: https://stars.renci.org/var/translator/releases/hpoa/2025_12_15/ secondary_source: - translator repository: https://github.com/obophenotype/human-phenotype-ontology taxon: - NCBITaxon:9606 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: email value: contact@proteinatlas.org - contact_type: url value: https://www.proteinatlas.org/about/organization label: Human Protein Atlas Team creation_date: '2025-10-09T00:00:00Z' description: The Human Protein Atlas (HPA) is a Swedish-based program aiming to map all human proteins in cells, tissues and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. The HPA aggregates and presents data from eight different resources covering tissue, brain, single cell, subcellular, cancer, blood, cell line, and structure & interaction atlases. domains: - biomedical - proteomics - genomics - anatomy and development - health homepage_url: https://www.proteinatlas.org/ id: hpa infores_id: hpa last_modified_date: '2025-10-09T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 logo: https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png name: Human Protein Atlas products: - category: GraphicalInterface description: Main web portal for exploring protein expression profiles across tissues, cells, and disease states format: http id: hpa.portal name: Human Protein Atlas Portal product_url: https://www.proteinatlas.org/ - category: Product description: Complete Human Protein Atlas data in TSV format, version 24.1 format: tsv id: hpa.proteinatlas.tsv name: HPA Complete Data (TSV) product_file_size: 6286585 product_url: https://www.proteinatlas.org/download/proteinatlas.tsv.zip - category: Product description: Complete Human Protein Atlas data in JSON format, version 24.1 format: json id: hpa.proteinatlas.json name: HPA Complete Data (JSON) product_file_size: 10840984 product_url: https://www.proteinatlas.org/download/proteinatlas.json.gz - category: Product description: Complete Human Protein Atlas data in XML format, version 24.0 with comprehensive protein expression and annotation data format: xml id: hpa.proteinatlas.xml name: HPA Complete Data (XML) product_file_size: 712079128 product_url: https://www.proteinatlas.org/download/proteinatlas.xml.gz - category: Product description: Normal tissue expression data based on immunohistochemistry using tissue microarrays format: tsv id: hpa.normal_tissue name: HPA Normal Tissue Data product_url: https://www.proteinatlas.org/download/normal_tissue.tsv.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Pathology data including cancer tissue expression and patient survival information format: tsv id: hpa.pathology name: HPA Pathology Data product_url: https://www.proteinatlas.org/download/pathology.tsv.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-11-10_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Subcellular localization data based on immunofluorescent staining of human cell lines format: tsv id: hpa.subcellular_location name: HPA Subcellular Location Data product_url: https://www.proteinatlas.org/download/subcellular_location.tsv.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-11-10_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: RNA expression data in human tissues based on transcriptomic analysis format: tsv id: hpa.rna_tissue name: HPA RNA Tissue Expression Data product_url: https://www.proteinatlas.org/download/rna_tissue.tsv.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: RNA expression data in human cell lines based on RNA-seq analysis format: tsv id: hpa.rna_celline name: HPA RNA Cell Line Expression Data product_url: https://www.proteinatlas.org/download/rna_celline.tsv.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-11-10_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Single cell expression data from human tissues based on scRNA-seq analysis format: tsv id: hpa.rna_single_cell name: HPA Single Cell RNA Expression Data product_url: https://www.proteinatlas.org/download/rna_single_cell.tsv.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Brain-specific expression data including regional and cellular distribution format: tsv id: hpa.brain_rna name: HPA Brain RNA Expression Data product_url: https://www.proteinatlas.org/download/brain_rna.tsv.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Blood protein expression data from healthy individuals and disease states format: tsv id: hpa.blood_protein name: HPA Blood Protein Data product_url: https://www.proteinatlas.org/download/blood_protein.tsv.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Immune cell expression data from single cell transcriptomics studies format: tsv id: hpa.rna_immune_cell name: HPA Immune Cell RNA Data product_url: https://www.proteinatlas.org/download/rna_immune_cell.tsv.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-11-10_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: ProgrammingInterface description: Programmatic access to individual protein entries in XML format via Ensembl ID format: xml id: hpa.api.xml name: HPA XML API product_url: https://www.proteinatlas.org/about/download - category: ProgrammingInterface description: Programmatic access to individual protein entries in TSV format via Ensembl ID format: tsv id: hpa.api.tsv name: HPA TSV API product_url: https://www.proteinatlas.org/about/download - category: ProgrammingInterface description: Programmatic access to individual protein entries in JSON format via Ensembl ID format: json id: hpa.api.json name: HPA JSON API product_url: https://www.proteinatlas.org/about/download - category: ProgrammingInterface description: Programmatic access to individual protein entries in RDF format via Ensembl ID format: rdfxml id: hpa.api.rdf name: HPA RDF API product_url: https://www.proteinatlas.org/about/download - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - authors: - Uhlén M - Fagerberg L - Hallström BM - Lindskog C - Oksvold P - Mardinoglu A doi: 10.1126/science.1260419 id: doi:10.1126/science.1260419 journal: Science title: Tissue-based map of the human proteome year: '2015' - authors: - Karlsson M - Zhang C - Méar L - Zhong W - Digre A - Katona B doi: 10.1126/science.aal3321 id: doi:10.1126/science.aal3321 journal: Science title: A single-cell type transcriptomics map of human tissues year: '2021' repository: https://github.com/human-protein-atlas taxon: - NCBITaxon:9606 - activity_status: active category: DataModel contacts: - category: Individual label: Katy Börner orcid: 0000-0002-3321-6137 creation_date: '2025-11-05T00:00:00Z' description: The Human Reference Atlas (HRA) is a comprehensive 3D spatial framework and data model for mapping the healthy human body at single-cell resolution. The HRA provides reference anatomical structures, cell types, biomarkers, and standardized spatial coordinates to enable integration and analysis of diverse biological data types across multiple scales from organs to cells. domains: - anatomy and development - health - biological systems - biomedical - precision medicine homepage_url: https://humanatlas.io/ id: hra infores_id: hra last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Human Reference Atlas products: - category: GraphicalInterface description: Web portal for exploring and visualizing the Human Reference Atlas format: http id: hra.portal name: Human Reference Atlas Portal original_source: - hra product_url: https://humanatlas.io/ - category: ProgrammingInterface description: API endpoints for programmatic access to HRA data format: http id: hra.api name: HRA API original_source: - hra product_url: https://apps.humanatlas.io/api - category: Product description: Downloadable data files including anatomical structures, cell types, and biomarkers format: mixed id: hra.data name: HRA Data Downloads original_source: - hra product_url: https://humanatlas.io/data - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg publications: - id: https://doi.org/10.1038/s41556-021-00788-6 repository: https://github.com/hubmapconsortium/ccf-ui synonyms: - HRA taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Individual label: Katy Börner orcid: 0000-0002-3321-6137 creation_date: '2025-03-09T00:00:00Z' description: The HRA Knowledge Graph (HRA KG) is a linked open data resource that integrates anatomical structures, cell types, and biomarkers to support cross-scale biological queries. domains: - health - anatomy and development - biological systems - biomedical evaluation_page: resource/hra-kg/hra-kg_eval.html homepage_url: https://apps.humanatlas.io/dashboard/data id: hra-kg last_modified_date: '2025-08-12T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Human Reference Atlas Knowledge Graph (HRA KG) products: - category: GraphProduct description: The graph representation of the Human Reference Atlas (HRA) dataset, v2.2, Turtle format format: ttl id: hra-kg.graph.ttl name: HRA KG graph data, v2.2, Turtle format original_source: - hra-kg product_file_size: 204030087 product_url: https://cdn.humanatlas.io/digital-objects/collection/hra/v2.2/graph.ttl secondary_source: - hra-kg - category: GraphProduct description: The graph representation of the Human Reference Atlas (HRA) dataset, v2.2, JSON-LD format format: jsonld id: hra-kg.graph.json name: HRA KG graph data, v2.2, JSON-LD format original_source: - hra-kg product_file_size: 18043 product_url: https://cdn.humanatlas.io/digital-objects/collection/hra/v2.2/graph.json secondary_source: - hra-kg - category: GraphProduct description: The graph representation of the Human Reference Atlas (HRA) dataset, v2.2, RDF/XML format format: rdfxml id: hra-kg.graph.xml name: HRA KG graph data, v2.2, RDF/XML format original_source: - hra-kg product_file_size: 185060502 product_url: https://cdn.humanatlas.io/digital-objects/collection/hra/v2.2/graph.xml secondary_source: - hra-kg - category: GraphProduct description: The graph representation of the Human Reference Atlas (HRA) dataset, v2.2, N-Triples format format: ntriples id: hra-kg.graph.nt name: HRA KG graph data, v2.2, N-Triples format original_source: - hra-kg product_file_size: 291382102 product_url: https://cdn.humanatlas.io/digital-objects/collection/hra/v2.2/graph.nt secondary_source: - hra-kg - category: GraphProduct description: The graph representation of the Human Reference Atlas (HRA) dataset, v2.2, N-Quads format format: nquads id: hra-kg.graph.nq name: HRA KG graph data, v2.2, N-Quads format original_source: - hra-kg product_file_size: 376981902 product_url: https://cdn.humanatlas.io/digital-objects/collection/hra/v2.2/graph.nq secondary_source: - hra-kg repository: https://github.com/hubmapconsortium/hra-kg - activity_status: active category: DataSource creation_date: '2025-11-19T00:00:00Z' description: The Human Reference Protein Interactome Mapping Project (HRPIMP) is a systematic effort to map binary protein-protein interactions in human cells. The project produced the Human Reference Interactome (HuRI) database containing high-quality experimentally validated protein-protein interactions. Using systematic yeast two-hybrid (Y2H) screening approaches, HRPIMP mapped interactions for 9,094 proteins, identifying 64,006 binary protein-protein interactions. This comprehensive reference map of the human binary protein interactome provides essential data for understanding cellular mechanisms, disease pathways, and molecular networks. The data is freely available and has been integrated into multiple knowledge bases and research projects including studies of Alzheimer's Disease, cancer, and other complex diseases. domains: - proteomics - systems biology - biomedical - biological systems homepage_url: http://www.interactome-atlas.org/ id: hrpimp last_modified_date: '2025-11-19T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Human Reference Protein Interactome Mapping Project products: - category: Product description: TSV files containing systematically mapped binary protein-protein interactions for 9,094 human proteins with 64,006 validated interactions format: tsv id: hrpimp.data name: HuRI Protein-Protein Interaction Data original_source: - hrpimp product_url: https://github.com/VIDallab/huri warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphicalInterface description: Web interface for browsing and exploring the Human Reference Interactome format: http id: hrpimp.web name: Interactome Atlas Web Portal original_source: - hrpimp product_url: http://www.interactome-atlas.org/ - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet publications: - authors: - Luck K - Kim DK - Lambourne L - Spirohn K - Begg BE - Bian W - Brignall R - Cafarelli T - Campos-Laborie FJ - Charloteaux B - Choi D - Coté AG - Daley M - Deimling S - Desbuleux A - Dricot A - Gebbia M - Hardy MF - Kishore N - Knapp JJ - Kovács IA - Lemmens I - Mee MW - Mellor JC - Pollis C - Pons C - Richardson AD - Schlabach S - Teeking B - Yadav A - Babor M - Balcha D - Basha O - Bowman-Colin C - Chin SF - Choi SG - Colabella C - Coppin G - D'Amata C - De Ridder D - De Rouck S - Duran-Frigola M - Ennajdaoui H - Goebels F - Goehring L - Gopal A - Haddad G - Hatchi E - Helmy M - Jacob Y - Kassa Y - Landini S - Li R - van Lieshout N - MacWilliams A - Markey D - Paulson JN - Rangarajan S - Rasla J - Rayhan A - Rolland T - San-Miguel A - Shen Y - Sheykhkarimli D - Sheynkman GM - Simonovsky E - Taşan M - Tejeda A - Tropepe V - Twizere JC - Wang Y - Weatheritt RJ - Weile J - Xia Y - Yang X - Yeger-Lotem E - Zhong Q - Aloy P - Bader GD - De Las Rivas J - Gaudet S - Hao T - Rak J - Tavernier J - Hill DE - Vidal M - Roth FP - Calderwood MA doi: 10.1038/s41586-020-2188-x id: PMID:32296183 journal: Nature title: A reference map of the human binary protein interactome year: '2020' repository: https://github.com/VIDallab/huri synonyms: - HRPIMP - HuRI - Human Reference Interactome taxon: - NCBITaxon:9606 - NCBITaxon:4932 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: frederic.bastian@unil.ch - contact_type: github value: fbastian label: Fr d ric Bastian orcid: 0000-0002-9415-5104 creation_date: '2025-06-04T00:00:00Z' description: Life cycle stages for Human domains: - anatomy and development homepage_url: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv id: hsapdv last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Human Developmental Stages products: - category: OntologyProduct description: Human Developmental Stages in OWL format format: owl id: hsapdv.owl name: hsapdv.owl product_file_size: 528600 product_url: http://purl.obolibrary.org/obo/hsapdv.owl - category: OntologyProduct description: Human Developmental Stages in OBO format format: obo id: hsapdv.obo name: hsapdv.obo product_file_size: 143585 product_url: http://purl.obolibrary.org/obo/hsapdv.obo - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg repository: https://github.com/obophenotype/developmental-stage-ontologies - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: fernanda.dorea@sva.se - contact_type: github value: nandadorea label: Fernanda Dorea orcid: 0000-0001-8638-8525 creation_date: '2025-09-29T00:00:00Z' description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. domains: - biomedical homepage_url: https://w3id.org/hso id: hso last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Health Surveillance Ontology products: - category: OntologyProduct description: Health Surveillance Ontology in OWL format format: owl id: hso.owl name: hso.owl product_file_size: 138245 product_url: http://purl.obolibrary.org/obo/hso.owl repository: https://github.com/SVA-SE/HSO - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: aellenhicks@gmail.com - contact_type: github value: aellenhicks label: Amanda Hicks orcid: 0000-0002-1795-5570 creation_date: '2025-09-29T00:00:00Z' description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines domains: - biomedical homepage_url: https://github.com/aellenhicks/htn_owl id: htn last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Hypertension Ontology products: - category: OntologyProduct description: HTN format: owl id: htn.owl name: HTN product_file_size: 140471 product_url: http://purl.obolibrary.org/obo/htn.owl repository: https://github.com/aellenhicks/htn_owl - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://hubmapconsortium.org/ - contact_type: email value: help@hubmapconsortium.org label: HuBMAP Consortium creation_date: '2025-08-05T00:00:00Z' description: The Human BioMolecular Atlas Program (HuBMAP) is a transformative NIH Common Fund initiative dedicated to creating an open, global atlas of the human body at the cellular level. HuBMAP develops the tools, technology, and infrastructure needed to map healthy human tissues in unprecedented molecular detail. domains: - biomedical - anatomy and development - biological systems - health - proteomics - genomics - systems biology homepage_url: https://hubmapconsortium.org/ id: hubmap last_modified_date: '2025-08-05T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: HuBMAP products: - category: Product description: HuBMAP Data Portal providing access to standardized single-cell and spatial tissue data from human donors format: mixed id: hubmap.data_portal license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: HuBMAP Data Portal product_url: https://portal.hubmapconsortium.org/ - category: Product description: Human Reference Atlas providing atlas data and reference functionality format: mixed id: hubmap.human_reference_atlas license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: Human Reference Atlas product_url: https://humanatlas.io/ - category: GraphicalInterface description: Interactive data visualization tool for spatial and single-cell multimodal datasets id: hubmap.vitessce name: Vitessce product_url: https://vitessce.io/ - category: GraphicalInterface description: Interactive JupyterLab environments for analyzing HuBMAP data id: hubmap.workspaces name: HuBMAP Workspaces product_url: https://portal.hubmapconsortium.org/workspaces - category: GraphicalInterface description: Single-cell RNA-seq and ATAC-seq analysis using reference datasets id: hubmap.azimuth name: Azimuth product_url: https://azimuth.hubmapconsortium.org/ - category: GraphicalInterface description: Functional Unit State Identification and Navigation with Whole Slide Imaging id: hubmap.fusion name: FUSION product_url: http://fusion.hubmapconsortium.org/ - category: Product description: Antibody validation reports for multiplex imaging assays id: hubmap.antibody_validation_reports name: Antibody Validation Reports product_url: https://avr.hubmapconsortium.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 401 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 401 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 401 error when accessing file' - category: Product description: Data submission portal for registering and ingesting consortium data id: hubmap.data_ingest_portal name: Data Ingest Portal product_url: https://ingest.hubmapconsortium.org/ - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg publications: - authors: - Katy Börner - et al. doi: 10.1038/s41592-025-02120-1 id: doi:10.1038/s41592-025-02120-1 journal: Nature Methods preferred: true title: 'Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage' year: '2025' - authors: - Mark S Keller - et al. doi: 10.1038/s41592-024-02497-x id: doi:10.1038/s41592-024-02497-x journal: Nature Methods title: 'Vitessce: integrative visualization of multimodal and spatially-resolved single-cell data' year: '2024' repository: https://github.com/hubmapconsortium taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.inetbio.org/humannet/ label: INetBio creation_date: '2025-11-05T00:00:00Z' description: HumanNet is a probabilistic functional gene network for Homo sapiens that integrates genomic and proteomic data from multiple sources to predict functional relationships between genes. The network uses a modified Bayesian integration approach to combine evidence from diverse data types including protein-protein interactions, gene co-expression, phylogenetic profiling, and literature mining. HumanNet provides confidence scores for gene-gene functional linkages and can be used for gene function prediction, disease gene prioritization, and pathway analysis. domains: - genomics - systems biology - biomedical - biological systems homepage_url: https://www.inetbio.org/humannet/ id: humannet last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: HumanNet products: - category: GraphicalInterface description: Web interface for querying and visualizing the HumanNet functional gene network format: http id: humannet.web name: HumanNet Web Interface original_source: - humannet product_url: https://www.inetbio.org/humannet/ - category: GraphProduct description: Downloadable functional gene network with confidence scores format: tsv id: humannet.network name: HumanNet Network File original_source: - humannet product_url: https://www.inetbio.org/humannet/download.php warnings: - File was not able to be retrieved when checked on 2025-11-13_ Timeout connecting to URL - category: ProgrammingInterface description: API for programmatic access to HumanNet data format: http id: humannet.api name: HumanNet API original_source: - humannet product_url: https://www.inetbio.org/humannet/ - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg publications: - id: https://doi.org/10.1093/nar/gky1126 synonyms: - HumanNet - humannet taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://ccsb.dana-farber.org/ label: Center for Cancer Systems Biology - category: Individual label: Marc Vidal orcid: 0000-0002-9500-6065 - category: Individual label: Frederick P. Roth creation_date: '2025-08-05T00:00:00Z' description: The Human Reference Interactome (HuRI) is a comprehensive map of binary protein-protein interactions in human cells, generated through systematic high-throughput yeast two-hybrid screening. HuRI provides the largest experimentally verified collection of human protein interactions and serves as a foundational resource for understanding cellular networks and disease mechanisms. domains: - biomedical - biological systems - proteomics - systems biology homepage_url: http://www.interactome-atlas.org/ id: huri infores_id: huri last_modified_date: '2025-08-05T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: HuRI products: - category: Product description: Human Reference Interactome (HuRI) protein-protein interaction data format: tsv id: huri.interactions license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: HuRI Protein-Protein Interactions product_url: http://www.interactome-atlas.org/download - category: Product description: Literature-curated high-quality protein-protein interactions from comparable experimental approaches format: tsv id: huri.literature_benchmark license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: HuRI Literature Benchmark product_url: http://www.interactome-atlas.org/download - category: GraphicalInterface description: Web portal for searching and browsing human protein interactions id: huri.portal name: HuRI Web Portal product_url: http://www.interactome-atlas.org/ - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - authors: - Katja Luck - Dae-Kyum Kim - Luke Lambourne - Kerstin Spirohn - et al. doi: 10.1038/s41586-020-2188-x id: doi:10.1038/s41586-020-2188-x journal: Nature preferred: true title: A reference map of the human binary protein interactome year: '2020' repository: https://github.com/VIDallab/huri taxon: - NCBITaxon:9606 - NCBITaxon:4932 - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: torsten.hahmann@maine.edu label: Torsten Hahmann creation_date: '2025-12-08T00:00:00Z' description: The Hydrology KG is part of the SAWGraph (Safe Agricultural Products and Water Graph) project, providing structured data about hydrological systems and water resources. domains: - environment evaluation_page: resource/hydrologykg/hydrologykg_eval_automated.html homepage_url: https://sawgraph.github.io/ id: hydrologykg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SAWGraph Hydrology KG products: - category: ProgrammingInterface description: SPARQL endpoint for SAWGraph Hydrology KG id: hydrologykg.sparql name: SAWGraph Hydrology KG SPARQL original_source: - hydrologykg product_url: https://frink.apps.renci.org/hydrologykg/sparql - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: zhengj2007@gmail.com - contact_type: github value: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 creation_date: '2025-06-25T00:00:00Z' description: An ontology of information entities. domains: - biomedical homepage_url: https://github.com/information-artifact-ontology/IAO/ id: iao last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Information Artifact Ontology products: - category: OntologyProduct description: Information Artifact Ontology in OWL format format: owl id: iao.owl name: iao.owl product_file_size: 78925 product_url: http://purl.obolibrary.org/obo/iao.owl - category: OntologyProduct description: IAO ontology metadata format: owl id: iao.ontology-metadata.owl name: IAO ontology metadata product_file_size: 11084 product_url: http://purl.obolibrary.org/obo/iao/ontology-metadata.owl - category: OntologyProduct description: IAO dev format: owl id: iao.dev.iao.owl name: IAO dev product_url: http://purl.obolibrary.org/obo/iao/dev/iao.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: An ontology based on a theory of document acts describing what people can do with documents format: owl id: iao.d-acts.owl name: ontology of document acts product_file_size: 10158 product_url: http://purl.obolibrary.org/obo/iao/d-acts.owl - category: OntologyProduct description: OWL release of Monochrom Ontology format: owl id: chr.model.owl name: Monochrom Ontology OWL release original_source: - ro - go - ncbitaxon - iao - geno - skos - gff product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl secondary_source: - chr - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct description: RDF dump of the Open Research Knowledge Graph distributed in N-Triples format. format: ntriples id: orkg.dump name: ORKG RDF Dump original_source: - orkg - wikidata - geonames - ncit - chebi - ncbitaxon - go - clo - omit - iao - uo - stato - obi product_file_size: 642902930 product_url: https://orkg.org/api/rdf/dump secondary_source: - orkg repository: https://github.com/information-artifact-ontology/IAO - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: chang.su@temple.edu label: Chang Su - category: Individual contact_details: - contact_type: email value: few2001@med.cornell.edu label: Fei Wang creation_date: '2025-11-19T00:00:00Z' description: A comprehensive biomedical knowledge graph created by harmonizing and integrating information from diverse biomedical resources for biomedical discovery and drug repurposing. domains: - biomedical - health - drug discovery - systems biology evaluation_page: resource/ibkh/ibkh_eval_automated.html homepage_url: https://pubmed.ncbi.nlm.nih.gov/37020958/ id: ibkh last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: integrative Biomedical Knowledge Hub products: - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi publications: - authors: - Chang Su - Yu Hou - Manqi Zhou - Suraj Rajendran - Jacqueline R M A Maasch - Zehra Abedi - Haotan Zhang - Zilong Bai - Anthony Cuturrufo - Winston Guo - Fayzan F Chaudhry - Gregory Ghahramani - Jian Tang - Feixiong Cheng - Yue Li - Rui Zhang - Steven T DeKosky - Jiang Bian - Fei Wang doi: 10.1016/j.isci.2023.106460 id: https://doi.org/10.1016/j.isci.2023.106460 journal: iScience preferred: true title: Biomedical discovery through the integrative biomedical knowledge hub (iBKH) year: '2023' synonyms: - iBKH - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.who.int/ - contact_type: email value: classifications@who.int id: who label: World Health Organization - category: Organization contact_details: - contact_type: url value: https://www.who.int/standards/classifications id: who label: WHO Family of International Classifications creation_date: '2025-11-10T00:00:00Z' description: The International Classification of Diseases, 10th Revision (ICD-10) is a standardized system for classifying diseases, injuries, and causes of death maintained by the World Health Organization (WHO). Originating in the 19th century with over 150 years of continuous development, ICD-10 came into effect on January 1, 1993, following adoption by the World Health Assembly in May 1990. ICD-10 provides a comprehensive hierarchical classification system with alphanumeric codes that allow systematic recording, analysis, interpretation, and comparison of mortality and morbidity data collected across countries and time periods. The system is used globally for health recording and statistics, including cause of death certification, morbidity coding in primary through tertiary care, resource allocation, reimbursement systems, quality and safety assessment, and epidemiological research. ICD-10 serves as the foundation for diagnostic-related grouping (DRG), cancer registries, and clinical trials that require standardized disease classification. The classification has been translated into dozens of languages and adapted by many countries for national use, with variants like ICD-10-CM (Clinical Modification) used in the United States and ICD-10-CA used in Canada. While ICD-11 officially came into effect in January 2022, ICD-10 remains widely used during the transition period as countries implement the newer revision. ICD-10 continues to be maintained with periodic updates and serves as the basis for various mapping projects to other terminology systems including SNOMED CT, MedDRA, and LOINC. domains: - clinical homepage_url: https://icd.who.int/browse10 id: icd10 infores_id: icd10 last_modified_date: '2025-11-10T00:00:00Z' layout: resource_detail name: ICD-10 products: - category: GraphicalInterface description: Web-based browser for exploring the ICD-10 classification hierarchy and codes id: icd10.browser name: ICD-10 Browser product_url: https://icd.who.int/browse10 - category: Product description: Official ICD-10 classification files and documentation available for download format: txt id: icd10.downloads name: ICD-10 Downloads product_url: https://www.who.int/standards/classifications/classification-of-diseases - category: DocumentationProduct description: Training materials and courses for learning ICD-10 coding and classification format: http id: icd10.training name: ICD-10 Training product_url: https://icd.who.int/training/icd10training/ warnings: - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ HTTPSConnectionPool(host='icd.who.int', port=443)_ Max retries exceeded with url_ /training/icd10training/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - File was not able to be retrieved when checked on 2025-12-07_ Error connecting to URL_ HTTPSConnectionPool(host='icd.who.int', port=443)_ Max retries exceeded with url_ /training/icd10training/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2025-12-05_ Error connecting to URL_ HTTPSConnectionPool(host='icd.who.int', port=443)_ Max retries exceeded with url_ /training/icd10training/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - category: MappingProduct description: The biannual release of the SNOMED CT to ICD-10-CM Map, which maps SNOMED CT concepts to ICD-10-CM codes. id: snomedct.icd10cm.map name: SNOMED CT to ICD-10-CM Map original_source: - snomedct - icd10 product_url: https://download.nlm.nih.gov/mlb/utsauth/ICD10CM/SNOMED_CT_to_ICD-10-CM_Resources_20250301.zip - category: MappingProduct description: Concept mappings between different terminology systems format: csv id: athena.mappings name: Athena Concept Mappings original_source: - snomedct - icd10 - icd10cm - mesh - loinc - cdiscvocab - ciel product_url: https://athena.ohdsi.org/search-terms/start secondary_source: - athena warnings: - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ Exceeded 30 redirects. - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ Exceeded 30 redirects. - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: Product description: icd10 Nodes TSV format: tsv id: obo-db-ingest.icd10.tsv license: id: https://cdn.who.int/media/docs/default-source/publishing-policies/copyright/who-faq-licensing-icd-10.pdf label: Custom name: icd10 Nodes TSV original_source: - icd10 product_file_size: 40794 product_url: https://w3id.org/biopragmatics/resources/icd10/icd10.tsv secondary_source: - obo-db-ingest publications: - id: https://doi.org/10.1186/s12911-021-01534-6 title: ICD-11 - an international classification of diseases for the twenty-first century repository: https://github.com/ICD-Codes synonyms: - ICD-10 - ICD10 - International Classification of Diseases 10th Revision taxon: - NCBITaxon:9606 - activity_status: active category: Ontology creation_date: '2025-10-30T00:00:00Z' description: ICD-10-CM (International Classification of Diseases, 10th Revision, Clinical Modification) is a clinical modification of the WHO's ICD-10 system, providing diagnostic codes used for billing, epidemiology, and health management in the United States, with greater specificity than the international version. domains: - clinical - health homepage_url: https://icd10cmtool.cdc.gov/ id: icd10cm infores_id: icd10cm last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: ICD-10-CM products: - category: GraphicalInterface description: Interactive web-based search tool for ICD-10-CM codes format: http id: icd10cm.tool name: ICD-10-CM Browser Tool original_source: - icd10cm product_url: https://icd10cmtool.cdc.gov/ - category: MappingProduct description: Concept mappings between different terminology systems format: csv id: athena.mappings name: Athena Concept Mappings original_source: - snomedct - icd10 - icd10cm - mesh - loinc - cdiscvocab - ciel product_url: https://athena.ohdsi.org/search-terms/start secondary_source: - athena warnings: - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ Exceeded 30 redirects. - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ Exceeded 30 redirects. synonyms: - ICD-10-CM - ICD10 Clinical Modification - International Classification of Diseases, 10th Revision, Clinical Modification taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for icd11. This page was automatically generated because it was referenced by other resources. domains: - stub id: icd11 last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Icd11 products: - category: Product description: icd11 Nodes TSV format: tsv id: obo-db-ingest.icd11.tsv license: id: https://creativecommons.org/licenses/by-nc-nd/3.0/igo/deed.en label: CC-BY-ND-3.0-IGO name: icd11 Nodes TSV original_source: - icd11 product_file_size: 4174868 product_url: https://w3id.org/biopragmatics/resources/icd11/icd11.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: kfecho@renci.org - contact_type: github value: karafecho label: Kara Fecho orcid: 0000-0002-6704-9306 creation_date: '2025-11-05T00:00:00Z' description: The Integrated Clinical and Environmental Exposures Service Knowledge Graph (ICEES KG) is a Translator Knowledge Provider that integrates patient-level clinical data from electronic health records with environmental exposures data including airborne pollutants, landfills, concentrated animal feeding operations, and socio-economic indicators. ICEES KG provides regulatory-compliant open access to integrated clinical and environmental data to support translational research on exposure-driven disease mechanisms and health disparities. domains: - health - clinical - biomedical - public health evaluation_page: resource/icees-kg/icees-kg_eval_automated.html homepage_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg id: icees-kg infores_id: icees-kg last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: Exposures KP (icees-kg) products: - category: GraphProduct description: KGX distribution of the ICEES Exposures KP in Knowledge Graph Exchange (KGX) format, containing integrated clinical and environmental exposures data as a knowledge graph with 226 nodes and 14,342 edges format: kgx-jsonl id: icees-kg.graph name: KGX distribution of the ICEES Exposures KP original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/ secondary_source: - icees-kg - category: ProgrammingInterface description: Translator Reasoner API (TRAPI) endpoint for querying ICEES KG using standardized Translator protocols format: http id: icees-kg.trapi name: ICEES KG TRAPI API original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg-trapi secondary_source: - icees-kg - category: Product description: Meta knowledge graph and metadata describing the data sources, node types, edge types, and predicates available in ICEES KG format: json id: icees-kg.metadata name: ICEES KG Metadata original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/metadata-metadata-get-icees-kg secondary_source: - icees-kg - category: GraphProduct description: KGX graph package for ICEES cohort data (build icees_2024-08-20_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.icees.graph name: Translator ICEES KGX Graph original_source: - icees-kg product_url: https://stars.renci.org/var/translator/releases/icees/2025_12_15/ secondary_source: - translator publications: - id: https://doi.org/10.1093/jamia/ocz042 - id: https://doi.org/10.2196/17964 repository: https://github.com/NCATSTranslator/Translator-All/wiki/Exposures-Provider-ICEES tags: - translator taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: liumeng94@sjtu.edu.cn - contact_type: github value: Lemon-Liu label: Meng LIU orcid: 0000-0003-3781-6962 creation_date: '2025-09-29T00:00:00Z' description: ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs). domains: - biological systems homepage_url: https://github.com/ontoice/ICEO id: iceo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Integrative and Conjugative Element Ontology products: - category: OntologyProduct description: Integrative and Conjugative Element Ontology in OWL format format: owl id: iceo.owl name: iceo.owl product_file_size: 1257537 product_url: http://purl.obolibrary.org/obo/iceo.owl repository: https://github.com/ontoice/ICEO - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: yongqunh@med.umich.edu - contact_type: github value: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 creation_date: '2025-09-29T00:00:00Z' description: An ontology of clinical informed consents domains: - biomedical homepage_url: https://github.com/ICO-ontology/ICO id: ico last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Informed Consent Ontology products: - category: OntologyProduct description: Informed Consent Ontology in OWL format format: owl id: ico.owl name: ico.owl product_file_size: 205044 product_url: http://purl.obolibrary.org/obo/ico.owl repository: https://github.com/ICO-ontology/ICO - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for iconclass. This page was automatically generated because it was referenced by other resources. domains: - stub id: iconclass last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Iconclass products: - category: Product description: iconclass OBO format: obo id: obo-db-ingest.iconclass.obo name: iconclass OBO original_source: - iconclass product_file_size: 650455 product_url: https://w3id.org/biopragmatics/resources/iconclass/iconclass.obo secondary_source: - obo-db-ingest - category: Product description: iconclass OWL format: owl id: obo-db-ingest.iconclass.owl name: iconclass OWL original_source: - iconclass product_file_size: 864770 product_url: https://w3id.org/biopragmatics/resources/iconclass/iconclass.owl secondary_source: - obo-db-ingest - category: Product description: iconclass OBO Graph JSON format: json id: obo-db-ingest.iconclass.json name: iconclass OBO Graph JSON original_source: - iconclass product_file_size: 694590 product_url: https://w3id.org/biopragmatics/resources/iconclass/iconclass.json secondary_source: - obo-db-ingest - category: Product description: iconclass Nodes TSV format: tsv id: obo-db-ingest.iconclass.tsv name: iconclass Nodes TSV original_source: - iconclass product_file_size: 611565 product_url: https://w3id.org/biopragmatics/resources/iconclass/iconclass.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: morshedm@renci.org label: Mahir Morshed creation_date: '2025-12-08T00:00:00Z' description: ID Mappings is a FRINK-hosted subset of the Wikidata graph containing mappings between Wikidata entities and external identifiers expressed with standard RDF predicates such as skos:exactMatch, enabling consistent cross-reference and integration across knowledge bases. domains: - general evaluation_page: resource/identifier-mappings/identifier-mappings_eval_automated.html homepage_url: https://frink.renci.org/registry/kgs/identifier-mappings/ id: identifier-mappings last_modified_date: '2026-01-23T00:00:00Z' layout: resource_detail name: ID Mappings products: - category: ProgrammingInterface description: SPARQL endpoint for ID Mappings id: identifier-mappings.sparql name: ID Mappings SPARQL original_source: - identifier-mappings - wikidata product_url: https://frink.apps.renci.org/identifier-mappings/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for ID Mappings id: identifier-mappings.tpf name: ID Mappings TPF original_source: - identifier-mappings - wikidata product_url: https://frink.apps.renci.org/ldf/identifier-mappings - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: url value: https://github.com/zhang-informatics label: Rui Zhang creation_date: '2025-10-30T00:00:00Z' description: The integrated DIetary Supplements Knowledge base (iDISK) is a standardized knowledge base integrating dietary supplement information from multiple authoritative sources including ingredients, products, drug interactions, effectiveness, adverse effects, and therapeutic uses, represented according to established terminology principles with UMLS and MedDRA mappings. domains: - nutrition - biomedical - health - pharmacology evaluation_page: resource/idisk/idisk_eval_automated.html homepage_url: https://doi.org/10.13020/d6bm3v id: idisk infores_id: idisk last_modified_date: '2025-11-25T00:00:00Z' layout: resource_detail name: integrated Dietary Supplement Knowledge Base products: - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi publications: - id: doi:10.1093/jamia/ocz216 preferred: true title: 'iDISK: the integrated DIetary Supplements Knowledge base' year: '2020' repository: https://github.com/zhang-informatics/iDISK synonyms: - iDISK - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Lindsay.Cowell@utsouthwestern.edu - contact_type: github value: lgcowell label: Lindsay Cowell orcid: 0000-0003-1617-8244 creation_date: '2025-06-25T00:00:00Z' description: A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain. domains: - biomedical homepage_url: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology id: ido last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Infectious Disease Ontology products: - category: OntologyProduct description: Infectious Disease Ontology in OWL format format: owl id: ido.owl name: ido.owl product_file_size: 69658 product_url: http://purl.obolibrary.org/obo/ido.owl - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: jinfeng@insilicom.com label: Jinfeng Zhang creation_date: '2025-07-22T00:00:00Z' curators: - category: Organization contact_details: - contact_type: url value: https://insilicom.com/ label: Insilicom description: A large-scale biomedical knowledge graph assembled from PubMed abstracts, containing over 22 million entities and 120 million relations. domains: - health - biomedical - drug discovery - translational - genomics evaluation_page: resource/ikraph/ikraph_eval_automated.html homepage_url: https://biokde.insilicom.com/ id: ikraph last_modified_date: '2025-07-22T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: iKraph products: - category: GraphicalInterface description: Biomedical Knowledge Discovery Engine. Interface for iKraph with search, visualization, and exploration capabilities. format: http id: ikraph.site name: BioKDE original_source: - ikraph product_url: https://biokde.insilicom.com/ secondary_source: - ikraph - category: ProcessProduct description: Code for named entity recognition, relation extraction, and drug repurposing in assembly and analysis of iKraph id: ikraph.code license: id: https://www.gnu.org/licenses/gpl-3.0.en.html label: GPL-3 name: iKraph Code original_source: - ikraph product_url: https://github.com/myinsilicom/iKraph repository: https://github.com/myinsilicom/iKraph secondary_source: - ikraph - category: GraphProduct compression: targz description: Graph metadata for iKraph, including a list of relations, entity type-specific metadata, data sources, and drug repurposing predictions. format: json id: ikraph.graph name: iKraph graph metadata original_source: - ikraph product_file_size: 61183533 product_url: https://zenodo.org/records/14851275/files/data.tar.gz?download=1 secondary_source: - ikraph - category: GraphProduct compression: targz description: Complete graph data for iKraph with all entities and relations extracted from PubMed abstracts id: ikraph.graphdata name: iKraph graph data original_source: - ikraph product_file_size: 1440676039 product_url: https://zenodo.org/records/14851275/files/iKraph_full.tar.gz?download=1 secondary_source: - ikraph publications: - authors: - Zhang Y - Sui X - Pan F - Yu K - Li K - Tian S - Erdengasileng A - Han Q - Wang W - Wang J - Wang J - Sun D - Chung H - Zhou J - Zhou E - Lee B - Zhang P - Qiu X - Zhao T - Zhang J doi: 10.1038/s42256-025-01014-w id: doi:10.1038/s42256-025-01014-w journal: Nature Machine Intelligence preferred: true title: A comprehensive large-scale biomedical knowledge graph for AI-powered data-driven biomedical research year: '2025' repository: https://github.com/myinsilicom/iKraph - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: ecatoiu@ucsd.edu label: Edward Catoiu - category: Organization contact_details: - contact_type: url value: http://systemsbiology.ucsd.edu/ label: Systems Biology Research Group at University of California San Diego creation_date: '2025-11-06T00:00:00Z' description: iModulonDB is a knowledgebase of microbial transcriptional regulation derived from machine learning. It provides curated sets of iModulons - independently modulated groups of co-expressed genes identified through independent component analysis (ICA) of high-quality transcriptomic datasets - for prokaryotic organisms. The database offers interactive dashboards and analysis tools to explore transcriptional regulatory networks across multiple bacterial species, enabling researchers to understand gene regulation, discover new regulators, and analyze condition-specific cellular responses. domains: - systems biology - microbiology homepage_url: https://imodulondb.org/ id: imodulondb last_modified_date: '2025-11-06T00:00:00Z' layout: resource_detail name: iModulonDB products: - category: GraphicalInterface description: Interactive web interface for browsing and analyzing iModulons across 15 prokaryotic organisms with 22 datasets, 1924 curated iModulons, and 9576 expression profiles. Includes organism-specific dataset pages, iModulon dashboards, gene search functionality, and project information pages displaying experimental conditions and publication abstracts. format: http id: imodulondb.browser name: iModulonDB Web Interface original_source: - imodulondb product_url: https://imodulondb.org/ - category: ProgrammingInterface description: Python package for characterization, plotting, and analysis of iModulons. Provides functions for threshold determination, transcriptional regulatory network (TRN) enrichment analysis, explained variance calculation, and generation of dashboard files for iModulonDB. format: http id: imodulondb.pymodulon name: PyModulon Python Package original_source: - imodulondb product_url: https://github.com/SBRG/pymodulon - category: Product description: Computational pipeline for gathering publicly available RNA-seq data, aligning reads, performing quality control, computing iModulons using independent component analysis, and formatting dashboard files. Enables users to generate their own iModulon decompositions from transcriptomic datasets. format: http id: imodulondb.imodulonminer name: iModulonMiner Pipeline original_source: - imodulondb product_url: https://github.com/SBRG/iModulonMiner - category: Product description: Modulome workflow for scraping publicly available data for an organism, aligning reads, quality control, and computing iModulons. Used to expand iModulonDB across the prokaryotic evolutionary tree by processing data from the Sequence Read Archive. format: http id: imodulondb.modulome_workflow name: Modulome Workflow original_source: - imodulondb product_url: https://github.com/avsastry/modulome-workflow - category: Product description: Downloadable transcriptomic datasets and iModulon decompositions for 15 organisms including E. coli, B. subtilis, S. aureus, M. tuberculosis, P. aeruginosa, P. putida, and others. Includes gene expression matrices, iModulon activity matrices, gene weights, and metadata for over 9500 expression profiles from 525 studies. format: mixed id: imodulondb.datasets name: iModulonDB Datasets original_source: - imodulondb product_url: https://imodulondb.org/ publications: - authors: - Catoiu EA - Krishnan J - Li G - Lou XA - Rychel K - Yuan Y - Bajpe H - Patel A - Choe D - Shin J - Decker KT - Chauhan SM - Phaneuf PV - Palsson BO doi: doi:10.1093/nar/gkae1009 id: https://doi.org/10.1093/nar/gkae1009 journal: Nucleic Acids Research preferred: true title: 'iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets' year: '2025' - authors: - Rychel K - Decker K - Sastry AV - Phaneuf PV - Poudel S - Palsson BO doi: doi:10.1093/nar/gkaa810 id: https://doi.org/10.1093/nar/gkaa810 journal: Nucleic Acids Research preferred: false title: 'iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning' year: '2021' repository: https://github.com/SBRG/iModulonMiner taxon: - NCBITaxon:2 - activity_status: active category: DataModel creation_date: '2026-02-18T00:00:00Z' description: InChIKey is a fixed-length hashed representation of the IUPAC International Chemical Identifier (InChI), used for indexing and linking chemical structures across resources. domains: - chemistry and biochemistry - drug discovery homepage_url: https://www.inchi-trust.org/ id: inchikey last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail name: InChIKey products: - category: DocumentationProduct description: InChI Trust documentation and supporting material for the InChI/InChIKey identifier standard. format: http id: inchikey.docs name: InChI/InChIKey Documentation original_source: - inchikey product_url: https://www.inchi-trust.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv synonyms: - InChI key - IUPAC InChIKey - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://indra.readthedocs.io/en/latest/ - contact_type: github value: sorgerlab label: Sorger Lab, Harvard Medical School - category: Organization contact_details: - contact_type: url value: https://gyorilab.github.io/ label: Gyori Lab, Northeastern University creation_date: '2025-07-19T00:00:00Z' description: INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models. domains: - biomedical - systems biology homepage_url: https://www.indra.bio/ id: indra last_modified_date: '2025-07-20T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/BSD-2-Clause label: BSD 2-Clause License name: INDRA products: - category: GraphicalInterface description: Web interface for the INDRA Biomedical Discovery Engine format: http id: indra.discovery name: INDRA Biomedical Discovery Engine original_source: - indra product_url: https://discovery.indra.bio/ - category: ProgrammingInterface description: REST API for INDRA CoGEx queries format: http id: indra.api.cogex name: INDRA CoGEx Query API original_source: - indra product_url: https://discovery.indra.bio/apidocs - category: ProcessProduct description: Python library for automated model assembly from mechanistic knowledge format: python id: indra.python name: INDRA Python Library original_source: - indra product_url: https://github.com/sorgerlab/indra repository: https://github.com/sorgerlab/indra - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra repository: https://github.com/sorgerlab/indra - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: innatedb-mail@sfu.ca label: Brinkman Laboratory, Simon Fraser University creation_date: '2025-10-30T00:00:00Z' description: InnateDB is a publicly available database of genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection, with over 18,780 manually curated interactions and integrated bioinformatics and visualization tools for systems-level analysis. domains: - immunology - biological systems - systems biology homepage_url: https://www.innatedb.com/ id: innatedb infores_id: innatedb last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: InnateDB products: - category: GraphicalInterface description: Web interface for searching and analyzing innate immunity genes, proteins, interactions, and pathways format: http id: innatedb.portal name: InnateDB Web Portal original_source: - innatedb product_url: https://www.innatedb.com/ - category: Product description: Downloadable data files for interactions, pathways, and annotations id: innatedb.downloads name: InnateDB Data Downloads original_source: - innatedb product_url: https://www.innatedb.com/ publications: - id: https://doi.org/10.1093/nar/gks1147 journal: Nucleic Acids Research title: 'InnateDB: systems biology of innate immunity and beyond - recent updates and continuing curation' year: '2013' synonyms: - InnateDB taxon: - NCBITaxon:2 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: yongqunh@med.umich.edu - contact_type: github value: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 creation_date: '2025-09-29T00:00:00Z' description: An ontology of interactions and interaction networks domains: - biological systems homepage_url: https://github.com/INO-ontology/ino id: ino last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Interaction Network Ontology products: - category: OntologyProduct description: Interaction Network Ontology in OWL format format: owl id: ino.owl name: ino.owl product_file_size: 56433 product_url: http://purl.obolibrary.org/obo/ino.owl repository: https://github.com/INO-ontology/ino - activity_status: active category: KnowledgeGraph collection: - aop contacts: - category: Organization contact_details: - contact_type: url value: https://insight-project.org/ label: INSIGHT Project Team creation_date: '2025-08-30T00:00:00Z' description: INSIGHT is an integrative knowledge graph resource designed to support translational and clinical informatics by linking heterogeneous biomedical entities (genes, variants, diseases, phenotypes, pathways, drugs, and clinical concepts) with provenance and harmonized semantics to enable multi-scale reasoning and decision support. domains: - biomedical - systems biology - clinical - genomics - toxicology evaluation_page: resource/insight/insight_eval_automated.html homepage_url: https://insight-project.org/ id: insight last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: INSIGHT products: - category: GraphicalInterface description: INSIGHT project web portal for project updates, consortium information, and dissemination materials. format: http id: insight.portal name: INSIGHT Project Portal original_source: - insight product_url: https://insight-project.org/ publications: - doi: 10.1016/j.csbj.2025.03.042 id: doi:10.1016/j.csbj.2025.03.042 journal: Computational and Structural Biotechnology Journal title: 'INSIGHT: an integrative clinical and translational biomedical knowledge graph for multi-scale analytics' year: '2025' taxon: - NCBITaxon:9606 - activity_status: active category: Aggregator collection: - ber contacts: - category: Organization contact_details: - contact_type: url value: https://www.ebi.ac.uk/support/intact id: ebi label: IntAct Team (EMBL-EBI) creation_date: '2025-07-08T00:00:00Z' description: IntAct is an open, curated molecular interaction database maintained at EMBL‑EBI. It aggregates experimentally-derived interaction evidence from literature curation and direct submissions, and distributes data in PSI‑MI XML and MITAB formats along with curated datasets and documentation. domains: - proteomics - systems biology homepage_url: https://www.ebi.ac.uk/intact/home id: intact infores_id: intact last_modified_date: '2025-09-09T00:00:00Z' layout: resource_detail license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: IntAct products: - category: GraphicalInterface description: Web portal for browsing, searching, and accessing IntAct molecular interaction data format: http id: intact.portal name: IntAct Portal original_source: - intact product_url: https://www.ebi.ac.uk/intact/home - category: Product description: IntAct data in PSI-MI XML 2.5 format (directory) format: psi_mi_xml id: intact.ftp.psi25 name: IntAct PSI-MI XML 2.5 original_source: - intact product_url: https://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/ - category: Product description: IntAct data in PSI-MI XML 3.0 format (directory) format: psi_mi_xml id: intact.ftp.psi30 name: IntAct PSI-MI XML 3.0 original_source: - intact product_url: https://ftp.ebi.ac.uk/pub/databases/intact/current/psi30/ - category: Product description: IntAct data in PSI-MI MITAB format (directory) format: psi_mi_mitab id: intact.ftp.psimitab name: IntAct PSI-MI MITAB 2.7 original_source: - intact product_url: https://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/ - category: Product description: Entire MITAB export of the database as a single archive (intact.zip) format: psi_mi_mitab id: intact.ftp.psimitab.all name: IntAct MITAB Archive original_source: - intact product_file_size: 846305671 product_url: https://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip - category: Product description: Curated and computational datasets (disease-, method-, and species-specific) with per-dataset downloads format: http id: intact.datasets name: IntAct Datasets original_source: - intact product_url: https://www.ebi.ac.uk/intact/download/datasets - category: DocumentationProduct description: User guide and documentation for search, exports, data sources, and submission format: http id: intact.docs.user-guide name: IntAct User Guide original_source: - intact product_url: https://www.ebi.ac.uk/intact/documentation/user-guide - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 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interpro product_file_size: 697846 product_url: https://w3id.org/biopragmatics/resources/interpro/interpro.tsv secondary_source: - obo-db-ingest publications: - authors: - Blum M - Andreeva A - Florentino LC - Chuguransky SR - Grego T - Hobbs E - Pinto BL - Orr A - Paysan-Lafosse T - Ponamareva I - Salazar GA - Bordin N - Bork P - Bridge A - Colwell L - Gough J - Haft DH - Letunic I - Llinares-López F - Marchler-Bauer A - Meng-Papaxanthos L - Mi H - Natale DA - Orengo CA - Pandurangan AP - Piovesan D - Rivoire C - Sigrist CJA - Thanki N - Thibaud-Nissen F - Thomas PD - Tosatto SCE - Wu CH - Bateman A doi: doi:10.1093/nar/gkae1082 id: doi:10.1093/nar/gkae1082 preferred: true title: 'InterPro: the protein sequence classification resource in 2025' year: '2024' repository: https://www.ebi.ac.uk/interpro/ - activity_status: active category: DataSource creation_date: '2025-11-13T00:00:00Z' description: iPTMnet is an integrated resource for protein post-translational modification (PTM) network discovery that employs an integrative bioinformatics approach combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs), and PTM conservation across species. domains: - proteomics homepage_url: https://research.bioinformatics.udel.edu/iptmnet/ id: iptmnet infores_id: iptmnet last_modified_date: '2025-11-13T00:00:00Z' layout: resource_detail name: iPTMnet products: - category: GraphicalInterface description: Interactive web interface for exploring and visualizing kinase-substrate interactions format: http id: kinace.portal name: KinAce Web Portal original_source: - phosphositeplus - iptmnet - uniprot - epsd - kinhub - coralkinome - darkkinasekb - hgnc - kegg - interpro product_url: https://kinace.kinametrix.com/ secondary_source: - kinace publications: - id: PMID:29145615 synonyms: [] - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: url value: https://www.itis.gov/ - contact_type: email value: itiswebmaster@itis.gov label: Integrated Taxonomic Information System (ITIS) creation_date: '2025-09-03T00:00:00Z' description: The Integrated Taxonomic Information System (ITIS) provides authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. 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biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz - category: Product description: kegg.genome Nodes TSV format: tsv id: obo-db-ingest.kegg.genome.tsv license: id: https://www.kegg.jp/kegg/legal.html label: Custom name: kegg.genome Nodes TSV original_source: - kegg product_file_size: 187935 product_url: https://w3id.org/biopragmatics/resources/kegg.genome/kegg.genome.tsv secondary_source: - obo-db-ingest publications: - id: doi:10.1093/nar/gkae909 preferred: true title: KEGG biological systems database as a model of the real world taxon: - NCBITaxon:10116 - NCBITaxon:9606 - NCBITaxon:10090 - NCBITaxon:7227 - NCBITaxon:6239 - NCBITaxon:7955 - NCBITaxon:4932 - NCBITaxon:3702 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: jhc@lbl.gov - contact_type: github value: caufieldjh label: J. Harry Caufield orcid: 0000-0001-5705-7831 creation_date: '2025-03-18T00:00:00Z' description: A Knowledge Graph for integrating data related to Alzheimer's disease, supporting Retrieval-Augmented Generation (RAG) and AI assistant development for Alzheimer's disease research. domains: - health - neuroscience - biomedical evaluation_page: resource/kg-alzheimers/kg-alzheimers_eval_automated.html homepage_url: https://kghub.org/kg-alzheimers/index.html id: kg-alzheimers last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: KG-Alzheimers products: - category: GraphProduct compression: targz description: KGX Distribution of KG-Alzheimers format: kgx id: kg-alzheimers.graph name: KGX Distribution of KG-Alzheimers original_source: - kg-alzheimers product_file_size: 210868256 product_url: https://kg-hub.berkeleybop.io/kg-alzheimers/current/kg-alzheimers.tar.gz secondary_source: - kg-alzheimers repository: https://github.com/Knowledge-Graph-Hub/kg-alzheimers taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: justaddcoffee label: Justin Reese creation_date: '2025-03-09T00:00:00Z' description: A knowledge graph for COVID-19 and SARS-COV-2. domains: - organisms - health - microbiology - public health evaluation_page: resource/kg-covid-19/kg-covid-19_eval_automated.html homepage_url: https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki id: kg-covid-19 last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://opensource.org/license/bsd-3-clause label: BSD3 name: KG-COVID-19 products: - category: GraphProduct description: KGX nodes and edges for KG-COVID-19 format: kgx id: kg-covid-19.graph name: KG-COVID-19 graph original_source: - kg-covid-19 product_url: https://kghub.io/kg-covid-19/ secondary_source: - kg-covid-19 warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-11-17_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/Knowledge-Graph-Hub/kg-covid-19 - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual contact_details: - contact_type: email value: colxu@scripps.edu - contact_type: github value: colleenXu label: Colleen Xu creation_date: '2025-05-07T00:00:00Z' description: An ingest of EMBL-EBI's Gene2Phenotype resource, for Translator use (output in Translator standards and NodeNormed, using own custom pipeline) domains: - health evaluation_page: resource/kg-ebi-gene2pheno/kg-ebi-gene2pheno_eval_automated.html id: kg-ebi-gene2pheno last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: EBI Gene2Phenotype KG products: - category: GraphProduct description: KGX nodes file for EBI Gene2Phenotype KG format: kgx-jsonl id: kg-ebi-gene2pheno.nodes.kgx name: EBI gene2pheno KGX nodes product_file_size: 62139 product_url: https://github.com/biothings/pending.api/blob/translator-output/plugins/ebi_gene2phenotype/EBIgene2pheno_kgx_nodes.jsonl - category: GraphProduct description: KGX edges file for EBI Gene2Phenotype KG format: kgx-jsonl id: kg-ebi-gene2pheno.edges.kgx name: EBI gene2pheno KGX edges product_file_size: 133106 product_url: https://github.com/biothings/pending.api/blob/translator-output/plugins/ebi_gene2phenotype/EBIgene2pheno_kgx_edges.jsonl - category: GraphProduct description: TRAPI edges file for EBI Gene2Phenotype KG format: trapi-jsonl id: kg-ebi-gene2pheno.edges.trapi name: EBI gene2pheno TRAPI edges product_file_size: 142045 product_url: https://github.com/biothings/pending.api/blob/translator-output/plugins/ebi_gene2phenotype/EBIgene2pheno_trapi_edges.jsonl repository: https://github.com/biothings/pending.api/tree/translator-output/plugins/ebi_gene2phenotype - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: oolonek label: Pierre-Marie Allard creation_date: '2026-01-06T00:00:00Z' description: ENP-KG is a specialized knowledge graph for experimental natural products discovery and characterization. It integrates chemical spectroscopy data, natural product structures, and organism information to support drug discovery research and chemical ecology applications. The knowledge graph provides a unified platform for exploring relationships between organisms and their secondary metabolites. domains: - organisms - drug discovery evaluation_page: resource/kg-enp/kg-enp_eval_automated.html homepage_url: https://enpkg.commons-lab.org/ id: kg-enp last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: kg-enp products: - category: GraphicalInterface description: Web-based interactive portal for exploring experimental natural products, chemical structures, and organism relationships with data visualization format: http id: kg-enp.portal name: ENP-KG Portal product_url: https://enpkg.commons-lab.org/ repository: https://github.com/enpkg/enpkg_full - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: jhc@lbl.gov - contact_type: github value: caufieldjh label: J. Harry Caufield orcid: 0000-0001-5705-7831 creation_date: '2025-03-09T00:00:00Z' description: a Knowledge Graph for Illuminating the Druggable Genome domains: - health evaluation_page: resource/kg-idg/kg-idg_eval_automated.html homepage_url: https://kghub.org/kg-idg/index.html id: kg-idg last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://opensource.org/license/bsd-3-clause label: BSD3 name: KG-IDG products: - category: GraphProduct description: KGX Distribution of KG-IDG format: kgx id: kg-idg.graph name: KGX Distribution of KG-IDG original_source: - kg-idg product_url: https://kg-hub.berkeleybop.io/kg-idg/current/kg-microbe.tar.gz secondary_source: - kg-idg warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/Knowledge-Graph-Hub/kg-idg - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual contact_details: - contact_type: email value: colxu@scripps.edu - contact_type: github value: colleenXu label: Colleen Xu creation_date: '2025-05-06T00:00:00Z' description: An ingest of Jensen Lab's DISEASES resource, for Translator use (output in Translator standards and NodeNormed, using own custom pipeline) domains: - health evaluation_page: resource/kg-jensenlab-diseases/kg-jensenlab-diseases_eval_automated.html id: kg-jensenlab-diseases last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: JensenLab DISEASES KG products: - category: GraphProduct description: KGX nodes file for JensenLab DISEASES KG format: kgx-jsonl id: kg-jensenlab-diseases.nodes.kgx name: DISEASES KGX nodes product_file_size: 130 product_url: https://github.com/biothings/pending.api/blob/translator-output/plugins/DISEASES/DISEASES_kgx_nodes.jsonl - category: GraphProduct description: KGX edges file for JensenLab DISEASES KG format: kgx-jsonl id: kg-jensenlab-diseases.edges.kgx name: DISEASES KGX edges product_file_size: 132 product_url: https://github.com/biothings/pending.api/blob/translator-output/plugins/DISEASES/DISEASES_kgx_edges.jsonl - category: GraphProduct description: TRAPI edges file for JensenLab DISEASES KG format: trapi-jsonl id: kg-jensenlab-diseases.edges.trapi name: DISEASES TRAPI edges product_file_size: 132 product_url: https://github.com/biothings/pending.api/blob/translator-output/plugins/DISEASES/DISEASES_trapi_edges.jsonl repository: https://github.com/biothings/pending.api/tree/translator-output/plugins/DISEASES - activity_status: active category: KnowledgeGraph collection: - ber contacts: - category: Individual contact_details: - contact_type: email value: MJoachimiak@lbl.gov - contact_type: github value: realmarcin label: Marcin P. Joachimiak creation_date: '2025-03-09T00:00:00Z' description: A Knowledge Graph about microbes. The KG is designed to integrate diverse knowledge about microbes from a variety of structured and unstructured sources. domains: - microbiology - organisms - phenotype - microbiome - biological systems evaluation_page: resource/kg-microbe/kg-microbe_eval_automated.html homepage_url: https://kghub.org/kg-microbe/index.html id: kg-microbe last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://opensource.org/license/bsd-3-clause label: BSD3 name: KG Microbe products: - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: UniProt proteins from microbes, as graph nodes and edges format: kgx id: kg-microbe.graph.uniprot name: KG-Microbe UniProt microbe transform original_source: - uniprot product_file_size: 4796343398 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-transformed-uniprot-microbes-20240924.tar.gz secondary_source: - kg-microbe repository: https://github.com/Knowledge-Graph-Hub/kg-microbe taxon: - NCBITaxon:2 - NCBITaxon:2759 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Christopher J. Mungall orcid: 0000-0002-6601-2165 - category: Organization contact_details: - contact_type: other contact_type_name: Monarch Initiative Community contact_type_url: https://groups.google.com/g/monarch-friends/ value: monarch-friends id: monarchinitiative label: Monarch Initiative creation_date: '2025-03-09T00:00:00Z' description: The Monarch Initiative is an international consortium that leads key global standards and semantic data integration technologies. To maximize utility and impact, the Monarch platform is composed of multiple open-source, open-access components. domains: - health evaluation_page: resource/kg-monarch/kg-monarch_eval.html homepage_url: https://kghub.org/kg-monarch/index.html id: kg-monarch last_modified_date: '2026-03-11T22:49:43Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: KG Monarch products: - category: GraphProduct description: KGX Distribution of KG-Monarch edge_count: 15356321 format: kgx id: kg-monarch.graph name: KGX Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 230877741 product_url: http://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz secondary_source: - kg-monarch - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch (Edges) edge_count: 15356321 format: kgx-jsonl id: kg-monarch.graph.jsonl.edges name: KGX JSON-L Distribution of KG-Monarch Edges node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 15279494795 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.jsonl secondary_source: - kg-monarch - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch (Nodes) edge_count: 15356321 format: kgx-jsonl id: kg-monarch.graph.jsonl.nodes name: KGX JSON-L Distribution of KG-Monarch Nodes node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 1149505896 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.jsonl secondary_source: - kg-monarch - category: GraphProduct description: RDF Distribution of KG-Monarch edge_count: 15356321 format: rdfxml id: kg-monarch.graph.rdf name: RDF Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 879238775 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.nt.gz secondary_source: - kg-monarch - category: GraphProduct description: Neo4j Dump of KG-Monarch Edges edge_count: 15356321 format: neo4j id: kg-monarch.graph.neo4j.edges name: Neo4j Dump of KG-Monarch Edges node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 4386388748 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.neo4j.csv secondary_source: - kg-monarch - category: GraphProduct description: Neo4j Dump of KG-Monarch Nodes edge_count: 15356321 format: neo4j id: kg-monarch.graph.neo4j.nodes name: Neo4j Dump of KG-Monarch Nodes node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 349573789 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.neo4j.csv secondary_source: - kg-monarch - category: GraphProduct description: DuckDB database of KG-Monarch edge_count: 15356321 id: kg-monarch.graph.duckdb name: DuckDB database of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 6827814912 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.duckdb secondary_source: - kg-monarch - category: ProcessProduct description: This repository is a code reference for the C-Path Knowledge Graph project, to increase discoverability of rare disease datasets through integration with the Monarch Knowlege Graph. Note that this is only a reference to scripts and queries associated with this project and is not provided as a runnable project because these workflows depend on an internal data catalog. format: python id: cpathkg.code name: C-Path Knowledge Graph Integration original_source: - biolink - kg-monarch product_url: https://gitlab.c-path.org/c-pathontology/c-path-knowledge-graph-integration secondary_source: - cpathkg - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch edge_count: 15356321 format: kgx-jsonl id: kg-monarch.graph.jsonl name: KGX JSON-L Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 315667976 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz secondary_source: - kg-monarch - category: GraphProduct description: Neo4j Dump of KG-Monarch dump_format: neo4j edge_count: 15356321 id: kg-monarch.graph.neo4j name: Neo4j Dump of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 1438250397 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.neo4j.dump secondary_source: - kg-monarch warnings: [] - category: Product description: All associations from the Monarch Knowledge Graph in TSV format format: tsv id: kg-monarch.associations.all name: All Associations original_source: - kg-monarch product_file_size: 50883784 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Causal gene to disease associations format: tsv id: kg-monarch.associations.causal_gene_to_disease name: Causal Gene to Disease Associations original_source: - kg-monarch product_file_size: 173184 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/causal_gene_to_disease_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Chemical or drug or treatment to disease or phenotypic feature associations format: tsv id: kg-monarch.associations.chemical_or_drug_to_disease name: Chemical/Drug/Treatment to Disease/Phenotypic Feature Associations original_source: - kg-monarch product_file_size: 19562 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Chemical to disease or phenotypic feature associations format: tsv id: kg-monarch.associations.chemical_to_disease name: Chemical to Disease/Phenotypic Feature Associations original_source: - kg-monarch product_file_size: 630460 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/chemical_to_disease_or_phenotypic_feature_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Chemical to pathway associations format: tsv id: kg-monarch.associations.chemical_to_pathway name: Chemical to Pathway Associations original_source: - kg-monarch product_file_size: 2595240 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/chemical_to_pathway_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Correlated gene to disease associations format: tsv id: kg-monarch.associations.correlated_gene_to_disease name: Correlated Gene to Disease Associations original_source: - kg-monarch product_file_size: 232463 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/correlated_gene_to_disease_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Disease or phenotypic feature to genetic inheritance associations format: tsv id: kg-monarch.associations.disease_to_inheritance name: Disease/Phenotypic Feature to Genetic Inheritance Associations original_source: - kg-monarch product_file_size: 240991 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/disease_or_phenotypic_feature_to_genetic_inheritance_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Disease or phenotypic feature to location associations format: tsv id: kg-monarch.associations.disease_to_location name: Disease/Phenotypic Feature to Location Associations original_source: - kg-monarch product_file_size: 22009 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/disease_or_phenotypic_feature_to_location_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Disease to phenotypic feature associations format: tsv id: kg-monarch.associations.disease_to_phenotype name: Disease to Phenotypic Feature Associations original_source: - kg-monarch product_file_size: 8305765 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/disease_to_phenotypic_feature_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Gene to expression site associations format: tsv id: kg-monarch.associations.gene_to_expression_site name: Gene to Expression Site Associations original_source: - kg-monarch product_file_size: 49551885 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/gene_to_expression_site_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Gene to gene homology associations format: tsv id: kg-monarch.associations.gene_to_gene_homology name: Gene to Gene Homology Associations original_source: - kg-monarch product_file_size: 39739502 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/gene_to_gene_homology_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Gene to pathway associations format: tsv id: kg-monarch.associations.gene_to_pathway name: Gene to Pathway Associations original_source: - kg-monarch product_file_size: 6256794 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/gene_to_pathway_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Gene to phenotypic feature associations format: tsv id: kg-monarch.associations.gene_to_phenotype name: Gene to Phenotypic Feature Associations original_source: - kg-monarch product_file_size: 21465491 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/gene_to_phenotypic_feature_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Genotype to disease associations format: tsv id: kg-monarch.associations.genotype_to_disease name: Genotype to Disease Associations original_source: - kg-monarch product_file_size: 486257 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/genotype_to_disease_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Genotype to gene associations format: tsv id: kg-monarch.associations.genotype_to_gene name: Genotype to Gene Associations original_source: - kg-monarch product_file_size: 4186637 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/genotype_to_gene_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Genotype to phenotypic feature associations format: tsv id: kg-monarch.associations.genotype_to_phenotype name: Genotype to Phenotypic Feature Associations original_source: - kg-monarch product_file_size: 22271794 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/genotype_to_phenotypic_feature_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Genotype to variant associations format: tsv id: kg-monarch.associations.genotype_to_variant name: Genotype to Variant Associations original_source: - kg-monarch product_file_size: 5898563 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/genotype_to_variant_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Macromolecular machine to biological process associations format: tsv id: kg-monarch.associations.macromolecular_machine_to_biological_process name: Macromolecular Machine to Biological Process Associations original_source: - kg-monarch product_file_size: 33957550 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/macromolecular_machine_to_biological_process_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Macromolecular machine to cellular component associations format: tsv id: kg-monarch.associations.macromolecular_machine_to_cellular_component name: Macromolecular Machine to Cellular Component Associations original_source: - kg-monarch product_file_size: 19600342 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/macromolecular_machine_to_cellular_component_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Macromolecular machine to molecular activity associations format: tsv id: kg-monarch.associations.macromolecular_machine_to_molecular_activity name: Macromolecular Machine to Molecular Activity Associations original_source: - kg-monarch product_file_size: 24519759 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/macromolecular_machine_to_molecular_activity_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Pairwise gene to gene interaction associations format: tsv id: kg-monarch.associations.pairwise_gene_to_gene_interaction name: Pairwise Gene to Gene Interaction Associations original_source: - kg-monarch product_file_size: 53935441 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/pairwise_gene_to_gene_interaction.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Variant to disease associations format: tsv id: kg-monarch.associations.variant_to_disease name: Variant to Disease Associations original_source: - kg-monarch product_file_size: 439945 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/variant_to_disease_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Variant to gene associations format: tsv id: kg-monarch.associations.variant_to_gene name: Variant to Gene Associations original_source: - kg-monarch product_file_size: 4273160 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/variant_to_gene_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Variant to phenotypic feature associations format: tsv id: kg-monarch.associations.variant_to_phenotype name: Variant to Phenotypic Feature Associations original_source: - kg-monarch product_file_size: 9841001 product_url: https://data.monarchinitiative.org/monarch-kg/latest/tsv/all_associations/variant_to_phenotypic_feature_association.all.tsv.gz secondary_source: - kg-monarch - category: Product description: Phenio SQLite database in SemSQL format for ontology queries format: sqlite id: kg-monarch.phenio.semsql name: Phenio SQLite (SemSQL) original_source: - phenio product_file_size: 3425435914 product_url: https://data.monarchinitiative.org/monarch-kg/latest/phenio.db.gz secondary_source: - kg-monarch - category: Product compression: targz description: Solr index data for the Monarch Knowledge Graph search functionality id: kg-monarch.solr name: Solr Data original_source: - kg-monarch product_file_size: 34691273954 product_url: https://data.monarchinitiative.org/monarch-kg/latest/solr.tar.gz - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb repository: https://github.com/monarch-initiative/monarch-ingest - activity_status: active category: KnowledgeGraph creation_date: '2025-11-22T00:00:00Z' description: KG-Predict is a knowledge graph computational framework for drug repurposing that integrates multiple types of genotypic and phenotypic data. The framework constructs GP-KG (Genotype-Phenotype Knowledge Graph), containing 1,246,726 associations between 61,146 biomedical entities from various databases. KG-Predict uses graph embedding methods to learn low-dimensional representations of entities and relations, enabling inference of new drug-disease interactions. The system has been validated for identifying repositioned candidate drugs, particularly for Alzheimer's disease, achieving high performance metrics (AUROC = 0.981, AUPR = 0.409) and successfully prioritizing FDA-approved and clinical trial anti-AD drugs. domains: - drug discovery - systems biology - biomedical - pharmacology - translational - genomics - phenotype evaluation_page: resource/kg-predict/kg-predict_eval_automated.html homepage_url: http://nlp.case.edu/public/data/GPKG-Predict/ id: kg-predict last_modified_date: '2025-11-22T00:00:00Z' layout: resource_detail license: id: https://www.elsevier.com/open-access/userlicense/1.0/ label: Elsevier User License name: KG-Predict products: - category: GraphProduct description: GP-KG knowledge graph containing 1,246,726 associations between 61,146 entities from multiple genotypic and phenotypic databases format: csv id: kg-predict.gpkg name: GP-KG Knowledge Graph Data original_source: - kg-predict product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/ - category: ProcessProduct description: Python implementation of KG-Predict framework for graph embedding and drug repurposing prediction id: kg-predict.code name: KG-Predict Code original_source: - kg-predict product_url: http://nlp.case.edu/public/data/GPKG-Predict/code/ - category: Product description: Alzheimer's disease case study predictions and clinical trial evidence format: csv id: kg-predict.ad_predictions name: AD Drug Predictions original_source: - kg-predict product_url: http://nlp.case.edu/public/data/GPKG-Predict/ publications: - authors: - Gao Z - Ding P - Xu R doi: 10.1016/j.jbi.2022.104133 id: PMID:35690340 journal: Journal of Biomedical Informatics title: 'KG-Predict: A knowledge graph computational framework for drug repurposing' year: '2022' synonyms: - GPKG-Predict - GP-KG taxon: - NCBITaxon:9606 - activity_status: active category: DataModel contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Christopher J. Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-03-09T00:00:00Z' description: A data model for describing change operations at a high level on an ontology or ontology-like artefact, such as a Knowledge Graph. KGCL enables standardized representation of changes in ontologies and knowledge graphs for tracking, auditing, and reproducibility. It provides a formal language for representing and documenting changes in knowledge graphs, facilitating version control, change history, and collaboration. domains: - information technology homepage_url: https://incatools.github.io/kgcl/ id: kgcl last_modified_date: '2025-08-06T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: Knowledge Graph Change Language products: - category: DataModelProduct description: OWL release of Knowledge Graph Change Language, provides a formal semantic model for representing change operations in ontologies and knowledge graphs. format: owl id: kgcl.model.owl name: Knowledge Graph Change Language OWL release original_source: - kgcl product_file_size: 11700 product_url: https://w3id.org/kgcl/kgcl.owl.ttl secondary_source: - kgcl - category: ProcessProduct description: Python implementation of the Knowledge Graph Change Language standard, including a LinkML model and LARK grammar for parsing and generating KGCL statements. id: kgcl.python name: KGCL Python Implementation original_source: - kgcl product_url: https://github.com/INCATools/kgcl/ secondary_source: - kgcl - category: DataModelProduct description: JSON-LD context for the Knowledge Graph Change Language model, enabling semantic interoperability for KGCL data. format: jsonld id: kgcl.model.jsonld name: Knowledge Graph Change Language JSON-LD Context original_source: - kgcl product_file_size: 2161 product_url: https://w3id.org/kgcl/kgcl.context.jsonld secondary_source: - kgcl - category: DataModelProduct description: SHACL shapes for validating Knowledge Graph Change Language instances. format: shacl id: kgcl.model.shacl name: Knowledge Graph Change Language SHACL Shapes original_source: - kgcl product_file_size: 15868 product_url: https://w3id.org/kgcl/kgcl.shacl.ttl secondary_source: - kgcl - category: DataModelProduct description: YAML schema representation of the Knowledge Graph Change Language model. format: yaml id: kgcl.model.yaml name: Knowledge Graph Change Language YAML Schema original_source: - kgcl product_file_size: 7492 product_url: https://w3id.org/kgcl/kgcl.yaml secondary_source: - kgcl publications: - authors: - Hegde H - Vendetti J - Goutte-Gattat D - Caufield JH - Graybeal JB - Harris NL - Karam N - Kindermann C - Matentzoglu N - Overton JA - Mungall CJ id: doi:10.1093/database/baae133 journal: Database preferred: true title: A change language for ontologies and knowledge graphs year: '2025' repository: https://github.com/INCATools/kgcl/ version: 0.7.0 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: support@kidsfirstdrc.org - contact_type: url value: https://kidsfirstdrc.org/ label: Kids First Data Resource Center - category: Organization contact_details: - contact_type: url value: https://d3b.center/ label: Children's Hospital of Philadelphia creation_date: '2025-06-04T00:00:00Z' description: The Gabriella Miller Kids First Pediatric Research Program Data Resource Center (Kids First DRC) provides researchers access to genomic and clinical data from pediatric cancer and structural birth defect cohorts to accelerate discovery and development of more effective treatments. domains: - health - biomedical - genomics - clinical homepage_url: https://kidsfirstdrc.org/ id: kidsfirst last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail name: Kids First Data Resource Center products: - category: GraphicalInterface description: Centralized platform providing access to harmonized clinical and genomic data from childhood cancer and congenital disorder cohorts, supporting cohort discovery and analysis. id: kidsfirst.portal name: Kids First Data Resource Portal product_url: https://portal.kidsfirstdrc.org/ - category: GraphicalInterface description: Cloud-based analysis platform for Kids First data, allowing researchers to analyze and integrate genomic and clinical data in a secure environment. id: kidsfirst.cavatica name: CAVATICA Platform product_url: https://cavatica.sbgenomics.com/ - category: GraphicalInterface description: Web-based tool for exploring and visualizing pediatric cancer genomic datasets, integrated with clinical data. id: kidsfirst.pedcbioportal name: PedcBioPortal product_url: https://pedcbioportal.kidsfirstdrc.org/ - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg repository: https://github.com/kids-first/ taxon: - NCBITaxon:9606 - activity_status: active category: Aggregator creation_date: '2025-11-05T00:00:00Z' description: The KinAce web portal aggregates and visualizes the network of interactions between protein kinases and their substrates in the human genome. KinAce integrates data from multiple sources including PhosphoSitePlus, iPTMnet, EPSD, KinHub, CORAL, Dark Kinase Knowledgebase, UniProt, HGNC, KEGG, and InterPro, providing comprehensive phosphorylation site data and kinase-substrate relationships. domains: - proteomics - systems biology - biomedical - biological systems homepage_url: https://kinace.kinametrix.com/ id: kinace infores_id: kinace last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: KinAce products: - category: GraphicalInterface description: Interactive web interface for exploring and visualizing kinase-substrate interactions format: http id: kinace.portal name: KinAce Web Portal original_source: - phosphositeplus - iptmnet - uniprot - epsd - kinhub - coralkinome - darkkinasekb - hgnc - kegg - interpro product_url: https://kinace.kinametrix.com/ secondary_source: - kinace synonyms: - KinAce taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-11-05T00:00:00Z' description: A comprehensive resource for human protein kinases featuring KinMap, an interactive web-based tool for visualizing and annotating the human kinome tree, integrating biochemical, structural, and disease association data with a unified naming scheme domains: - genomics - biological systems homepage_url: http://www.kinhub.org/ id: kinhub last_modified_date: '2025-11-13T00:00:00Z' layout: resource_detail name: KinHub products: - category: GraphicalInterface description: Main portal providing resources and tools for human protein kinases format: http id: kinhub.portal name: KinHub Portal product_url: http://www.kinhub.org/ - category: GraphicalInterface description: Interactive web-based tool for navigating and annotating the human kinome tree with biochemical, structural, and disease data format: http id: kinhub.kinmap name: KinMap product_url: http://www.kinhub.org/kinmap/index.html - category: Product description: Comprehensive list of human protein kinases with unified naming scheme format: http id: kinhub.kinases-list name: Human Protein Kinases List product_url: http://www.kinhub.org/kinases.html - category: GraphicalInterface description: Interactive web interface for exploring and visualizing kinase-substrate interactions format: http id: kinace.portal name: KinAce Web Portal original_source: - phosphositeplus - iptmnet - uniprot - epsd - kinhub - coralkinome - darkkinasekb - hgnc - kegg - interpro product_url: https://kinace.kinametrix.com/ secondary_source: - kinace publications: - doi: 10.1186/s12859-016-1433-7 id: eid2017kinmap preferred: true title: 'KinMap: a web-based tool for interactive navigation through human kinome data' year: '2017' synonyms: - Human Kinase Hub - Human Protein Kinases Hub taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://lincs.hms.harvard.edu/ label: HMS LINCS Project creation_date: '2025-10-30T00:00:00Z' description: KINOMEscan is a biochemical kinase profiling assay that measures drug binding using a panel of approximately 440 purified kinases. The HMS LINCS Project provides a comprehensive table of all small molecules in the HMS LINCS collection that have been profiled by KINOMEscan, with links to raw binding data. domains: - drug discovery - pharmacology - biomedical homepage_url: https://lincs.hms.harvard.edu/kinomescan/ id: kinomescan infores_id: kinomescan last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail name: KINOMEscan products: - category: GraphicalInterface description: Web interface providing searchable table of all small molecules profiled by KINOMEscan format: http id: kinomescan.portal name: KINOMEscan Data Portal original_source: - kinomescan product_url: https://lincs.hms.harvard.edu/kinomescan/ - category: DocumentationProduct description: Excel spreadsheet containing HMS LINCS KINOMEscan datasets with compound information and data links id: kinomescan.spreadsheet name: KINOMEscan Datasets Spreadsheet original_source: - kinomescan product_file_size: 17872 product_url: http://lincs.hms.harvard.edu/wordpress/wp-content/uploads/2013/11/HMS-LINCS_KinomeScan_Datasets_2018-01-18.xlsx synonyms: - HMS LINCS KINOMEscan - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jonrkarr@gmail.com - contact_type: github value: jonrkarr label: Jonathan Karr orcid: 0000-0002-2605-5080 creation_date: '2025-09-29T00:00:00Z' description: A classification of algorithms for simulating biology, their parameters, and their outputs domains: - biological systems homepage_url: https://github.com/SED-ML/KiSAO id: kisao last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://opensource.org/licenses/Artistic-2.0 label: Artistic License 2.0 name: Kinetic Simulation Algorithm Ontology products: - category: OntologyProduct description: Kinetic Simulation Algorithm Ontology in OWL format format: owl id: kisao.owl name: kisao.owl product_file_size: 96237 product_url: http://purl.obolibrary.org/obo/kisao.owl repository: https://github.com/SED-ML/KiSAO - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: jano@geog.ucsb.edu label: Krzysztof Janowicz orcid: 0000-0003-4727-3564 - category: Organization contact_details: - contact_type: url value: https://knowwheregraph.org/ id: ucsb-geography label: University of California, Santa Barbara - Department of Geography creation_date: '2025-12-17T00:00:00Z' description: KnowWhereGraph is a large-scale geospatial and environmental knowledge graph containing over 29 billion RDF triples. It fuses knowledge graph technology with geo-enrichment capabilities to provide location-centric answers about environmental and human systems globally. The graph integrates 30+ data layers spanning natural hazards, climate, soil properties, demographics, health, agriculture, and more. domains: [] evaluation_page: resource/knowwheregraph/knowwheregraph_eval_automated.html funding: - National Science Foundation (NSF) - Convergence Accelerated Program (OIA-2033521) homepage_url: https://knowwheregraph.org/ id: knowwheregraph infores_id: knowwheregraph last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: KnowWhereGraph products: - category: GraphProduct description: KnowWhereGraph knowledge graph with 29+ billion RDF triples integrating 30+ environmental and geospatial data layers accessible through SPARQL endpoint edge_count: 29000000000 format: rdfxml id: knowwheregraph.graph name: KnowWhereGraph RDF Knowledge Graph node_count: 5000000000 product_url: https://knowwheregraph.org/ - category: ProgrammingInterface description: SPARQL endpoint with GeoSPARQL support for querying KnowWhereGraph data and performing geospatial queries format: http id: knowwheregraph.sparql is_public: true name: KnowWhereGraph SPARQL Endpoint product_url: https://knowwheregraph.org/sparql/ - category: GraphicalInterface description: Faceted search interface providing table and map-based views for browsing and discovering KnowWhereGraph data with automatic SPARQL query generation format: http id: knowwheregraph.explorer is_public: true name: KnowWhereGraph Knowledge Explorer product_url: https://www.knowwheregraph.org/tools/knowledge-explorer/ - category: DocumentationProduct description: Comprehensive ontology documentation and reference for the KnowWhereGraph ontology with 150 classes, 70 object properties, and 75 data properties format: http id: knowwheregraph.ontology is_public: true name: KnowWhereGraph Ontology Documentation product_url: https://stko-kwg.geog.ucsb.edu/lod/ontology warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-05_ Error connecting to URL_ HTTPSConnectionPool(host='stko-kwg.geog.ucsb.edu', port=443)_ Max retries exceeded with url_ /lod/ontology (Caused by NewConnectionError("HTTPSConnection(host='stko-kwg.geog.ucsb.edu', port=443)_ Failed to establish a new connection_ [Errno 111] Connection refused")) - File was not able to be retrieved when checked on 2025-12-17_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' publications: - authors: - Zhu R - Shimizu C - Janowicz K - Hitzler P doi: 10.48550/arXiv.2502.13874 id: arXiv:2502.13874 journal: arXiv preferred: true title: 'The KnowWhereGraph: A Large-Scale Geo-Knowledge Graph for Interdisciplinary Knowledge Discovery and Geo-Enrichment' year: '2025' - authors: - Shimizu C - Hitzler P - Janowicz K doi: 10.1016/j.websem.2024.100819 id: doi:10.1016/j.websem.2024.100819 journal: Journal of Web Semantics title: The KnowWhereGraph Ontology year: '2024' - authors: - Janowicz K - Hitzler P - Li W - Rehberger D - Schildhauer M doi: 10.1002/aaai.12043 id: doi:10.1002/aaai.12043 journal: AI Magazine title: 'Know, Know Where, KnowWhereGraph: A Densely Connected, Cross-Domain Knowledge Graph and Geo-Enrichment Service Stack for Applications in Environmental Intelligence' year: '2022' repository: https://github.com/KnowWhereGraph usages: - description: Humanitarian aid coordination and supply chain management during crises id: knowwheregraph.use.humanitarian label: Humanitarian Response - description: Food supply chain sustainability, agriculture sustainability assessment id: knowwheregraph.use.supply_chain label: Supply Chain Management - description: Disaster response, emergency management, natural hazard assessment id: knowwheregraph.use.emergency label: Emergency Management - description: Farm credit assessment, land valuation, agricultural potential evaluation id: knowwheregraph.use.agriculture label: Agricultural Finance - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: paul.fabry@usherbrooke.ca - contact_type: github value: pfabry label: Paul Fabry orcid: 0000-0002-3336-2476 creation_date: '2025-09-29T00:00:00Z' description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. domains: - biomedical homepage_url: https://github.com/OpenLHS/LABO id: labo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: clinical LABoratory Ontology products: - category: OntologyProduct description: clinical LABoratory Ontology in OWL format format: owl id: labo.owl name: labo.owl product_file_size: 47001 product_url: http://purl.obolibrary.org/obo/labo.owl repository: https://github.com/OpenLHS/LABO taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: lagonzalezmo@unal.edu.co - contact_type: github value: luis-gonzalez-m label: Luis A. Gonzalez-Montana orcid: 0000-0002-9136-9932 creation_date: '2025-09-29T00:00:00Z' description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research). domains: - anatomy and development homepage_url: https://github.com/insect-morphology/lepao id: lepao last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Lepidoptera Anatomy Ontology products: - category: OntologyProduct description: Lepidoptera Anatomy Ontology in OWL format format: owl id: lepao.owl name: lepao.owl product_file_size: 141799 product_url: http://purl.obolibrary.org/obo/lepao.owl - category: OntologyProduct description: Lepidoptera Anatomy Ontology in OBO format format: obo id: lepao.obo name: lepao.obo product_file_size: 74809 product_url: http://purl.obolibrary.org/obo/lepao.obo repository: https://github.com/insect-morphology/lepao - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: ilincs@googlegroups.com label: BD2K-LINCS Data Coordination and Integration Center - category: Organization label: National Institutes of Health (NIH) Common Fund creation_date: '2025-05-29T00:00:00Z' description: The Library of Integrated Network-based Cellular Signatures (LINCS) is a comprehensive collection of data that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. It aims to better understand human disease and advance the development of new therapies by assembling an integrated picture of the range of responses of human cells exposed to many perturbations. domains: - biomedical - drug discovery - systems biology - genomics - proteomics - precision medicine homepage_url: https://lincsportal.ccs.miami.edu/signatures/home id: lincs infores_id: lincs last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail name: LINCS products: - category: GraphicalInterface description: Web interface that allows users to explore, analyze, and visualize LINCS signatures and datasets. id: lincs.portal name: LINCS Data Portal 2.0 product_url: https://lincsportal.ccs.miami.edu/signatures/home - category: ProgrammingInterface description: API for programmatic access to LINCS data and signatures. id: lincs.api is_public: true name: LINCS API product_url: https://lincsportal.ccs.miami.edu/sigc-api/swagger-ui.html#/ - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - authors: - Keenan AB - Jenkins SL - Jagodnik KM - Koplev S - He E - Torre D - Wang Z - Dohlman AB - Silverstein MC - Lachmann A - Kuleshov MV - Ma'ayan A - Stathias V - Terryn R - Cooper D - Forlin M - Koleti A - Vidovic D - Chung C - Schürer SC - Vasiliauskas J - Pilarczyk M - Shamsaei B - Fazel M - Ren Y - Niu W - Clark NA - White S - Mahi N - Zhang L - Kouril M - Reichard JF - Sivaganesan S - Medvedovic M - Meller J - Koch RJ - Birtwistle MR - Iyengar R - Sobie EA - Azeloglu EU - Kaye J - Osterloh J - Haston K - Kalra J - Finkbiener S - Li J - Milani P - Adam M - Escalante-Chong R - Sachs K - Lenail A - Ramamoorthy D - Fraenkel E - Daigle G - Hussain U - Coye A - Rothstein J - Sareen D - Ornelas L - Banuelos M - Mandefro B - Ho R - Svendsen CN - Lim RG - Stocksdale J - Casale MS - Thompson TG - Wu J - Thompson LM - Dardov V - Venkatraman V - Matlock A - Van Eyk JE - Jaffe JD - Papanastasiou M - Subramanian A - Golub TR - Erickson SD - Fallahi-Sichani M - Hafner M - Gray NS - Lin JR - Mills CE - Muhlich JL - Niepel M - Shamu CE - Williams EH - Wrobel D - Sorger PK - Heiser LM - Gray JW - Korkola JE - Mills GB - LaBarge M - Feiler HS - Dane MA - Bucher E - Nederlof M - Sudar D - Gross S - Kilburn DF - Smith R - Devlin K - Margolis R - Derr L - Lee A - Pillai A doi: doi:10.1016/j.cels.2017.11.001 id: https://doi.org/10.1016/j.cels.2017.11.001 journal: Cell Systems preferred: true title: The Library of Integrated Network-Based Cellular Signatures NIH Program - System-Level Cataloging of Human Cells Response to Perturbations year: '2018' - authors: - Koleti A - Terryn R - Stathias V - Chung C - Cooper DJ - Turner JP - Vidovic D - Forlin M - Kelley TT - D'Urso A - Allen BK - Torre D - Jagodnik KM - Wang L - Jenkins SL - Mader C - Niu W - Fazel M - Mahi N - Pilarczyk M - Clark N - Shamsaei B - Meller J - Vasiliauskas J - Reichard J - Medvedovic M - Ma'ayan A - Pillai A - Schürer SC doi: doi:10.1093/nar/gkx1063 id: https://doi.org/10.1093/nar/gkx1063 journal: Nucleic Acids Research title: Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program - integrated access to diverse large-scale cellular perturbation response data year: '2018' - authors: - Shen JP - Ozerov IV - Zhavoronkov A - Keenan AB - Koplev S - Jenkins SL - Jagodnik KM - Hallen A - Ma'ayan A doi: doi:10.1038/s41467-022-32205-3 id: https://doi.org/10.1038/s41467-022-32205-3 journal: Nature Communications title: Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS year: '2022' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: lincs-help@broadinstitute.org id: broad label: Broad Institute LINCS Transcriptomics Center creation_date: '2025-01-08T00:00:00Z' description: The LINCS L1000 is a high-throughput, reduced representation gene expression profiling assay developed as part of the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) Program. L1000 directly measures 978 landmark genes and computationally infers the expression of 11,350 additional genes, enabling cost-effective large-scale transcriptional profiling at approximately $2 per sample. The technology was developed to create a Connectivity Map (CMap) that catalogs cellular responses to genetic and chemical perturbations, facilitating drug discovery, mechanism of action determination, and functional annotation of genetic variants. The LINCS L1000 dataset comprises over 1.3 million gene expression profiles representing responses to 19,811 chemical compounds, genetic perturbations targeting 5,075 genes (via shRNA knockdowns and cDNA overexpression), and 314 biologics across multiple cell lines and time points. domains: - drug discovery homepage_url: https://lincsproject.org/LINCS/ id: lincs-l1000 last_modified_date: '2025-11-08T00:00:00Z' layout: resource_detail name: LINCS L1000 products: - category: GraphicalInterface description: The Connectivity Map (CMap) database containing over 1.3 million L1000 gene expression profiles from chemical, genetic, and biologic perturbations. Includes web-based analysis tools for signature search and perturbagen class discovery. format: http id: lincs-l1000.cmap name: LINCS Connectivity Map (CMap) product_url: https://clue.io - category: GraphicalInterface description: The CLUE platform provides interactive analysis tools and data access for the LINCS L1000 Connectivity Map dataset, including query tools, visualization, and APIs for programmatic access. format: http id: lincs-l1000.clue name: CLUE Platform product_url: https://clue.io - category: Product description: LINCS L1000 data deposited in the Gene Expression Omnibus, including raw and processed gene expression data at multiple levels of preprocessing for all 1.3+ million profiles. format: http id: lincs-l1000.geo name: LINCS L1000 GEO Dataset product_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92742 warnings: - File was not able to be retrieved when checked on 2025-11-19_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-11-10_ Timeout connecting to URL - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet publications: - authors: - Subramanian, A. - Narayan, R. - Corsello, S.M. - Peck, D.D. - Natoli, T.E. - Lu, X. - Gould, J. - Davis, J.F. - Tubelli, A.A. - Asiedu, J.K. - Lahr, D.L. - Hirschman, J.E. - Liu, Z. - Donahue, M. - Julian, B. - Khan, M. - Wadden, D. - Smith, I.C. - Lam, D. - Liberzon, A. - Toder, C. - Bagul, M. - Orzechowski, M. - Enache, O.M. - Piccioni, F. - Johnson, S.A. - Lyons, N.J. - Berger, A.H. - Shamji, A.F. - Brooks, A.N. - Vrcic, A. - Flynn, C. - Rosains, J. - Takeda, D.Y. - Hu, R. - Davison, D. - Lamb, J. - Ardlie, K. - Hogstrom, L. - Greenside, P. - Gray, N.S. - Clemons, P.A. - Silver, S. - Wu, X. - Zhao, W.N. - Read-Button, W. - Wu, X. - Haggarty, S.J. - Ronco, L.V. - Boehm, J.S. - Schreiber, S.L. - Doench, J.G. - Bittker, J.A. - Root, D.E. - Wong, B. - Golub, T.R. doi: 10.1016/j.cell.2017.10.049 id: lincs_l1000_paper journal: Cell preferred: true title: 'A Next Generation Connectivity Map: L1000 platform and the first 1,000,000 profiles' year: '2017' repository: https://github.com/cmap/l1000-jupyter taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: zhiyong.lu@nih.gov - contact_type: url value: https://www.ncbi.nlm.nih.gov/research/bionlp/ id: ncbi label: NCBI Computational Biology Branch creation_date: '2025-11-08T00:00:00Z' description: LitVar is a comprehensive NCBI web service for searching and retrieving variant-specific information from the biomedical literature using advanced text mining and machine learning techniques. Developed by the National Library of Medicine's Computational Biology Branch, LitVar automatically extracts variant-related information from over 35 million PubMed articles and 5.7 million full-text articles in PubMed Central including supplementary materials, with monthly updates to capture the latest research. A key innovation of LitVar is its sophisticated variant normalization system that standardizes different forms of the same variant into unique identifiers, enabling comprehensive search results regardless of which variant nomenclature is used in the query, whether protein level names, DNA level annotations, dbSNP RS identifiers, ClinGen identifiers, or SPDI format. LitVar leverages PubTator, a state-of-the-art literature annotation tool, to identify and display key biological entities including genes, diseases, drugs, chemicals, and mutations within retrieved articles, providing rich contextual information around variants of interest. domains: - genomics - literature homepage_url: https://www.ncbi.nlm.nih.gov/research/litvar2/ id: litvar infores_id: litvar last_modified_date: '2025-11-08T00:00:00Z' layout: resource_detail name: LitVar products: - category: GraphicalInterface description: Web interface for searching and retrieving variant information from 35+ million PubMed articles with autocomplete, filtering, and entity highlighting format: http id: litvar.web_interface name: LitVar Web Interface product_url: https://www.ncbi.nlm.nih.gov/research/litvar2/ - category: ProgrammingInterface description: RESTful API providing programmatic access to variant summaries, publications, search, and gene-level variant queries format: http id: litvar.api name: LitVar API product_url: https://www.ncbi.nlm.nih.gov/research/litvar2/api publications: - authors: - Alexis Allot - Chih-Hsuan Wei - Lon Phan - Timothy Hefferon - Melissa Landrum - Heidi L. Rehm - Zhiyong Lu doi: 10.1038/s41588-023-01414-x id: litvar_2023 journal: Nature Genetics preferred: true title: Tracking genetic variants in the biomedical literature using LitVar 2.0 year: '2023' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: DIANA-LncBase is a comprehensive repository of experimentally supported miRNA-lncRNA interactions. Version 3.0 contains ~500,000 entries corresponding to ~240,000 unique tissue and cell type specific miRNA-lncRNA pairs in human and mouse. Data derived from manual curation and analysis of >300 high-throughput datasets including AGO-CLIP-Seq, microarrays, and low-yield experiments across 192 cell types and 51 tissues. Includes lncRNA expression profiles and subcellular localization data. domains: - genomics - biological systems homepage_url: http://www.microrna.gr/LncBase id: lncbase last_modified_date: '2025-11-13T00:00:00Z' layout: resource_detail name: DIANA-LncBase products: - category: GraphicalInterface description: Main web portal for searching experimentally supported miRNA-lncRNA interactions with interactive visualizations format: http id: lncbase.portal name: DIANA-LncBase Portal original_source: - lncbase product_url: http://www.microrna.gr/LncBase - category: Product description: Interactive correlation plots showing clustering of miRNA-lncRNA interactions across cell types and tissues format: http id: lncbase.correlation-viz name: LncBase Correlation Visualizations original_source: - lncbase product_url: http://www.microrna.gr/LncBase - category: Product description: Interactive bar plots showing lncRNA expression profiles and subcellular localization (nucleus/cytoplasm) format: http id: lncbase.expression-viz name: LncBase Expression Visualizations original_source: - lncbase product_url: http://www.microrna.gr/LncBase - category: Product description: UCSC Genome Browser integration for visualizing miRNA binding events and variant locations on lncRNAs format: http id: lncbase.ucsc-browser name: LncBase UCSC Browser Integration original_source: - lncbase product_url: http://www.microrna.gr/LncBase - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Karagkouni D - Paraskevopoulou MD - Tastsoglou S - Skoufos G - Karavangeli A - Pierros V - Zacharopoulou E - Hatzigeorgiou AG id: https://doi.org/10.1093/nar/gkz1036 journal: Nucleic Acids Research preferred: true title: 'DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts' year: '2020' synonyms: - LncBase - DIANA LncBase taxon: - NCBITaxon:9606 - NCBITaxon:10090 - activity_status: active category: DataSource creation_date: '2019-01-05T00:00:00Z' description: LncBook is a comprehensive database of human long non-coding RNAs (lncRNAs) with multi-omics annotations. It accommodates 95,243 lncRNA genes and 323,950 transcripts, integrated from multiple resources including GENCODE, RefLnc, CHESS, FANTOM-CAT, and BIGTranscriptome, with strict quality control and curation. The database provides abundant annotations including conservation features across 40 vertebrates, disease/trait-associated variants, DNA methylation profiles, expression profiles across 9 biological contexts, lncRNA-encoded small proteins, lncRNA-protein interactions, and lncRNA-miRNA interactions. domains: - genomics - biological systems homepage_url: https://ngdc.cncb.ac.cn/lncbook/home id: lncbook last_modified_date: '2025-10-21T00:00:00Z' layout: resource_detail name: LncBook products: - category: GraphicalInterface description: Main web portal for searching and browsing human long non-coding RNAs with multi-omics annotations format: http id: lncbook.portal name: LncBook Portal product_url: https://ngdc.cncb.ac.cn/lncbook/home - category: GraphicalInterface description: Browse conservation features of lncRNA genes across 40 vertebrates format: http id: lncbook.conservation name: Conservation Browser product_url: https://ngdc.cncb.ac.cn/lncbook/omics/conservation - category: GraphicalInterface description: Browse 959,138 disease/trait-associated variants across lncRNA genes format: http id: lncbook.variation name: Variation Browser product_url: https://ngdc.cncb.ac.cn/lncbook/omics/variation - category: GraphicalInterface description: Browse DNA methylation profiles in 16 diseases (14 cancers and 2 neurodevelopmental disorders) format: http id: lncbook.methylation name: Methylation Browser product_url: https://ngdc.cncb.ac.cn/lncbook/omics/methylation - category: GraphicalInterface description: Browse expression profiles across 9 biological contexts (normal tissue, organ development, cell differentiation, etc.) format: http id: lncbook.expression name: Expression Browser product_url: https://ngdc.cncb.ac.cn/lncbook/omics/expression - category: GraphicalInterface description: Browse 34,012 small proteins encoded by lncRNAs format: http id: lncbook.sprotein name: Small Protein Browser product_url: https://ngdc.cncb.ac.cn/lncbook/omics/sprotein - category: GraphicalInterface description: Browse lncRNA-miRNA and lncRNA-protein interactions (146,092,274 lncRNA-miRNA and 772,745 lncRNA-protein interactions) format: http id: lncbook.interaction name: Interaction Browser product_url: https://ngdc.cncb.ac.cn/lncbook/omics/interaction - category: GraphicalInterface description: ID conversion tool across 14 resources format: http id: lncbook.conversion name: ID Conversion Tool product_url: https://ngdc.cncb.ac.cn/lncbook/tools/conversion - category: GraphicalInterface description: BLAST search tool for sequence similarity format: http id: lncbook.blast name: BLAST Search product_url: https://ngdc.cncb.ac.cn/lncbook/tools/blast - category: GraphicalInterface description: Genomic location annotation and classification tool format: http id: lncbook.classification name: Classification Tool product_url: https://ngdc.cncb.ac.cn/lncbook/tools/classification - category: GraphicalInterface description: LGC coding potential prediction tool format: http id: lncbook.lgc name: LGC Coding Potential Predictor product_url: https://ngdc.cncb.ac.cn/lgc - category: DocumentationProduct description: Comprehensive database statistics and analysis results format: http id: lncbook.statistics name: Statistics Page product_url: https://ngdc.cncb.ac.cn/lncbook/statistics - category: Product description: Downloadable data files including gene annotations, expression profiles, and multi-omics annotations format: http id: lncbook.downloads name: Downloads product_url: https://ngdc.cncb.ac.cn/lncbook/download warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Zhao Li - Lin Liu - Changrui Feng - Yuxin Qin - Jingfa Xiao - Zhang Zhang - Lina Ma id: https://doi.org/10.1093/nar/gkac999 journal: Nucleic Acids Research preferred: true title: 'LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations' year: '2023' - authors: - Lina Ma - Jingfa Cao - Lin Liu - Qiuye Du - Zhilei Li - Dahai Zou - Vladimir B. Bajic - Zhang Zhang id: https://doi.org/10.1093/nar/gky960 journal: Nucleic Acids Research title: 'LncBook: a curated knowledgebase of human long non-coding RNAs' year: '2019' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://lncipedia.org/ label: LncIPedia Team creation_date: '2025-10-30T00:00:00Z' description: LncIPedia is a comprehensive public database for human long non-coding RNA (lncRNA) sequences and annotations, containing manually curated literature and detailed transcript information. domains: - genomics - literature homepage_url: https://lncipedia.org/ id: lncipedia last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail name: LncIPedia products: - category: GraphicalInterface description: Web interface for searching and browsing human lncRNA sequences and annotations format: http id: lncipedia.search name: LncIPedia Search original_source: - lncipedia product_url: https://lncipedia.org/db/search - category: Product description: Downloadable database files in FASTA, GFF, and BED formats for both GRCh37/hg19 and GRCh38/hg38 genome assemblies format: fasta id: lncipedia.downloads name: LncIPedia Downloads product_url: https://lncipedia.org/download - category: GraphicalInterface description: UCSC Genome Browser trackhub for directly displaying LncIPedia annotations id: lncipedia.trackhub name: LncIPedia UCSC Trackhub original_source: - lncipedia product_url: https://www.lncipedia.org/trackhub/hub.txt - category: Product description: Integration files for Integrative Genomics Viewer (IGV) to visualize lncRNA annotations format: http id: lncipedia.igv name: LncIPedia IGV Integration original_source: - lncipedia product_url: https://lncipedia.org/download#anchor-igv - category: Product description: Metadata files including locus conservation across species (chimpanzee, mouse, Drosophila, zebrafish) and conversion tables to Ensembl and RefSeq IDs format: tsv id: lncipedia.metadata name: LncIPedia Metadata product_url: https://lncipedia.org/download#anchor-metadata - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - category: Publication id: PMID:30371849 preferred: true - category: Publication id: PMID:25378313 - category: Publication id: PMID:23042674 taxon: - NCBITaxon:9606 warnings: - LncIPedia download files are for non-commercial use only. Any other use should be approved in writing from Ghent University. - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: avi.maayan@mssm.edu - contact_type: url value: https://labs.icahn.mssm.edu/maayanlab/ label: Ma'ayan Laboratory creation_date: '2025-09-23T00:00:00Z' description: lncRNAlyzr is a specialized knowledge graph focused on long non-coding RNA (lncRNA) biology, integrating lncRNA annotations, expression profiles, functional interactions, disease associations, and regulatory mechanisms to provide comprehensive insights into lncRNA roles in cellular processes and human disease. domains: - biomedical - genomics - systems biology evaluation_page: resource/lncrnalyzr/lncrnalyzr_eval_automated.html homepage_url: https://lncrnalyzr.maayanlab.cloud/ id: lncrnalyzr last_modified_date: '2025-09-23T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC BY-NC-SA 4.0 name: lncRNAlyzr products: - category: GraphicalInterface description: Interactive web platform for exploring lncRNA networks with expression visualization and functional analysis tools format: http id: lncrnalyzr.portal name: lncRNAlyzr Explorer product_url: https://lncrnalyzr.maayanlab.cloud/ - category: ProgrammingInterface description: RESTful API for programmatic access to lncRNA annotations, interactions, and functional predictions format: http id: lncrnalyzr.api name: lncRNAlyzr API product_url: https://lncrnalyzr.maayanlab.cloud/api-docs - category: GraphProduct description: Neo4j knowledge graph containing lncRNAs, protein-coding genes, regulatory interactions, and disease associations dump_format: neo4j format: neo4j id: lncrnalyzr.graph name: lncRNAlyzr Knowledge Graph publications: - id: doi:10.1016/j.jmb.2025.168938 journal: Nature Genetics title: 'lncRNAlyzr: Enrichment Analysis for lncRNA Sets' year: '2025' repository: https://github.com/MaayanLab/lncRNAlyzr taxon: - NCBITaxon:9606 - activity_status: active category: DataModel contacts: - category: Organization contact_details: - contact_type: url value: https://loinc.org/contact/ label: Regenstrief Institute (LOINC) creation_date: '2025-06-04T00:00:00Z' description: LOINC (Logical Observation Identifiers Names and Codes) is the international standard for identifying health measurements, laboratory and clinical observations, and documents; it provides universal codes and structured names enabling interoperable exchange and aggregation of clinical, laboratory, and other health data worldwide. domains: - clinical - biomedical - health - genomics homepage_url: https://loinc.org/ id: loinc infores_id: loinc last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://loinc.org/license/ label: LOINC License (free registration required) name: LOINC products: - category: GraphicalInterface description: Web-based tools including SearchLOINC and Hierarchy Browser for interactive exploration of LOINC content (free login required) format: http id: loinc.web name: LOINC Website & Browsers original_source: - loinc product_url: https://loinc.org/search/ - category: ProgrammingInterface description: HL7 FHIR-based API providing programmatic access to LOINC terminology content (requires free LOINC login) format: http id: loinc.api.fhir is_public: false name: LOINC FHIR API original_source: - loinc product_url: https://loinc.org/fhir/ - category: DataModelProduct compression: zip description: Complete LOINC release archive (table and accessory files) downloadable after free registration format: mixed id: loinc.complete latest_version: '2.81' name: LOINC Complete Release original_source: - loinc product_url: https://loinc.org/download/loinc-complete/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 503 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 503 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 503 error when accessing file' - category: DataModelProduct description: Archive of past LOINC releases for version-specific implementations format: mixed id: loinc.archive name: LOINC Release Archive original_source: - loinc product_url: https://loinc.org/downloads/archive/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 503 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 503 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 503 error when accessing file' - category: DocumentationProduct description: LOINC Mission, Vision, and Guiding Principles for open terminology development (CC-BY 4.0 licensed document) id: loinc.principles name: LOINC Principles Document original_source: - loinc product_url: https://loinc.org/principles/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 503 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 503 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 503 error when accessing file' - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: MappingProduct description: Concept mappings between different terminology systems format: csv id: athena.mappings name: Athena Concept Mappings original_source: - snomedct - icd10 - icd10cm - mesh - loinc - cdiscvocab - ciel product_url: https://athena.ohdsi.org/search-terms/start secondary_source: - athena warnings: - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ Exceeded 30 redirects. - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ Exceeded 30 redirects. publications: - id: https://doi.org/10.1093/nar/gkad1044 journal: Nucleic Acids Research preferred: true title: 'LOINC 2024 update: advancing global interoperability for health measurements and observations' year: '2024' - id: https://doi.org/10.1093/nar/gkac998 journal: Nucleic Acids Research title: 'LOINC 2023 update: refining identifiers and expanding clinical content' year: '2023' taxon: - NCBITaxon:9606 warnings: - LOINC downloads and API require a free account; ensure you cite the specific version (e.g., 2.81) when using the terminology. - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: ribeiro@ebi.ac.uk label: António JM Ribeiro creation_date: '2025-03-17T00:00:00Z' description: The Mechanism and Catalytic Site Atlas (M-CSA) is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA. 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows. 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism. domains: - biological systems homepage_url: https://www.ebi.ac.uk/thornton-srv/m-csa/ id: m-csa last_modified_date: '2025-08-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: M-CSA products: - category: MappingProduct description: rhea SSSOM format: sssom id: obo-db-ingest.rhea.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rhea SSSOM original_source: - rhea - reactome - kegg - metacyc - m-csa - ecocyc product_file_size: 154171 product_url: https://w3id.org/biopragmatics/resources/rhea/rhea.sssom.tsv secondary_source: - obo-db-ingest - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Terry.Hayamizu@jax.org - contact_type: github value: tfhayamizu label: Terry Hayamizu orcid: 0000-0002-0956-8634 creation_date: '2025-06-25T00:00:00Z' description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus). domains: - anatomy and development homepage_url: https://github.com/obophenotype/adult-mouse-anatomy-ontology id: ma last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Mouse adult gross anatomy products: - category: OntologyProduct description: Mouse adult gross anatomy in OWL format format: owl id: ma.owl name: ma.owl product_file_size: 99035 product_url: http://purl.obolibrary.org/obo/ma.owl - category: OntologyProduct description: Mouse adult gross anatomy in OBO format format: obo id: ma.obo name: ma.obo product_file_size: 62768 product_url: http://purl.obolibrary.org/obo/ma.obo - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/obophenotype/adult-mouse-anatomy-ontology taxon: - NCBITaxon:10088 - activity_status: active category: Aggregator creation_date: '2025-09-09T00:00:00Z' description: MalaCards is a comprehensive, searchable database integrating information about human diseases from 78 data sources. It provides integrated disease annotations including genes, symptoms, drugs, mutations, publications, clinical trials, and pathways for over 22,000 human disorders. domains: - health - clinical - genomics - biomedical id: malacards last_modified_date: '2025-10-10T00:00:00Z' layout: resource_detail name: MalaCards products: - category: GraphicalInterface description: Searchable web interface for exploring human diseases with integrated data on genes, symptoms, drugs, mutations, clinical trials and more. format: http id: malacards.portal name: MalaCards Web Portal product_url: https://www.malacards.org/ - category: GraphicalInterface description: Browse diseases by global categories (cancer, genetic, rare, etc.) and anatomical categories (neuronal, cardiovascular, etc.). format: http id: malacards.categories name: MalaCards Disease Categories product_url: https://www.malacards.org/categories - category: GraphicalInterface description: Advanced search interface for querying diseases by multiple criteria. format: http id: malacards.search name: MalaCards Advanced Search product_url: https://www.malacards.org/search/advanced - category: DocumentationProduct description: Access to previous versions of the MalaCards database. format: http id: malacards.archive name: MalaCards Previous Version Archive product_url: https://previous.malacards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database - category: Product description: Disease association data integrated from OMIM, MalaCards, ClinVar, Orphanet, DisGeNET and other disease databases format: http id: genecards.disease.associations name: GeneCards Disease Associations original_source: - omim - malacards - clinvar - orphanet - disgenet product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' publications: - authors: - Rappaport N - Nativ N - Stelzer G - Twik M - Guan-Golan Y - Stein TI - Bahir I - Belinky F - Morrey CP - Safran M - Lancet D id: https://doi.org/10.1093/database/bat018 journal: Database preferred: true title: 'MalaCards: an integrated compendium for diseases and their annotation' year: '2013' - authors: - Rappaport N - Twik M - Nativ N - Stelzer G - Bahir I - Stein TI - Safran M - Lancet D id: https://doi.org/10.1002/0471250953.bi0124s47 journal: Current Protocols in Bioinformatics preferred: false title: 'MalaCards: A Comprehensive Automatically-Mined Database of Human Diseases' year: '2014' taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph collection: - ber contacts: - category: Organization contact_details: - contact_type: url value: https://mangal.io/ label: Mangal creation_date: '2025-12-15T00:00:00Z' description: mangal.io is a collaborative database and analysis platform for ecological networks, providing a comprehensive collection of species interaction networks (food webs, pollination networks, plant-herbivore networks) with tools for visualization, analysis, and reuse of published ecological data. domains: [] evaluation_page: resource/mangal/mangal_eval_automated.html homepage_url: https://mangal.io/ id: mangal last_modified_date: '2025-12-15T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: mangal.io products: - category: GraphicalInterface description: Web interface for browsing, querying, and visualizing ecological networks format: http id: mangal.portal name: mangal.io Web Portal product_url: https://mangal.io/ - category: ProgrammingInterface description: RESTful API for programmatic access to network data and metadata format: http id: mangal.api is_public: true name: mangal.io API product_url: https://api.mangal.io/ - category: DocumentationProduct description: API documentation, user guides, and data model specification format: http id: mangal.docs name: mangal.io Documentation product_url: https://mangal.io/documentation taxon: - NCBITaxon:33208 - NCBITaxon:33090 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Leigh.Carmody@jax.org - contact_type: github value: LCCarmody label: Leigh Carmody orcid: 0000-0001-7941-2961 creation_date: '2025-08-13T00:00:00Z' description: The Medical Action Ontology (MAxO) provides a broad view of medical actions and includes terms for medical procedures, interventions, therapies, treatments, and recommendations. domains: - 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medgen product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/csv/ - category: DocumentationProduct description: Documentation, help pages, and user guides for MedGen format: http id: medgen.help name: MedGen Documentation original_source: - medgen product_url: https://www.ncbi.nlm.nih.gov/medgen/docs/overview/ - category: DocumentationProduct description: Frequently asked questions about MedGen format: http id: medgen.faq name: FAQ original_source: - medgen product_url: https://www.ncbi.nlm.nih.gov/medgen/docs/faq/ - category: DocumentationProduct description: README file with detailed information about FTP data files and formats format: txt id: medgen.readme name: README original_source: - medgen product_file_size: 17286 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/README.txt - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: MappingProduct description: MIM to Gene and MedGen mapping data connecting genetic disorders to genes format: tsv id: ncbigene.mim2gene_medgen name: MIM to Gene MedGen Mapping original_source: - ncbigene - medgen - omim product_file_size: 954971 product_url: https://ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv - category: DocumentationProduct description: Directory of MedGen presentations related to terminology and curation workflows format: http id: medgen.presentations name: MedGen Presentations original_source: - medgen product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/presentations/ taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-10-30T00:00:00Z' description: MEDI (MATRIX Indication List) is a curated dataset of drug indications and contraindications extracted from FDA DailyMed product labels using large language models. Developed by the Every Cure organization, MEDI provides ground truth data for drug repurposing predictive models by mapping drug-indication and drug-contraindication relationships with standardized disease ontology terms (MONDO). domains: - pharmacology - drug discovery - clinical homepage_url: https://github.com/everycure-org/matrix-indication-list id: medi infores_id: medi last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail license: id: https://github.com/everycure-org/matrix-indication-list/blob/main/LICENSE label: License (see repository) name: MeDI products: - category: Product description: GitHub repository containing the MEDI dataset, extraction pipelines, and processing code for drug indications and contraindications format: mixed id: medi.github name: MEDI GitHub Repository original_source: - medi product_url: https://github.com/everycure-org/matrix-indication-list - category: Product description: Latest release of the MEDI dataset containing curated drug-indication and drug-contraindication mappings id: medi.release name: MEDI Dataset Releases product_url: https://github.com/everycure-org/matrix-indication-list/releases repository: https://github.com/everycure-org/matrix-indication-list taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.dsmz.de/ label: DSMZ (Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures) creation_date: '2025-11-25T00:00:00Z' description: MediaDive is the world's largest collection of microbial cultivation media, maintained by DSMZ (German Collection of Microorganisms and Cell Cultures). It provides comprehensive information about media compositions, solutions, ingredients, and growth conditions for over 47,000 microbial strains including bacteria, archaea, fungi, protists, and algae. domains: - microbiology - biological systems - systems biology homepage_url: https://mediadive.dsmz.de/ id: mediadive last_modified_date: '2025-11-25T00:00:00Z' layout: resource_detail name: MediaDive products: - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe publications: - id: https://doi.org/10.1093/nar/gkac803 title: 'MediaDive: the expert-curated cultivation media database' year: '2022' synonyms: - MediaDive - Media Diversity - DSMZ MediaDive taxon: - NCBITaxon:2 - NCBITaxon:2157 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: prabhagarg@niper.ac.in label: Prabha Garg creation_date: '2025-03-24T00:00:00Z' description: MedKG is a comprehensive and continuously updated knowledge graph designed to address challenges in precision medicine and drug discovery. MedKG integrates data from 35 authoritative sources, encompassing 34 node types and 79 relationships. A Continuous Integration/Continuous Update pipeline ensures MedKG remains current, addressing a critical limitation of static knowledge bases. The integration of molecular embeddings enhances semantic analysis capabilities, bridging the gap between chemical structures and biological entities. domains: - biological systems evaluation_page: resource/medkg/medkg_eval_automated.html homepage_url: http://pitools.niper.ac.in/medkg/ id: medkg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: MedKG products: - category: GraphicalInterface description: Graphical interface for MedKG id: medkb.site name: MedKG Site original_source: - medkg product_url: http://pitools.niper.ac.in/medkg/ secondary_source: - medkg publications: - authors: - Kumari M - Chauhan R - Garg P doi: 10.1007/s11030-025-11164-z id: doi:10.1007/s11030-025-11164-z title: '''MedKG: enabling drug discovery through a unified biomedical knowledge graph''' year: '2025' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://support.nlm.nih.gov/knowledgebase/category/?id=CAT-01231&category=medlineplus id: ncbi label: National Library of Medicine creation_date: '2025-11-08T00:00:00Z' description: MedlinePlus is the premier online health information resource from the National Library of Medicine, providing comprehensive, trusted health and wellness information for patients, families, and the general public. As a service of the world's largest medical library and part of the National Institutes of Health, MedlinePlus delivers high-quality, evidence-based health content that is easy to understand, free of advertising, and available in both English and Spanish. The resource covers over 1,000 health topics including diseases, conditions, wellness information, and prevention strategies, with content organized into multiple categories including health topics, medical encyclopedia, drugs and supplements information, medical tests, healthy recipes, and genetics resources. MedlinePlus provides detailed information on prescription drugs, over-the-counter medicines, herbs, and supplements through its comprehensive drug information database. The medical encyclopedia contains thousands of articles, images, and videos covering diseases, symptoms, tests, and treatments. MedlinePlus Genetics offers information on genetic conditions, genes, chromosomes, and how genetic variations affect health. domains: - health homepage_url: https://medlineplus.gov/ id: medlineplus infores_id: medlineplus last_modified_date: '2025-11-08T00:00:00Z' layout: resource_detail name: MedlinePlus products: - category: GraphicalInterface description: Main MedlinePlus website providing consumer-friendly health information organized into health topics, medical encyclopedia, drug information, medical tests, and genetics resources in English and Spanish format: http id: medlineplus.website name: MedlinePlus Website product_url: https://medlineplus.gov/ - category: ProgrammingInterface description: Web service providing search-based health topic data in XML format for integration with external applications format: xml id: medlineplus.web_service name: MedlinePlus Web Service product_url: https://medlineplus.gov/about/developers/webservices/ - category: ProgrammingInterface description: MedlinePlus Connect API enabling electronic health record systems and patient portals to link patients to relevant MedlinePlus health information based on their diagnoses and medications format: http id: medlineplus.connect_api name: MedlinePlus Connect API product_url: https://medlineplus.gov/connect/overview.html - category: Product description: Downloadable XML files containing complete records for all English and Spanish health topics on MedlinePlus format: xml id: medlineplus.xml_files name: MedlinePlus XML Data Files product_url: https://medlineplus.gov/xml.html - category: ProgrammingInterface description: API and data files for retrieving genetic condition and gene information from MedlinePlus Genetics in XML or JSON format format: json id: medlineplus.genetics_api name: MedlinePlus Genetics API product_url: https://medlineplus.gov/about/developers/geneticsdatafilesapi/ taxon: - NCBITaxon:9606 - activity_status: active category: Ontology creation_date: '2025-10-10T00:00:00Z' description: The Medical Subject Headings (MeSH) is a hierarchically-organized controlled vocabulary produced by the National Library of Medicine (NLM). It serves as the standard thesaurus for indexing and cataloging biomedical and health-related information in MEDLINE/PubMed and other NLM databases. domains: - biomedical - health - literature homepage_url: https://www.nlm.nih.gov/mesh/meshhome.html id: mesh infores_id: mesh last_modified_date: '2025-10-10T00:00:00Z' layout: resource_detail license: id: https://www.nlm.nih.gov/databases/download/terms_and_conditions_mesh.html label: NLM Terms and Conditions for MeSH Data name: Medical Subject Headings (MeSH) products: - category: GraphicalInterface description: The official MeSH Browser for searching and browsing the Medical Subject Headings vocabulary. Provides hierarchical navigation and term details. format: http id: mesh.browser name: MeSH Browser product_url: https://meshb.nlm.nih.gov/search - category: OntologyProduct description: MeSH data in XML format containing descriptors, qualifiers, and supplemental concept records. Updated annually with daily updates for SCRs. format: xml id: mesh.xml name: MeSH XML Data product_url: https://nlmpubs.nlm.nih.gov/projects/mesh/MESH_FILES/xmlmesh/ - category: OntologyProduct description: MeSH data in RDF (Resource Description Framework) format for semantic web applications. Updated daily Monday through Friday. format: rdfxml id: mesh.rdf name: MeSH RDF Data product_url: https://nlmpubs.nlm.nih.gov/projects/mesh/rdf/2025/ - category: OntologyProduct description: MeSH data in ASCII text format containing descriptors, qualifiers, and supplemental concept records. Updated annually with daily SCR updates. format: txt id: mesh.ascii name: MeSH ASCII Data product_url: https://nlmpubs.nlm.nih.gov/projects/mesh/MESH_FILES/asciimesh/ - category: OntologyProduct description: MeSH data in MARC 21 bibliographic format for library systems. Posted monthly. format: mixed id: mesh.marc name: MeSH MARC 21 Data product_url: https://nlmpubs.nlm.nih.gov/projects/mesh/MESH_FILES/meshmarc/ - category: ProgrammingInterface description: E-utilities API for programmatic access to MeSH data through NCBI's Entrez system. format: http id: mesh.api.eutilities name: MeSH E-utilities API product_url: https://www.ncbi.nlm.nih.gov/books/NBK25500/ - category: ProgrammingInterface description: SPARQL endpoint and REST API for querying MeSH RDF data with semantic web technologies. format: http id: mesh.api.rdf name: MeSH RDF API product_url: https://id.nlm.nih.gov/mesh/swagger/ui - category: GraphicalInterface description: SPARQL query editor interface for interactive querying of MeSH data using semantic web query language. format: http id: mesh.sparql.editor name: MeSH SPARQL Query Editor product_url: https://id.nlm.nih.gov/mesh/query - category: Product description: MeSH on Demand service for suggesting MeSH terms for text or citations. Helps identify appropriate subject headings for indexing. format: http id: mesh.ondemand name: MeSH on Demand product_url: https://meshb.nlm.nih.gov/MeSHonDemand - category: DocumentationProduct description: Comprehensive documentation about MeSH including tutorials, webinars, and user guides for understanding and using the vocabulary. format: http id: mesh.documentation name: MeSH Documentation and Tutorials product_url: https://www.nlm.nih.gov/bsd/disted/mesh.html - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: GraphProduct description: KGX distribution of the ICEES Exposures KP in Knowledge Graph Exchange (KGX) format, containing integrated clinical and environmental exposures data as a knowledge graph with 226 nodes and 14,342 edges format: kgx-jsonl id: icees-kg.graph name: KGX distribution of the ICEES Exposures KP original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/ secondary_source: - icees-kg - category: ProgrammingInterface description: Translator Reasoner API (TRAPI) endpoint for querying ICEES KG using standardized Translator protocols format: http id: icees-kg.trapi name: ICEES KG TRAPI API original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg-trapi secondary_source: - icees-kg - category: Product description: Meta knowledge graph and metadata describing the data sources, node types, edge types, and predicates available in ICEES KG format: json id: icees-kg.metadata name: ICEES KG Metadata original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/metadata-metadata-get-icees-kg secondary_source: - icees-kg - category: MappingProduct description: Concept mappings between different terminology systems format: csv id: athena.mappings name: Athena Concept Mappings original_source: - snomedct - icd10 - icd10cm - mesh - loinc - cdiscvocab - ciel product_url: https://athena.ohdsi.org/search-terms/start secondary_source: - athena warnings: - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ Exceeded 30 redirects. - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ Exceeded 30 redirects. - category: GraphProduct description: Downloadable knowledge graph dump in TAR/GZ format containing complete FORUM data id: forum.graph.dump name: FORUM Knowledge Graph Dump original_source: - mesh - chebi - cito - fabio - dc - cheminf - skos - chemont - pubchem - pubmed product_url: ftp://forum:Forum2021Cov!@ftp.semantic-metabolomics.org/dumps/2021/share.tar.gz secondary_source: - forum warnings: - File was not able to be retrieved when checked on 2026-03-08_ FTP error_ timed out - File was not able to be retrieved when checked on 2026-02-26_ FTP error_ timed out - 'File was not able to be retrieved when checked on 2026-03-11: FTP error: timed out' - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv - category: Product description: mesh Nodes TSV format: tsv id: obo-db-ingest.mesh.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: mesh Nodes TSV original_source: - mesh product_file_size: 12212627 product_url: https://w3id.org/biopragmatics/resources/mesh/mesh.tsv secondary_source: - obo-db-ingest repository: https://nlmpubs.nlm.nih.gov/projects/mesh/ - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: email value: biocyc-support@sri.com label: MetaCyc creation_date: '2025-03-17T00:00:00Z' description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. 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The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. domains: - biological systems homepage_url: https://metacyc.org/ id: metacyc infores_id: metacyc last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail license: id: https://metacyc.org/download.shtml label: Varies name: MetaCyc products: - category: MappingProduct description: rhea SSSOM format: sssom id: obo-db-ingest.rhea.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rhea SSSOM original_source: - rhea - reactome - kegg - metacyc - m-csa - ecocyc product_file_size: 154171 product_url: https://w3id.org/biopragmatics/resources/rhea/rhea.sssom.tsv secondary_source: - obo-db-ingest - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: help@metanetx.org - contact_type: url value: https://www.metanetx.org/ id: sib label: MetaNetX Team - SIB Swiss Institute of Bioinformatics creation_date: '2025-05-07T00:00:00Z' description: MetaNetX is an online platform for accessing, analyzing, and manipulating genome-scale metabolic networks (GSM) and biochemical pathways, integrating data from multiple sources with a unified namespace for metabolites and biochemical reactions. domains: - biological systems - chemistry and biochemistry homepage_url: https://www.metanetx.org/ id: metanetx last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: MetaNetX products: - 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File was not able to be retrieved when checked on 2026-02-20_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-11-06_ HTTP 500 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: MNXref unified namespace for reactions across databases format: tsv id: metanetx.mnxref.reactions name: MetaNetX MNXref Reactions original_source: - metanetx product_url: https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_xref.tsv secondary_source: - metanetx warnings: - File was not able to be retrieved when checked on 2025-09-16_ No Content-Length header found - File was not able to be retrieved when checked on 2025-09-14_ No Content-Length header found - category: Product compression: gzip description: RDF version of the MetaNetX data for semantic web applications format: ttl id: metanetx.rdf name: MetaNetX RDF Data original_source: - metanetx product_file_size: 237044998 product_url: https://www.metanetx.org/ftp/latest/metanetx.ttl.gz secondary_source: - metanetx publications: - authors: - Moretti S - Tran VDT - Mehl F - Ibberson M - Pagni M doi: doi:10.1093/nar/gkaa992 id: doi:10.1093/nar/gkaa992 preferred: true title: MetaNetX/MNXref - unified namespace for metabolites and biochemical reactions in the context of metabolic models year: '2021' - authors: - Moretti S - Martin O - Tran VDT - Bridge A - Morgat A - Pagni M doi: doi:10.1093/nar/gkv1117 id: doi:10.1093/nar/gkv1117 title: MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks year: '2016' - authors: - Ganter M - Bernard T - Moretti S - Stelling J - Pagni M doi: doi:10.1093/bioinformatics/btt036 id: doi:10.1093/bioinformatics/btt036 title: MetaNetX.org - a website and repository for accessing, analysing and manipulating metabolic networks year: '2013' - authors: - Bernard T - Bridge A - Morgat A - Moretti S - Xenarios I - Pagni M doi: doi:10.1093/bib/bbs058 id: doi:10.1093/bib/bbs058 title: Reconciliation of metabolites and biochemical reactions for metabolic networks year: '2014' - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://metatraits.embl.de/ label: EMBL creation_date: '2026-02-21T00:00:00Z' description: metaTraits is a unified and accessible microbial trait resource that integrates culture-derived trait information from BacDive, BV-BRC, JGI IMG, and GOLD, with genome-based predictions for medium- and high-quality isolate and metagenome-assembled genomes (MAGs) from proGenomes and SPIRE. metaTraits covers over 2.2 million genomes and more than 140 harmonized traits mapped to standardized ontologies, spanning cell morphology (e.g., shape, size, Gram staining), physiology (e.g., motility, sporulation), metabolic and enzymatic activities, environmental preferences (e.g., temperature, salinity, oxygen tolerance), and lifestyle categories. All records are linked to their original evidence and cross-referenced to both NCBI and GTDB taxonomies. domains: - microbiology - genomics - microbiome - biological systems homepage_url: https://metatraits.embl.de/ id: metatraits last_modified_date: '2026-02-21T00:00:00Z' layout: resource_detail name: metaTraits products: - category: GraphicalInterface description: Web interface to explore and query microbial trait data in metaTraits, covering over 2.2 million genomes and 140+ harmonized traits. id: metatraits.site name: metaTraits Web Portal original_source: - metatraits product_url: https://metatraits.embl.de/ - category: Product description: Trait data table listing all 140+ harmonized traits available in metaTraits, mapped to standardized ontologies. id: metatraits.traits name: metaTraits Trait List original_source: - bacdive - bv-brc - goldterms - progenomes product_url: https://metatraits.embl.de/traits taxon: - NCBITaxon:2 - activity_status: active category: Ontology contacts: - category: Organization contact_details: - contact_type: url value: https://www.berkeleybop.org/ id: berkeleybop label: Berkeley Bioinformatics Open-source Projects creation_date: '2025-11-25T00:00:00Z' description: METPO (Microbial Ecophysiological Trait and Phenotype Ontology) is an ontology for describing microbial ecophysiological traits and phenotypes relevant to microbial ecology and environmental systems biology. domains: - microbiology - systems biology - biological systems homepage_url: https://github.com/berkeleybop/metpo id: metpo last_modified_date: '2026-01-05T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: METPO (Microbial Ecophysiological Trait and Phenotype Ontology) products: - category: OntologyProduct description: METPO ontology in OWL format format: owl id: metpo.owl is_public: true name: METPO OWL product_file_size: 24016 product_url: https://raw.githubusercontent.com/berkeleybop/metpo/refs/heads/main/metpo.owl - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe repository: https://github.com/berkeleybop/metpo synonyms: - METPO - Microbial Ecophysiological Trait and Phenotype Ontology taxon: - NCBITaxon:2 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: janna.hastings@gmail.com - contact_type: github value: jannahastings label: Janna Hastings orcid: 0000-0002-3469-4923 creation_date: '2025-09-29T00:00:00Z' description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. domains: - biomedical homepage_url: https://github.com/jannahastings/mental-functioning-ontology id: mf last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Mental Functioning Ontology products: - category: OntologyProduct description: Mental Functioning Ontology in OWL format format: owl id: mf.owl name: mf.owl product_file_size: 55614 product_url: http://purl.obolibrary.org/obo/mf.owl repository: https://github.com/jannahastings/mental-functioning-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: janna.hastings@gmail.com - contact_type: github value: jannahastings label: Janna Hastings orcid: 0000-0002-3469-4923 creation_date: '2025-09-29T00:00:00Z' description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. domains: - biomedical homepage_url: https://github.com/jannahastings/emotion-ontology id: mfoem last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Emotion Ontology products: - category: OntologyProduct description: Emotion Ontology in OWL format format: owl id: mfoem.owl name: mfoem.owl product_file_size: 72354 product_url: http://purl.obolibrary.org/obo/mfoem.owl repository: https://github.com/jannahastings/emotion-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: janna.hastings@gmail.com - contact_type: github value: jannahastings label: Janna Hastings orcid: 0000-0002-3469-4923 creation_date: '2025-09-29T00:00:00Z' description: An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable domains: - biomedical homepage_url: https://github.com/jannahastings/mental-functioning-ontology id: mfomd last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Mental Disease Ontology products: - category: OntologyProduct description: Mental Disease Ontology in OWL format format: owl id: mfomd.owl name: mfomd.owl product_file_size: 1294 product_url: http://purl.obolibrary.org/obo/mfomd.owl repository: https://github.com/jannahastings/mental-functioning-ontology - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.jax.org/ - contact_type: email value: mgi-help@jax.org label: The Jackson Laboratory - category: Organization contact_details: - contact_type: url value: https://www.informatics.jax.org/ label: Mouse Genome Informatics creation_date: '2025-01-10T00:00:00Z' description: The Mouse Genome Database (MGD) is the international database resource for the laboratory mouse serving as the authoritative source of integrated genetic, genomic, and biological data to facilitate the study of human health and disease through mouse models. Developed and maintained by the Mouse Genome Informatics consortium at The Jackson Laboratory, MGD provides comprehensive information on mouse genes, genome features, mammalian orthology, phenotypes, allelic variants, disease models, and extensive curated experimental data. The database integrates multiple specialized resources including the Gene Expression Database documenting spatial and temporal patterns of gene expression during mouse development and adulthood, the Mouse Models of Human Cancer database cataloging spontaneous and induced tumors, and extensive phenotype annotations using the Mammalian Phenotype Ontology. MGD contains curated data for all mouse genes with standardized nomenclature, genomic coordinates, functional annotations from Gene Ontology, expression patterns, phenotype associations, human disease connections, and literature references. The resource supports comparative genomics by providing detailed orthology relationships between mouse and human genes enabling translation of findings between species for biomedical research. MGD offers sophisticated search interfaces for genes, phenotypes, alleles, strains, polymorphisms including dramatically expanded SNP data, recombinase activity patterns for cre lines, and RNA-seq experiments, along with genome browsers, batch query tools, and data downloads in various formats. The database integrates data from high-throughput projects including the International Mouse Phenotyping Consortium systematic knockout phenotyping and Ensembl regulatory annotations. With over 30 years of continuous development since its 1994 web release, MGD collaborates with the Alliance of Genome Resources to harmonize model organism data and serves as an essential resource for the global mouse research community providing standardized, expert-curated knowledge. domains: - genomics homepage_url: https://www.informatics.jax.org/ id: mgd infores_id: mgi last_modified_date: '2025-01-10T00:00:00Z' layout: resource_detail name: Mouse Genome Database products: - category: GraphicalInterface description: Primary web interface providing integrated access to mouse genes, phenotypes, expression data, disease models, and genome features id: mgd.portal name: MGI Web Portal original_source: - mgd product_url: https://www.informatics.jax.org/ - category: Product description: Downloadable data reports including genes, markers, phenotypes, expression annotations, and orthology in various formats format: txt id: mgd.downloads name: MGD Data Downloads original_source: - mgd product_url: https://www.informatics.jax.org/downloads/reports/index.html - category: ProgrammingInterface description: MouseMine data mining platform providing programmatic access to MGD data through InterMine query interface id: mgd.mousemine is_public: true name: MouseMine original_source: - mgd product_url: http://www.mousemine.org/ - category: GraphicalInterface description: Gene Expression Database documenting spatiotemporal gene expression patterns during mouse development and adulthood id: mgd.gxd name: Gene Expression Database (GXD) original_source: - mgd product_url: https://www.informatics.jax.org/expression.shtml - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet publications: - id: https://doi.org/10.1093/genetics/iyae031 title: 'Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse' - id: https://doi.org/10.1093/nar/gkaa1083 title: 'Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology' repository: https://github.com/mgijax synonyms: - MGD - Mouse Genome Database - MGI - Mouse Genome Informatics taxon: - NCBITaxon:9606 - NCBITaxon:40674 - NCBITaxon:10090 - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for mgi. This page was automatically generated because it was referenced by other resources. domains: - stub id: mgi last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Mgi products: - category: Product description: mgi Nodes TSV format: tsv id: obo-db-ingest.mgi.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: mgi Nodes TSV original_source: - mgi product_file_size: 6615249 product_url: https://w3id.org/biopragmatics/resources/mgi/mgi.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: bsantan label: Brook Santangelo creation_date: '2025-04-13T00:00:00Z' description: A knowledge graph of linked microbes, genes and metabolites. domains: - biological systems - microbiology evaluation_page: resource/mgmlink/mgmlink_eval_automated.html id: mgmlink last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: MGMLink products: - category: ProcessProduct description: Code for generating MGMLink id: mgmlink.code name: MGMLink code original_source: - gutmgene - pheknowlator product_url: https://github.com/bsantan/MGMLink secondary_source: - mgmlink publications: - authors: - Santangelo BE - Bada M - Hunter LE - Lozupone C doi: 10.1038/s41598-025-91230-6 id: doi:10.1038/s41598-025-91230-6 title: '''Hypothesizing mechanistic links between microbes and disease using knowledge graphs''' year: '2025' taxon: - NCBITaxon:2759 - activity_status: active category: Aggregator creation_date: '2025-09-09T00:00:00Z' description: MGnify is an active aggregator and analysis platform for microbiome and metagenomic data, providing tools for submission, analysis, visualization, and discovery of microbiome datasets from diverse biomes and environments. It is operated by EMBL-EBI and is an ELIXIR Core Data Resource. domains: - biological systems - genomics - environment - clinical id: mgnify last_modified_date: '2025-10-10T00:00:00Z' layout: resource_detail name: MGnify products: - category: GraphicalInterface description: Web portal for searching, browsing, and analyzing microbiome and metagenomic datasets, including studies, analyses, genomes, and biomes. format: http id: mgnify.portal name: MGnify Web Portal product_url: https://www.ebi.ac.uk/metagenomics - category: ProgrammingInterface description: REST API for programmatic access to MGnify data, including studies, analyses, genomes, and metadata. format: http id: mgnify.api name: MGnify REST API product_url: https://www.ebi.ac.uk/metagenomics/api - category: Product description: FTP archive with current and archived release files, including sequences, annotations, and genome catalogues. format: http id: mgnify.ftp name: MGnify FTP Archive product_url: ftp://ftp.ebi.ac.uk/pub/databases/metagenomics warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/metagenomics' - File was not able to be retrieved when checked on 2025-12-04_ FTP error_ [Errno 104] Connection reset by peer - File was not able to be retrieved when checked on 2025-12-04_ FTP error_ [Errno 104] Connection reset by peer - category: Product description: Biome-specific microbial genome catalogues, including marine, human gut, and other environments. format: http id: mgnify.genomes name: MGnify Genomes Catalogue product_url: https://www.ebi.ac.uk/metagenomics/browse - category: Product description: Protein database derived from metagenomic analyses, including protein families and annotations. format: http id: mgnify.proteins name: MGnify Proteins Database product_url: https://www.ebi.ac.uk/metagenomics/proteins - category: DocumentationProduct description: Documentation and help resources for MGnify, including user guides and API documentation. format: http id: mgnify.docs name: MGnify Documentation product_url: https://www.ebi.ac.uk/metagenomics/help - category: DocumentationProduct description: On-demand and live training resources for MGnify users, including webinars and tutorials. format: http id: mgnify.training name: MGnify Training product_url: https://www.ebi.ac.uk/training/online/courses/mgnify-quick-tour - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Richardson LJ - Allen B - Baldi G - Beracochea M - Bileschi M - Burdett T - Burgin J - Caballero-Pérez J - Cochrane G - Colwell L - Curtis T - Escobar-Zepeda A - Gurbich T - Kale V - Korobeynikov A - Raj S - Rogers AB - Sakharova E - Sanchez S - Wilkinson D - Finn RD id: https://doi.org/10.1093/nar/gkac1080 journal: Nucleic Acids Research preferred: true title: 'MGnify: the microbiome sequence data analysis resource in 2023' year: '2023' taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: luana.licata@gmail.com - contact_type: github value: luanalicata label: Luana Licata orcid: 0000-0001-5084-9000 creation_date: '2025-06-04T00:00:00Z' description: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. domains: - biomedical homepage_url: https://github.com/HUPO-PSI/psi-mi-CV id: mi last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Molecular Interactions Controlled Vocabulary products: - category: OntologyProduct description: Molecular Interactions Controlled Vocabulary in OWL format format: owl id: mi.owl name: mi.owl product_file_size: 248742 product_url: http://purl.obolibrary.org/obo/mi.owl - category: OntologyProduct description: Molecular Interactions Controlled Vocabulary in OBO format format: obo id: mi.obo name: mi.obo product_file_size: 169744 product_url: http://purl.obolibrary.org/obo/mi.obo - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 repository: https://github.com/HUPO-PSI/psi-mi-CV - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: hilmar.lapp@duke.edu - contact_type: github value: hlapp label: Hilmar Lapp orcid: 0000-0001-9107-0714 creation_date: '2025-09-29T00:00:00Z' description: An application ontology to formalize annotation of phylogenetic data. domains: - biomedical homepage_url: http://www.evoio.org/wiki/MIAPA id: miapa last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: MIAPA Ontology products: - category: OntologyProduct description: MIAPA Ontology in OWL format format: owl id: miapa.owl name: miapa.owl product_file_size: 5849 product_url: http://purl.obolibrary.org/obo/miapa.owl repository: https://github.com/evoinfo/miapa - activity_status: active category: KnowledgeGraph collection: - translator - ber contacts: - category: Individual contact_details: - contact_type: email value: gglusman@isbscience.org - contact_type: github value: gglusman label: Gwênlyn Glusman creation_date: '2025-08-30T00:00:00Z' description: MicrobiomeKG is an integrative knowledge graph resource for multi-omics microbiome data linking microbial taxa, genes, metabolites, host phenotypes, pathways, and clinical variables to support systems biology analyses and translational research. domains: - biomedical - systems biology - microbiome evaluation_page: resource/microbiomekg/microbiomekg_eval_automated.html homepage_url: https://multiomics.transltr.io/mbkp id: microbiomekg last_modified_date: '2025-08-30T00:00:00Z' layout: resource_detail name: MicrobiomeKG products: - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg publications: - doi: 10.3389/fsysb.2025.1544432 id: doi:10.3389/fsysb.2025.1544432 journal: Frontiers in Systems Biology title: 'MicrobiomeKG: an integrative knowledge graph for multi-omics microbiome translational research' year: '2025' taxon: - NCBITaxon:9606 - NCBITaxon:2 - activity_status: active category: KnowledgeGraph contacts: - category: Individual label: Roger Tu orcid: 0000-0002-7899-1604 - category: Individual label: Meghamala Sinha orcid: 0000-0002-6422-3313 - category: Individual label: Andrew I. Su orcid: 0000-0002-9859-4104 creation_date: '2025-07-17T00:00:00Z' description: 'Mechanistic Repositioning Network with Indications (MIND) is a knowledge graph incorporating two biomedical resources: MechRepoNet and DrugCentral. MechRepoNet is a knowledge graph comprising of 18 biomedical resources that reflects and expands on important drug mechanism relationships identified from a curated biomedical drug mechanism dataset. MIND was created by mapping DrugCentral edges to existing MechRepoNet nodes through the Unified Medical Language System (UMLS) and Medical Subject Headings (MeSH). The MIND training set has a total of 9,651,040 edges.' domains: - drug discovery - biomedical evaluation_page: resource/mind/mind_eval_automated.html homepage_url: https://zenodo.org/records/8117748 id: mind last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: MIND products: - category: GraphProduct description: Training data for the MIND knowledge graph containing 9,651,040 edges format: tsv id: mind.train license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: MIND Training Data original_source: - drugcentral - mechreponet product_url: https://zenodo.org/records/8117748/files/train.txt secondary_source: - mind warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-22_ HTTP 429 error when accessing file - File was not able to be retrieved when checked on 2025-12-18_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: Test data for the MIND knowledge graph containing DrugCentral indications format: tsv id: mind.test license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: MIND Test Data original_source: - drugcentral - mechreponet product_url: https://zenodo.org/records/8117748/files/test.txt secondary_source: - mind warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-18_ HTTP 429 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: Validation data for the MIND knowledge graph containing DrugCentral indications format: tsv id: mind.valid license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: MIND Validation Data original_source: - drugcentral - mechreponet product_url: https://zenodo.org/records/8117748/files/valid.txt secondary_source: - mind warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2025-12-22_ HTTP 429 error when accessing file - File was not able to be retrieved when checked on 2025-10-30_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Dictionary of entities in the MIND knowledge graph format: tsv id: mind.entities license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: MIND Entities Dictionary original_source: - drugcentral - mechreponet product_file_size: 5629618 product_url: https://zenodo.org/records/8117748/files/entities.dict secondary_source: - mind - category: Product description: Dictionary of relations in the MIND knowledge graph format: tsv id: mind.relations license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: MIND Relations Dictionary original_source: - drugcentral - mechreponet product_file_size: 1648 product_url: https://zenodo.org/records/8117748/files/relations.dict secondary_source: - mind publications: - authors: - Roger Tu - Meghamala Sinha - Carolina González - Eric Hu - Shehzaad Dhuliawala - Andrew McCallum - Andrew I. Su id: https://doi.org/10.1101/2023.05.12.540594 journal: bioRxiv title: Drug Repurposing using consilience of Knowledge Graph Completion methods year: '2023' repository: https://github.com/SuLab/KnowledgeGraphEmbedding - activity_status: active category: Aggregator contacts: - category: Organization label: MINT Team - University of Rome Tor Vergata creation_date: '2025-10-31T00:00:00Z' description: MINT (The Molecular INTeraction database) is a public and open source database focusing on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. Molecular interactions are annotated according to international PSI-MI standards and follow the PSI-MI controlled vocabulary. MINT is a founder and main member of the IMEx consortium and provides data that is integrated into the IntAct database as part of a single non-redundant open access dataset. As an ELIXIR Core Data Resource and Global Core Biodata Resource, MINT contains over 139,000 interactions involving 27,800+ interactors from 676 organisms extracted from 6,500+ publications. domains: - proteomics - biomedical - systems biology - biological systems homepage_url: https://mint.bio.uniroma2.it/ id: mint last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Mint products: - category: GraphicalInterface description: Web interface for browsing, searching, and visualizing protein-protein interaction data from MINT with advanced search capabilities. format: http id: mint.portal name: MINT Web Portal original_source: - mint product_url: https://mint.bio.uniroma2.it/ - category: Product description: Complete MINT dataset in PSI-MI MITAB 2.7 format accessible via PSICQUIC web service. format: psi_mi_mitab id: mint.mitab.all name: MINT MITAB Full Dataset product_url: http://www.ebi.ac.uk/Tools/webservices/psicquic/mint/webservices/current/search/query/* warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 500 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-25_ HTTP 500 error when accessing file - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Human protein interactions from MINT in PSI-MI MITAB format for Homo sapiens (NCBITaxon 9606). format: psi_mi_mitab id: mint.mitab.human name: MINT Human Interactions product_url: http://www.ebi.ac.uk/Tools/webservices/psicquic/mint/webservices/current/search/query/species:human warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 500 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-25_ HTTP 500 error when accessing file - File was not able to be retrieved when checked on 2025-12-04_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Mouse protein interactions from MINT in PSI-MI MITAB format for Mus musculus (NCBITaxon 10090). format: psi_mi_mitab id: mint.mitab.mouse name: MINT Mouse Interactions product_url: http://www.ebi.ac.uk/Tools/webservices/psicquic/mint/webservices/current/search/query/species:mouse warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 500 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-25_ HTTP 500 error when accessing file - File was not able to be retrieved when checked on 2026-01-06_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: ProgrammingInterface description: PSICQUIC SOAP and REST web services for programmatic access to MINT data using Molecular Interactions Query Language (MIQL). id: mint.psicquic name: MINT PSICQUIC Web Service product_url: http://www.ebi.ac.uk/Tools/webservices/psicquic/mint/webservices/ - category: GraphicalInterface description: Advanced search interface for querying MINT data with field-specific searches and boolean operators. format: http id: mint.advanced.search name: MINT Advanced Search product_url: https://mint.bio.uniroma2.it/index.php/advanced-search/ - category: Product description: Historical consolidated protein interaction index in PSI-MITAB 2.5 format aggregating data from BIND, BioGrid, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID format: psi_mi_mitab id: irefindex.database name: iRefIndex Database original_source: - bind - biogrid - dip - hprd - intact - mint - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz publications: - doi: 10.1016/s0014-5793(01)03293-8 id: PMID:11911893 journal: FEBS Lett title: 'MINT: a Molecular INTeraction database' year: '2002' - doi: 10.1093/nar/gkl950 id: PMID:17135203 journal: Nucleic Acids Res title: 'MINT: the Molecular INTeraction database' year: '2007' - doi: 10.1093/nar/gkr930 id: PMID:22096227 journal: Nucleic Acids Res title: 'MINT, the molecular interaction database: 2012 update' year: '2012' synonyms: - MINT - Molecular INTeraction Database - activity_status: active category: Aggregator creation_date: '2004-01-01T00:00:00Z' description: miRBase is the primary online repository for microRNA sequences and annotations, serving as the central registry for microRNA nomenclature and providing a comprehensive archive of published microRNA data including sequences, annotations, predicted targets, and deep sequencing evidence. domains: - genomics - biological systems homepage_url: https://www.mirbase.org/ id: mirbase infores_id: mirbase last_modified_date: '2025-10-21T00:00:00Z' layout: resource_detail name: miRBase products: - category: GraphicalInterface description: Web portal for searching and browsing microRNA sequences by identifier, keyword, genomic location, tissue expression, or sequence format: http id: mirbase.portal name: miRBase Portal product_url: https://www.mirbase.org/ - category: GraphicalInterface description: Browse interface for exploring microRNA entries organized by species and other criteria format: http id: mirbase.browse name: miRBase Browse Interface product_url: https://www.mirbase.org/ - category: GraphicalInterface description: Search interface for finding microRNAs by genomic location coordinates format: http id: mirbase.genomic-search name: Genomic Location Search product_url: https://www.mirbase.org/ - category: GraphicalInterface description: Search interface for finding microRNAs by tissue expression patterns format: http id: mirbase.tissue-search name: Tissue Expression Search product_url: https://www.mirbase.org/ - category: Product compression: gzip description: All published microRNA data in EMBL format format: txt id: mirbase.mirna-dat name: miRNA.dat product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: FASTA format sequences of all microRNA hairpin precursors format: fasta id: mirbase.hairpin-fa name: hairpin.fa product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: FASTA format sequences of all mature microRNA sequences format: fasta id: mirbase.mature-fa name: mature.fa product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: List of changes between the last release and current release format: txt id: mirbase.diff name: miRNA.diff product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: List of entries that have been removed from the database format: txt id: mirbase.dead name: miRNA.dead product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: Genome coordinates for human microRNAs in GFF3 format format: gff id: mirbase.hsa-gff3 name: Human (hsa) Genome Coordinates product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: Genome coordinates for mouse microRNAs in GFF3 format format: gff id: mirbase.mmu-gff3 name: Mouse (mmu) Genome Coordinates product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: Genome coordinates for rat microRNAs in GFF3 format format: gff id: mirbase.rno-gff3 name: Rat (rno) Genome Coordinates product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: Genome coordinates for Drosophila microRNAs in GFF3 format format: gff id: mirbase.dme-gff3 name: Drosophila (dme) Genome Coordinates product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: Genome coordinates for C. elegans microRNAs in GFF3 format format: gff id: mirbase.cel-gff3 name: C. elegans (cel) Genome Coordinates product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: Genome coordinates for zebrafish microRNAs in GFF3 format format: gff id: mirbase.dre-gff3 name: Zebrafish (dre) Genome Coordinates product_url: https://www.mirbase.org/download/CURRENT/ - category: Product compression: gzip description: Genome coordinates for Arabidopsis microRNAs in GFF3 format format: gff id: mirbase.ath-gff3 name: Arabidopsis (ath) Genome Coordinates product_url: https://www.mirbase.org/download/CURRENT/ - category: Product description: FTP archive with current release data files and previous releases format: http id: mirbase.ftp name: miRBase FTP Archive product_url: https://www.mirbase.org/download/CURRENT/ - category: DocumentationProduct description: Release notes and documentation for data file formats format: txt id: mirbase.readme name: README product_url: https://www.mirbase.org/download/CURRENT/ - category: DocumentationProduct description: Comprehensive help documentation including submission guidelines, search instructions, genome assemblies, and naming conventions format: http id: mirbase.help name: miRBase Help Documentation product_url: https://www.mirbase.org/help/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database - category: Product description: mirbase Nodes TSV format: tsv id: obo-db-ingest.mirbase.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase Nodes TSV original_source: - mirbase product_file_size: 384582 product_url: https://w3id.org/biopragmatics/resources/mirbase/mirbase.tsv secondary_source: - obo-db-ingest - category: Product description: mirbase.family Nodes TSV format: tsv id: obo-db-ingest.mirbase.family.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase.family Nodes TSV original_source: - mirbase product_file_size: 15085 product_url: https://w3id.org/biopragmatics/resources/mirbase.family/mirbase.family.tsv secondary_source: - obo-db-ingest - category: Product description: mirbase.mature Nodes TSV format: tsv id: obo-db-ingest.mirbase.mature.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase.mature Nodes TSV original_source: - mirbase product_file_size: 293915 product_url: https://w3id.org/biopragmatics/resources/mirbase.mature/mirbase.mature.tsv secondary_source: - obo-db-ingest publications: - authors: - Kozomara - Birgaoanu - Griffiths-Jones id: https://pubmed.ncbi.nlm.nih.gov/30423142/ journal: Nucleic Acids Research preferred: true title: 'miRBase: from microRNA sequences to function' year: '2019' - authors: - Kozomara - Griffiths-Jones id: https://pubmed.ncbi.nlm.nih.gov/24275495/ journal: Nucleic Acids Research title: 'miRBase: annotating high confidence microRNAs using deep sequencing data' year: '2014' - authors: - Kozomara - Griffiths-Jones id: https://pubmed.ncbi.nlm.nih.gov/21037258/ journal: Nucleic Acids Research title: 'miRBase: integrating microRNA annotation and deep-sequencing data' year: '2011' - authors: - Griffiths-Jones - Saini - van Dongen - Enright id: https://pubmed.ncbi.nlm.nih.gov/17991681/ journal: Nucleic Acids Research title: 'miRBase: tools for microRNA genomics' year: '2008' - authors: - Griffiths-Jones - Grocock - van Dongen - Bateman - Enright id: https://pubmed.ncbi.nlm.nih.gov/16381832/ journal: Nucleic Acids Research title: 'miRBase: microRNA sequences, targets and gene nomenclature' year: '2006' - authors: - Griffiths-Jones id: https://pubmed.ncbi.nlm.nih.gov/14681370/ journal: Nucleic Acids Research title: The microRNA Registry year: '2004' - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: MirGeneDB is a manually curated database of microRNA genes, providing validated and annotated microRNA gene entries for over 21,000 genes from 114 metazoan species. It offers uniform nomenclature, evolutionary context, and downloadable data for all species and families. domains: - genomics - biological systems id: mirgenedb last_modified_date: '2025-10-15T00:00:00Z' layout: resource_detail name: MirGeneDB products: - category: GraphicalInterface description: Web interface for browsing, searching, and exploring curated microRNA gene entries and families across 114 metazoan species. format: http id: mirgenedb.portal name: MirGeneDB Web Portal product_url: https://mirgenedb.org/ - category: Product description: Downloadable FASTA, GFF, BED, and tabular files for microRNA genes from individual species. format: http id: mirgenedb.species_downloads name: MirGeneDB Species-Specific Downloads product_url: https://mirgenedb.org/download - category: Product description: Downloadable covariance models for more than 700 conserved microRNA families. format: http id: mirgenedb.covariance name: MirGeneDB Covariance Models product_url: https://mirgenedb.org/covariance - category: Product description: Downloadable processed FASTA files of all read data used in MirGeneDB annotations. format: fasta id: mirgenedb.reads name: MirGeneDB Processed Read Data product_url: https://mirgenedb.org/download - category: Product description: Bulk download ZIP archives for all microRNA gene data across species. format: http id: mirgenedb.bulk name: MirGeneDB Bulk Data Archive product_url: https://mirgenedb.org/download - category: DocumentationProduct description: Documentation and information about MirGeneDB nomenclature, annotation standards, and database usage. format: http id: mirgenedb.info name: MirGeneDB Information and Help product_url: https://mirgenedb.org/information - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Clarke AW - Høye E - Hembrom AA - Paynter VM - Vinther J - Wyrożemski Ł - Biryukova I - Formaggioni A - Ovchinnikov V - Herlyn H id: https://doi.org/10.1093/nar/gkae1094 journal: Nucleic Acids Research preferred: true title: 'MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models' year: '2024' - activity_status: active category: DataSource creation_date: '2025-07-17T00:00:00Z' description: miRTarBase is a comprehensive database of experimentally validated microRNA-target interactions (MTIs). It collects and curates miRNA-target interactions with experimental evidence from the literature, including data from reporter assays, western blot, qPCR, microarray, and high-throughput experiments such as CLIP-Seq. domains: - genomics - biological systems id: mirtarbase last_modified_date: '2025-10-15T00:00:00Z' layout: resource_detail name: miRTarBase products: - category: GraphicalInterface description: Web interface for searching and browsing experimentally validated microRNA-target interactions across multiple species. format: http id: mirtarbase.portal name: miRTarBase Web Portal product_url: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2025/php/index.php - category: Product description: Complete dataset of microRNA-target interactions (MTI) in CSV format containing all experimentally validated interactions. format: csv id: mirtarbase.mti name: miRTarBase Complete MTI Dataset product_url: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2025/php/download.php warnings: - File was not able to be retrieved when checked on 2026-03-08_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-25_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='mirtarbase.cuhk.edu.cn', port=443)_ Max retries exceeded with url_ /~miRTarBase/miRTarBase_2025/php/download.php (Caused by SSLError(SSLError(1, '[SSL_ SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='mirtarbase.cuhk.edu.cn', port=443)_ Max retries exceeded with url_ /~miRTarBase/miRTarBase_2025/php/download.php (Caused by SSLError(SSLError(1, '[SSL_ SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Dataset of microRNA target sites with detailed binding site information in CSV format. format: csv id: mirtarbase.target_sites name: miRTarBase Target Sites Dataset product_url: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2025/php/download.php warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='mirtarbase.cuhk.edu.cn', port=443)_ Max retries exceeded with url_ /~miRTarBase/miRTarBase_2025/php/download.php (Caused by SSLError(SSLError(1, '[SSL_ SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='mirtarbase.cuhk.edu.cn', port=443)_ Max retries exceeded with url_ /~miRTarBase/miRTarBase_2025/php/download.php (Caused by SSLError(SSLError(1, '[SSL_ SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c_1017)'))) - File was not able to be retrieved when checked on 2026-01-06_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Species-specific microRNA-target interaction datasets in CSV format for human, mouse, rat, and 25+ other species. format: csv id: mirtarbase.species_mti name: miRTarBase Species-Specific MTI Files product_url: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2025/php/download.php warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='mirtarbase.cuhk.edu.cn', port=443)_ Max retries exceeded with url_ /~miRTarBase/miRTarBase_2025/php/download.php (Caused by SSLError(SSLError(1, '[SSL_ SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-02-04_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='mirtarbase.cuhk.edu.cn', port=443)_ Max retries exceeded with url_ /~miRTarBase/miRTarBase_2025/php/download.php (Caused by SSLError(SSLError(1, '[SSL_ SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Curated datasets filtered for strong experimental evidence including reporter assays, western blot, qPCR, and CLIP-Seq data. format: csv id: mirtarbase.strong_evidence name: miRTarBase Strong Evidence Datasets product_url: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2025/php/download.php warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-25_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='mirtarbase.cuhk.edu.cn', port=443)_ Max retries exceeded with url_ /~miRTarBase/miRTarBase_2025/php/download.php (Caused by SSLError(SSLError(1, '[SSL_ SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='mirtarbase.cuhk.edu.cn', port=443)_ Max retries exceeded with url_ /~miRTarBase/miRTarBase_2025/php/download.php (Caused by SSLError(SSLError(1, '[SSL_ SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Archive of previous miRTarBase releases for reproducibility and historical comparisons. format: http id: mirtarbase.archive name: miRTarBase Previous Releases Archive product_url: https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2025/php/download.php warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='mirtarbase.cuhk.edu.cn', port=443)_ Max retries exceeded with url_ /~miRTarBase/miRTarBase_2025/php/download.php (Caused by SSLError(SSLError(1, '[SSL_ SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-02-13_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='mirtarbase.cuhk.edu.cn', port=443)_ Max retries exceeded with url_ /~miRTarBase/miRTarBase_2025/php/download.php (Caused by SSLError(SSLError(1, '[SSL_ SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet publications: - authors: - Cui S - Yu S - Huang HY - Lin YCD - Huang Y - Zhang B - Xiao J - Zuo H - Wang J - Li Z id: https://doi.org/10.1093/nar/gkae1072 journal: Nucleic Acids Research preferred: true title: 'miRTarBase 2025: updates to the collection of experimentally validated microRNA-target interactions' year: '2024' - authors: - Huang HY - Lin YCD - Cui S - Huang Y - Tang Y - Xu J - Bao J - Li Y - Wen J - Zuo H id: https://doi.org/10.1093/nar/gkab1079 journal: Nucleic Acids Research preferred: false title: 'miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions' year: '2022' - activity_status: active category: DataModel collection: - ber contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Christopher J. Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-03-09T00:00:00Z' description: 'MIxS, or the Minimum Information about any (X) Sequence is a standard for describing the contextual information about the sampling and sequencing of any genomic sequence. The standard has Terms that describe characteristics of a sample that addresses: What is the source of the sequence? In what kind of environment was the sample collected? What methods were utilized to process the sample?' domains: - environment homepage_url: https://w3id.org/mixs id: mixs last_modified_date: '2025-09-27T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: MIxS products: - category: DataModelProduct description: OWL release of mixs id: mixs.model name: MIxS OWL release original_source: - mixs product_file_size: 154279 product_url: https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/refs/heads/main/project/owl/mixs.owl.ttl secondary_source: - mixs repository: https://github.com/GenomicsStandardsConsortium/mixs - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jrsmith@mcw.edu - contact_type: github value: jrsjrs label: Jennifer Smith orcid: 0000-0002-6443-9376 creation_date: '2025-09-29T00:00:00Z' description: A representation of the variety of methods used to make clinical and phenotype measurements. domains: - biomedical homepage_url: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 id: mmo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Measurement method ontology products: - category: OntologyProduct description: Measurement method ontology in OWL format format: owl id: mmo.owl name: mmo.owl product_file_size: 1924483 product_url: http://purl.obolibrary.org/obo/mmo.owl - category: OntologyProduct description: Measurement method ontology in OBO format format: obo id: mmo.obo name: mmo.obo product_file_size: 506222 product_url: http://purl.obolibrary.org/obo/mmo.obo repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: frederic.bastian@unil.ch - 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pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 repository: https://github.com/HUPO-PSI/psi-mod-CV - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: MODOMICS is a comprehensive database of RNA modifications that provides detailed information about the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, RNA modifying enzymes, and associated human diseases. domains: - genomics - biological systems - chemistry and biochemistry id: modomics last_modified_date: '2025-10-15T00:00:00Z' layout: resource_detail name: MODOMICS products: - category: GraphicalInterface description: Web interface for browsing RNA modifications, pathways, reactions, sequences, proteins, and associated diseases. format: http id: modomics.portal name: MODOMICS Web Portal product_url: https://genesilico.pl/modomics/ - 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category: OntologyProduct description: Ontology of base modifications in OWL Lite format for semantic web applications. format: owl id: modomics.owl name: MODOMICS Ontology (OWL) product_url: https://genesilico.pl/modomics/download/ModifiedBases.owl - category: OntologyProduct description: Ontology of base modifications in N3 format. id: modomics.n3 name: MODOMICS Ontology (N3) product_url: https://genesilico.pl/modomics/download/Modifications.n3 - category: Product description: Structure-data files for modified bases in SDF format. format: sdf id: modomics.sdf name: MODOMICS SDF Files product_file_size: 271038 product_url: https://genesilico.pl/modomics/download/sdf2/ - category: GraphicalInterface description: Advanced search interface for querying modifications, pathways, sequences, and proteins. format: http id: modomics.search name: MODOMICS Advanced Search product_url: https://genesilico.pl/modomics/search/advance/ - category: DocumentationProduct description: User guide and documentation for using the MODOMICS database. format: http id: modomics.help name: MODOMICS Help Documentation product_url: https://genesilico.pl/modomics/help - category: DocumentationProduct description: Information about data annotation methods and standards used in MODOMICS. format: http id: modomics.annotation name: MODOMICS Data Annotation Information product_url: https://genesilico.pl/modomics/data_information/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Cappannini A - Ray A - Purta E - Mukherjee S - Boccaletto P - Moafinejad SN - Lechner A - Barchet C - Klaholz BP - Stefaniak F - Bujnicki JM id: https://doi.org/10.1093/nar/gkad1083 journal: Nucleic Acids Research preferred: true title: 'MODOMICS: a database of RNA modifications and related information. 2023 update' year: '2024' - authors: - Boccaletto P - Stefaniak F - Ray A - Cappannini A - Mukherjee S - Purta E - Kurkowska M - Shirvanizadeh N - Destefanis E - Groza P id: https://doi.org/10.1093/nar/gkab1083 journal: Nucleic Acids Research preferred: false title: 'MODOMICS: a database of RNA modification pathways. 2021 update' year: '2022' taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual label: Sandrine Muller orcid: 0000-0001-5998-3003 creation_date: '2025-03-09T00:00:00Z' description: MolePro is a Molecular Data Provider translating molecular scale to systems scale through a Reasoner API. It is a Translator Knowledge Provider. domains: - health evaluation_page: resource/molecular-data-kp/molecular-data-kp_eval_automated.html homepage_url: https://github.com/broadinstitute/molecular-data-provider/ id: molecular-data-kp last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: MolePro products: - category: GraphProduct description: KGX nodes for Molecular Data KP format: kgx id: molecular-data-kp.graph.nodes name: Nodes for Molecular Data KP original_source: - molecular-data-kp product_file_size: 3676906360 product_url: https://molepro.s3.amazonaws.com/nodes.tsv secondary_source: - molecular-data-kp - category: GraphProduct description: KGX edges for Molecular Data KP format: kgx id: molecular-data-kp.graph.edges name: Edges for Molecular Data KP original_source: - molecular-data-kp product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv secondary_source: - molecular-data-kp - category: ProgrammingInterface connection_url: https://translator.broadinstitute.org/molecular_data_provider/api description: Open API for Molecular Data KP id: molecular-data-kp.api is_public: true name: Open API for Molecular Data KP original_source: - molecular-data-kp product_url: https://translator.broadinstitute.org/molecular_data_provider/api secondary_source: - molecular-data-kp repository: https://github.com/broadinstitute/molecular-data-provider/ - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: email value: translator@broadinstitute.org id: broad label: Broad Institute Translator Team creation_date: '2025-10-30T00:00:00Z' description: The Molecular Data Provider (MolePro) is part of the NCATS Biomedical Data Translator project, integrating diverse chemical biology data sources into a curated framework for chemical entities and their effects on biological targets. MolePro consolidates information from over two dozen public chemical biology datasets, portals, and tools, providing comprehensive insights into compounds, protein targets, and similarity-based connections through both a custom API and TRAPI interface. domains: - drug discovery - chemistry and biochemistry - biomedical - pharmacology - translational homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/Molecular-Data-Provider id: molepro infores_id: molepro last_modified_date: '2025-11-17T00:00:00Z' layout: resource_detail name: Molecular Data Provider products: - category: ProgrammingInterface description: MolePro API providing access to the knowledge graph of chemical entities and biological targets format: http id: molepro.api name: MolePro API original_source: - molepro product_url: https://molepro.transltr.io/molecular_data_provider/api - category: ProgrammingInterface description: TRAPI-compliant interface for MolePro knowledge graph following the Translator Reasoner API standard format: http id: molepro.trapi name: MolePro TRAPI Interface original_source: - molepro product_url: https://molepro-trapi.transltr.io/molepro/trapi/v1.5/ui/ - category: Product description: Catalog of MolePro knowledge sources in JSON format format: json id: molepro.catalog name: MolePro Knowledge Sources Catalog original_source: - molepro product_file_size: 2127887 product_url: https://translator.broadinstitute.org/molecular_data_provider/transformers repository: https://github.com/broadinstitute/molecular-data-provider synonyms: - MolePro - Molecular Data Provider tags: - translator - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: email value: info@monarchinitiative.org id: monarchinitiative label: Monarch Initiative creation_date: '2025-10-30T00:00:00Z' description: The Monarch Initiative is an international consortium that integrates, aligns, and redistributes cross-species gene, genotype, variant, disease, and phenotype data to improve understanding of genetic disease and support translational research. domains: - genomics - biological systems homepage_url: https://monarchinitiative.org/ id: monarchinitiative infores_id: monarchinitiative last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: Monarch Initiative products: - category: KnowledgeGraph description: Monarch Knowledge Graph integrating phenotype, disease, gene data across species format: mixed id: monarchinitiative.kg name: Monarch Knowledge Graph original_source: - monarchinitiative product_url: https://monarchinitiative.org/ - category: ProgrammingInterface description: Monarch API for programmatic access to integrated data format: http id: monarchinitiative.api name: Monarch API original_source: - monarchinitiative product_url: https://api.monarchinitiative.org/api/ - category: GraphicalInterface description: Web interface for browsing genes, diseases, phenotypes across species format: http id: monarchinitiative.portal name: Monarch Web Portal original_source: - monarchinitiative product_url: https://monarchinitiative.org/ publications: - id: https://doi.org/10.1093/nar/gkw1128 journal: Nucleic Acids Research title: 'The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species' year: '2017' repository: https://github.com/monarch-initiative synonyms: - Monarch - The Monarch Initiative - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Sabrina@tislab.org - contact_type: github value: sabrinatoro label: Sabrina Toro orcid: 0000-0002-4142-7153 creation_date: '2025-04-22T00:00:00Z' description: A global community effort to harmonize multiple disease resources to yield a coherent merged ontology. domains: - biomedical homepage_url: https://monarch-initiative.github.io/mondo id: mondo last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Mondo Disease Ontology products: - 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category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. 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kg-microbe - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: GraphProduct description: KGX distribution of the ICEES Exposures KP in Knowledge Graph Exchange (KGX) format, containing integrated clinical and environmental exposures data as a knowledge graph with 226 nodes and 14,342 edges format: kgx-jsonl id: icees-kg.graph name: KGX distribution of the ICEES Exposures KP original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/ secondary_source: - icees-kg - category: ProgrammingInterface description: Translator Reasoner API (TRAPI) endpoint for querying ICEES KG using standardized Translator protocols format: http id: icees-kg.trapi name: ICEES KG TRAPI API original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg-trapi secondary_source: - icees-kg - category: Product description: Meta knowledge graph and metadata describing the data sources, node types, edge types, and predicates available in ICEES KG format: json id: icees-kg.metadata name: ICEES KG Metadata original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/metadata-metadata-get-icees-kg secondary_source: - icees-kg - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct description: Nodes for the Drug Approvals KP, v0.3.9 format: kgx id: drug-approvals-kp.graph.nodes name: Drug Approvals KP Graph Nodes original_source: - chebi - doid - hp - mondo product_file_size: 701451 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_nodes_v0.3.9.tsv secondary_source: - drug-approvals-kp - category: GraphProduct description: Edges for the Drug Approvals KP, v0.3.9 format: kgx id: drug-approvals-kp.graph.edges name: Drug Approvals KP Graph Edges original_source: - chebi - doid - hp - mondo product_file_size: 31052966 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_edges_v0.3.9.tsv secondary_source: - drug-approvals-kp - category: MappingProduct description: MONDO SSSOM. Mappings from MONDO identifiers to other namespaces. format: sssom id: mondo.sssom name: MONDO SSSOM original_source: - doid - hp - hgnc product_file_size: 1437457 product_url: https://raw.githubusercontent.com/monarch-initiative/mondo/refs/heads/master/src/ontology/mappings/mondo.sssom.tsv secondary_source: - mondo - category: Product description: History file tracking changes to Mondo term mappings to CUIs format: txt id: medgen.mondo-history name: Mondo CUI History original_source: - medgen - mondo product_file_size: 1012883 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/MONDO_CUI_history.txt repository: https://github.com/monarch-initiative/mondo taxon: - NCBITaxon:33208 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: batchelorc@rsc.org - contact_type: github value: batchelorc label: Colin Batchelor orcid: 0000-0001-5985-7429 creation_date: '2025-09-29T00:00:00Z' description: Processes at the molecular level domains: - chemistry and biochemistry homepage_url: https://github.com/rsc-ontologies/rxno id: mop last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Molecular Process Ontology products: - category: OntologyProduct description: Molecular Process Ontology format: owl id: mop.owl name: Molecular Process Ontology product_file_size: 154788 product_url: http://purl.obolibrary.org/obo/mop.owl repository: https://github.com/rsc-ontologies/rxno - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://motrpac-data.org/contact label: MoTrPAC BioInformatics Center creation_date: '2025-10-29T00:00:00Z' curators: - category: Organization label: MoTrPAC BioInformatics Center at Stanford University description: The Molecular Transducers of Physical Activity Consortium (MoTrPAC) Data Hub is a national research initiative that generates a comprehensive molecular map of the effects of exercise and physical activity training. The data repository provides multi-omics datasets documenting molecular changes from exercise across multiple tissues, including transcriptomics, proteomics, metabolomics, and epigenomics data. The complete young adult rat endurance training dataset is publicly available, featuring quantitative results and analyses from 20 tissues across 29 assays and 5 time points, studying male and female animals. The data hub provides both browsable study data and pre-bundled datasets organized by tissue type and omics platform, all released under CC BY 4.0 license. The resource includes phenotypic data, sample-level metadata, quality control metrics, and quantitative results to enable comprehensive analysis of the temporal dynamics of multi-omic responses to endurance exercise training. domains: - biological systems - health - proteomics - genomics - systems biology homepage_url: https://motrpac-data.org/ id: motrpac last_modified_date: '2025-10-29T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Molecular Transducers of Physical Activity Consortium (MoTrPAC) Data Hub products: - category: GraphicalInterface description: Interactive data browser for exploring and downloading MoTrPAC multi-omics datasets by tissue, ome, or assay type format: http id: motrpac.data-browser name: MoTrPAC Data Browser product_url: https://motrpac-data.org/data-download - category: Product description: Phenotypic data from young adult rats (6-month old) that performed endurance exercise training format: csv id: motrpac.phenotype name: Rat Young Adult Endurance Training - Phenotype Data product_url: https://motrpac-data.org/data-download - category: Product description: Epigenomics data including ATAC-seq and RRBS analyses, sample-level metadata, QC, and quantitative results across tissues format: csv id: motrpac.epigenomics name: Rat Young Adult Endurance Training - Epigenomics Data product_url: https://motrpac-data.org/data-download - category: Product description: RNA-seq analyses, sample-level metadata, QC, and quantitative results across tissues format: csv id: motrpac.transcriptomics name: Rat Young Adult Endurance Training - Transcriptomics Data product_url: https://motrpac-data.org/data-download - category: Product description: Untargeted proteomics data including Acetyl Proteomics, Global Proteomics, Phosphoproteomics, and Protein Ubiquitination analyses across tissues format: csv id: motrpac.proteomics-untargeted name: Rat Young Adult Endurance Training - Proteomics (Untargeted) product_url: https://motrpac-data.org/data-download - category: Product description: Untargeted metabolomics analyses, sample-level metadata, QC, and quantitative results across tissues format: csv id: motrpac.metabolomics-untargeted name: Rat Young Adult Endurance Training - Metabolomics (Untargeted) product_url: https://motrpac-data.org/data-download - category: Product description: Targeted metabolomics analyses, sample-level metadata, QC, and quantitative results across tissues format: csv id: motrpac.metabolomics-targeted name: Rat Young Adult Endurance Training - Metabolomics (Targeted) product_url: https://motrpac-data.org/data-download - category: Product description: Targeted proteomics immunoassay data with analyses, sample-level metadata, QC, and quantitative results across tissues format: csv id: motrpac.proteomics-targeted name: Rat Young Adult Endurance Training - Proteomics (Targeted/Immunoassay) product_url: https://motrpac-data.org/data-download - category: DocumentationProduct description: Video tutorials demonstrating how to use the MoTrPAC Data Hub and access datasets format: http id: motrpac.video-tutorials name: MoTrPAC Data Hub Video Tutorials product_url: https://motrpac-data.org/ - category: GraphicalInterface description: Main portal for the MoTrPAC Data Hub providing access to data downloads, documentation, and visualization tools format: http id: motrpac.data-hub name: MoTrPAC Data Hub Portal product_url: https://motrpac-data.org/ - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg publications: - authors: - MoTrPAC Study Group category: Publication id: https://doi.org/10.1016/j.cell.2020.06.004 journal: Cell preferred: true title: 'Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise' year: '2020' - authors: - MoTrPAC Study Group category: Publication id: https://doi.org/10.1038/s41586-023-06877-w journal: Nature preferred: false title: Temporal dynamics of the multi-omic response to endurance exercise training year: '2024' taxon: - NCBITaxon:10116 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.informatics.jax.org/mgihome/support/mgi_inbox.shtml label: MGI User Support creation_date: '2025-10-30T00:00:00Z' description: MouseMine is an InterMine data warehouse that provides integrated access to mouse genomic, phenotypic, expression, and disease data from Mouse Genome Informatics (MGI). domains: - genomics - organisms - phenotype - health - pathways homepage_url: http://www.mousemine.org/mousemine/begin.do id: mousemine infores_id: mousemine last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail name: MouseMine products: - category: GraphicalInterface description: Web-based interface for searching, querying, and analyzing mouse data from MGI through MouseMine id: mousemine.web name: MouseMine Web Interface original_source: - mousemine product_url: http://www.mousemine.org/mousemine/begin.do - category: ProgrammingInterface description: Programmatic access to MouseMine data via RESTful web services with client libraries for Perl, Python, Ruby, and Java id: mousemine.api is_public: true name: MouseMine API original_source: - mousemine product_url: http://www.mousemine.org/mousemine/api.do - category: GraphicalInterface description: Pre-built query templates for common data retrieval tasks covering genome features, proteins, expression, interactions, phenotypes, diseases, and more id: mousemine.templates name: MouseMine Query Templates original_source: - mousemine product_url: http://www.mousemine.org/mousemine/templates.do - category: GraphicalInterface description: Custom query construction tool for building complex, iterative queries across multiple data types id: mousemine.querybuilder name: MouseMine QueryBuilder original_source: - mousemine product_url: http://www.mousemine.org/mousemine/customQuery.do synonyms: - MouseMine - Mouse Genome Informatics MouseMine taxon: - NCBITaxon:10090 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: pheno@jax.org - contact_type: github value: sbello label: Sue Bello orcid: 0000-0003-4606-0597 creation_date: '2025-06-04T00:00:00Z' description: Standard terms for annotating mammalian phenotypic data. domains: - biological systems homepage_url: https://www.informatics.jax.org/vocab/mp_ontology/ id: mp last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Mammalian Phenotype Ontology products: - category: OntologyProduct description: The main ontology in OWL. Contains all MP terms and links to other OBO ontologies. format: owl id: mp.owl name: MP (OWL edition) product_file_size: 102908651 product_url: http://purl.obolibrary.org/obo/mp.owl - category: OntologyProduct description: A direct translation of the MP (OWL edition) into OBO format. format: obo id: mp.obo name: MP (OBO edition) product_url: http://purl.obolibrary.org/obo/mp.obo warnings: - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: OntologyProduct description: For a description of the format see https://github.com/geneontology/obographs. format: json id: mp.json name: MP (obographs JSON edition) product_file_size: 54836173 product_url: http://purl.obolibrary.org/obo/mp.json - category: OntologyProduct description: The main ontology plus axioms connecting to select external ontologies, excluding axioms from the the external ontologies themselves. format: owl id: mp.mp-base.owl name: MP Base Module product_file_size: 50338260 product_url: http://purl.obolibrary.org/obo/mp/mp-base.owl - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/mgijax/mammalian-phenotype-ontology taxon: - NCBITaxon:40674 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: pns12@hermes.cam.ac.uk - contact_type: github value: PaulNSchofield label: Paul Schofield orcid: 0000-0002-5111-7263 creation_date: '2025-06-25T00:00:00Z' description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes domains: - biomedical homepage_url: http://www.pathbase.net id: mpath last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Mouse pathology ontology products: - category: OntologyProduct description: Mouse pathology ontology in OWL format format: owl id: mpath.owl name: mpath.owl product_file_size: 88952 product_url: http://purl.obolibrary.org/obo/mpath.owl - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/PaulNSchofield/mpath taxon: - NCBITaxon:10088 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mbrochhausen@uams.edu - contact_type: github value: mbrochhausen label: Mathias Brochhausen orcid: 0000-0003-1834-3856 creation_date: '2025-09-29T00:00:00Z' description: An ontology of minimum information regarding potential drug-drug interaction information. domains: - biomedical homepage_url: https://github.com/MPIO-Developers/MPIO id: mpio last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Minimum PDDI Information Ontology products: - category: OntologyProduct description: Minimum PDDI Information Ontology in OWL format format: owl id: mpio.owl name: mpio.owl product_file_size: 19172 product_url: http://purl.obolibrary.org/obo/mpio.owl repository: https://github.com/MPIO-Developers/MPIO - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.mrbase.org/ label: MR-Base Team (MRC Integrative Epidemiology Unit, University of Bristol) creation_date: '2025-09-03T00:00:00Z' description: MR-Base is a platform that integrates a large database of harmonized GWAS summary association datasets with analytical tools (web apps and R packages) to support systematic two-sample Mendelian randomization (2SMR) and phenome-wide causal inference across the human phenome. domains: - 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activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: joshua.adam.klein@gmail.com - contact_type: github value: mobiusklein label: Joshua Klein orcid: 0000-0003-1279-6838 creation_date: '2025-08-12T00:00:00Z' description: A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. domains: - biomedical homepage_url: http://www.psidev.info/groups/controlled-vocabularies id: ms last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Mass spectrometry ontology products: - category: OntologyProduct description: Mass spectrometry ontology in OBO format format: obo id: ms.obo name: ms.obo product_file_size: 1123745 product_url: http://purl.obolibrary.org/obo/ms.obo - category: OntologyProduct description: Mass spectrometry ontology in OWL format format: owl id: ms.owl name: ms.owl product_file_size: 4865907 product_url: http://purl.obolibrary.org/obo/ms.owl - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 repository: https://github.com/HUPO-PSI/psi-ms-CV - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: genesets@broadinstitute.org label: MSigDB Team creation_date: '2025-10-30T00:00:00Z' description: The Molecular Signatures Database (MSigDB) is a comprehensive collection of tens of thousands of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. MSigDB includes curated gene sets from pathway databases, gene ontology annotations, hallmark gene sets, immunologic signatures, regulatory target sets, and cell type-specific signatures derived from single-cell sequencing studies. Available for both human and mouse. domains: - genomics - systems biology - pathways homepage_url: https://www.gsea-msigdb.org/gsea/msigdb/ id: msigdb infores_id: msigdb last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail license: id: https://www.gsea-msigdb.org/gsea/license_terms_list.jsp label: GSEA/MSigDB License Terms name: Molecular Signatures Database products: - category: GraphicalInterface description: Web interface for browsing, searching, and investigating gene sets across all MSigDB collections format: http id: msigdb.browser name: MSigDB Web Browser original_source: - msigdb product_url: https://www.gsea-msigdb.org/gsea/msigdb/ - category: Product description: Downloadable gene set files in GMT, XML, and other formats for human collections including hallmarks, curated pathways, ontologies, and computational signatures format: mixed id: msigdb.downloads.human name: MSigDB Human Gene Sets Downloads product_url: https://www.gsea-msigdb.org/gsea/downloads.jsp#msigdb - category: Product description: Downloadable gene set files for mouse collections including mouse-ortholog hallmarks, curated pathways, ontologies, and cell type signatures format: mixed id: msigdb.downloads.mouse name: MSigDB Mouse Gene Sets Downloads product_url: https://www.gsea-msigdb.org/gsea/downloads.jsp#msigdb - category: GraphicalInterface description: Interactive tool for computing overlaps between user-provided gene sets and MSigDB collections id: msigdb.investigate name: MSigDB Investigate Tool original_source: - msigdb product_url: https://www.gsea-msigdb.org/gsea/msigdb/human/annotate.jsp - category: GraphicalInterface description: Tool for categorizing gene set members by gene families id: msigdb.gene_families name: MSigDB Gene Families Tool original_source: - msigdb product_url: https://www.gsea-msigdb.org/gsea/msigdb/human/gene_families.jsp - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: Product description: msigdb Nodes TSV format: tsv id: obo-db-ingest.msigdb.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: msigdb Nodes TSV original_source: - msigdb product_file_size: 3121367 product_url: https://w3id.org/biopragmatics/resources/msigdb/msigdb.tsv secondary_source: - obo-db-ingest publications: - id: PMID:37653294 title: Extending support for mouse data in the Molecular Signatures Database (MSigDB). synonyms: - MSigDB taxon: - NCBITaxon:9606 - NCBITaxon:10090 - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual label: Gwênlyn Glusman - category: Individual label: Guangrong Qin creation_date: '2025-03-09T00:00:00Z' description: A Translator Knowledge Provider incorporating multiomics data. domains: - health evaluation_page: resource/multiomics-kp/multiomics-kp_eval_automated.html id: multiomics-kp last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Multiomics KP products: - category: DocumentationProduct description: Team overview and interface links for the Multiomics Provider. format: http id: multiomics-kp.docs name: Multiomics KP Documentation original_source: - multiomics-kp product_url: https://github.com/NCATSTranslator/Translator-All/wiki/Multiomics-Provider - category: ProcessProduct description: Source repository for deployment and integration code used by the Multiomics Provider team. format: http id: multiomics-kp.code name: Multiomics KP Source Code original_source: - multiomics-kp product_url: https://github.com/PriceLab/DOCKET - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.cancergenomeinterpreter.org/ - contact_type: email value: cancerinterpreter@irbbarcelona.org id: cgi-team label: Cancer Genome Interpreter Team creation_date: '2025-08-12T00:00:00Z' description: The Catalog of Validated Oncogenic Mutations is part of the Cancer Genome Interpreter and contains a compiled inventory of mutations in cancer genes that are demonstrated to drive tumor growth or predispose to cancer, combining data from DoCM, ClinVar, OncoKB, and experimental assays. domains: - genomics - biomedical homepage_url: https://www.cancergenomeinterpreter.org/mutations id: mutationds last_modified_date: '2026-01-15T00:00:00Z' layout: resource_detail name: Catalog of Validated Oncogenic Mutations products: - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 publications: - category: Publication id: PMID:34090623 preferred: true synonyms: - MutationDS - CGI Mutations warnings: - ClinicalKG dump includes mutationds as one of many integrated sources; the dedicated mutation catalog is maintained under Cancer Genome Interpreter. - activity_status: active category: DataSource contacts: - category: Person contact_details: - contact_type: email value: fiehn@ucdavis.edu label: Oliver Fiehn - category: Person contact_details: - contact_type: email value: shankar@sdsc.edu label: Shankar Subramaniam creation_date: '2025-06-04T00:00:00Z' description: The Metabolomics Workbench is a public repository for metabolomics data and metadata, serving as the National Metabolomics Data Repository (NMDR). It provides tools, protocols, training, and access to over 2,000 metabolomics studies containing data from more than 75,000 samples and 32,000 known metabolites. Funded by the NIH Common Fund from 2012-2022. domains: [] homepage_url: https://www.metabolomicsworkbench.org/ id: mw last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: Metabolomics Workbench products: - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg publications: - id: https://doi.org/10.1038/s41592-019-0694-2 journal: Nature Methods title: The Metabolomics program year: '2020' synonyms: - MW - NMDR - National Metabolomics Data Repository warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: nams.network@qsarlab.com label: QSAR Lab creation_date: '2025-12-13T00:00:00Z' description: NAMs.network is the first database of regulatory-relevant New Approach Methodologies (NAMs) for assessing the safety of materials and chemicals. Given the ethical, economic, and time-related challenges associated with animal testing, as well as emerging bans on such methods in the EU, it is paramount to develop and validate alternative in silico, in chemico, in vitro, and ex vivo approaches. NAMs.network provides state-of-the-art knowledge on different NAMs for materials and chemical safety assessment. domains: - toxicology - chemistry and biochemistry - general evaluation_page: resource/namsnetwork/namsnetwork_eval_automated.html homepage_url: https://nams.network/ id: namsnetwork last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: NAMs Network products: - category: GraphicalInterface description: NAMs Network web interface for exploring and searching New Approach Methodologies for chemical and material safety assessment id: namsnetwork.portal name: NAMs Network Portal product_url: https://nams.network/ - activity_status: active category: DataModel creation_date: '2025-10-30T00:00:00Z' description: Nanopublications are a format for publishing scientific claims as small, machine-readable, FAIR digital objects using RDF semantic web technology. Each nanopublication consists of three parts - an assertion, provenance metadata, and publication info - forming minimal publishable information units that can be cited, queried, and reused. domains: [] homepage_url: http://nanopub.net/ id: nanopublications infores_id: nanopublications last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: Nanopublications Network products: - category: GraphicalInterface description: Web interface for browsing and searching nanopublications format: http id: nanopublications.portal name: Nanopublications Browser original_source: - nanopublications product_url: http://nanopub.net/ - category: ProgrammingInterface description: Decentralized server network for storing and retrieving nanopublications format: http id: nanopublications.servers name: Nanopublication Server Network original_source: - nanopublications product_url: http://nanopub.net/ publications: - id: https://doi.org/10.7717/peerj-cs.387 journal: PeerJ Computer Science title: Genuine semantic publishing year: '2021' repository: https://github.com/Nanopublication synonyms: - Nanopublications - Nanopubs - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: lisa@renci.org label: Lisa Stillwell creation_date: '2025-12-08T00:00:00Z' description: The NASA Knowledge Graph Dataset is an expansive graph-based dataset designed to integrate and interconnect information about satellite datasets, scientific publications, instruments, platforms, projects, data centers, and science keywords. This knowledge graph is particularly focused on datasets managed by NASA's Distributed Active Archive Centers (DAACs), which are NASA's data repositories responsible for archiving and distributing scientific data. In addition to NASA DAACs, the graph includes datasets from 184 data providers worldwide, including various government agencies and academic institutions. domains: - environment - investigations evaluation_page: resource/nasa-gesdisc-kg/nasa-gesdisc-kg_eval_automated.html homepage_url: https://disc.gsfc.nasa.gov id: nasa-gesdisc-kg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: NASA-GESDISC-KG products: - category: ProgrammingInterface description: SPARQL endpoint for NASA-GESDISC-KG id: nasa-gesdisc-kg.sparql name: NASA-GESDISC-KG SPARQL original_source: - nasa-gesdisc-kg product_url: https://frink.apps.renci.org/nasa-gesdisc-kg/sparql - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: g.gkoutos@bham.ac.uk - contact_type: github value: gkoutos label: George Gkoutos orcid: 0000-0002-2061-091X creation_date: '2025-09-29T00:00:00Z' description: An ontology of human and animal behaviours and behavioural phenotypes domains: - biological systems homepage_url: https://github.com/obo-behavior/behavior-ontology/ id: nbo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Neuro Behavior Ontology products: - category: OntologyProduct description: Neuro Behavior Ontology in OWL format format: owl id: nbo.owl name: nbo.owl product_file_size: 372935 product_url: http://purl.obolibrary.org/obo/nbo.owl repository: https://github.com/obo-behavior/behavior-ontology - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: jsanjak@gmail.com label: Jaleal Sanjak creation_date: '2025-07-11T00:00:00Z' description: The NCATS GARD Knowledge Graph integrates data about rare diseases, creating a comprehensive resource for rare disease research and drug discovery. It leverages clustering and machine learning approaches to identify relationships between rare diseases and potential therapeutic targets. domains: - health - biomedical - clinical - genomics evaluation_page: resource/ncatsgardkg/ncatsgardkg_eval.html homepage_url: https://github.com/ncats/RD-Clust id: ncatsgardkg last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: NCATS GARD KG products: - category: ProcessProduct description: RD-Clust source repository implementing NCATS GARD KG clustering and analysis workflows. format: http id: ncatsgardkg.code name: NCATS GARD KG Source Repository original_source: - ncatsgardkg product_url: https://github.com/ncats/RD-Clust - category: Product description: Repository subdirectory containing raw datasets used to construct the NCATS GARD KG workflow. format: http id: ncatsgardkg.raw-data name: NCATS GARD KG Raw Data Directory original_source: - ncatsgardkg product_url: https://github.com/ncats/RD-Clust/tree/main/data/raw publications: - doi: 10.1093/jamia/ocad186 id: https://doi.org/10.1093/jamia/ocad186 title: A knowledge graph approach to rare disease research and drug discovery year: '2023' - doi: 10.1101/2023.02.15.528673 id: https://doi.org/10.1101/2023.02.15.528673 title: 'RD-Clust: A tool for rare disease clustering and drug discovery' year: '2023' repository: https://github.com/ncats/RD-Clust taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for ncbi. This page was automatically generated because it was referenced by other resources. domains: - stub id: ncbi last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Ncbi products: - category: DataModelProduct description: Automatically generated stub product. Please update with accurate information. id: gc name: Gc (Stub) warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.ncbi.nlm.nih.gov/gene id: ncbi label: NCBI Gene Database - category: Organization contact_details: - contact_type: email value: info@ncbi.nlm.nih.gov id: ncbi label: NCBI Help Desk creation_date: '2025-06-04T00:00:00Z' description: NCBI Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide. domains: - biological systems homepage_url: https://www.ncbi.nlm.nih.gov/gene/ id: ncbigene infores_id: ncbi-gene last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: NCBI Gene products: - category: MappingProduct compression: gzip description: Gene to accession mapping data providing links between gene records and nucleotide/protein sequence accessions format: tsv id: ncbigene.gene2accession name: Gene to Accession Mapping original_source: - ncbigene product_file_size: 3953177919 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz - category: MappingProduct compression: gzip description: Gene to Ensembl mapping data providing cross-references between NCBI Gene and Ensembl gene identifiers format: tsv id: ncbigene.gene2ensembl name: Gene to Ensembl Mapping original_source: - ensembl - ncbigene product_file_size: 282824267 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene2ensembl.gz - category: MappingProduct compression: gzip description: Gene to Gene Ontology mapping data providing functional annotations for genes format: tsv id: ncbigene.gene2go name: Gene to GO Mapping original_source: - go - ncbigene product_file_size: 1223833668 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz - category: MappingProduct compression: gzip description: Gene to PubMed mapping data providing literature references associated with genes format: tsv id: ncbigene.gene2pubmed name: Gene to PubMed Mapping original_source: - pubmed - ncbigene product_file_size: 230242176 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene2pubmed.gz - category: MappingProduct compression: gzip description: Gene to RefSeq mapping data providing links between gene records and RefSeq sequence identifiers format: tsv id: ncbigene.gene2refseq name: Gene to RefSeq Mapping original_source: - 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category: Product compression: gzip description: Gene neighbor information showing genomic proximity relationships format: tsv id: ncbigene.gene_neighbors name: Gene Neighbors Data original_source: - ncbigene product_file_size: 1764403523 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene_neighbors.gz - category: Product compression: gzip description: Gene ortholog information showing evolutionary relationships between genes across species format: tsv id: ncbigene.gene_orthologs name: Gene Orthologs Data original_source: - ncbigene product_file_size: 108555140 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene_orthologs.gz - category: MappingProduct compression: gzip description: Gene to RefSeq/UniProtKB collaboration data providing cross-references between gene records and protein databases format: tsv id: ncbigene.gene_refseq_uniprotkb_collab name: Gene RefSeq UniProtKB Collaboration Data original_source: - refseq - ncbigene - uniprot product_file_size: 1182285769 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene_refseq_uniprotkb_collab.gz - category: Product compression: gzip description: Gene summary information providing brief descriptions of gene function format: tsv id: ncbigene.gene_summary name: Gene Summary Data original_source: - ncbigene product_file_size: 20880547 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene_summary.gz - category: MappingProduct description: MIM to Gene and MedGen mapping data connecting genetic disorders to genes format: tsv id: ncbigene.mim2gene_medgen name: MIM to Gene MedGen Mapping original_source: - ncbigene - medgen - omim product_file_size: 954971 product_url: https://ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen - category: GraphicalInterface description: Web-based search and browsing interface for the NCBI Gene database format: http id: ncbigene.search name: NCBI Gene Search Interface original_source: - ncbigene product_url: https://www.ncbi.nlm.nih.gov/gene/ - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - 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biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: Product description: The EPA has developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Since its inception, the AOP-DB has been developed with the aim of integrating AOP molecular target information with other publicly available datasets to facilitate computational analyses of AOP information. id: aop-db.data name: AOP-DB Data original_source: - aop-wiki - ctd - toxcast - disgenet - ncbigene - string - 1000genomes - ensembl - gwascatalog product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 secondary_source: - aop-db - category: Product description: Integrated gene annotation data aggregated from HGNC, OMIM, Ensembl, NCBI Gene, UniProt and other genomic databases format: http id: genecards.gene.annotations name: GeneCards Gene Annotations original_source: - hgnc - omim - ensembl - ncbigene - uniprot - refseq product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: MappingProduct compression: zip description: A single delimited text file format containing a list of mappings between different identifiers stored in BioGRID and the identifiers used in downloads. format: tsv id: biogrid.identifiers latest_version: 5.0.252 name: BIOGRID-IDENTIFIERS-LATEST.tab.zip original_source: - biogrid - uniprot - ncbigene - zfin - xenbase - hgnc product_url: https://downloads.thebiogrid.org/File/BioGRID/Latest-Release/BIOGRID-IDENTIFIERS-LATEST.tab.zip secondary_source: - biogrid - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - authors: - Donna Maglott - Jim Ostell - Kim D. Pruitt - Tatiana Tatusova id: doi:10.1093/nar/gkq1237 journal: Nucleic Acids Research preferred: true title: 'Entrez Gene: gene-centered information at NCBI' year: '2011' - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: frederic.bastian@unil.ch - contact_type: github value: fbastian label: Frederic Bastian orcid: 0000-0002-9415-5104 creation_date: '2025-05-28T00:00:00Z' description: An ontology representation of the NCBI organismal taxonomy domains: - biological systems homepage_url: https://github.com/obophenotype/ncbitaxon id: ncbitaxon last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: NCBI organismal classification products: - category: OntologyProduct description: Main release format: owl id: ncbitaxon.owl name: Main release product_file_size: 1915871262 product_url: http://purl.obolibrary.org/obo/ncbitaxon.owl - 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category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - 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Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: OntologyProduct description: OWL release of Monochrom Ontology format: owl id: chr.model.owl name: Monochrom Ontology OWL release original_source: - ro - go - ncbitaxon - iao - geno - skos - gff product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl secondary_source: - chr - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - 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orkg - wikidata - geonames - ncit - chebi - ncbitaxon - go - clo - omit - iao - uo - stato - obi product_file_size: 642902930 product_url: https://orkg.org/api/rdf/dump secondary_source: - orkg repository: https://github.com/obophenotype/ncbitaxon - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: noreply@example.com - contact_type: github value: ghost label: None orcid: 0000-0000-0000-0000 creation_date: '2025-06-25T00:00:00Z' description: NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental. domains: - biomedical homepage_url: https://github.com/ncit-obo-org/ncit-obo-edition id: ncit last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: NCI Thesaurus OBO Edition products: - category: OntologyProduct description: A direct transformation of the standard NCIt content using OBO-style term and ontology IRIs and annotation properties. format: owl id: ncit.owl name: NCIt OBO Edition OWL format product_file_size: 782238438 product_url: http://purl.obolibrary.org/obo/ncit.owl - category: OntologyProduct description: NCIt OBO Edition OBO format format: obo id: ncit.obo name: NCIt OBO Edition OBO format product_file_size: 238812762 product_url: http://purl.obolibrary.org/obo/ncit.obo - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct description: RDF dump of the Open Research Knowledge Graph distributed in N-Triples format. format: ntriples id: orkg.dump name: ORKG RDF Dump original_source: - orkg - wikidata - geonames - ncit - chebi - ncbitaxon - go - clo - omit - iao - uo - stato - obi product_file_size: 642902930 product_url: https://orkg.org/api/rdf/dump secondary_source: - orkg repository: https://github.com/ncit-obo-org/ncit-obo-edition - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: huang@southalabama.edu - contact_type: github value: Huang-OMIT label: Jingshan Huang orcid: 0000-0003-2408-2883 creation_date: '2025-09-29T00:00:00Z' description: An ontology for non-coding RNA, both of biological origin, and engineered. domains: - biomedical homepage_url: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology id: ncro last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Non-Coding RNA Ontology products: - category: OntologyProduct description: NCRO development version format: owl id: ncro.dev.ncro.owl name: NCRO development version product_file_size: 4548 product_url: http://purl.obolibrary.org/obo/ncro/dev/ncro.owl repository: https://github.com/OmniSearch/ncro - activity_status: active category: DataSource creation_date: '2025-11-19T00:00:00Z' description: The FDA National Drug Code Directory is a comprehensive database maintained by the U.S. Food and Drug Administration containing information about finished drug products, unfinished drugs, and compounded drug products. Drug establishments are required to provide FDA with current lists of all drugs using unique three-segment National Drug Code (NDC) numbers. The directory includes prescription and over-the-counter drugs, approved and unapproved drugs, and repackaged and relabeled drugs. The database is updated daily and provides essential drug identification and regulatory information for healthcare professionals, researchers, and regulatory compliance. domains: - pharmacology - drug discovery - clinical - biomedical homepage_url: https://www.fda.gov/drugs/drug-approvals-and-databases/national-drug-code-directory id: ndcd infores_id: ndcd last_modified_date: '2025-11-19T00:00:00Z' layout: resource_detail name: National Drug Code Directory products: - category: GraphicalInterface description: Web-based search interface for the NDC Directory allowing users to search and browse National Drug Code information format: http id: ndcd.search name: NDC Directory Search original_source: - ndcd product_url: https://www.accessdata.fda.gov/scripts/cder/ndc - category: Product compression: zip description: Downloadable database file in text format containing finished drug product information, updated daily format: txt id: ndcd.text name: NDC Database Text File original_source: - ndcd product_url: https://www.fda.gov/drugs/drug-approvals-and-databases/national-drug-code-directory warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product compression: zip description: Downloadable database file in Excel format containing finished drug product information id: ndcd.excel name: NDC Database Excel File original_source: - ndcd product_url: https://www.fda.gov/drugs/drug-approvals-and-databases/national-drug-code-directory warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: ProgrammingInterface description: REST API providing programmatic access to National Drug Code data through the openFDA platform format: http id: ndcd.api name: NDC API original_source: - ndcd product_url: https://open.fda.gov/apis/drug/ndc/ synonyms: - NDCD - NDC Directory taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: asu@scripps.edu - contact_type: github value: andrewsu label: Andrew Su - category: Individual contact_details: - contact_type: email value: plwhetzel@gmail.com - contact_type: github value: twhetzel label: Trish Whetzel creation_date: '2025-12-08T00:00:00Z' description: The NDE (NIAID Data Ecosystem) KG contains infectious and immune-mediated disease datasets. These include datasets from NIAID-funded repositories as well as globally-relevant infectious and immune-mediated disease (IID) repositories from NIH and beyond. The datasets include -omics data, clinical data, epidemiological data, pathogen-host interaction data, flow cytometry, and imaging. domains: - biomedical - immunology - health evaluation_page: resource/nde/nde_eval_automated.html homepage_url: https://data.niaid.nih.gov/ id: nde last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: NIAID Data Ecosystem KG products: - category: ProgrammingInterface description: SPARQL endpoint for NIAID Data Ecosystem KG id: nde.sparql name: NIAID Data Ecosystem KG SPARQL original_source: - nde product_url: https://frink.apps.renci.org/nde/sparql taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-10-30T00:00:00Z' description: The Veterans Health Administration National Drug File (VANDF) is a comprehensive drug terminology containing approximately 27,921 clinical drugs, 8,058 ingredients, and 578 drug classes. It is maintained by the Department of Veterans Affairs and distributed through UMLS and RxNorm. domains: - pharmacology homepage_url: https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/vandf.html id: ndfrt infores_id: ndfrt last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: Veterans Health Administration National Drug File products: - category: Product description: VANDF drug terminology data distributed through UMLS Metathesaurus id: ndfrt.umls name: VANDF in UMLS original_source: - ndfrt product_url: https://www.nlm.nih.gov/research/umls/ secondary_source: - umls - category: Product description: VANDF data integrated into RxNorm id: ndfrt.rxnorm name: VANDF in RxNorm original_source: - ndfrt product_url: https://www.nlm.nih.gov/research/umls/rxnorm/ secondary_source: - rxnorm synonyms: - VANDF - NDF-RT - VA National Drug File - National Drug File - Reference Terminology taxon: - NCBITaxon:9606 - activity_status: active category: Resource contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Christopher J. Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-03-09T00:00:00Z' description: 'This repository contains classes required by Noctua/Minerva for representing entities that are object of ''enabled by'' relations, and similar molecular relationships. This includes: genes, protein (gene-level generic proteins and isoforms), functional RNAs, and complexes. These are represented as ontology classes, although NEO is not really an ontology in a conventional sense: there is no hierarchy, it is organized as a largely flat list.' domains: - biological systems homepage_url: https://github.com/geneontology/neo/ id: neo last_modified_date: '2025-08-06T00:00:00Z' layout: resource_detail name: Noctua Entity Ontology products: - category: Product description: OWL release of neo format: owl id: neo.model name: neo OWL release original_source: - neo product_file_size: 2278767531 product_url: http://purl.obolibrary.org/obo/go/noctua/neo.owl secondary_source: - neo repository: https://github.com/geneontology/neo/ - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: dal.alghamdi92@gmail.com - contact_type: github value: dalalghamdi label: Dalia Alghamdi orcid: 0000-0002-2801-0767 creation_date: '2025-09-29T00:00:00Z' description: 'The Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.' domains: - biomedical homepage_url: https://github.com/Dalalghamdi/NGBO id: ngbo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Next Generation Biobanking Ontology products: - category: OntologyProduct description: Next Generation Biobanking Ontology in OWL format format: owl id: ngbo.owl name: ngbo.owl product_file_size: 187540 product_url: http://purl.obolibrary.org/obo/ngbo.owl repository: https://github.com/Dalalghamdi/NGBO - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://report.nih.gov/contactus - contact_type: email value: reporter@od.nih.gov label: NIH Office of Extramural Research creation_date: '2025-07-20T00:00:00Z' description: NIH Reporter (RePORTER) is a comprehensive data source providing access to information about NIH-funded research projects, including both intramural and extramural research activities. It serves as an electronic repository for NIH research project data, publications, and patents resulting from NIH funding since fiscal year 1985. domains: - biomedical - health - clinical - translational homepage_url: https://reporter.nih.gov/ id: nihreporter last_modified_date: '2025-09-24T00:00:00Z' layout: resource_detail name: NIH Reporter products: - category: GraphicalInterface description: Web-based search interface for exploring NIH-funded research projects with advanced search capabilities format: http id: nihreporter.portal name: NIH Reporter Web Portal product_url: https://reporter.nih.gov/ - category: Product description: Bulk download of NIH research project data in structured format format: csv id: nihreporter.projects name: NIH Reporter Exporter Projects product_url: https://reporter.nih.gov/exporter/projects - category: ProgrammingInterface description: API access to NIH research project data and search functionality format: http id: nihreporter.api name: NIH Reporter API product_url: https://reporter.nih.gov/ - category: Product description: Database of abstracts linked to NIH-funded research projects format: json id: nihreporter.abstracts name: NIH-Funded Project Abstracts product_url: https://reporter.nih.gov/exporter/abstracts - category: Product description: Database of patents linked to NIH-funded research projects id: nihreporter.patents name: NIH-Funded Project Patents product_url: https://reporter.nih.gov/exporter/patents - category: Product description: Database of clinical studies linked to NIH-funded research projects id: nihreporter.clinicalstudies name: NIH-Funded Project Clinical Studies product_url: https://reporter.nih.gov/exporter/clinicalstudies - category: Product description: Database of publications linked to NIH-funded research projects format: json id: nihreporter.publications name: NIH-Funded Publications Database product_url: https://reporter.nih.gov/exporter/publications - category: Product description: Database of publication link tables for NIH-funded research projects id: nihreporter.linktables name: NIH-Funded Publications Link Tables product_url: https://reporter.nih.gov/exporter/linktables - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra - category: Product compression: gzip description: nihreporter.project Nodes TSV format: tsv id: obo-db-ingest.nihreporter.project.tsv name: nihreporter.project Nodes TSV original_source: - nihreporter product_file_size: 65861949 product_url: https://w3id.org/biopragmatics/resources/nihreporter.project/nihreporter.project.tsv.gz secondary_source: - obo-db-ingest taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: jinggao@purdue.edu label: Jing Gao creation_date: '2025-12-08T00:00:00Z' description: Neighborhood Information KG (NIKG) is a knowledge graph warehouse for neighborhood information, providing structured data about community characteristics, demographics, and local resources. domains: - social determinants evaluation_page: resource/nikg/nikg_eval_automated.html homepage_url: https://frink.apps.renci.org/neighborhood-information-kg/sparql id: nikg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: Neighborhood Information KG products: - category: ProgrammingInterface description: SPARQL endpoint for Neighborhood Information KG id: nikg.sparql name: Neighborhood Information KG SPARQL original_source: - nikg product_url: https://frink.apps.renci.org/neighborhood-information-kg/sparql - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for nlm. This page was automatically generated because it was referenced by other resources. domains: - stub id: nlm last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Nlm products: - category: DataModelProduct description: Automatically generated stub product. Please update with accurate information. id: publisher name: Publisher (Stub) - category: Product description: nlm Nodes TSV format: tsv id: obo-db-ingest.nlm.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: nlm Nodes TSV original_source: - nlm product_file_size: 1156325 product_url: https://w3id.org/biopragmatics/resources/nlm/nlm.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: richard.scheuermann@nih.gov label: Richard Scheuermann - category: Individual contact_details: - contact_type: email value: matthew.diller@nih.gov - contact_type: github value: dillerm label: Matthew Diller orcid: 0000-0001-6378-1703 creation_date: '2025-04-17T00:00:00Z' curators: - category: Individual contact_details: - contact_type: github value: caufieldjh label: Harry Caufield orcid: 0000-0001-5705-7831 - category: Individual contact_details: - contact_type: email value: matthew.diller@nih.gov - contact_type: github value: dillerm label: Matthew Diller orcid: 0000-0001-6378-1703 description: The NLM Cell Knowledge Network, a knowledge graph that contains knowledge about cellular phenotypes (cell types and cell states) that has been gathered through single cell technologies and related experiments. NLM-CKN is populated using validated computational analysis pipelines and natural language processing of scientific literature and integrated with other public sources of relevant knowledge about genes, anatomical structures, diseases, and drugs. domains: - biological systems - health - phenotype evaluation_page: resource/nlm-ckn/nlm-ckn_eval_automated.html id: nlm-ckn last_modified_date: '2025-06-12T20:33:29Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: NLM-CKN products: - category: DataModelProduct description: Data model for cell phenotypes and biological entities they relate to. id: nlm-ckn.schema name: nlm-ckn-schema original_source: - nlm-ckn product_file_size: 4262 product_url: https://github.com/NIH-NLM/cell-kn-schema/blob/main/ckn-schema.yaml secondary_source: - nlm-ckn repository: https://github.com/NIH-NLM/cell-kn-mvp - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: diapriid@gmail.com - contact_type: github value: mjy label: Matt Yoder orcid: 0000-0002-5640-5491 creation_date: '2025-09-29T00:00:00Z' description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. domains: - biomedical homepage_url: https://github.com/SpeciesFileGroup/nomen id: nomen last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: NOMEN - A nomenclatural ontology for biological names products: - category: OntologyProduct description: core ontology format: owl id: nomen.owl name: NOMEN product_file_size: 11371 product_url: http://purl.obolibrary.org/obo/nomen.owl repository: https://github.com/SpeciesFileGroup/nomen - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: A comprehensive database dedicated to long non-coding RNA (lncRNA) annotation in animals and plants, providing systematic nomenclature, sequence information, genome location, expression profiles, functional predictions, and conservation analysis across 39 species (16 animals and 23 plants) domains: - genomics - biological systems homepage_url: http://www.noncode.org/ id: noncode last_modified_date: '2025-11-13T00:00:00Z' layout: resource_detail name: NONCODE products: - category: GraphicalInterface description: Main web interface for searching, browsing, and analyzing lncRNA annotations across 39 species format: http id: noncode.portal name: NONCODE Web Portal product_url: http://www.noncode.org/ - category: GraphicalInterface description: Browse lncRNAs by species and RNA type format: http id: noncode.browse name: Browse NONCODE product_url: http://www.noncode.org/browse.php - category: GraphicalInterface description: Search for specific genes or transcripts by identifier or keywords format: http id: noncode.search name: Search Gene/Transcript product_url: http://www.noncode.org/search.php - category: GraphicalInterface description: Find similar sequences using BLAST alignment format: http id: noncode.blast name: BLAST Similarity Search product_url: http://www.noncode.org/blast.php - category: GraphicalInterface description: Browse disease-related lncRNA information, especially cancer associations format: http id: noncode.disease name: Disease Information product_url: http://www.noncode.org/disease.php - category: GraphicalInterface description: View transcript locations in genomic context (human hg38) format: http id: noncode.genome-browser name: Genome Browser product_url: http://www.noncode.org/genome.php - category: Product description: Download complete lncRNA annotations and sequences format: http id: noncode.download name: Download Data product_url: http://www.noncode.org/download.php warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphicalInterface description: Predicted functions for plant lncRNAs based on co-expression analysis format: http id: noncode.function name: Function Prediction product_url: http://www.noncode.org/function.php - category: GraphicalInterface description: Cross-species conservation analysis for plant lncRNAs format: http id: noncode.conservation name: Conservation Analysis product_url: http://www.noncode.org/conservation.php - category: GraphicalInterface description: Convert between NONCODE IDs and other database identifiers (Ensembl, RefSeq, etc.) format: http id: noncode.id-conversion name: ID Conversion Tool product_url: http://www.noncode.org/id_conversion.php - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - doi: 10.1093/nar/gkaa1046 id: zhao2021noncode preferred: true title: 'NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants' year: '2021' synonyms: - NONCODEV6 - NONCODE v6.0 - NONCODE 2021 taxon: - NCBITaxon:33090 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: sanyabt label: Sanya Bathla Taneja creation_date: '2025-03-09T00:00:00Z' description: NP-KG is a graph framework that creates a biomedical knowledge graph to identify and generate mechanistic hypotheses for pharmacokinetic natural product-drug interactions (NPDIs). domains: - health - pharmacology - drug discovery - biomedical evaluation_page: resource/np-kg/np-kg_eval_automated.html homepage_url: https://doi.org/10.5281/zenodo.6814507 id: np-kg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: NP-KG products: - category: GraphProduct description: Merged KG with ontology-grounded KG and literature-based graph as TSV file id: np-kg.graph.tsv name: NP-KG TSV original_source: - np-kg product_file_size: 1074149258 product_url: https://zenodo.org/records/12536780/files/NP-KG_v3.0.0.tsv?download=1 secondary_source: - np-kg - category: GraphProduct description: Merged KG with ontology-grounded KG and literature-based graph as NetworkX multidigraph object dump_format: gpickle id: np-kg.graph.networkx name: NP-KG gpickle original_source: - np-kg product_file_size: 936065236 product_url: https://zenodo.org/records/12536780/files/NP-KG_v3.0.0.gpickle?download=1 secondary_source: - np-kg publications: - authors: - Taneja SB - Callahan TJ - Paine MF - Kane-Gill SL - Kilicoglu H - Joachimiak MP - Boyce RD doi: doi:10.1016/j.jbi.2023.104341 id: doi:10.1016/j.jbi.2023.104341 preferred: true title: '''Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions''' year: '2023' repository: https://github.com/sanyabt/np-kg - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for npass. This page was automatically generated because it was referenced by other resources. domains: - stub id: npass last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Npass products: - category: Product description: npass Nodes TSV format: tsv id: obo-db-ingest.npass.tsv license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC-BY-NC name: npass Nodes TSV original_source: - npass product_file_size: 2460413 product_url: https://w3id.org/biopragmatics/resources/npass/npass.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: Ontology contacts: - category: Person contact_details: - contact_type: email value: mmartone@ucsd.edu label: Maryann E. Martone - category: Person contact_details: - contact_type: email value: sean.hill@camh.ca label: Sean L. Hill creation_date: '2025-06-04T00:00:00Z' description: The Neuron Phenotype Ontology (NPO) is a FAIR ontology-based data model for representing complex cellular phenotypes of neurons. It characterizes neuron types as bundles of normalized phenotypic properties across multiple dimensions including species, anatomical location, morphology, molecular constituents, electrophysiology, connectivity, and circuit roles. The NPO provides a standardized and automatable approach for naming cell types and normalizing their constituent phenotypes using identifiers from community ontologies, enabling interoperability between different neuron naming schemes and classification systems. domains: - neuroscience homepage_url: https://bioportal.bioontology.org/ontologies/NPOKB id: npo last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: Neuron Phenotype Ontology products: - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg publications: - doi: 10.1007/s12021-022-09566-7 id: PMID:35267146 title: 'The Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types' year: '2022' synonyms: - NPO - NPOKB - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: nick.tatonetti@gmail.com - contact_type: github value: tatonetti-lab label: Tatonetti Lab creation_date: '2025-10-30T00:00:00Z' description: nSIDES is a comprehensive collection of drug side effect and drug interaction resources developed by the Tatonetti Lab. It includes OnSIDES (adverse events from drug labels), KidSIDES (pediatric drug safety signals), AwareDX (sex-specific adverse drug effects), OffSIDES (off-label side effects), TwoSIDES (drug-drug interactions), and ManySIDES (combinations of 3+ drugs). domains: - pharmacology - drug discovery - health - precision medicine homepage_url: https://nsides.io/ id: nsides infores_id: nsides last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail name: nSIDES products: - category: Product description: Adverse drug events extracted from FDA drug labels using fine-tuned PubMedBERT, covering 3.6M+ drug-ADE pairs for 2,793 drug ingredients from 46,686 labels format: csv id: nsides.onsides name: OnSIDES product_url: https://github.com/tatonetti-lab/onsides/releases - category: Product description: Pediatric drug safety signals across developmental phases, covering adverse events specific to children format: csv id: nsides.kidsides name: KidSIDES original_source: - nsides product_file_size: 107 product_url: https://tatonettilab-resources.s3.amazonaws.com/KidSIDES/ade_nichd.csv.gz - category: GraphicalInterface description: Interactive RShiny web portal for browsing pediatric drug safety signals format: http id: nsides.pdsportal name: PDSPortal original_source: - nsides product_url: https://pdsportal.shinyapps.io/pdsportal/ - category: Product description: Drug safety signals with differential risk between men and women, covering 20,817 adverse drug effects with sex-specific risks format: http id: nsides.awaredx name: AwareDX original_source: - nsides product_url: http://tatonettilab-resources.s3-website-us-west-1.amazonaws.com/?p=nsides/ - category: ProcessProduct description: Code repository for OnSIDES model training and data generation id: nsides.onsides.code name: OnSIDES Code original_source: - nsides product_url: https://github.com/tatonetti-lab/onsides - category: ProcessProduct description: Code repository for KidSIDES pediatric adverse drug event database study id: nsides.kidsides.code name: KidSIDES Code original_source: - nsides product_url: https://github.com/ngiangre/pediatric_ade_database_study publications: - authors: - Chandak P - Tatonetti NP doi: 10.1016/j.patter.2020.100108 id: doi:10.1016/j.patter.2020.100108 journal: Patterns (N Y) title: Using Machine Learning to Identify Adverse Drug Effects Posing Increased Risk to Women year: '2020' - authors: - Giangreco N - Tatonetti NP doi: 10.1016/j.medj.2022.08.001 id: doi:10.1016/j.medj.2022.08.001 journal: Med title: A database of pediatric drug effects to evaluate ontogenic mechanisms from child growth and development year: '2022' - authors: - Giangreco N - Tatonetti NP doi: 10.1186/s13040-021-00264-9 id: doi:10.1186/s13040-021-00264-9 journal: BioData Mining title: Evaluating risk detection methods to uncover ontogenic-mediated adverse drug effect mechanisms in children year: '2021' repository: https://github.com/tatonetti-lab synonyms: - nSIDES - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: yongqunh@med.umich.edu - contact_type: github value: yongqunh label: Yongqunh He orcid: 0000-0001-9189-9661 creation_date: '2025-09-29T00:00:00Z' description: A biomedical ontology in the domain of adverse events domains: - biomedical homepage_url: https://github.com/OAE-ontology/OAE/ id: oae last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Adverse Events products: - category: OntologyProduct description: Ontology of Adverse Events in OWL format format: owl id: oae.owl name: oae.owl product_file_size: 1274570 product_url: http://purl.obolibrary.org/obo/oae.owl repository: https://github.com/OAE-ontology/OAE - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mjyoder@illinois.edu - contact_type: github value: mjy label: Matt Yoder orcid: 0000-0002-5640-5491 creation_date: '2025-09-29T00:00:00Z' description: OArCS is an ontology describing the Arthropod ciruclatory system. domains: - anatomy and development homepage_url: https://github.com/aszool/oarcs id: oarcs last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Arthropod Circulatory Systems products: - category: OntologyProduct description: Ontology of Arthropod Circulatory Systems in OWL format format: owl id: oarcs.owl name: oarcs.owl product_file_size: 27840 product_url: http://purl.obolibrary.org/obo/oarcs.owl repository: https://github.com/aszool/oarcs - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-06-25T00:00:00Z' description: A collection of biological attributes (traits) covering all kingdoms of life. domains: - biological systems homepage_url: https://github.com/obophenotype/bio-attribute-ontology id: oba last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Ontology of Biological Attributes products: - category: OntologyProduct description: Ontology of Biological Attributes in OWL format format: owl id: oba.owl name: oba.owl product_file_size: 166637718 product_url: http://purl.obolibrary.org/obo/oba.owl - category: OntologyProduct description: Ontology of Biological Attributes in OBO format format: obo id: oba.obo name: oba.obo product_file_size: 33532280 product_url: http://purl.obolibrary.org/obo/oba.obo - category: OntologyProduct description: Ontology of Biological Attributes in OBO format format: obo id: oba.subsets.oba-basic.obo name: oba.subsets.oba-basic.obo product_file_size: 11853852 product_url: http://purl.obolibrary.org/obo/oba/subsets/oba-basic.obo - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/obophenotype/bio-attribute-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jiezhen@med.umich.edu - contact_type: github value: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 creation_date: '2025-09-29T00:00:00Z' description: A biomedical ontology in the domain of biological and clinical statistics. domains: - biomedical homepage_url: https://github.com/obcs/obcs id: obcs last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Biological and Clinical Statistics products: - category: OntologyProduct description: Ontology of Biological and Clinical Statistics in OWL format format: owl id: obcs.owl name: obcs.owl product_file_size: 213907 product_url: http://purl.obolibrary.org/obo/obcs.owl repository: https://github.com/obcs/obcs - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: bpeters@lji.org - contact_type: github value: bpeters42 label: Bjoern Peters orcid: 0000-0002-8457-6693 creation_date: '2025-06-04T00:00:00Z' description: An integrated ontology for the description of life-science and clinical investigations domains: - biomedical homepage_url: http://obi-ontology.org id: obi last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology for Biomedical Investigations products: - category: OntologyProduct description: The full version of OBI in OWL format format: owl id: obi.owl name: OBI product_file_size: 711939 product_url: http://purl.obolibrary.org/obo/obi.owl - category: OntologyProduct description: The OBO-format version of OBI format: obo id: obi.obo name: OBI in OBO product_file_size: 303335 product_url: http://purl.obolibrary.org/obo/obi.obo - category: OntologyProduct description: A collection of important high-level terms and their relations from OBI and other ontologies format: owl id: obi.obi_core.owl name: OBI Core product_file_size: 39718 product_url: http://purl.obolibrary.org/obo/obi/obi_core.owl - category: OntologyProduct description: Base module for OBI format: owl id: obi.obi-base.owl name: OBI Base module product_file_size: 609635 product_url: http://purl.obolibrary.org/obo/obi/obi-base.owl - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct description: RDF dump of the Open Research Knowledge Graph distributed in N-Triples format. format: ntriples id: orkg.dump name: ORKG RDF Dump original_source: - orkg - wikidata - geonames - ncit - chebi - ncbitaxon - go - clo - omit - iao - uo - stato - obi product_file_size: 642902930 product_url: https://orkg.org/api/rdf/dump secondary_source: - orkg repository: https://github.com/obi-ontology/obi - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jmwhorton@uams.edu - contact_type: github value: jmwhorton label: Justin Whorton orcid: 0009-0003-4268-6207 creation_date: '2025-06-04T00:00:00Z' description: An ontology built for annotation and modeling of biobank repository and biobanking administration domains: - biomedical homepage_url: https://github.com/biobanking/biobanking id: obib last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology for Biobanking products: - category: OntologyProduct description: Ontology for Biobanking in OWL format format: owl id: obib.owl name: obib.owl product_file_size: 230390 product_url: http://purl.obolibrary.org/obo/obib.owl - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg repository: https://github.com/biobanking/biobanking - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.ioc.unesco.org/ - contact_type: email value: obis@vliz.be id: UNESCO-IOC label: UNESCO Intergovernmental Oceanographic Commission (IOC) - category: Organization contact_details: - contact_type: url value: https://www.vliz.be/ id: vliz label: Flanders Marine Institute (VLIZ) creation_date: '2025-12-18T00:00:00Z' description: Ocean Biodiversity Information System (OBIS) is a global open-access data and information system providing free access to information about the distribution and abundance of living species in the ocean. It aggregates 161 million biodiversity records covering 160,000+ marine species from 600+ institutions across 56+ countries, using Darwin Core standards and World Register of Marine Species (WoRMS) as the authoritative taxonomic backbone. domains: [] homepage_url: https://obis.org/ id: obis infores_id: obis last_modified_date: '2025-12-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0, CC BY, and CC BY-NC (mixed) logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Ocean Biodiversity Information System (OBIS) products: - category: GraphicalInterface description: Interactive web mapper for searching, filtering, and visualizing marine species distributions across geographic areas, depth ranges, and time periods with multi-parameter search capabilities format: http id: obis.mapper name: OBIS Web Mapper product_url: https://portal.obis.org/ - category: ProgrammingInterface description: RESTful API providing programmatic access to marine biodiversity records, species information, and occurrence data with filtering by taxonomy, location, depth, and time format: http id: obis.api is_public: true name: OBIS API product_url: https://api.obis.org/ - category: ProgrammingInterface description: R package robis for programmatic data access and querying of OBIS data from R environment format: http id: obis.robis is_public: true name: robis R Package product_url: https://cran.r-project.org/web/packages/robis/ - category: Product description: Complete biodiversity record exports in Darwin Core Archive format containing occurrence data with standardized metadata and EML documentation id: obis.dca name: OBIS Darwin Core Archive Downloads product_url: https://portal.obis.org/ - category: Product description: Cloud-native GeoParquet format biodiversity records available on AWS S3 for efficient large-scale spatial analysis without local downloads id: obis.geoparquet name: OBIS GeoParquet on AWS product_url: https://registry.opendata.aws/obis/ - category: Product description: OBIS-SEAMAP specialized database for marine megavertebrates containing distribution, abundance, and telemetry data for marine mammals, seabirds, and sea turtles id: obis.seamap name: OBIS-SEAMAP Marine Megavertebrates Database product_url: https://seamap.env.duke.edu/ - category: DocumentationProduct description: Comprehensive OBIS manual covering data standards, quality control procedures, Darwin Core implementation, publication guidelines, and API usage documentation format: http id: obis.manual is_public: true name: OBIS Manual product_url: https://manual.obis.org/ publications: - authors: - OBIS Contributors id: obis-data title: Ocean Biodiversity Information System - Global Marine Biodiversity Dataset year: '2025' repository: https://github.com/iobis/ taxon: - NCBITaxon:2157 - NCBITaxon:2158 - NCBITaxon:2159 - activity_status: active category: Aggregator contacts: - category: Individual contact_details: - contact_type: email value: cthoyt@gmail.com - contact_type: github value: cthoyt label: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 creation_date: '2025-03-09T00:00:00Z' description: A set of databases formalized in OBO, OWL, and OBO Graph JSON formats, as well as mappings and nodelists. domains: - upper homepage_url: https://biopragmatics.github.io/obo-db-ingest/ id: obo-db-ingest last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail license: id: https://biopragmatics.github.io/obo-db-ingest/ label: Varies name: OBO Database Ingestion products: - category: Product description: bigg.compartment OBO format: obo id: obo-db-ingest.bigg.compartment.obo license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.compartment OBO original_source: - bigg product_file_size: 1055 product_url: https://w3id.org/biopragmatics/resources/bigg.compartment/bigg.compartment.obo secondary_source: - obo-db-ingest - category: Product description: bigg.compartment OWL format: owl id: obo-db-ingest.bigg.compartment.owl license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.compartment OWL original_source: - bigg product_file_size: 1477 product_url: https://w3id.org/biopragmatics/resources/bigg.compartment/bigg.compartment.owl secondary_source: - obo-db-ingest - category: Product description: bigg.compartment OBO Graph JSON format: json id: obo-db-ingest.bigg.compartment.json license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.compartment OBO Graph JSON original_source: - bigg product_file_size: 1114 product_url: https://w3id.org/biopragmatics/resources/bigg.compartment/bigg.compartment.json secondary_source: - obo-db-ingest - category: MappingProduct description: bigg.compartment SSSOM format: sssom id: obo-db-ingest.bigg.compartment.sssom.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.compartment SSSOM original_source: - bigg - go product_file_size: 242 product_url: https://w3id.org/biopragmatics/resources/bigg.compartment/bigg.compartment.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: bigg.compartment Nodes TSV format: tsv id: obo-db-ingest.bigg.compartment.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.compartment Nodes TSV original_source: - bigg product_file_size: 297 product_url: https://w3id.org/biopragmatics/resources/bigg.compartment/bigg.compartment.tsv secondary_source: - obo-db-ingest - category: Product description: bigg.metabolite OBO format: obo id: obo-db-ingest.bigg.metabolite.obo license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.metabolite OBO original_source: - bigg product_file_size: 588366 product_url: https://w3id.org/biopragmatics/resources/bigg.metabolite/bigg.metabolite.obo secondary_source: - obo-db-ingest - category: Product description: bigg.metabolite OWL format: owl id: obo-db-ingest.bigg.metabolite.owl license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.metabolite OWL original_source: - bigg product_file_size: 757896 product_url: https://w3id.org/biopragmatics/resources/bigg.metabolite/bigg.metabolite.owl secondary_source: - obo-db-ingest - category: Product description: bigg.metabolite OBO Graph JSON format: json id: obo-db-ingest.bigg.metabolite.json license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.metabolite OBO Graph JSON original_source: - bigg product_file_size: 1025217 product_url: https://w3id.org/biopragmatics/resources/bigg.metabolite/bigg.metabolite.json secondary_source: - obo-db-ingest - category: MappingProduct description: bigg.metabolite SSSOM format: sssom id: obo-db-ingest.bigg.metabolite.sssom.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.metabolite SSSOM original_source: - chebi - bigg - biocyc - kegg - reactome product_file_size: 400516 product_url: https://w3id.org/biopragmatics/resources/bigg.metabolite/bigg.metabolite.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: bigg.metabolite Nodes TSV format: tsv id: obo-db-ingest.bigg.metabolite.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.metabolite Nodes TSV original_source: - bigg product_file_size: 266629 product_url: https://w3id.org/biopragmatics/resources/bigg.metabolite/bigg.metabolite.tsv secondary_source: - obo-db-ingest - category: Product description: bigg.model OBO format: obo id: obo-db-ingest.bigg.model.obo license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.model OBO original_source: - bigg product_file_size: 2782 product_url: https://w3id.org/biopragmatics/resources/bigg.model/bigg.model.obo secondary_source: - obo-db-ingest - category: Product description: bigg.model OWL format: owl id: obo-db-ingest.bigg.model.owl license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.model OWL original_source: - bigg product_file_size: 3714 product_url: https://w3id.org/biopragmatics/resources/bigg.model/bigg.model.owl secondary_source: - obo-db-ingest - category: Product description: bigg.model OBO Graph JSON format: json id: obo-db-ingest.bigg.model.json license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.model OBO Graph JSON original_source: - bigg product_file_size: 2508 product_url: https://w3id.org/biopragmatics/resources/bigg.model/bigg.model.json secondary_source: - obo-db-ingest - category: Product description: bigg.model Nodes TSV format: tsv id: obo-db-ingest.bigg.model.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.model Nodes TSV original_source: - bigg product_file_size: 1151 product_url: https://w3id.org/biopragmatics/resources/bigg.model/bigg.model.tsv secondary_source: - obo-db-ingest - category: Product description: bigg.reaction OBO format: obo id: obo-db-ingest.bigg.reaction.obo license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.reaction OBO original_source: - bigg product_file_size: 1195491 product_url: https://w3id.org/biopragmatics/resources/bigg.reaction/bigg.reaction.obo secondary_source: - obo-db-ingest - category: Product description: bigg.reaction OWL format: owl id: obo-db-ingest.bigg.reaction.owl license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.reaction OWL original_source: - bigg product_file_size: 1806640 product_url: https://w3id.org/biopragmatics/resources/bigg.reaction/bigg.reaction.owl secondary_source: - obo-db-ingest - category: Product description: bigg.reaction OBO Graph JSON format: json id: obo-db-ingest.bigg.reaction.json license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.reaction OBO Graph JSON original_source: - bigg product_file_size: 2340334 product_url: https://w3id.org/biopragmatics/resources/bigg.reaction/bigg.reaction.json secondary_source: - obo-db-ingest - category: MappingProduct description: bigg.reaction SSSOM format: sssom id: obo-db-ingest.bigg.reaction.sssom.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.reaction SSSOM original_source: - bigg product_file_size: 462968 product_url: https://w3id.org/biopragmatics/resources/bigg.reaction/bigg.reaction.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: bigg.reaction Nodes TSV format: tsv id: obo-db-ingest.bigg.reaction.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.reaction Nodes TSV original_source: - bigg product_file_size: 593163 product_url: https://w3id.org/biopragmatics/resources/bigg.reaction/bigg.reaction.tsv secondary_source: - obo-db-ingest - category: Product description: ccle OBO format: obo id: obo-db-ingest.ccle.obo license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: ccle OBO original_source: - ccle product_file_size: 19324 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.obo secondary_source: - obo-db-ingest - category: Product description: ccle OWL format: owl id: obo-db-ingest.ccle.owl license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: ccle OWL original_source: - ccle product_file_size: 29770 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.owl secondary_source: - obo-db-ingest - category: Product description: ccle OBO Graph JSON format: json id: obo-db-ingest.ccle.json license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: ccle OBO Graph JSON original_source: - ccle product_file_size: 23282 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.json secondary_source: - obo-db-ingest - category: MappingProduct description: ccle SSSOM format: sssom id: obo-db-ingest.ccle.sssom.tsv license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: ccle SSSOM original_source: - ccle product_file_size: 14414 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: ccle Nodes TSV format: tsv id: obo-db-ingest.ccle.tsv license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: ccle Nodes TSV original_source: - ccle product_file_size: 12188 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.tsv secondary_source: - obo-db-ingest - category: Product description: cgnc OBO format: obo id: obo-db-ingest.cgnc.obo license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: cgnc OBO original_source: - cgnc product_file_size: 683991 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.obo secondary_source: - obo-db-ingest - category: Product description: cgnc OWL format: owl id: obo-db-ingest.cgnc.owl license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: cgnc OWL original_source: - cgnc product_file_size: 911421 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.owl secondary_source: - obo-db-ingest - category: Product description: cgnc OBO Graph JSON format: json id: obo-db-ingest.cgnc.json license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: cgnc OBO Graph JSON original_source: - cgnc product_file_size: 861880 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.json secondary_source: - obo-db-ingest - category: MappingProduct description: cgnc SSSOM format: sssom id: obo-db-ingest.cgnc.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: cgnc SSSOM original_source: - cgnc product_file_size: 258292 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: cgnc Nodes TSV format: tsv id: obo-db-ingest.cgnc.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: cgnc Nodes TSV original_source: - cgnc product_file_size: 406670 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.tsv secondary_source: - obo-db-ingest - category: Product description: chembl.compound OBO format: obo id: obo-db-ingest.chembl.compound.obo license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.compound OBO product_file_size: 5380016 product_url: https://w3id.org/biopragmatics/resources/chembl.compound/chembl.compound.obo - category: Product description: chembl.compound OWL format: owl id: obo-db-ingest.chembl.compound.owl license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.compound OWL product_file_size: 5800822 product_url: https://w3id.org/biopragmatics/resources/chembl.compound/chembl.compound.owl - category: Product description: chembl.compound OBO Graph JSON format: json id: obo-db-ingest.chembl.compound.json license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.compound OBO Graph JSON product_file_size: 5732141 product_url: https://w3id.org/biopragmatics/resources/chembl.compound/chembl.compound.json - category: MappingProduct description: chembl.compound SSSOM format: sssom id: obo-db-ingest.chembl.compound.sssom.tsv license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.compound SSSOM product_file_size: 767775 product_url: https://w3id.org/biopragmatics/resources/chembl.compound/chembl.compound.sssom.tsv - category: Product description: chembl.compound Nodes TSV format: tsv id: obo-db-ingest.chembl.compound.tsv license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.compound Nodes TSV original_source: - chembl product_file_size: 411222 product_url: https://w3id.org/biopragmatics/resources/chembl.compound/chembl.compound.tsv secondary_source: - obo-db-ingest - category: Product description: chembl.target OBO format: obo id: obo-db-ingest.chembl.target.obo license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.target OBO product_file_size: 387199 product_url: https://w3id.org/biopragmatics/resources/chembl.target/chembl.target.obo - category: Product description: chembl.target OWL format: owl id: obo-db-ingest.chembl.target.owl license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.target OWL product_file_size: 546755 product_url: https://w3id.org/biopragmatics/resources/chembl.target/chembl.target.owl - category: Product description: chembl.target OBO Graph JSON format: json id: obo-db-ingest.chembl.target.json license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.target OBO Graph JSON product_file_size: 495605 product_url: https://w3id.org/biopragmatics/resources/chembl.target/chembl.target.json - category: MappingProduct description: chembl.target SSSOM format: sssom id: obo-db-ingest.chembl.target.sssom.tsv license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.target SSSOM product_file_size: 72721 product_url: https://w3id.org/biopragmatics/resources/chembl.target/chembl.target.sssom.tsv - category: Product description: chembl.target Nodes TSV format: tsv id: obo-db-ingest.chembl.target.tsv license: id: https://creativecommons.org/licenses/by-sa/3.0/ label: CC-BY-SA-3.0 name: chembl.target Nodes TSV original_source: - chembl product_file_size: 260194 product_url: https://w3id.org/biopragmatics/resources/chembl.target/chembl.target.tsv secondary_source: - obo-db-ingest - category: Product description: civic.gid OBO format: obo id: obo-db-ingest.civic.gid.obo license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: civic.gid OBO product_file_size: 45668 product_url: https://w3id.org/biopragmatics/resources/civic.gid/civic.gid.obo - category: Product description: civic.gid OWL format: owl id: obo-db-ingest.civic.gid.owl license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: civic.gid OWL product_file_size: 58831 product_url: https://w3id.org/biopragmatics/resources/civic.gid/civic.gid.owl - category: Product description: civic.gid OBO Graph JSON format: json id: obo-db-ingest.civic.gid.json license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: civic.gid OBO Graph JSON product_file_size: 55758 product_url: https://w3id.org/biopragmatics/resources/civic.gid/civic.gid.json - category: MappingProduct description: civic.gid SSSOM format: sssom id: obo-db-ingest.civic.gid.sssom.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: civic.gid SSSOM product_file_size: 3977 product_url: https://w3id.org/biopragmatics/resources/civic.gid/civic.gid.sssom.tsv - category: Product description: civic.gid Nodes TSV format: tsv id: obo-db-ingest.civic.gid.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: civic.gid Nodes TSV original_source: - civic product_file_size: 34804 product_url: https://w3id.org/biopragmatics/resources/civic.gid/civic.gid.tsv secondary_source: - obo-db-ingest - category: Product compression: gzip description: clinicaltrials OBO format: obo id: obo-db-ingest.clinicaltrials.obo license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials OBO product_file_size: 41571299 product_url: https://w3id.org/biopragmatics/resources/clinicaltrials/clinicaltrials.obo.gz - category: Product compression: gzip description: clinicaltrials OWL format: owl id: obo-db-ingest.clinicaltrials.owl license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials OWL product_file_size: 40291602 product_url: https://w3id.org/biopragmatics/resources/clinicaltrials/clinicaltrials.owl.gz - category: Product compression: gzip description: clinicaltrials OBO Graph JSON format: json id: obo-db-ingest.clinicaltrials.json license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials OBO Graph JSON product_file_size: 40813205 product_url: https://w3id.org/biopragmatics/resources/clinicaltrials/clinicaltrials.json.gz - category: MappingProduct description: clinicaltrials SSSOM format: sssom id: obo-db-ingest.clinicaltrials.sssom.tsv license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials SSSOM product_file_size: 6299996 product_url: https://w3id.org/biopragmatics/resources/clinicaltrials/clinicaltrials.sssom.tsv - category: Product description: clinicaltrials Nodes TSV format: tsv id: obo-db-ingest.clinicaltrials.tsv license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials Nodes TSV original_source: - clinicaltrials product_file_size: 19140027 product_url: https://w3id.org/biopragmatics/resources/clinicaltrials/clinicaltrials.tsv secondary_source: - obo-db-ingest - category: Product description: complexportal OBO format: obo id: obo-db-ingest.complexportal.obo license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: complexportal OBO product_file_size: 921494 product_url: https://w3id.org/biopragmatics/resources/complexportal/complexportal.obo - category: Product description: complexportal OWL format: owl id: obo-db-ingest.complexportal.owl license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: complexportal OWL product_file_size: 1099541 product_url: https://w3id.org/biopragmatics/resources/complexportal/complexportal.owl - category: Product description: complexportal OBO Graph JSON format: json id: obo-db-ingest.complexportal.json license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: complexportal OBO Graph JSON product_file_size: 1096476 product_url: https://w3id.org/biopragmatics/resources/complexportal/complexportal.json - category: MappingProduct description: complexportal SSSOM format: sssom id: obo-db-ingest.complexportal.sssom.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: complexportal SSSOM product_file_size: 58537 product_url: https://w3id.org/biopragmatics/resources/complexportal/complexportal.sssom.tsv - category: Product description: complexportal Nodes TSV format: tsv id: obo-db-ingest.complexportal.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: complexportal Nodes TSV original_source: - complexportal product_file_size: 654220 product_url: https://w3id.org/biopragmatics/resources/complexportal/complexportal.tsv secondary_source: - obo-db-ingest - category: Product description: cpt OBO format: obo id: obo-db-ingest.cpt.obo name: cpt OBO product_file_size: 6117 product_url: https://w3id.org/biopragmatics/resources/cpt/cpt.obo - category: Product description: cpt OWL format: owl id: obo-db-ingest.cpt.owl name: cpt OWL product_file_size: 7552 product_url: https://w3id.org/biopragmatics/resources/cpt/cpt.owl - category: Product description: cpt OBO Graph JSON format: json id: obo-db-ingest.cpt.json name: cpt OBO Graph JSON product_file_size: 6848 product_url: https://w3id.org/biopragmatics/resources/cpt/cpt.json - category: MappingProduct description: cpt SSSOM format: sssom id: obo-db-ingest.cpt.sssom.tsv name: cpt SSSOM product_file_size: 977 product_url: https://w3id.org/biopragmatics/resources/cpt/cpt.sssom.tsv - category: Product description: cpt Nodes TSV format: tsv id: obo-db-ingest.cpt.tsv name: cpt Nodes TSV original_source: - cpt product_file_size: 4342 product_url: https://w3id.org/biopragmatics/resources/cpt/cpt.tsv secondary_source: - obo-db-ingest - category: Product description: credit OBO format: obo id: obo-db-ingest.credit.obo license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: credit OBO product_file_size: 1421 product_url: https://w3id.org/biopragmatics/resources/credit/credit.obo - category: Product description: credit OWL format: owl id: obo-db-ingest.credit.owl license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: credit OWL product_file_size: 1903 product_url: https://w3id.org/biopragmatics/resources/credit/credit.owl - category: Product description: credit OBO Graph JSON format: json id: obo-db-ingest.credit.json license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: credit OBO Graph JSON product_file_size: 1577 product_url: https://w3id.org/biopragmatics/resources/credit/credit.json - 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obo-db-ingest - category: Product description: interpro OWL format: owl id: obo-db-ingest.interpro.owl license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: interpro OWL original_source: - interpro product_file_size: 1347709 product_url: https://w3id.org/biopragmatics/resources/interpro/interpro.owl secondary_source: - obo-db-ingest - category: Product description: interpro OBO Graph JSON format: json id: obo-db-ingest.interpro.json license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: interpro OBO Graph JSON original_source: - interpro product_file_size: 1116474 product_url: https://w3id.org/biopragmatics/resources/interpro/interpro.json secondary_source: - obo-db-ingest - category: Product description: interpro Nodes TSV format: tsv id: obo-db-ingest.interpro.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: interpro Nodes TSV original_source: - interpro product_file_size: 697846 product_url: https://w3id.org/biopragmatics/resources/interpro/interpro.tsv secondary_source: - obo-db-ingest - category: Product description: itis OBO format: obo id: obo-db-ingest.itis.obo license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: itis OBO original_source: - itis product_file_size: 10936424 product_url: https://w3id.org/biopragmatics/resources/itis/itis.obo secondary_source: - obo-db-ingest - category: Product compression: gzip description: itis OWL format: owl id: obo-db-ingest.itis.owl license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: itis OWL original_source: - itis product_file_size: 14607611 product_url: https://w3id.org/biopragmatics/resources/itis/itis.owl.gz secondary_source: - obo-db-ingest - category: Product compression: gzip description: itis OBO Graph JSON format: json id: obo-db-ingest.itis.json license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: itis OBO Graph JSON original_source: - itis product_file_size: 12669423 product_url: https://w3id.org/biopragmatics/resources/itis/itis.json.gz secondary_source: - obo-db-ingest - category: Product description: itis Nodes TSV format: tsv id: obo-db-ingest.itis.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: itis Nodes TSV original_source: - itis product_file_size: 9497861 product_url: https://w3id.org/biopragmatics/resources/itis/itis.tsv secondary_source: - obo-db-ingest - category: Product description: kegg.genome OBO format: obo id: obo-db-ingest.kegg.genome.obo license: id: https://www.kegg.jp/kegg/legal.html label: Custom name: kegg.genome OBO product_file_size: 198714 product_url: https://w3id.org/biopragmatics/resources/kegg.genome/kegg.genome.obo - category: Product description: kegg.genome OWL format: owl id: obo-db-ingest.kegg.genome.owl license: id: https://www.kegg.jp/kegg/legal.html label: Custom name: kegg.genome OWL product_file_size: 192384 product_url: https://w3id.org/biopragmatics/resources/kegg.genome/kegg.genome.owl - category: Product description: kegg.genome OBO Graph JSON format: json id: obo-db-ingest.kegg.genome.json license: id: https://www.kegg.jp/kegg/legal.html label: Custom name: kegg.genome OBO Graph JSON product_file_size: 20525 product_url: https://w3id.org/biopragmatics/resources/kegg.genome/kegg.genome.json - category: Product description: kegg.genome Nodes TSV format: tsv id: obo-db-ingest.kegg.genome.tsv license: id: https://www.kegg.jp/kegg/legal.html label: Custom name: kegg.genome Nodes TSV original_source: - kegg product_file_size: 187935 product_url: https://w3id.org/biopragmatics/resources/kegg.genome/kegg.genome.tsv secondary_source: - obo-db-ingest - category: Product description: mesh OBO format: obo id: obo-db-ingest.mesh.obo license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: mesh OBO product_file_size: 13534704 product_url: https://w3id.org/biopragmatics/resources/mesh/mesh.obo - category: Product compression: gzip description: mesh OWL format: owl id: obo-db-ingest.mesh.owl license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: mesh OWL product_file_size: 15978588 product_url: https://w3id.org/biopragmatics/resources/mesh/mesh.owl.gz - category: Product compression: gzip description: mesh OBO Graph JSON format: json id: obo-db-ingest.mesh.json license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: mesh OBO Graph JSON product_file_size: 15337148 product_url: https://w3id.org/biopragmatics/resources/mesh/mesh.json.gz - category: Product description: mesh Nodes TSV format: tsv id: obo-db-ingest.mesh.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: mesh Nodes TSV original_source: - mesh product_file_size: 12212627 product_url: https://w3id.org/biopragmatics/resources/mesh/mesh.tsv secondary_source: - obo-db-ingest - category: Product compression: gzip description: mgi OBO format: obo id: obo-db-ingest.mgi.obo license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: mgi OBO product_file_size: 9628994 product_url: https://w3id.org/biopragmatics/resources/mgi/mgi.obo.gz - category: Product compression: gzip description: mgi OWL format: owl id: obo-db-ingest.mgi.owl license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: mgi OWL product_file_size: 15551282 product_url: https://w3id.org/biopragmatics/resources/mgi/mgi.owl.gz - category: Product compression: gzip description: mgi OBO Graph JSON format: json id: obo-db-ingest.mgi.json license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: mgi OBO Graph JSON product_file_size: 12304920 product_url: https://w3id.org/biopragmatics/resources/mgi/mgi.json.gz - 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category: Product description: mirbase OBO Graph JSON format: json id: obo-db-ingest.mirbase.json license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase OBO Graph JSON product_file_size: 825009 product_url: https://w3id.org/biopragmatics/resources/mirbase/mirbase.json - category: MappingProduct description: mirbase SSSOM format: sssom id: obo-db-ingest.mirbase.sssom.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase SSSOM product_file_size: 53837 product_url: https://w3id.org/biopragmatics/resources/mirbase/mirbase.sssom.tsv - category: Product description: mirbase Nodes TSV format: tsv id: obo-db-ingest.mirbase.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase Nodes TSV original_source: - mirbase product_file_size: 384582 product_url: https://w3id.org/biopragmatics/resources/mirbase/mirbase.tsv secondary_source: - obo-db-ingest - category: Product description: mirbase.family OBO format: obo id: obo-db-ingest.mirbase.family.obo license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase.family OBO product_file_size: 175105 product_url: https://w3id.org/biopragmatics/resources/mirbase.family/mirbase.family.obo - category: Product description: mirbase.family OWL format: owl id: obo-db-ingest.mirbase.family.owl license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase.family OWL product_file_size: 248775 product_url: https://w3id.org/biopragmatics/resources/mirbase.family/mirbase.family.owl - category: Product description: mirbase.family OBO Graph JSON format: json id: obo-db-ingest.mirbase.family.json license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase.family OBO Graph JSON product_file_size: 113961 product_url: https://w3id.org/biopragmatics/resources/mirbase.family/mirbase.family.json - category: Product description: mirbase.family Nodes TSV format: tsv id: obo-db-ingest.mirbase.family.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase.family Nodes TSV original_source: - mirbase product_file_size: 15085 product_url: https://w3id.org/biopragmatics/resources/mirbase.family/mirbase.family.tsv secondary_source: - obo-db-ingest - category: Product description: mirbase.mature OBO format: obo id: obo-db-ingest.mirbase.mature.obo license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase.mature OBO product_file_size: 329057 product_url: https://w3id.org/biopragmatics/resources/mirbase.mature/mirbase.mature.obo - category: Product description: mirbase.mature OWL format: owl id: obo-db-ingest.mirbase.mature.owl license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase.mature OWL product_file_size: 549748 product_url: https://w3id.org/biopragmatics/resources/mirbase.mature/mirbase.mature.owl - category: Product description: mirbase.mature OBO Graph JSON format: json id: obo-db-ingest.mirbase.mature.json license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase.mature OBO Graph JSON product_file_size: 373573 product_url: https://w3id.org/biopragmatics/resources/mirbase.mature/mirbase.mature.json - category: Product description: mirbase.mature Nodes TSV format: tsv id: obo-db-ingest.mirbase.mature.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: mirbase.mature Nodes TSV original_source: - mirbase product_file_size: 293915 product_url: https://w3id.org/biopragmatics/resources/mirbase.mature/mirbase.mature.tsv secondary_source: - obo-db-ingest - category: Product compression: gzip description: msigdb OBO format: obo id: obo-db-ingest.msigdb.obo license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: msigdb OBO product_file_size: 19115104 product_url: https://w3id.org/biopragmatics/resources/msigdb/msigdb.obo.gz - category: Product compression: gzip description: msigdb OWL format: owl id: obo-db-ingest.msigdb.owl license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: msigdb OWL product_file_size: 18147081 product_url: https://w3id.org/biopragmatics/resources/msigdb/msigdb.owl.gz - category: Product compression: gzip description: msigdb OBO Graph JSON format: json id: obo-db-ingest.msigdb.json license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: msigdb OBO Graph JSON product_file_size: 19170792 product_url: https://w3id.org/biopragmatics/resources/msigdb/msigdb.json.gz - category: MappingProduct description: msigdb SSSOM format: sssom id: obo-db-ingest.msigdb.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: msigdb SSSOM product_file_size: 92467 product_url: https://w3id.org/biopragmatics/resources/msigdb/msigdb.sssom.tsv - category: Product description: msigdb Nodes TSV format: tsv id: obo-db-ingest.msigdb.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: msigdb Nodes TSV original_source: - msigdb product_file_size: 3121367 product_url: https://w3id.org/biopragmatics/resources/msigdb/msigdb.tsv secondary_source: - obo-db-ingest - category: Product description: ncbi.gc OBO format: obo id: obo-db-ingest.ncbi.gc.obo license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: ncbi.gc OBO product_file_size: 1425 product_url: https://w3id.org/biopragmatics/resources/ncbi.gc/ncbi.gc.obo - category: Product description: ncbi.gc OWL format: owl id: obo-db-ingest.ncbi.gc.owl license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: ncbi.gc OWL product_file_size: 2223 product_url: https://w3id.org/biopragmatics/resources/ncbi.gc/ncbi.gc.owl - category: Product description: ncbi.gc OBO Graph JSON format: json id: obo-db-ingest.ncbi.gc.json license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: ncbi.gc OBO Graph JSON product_file_size: 1886 product_url: https://w3id.org/biopragmatics/resources/ncbi.gc/ncbi.gc.json - category: MappingProduct description: ncbi.gc SSSOM format: sssom id: obo-db-ingest.ncbi.gc.sssom.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: ncbi.gc SSSOM product_file_size: 191 product_url: https://w3id.org/biopragmatics/resources/ncbi.gc/ncbi.gc.sssom.tsv - category: Product description: ncbi.gc Nodes TSV format: tsv id: obo-db-ingest.ncbi.gc.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: ncbi.gc Nodes TSV original_source: - ncbi.gc product_file_size: 531 product_url: https://w3id.org/biopragmatics/resources/ncbi.gc/ncbi.gc.tsv secondary_source: - obo-db-ingest - category: Product compression: gzip description: nihreporter.project OBO format: obo id: obo-db-ingest.nihreporter.project.obo name: nihreporter.project OBO product_file_size: 69000371 product_url: https://w3id.org/biopragmatics/resources/nihreporter.project/nihreporter.project.obo.gz - 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category: Product description: nlm OWL format: owl id: obo-db-ingest.nlm.owl license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: nlm OWL product_file_size: 2471988 product_url: https://w3id.org/biopragmatics/resources/nlm/nlm.owl - category: Product description: nlm OBO Graph JSON format: json id: obo-db-ingest.nlm.json license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: nlm OBO Graph JSON product_file_size: 2497051 product_url: https://w3id.org/biopragmatics/resources/nlm/nlm.json - category: MappingProduct description: nlm SSSOM format: sssom id: obo-db-ingest.nlm.sssom.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: nlm SSSOM product_file_size: 422890 product_url: https://w3id.org/biopragmatics/resources/nlm/nlm.sssom.tsv - category: Product description: nlm Nodes TSV format: tsv id: obo-db-ingest.nlm.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: nlm Nodes TSV original_source: - nlm product_file_size: 1156325 product_url: https://w3id.org/biopragmatics/resources/nlm/nlm.tsv secondary_source: - obo-db-ingest - category: Product description: nlm.publisher OBO format: obo id: obo-db-ingest.nlm.publisher.obo license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: nlm.publisher OBO product_file_size: 9570 product_url: https://w3id.org/biopragmatics/resources/nlm.publisher/nlm.publisher.obo - category: Product description: nlm.publisher OWL format: owl id: obo-db-ingest.nlm.publisher.owl license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: nlm.publisher OWL product_file_size: 12531 product_url: https://w3id.org/biopragmatics/resources/nlm.publisher/nlm.publisher.owl - category: Product description: nlm.publisher OBO Graph JSON format: json id: obo-db-ingest.nlm.publisher.json license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: nlm.publisher OBO Graph JSON product_file_size: 12675 product_url: https://w3id.org/biopragmatics/resources/nlm.publisher/nlm.publisher.json - category: MappingProduct description: nlm.publisher SSSOM format: sssom id: obo-db-ingest.nlm.publisher.sssom.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: nlm.publisher SSSOM original_source: - nlm.publisher product_file_size: 140 product_url: https://w3id.org/biopragmatics/resources/nlm.publisher/nlm.publisher.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: nlm.publisher Nodes TSV format: tsv id: obo-db-ingest.nlm.publisher.tsv license: id: https://creativecommons.org/public-domain/pdm/ label: public domain name: nlm.publisher Nodes TSV original_source: - nlm.publisher product_file_size: 8289 product_url: https://w3id.org/biopragmatics/resources/nlm.publisher/nlm.publisher.tsv secondary_source: - obo-db-ingest - category: Product description: npass OBO format: obo id: obo-db-ingest.npass.obo license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC-BY-NC name: npass OBO product_file_size: 3336518 product_url: https://w3id.org/biopragmatics/resources/npass/npass.obo - category: Product description: npass OWL format: owl id: obo-db-ingest.npass.owl license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC-BY-NC name: npass OWL product_file_size: 4085393 product_url: https://w3id.org/biopragmatics/resources/npass/npass.owl - category: Product description: npass OBO Graph JSON format: json id: obo-db-ingest.npass.json license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC-BY-NC name: npass OBO Graph JSON product_file_size: 3814506 product_url: https://w3id.org/biopragmatics/resources/npass/npass.json - category: MappingProduct description: npass SSSOM format: sssom id: obo-db-ingest.npass.sssom.tsv license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC-BY-NC name: npass SSSOM product_file_size: 833693 product_url: https://w3id.org/biopragmatics/resources/npass/npass.sssom.tsv - category: Product description: npass Nodes TSV format: tsv id: obo-db-ingest.npass.tsv license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC-BY-NC name: npass Nodes TSV original_source: - npass product_file_size: 2460413 product_url: https://w3id.org/biopragmatics/resources/npass/npass.tsv secondary_source: - obo-db-ingest - category: Product description: omim.ps OBO format: obo id: obo-db-ingest.omim.ps.obo license: id: https://www.omim.org/help/agreement label: Custom name: omim.ps OBO product_file_size: 10241 product_url: https://w3id.org/biopragmatics/resources/omim.ps/omim.ps.obo - category: Product description: omim.ps OWL format: owl id: obo-db-ingest.omim.ps.owl license: id: https://www.omim.org/help/agreement label: Custom name: omim.ps OWL product_file_size: 13894 product_url: https://w3id.org/biopragmatics/resources/omim.ps/omim.ps.owl - category: Product description: omim.ps OBO Graph JSON format: json id: obo-db-ingest.omim.ps.json license: id: https://www.omim.org/help/agreement label: Custom name: omim.ps OBO Graph JSON product_file_size: 11140 product_url: https://w3id.org/biopragmatics/resources/omim.ps/omim.ps.json - category: Product description: omim.ps Nodes TSV format: tsv id: obo-db-ingest.omim.ps.tsv license: id: https://www.omim.org/help/agreement label: Custom name: omim.ps Nodes TSV original_source: - omim product_file_size: 9568 product_url: https://w3id.org/biopragmatics/resources/omim.ps/omim.ps.tsv secondary_source: - obo-db-ingest - category: Product compression: gzip description: pathbank OBO format: obo id: obo-db-ingest.pathbank.obo license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: pathbank OBO product_file_size: 1849960 product_url: https://w3id.org/biopragmatics/resources/pathbank/pathbank.obo.gz - category: Product compression: gzip description: pathbank OWL format: owl id: obo-db-ingest.pathbank.owl license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: pathbank OWL product_file_size: 6878307 product_url: https://w3id.org/biopragmatics/resources/pathbank/pathbank.owl.gz - category: Product compression: gzip description: pathbank OBO Graph JSON format: json id: obo-db-ingest.pathbank.json license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: pathbank OBO Graph JSON product_file_size: 8672175 product_url: https://w3id.org/biopragmatics/resources/pathbank/pathbank.json.gz - category: MappingProduct description: pathbank SSSOM format: sssom id: obo-db-ingest.pathbank.sssom.tsv license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: pathbank SSSOM product_file_size: 570276 product_url: https://w3id.org/biopragmatics/resources/pathbank/pathbank.sssom.tsv - category: Product description: pathbank Nodes TSV format: tsv id: obo-db-ingest.pathbank.tsv license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: pathbank Nodes TSV original_source: - pathbank product_file_size: 727666 product_url: https://w3id.org/biopragmatics/resources/pathbank/pathbank.tsv secondary_source: - obo-db-ingest - category: Product description: pfam OBO format: obo id: obo-db-ingest.pfam.obo license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: pfam OBO product_file_size: 510198 product_url: https://w3id.org/biopragmatics/resources/pfam/pfam.obo - category: Product description: pfam OWL format: owl id: obo-db-ingest.pfam.owl license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: pfam OWL product_file_size: 656714 product_url: https://w3id.org/biopragmatics/resources/pfam/pfam.owl - category: Product description: pfam OBO Graph JSON format: json id: obo-db-ingest.pfam.json license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: pfam OBO Graph JSON product_file_size: 595575 product_url: https://w3id.org/biopragmatics/resources/pfam/pfam.json - category: Product description: pfam Nodes TSV format: tsv id: obo-db-ingest.pfam.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: pfam Nodes TSV original_source: - pfam product_file_size: 460967 product_url: https://w3id.org/biopragmatics/resources/pfam/pfam.tsv secondary_source: - obo-db-ingest - category: Product description: pfam.clan OBO format: obo id: obo-db-ingest.pfam.clan.obo license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: pfam.clan OBO product_file_size: 7122 product_url: https://w3id.org/biopragmatics/resources/pfam.clan/pfam.clan.obo - category: Product description: pfam.clan OWL format: owl id: obo-db-ingest.pfam.clan.owl license: id: https://creativecommons.org.publicdomain/zero/1.0/ label: CC0-1.0 name: pfam.clan OWL product_file_size: 11064 product_url: https://w3id.org/biopragmatics/resources/pfam.clan/pfam.clan.owl - category: Product description: pfam.clan OBO Graph JSON format: json id: obo-db-ingest.pfam.clan.json license: id: https://creativecommons.org.publicdomain/zero/1.0/ label: CC0-1.0 name: pfam.clan OBO Graph JSON product_file_size: 7820 product_url: https://w3id.org/biopragmatics/resources/pfam.clan/pfam.clan.json - category: Product description: pfam.clan Nodes TSV format: tsv id: obo-db-ingest.pfam.clan.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: pfam.clan Nodes TSV original_source: - pfam product_file_size: 6407 product_url: https://w3id.org/biopragmatics/resources/pfam.clan/pfam.clan.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.disease OBO format: obo id: obo-db-ingest.pharmgkb.disease.obo license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.disease OBO original_source: - pharmgkb product_file_size: 148487 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.obo secondary_source: - obo-db-ingest - category: Product description: pharmgkb.disease OWL format: owl id: obo-db-ingest.pharmgkb.disease.owl license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.disease OWL original_source: - pharmgkb product_file_size: 178658 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.owl secondary_source: - obo-db-ingest - category: Product description: pharmgkb.disease OBO Graph JSON format: json id: obo-db-ingest.pharmgkb.disease.json license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.disease OBO Graph JSON original_source: - pharmgkb product_file_size: 180080 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.json secondary_source: - obo-db-ingest - category: MappingProduct description: pharmgkb.disease SSSOM format: sssom id: obo-db-ingest.pharmgkb.disease.sssom.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.disease SSSOM original_source: - pharmgkb product_file_size: 62271 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.disease Nodes TSV format: tsv id: obo-db-ingest.pharmgkb.disease.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.disease Nodes TSV original_source: - pharmgkb product_file_size: 85777 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.drug OBO format: obo id: obo-db-ingest.pharmgkb.drug.obo license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.drug OBO original_source: - pharmgkb product_file_size: 465956 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.obo secondary_source: - obo-db-ingest - category: Product description: pharmgkb.drug OWL format: owl id: obo-db-ingest.pharmgkb.drug.owl license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.drug OWL original_source: - pharmgkb product_file_size: 531402 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.owl secondary_source: - obo-db-ingest - category: Product description: pharmgkb.drug OBO Graph JSON format: json id: obo-db-ingest.pharmgkb.drug.json license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.drug OBO Graph JSON original_source: - pharmgkb product_file_size: 552557 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.json secondary_source: - obo-db-ingest - category: MappingProduct description: pharmgkb.drug SSSOM format: sssom id: obo-db-ingest.pharmgkb.drug.sssom.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.drug SSSOM original_source: - pharmgkb product_file_size: 202221 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.drug Nodes TSV format: tsv id: obo-db-ingest.pharmgkb.drug.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.drug Nodes TSV original_source: - pharmgkb product_file_size: 55062 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.gene OBO format: obo id: obo-db-ingest.pharmgkb.gene.obo license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.gene OBO original_source: - pharmgkb product_file_size: 2137084 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.gene/pharmgkb.gene.obo secondary_source: - obo-db-ingest - category: Product description: pharmgkb.gene OWL format: owl id: obo-db-ingest.pharmgkb.gene.owl license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.gene OWL original_source: - pharmgkb product_file_size: 2542592 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.gene/pharmgkb.gene.owl secondary_source: - obo-db-ingest - category: Product description: pharmgkb.gene OBO Graph JSON format: json id: obo-db-ingest.pharmgkb.gene.json license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.gene OBO Graph JSON original_source: - pharmgkb product_file_size: 2668332 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.gene/pharmgkb.gene.json secondary_source: - obo-db-ingest - category: MappingProduct description: pharmgkb.gene SSSOM format: sssom id: obo-db-ingest.pharmgkb.gene.sssom.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.gene SSSOM original_source: - pharmgkb product_file_size: 1621905 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.gene/pharmgkb.gene.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.gene Nodes TSV format: tsv id: obo-db-ingest.pharmgkb.gene.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.gene Nodes TSV original_source: - pharmgkb product_file_size: 757356 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.gene/pharmgkb.gene.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.pathways OBO format: obo id: obo-db-ingest.pharmgkb.pathways.obo license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.pathways OBO original_source: - pharmgkb product_file_size: 2776 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.obo secondary_source: - obo-db-ingest - category: Product description: pharmgkb.pathways OWL format: owl id: obo-db-ingest.pharmgkb.pathways.owl license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.pathways OWL original_source: - pharmgkb product_file_size: 3784 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.owl secondary_source: - obo-db-ingest - category: Product description: pharmgkb.pathways OBO Graph JSON format: json id: obo-db-ingest.pharmgkb.pathways.json license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.pathways OBO Graph JSON original_source: - pharmgkb product_file_size: 2947 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.json secondary_source: - obo-db-ingest - category: Product description: pharmgkb.pathways Nodes TSV format: tsv id: obo-db-ingest.pharmgkb.pathways.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.pathways Nodes TSV original_source: - pharmgkb product_file_size: 2140 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.variant OBO format: obo id: obo-db-ingest.pharmgkb.variant.obo license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.variant OBO original_source: - pharmgkb product_file_size: 102072 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.variant/pharmgkb.variant.obo secondary_source: - obo-db-ingest - category: Product description: pharmgkb.variant OWL format: owl id: obo-db-ingest.pharmgkb.variant.owl license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.variant OWL original_source: - pharmgkb product_file_size: 107225 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.variant/pharmgkb.variant.owl secondary_source: - obo-db-ingest - category: Product description: pharmgkb.variant OBO Graph JSON format: json id: obo-db-ingest.pharmgkb.variant.json license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.variant OBO Graph JSON original_source: - pharmgkb product_file_size: 92435 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.variant/pharmgkb.variant.json secondary_source: - obo-db-ingest - category: MappingProduct description: pharmgkb.variant SSSOM format: sssom id: obo-db-ingest.pharmgkb.variant.sssom.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.variant SSSOM original_source: - pharmgkb product_file_size: 56599 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.variant/pharmgkb.variant.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.variant Nodes TSV format: tsv id: obo-db-ingest.pharmgkb.variant.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.variant Nodes TSV original_source: - pharmgkb product_file_size: 19203 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.variant/pharmgkb.variant.tsv secondary_source: - obo-db-ingest - category: Product description: pid.pathway OBO format: obo id: obo-db-ingest.pid.pathway.obo name: pid.pathway OBO product_file_size: 53872 product_url: https://w3id.org/biopragmatics/resources/pid.pathway/pid.pathway.obo - category: Product description: pid.pathway OWL format: owl id: obo-db-ingest.pid.pathway.owl name: pid.pathway OWL product_file_size: 54779 product_url: https://w3id.org/biopragmatics/resources/pid.pathway/pid.pathway.owl - category: Product description: pid.pathway OBO Graph JSON format: json id: obo-db-ingest.pid.pathway.json name: pid.pathway OBO Graph JSON product_file_size: 47185 product_url: https://w3id.org/biopragmatics/resources/pid.pathway/pid.pathway.json - category: Product description: pid.pathway Nodes TSV format: tsv id: obo-db-ingest.pid.pathway.tsv name: pid.pathway Nodes TSV original_source: - pid product_file_size: 3923 product_url: https://w3id.org/biopragmatics/resources/pid.pathway/pid.pathway.tsv secondary_source: - obo-db-ingest - category: Product description: pombase OBO format: obo id: obo-db-ingest.pombase.obo license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: pombase OBO product_file_size: 232235 product_url: https://w3id.org/biopragmatics/resources/pombase/pombase.obo - category: Product description: pombase OWL format: owl id: obo-db-ingest.pombase.owl license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: pombase OWL product_file_size: 422834 product_url: https://w3id.org/biopragmatics/resources/pombase/pombase.owl - category: Product description: pombase OBO Graph JSON format: json id: obo-db-ingest.pombase.json license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: pombase OBO Graph JSON product_file_size: 368065 product_url: https://w3id.org/biopragmatics/resources/pombase/pombase.json - category: Product description: pombase Nodes TSV format: tsv id: obo-db-ingest.pombase.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: pombase Nodes TSV original_source: - pombase product_file_size: 143806 product_url: https://w3id.org/biopragmatics/resources/pombase/pombase.tsv secondary_source: - obo-db-ingest - category: Product description: reactome OBO format: obo id: obo-db-ingest.reactome.obo license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: reactome OBO product_file_size: 4695236 product_url: https://w3id.org/biopragmatics/resources/reactome/reactome.obo - category: Product compression: gzip description: reactome OWL format: owl id: obo-db-ingest.reactome.owl license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: reactome OWL product_file_size: 5333931 product_url: https://w3id.org/biopragmatics/resources/reactome/reactome.owl.gz - category: Product compression: gzip description: reactome OBO Graph JSON format: json id: obo-db-ingest.reactome.json license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: reactome OBO Graph JSON product_file_size: 5919602 product_url: https://w3id.org/biopragmatics/resources/reactome/reactome.json.gz - category: Product description: reactome Nodes TSV format: tsv id: obo-db-ingest.reactome.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: reactome Nodes TSV original_source: - reactome product_file_size: 445199 product_url: https://w3id.org/biopragmatics/resources/reactome/reactome.tsv secondary_source: - obo-db-ingest - category: Product description: rgd OBO format: obo id: obo-db-ingest.rgd.obo license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rgd OBO product_file_size: 3728799 product_url: https://w3id.org/biopragmatics/resources/rgd/rgd.obo - category: Product compression: gzip description: rgd OWL format: owl id: obo-db-ingest.rgd.owl license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rgd OWL product_file_size: 6347162 product_url: https://w3id.org/biopragmatics/resources/rgd/rgd.owl.gz - category: Product compression: gzip description: rgd OBO Graph JSON format: json id: obo-db-ingest.rgd.json license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rgd OBO Graph JSON product_file_size: 4392993 product_url: https://w3id.org/biopragmatics/resources/rgd/rgd.json.gz - category: MappingProduct description: rgd SSSOM format: sssom id: obo-db-ingest.rgd.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rgd SSSOM product_file_size: 632341 product_url: https://w3id.org/biopragmatics/resources/rgd/rgd.sssom.tsv - 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category: Product description: uniprot.ptm OBO Graph JSON format: json id: obo-db-ingest.uniprot.ptm.json license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: uniprot.ptm OBO Graph JSON product_file_size: 17583 product_url: https://w3id.org/biopragmatics/resources/uniprot.ptm/uniprot.ptm.json - category: MappingProduct description: uniprot.ptm SSSOM format: sssom id: obo-db-ingest.uniprot.ptm.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: uniprot.ptm SSSOM product_file_size: 8833 product_url: https://w3id.org/biopragmatics/resources/uniprot.ptm/uniprot.ptm.sssom.tsv - category: Product description: uniprot.ptm Nodes TSV format: tsv id: obo-db-ingest.uniprot.ptm.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: uniprot.ptm Nodes TSV original_source: - uniprot product_file_size: 6660 product_url: https://w3id.org/biopragmatics/resources/uniprot.ptm/uniprot.ptm.tsv secondary_source: - obo-db-ingest - category: Product description: wikipathways OBO format: obo id: obo-db-ingest.wikipathways.obo license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: wikipathways OBO product_file_size: 300327 product_url: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.obo - category: Product description: wikipathways OWL format: owl id: obo-db-ingest.wikipathways.owl license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: wikipathways OWL product_file_size: 495634 product_url: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.owl - category: Product description: wikipathways OBO Graph JSON format: json id: obo-db-ingest.wikipathways.json license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: wikipathways OBO Graph JSON product_file_size: 394845 product_url: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.json - category: Product description: wikipathways Nodes TSV format: tsv id: obo-db-ingest.wikipathways.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: wikipathways Nodes TSV original_source: - wikipathways product_file_size: 33562 product_url: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.tsv secondary_source: - obo-db-ingest - category: Product description: zfin OBO format: obo id: obo-db-ingest.zfin.obo license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: zfin OBO original_source: - zfin product_file_size: 2643947 product_url: https://w3id.org/biopragmatics/resources/zfin/zfin.obo secondary_source: - obo-db-ingest - category: Product compression: gzip description: zfin OWL format: owl id: obo-db-ingest.zfin.owl license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: zfin OWL original_source: - zfin product_file_size: 4556098 product_url: https://w3id.org/biopragmatics/resources/zfin/zfin.owl.gz secondary_source: - obo-db-ingest - category: Product compression: gzip description: zfin OBO Graph JSON format: json id: obo-db-ingest.zfin.json license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: zfin OBO Graph JSON original_source: - zfin product_file_size: 4010220 product_url: https://w3id.org/biopragmatics/resources/zfin/zfin.json.gz secondary_source: - obo-db-ingest - category: MappingProduct description: zfin SSSOM format: sssom id: obo-db-ingest.zfin.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: zfin SSSOM original_source: - zfin product_file_size: 374627 product_url: https://w3id.org/biopragmatics/resources/zfin/zfin.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: zfin Nodes TSV format: tsv id: obo-db-ingest.zfin.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: zfin Nodes TSV original_source: - zfin product_file_size: 1884582 product_url: https://w3id.org/biopragmatics/resources/zfin/zfin.tsv secondary_source: - obo-db-ingest repository: https://github.com/biopragmatics/obo-db-ingest - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: zhengj2007@gmail.com - contact_type: github value: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 creation_date: '2025-09-29T00:00:00Z' description: An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union. domains: - biomedical homepage_url: https://github.com/Occupation-Ontology/OccO id: occo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Occupation Ontology products: - category: OntologyProduct description: Occupation Ontology in OWL format format: owl id: occo.owl name: occo.owl product_file_size: 280761 product_url: http://purl.obolibrary.org/obo/occo.owl repository: https://github.com/Occupation-Ontology/OccO - activity_status: active category: DataSource creation_date: '2025-07-08T00:00:00Z' description: OFFSIDES is a database of drug side effects that were found through data mining of FDA Adverse Event Reporting System (FAERS) but are not listed on the official FDA drug labels. Part of the nSIDES resource developed by Tatonetti Lab. domains: - pharmacology homepage_url: http://tatonettilab.org/offsides/ id: offsides last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: OFFSIDES products: - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque synonyms: - OffSIDES - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: yongqunh@med.umich.edu - contact_type: github value: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 creation_date: '2025-09-29T00:00:00Z' description: A formal ontology of genes and genomes of biological organisms. domains: - biological systems homepage_url: https://bitbucket.org/hegroup/ogg id: ogg last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: The Ontology of Genes and Genomes products: - category: OntologyProduct description: The Ontology of Genes and Genomes in OWL format format: owl id: ogg.owl name: ogg.owl product_file_size: 127956460 product_url: http://purl.obolibrary.org/obo/ogg.owl repository: https://bitbucket.org/hegroup/ogg - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: baeverma@jcvi.org - contact_type: github value: BAevermann label: Brian Aevermann orcid: 0000-0003-1346-1327 creation_date: '2025-06-25T00:00:00Z' description: An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities domains: - biomedical homepage_url: https://github.com/OGMS/ogms id: ogms last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology for General Medical Science products: - category: OntologyProduct description: Ontology for General Medical Science in OWL format format: owl id: ogms.owl name: ogms.owl product_file_size: 39126 product_url: http://purl.obolibrary.org/obo/ogms.owl - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/OGMS/ogms taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: wdduncan@gmail.com - contact_type: github value: wdduncan label: Bill Duncan orcid: 0000-0001-9625-1899 creation_date: '2025-09-29T00:00:00Z' description: The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies. domains: - biomedical homepage_url: https://purl.obolibrary.org/obo/ohd/home id: ohd last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Oral Health and Disease Ontology products: - category: OntologyProduct description: Oral Health and Disease Ontology in OWL format format: owl id: ohd.owl name: ohd.owl product_file_size: 326300 product_url: http://purl.obolibrary.org/obo/ohd.owl - category: OntologyProduct description: OHD dev format: owl id: ohd.dev.ohd.owl name: OHD dev product_url: http://purl.obolibrary.org/obo/ohd/dev/ohd.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: yongqunh@med.umich.edu - contact_type: github value: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 creation_date: '2025-07-10T00:00:00Z' description: The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions. domains: - biological systems homepage_url: https://github.com/ohmi-ontology/ohmi id: ohmi last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Host-Microbiome Interactions products: - category: OntologyProduct description: Ontology of Host-Microbiome Interactions in OWL format format: owl id: ohmi.owl name: ohmi.owl product_file_size: 146555 product_url: http://purl.obolibrary.org/obo/ohmi.owl repository: https://github.com/ohmi-ontology/ohmi - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: edong@umich.edu - contact_type: github value: e4ong1031 label: Edison Ong orcid: 0000-0002-5159-414X creation_date: '2025-09-29T00:00:00Z' description: OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource. domains: - biological systems homepage_url: https://github.com/OHPI/ohpi id: ohpi last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Host Pathogen Interactions products: - category: OntologyProduct description: Ontology of Host Pathogen Interactions in OWL format format: owl id: ohpi.owl name: ohpi.owl product_file_size: 1482262 product_url: http://purl.obolibrary.org/obo/ohpi.owl repository: https://github.com/OHPI/ohpi - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: github value: EBISPOT/ols4 - contact_type: email value: ols-support@ebi.ac.uk id: ebi label: EMBL-EBI Samples, Phenotypes and Ontologies Team creation_date: '2025-10-30T00:00:00Z' description: The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. Users can browse ontologies through the website and programmatically via the OLS API. Maintained by the Samples, Phenotypes and Ontologies Team (SPOT) at EMBL-EBI. domains: - biomedical - biological systems - information technology homepage_url: https://www.ebi.ac.uk/ols4/ id: ols infores_id: ols last_modified_date: '2026-01-15T00:00:00Z' layout: resource_detail name: Ontology Lookup Service products: - category: GraphicalInterface description: Web interface for browsing and searching biomedical ontologies with exact match and obsolete term filtering format: http id: ols.portal is_public: true name: OLS Web Portal original_source: - ols product_url: https://www.ebi.ac.uk/ols4/ - category: ProgrammingInterface description: RESTful API for programmatic access to ontology data including terms, properties, and relationships format: http id: ols.api is_public: true name: OLS REST API original_source: - ols product_url: https://www.ebi.ac.uk/ols4/api-docs - category: Product compression: gzip description: Internal JSON representation of all loaded ontologies (approximately 50 GB uncompressed) format: json id: ols.json name: OLS Ontologies JSON original_source: - ols product_url: https://ftp.ebi.ac.uk/pub/databases/spot/ols/ - category: GraphProduct compression: tar description: Neo4j database with linked ontology data including cross-references between ontologies and external databases (approximately 150 GB) dump_format: neo4j format: neo4j id: ols.neo4j name: OLS Neo4j Database original_source: - ols product_url: https://ftp.ebi.ac.uk/pub/databases/spot/ols/ - category: Product compression: tar description: Solr search index database for ontology searching (requires Solr 9.0.0) id: ols.solr name: OLS Solr Database original_source: - ols product_url: https://ftp.ebi.ac.uk/pub/databases/spot/ols/ - category: MappingProduct compression: gzip description: Ontology mappings extracted from all ontologies in SSSOM TSV format format: tsv id: ols.mappings name: OLS SSSOM Mappings original_source: - ols product_url: https://ftp.ebi.ac.uk/pub/databases/spot/ols/ publications: - id: PMID:39913645 preferred: true repository: https://github.com/EBISPOT/ols4 synonyms: - OLS - OLS4 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: contact@omabrowser.org - contact_type: url value: https://omabrowser.org/contact/ id: sib label: OMA Team - SIB Swiss Institute of Bioinformatics - category: Individual contact_details: - contact_type: email value: adrian.altenhoff@inf.ethz.ch - contact_type: url value: https://omabrowser.org/oma/team/ label: Adrian Altenhoff creation_date: '2025-05-07T00:00:00Z' description: OMA (Orthologous MAtrix) is a database of orthologous genes among multiple species, providing a systematic classification of orthologs across complete genomes. domains: - biological systems - organisms homepage_url: https://omabrowser.org/ id: oma last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: OMA products: - category: GraphicalInterface description: Web interface for exploring OMA data id: oma.site is_public: true name: OMA Browser original_source: - oma product_url: https://omabrowser.org/oma/ secondary_source: - oma - category: ProgrammingInterface description: RESTful API for accessing OMA data id: oma.api.rest is_public: true name: OMA REST API original_source: - oma product_url: https://omabrowser.org/api/ secondary_source: - oma - category: ProgrammingInterface description: SPARQL endpoint for accessing OMA data id: oma.api.sparql is_public: true name: OMA SPARQL original_source: - oma product_url: https://sparql.omabrowser.org/lode/sparql secondary_source: - oma - category: Product compression: gzip description: OMA orthology groups in plain text format id: oma.groups.txt name: OMA Groups (Text) original_source: - oma product_url: https://omabrowser.org/oma/current/OmaGroups.txt.gz secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-03_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-12-15_ HTTP 502 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: OMA orthology groups in OrthoXML format format: xml id: oma.groups.orthoxml name: OMA Groups (OrthoXML) original_source: - oma product_url: https://omabrowser.org/oma/current/OmaGroups.orthoxml secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-12-15_ HTTP 502 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Hierarchical Orthologous Groups (HOGs) in OrthoXML format format: xml id: oma.hogs.orthoxml name: OMA HOGs (OrthoXML) original_source: - oma product_url: https://omabrowser.org/oma/current/OmaHOGs.orthoxml secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-03_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-12-15_ HTTP 502 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product compression: gzip description: Pairwise orthologs in tab-separated text format format: tsv id: oma.pairs.txt name: OMA Pairwise Orthologs original_source: - oma product_url: https://omabrowser.org/oma/current/OrthologousPairs.txt.gz secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-03_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-12-15_ HTTP 502 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product compression: gzip description: Protein sequences from all genomes in FASTA format format: fasta id: oma.proteins.fasta name: OMA Protein Sequences original_source: - oma product_url: https://omabrowser.org/oma/current/oma-proteins.fa.gz secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-03_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-02_ HTTP 502 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product compression: gzip description: cDNA sequences for Eukaryotic genomes in FASTA format format: fasta id: oma.cdna.eukaryotes.fasta name: OMA cDNA Sequences (Eukaryotes) original_source: - oma product_url: https://omabrowser.org/oma/current/oma-eukaryotes.cdna.fa.gz secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-03_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-13_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product compression: gzip description: cDNA sequences for Prokaryotic genomes in FASTA format format: fasta id: oma.cdna.prokaryotes.fasta name: OMA cDNA Sequences (Prokaryotes) original_source: - oma product_url: https://omabrowser.org/oma/current/oma-prokaryotes.cdna.fa.gz secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-03_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-13_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: OMA Browser database in HDF5 format id: oma.hdf5 name: OMA Browser Database (HDF5) original_source: - oma product_url: https://omabrowser.org/oma/current/OmaServer.h5 secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-03_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-13_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product compression: gzip description: OMA data in RDF format (Turtle syntax) format: ttl id: oma.rdf name: OMA RDF Data original_source: - oma product_url: https://omabrowser.org/oma/current/OMA.ttl.gz secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-03_ HTTP 502 error when accessing file - File was not able to be retrieved when checked on 2025-12-13_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: MappingProduct compression: gzip description: Mapping of OMA identifiers to UniProt accession numbers format: tsv id: oma.mapping.uniprot name: OMA to UniProt Mapping original_source: - oma - uniprot product_url: https://omabrowser.org/oma/current/oma-uniprot.txt.gz secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-03_ HTTP 502 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.ebi.ac.uk/ id: ebi label: EMBL-EBI creation_date: '2025-10-30T00:00:00Z' description: OmicsDI (Omics Discovery Index) is an integrated resource for omics datasets across multiple repositories, providing a unified search interface for genomics, proteomics, metabolomics, and transcriptomics data. domains: - genomics - proteomics homepage_url: https://www.omicsdi.org/ id: omicsdi infores_id: omicsdi last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: OmicsDI products: - category: GraphicalInterface description: Web portal for searching and browsing integrated omics dataset metadata across repositories. format: http id: omicsdi.portal name: OmicsDI Portal original_source: - omicsdi product_url: https://www.omicsdi.org/ - category: ProgrammingInterface connection_url: https://www.omicsdi.org/ws description: Swagger-documented web service for programmatic querying of OmicsDI dataset metadata. format: http id: omicsdi.api is_public: true name: OmicsDI API original_source: - omicsdi product_url: https://www.omicsdi.org/ws/swagger-ui/index.html publications: - doi: 10.1038/nbt.3790 id: doi:10.1038/nbt.3790 journal: Nature Biotechnology preferred: true title: Discovering and linking public omics data sets using the Omics Discovery Index year: '2017' synonyms: - OmicsDI - Omics Discovery Index - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.omim.org/contact label: OMIM (Johns Hopkins University) creation_date: '2025-06-04T00:00:00Z' description: OMIM (Online Mendelian Inheritance in Man) is a continuously updated, expert-curated catalog of human genes and genetic disorders, focusing on genotype–phenotype relationships and the molecular basis of disease. domains: - biomedical - clinical - genomics homepage_url: https://www.omim.org/ id: omim infores_id: omim last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://www.omim.org/help/agreement label: OMIM Use Agreement (research/educational use; license required for commercial/redistribution) name: OMIM products: - category: GraphicalInterface description: Web interface for browsing and searching OMIM entries format: http id: omim.web name: OMIM Website original_source: - omim product_url: https://www.omim.org/ - category: ProgrammingInterface description: REST-based API for programmatic access to OMIM data (registration and API key required) format: http id: omim.api is_public: false name: OMIM API original_source: - omim product_url: https://www.omim.org/api - category: MappingProduct description: Public mapping of MIM numbers to NCBI Gene IDs, Ensembl Gene IDs, and HGNC symbols format: tsv id: omim.mim2gene name: OMIM mim2gene.txt original_source: - omim - ncbigene - ensembl - hgnc product_file_size: 974440 product_url: https://www.omim.org/static/omim/data/mim2gene.txt - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: MappingProduct description: MIM to Gene and MedGen mapping data connecting genetic disorders to genes format: tsv id: ncbigene.mim2gene_medgen name: MIM to Gene MedGen Mapping original_source: - ncbigene - medgen - omim product_file_size: 954971 product_url: https://ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg - category: Product description: Integrated gene annotation data aggregated from HGNC, OMIM, Ensembl, NCBI Gene, UniProt and other genomic databases format: http id: genecards.gene.annotations name: GeneCards Gene Annotations original_source: - hgnc - omim - ensembl - ncbigene - uniprot - refseq product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Disease association data integrated from OMIM, MalaCards, ClinVar, Orphanet, DisGeNET and other disease databases format: http id: genecards.disease.associations name: GeneCards Disease Associations original_source: - omim - malacards - clinvar - orphanet - disgenet product_url: https://www.genecards.org/ warnings: - 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unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - 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This resource is part of the NCATS Translator infrastructure and supports literature-based discovery and evidence aggregation for knowledge graph construction. domains: - literature - biomedical - translational homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/OmniCorp id: omnicorp infores_id: omnicorp last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: OmniCorp products: - category: Product description: Co-occurrence data from PubMed abstracts format: mixed id: omnicorp.cooccurrence name: OmniCorp Co-occurrence Data original_source: - pubmed product_url: https://github.com/NCATSTranslator/Translator-All/wiki/OmniCorp secondary_source: - omnicorp - category: ProgrammingInterface description: API access to OmniCorp co-occurrence data format: http id: omnicorp.api name: OmniCorp API original_source: - pubmed product_url: https://github.com/NCATSTranslator/Translator-All/wiki/OmniCorp secondary_source: - omnicorp synonyms: - OmniCorp tags: - translator - activity_status: active category: Aggregator collection: - ber contacts: - category: Organization contact_details: - contact_type: email value: omnipathdb@gmail.com - contact_type: url value: https://omnipathdb.org/ label: OmniPath Development Team creation_date: '2025-07-08T00:00:00Z' description: OmniPath is a comprehensive prior knowledge resource that integrates molecular interactions and biological pathway information from over 100 original databases and resources. It provides unified access to protein-protein interactions, gene regulatory interactions, enzyme-PTM relationships, protein complexes, protein annotations, and intercellular communication data through multiple interfaces including web services, R/Bioconductor packages, Python clients, and Cytoscape plugins. domains: - systems biology - biological systems - proteomics - pathways homepage_url: https://omnipathdb.org/ id: omnipath last_modified_date: '2025-09-27T00:00:00Z' layout: resource_detail name: OmniPath products: - category: ProgrammingInterface description: Web service API providing programmatic access to OmniPath molecular interaction networks, annotations, and intercellular communication data format: json id: omnipath.webservice name: OmniPath Web Service original_source: - omnipath product_url: https://omnipathdb.org/queries - category: ProgrammingInterface description: R/Bioconductor package (OmnipathR) for accessing and analyzing OmniPath data within the R statistical computing environment format: mixed id: omnipath.r_package name: OmnipathR Package original_source: - omnipath product_url: https://bioconductor.org/packages/release/bioc/html/OmnipathR.html - category: ProgrammingInterface description: Python client library providing programmatic access to OmniPath databases for Python-based analysis workflows format: python id: omnipath.python_client name: OmniPath Python Client original_source: - omnipath product_url: https://pypi.org/project/omnipath/ - category: ProcessProduct description: Cytoscape plugin for importing and visualizing OmniPath network data within the Cytoscape network analysis platform format: java id: omnipath.cytoscape_plugin name: OmniPath Cytoscape Plugin original_source: - omnipath product_url: https://apps.cytoscape.org/apps/omnipath - category: GraphicalInterface description: Interactive database explorer for browsing OmniPath data integrated from 160+ resources format: http id: omnipath.explorer name: OmniPath Explorer original_source: - omnipath product_url: https://explore.omnipathdb.org/ - category: ProcessProduct description: Python package (pypath) for building custom OmniPath databases and accessing the OmniPath infrastructure format: python id: omnipath.pypath name: PyPath Database Builder original_source: - omnipath product_url: https://pypi.org/project/pypath-omnipath/ - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - authors: - Dénes Türei - Tamás Korcsmáros - Julio Saez-Rodriguez doi: 10.1038/nmeth.4077 id: doi:10.1038/nmeth.4077 title: 'OmniPath: guidelines and gateway for literature-curated signaling pathway resources' year: '2016' - authors: - Dénes Türei - Alberto Valdeolivas - Lejla Gul - Nicolàs Palacio-Escat - Michal Klein - Olga Ivanova - Márton Ölbei - Attila Gábor - Fabian Theis - Dezső Módos - Tamás Korcsmáros - Julio Saez-Rodriguez doi: 10.15252/msb.20209923 id: doi:10.15252/msb.20209923 title: Integrated intra- and intercellular signaling knowledge for multicellular omics analysis year: '2021' repository: https://github.com/saezlab/pypath - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-06-25T00:00:00Z' description: An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. 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Hu orcid: 0000-0001-9016-2684 creation_date: '2025-09-29T00:00:00Z' description: An ontology of phenotypes covering microbes domains: - biological systems homepage_url: http://microbialphenotypes.org id: omp last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Microbial Phenotypes products: - category: OntologyProduct description: Ontology of Microbial Phenotypes in OWL format format: owl id: omp.owl name: omp.owl product_file_size: 222487 product_url: http://purl.obolibrary.org/obo/omp.owl - category: OntologyProduct description: Ontology of Microbial Phenotypes in OBO format format: obo id: omp.obo name: omp.obo product_file_size: 124064 product_url: http://purl.obolibrary.org/obo/omp.obo repository: https://github.com/microbialphenotypes/OMP-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: hoganwr@gmail.com - contact_type: github value: hoganwr label: Bill Hogan orcid: 0000-0002-9881-1017 creation_date: '2025-07-10T00:00:00Z' description: The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. domains: - biomedical homepage_url: https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview id: omrse last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology for Modeling and Representation of Social Entities products: - category: OntologyProduct description: Ontology for Modeling and Representation of Social Entities in OWL format format: owl id: omrse.owl name: omrse.owl product_file_size: 124258 product_url: http://purl.obolibrary.org/obo/omrse.owl repository: https://github.com/mcwdsi/OMRSE taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: contact@oncokb.org - contact_type: url value: https://www.oncokb.org/ label: OncoKB Team creation_date: '2025-08-12T00:00:00Z' description: OncoKB is a precision oncology knowledge base developed at Memorial Sloan Kettering Cancer Center that contains biological and clinical information about genomic alterations in cancer. It provides alteration- and tumor type-specific therapeutic implications classified using the OncoKB Levels of Evidence system, which assigns clinical actionability to individual mutational events. The platform integrates data from 945 genes, 7967 alterations, 143 cancer types, and 156 drugs with FDA-recognized human genetic variant database status. domains: - precision medicine - clinical - genomics - biomedical - health homepage_url: https://www.oncokb.org/ id: oncokb last_modified_date: '2025-09-24T00:00:00Z' layout: resource_detail name: OncoKB products: - category: GraphicalInterface description: Interactive web interface for exploring OncoKB precision oncology knowledge base, including gene and variant information, therapeutic implications, and evidence levels format: http id: oncokb.web_interface name: OncoKB Web Interface original_source: - oncokb product_url: https://www.oncokb.org/ - category: ProgrammingInterface description: RESTful web API providing programmatic access to OncoKB data including gene annotations, variant classifications, therapeutic implications, and evidence levels format: json id: oncokb.api name: OncoKB Web API original_source: - oncokb product_url: https://www.oncokb.org/swagger-ui/index.html - category: ProcessProduct description: Python-based annotation tool for annotating MAF files, copy number alterations, fusions, and structural variants with OncoKB therapeutic and biological annotations format: python id: oncokb.annotator name: OncoKB Annotator original_source: - oncokb product_url: https://github.com/oncokb/oncokb-annotator - category: GraphicalInterface description: Demo version of OncoKB containing full data for BRAF, TP53, and ROS1 genes for evaluation purposes before licensing format: http id: oncokb.demo name: OncoKB Demo original_source: - oncokb product_url: https://demo.oncokb.org/ - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 publications: - authors: - Debyani Chakravarty - Jianjiong Gao - Sarah M. Phillips - Ritika Kundra - Hongxin Zhang - Jiaojiao Wang - Julia E. Rudolph - Ramdan Yaeger - Tara Soumerai - Ahmet H. Nissan - Matthew T. Chang - Sarah Adalsteinsson - Barry S. Taylor - Gregory J. Riely - Marc Ladanyi - David B. Solit - Nikolaus Schultz doi: 10.1200/PO.17.00011 id: doi:10.1200/PO.17.00011 title: 'OncoKB: A Precision Oncology Knowledge Base' year: '2017' - authors: - Samuel P. Suehnholz - Ritika Kundra - Hongxin Zhang - Jianjiong Gao - Angelica M. Camargo - Isabell Schulze - Matthew T. Chang - Sarah Adalsteinsson - Brie Kezlarian - Kendra A. Famiglietti - Tara Soumerai - Barry S. Taylor - Gregory J. Riely - Marc Ladanyi - David B. Solit - Nikolaus Schultz - Debyani Chakravarty doi: 10.1158/2159-8290.CD-23-0467 id: doi:10.1158/2159-8290.CD-23-0467 title: Quantifying the Expanding Landscape of Clinical Actionability for Patients with Cancer year: '2023' repository: https://github.com/oncokb taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: chenyangnutrition@gmail.com - contact_type: github value: cyang0128 label: Chen Yang orcid: 0000-0001-9202-5309 creation_date: '2025-09-29T00:00:00Z' description: An ontology to standardize research output of nutritional epidemiologic studies. domains: - chemistry and biochemistry homepage_url: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies id: one last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology for Nutritional Epidemiology products: - category: OntologyProduct description: Ontology for Nutritional Epidemiology in OWL format format: owl id: one.owl name: one.owl product_file_size: 9258 product_url: http://purl.obolibrary.org/obo/one.owl repository: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: francesco.vitali@ibba.cnr.it - contact_type: github value: FrancescoVit label: Francesco Vitali orcid: 0000-0001-9125-4337 creation_date: '2025-09-29T00:00:00Z' description: An ontology for description of concepts in the nutritional studies domain. domains: - chemistry and biochemistry homepage_url: https://github.com/enpadasi/Ontology-for-Nutritional-Studies id: ons last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology for Nutritional Studies products: - category: OntologyProduct description: ONS latest release format: owl id: ons.owl name: ONS latest release product_file_size: 215578 product_url: http://purl.obolibrary.org/obo/ons.owl repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: fortuna@ebd.csic.es - contact_type: github value: miguelfortuna label: Miguel A. Fortuna orcid: 0000-0002-8374-1941 creation_date: '2025-09-29T00:00:00Z' description: OntoAvida develops an integrated vocabulary for the description of the most widely-used computational approach for studying evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment). domains: - biological systems homepage_url: https://gitlab.com/fortunalab/ontoavida id: ontoavida last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: 'OntoAvida: ontology for Avida digital evolution platform' products: - category: OntologyProduct description: The main ontology in OWL format: owl id: ontoavida.owl name: OWL product_file_size: 472853 product_url: http://purl.obolibrary.org/obo/ontoavida.owl - category: OntologyProduct description: Equivalent to ontoavida.owl, in obo format format: obo id: ontoavida.obo name: OBO product_file_size: 240082 product_url: http://purl.obolibrary.org/obo/ontoavida.obo repository: https://gitlab.com/fortunalab/ontoavida - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual label: Jim Balhoff creation_date: '2025-03-09T00:00:00Z' description: A Translator Knowledge Provider dedicated to ontology-based services. domains: - other evaluation_page: resource/ontology-kp/ontology-kp_eval_automated.html id: ontology-kp last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Ontology KP products: - category: DocumentationProduct description: Translator wiki documentation for the SRI Ontology Service and Ontology KP usage. format: http id: ontology-kp.docs name: Ontology KP Documentation original_source: - ontology-kp product_url: https://github.com/NCATSTranslator/Translator-All/wiki/SRI-Ontology-Service - category: ProcessProduct description: UberGraph source repository used to support ontology reasoning and integrated ontology queries. format: http id: ontology-kp.ubergraph name: Ontology KP UberGraph Source original_source: - ontology-kp product_url: https://github.com/INCATools/ubergraph - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: fernanda.farinelli@gmail.com - contact_type: github value: FernandaFarinelli label: Fernanda Farinelli orcid: 0000-0003-2338-8872 creation_date: '2025-09-29T00:00:00Z' description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. domains: - biomedical homepage_url: https://ontoneo.com/ id: ontoneo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Obstetric and Neonatal Ontology products: - category: OntologyProduct description: The full version of ONTONEO in OWL format format: owl id: ontoneo.owl name: ONTONEO product_file_size: 238873 product_url: http://purl.obolibrary.org/obo/ontoneo.owl repository: https://github.com/ontoneo-project/Ontoneo - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mbrochhausen@gmail.com - contact_type: github value: mbrochhausen label: Mathias Brochhausen orcid: 0000-0003-1834-3856 creation_date: '2025-09-29T00:00:00Z' description: An ontology built for representating the organizational components of trauma centers and trauma systems. domains: - biomedical homepage_url: https://github.com/OOSTT/OOSTT id: oostt last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Organizational Structures of Trauma centers and Trauma systems products: - category: OntologyProduct description: Ontology of Organizational Structures of Trauma centers and Trauma systems in OWL format format: owl id: oostt.owl name: oostt.owl product_file_size: 78721 product_url: http://purl.obolibrary.org/obo/oostt.owl repository: https://github.com/OOSTT/OOSTT - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://tree.opentreeoflife.org/ id: open-tree-of-life-collaboration label: Open Tree of Life Collaboration creation_date: '2025-12-17T00:00:00Z' description: Open Tree of Life (OToL) is a comprehensive, collaborative online phylogenetic tree synthesizing published evolutionary estimates with taxonomic data. It combines phylogenetic data from 1,216 published papers with 10 source taxonomies to construct a dynamic tree of life with 2.4 million tips representing species and infraspecific taxa. domains: [] homepage_url: https://tree.opentreeoflife.org/ id: open-tree-of-life infores_id: open-tree-of-life last_modified_date: '2025-12-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 Public Domain logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Open Tree of Life products: - category: GraphicalInterface description: Interactive zoomable phylogenetic tree browser enabling exploration of taxonomic relationships and phylogenetic structure across 2.4 million tips format: http id: otol.tree-browser name: Open Tree of Life Browser product_url: https://tree.opentreeoflife.org/tree - category: ProgrammingInterface description: RESTful APIs providing programmatic access to synthetic tree, taxonomy, and taxonomic name resolution services with support for MRCA queries and subtree extraction format: http id: otol.api is_public: true name: Open Tree of Life APIs product_url: https://opentreeoflife.github.io/develop/api - category: ProgrammingInterface description: Taxonomic Name Resolution Service (TNRS) providing exact and fuzzy matching of taxonomic names to Open Tree Taxonomy with context-based disambiguation format: http id: otol.tnrs is_public: true name: Taxonomic Name Resolution Service (TNRS) product_url: https://tree.opentreeoflife.org/tnrs - category: Product description: Complete phylesystem repository containing 4,500+ curated phylogenetic studies in NexSON JSON format with full version control history id: otol.phylesystem name: Phylesystem Data Repository product_url: https://github.com/opentreeoflife/phylesystem - category: Product description: Preprocessed source trees and taxonomy files available for bulk download in Newick, Nexus, and JSON formats id: otol.bulk-download name: Open Tree of Life Bulk Downloads product_url: https://files.opentreeoflife.org/preprocessed/v3.0/ - category: DocumentationProduct description: API reference, developer guides, and integration documentation for accessing Open Tree of Life data programmatically format: http id: otol.documentation is_public: true name: Open Tree of Life Developer Documentation product_url: https://opentreeoflife.github.io/develop publications: - authors: - Hinchliff CE - Smith SA - Allman JF - Burleigh JG - Chaudhary R - Cogdell-Waters LM - Crandall KA - Deng J - Drew BT - Gazis R - Gude K - Hibbett DS - Katz LA - Laughinghouse HD - McTavish EJ - Midford PE - Oliver PM - Olds BS - Soltis DE - Soltis PS doi: 10.1073/pnas.1423041112 id: doi:10.1073/pnas.1423041112 journal: Proceedings of the National Academy of Sciences preferred: true title: Synthesis of phylogeny and taxonomy into a comprehensive tree of life year: '2015' - authors: - McTavish EJ - Cranston KA - Domman D - Sindbäck J - Freund J - Steele PR - Gude K - Midford PE doi: 10.1093/bioinformatics/btv128 id: doi:10.1093/bioinformatics/btv128 journal: Bioinformatics title: 'Phylesystem: a git-based data store for community curated phylogenetic estimates' year: '2015' - authors: - Sanchez-Reyes LL - Mishler BD - Merow C - Enquist BJ doi: 10.1093/sysbio/syab038 id: doi:10.1093/sysbio/syab038 journal: Systematic Biology title: 'OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life' year: '2021' - authors: - Michonneau F - Brown JW - Winter DJ doi: 10.1111/2041-210X.12593 id: doi:10.1111/2041-210X.12593 journal: Methods in Ecology and Evolution title: 'rotl: an R package to interact with the Open Tree of Life data' year: '2016' repository: https://github.com/opentreeoflife taxon: - NCBITaxon:1 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://openbiodiv.net/ id: pensoft label: Pensoft Publishers creation_date: '2025-12-17T00:00:00Z' description: OpenBiodiv is an open-access biodiversity knowledge graph that extracts, integrates, and provides semantic access to linked open biodiversity data from scientific literature and established taxonomic backbones. It converts narrative biodiversity information into computable semantic form and maintains a comprehensive knowledge management system for biodiversity science. domains: - literature evaluation_page: resource/openbiodiv/openbiodiv_eval_automated.html homepage_url: https://openbiodiv.net/ id: openbiodiv infores_id: openbiodiv last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: OpenBiodiv products: - category: GraphicalInterface description: Interactive web portal for searching, exploring, and discovering biodiversity knowledge graph data including taxonomic treatments, species descriptions, and literature-extracted information format: http id: openbiodiv.portal is_public: true name: OpenBiodiv Web Portal product_url: https://openbiodiv.net/ - category: ProgrammingInterface description: SPARQL endpoint for complex semantic queries across the biodiversity knowledge graph, enabling advanced queries combining taxonomic, literature, specimen, and ecological data format: http id: openbiodiv.sparql is_public: true name: OpenBiodiv SPARQL Endpoint product_url: http://graph.openbiodiv.net/ - category: ProgrammingInterface description: RESTful API for programmatic access to OpenBiodiv biodiversity data with Swagger API documentation for easy integration format: http id: openbiodiv.api is_public: true name: OpenBiodiv REST API product_url: https://graph.openbiodiv.net/webapi - category: OntologyProduct description: OpenBioDiv-O, the OpenBiodiv Ontology format: ttl id: openbiodiv.ontology.ttl is_public: true name: OpenBioDiv-O original_source: - skos - proton - fabio - doco - openbiodiv product_file_size: 8176 product_url: https://raw.githubusercontent.com/pensoft/OpenBiodiv/refs/heads/master/ontology/openbiodiv-ontology-latest.ttl secondary_source: - openbiodiv - category: DocumentationProduct description: Guide to OpenBioDiv-O, the OpenBiodiv Ontology format: http id: openbiodiv.ontology.guide is_public: true name: OpenBioDiv-O Guide product_url: https://openbiodiv.net/ontologies publications: - authors: - Penev L - Dimitrova M - Senderov V - Zhelezov G - Georgiev T - Stoev P - Simov K doi: 10.3390/publications7020038 id: doi:10.3390/publications7020038 journal: Publications preferred: true title: 'OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science' year: '2019' - authors: - Senderov V - Simov K - Georgiev T - Stoev P - Penev L doi: 10.1186/s13326-017-0174-5 id: doi:10.1186/s13326-017-0174-5 journal: Journal of Biomedical Semantics title: 'OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system' year: '2018' repository: https://github.com/pensoft/OpenBiodiv taxon: - NCBITaxon:1 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://openpredict.semanticscience.org/ label: Institute for Data Science at Maastricht University creation_date: '2025-11-05T00:00:00Z' description: OpenPredict is an NCATS Translator Knowledge Provider that provides machine learning-based predictions for drug-target interactions and drug-disease associations to support drug repurposing. OpenPredict integrates multiple biomedical knowledge graphs and applies various machine learning algorithms to predict potential therapeutic uses for existing drugs. The service offers predictions with confidence scores and provides evidence trails linking drugs to diseases through intermediate biological entities like targets and pathways. domains: - drug discovery - pharmacology - precision medicine - translational - biomedical homepage_url: https://openpredict.semanticscience.org/ id: openpredict infores_id: openpredict last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: OpenPredict products: - category: ProgrammingInterface description: TRAPI-compliant API for drug repurposing predictions format: http id: openpredict.api name: OpenPredict API original_source: - openpredict product_url: https://openpredict.semanticscience.org/ - category: GraphicalInterface description: Web interface for exploring drug repurposing predictions format: http id: openpredict.ui name: OpenPredict Web Interface original_source: - openpredict product_url: https://openpredict.semanticscience.org/ - category: Product description: Pre-computed drug-disease predictions format: mixed id: openpredict.predictions name: OpenPredict Prediction Data original_source: - openpredict product_url: https://openpredict.semanticscience.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 405 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 405 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 405 error when accessing file' publications: - id: https://doi.org/10.1093/bioinformatics/btab540 repository: https://github.com/MaastrichtU-IDS/translator-openpredict synonyms: - OpenPredict - OpenPredict API tags: - translator taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: contact@opentargets.org - contact_type: github value: opentargets - contact_type: url value: https://www.opentargets.org/contact label: Open Targets creation_date: '2025-05-29T00:00:00Z' description: Open Targets is a collaborative effort to systematically identify and prioritise the best targets to safely and effectively treat rare and common diseases. domains: - health - biomedical evaluation_page: resource/opentargets/opentargets_eval_automated.html homepage_url: https://www.opentargets.org/ id: opentargets last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: Open Targets products: - category: GraphicalInterface description: The Open Targets Platform integrates and visualizes public data on target-disease associations to assist in drug target identification and prioritization. format: http id: opentargets.platform name: Open Targets Platform product_url: https://platform.opentargets.org/ repository: https://github.com/opentargets/platform - category: ProgrammingInterface description: GraphQL API for accessing Open Targets Platform data programmatically. id: opentargets.api.graphql is_public: true name: Open Targets Platform GraphQL API product_url: https://api.platform.opentargets.org/api/v4/graphql - category: ProgrammingInterface description: REST API for accessing Open Targets Platform data programmatically. id: opentargets.api.rest is_public: true name: Open Targets Platform REST API product_url: https://api.platform.opentargets.org/api/v4/rest - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb publications: - authors: - Diederik S. Laman Trip - Marc van Oostrum - Danish Memon - Fabian Frommelt - Delora Baptista - Kalpana Panneerselvam - Glyn Bradley - Luana Licata - Henning Hermjakob - Sandra Orchard - Gosia Trynka - Ellen M. McDonagh - Andrea Fossati - Ruedi Aebersold - Matthias Gstaiger - Bernd Wollscheid - Pedro Beltrao doi: doi:10.1038/s41587-025-02659-z id: https://doi.org/10.1038/s41587-025-02659-z journal: Nature Biotechnology preferred: true title: A tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes year: '2025' - authors: - Cruz-Castillo, C. - Fumis, L. - Mehta, C. - Martinez-Osorio, R.E. - Roldan-Romero, J.M. - Cornu, H. - Uniyal, P. - Solano-Roman, A. - Carmona, M. - Ochoa, D. - McDonagh, E.M. - Buniello, A. doi: doi:10.1093/bioinformatics/btaf070 id: https://doi.org/10.1093/bioinformatics/btaf070 journal: Bioinformatics title: Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence year: '2025' repository: https://github.com/opentargets taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: zhengj2007@gmail.com - contact_type: github value: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 creation_date: '2025-09-29T00:00:00Z' description: A reference ontology for parasite life cycle stages. domains: - biological systems homepage_url: https://github.com/OPL-ontology/OPL id: opl last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology for Parasite LifeCycle products: - category: OntologyProduct description: Ontology for Parasite LifeCycle in OWL format format: owl id: opl.owl name: opl.owl product_file_size: 75624 product_url: http://purl.obolibrary.org/obo/opl.owl repository: https://github.com/OPL-ontology/OPL - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: yongqunh@med.umich.edu - contact_type: github value: yongqunh label: Yongqun Oliver He orcid: 0000-0001-9189-9661 creation_date: '2025-09-29T00:00:00Z' description: The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions. domains: - biomedical homepage_url: https://github.com/OPMI/opmi id: opmi last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Precision Medicine and Investigation products: - category: OntologyProduct description: Ontology of Precision Medicine and Investigation in OWL format format: owl id: opmi.owl name: opmi.owl product_file_size: 394555 product_url: http://purl.obolibrary.org/obo/opmi.owl repository: https://github.com/OPMI/opmi - activity_status: active category: DataSource contacts: - category: Organization label: ORCID creation_date: '2025-03-09T00:00:00Z' description: ORCID is a free, unique, persistent identifier (PID) for individuals to use as they engage in research, scholarship, and innovation activities. domains: - other homepage_url: https://orcid.org/ id: orcid last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: ORCID products: - category: GraphicalInterface description: Web interface for searching ORCID records and viewing researcher profiles. format: http id: orcid.portal name: ORCID Registry Portal original_source: - orcid product_url: https://orcid.org/ - category: ProgrammingInterface connection_url: https://pub.orcid.org/v3.0/ description: Public API documentation and access information for ORCID record retrieval. format: http id: orcid.api is_public: true name: ORCID Public API original_source: - orcid product_url: https://info.orcid.org/what-is-orcid/services/public-api/ publications: - doi: 10.1087/20120404 id: doi:10.1087/20120404 journal: Learned Publishing preferred: true title: 'ORCID: a system to uniquely identify researchers' year: '2012' repository: https://github.com/ORCID - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: contact.orphanet@inserm.fr - contact_type: url value: https://www.orpha.net/ label: Orphanet - category: Organization contact_details: - contact_type: url value: https://www.inserm.fr/ label: INSERM creation_date: '2025-06-04T00:00:00Z' description: The Orphanet Rare Disease Ontology (ORDO) is an open-access ontology developed from the Orphanet information system, enabling complex queries of rare diseases and their epidemiological data (age of onset, prevalence, mode of inheritance) and gene-disorder functional relationships. domains: - biomedical - health - clinical - genomics - phenotype homepage_url: https://www.orphadata.com/ordo/ id: ordo infores_id: ordo last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 (Creative Commons Attribution 4.0 International) logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Orphanet Rare Disease Ontology (ORDO) products: - category: DataModelProduct description: ORDO in OWL format in English (v4.7) format: owl id: ordo.owl name: ORDO OWL product_file_size: 49203440 product_url: https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.7.owl - category: ProgrammingInterface description: SPARQL endpoint for querying the ORDO ontology id: ordo.sparql name: ORDO SPARQL Endpoint product_url: https://www.orphadata.com/ordo-sparql-endpoint/ - category: DataModelProduct description: The Orphanet nomenclature pack provides ORPHAcodes (unique identifiers) for rare diseases, along with mappings to other terminologies, and is released annually in July. id: orphacode.nomenclature name: Orphanet Nomenclature Pack product_url: https://www.orphacode.org/pack-nomenclature/ warnings: [] - category: ProgrammingInterface description: API for accessing the Orphanet nomenclature pack data, allowing flexible implementation into various healthcare information systems. id: orphacode.api name: ORPHAcodes API product_url: https://api.orphacode.org/ - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://gitub.u-bordeaux.fr/erias/oregano label: ERIAS Team, University of Bordeaux creation_date: '2026-02-22T00:00:00Z' description: The OREGANO knowledge graph integrates free biomedical databases focused on drugs, proteins, genes, and diseases to support link prediction approaches for drug repositioning and drug-target relation discovery. domains: - pharmacology - drug discovery - biomedical homepage_url: https://gitub.u-bordeaux.fr/erias/oregano id: oregano last_modified_date: '2026-02-22T00:00:00Z' layout: resource_detail name: OREGANO products: - category: GraphProduct description: The OREGANO knowledge graph dataset integrating drug, protein, gene, and disease information for drug repositioning. id: oregano.graph name: OREGANO Knowledge Graph product_url: https://gitub.u-bordeaux.fr/erias/oregano/-/tree/master publications: - doi: doi:10.1038/s41597-023-02757-0 id: https://doi.org/10.1038/s41597-023-02757-0 journal: Scientific Data preferred: true title: 'OREGANO: a knowledge graph for biomedical relation prediction' year: '2023' repository: https://gitub.u-bordeaux.fr/erias/oregano/-/tree/master - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://orkg.org/about label: Open Research Knowledge Graph Team creation_date: '2026-03-11T00:00:00Z' description: The Open Research Knowledge Graph (ORKG) aims to describe research papers in a structured manner. It represents research papers and their contributions as structured, machine-readable descriptions that can be explored, compared, and reused through the ORKG portal and API. domains: - literature homepage_url: https://orkg.org/ id: orkg last_modified_date: '2026-03-11T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC BY-SA 4.0 logo: https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png name: Open Research Knowledge Graph products: - category: GraphicalInterface description: Web portal for browsing papers, creating structured research descriptions, and comparing research contributions in ORKG. format: http id: orkg.portal name: ORKG Web Portal original_source: - orkg product_url: https://orkg.org/ - category: ProgrammingInterface description: Public REST API for programmatic access to ORKG resources, comparisons, papers, and other structured scholarly content. format: http id: orkg.api is_public: true name: ORKG REST API original_source: - orkg product_url: https://orkg.org/api - category: DocumentationProduct description: Static reference documentation for the ORKG REST API published via GitLab Pages. format: http id: orkg.api-docs name: ORKG API Documentation original_source: - orkg.api product_url: http://tibhannover.gitlab.io/orkg/orkg-backend/api-doc/ - category: ProcessProduct description: Python package wrapping the ORKG API for programmatic access from Python workflows. format: python id: orkg.python name: ORKG Python Package original_source: - orkg.api product_url: https://pypi.org/project/orkg/ - category: DocumentationProduct description: Official ORKG documentation covering tutorials, reference material, and REST API model documentation. format: http id: orkg.docs name: ORKG Documentation original_source: - orkg product_url: https://docs.orkg.org/ - category: GraphicalInterface description: Virtuoso-based SPARQL query editor for querying ORKG RDF data. format: http id: orkg.triplestore name: ORKG Virtuoso Query Editor original_source: - orkg product_url: https://orkg.org/triplestore - category: GraphicalInterface description: Visual SPARQL editor for exploring ORKG data with query examples. format: http id: orkg.sparql name: ORKG Visual SPARQL Editor original_source: - orkg product_url: https://orkg.org/sparql/ - category: GraphProduct description: RDF dump of the Open Research Knowledge Graph distributed in N-Triples format. format: ntriples id: orkg.dump name: ORKG RDF Dump original_source: - orkg - wikidata - geonames - ncit - chebi - ncbitaxon - go - clo - omit - iao - uo - stato - obi product_file_size: 642902930 product_url: https://orkg.org/api/rdf/dump secondary_source: - orkg publications: - authors: - Mohamad Yaser Jaradeh - Allard Oelen - Kheir Eddine Farfar - Manuel Prinz - Jennifer D'Souza - Gábor Kismihók - Markus Stocker - Sören Auer doi: 10.1145/3360901.3364435 id: doi:10.1145/3360901.3364435 journal: Proceedings of the 10th International Conference on Knowledge Capture preferred: true title: Open Research Knowledge Graph year: '2019' repository: https://gitlab.com/TIBHannover/orkg/orkg-frontend/ synonyms: - ORKG - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: safisher@upenn.edu - contact_type: github value: safisher label: Stephen Fisher orcid: 0000-0001-8034-7685 creation_date: '2025-09-29T00:00:00Z' description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA. domains: - biomedical homepage_url: http://kim.bio.upenn.edu/software/ornaseq.shtml id: ornaseq last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of RNA Sequencing products: - category: OntologyProduct description: Ontology of RNA Sequencing in OWL format format: owl id: ornaseq.owl name: ornaseq.owl product_file_size: 27418 product_url: http://purl.obolibrary.org/obo/ornaseq.owl repository: https://github.com/safisher/ornaseq - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.orpha.net/en/institutions/get-in-touch/ label: Orphanet creation_date: '2025-07-10T00:00:00Z' description: Orphanet is a unique resource for information and data on rare diseases and orphan drugs, aimed at improving diagnosis, care, and treatment of patients with rare diseases. It maintains the Orphanet rare disease nomenclature (ORPHAcodes), which is essential for improving the visibility of rare diseases in health and research information systems. domains: - biomedical - clinical homepage_url: https://www.orpha.net/ id: orphanet infores_id: orphanet last_modified_date: '2025-07-10T00:00:00Z' layout: resource_detail name: Orphanet products: - category: Product description: XML dataset containing information on expert centers dedicated to the medical management and/or genetic counselling for rare diseases. format: xml id: orphanet.expertcenters name: Expert Centers Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on expert center networks for rare diseases. format: xml id: orphanet.expertcentersnetworks name: Expert Centers Networks Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on diagnostic tests and clinical laboratories for rare diseases. format: xml id: orphanet.diagnostictests name: Diagnostic Tests and Laboratories Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on patient organizations dedicated to rare diseases. format: xml id: orphanet.patientorganizations name: Patient Organizations Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on patient organization networks for rare diseases. format: xml id: orphanet.patientorganizationsnetworks name: Patient Organizations Networks Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on national research projects focused on rare diseases. format: xml id: orphanet.researchprojects name: National Research Projects Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on multinational research project networks for rare diseases. format: xml id: orphanet.researchprojectsnetworks name: Multinational Research Projects Networks Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on national clinical trials for rare diseases. format: xml id: orphanet.clinicaltrials name: National Clinical Trials Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on multinational clinical trial networks for rare diseases. format: xml id: orphanet.clinicaltrialsnetworks name: Multinational Clinical Trials Networks Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on patient registries for rare diseases. format: xml id: orphanet.patientregistries name: Patient Registries Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on patient registry networks for rare diseases. format: xml id: orphanet.patientregistriesnetworks name: Patient Registries Networks Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on biobanks dedicated to rare diseases. format: xml id: orphanet.biobanks name: Biobanks Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on biobank networks for rare diseases. format: xml id: orphanet.biobanksnetworks name: Biobanks Networks Dataset product_url: https://www.orphadata.com/expert-resources/ - category: Product description: XML dataset containing information on orphan drugs for rare diseases, including substances with orphan designation and/or marketing authorization. format: xml id: orphanet.orphandrugs name: Orphan Drugs Dataset product_url: https://www.orphadata.com/expert-resources/ - category: ProgrammingInterface description: APIs providing access to Orphanet scientific knowledge, ORPHAcodes, and expert resources data. id: orphanet.orphadataapi is_public: true name: Orphadata API product_url: https://www.orphadata.com/contact/ - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: Product description: Disease association data integrated from OMIM, MalaCards, ClinVar, Orphanet, DisGeNET and other disease databases format: http id: genecards.disease.associations name: GeneCards Disease Associations original_source: - omim - malacards - clinvar - orphanet - disgenet product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: History file tracking changes to Orphanet term mappings to CUIs format: txt id: medgen.ordo-history name: ORDO CUI History original_source: - medgen - orphanet product_file_size: 1130936 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/ORDO_CUI_history.txt repository: https://github.com/Orphanet taxon: - NCBITaxon:9606 version: July 2025 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: support@orthodb.org - contact_type: url value: https://www.orthodb.org/ id: sib label: Evgeny Zdobnov Lab - SIB Swiss Institute of Bioinformatics creation_date: '2025-05-07T00:00:00Z' description: OrthoDB is a comprehensive database of orthologous protein-coding genes across multiple species, providing evolutionary and functional annotations of orthologous groups. domains: - biological systems - organisms homepage_url: https://www.orthodb.org/ id: orthodb last_modified_date: '2025-12-07T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: OrthoDB products: - category: GraphicalInterface description: Web interface for exploring OrthoDB data id: orthodb.site is_public: true name: OrthoDB Web Interface original_source: - orthodb product_url: https://www.orthodb.org/ secondary_source: - orthodb - category: ProgrammingInterface description: SPARQL endpoint for querying OrthoDB data id: orthodb.api.sparql is_public: true name: OrthoDB SPARQL Endpoint original_source: - orthodb product_url: https://sparql.orthodb.org/ secondary_source: - orthodb - category: ProgrammingInterface description: RESTful API for programmatic access to OrthoDB data id: orthodb.api.rest is_public: true name: OrthoDB API original_source: - orthodb product_url: https://www.orthodb.org/api/ secondary_source: - orthodb - category: Product compression: gzip description: Tab-separated file with species information based on NCBI taxonomy format: tsv id: orthodb.species name: OrthoDB Species Data original_source: - orthodb product_file_size: 644375 product_url: https://data.orthodb.org/current/download/odb12v1_species.tab.gz secondary_source: - orthodb - category: Product compression: gzip description: Tab-separated file with information about orthologous groups format: tsv id: orthodb.ogs name: OrthoDB Orthologous Groups original_source: - orthodb product_file_size: 145213387 product_url: https://data.orthodb.org/current/download/odb12v1_OGs.tab.gz secondary_source: - orthodb - category: MappingProduct compression: gzip description: Tab-separated file mapping orthologous groups to genes format: tsv id: orthodb.og2genes name: OrthoDB OG to Genes Mapping original_source: - orthodb product_file_size: 4909850611 product_url: https://data.orthodb.org/current/download/odb12v1_OG2genes.tab.gz secondary_source: - orthodb - category: Product compression: gzip description: Tab-separated file with gene information and annotations format: tsv id: orthodb.genes name: OrthoDB Genes Data original_source: - orthodb product_file_size: 4785964374 product_url: https://data.orthodb.org/current/download/odb12v1_genes.tab.gz secondary_source: - orthodb - category: MappingProduct compression: gzip description: Tab-separated file with gene cross-references to other databases format: tsv id: orthodb.gene_xrefs name: OrthoDB Gene Cross-references original_source: - orthodb product_file_size: 4692134033 product_url: https://data.orthodb.org/current/download/odb12v1_gene_xrefs.tab.gz secondary_source: - orthodb - category: Product compression: gzip description: Tab-separated file with orthologous group functional annotations including GO, COG, and InterPro format: tsv id: orthodb.og_xrefs name: OrthoDB OG Functional Annotations original_source: - orthodb product_file_size: 349253826 product_url: https://data.orthodb.org/current/download/odb12v1_OG_xrefs.tab.gz secondary_source: - orthodb - category: Product compression: gzip description: FASTA-formatted amino acid sequences for all genes format: fasta id: orthodb.aa_fasta name: OrthoDB Protein Sequences original_source: - orthodb product_file_size: 38928290988 product_url: https://data.orthodb.org/current/download/odb12v1_aa_fasta.gz secondary_source: - orthodb - category: Product compression: gzip description: FASTA-formatted coding sequences for all genes format: fasta id: orthodb.cds_fasta name: OrthoDB CDS Sequences original_source: - orthodb product_file_size: 57560209301 product_url: https://data.orthodb.org/current/download/odb12v1_cds_fasta.gz secondary_source: - orthodb publications: - authors: - Kriventseva EV - Kuznetsov D - Tegenfeldt F - Manni M - Dias R - Simão FA - Zdobnov EM doi: doi:10.1093/nar/gky1053 id: doi:10.1093/nar/gky1053 title: OrthoDB v10 - sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs year: '2019' - authors: - Zdobnov EM - Tegenfeldt F - Kuznetsov D - Waterhouse RM - Simão FA - Ioannidis P - Seppey M - Loetscher A - Kriventseva EV doi: doi:10.1093/nar/gkw1119 id: doi:10.1093/nar/gkw1119 preferred: true title: OrthoDB v9.1 - cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs year: '2017' repository: https://github.com/zdobnov-lab/orthodb - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: yongqunh@med.umich.edu - contact_type: github value: yongqunh label: Yongqunh He orcid: 0000-0001-9189-9661 creation_date: '2025-09-29T00:00:00Z' description: A biomedical ontology in the domain of vaccine adverse events. domains: - biomedical homepage_url: http://www.violinet.org/ovae/ id: ovae last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Vaccine Adverse Events products: - category: OntologyProduct description: Ontology of Vaccine Adverse Events in OWL format format: owl id: ovae.owl name: ovae.owl product_file_size: 286812 product_url: http://purl.obolibrary.org/obo/ovae.owl repository: https://github.com/OVAE-Ontology/ovae - activity_status: active category: DataSource creation_date: '2025-11-19T00:00:00Z' description: OWLSim is a Java library and set of command-line tools for calculating semantic similarity between ontology classes and individuals. Part of the OWLTools suite, OWLSim implements various semantic similarity algorithms including Information Content-based methods for comparing phenotypes, diseases, and other ontology-based profiles. It is extensively used by the Monarch Initiative for phenotype matching, disease gene prioritization, and model organism comparison. OWLSim enables researchers to find similar disease profiles, identify candidate genes based on phenotypic similarity, and connect human diseases with model organism phenotypes using semantic similarity metrics across biological ontologies. domains: - biomedical - information technology - phenotype - genomics - systems biology homepage_url: https://github.com/owlcollab/owltools id: owlsim infores_id: owlsim last_modified_date: '2025-11-19T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/BSD-3-Clause label: BSD-3-Clause name: OWLSim Ontology Based Profile Matching products: - category: ProcessProduct description: Java library implementing semantic similarity algorithms for ontology-based profile matching id: owlsim.library name: OWLTools-Sim Library original_source: - owlsim product_url: https://github.com/owlcollab/owltools - category: ProcessProduct description: Command-line tools for batch processing of semantic similarity calculations id: owlsim.cli name: OWLSim Command-Line Tools original_source: - owlsim product_url: https://github.com/owlcollab/owltools/releases publications: - authors: - Köhler S - Bauer S - Horn D - Robinson PN doi: 10.1016/j.ajhg.2008.02.013 id: PMID:18371930 journal: American Journal of Human Genetics title: Walking the interactome for prioritization of candidate disease genes year: '2008' repository: https://github.com/owlcollab/owltools synonyms: - OWLSim taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: help@pankbase.org label: PanKBase - category: Organization contact_details: - contact_type: email value: hirncc@coh.org - contact_type: url value: https://hirnetwork.org/ label: NIDDK Human Islet Research Network (HIRN) creation_date: '2025-03-17T00:00:00Z' description: PanKbase is a comprehensive, centralized resource for the study of the human pancreas and diabetes. The PanKbase collective aims to integrate diverse type 1 diabetes (T1D) datasets with expert-curated knowledge in a centralized, open-source data hub. Part of the NIH/NIDDK Human Islet Research Network (HIRN). domains: - health - biological systems - genomics - clinical - precision medicine homepage_url: https://pankbase.org/ id: pankbase last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: PanKBase products: - category: GraphProduct description: Knowledge graph representation of human pancreas and diabetes data id: pankbase.graph name: PanKGraph original_source: - pankbase secondary_source: - pankbase - category: GraphicalInterface description: Graphical interface for exploring the PanKGraph format: http id: pankbase.graph.site is_public: true name: PanKGraph Site original_source: - pankbase product_url: https://pankgraph.org/ secondary_source: - pankbase - category: ProgrammingInterface description: Programming interface for exploring the PanKGraph format: http id: pankbase.graph.api is_neo4j: true is_public: true name: PanKGraph API original_source: - pankbase product_url: https://pankgraph.org/api secondary_source: - pankbase - category: ProgrammingInterface description: Programming interface for accessing contents of the PanKbase Data Portal format: http id: pankbase.api is_public: true name: PanKBase Data Library API original_source: - pankbase product_url: https://pankbase-db.github.io/pankbase-client-openapi-spec/ secondary_source: - pankbase repository: https://github.com/PanKbase-DB taxon: - NCBITaxon:9606 - activity_status: active category: Resource contacts: - category: Organization contact_details: - contact_type: email value: pantherfeedback@yahoo.com label: PANTHER creation_date: '2025-03-25T00:00:00Z' description: PANTHER is a Protein ANalysis THrough Evolutionary Relationships Classification System. The mission of the PANTHER knowledgebase is to support biomedical and other research by providing comprehensive information about the evolution of protein-coding gene families, particularly protein phylogeny, function and genetic variation impacting that function. domains: - biological systems homepage_url: https://www.pantherdb.org/ id: panther infores_id: panther last_modified_date: '2026-01-23T00:00:00Z' layout: resource_detail name: PANTHER products: - category: GraphProduct description: KGX Distribution of KG-Monarch edge_count: 15356321 format: kgx id: kg-monarch.graph name: KGX Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - 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This page was automatically generated because it was referenced by other resources. domains: - stub id: pathbank last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Pathbank products: - category: Product description: pathbank Nodes TSV format: tsv id: obo-db-ingest.pathbank.tsv license: id: https://opendatacommons.org/licenses/odbl/1-0/ label: ODbL-1.0 name: pathbank Nodes TSV original_source: - pathbank product_file_size: 727666 product_url: https://w3id.org/biopragmatics/resources/pathbank/pathbank.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://github.com/bio-ontology-research-group label: Bio-Ontology Research Group - category: Individual contact_details: - contact_type: github value: bio-ontology-research-group label: Bio-Ontology Research Group creation_date: '2025-05-28T00:00:00Z' description: PathoPhenoDB is a database of human pathogens, the diseases and phenotypes they elicit in human organisms, and information related to drug treatments and mechanisms of drug resistance. Specifically, PathoPhenoDB contains associations between pathogens and diseases, between pathogens and phenotypes, between drugs that are approved to treat particular pathogens, and it identifies genes or proteins within pathogens that can convey resistance to particular drugs. domains: - health - microbiology - pharmacology - drug discovery homepage_url: http://patho.phenomebrowser.net/ id: pathophenodb last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail name: PathoPhenoDB products: - category: GraphProduct description: PathoPhenoDB data containing pathogen-disease and pathogen-phenotype associations format: ntriples id: pathophenodb.data name: PathoPhenoDB RDF data, version 3 original_source: - pathophenodb product_file_size: 203836895 product_url: http://patho.phenomebrowser.net/media/downloads/patho_pheno_withsymbols.nt - category: GraphicalInterface description: Web interface for querying and browsing PathoPhenoDB data id: pathophenodb.web name: PathoPhenoDB Web Interface original_source: - pathophenodb product_url: http://patho.phenomebrowser.net/ - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke publications: - authors: - Şenay Kafkas - Marwa Abdelhakim - Yasmeen Hashish - Maxat Kulmanov - Marwa Abdellatif - Paul N. Schofield - Robert Hoehndorf id: http://doi.org/10.1038/s41597-019-0090-x journal: Scientific Data preferred: true title: PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research year: '2019' repository: https://github.com/bio-ontology-research-group/pathophenodb taxon: - NCBITaxon:9606 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.mskcc.org/ id: mskcc label: Memorial Sloan Kettering Cancer Center - category: Organization contact_details: - contact_type: url value: https://www.utoronto.ca/ id: utoronto label: University of Toronto creation_date: '2025-12-20T00:00:00Z' description: Pathway Commons is a centralized web resource that aggregates biological pathway and molecular interaction data from 22 major public databases into standardized BioPAX format. It provides 4,794 pathways and over 2.3 million molecular interactions accessible through multiple interfaces including web portal, REST API, and downloadable datasets, supporting systems biology research, pathway analysis, and network visualization. domains: - pathways - systems biology homepage_url: https://www.pathwaycommons.org/ id: pathway-commons infores_id: pathway-commons last_modified_date: '2025-12-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 (aggregated content) logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Pathway Commons products: - category: ProgrammingInterface description: RESTful web service API for programmatic access to Pathway Commons data with multiple query capabilities including search, pathway retrieval, and network analysis format: http id: pathway-commons.api is_public: true name: Pathway Commons REST API product_url: http://www.pathwaycommons.org/pc/webservice.do - category: GraphicalInterface description: Interactive web-based interface for browsing, searching, and visualizing biological pathways and molecular interactions format: http id: pathway-commons.web is_public: true name: Pathway Commons Web Interface product_url: https://www.pathwaycommons.org/ - category: Product description: Downloadable integrated pathway datasets in multiple standardized formats including BioPAX, SIF, GMT, and JSON-LD id: pathway-commons.downloads name: Pathway Commons Data Downloads product_url: https://www.pathwaycommons.org/ - category: Product description: Integrated BioPAX Level 3 unified model containing normalized pathway data, molecular interactions, and cross-database entity mappings from 22 sources id: pathway-commons.biopax name: Integrated BioPAX Model - category: Product description: Simple Interaction Format (SIF) network files representing binary pairwise molecular relationships for network analysis and visualization id: pathway-commons.sif name: SIF Network Format - category: Product description: Gene Matrix Transposed (GMT) format gene sets for pathway enrichment analysis with tools like GSEA (Gene Set Enrichment Analysis) id: pathway-commons.gmt name: GMT Gene Set Format - category: Product description: JSON-LD format for linked data web applications with semantic context and programmatic access to pathway information id: pathway-commons.jsonld name: JSON-LD Linked Data Format - category: DocumentationProduct description: Comprehensive API documentation, data format specifications, and tutorials for using Pathway Commons data and services format: http id: pathway-commons.documentation is_public: true name: Pathway Commons Documentation product_url: https://pathwaycommons.github.io/pcapi/ publications: - authors: - Rodchenkov I - Babur O - Luna A - et al. doi: 10.1093/nar/gkz946 id: doi:10.1093/nar/gkz946 journal: Nucleic Acids Research preferred: true title: 'Pathway Commons 2019 Update: integration, analysis and exploration of pathway data' year: '2020' - authors: - Cerami EG - Gross BE - Demir E - et al. doi: 10.1093/nar/gkq1016 id: doi:10.1093/nar/gkq1016 journal: Nucleic Acids Research title: Pathway Commons, a web resource for biological pathway data year: '2011' - authors: - Cerami E - Bader GD - Gross BE - Sander C doi: 10.1186/1471-2105-7-497 id: doi:10.1186/1471-2105-7-497 journal: BMC Bioinformatics title: 'cPath: open source software for collecting, storing, and querying biological pathways' year: '2006' repository: https://github.com/PathwayCommons synonyms: - Pathway Commons - PathwayCommons - PC taxon: - NCBITaxon:9606 - activity_status: active category: Resource contacts: - category: Organization contact_details: - contact_type: email value: david.wishart@ualberta.ca - contact_type: url value: http://www.wishartlab.com/ label: Wishart Lab creation_date: '2025-10-31T00:00:00Z' description: PathWhiz is a web-based pathway drawing and visualization tool designed for creating colorful, visually pleasing, and biologically accurate pathway diagrams that are machine-readable and interactive. PathWhiz supports a high level of biological detail including metabolites (with automated structure generation), protein complexes (with quaternary structures, covalent modifications, and cofactors), nucleic acids, membranes, subcellular structures, cells, tissues, and organs. PathWhiz has been used to generate over 700 pathway diagrams for popular databases including HMDB, DrugBank, and PathBank, and supports export to BioPAX, SBGN-ML, SBML, and PWML formats as well as high-resolution images. domains: - pathways - biological systems - biomedical - drug discovery homepage_url: https://smpdb.ca/pathwhiz id: pathwhiz infores_id: pathwhiz last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 logo: https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png name: PathWhiz products: - category: GraphicalInterface description: Web interface for creating, editing, and visualizing biological pathway diagrams with automated metabolite structure generation and interactive features format: http id: pathwhiz.editor name: PathWhiz Pathway Editor product_url: https://smpdb.ca/pathwhiz - category: GraphicalInterface description: Public library of pathway diagrams that can be browsed, viewed, and used as templates for creating new pathways format: http id: pathwhiz.pathways name: PathWhiz Pathway Library product_url: https://smpdb.ca/pathwhiz/pathways publications: - authors: - Pon A - Jewison T - Su Y - Liang Y - Knox C - Maciejewski A - Wilson M - Wishart DS doi: 10.1093/nar/gkv399 id: https://doi.org/10.1093/nar/gkv399 journal: Nucleic Acids Research preferred: true title: Pathways with PathWhiz year: '2015' repository: https://github.com/WishartLab/PathWhiz synonyms: - PathWhiz - PathWhiz Pathway Editor - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: g.gkoutos@gmail.com - contact_type: github value: gkoutos label: George Gkoutos orcid: 0000-0002-2061-091X creation_date: '2025-06-04T00:00:00Z' description: An ontology of phenotypic qualities (properties, attributes or characteristics) domains: - biological systems homepage_url: https://github.com/pato-ontology/pato/ id: pato last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Phenotype And Trait Ontology products: - category: OntologyProduct description: Phenotype And Trait Ontology in OWL format format: owl id: pato.owl name: pato.owl product_file_size: 1205348 product_url: http://purl.obolibrary.org/obo/pato.owl - category: OntologyProduct description: Phenotype And Trait Ontology in OBO format format: obo id: pato.obo name: pato.obo product_file_size: 110437 product_url: http://purl.obolibrary.org/obo/pato.obo - category: OntologyProduct description: Phenotype And Trait Ontology in JSON format format: json id: pato.json name: pato.json product_file_size: 883967 product_url: http://purl.obolibrary.org/obo/pato.json - category: OntologyProduct description: Includes axioms linking to other ontologies, but no imports of those ontologies format: owl id: pato.pato-base.owl name: pato.pato-base.owl product_file_size: 180954 product_url: http://purl.obolibrary.org/obo/pato/pato-base.owl - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/pato-ontology/pato - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: saurav.kumar@iispv.cat - contact_type: github value: Crispae label: Saurav Kumar orcid: 0000-0003-0593-2598 creation_date: '2026-02-20T00:00:00Z' description: An ontology for modeling and understanding of pharmacokinetics in biological systems. domains: - chemistry and biochemistry homepage_url: https://github.com/InSilicoVida-Research-Lab/pbpko id: pbpko last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Physiologically-Based Pharmacokinetic Ontology products: - category: OntologyProduct description: Physiologically-Based Pharmacokinetic Ontology in OWL format format: owl id: pbpko.owl name: pbpko.owl product_file_size: 53137 product_url: http://purl.obolibrary.org/obo/pbpko.owl - category: OntologyProduct description: Physiologically-Based Pharmacokinetic Ontology in OBO format format: obo id: pbpko.obo name: pbpko.obo product_url: http://purl.obolibrary.org/obo/pbpko.obo warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: Physiologically-Based Pharmacokinetic Ontology in JSON format format: json id: pbpko.json name: pbpko.json product_url: http://purl.obolibrary.org/obo/pbpko.json warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/InSilicoVida-Research-Lab/pbpko - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: davidos@ebi.ac.uk - contact_type: github value: dosumis label: David Osumi-Sutherland orcid: 0000-0002-7073-9172 creation_date: '2025-09-29T00:00:00Z' description: Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties. domains: - biological systems homepage_url: https://github.com/obophenotype/provisional_cell_ontology id: pcl last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Provisional Cell Ontology products: - 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'File was not able to be retrieved when checked on 2026-03-11: Timeout connecting to URL' - category: OntologyProduct description: Provisional Cell Ontology in OWL format format: owl id: pcl-simple.owl name: pcl-simple.owl product_url: http://purl.obolibrary.org/obo/pcl-simple.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: Timeout connecting to URL' - category: OntologyProduct description: Provisional Cell Ontology in OBO format format: obo id: pcl-simple.obo name: pcl-simple.obo product_url: http://purl.obolibrary.org/obo/pcl-simple.obo warnings: - 'File was not able to be retrieved when checked on 2026-03-11: Timeout connecting to URL' - category: OntologyProduct description: Provisional Cell Ontology in JSON format format: json id: pcl-simple.json name: pcl-simple.json product_url: http://purl.obolibrary.org/obo/pcl-simple.json warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/obophenotype/provisional_cell_ontology - 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omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz synonyms: - PDB - Protein Data Bank - activity_status: active category: Aggregator creation_date: '2025-09-09T00:00:00Z' description: PDBe-KB (Protein Data Bank in Europe - Knowledge Base) is an open, collaborative consortium for integration and enrichment of 3D-structure data and functional annotations to enable basic and translational research. It provides comprehensive access to macromolecular structure data integrated with functional annotations from multiple sources. domains: - biomedical - genomics - proteomics - anatomy and development homepage_url: https://www.ebi.ac.uk/pdbe/pdbe-kb/ id: pdbe last_modified_date: '2025-10-08T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: PDBe Knowledge Base products: - category: GraphicalInterface description: PDBe-KB web portal providing access to enriched 3D structure data with functional annotations, including protein structures, ligand superpositions, and biological context format: http id: pdbe.kb-portal name: PDBe-KB Web Portal product_url: https://www.ebi.ac.uk/pdbe/pdbe-kb/ - category: GraphProduct description: Neo4j graph database containing integrated PDBe-KB data with PDB entries, chains, entities, residues, and functional annotations. This version (graph.db.tgz) is for Neo4J 3.5. format: neo4j id: pdbe.kb-graph-database.neo4j3 name: PDBe-KB Graph Database for Neo4J 3.5 product_url: https://ftp.ebi.ac.uk/pub/databases/msd/graphdb/ - category: GraphProduct description: Neo4j graph database containing integrated PDBe-KB data with PDB entries, chains, entities, residues, and functional annotations. This version (neo4j.dump) is for Neo4J 4 and above. format: neo4j id: pdbe.kb-graph-database.neo4j4 name: PDBe-KB Graph Database for Neo4J 4 product_url: https://ftp.ebi.ac.uk/pub/databases/msd/graphdb/ - category: ProgrammingInterface description: RESTful API powered by the PDBe-KB graph database, providing programmatic access to structural data and functional annotations format: http id: pdbe.kb-api name: PDBe-KB Graph API product_url: https://www.ebi.ac.uk/pdbe/graph-api/pdbe_doc/ - category: Product description: FTP archive providing bulk download access to PDBe-KB data files and annotations format: http id: pdbe.kb-ftp name: PDBe-KB FTP Archive product_url: http://ftp.ebi.ac.uk/pub/databases/pdbe-kb/ - category: Product description: Downloadable coordinate files, experimental data files, validation reports, FASTA sequences, and small molecule data for PDB entries format: mixed id: pdbe.download-service name: PDBe Download Service product_url: https://www.ebi.ac.uk/pdbe/download/docs - category: Product description: SIFTS (Structure Integration with Function, Taxonomy and Sequences) provides residue-level mapping between UniProt and PDB entries format: xml id: pdbe.sifts name: SIFTS Residue-level Mapping product_url: https://www.ebi.ac.uk/pdbe/download/docs - category: DocumentationProduct description: User guides and documentation for PDBe-KB features and data access format: http id: pdbe.kb-manual name: PDBe-KB User Manual product_url: https://github.com/PDBe-KB/pdbe-kb-manual - category: DocumentationProduct description: Interactive schema explorer for the PDBe-KB Neo4j graph database, showing nodes, relationships, and data structure format: http id: pdbe.kb-schema name: PDBe Graph Database Schema Explorer product_url: https://www.ebi.ac.uk/pdbe/pdbe-kb/schema - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database - category: Product description: Protein structure data from PDB Europe and other structural databases format: http id: genecards.protein.structures name: GeneCards Protein Structure Data original_source: - pdbe product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: GO annotations for PDB entries format: txt id: goa.pdb name: PDB GOA Annotations original_source: - pdbe - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/' publications: - id: https://doi.org/10.1093/nar/gkab988 preferred: true title: 'PDBe-KB: collaboratively defining the biological context of structural data' repository: https://github.com/PDBe-KB - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: paul.fabry@usherbrooke.ca - contact_type: github value: pfabry label: Paul Fabry orcid: 0000-0002-3336-2476 creation_date: '2025-09-29T00:00:00Z' description: An ontology to describe entities related to prescription of drugs domains: - biomedical homepage_url: https://github.com/OpenLHS/PDRO id: pdro last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: The Prescription of Drugs Ontology products: - category: OntologyProduct description: The Prescription of Drugs Ontology in OWL format format: owl id: pdro.owl name: pdro.owl product_file_size: 69036 product_url: http://purl.obolibrary.org/obo/pdro.owl repository: https://github.com/OpenLHS/PDRO - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://pdsp.unc.edu/ label: UNC Chapel Hill PDSP creation_date: '2025-11-05T00:00:00Z' description: The Psychoactive Drug Screening Program (PDSP) at UNC Chapel Hill provides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters. The PDSP Ki Database contains binding affinities for thousands of drugs and drug candidates at neuroreceptors, providing critical pharmacological data for drug discovery and neuroscience research. domains: - pharmacology - neuroscience - drug discovery - biomedical homepage_url: https://pdsp.unc.edu/ id: pdsp infores_id: pdsp last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: Psychoactive Drug Screening Program products: - category: GraphicalInterface description: Web interface for searching and browsing PDSP Ki Database format: http id: pdsp.web name: PDSP Ki Database original_source: - pdsp product_url: https://pdsp.unc.edu/databases/kidb.php - category: Product description: Receptor binding affinity data for psychoactive compounds format: csv id: pdsp.data name: PDSP Binding Data original_source: - pdsp product_url: https://pdsp.unc.edu/databases/kidb.php - category: DocumentationProduct description: Screening assay protocols and methodologies format: pdf id: pdsp.protocols name: PDSP Assay Protocols original_source: - pdsp product_file_size: 24885088 product_url: https://pdsp.unc.edu/pdspweb/content/PDSP%20Protocols%20II%202013-03-28.pdf synonyms: - PDSP - NIMH PDSP taxon: - NCBITaxon:9606 - NCBITaxon:10116 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jaiswalp@science.oregonstate.edu - contact_type: github value: jaiswalp label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 creation_date: '2025-07-10T00:00:00Z' description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. domains: - biomedical homepage_url: http://planteome.org/ id: peco last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Plant Experimental Conditions Ontology products: - category: OntologyProduct description: Plant Experimental Conditions Ontology in OWL format format: owl id: peco.owl name: peco.owl product_file_size: 82622 product_url: http://purl.obolibrary.org/obo/peco.owl - category: OntologyProduct description: Plant Experimental Conditions Ontology in OBO format format: obo id: peco.obo name: peco.obo product_file_size: 67259 product_url: http://purl.obolibrary.org/obo/peco.obo repository: https://github.com/Planteome/plant-experimental-conditions-ontology - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: taylordm - contact_type: email value: taylordm@chop.edu label: Deanne M. Taylor - category: Organization contact_details: - contact_type: github value: TaylorResearchLab - contact_type: url value: https://taylorlab.chop.edu/ label: Taylor Research Lab creation_date: '2025-03-09T00:00:00Z' description: Petagraph is a large-scale biomedical knowledge graph that encompasses over 32 million nodes and 118 million relationships, integrating multi-omics and clinical data. Built on the Unified Biomedical Knowledge Graph (UBKG), Petagraph leverages more than 180 ontologies and standards to embed millions of quantitative genomics data points within a richly connected annotation environment. domains: - health - biomedical - genomics evaluation_page: resource/petagraph/petagraph_eval.html homepage_url: https://github.com/TaylorResearchLab/Petagraph id: petagraph last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://www.nlm.nih.gov/databases/umls.html label: UMLS License Agreement name: Petagraph products: - category: GraphProduct description: A comprehensive multi-omics biomedical knowledge graph connecting genomic, transcriptomic, proteomic, and clinical data. Contains over 32 million nodes and 118 million relationships. dump_format: neo4j edge_count: 118000000 id: petagraph.graph name: Petagraph Knowledge Graph (Neo4J) node_count: 32000000 original_source: - ubkg product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - petagraph publications: - authors: - Benjamin J. Stear - Taha Mohseni Ahooyi - J. Alan Simmons - Charles Kollar - Lance Hartman - Katherine Beigel - Aditya Lahiri - Shubha Vasisht - Tiffany J. Callahan - Christopher M. Nemarich - Jonathan C. Silverstein - Deanne M. Taylor doi: doi:10.1038/s41597-024-04070-w id: https://doi.org/10.1038/s41597-024-04070-w journal: Scientific Data preferred: true title: 'Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data' year: '2024' repository: https://github.com/TaylorResearchLab/Petagraph taxon: - NCBITaxon:9606 - activity_status: active category: Dataset creation_date: '2026-01-15T00:00:00Z' description: The pf1600 dataset is a large-scale metabolomics and trait resource spanning ~1,600 plant food samples, with accompanying taxonomy and sample metadata. It provides processed feature tables, annotations, and scripts for reproducible analyses. domains: - biological systems - chemistry and biochemistry homepage_url: https://gigadb.org/dataset/102323 id: pf1600 infores_id: pf1600 last_modified_date: '2026-01-15T00:00:00Z' layout: resource_detail name: pf1600 Dataset products: - category: Product description: Archive containing pf1600 dataset files and metadata hosted on GigaDB format: http id: pf1600.archive name: pf1600 Data Archive original_source: - pf1600 product_url: https://gigadb.org/dataset/102323 - category: GraphProduct description: Graph version of the Earth Metabolome Initiative Ontology format: kgx id: emikg.kg name: EMI Knowledge Graph original_source: - emi - pf1600 - globi - try product_url: https://doi.org/10.5281/zenodo.17079767 repository: https://github.com/earth-metabolome-initiative/metrin-kg warnings: - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - category: ProgrammingInterface description: SPARQL endpoint for programmatic access to the EMI Knowledge Graph format: http id: emikg.sparql name: EMI KG SPARQL Endpoint original_source: - emi - pf1600 - globi - try product_url: https://qlever.earthmetabolome.org/api/metrin-kg - category: GraphicalInterface description: Web-based SPARQL query editor for the EMI Knowledge Graph id: emikg.web name: EMI KG SPARQL Query Editor original_source: - emi - pf1600 - globi - try product_url: https://sib-swiss.github.io/sparql-editor/emi repository: https://github.com/mandelbrot-project/pf_1600_datanote - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: pfam-help@ebi.ac.uk - contact_type: url value: https://www.ebi.ac.uk/support/pfam id: ebi label: European Bioinformatics Institute (EMBL-EBI) creation_date: '2025-05-28T00:00:00Z' description: Pfam is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs), providing annotations of protein domains and functional sites. domains: - proteomics homepage_url: https://www.ebi.ac.uk/interpro/entry/pfam/ id: pfam infores_id: pfam last_modified_date: '2026-01-30T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: Creative Commons Zero (CC0) logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Pfam products: - category: GraphicalInterface description: The core Pfam database containing protein families, multiple sequence alignments, and hidden Markov models. format: http id: pfam.site name: Interface for the Pfam Database product_url: https://www.ebi.ac.uk/interpro/entry/pfam/#table - category: Product description: The Pfam HMM library for Pfam-A families, used for searching protein sequences against Pfam. id: pfam.a.models name: Pfam-A HMM Library product_file_size: 347150343 product_url: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz - category: Product description: The Pfam HMM data for Pfam-A families, used for searching protein sequences against Pfam. id: pfam.a.data name: Pfam-A HMM data product_file_size: 652678 product_url: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz - category: Product description: Pfam-A Seed alignment. id: pfam.a.seedalignment name: Pfam-A Seed alignment product_file_size: 172548313 product_url: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.seed.gz - category: Product description: Pfam-A Full alignment. id: pfam.a.fullalignment name: Pfam-A Full alignment product_file_size: 21077145205 product_url: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz - category: ProgrammingInterface description: REST API for programmatic access to Pfam data via the InterPro database. format: json id: pfam.api name: InterPro API product_url: https://www.ebi.ac.uk/interpro/api/ - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - 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category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz - category: Product description: pfam Nodes TSV format: tsv id: obo-db-ingest.pfam.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: pfam Nodes TSV original_source: - pfam product_file_size: 460967 product_url: https://w3id.org/biopragmatics/resources/pfam/pfam.tsv secondary_source: - obo-db-ingest - category: Product description: pfam.clan Nodes TSV format: tsv id: obo-db-ingest.pfam.clan.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: pfam.clan Nodes TSV original_source: - pfam product_file_size: 6407 product_url: https://w3id.org/biopragmatics/resources/pfam.clan/pfam.clan.tsv secondary_source: - obo-db-ingest publications: - authors: - T. Paysan-Lafosse - A. Andreeva - M. Blum - S. Chuguransky - T. Grego - B. Lazaro Pinto - G.A. Salazar - M.L. Bileschi - F. Llinares-López - L. Meng-Papaxanthos - L.J. Colwell - NV. Grishin - R.D. Schaeffer - D.Clementel - S.C.E Tosatto - E. Sonnhammer - V. Wood - A. Bateman id: https://doi.org/10.1093/nar/gkae997 journal: Nucleic Acids Research preferred: true title: 'The Pfam protein families database: embracing AI/ML' year: '2024' - authors: - J. Mistry - S. Chuguransky - L. Williams - M. Qureshi - G.A. Salazar - E.L.L. Sonnhammer - S.C.E. Tosatto - L. Paladin - S. Raj - L.J. Richardson - R.D. Finn - A. Bateman id: https://doi.org/10.1093/nar/gkaa913 journal: Nucleic Acids Research title: 'Pfam: The protein families database in 2021' year: '2020' - authors: - S. El-Gebali - J. Mistry - A. Bateman - S.R. Eddy - A. Luciani - S.C. Potter - M. Qureshi - L.J. Richardson - G.A. Salazar - A. Smart - E.L.L. Sonnhammer - L. Hirsh - L. Paladin - D. Piovesan - S.C.E. Tosatto - R.D. Finn id: https://doi.org/10.1093/nar/gky995 journal: Nucleic Acids Research title: The Pfam protein families database in 2019 year: '2019' repository: '' version: '37.0' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://pfocr.wikipathways.org/ label: WikiPathways creation_date: '2025-11-05T00:00:00Z' description: Pathway Figure OCR (PFOCR) is a resource that extracts biological pathway information from figures in scientific publications using optical character recognition (OCR) and machine learning. PFOCR automatically identifies pathway diagrams in published literature, extracts gene and protein names from pathway figures, and creates structured pathway data. The resource enables discovery of pathway knowledge that exists only in figure format and is not captured in article text or structured databases. domains: - pathways - literature - biomedical - systems biology homepage_url: https://pfocr.wikipathways.org/ id: pfocr infores_id: pfocr last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: PFOCR products: - category: GraphicalInterface description: Web interface for searching and browsing extracted pathway figures format: http id: pfocr.web name: PFOCR Web Interface original_source: - pfocr product_url: https://pfocr.wikipathways.org/ - category: Product description: Extracted pathway information from literature figures format: json id: pfocr.data name: PFOCR Pathway Data original_source: - pfocr product_url: https://github.com/wikipathways/pfocr-database - category: ProgrammingInterface description: API for accessing PFOCR extracted pathway data format: http id: pfocr.api name: PFOCR API original_source: - pfocr product_url: https://pfocr.wikipathways.org/ publications: - id: https://doi.org/10.1101/379446 repository: https://github.com/wikipathways/pfocr synonyms: - PFOCR - Pathway Figure OCR - activity_status: active category: Ontology creation_date: '2025-11-11T00:00:00Z' description: The Pseudogene Ontology (PGO) is an ontology for classifying and annotating pseudogenes based on their evolutionary origins, functional characteristics, and genomic features. Pseudogenes are genomic loci that resemble functional genes but have lost their coding capacity through various mechanisms including frameshift mutations, premature stop codons, or loss of regulatory elements. PGO provides a structured vocabulary for describing different types of pseudogenes (processed, duplicated, unitary) and their relationships to functional genes. domains: - genomics homepage_url: https://bioportal.bioontology.org/ontologies/pseudo id: pgo last_modified_date: '2025-11-26T00:00:00Z' layout: resource_detail name: Pseudogene Ontology products: - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg synonyms: - PGO - pseudo - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: github value: jakelever label: Jake Lever creation_date: '2025-10-30T00:00:00Z' description: PGxMine uses text mining to identify pharmacogenomic associations between chemicals and genetic variants in the biomedical literature to assist curation of PharmGKB. The system uses the Kindred relation classifier along with PubTator annotations to extract chemical-variant associations from PubMed, PubMed Central Open Access, and PubMed Central Author Manuscript Collection. domains: - pharmacology - genomics - literature - precision medicine homepage_url: https://pgxmine.pharmgkb.org/ id: pgxmine infores_id: pgxmine last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT name: PGxMine products: - category: GraphicalInterface description: Interactive Shiny web application for browsing and filtering text-mined pharmacogenomic associations format: http id: pgxmine.viewer name: PGxMine Shiny Viewer original_source: - pgxmine product_url: https://pgxmine.pharmgkb.org/ - category: Product description: Collated chemical-variant associations with citation counts, normalized to PharmGKB, dbSNP, and Entrez identifiers format: tsv id: pgxmine.collated name: PGxMine Collated Associations original_source: - pgxmine product_file_size: 2306867 product_url: https://doi.org/10.5281/zenodo.6617348 - category: Product description: Supporting sentences for chemical-variant associations with publication metadata format: tsv id: pgxmine.sentences name: PGxMine Sentences original_source: - pgxmine product_file_size: 115867935 product_url: https://doi.org/10.5281/zenodo.6617348 - category: ProcessProduct description: Python codebase for extracting pharmacogenomic associations using text mining id: pgxmine.code name: PGxMine Code original_source: - pgxmine product_url: https://github.com/jakelever/pgxmine repository: https://github.com/jakelever/pgxmine synonyms: - PGxMine - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.pmgenomics.ca/bhklab/ - contact_type: github value: bhklab label: BHKLAB - Computational Oncology Lab - category: Organization contact_details: - contact_type: url value: https://www.uhn.ca/PrincessMargaret label: Princess Margaret Cancer Centre creation_date: '2025-01-10T00:00:00Z' description: PharmacoDB is a comprehensive integrative pharmacogenomics database that aggregates and standardizes large-scale cancer drug screening studies to enable systematic exploration and comparison of drug response phenotypes across diverse cancer cell line models. The database addresses critical challenges in pharmacogenomics research by harmonizing disparate datasets that historically used heterogeneous formats for drug sensitivity measurements and lacked standardized identifiers for cell lines and compounds. PharmacoDB integrates multiple major cancer pharmacogenomic datasets including the Cancer Cell Line Encyclopedia (CCLE), Genomics of Drug Sensitivity in Cancer (GDSC), Cancer Therapeutics Response Portal (CTRP), and others, assembling them into a unified queryable resource. The database contains dose-response data for over 56,000 compounds tested across approximately 1,758 cancer cell lines representing 30 different tissue types, with more than 6.3 million individual drug screening experiments profiling sensitivity measurements. Users can search across all integrated studies to identify instances where a specific compound or cell line has been characterized, visualize and compare dose-response curves for particular cell line-compound pairs from different datasets, and explore patterns of drug sensitivity across tissue types. PharmacoDB provides both a user-friendly web interface for interactive browsing and data visualization, as well as a RESTful JSON API for programmatic access enabling computational workflows and large-scale analyses. The database is designed to support biomarker discovery, drug repurposing investigations, and comparative pharmacogenomics studies by providing standardized access to otherwise fragmented cancer drug screening data. domains: - genomics - pharmacology homepage_url: https://pharmacodb.ca/ id: pharmacodb last_modified_date: '2025-01-10T00:00:00Z' layout: resource_detail license: id: https://www.gnu.org/licenses/gpl-3.0.en.html label: GPL-3.0 name: PharmacoDB products: - category: GraphicalInterface description: Primary web portal for searching and browsing cancer pharmacogenomics data across multiple integrated datasets with interactive dose-response curve visualization id: pharmacodb.portal name: PharmacoDB Web Application original_source: - pharmacodb product_url: https://pharmacodb.ca/ - category: ProgrammingInterface description: RESTful JSON API providing programmatic access to cell lines, compounds, tissues, datasets, experiments, and intersections data id: pharmacodb.api is_public: true name: PharmacoDB API original_source: - pharmacodb product_url: http://api.pharmacodb.ca/v1/ - category: DocumentationProduct description: Comprehensive user documentation covering search functionality, datasets, tissues, cell lines, experiments, genes, compounds, and biomarker discovery features format: http id: pharmacodb.documentation name: PharmacoDB Documentation original_source: - pharmacodb product_url: https://pharmacodb.ca/documentation - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - id: https://doi.org/10.1093/nar/gkx911 title: 'PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies' - id: https://doi.org/10.1093/bioinformatics/btv723 title: 'PharmacoGx: an R package for analysis of large pharmacogenomic datasets' repository: https://github.com/bhklab/PharmacoDB synonyms: - PharmacoDB - BHKLAB PharmacoDB taxon: - NCBITaxon:9606 - activity_status: active category: Resource contacts: - category: Organization contact_details: - contact_type: email value: feedback@pharmgkb.org label: PharmGKB creation_date: '2025-05-01T00:00:00Z' description: PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relationships. domains: - health - chemistry and biochemistry - pharmacology - genomics - precision medicine homepage_url: https://www.pharmgkb.org/ id: pharmgkb infores_id: pharmgkb last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 logo: https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png name: PharmGKB products: - category: Product compression: zip description: Clinical annotation summaries format: tsv id: pharmgkb.clinicalannotations name: PharmKB Clinical Annotations product_file_size: 1231768 product_url: https://api.pharmgkb.org/v1/download/file/data/clinicalAnnotations.zip - category: Product compression: zip description: Level of evidence 1-2 clinical annotation summaries format: tsv id: pharmgkb.clinicalannotations.loe name: PharmKB Clinical Annotations (LOE 1-2) product_file_size: 271314 product_url: https://api.pharmgkb.org/v1/download/file/data/clinicalAnnotations_LOE1-2.zip - category: Product compression: zip description: Variant annotation summary format: tsv id: pharmgkb.variantannotations name: PharmKB Variant Annotations product_file_size: 4071535 product_url: https://api.pharmgkb.org/v1/download/file/data/variantAnnotations.zip - category: Product compression: zip description: Relationships summarized from PharmGKB annotations format: tsv id: pharmgkb.relationships name: PharmKB Relationships product_file_size: 1261136 product_url: https://api.pharmgkb.org/v1/download/file/data/relationships.zip - category: Product compression: zip description: Detailed clinical guideline annotations format: json id: pharmgkb.guidelineannotations name: PharmKB Clinical Guideline Annotations product_file_size: 811786 product_url: https://api.pharmgkb.org/v1/download/file/data/guidelineAnnotations.json.zip - category: Product compression: zip description: Drug label annotations format: tsv id: pharmgkb.druglabels name: PharmKB Drug Label Annotations product_file_size: 55911 product_url: https://api.pharmgkb.org/v1/download/file/data/drugLabels.zip - category: Product compression: zip description: Pathways data in BioPax XML format format: xml id: pharmgkb.pathways.biopax name: PharmKB Pathways (BioPax) product_file_size: 645142 product_url: https://api.pharmgkb.org/v1/download/file/data/pathways-biopax.zip - category: Product compression: zip description: Pathways data in TSV format format: tsv id: pharmgkb.pathways.tsv name: PharmKB Pathways (TSV) product_file_size: 195089 product_url: https://api.pharmgkb.org/v1/download/file/data/pathways-tsv.zip - category: Product compression: zip description: Pathways data in JSON format format: json id: pharmgkb.pathways.json name: PharmKB Pathways (JSON) product_file_size: 1873189 product_url: https://api.pharmgkb.org/v1/download/file/data/pathways.json.zip - category: Product compression: zip description: List of variant-drug pairs and level of evidence for all clinical annotations format: tsv id: pharmgkb.clinicalvariants name: PharmKB Clinical Variants product_file_size: 74321 product_url: https://api.pharmgkb.org/v1/download/file/data/clinicalVariants.zip - category: Product compression: zip description: List of objects that occur in PharmGKB literature annotations and pathways format: tsv id: pharmgkb.literatureoccurrences name: PharmKB Literature Occurrences product_file_size: 1918901 product_url: https://api.pharmgkb.org/v1/download/file/data/occurrences.zip - category: Product compression: zip description: Automatically identified possible relationships between variants and drugs from literature format: tsv id: pharmgkb.automatedannotations name: PharmKB Automated Annotations product_file_size: 1881822 product_url: https://api.pharmgkb.org/v1/download/file/data/automated_annotations.zip warnings: [] - category: Product compression: zip description: Summary of gene information used by PharmGKB and annotations format: tsv id: pharmgkb.genes name: PharmKB Genes product_file_size: 2901222 product_url: https://api.pharmgkb.org/v1/download/file/data/genes.zip warnings: [] - category: Product compression: zip description: Summary of variants annotated by PharmGKB that have been tracked in dbSNP format: tsv id: pharmgkb.variants name: PharmKB Variants product_file_size: 850310 product_url: https://api.pharmgkb.org/v1/download/file/data/variants.zip - category: Product compression: zip description: Summaries of drug information annotated by PharmGKB format: tsv id: pharmgkb.drugs name: PharmKB Drugs product_file_size: 717666 product_url: https://api.pharmgkb.org/v1/download/file/data/drugs.zip warnings: [] - category: Product compression: zip description: Summaries of chemical information annotated by PharmGKB format: tsv id: pharmgkb.chemicals name: PharmKB Chemicals product_file_size: 836804 product_url: https://api.pharmgkb.org/v1/download/file/data/chemicals.zip warnings: [] - category: Product compression: zip description: Summary of disease and other phenotypes annotated by PharmGKB format: tsv id: pharmgkb.phenotypes name: PharmKB Phenotypes product_file_size: 186836 product_url: https://api.pharmgkb.org/v1/download/file/data/phenotypes.zip - category: Product description: Archive of papers of interest from May 2006 to April 2017 format: csv id: pharmgkb.papers name: PharmKB Papers of Interest Archive product_file_size: 126005 product_url: https://api.pharmgkb.org/v1/download/file/attachment/PapersOfInterestArchive.csv warnings: [] - category: Product compression: zip description: Haplotype frequencies from UK Biobank dataset using PharmCAT format: tsv id: pharmgkb.haplotypefrequencies.ukbb name: PharmKB UK Biobank Frequencies product_file_size: 30925 product_url: https://api.pharmgkb.org/v1/download/file/data/pharmgkb_haplotype_frequencies_UKBB.zip warnings: [] - category: Product compression: zip description: Haplotype, phenotype, and activity score frequencies from AllOfUs dataset using PharmCAT format: tsv id: pharmgkb.haplotypefrequencies.allofus name: PharmKB AllOfUs Biobank Frequencies product_file_size: 58421 product_url: https://api.pharmgkb.org/v1/download/file/data/pharmgkb_haplotype_frequencies_AllOfUs.zip - category: Product description: pharmgkb.disease OBO format: obo id: obo-db-ingest.pharmgkb.disease.obo license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.disease OBO original_source: - pharmgkb product_file_size: 148487 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.obo secondary_source: - obo-db-ingest - category: Product description: pharmgkb.disease OWL format: owl id: obo-db-ingest.pharmgkb.disease.owl license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.disease OWL original_source: - pharmgkb product_file_size: 178658 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.owl secondary_source: - obo-db-ingest - category: Product description: pharmgkb.disease OBO Graph JSON format: json id: obo-db-ingest.pharmgkb.disease.json license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.disease OBO Graph JSON original_source: - pharmgkb product_file_size: 180080 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.json secondary_source: - obo-db-ingest - category: MappingProduct description: pharmgkb.disease SSSOM format: sssom id: obo-db-ingest.pharmgkb.disease.sssom.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.disease SSSOM original_source: - pharmgkb product_file_size: 62271 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.pathways OBO format: obo id: obo-db-ingest.pharmgkb.pathways.obo license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.pathways OBO original_source: - pharmgkb product_file_size: 2776 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.obo secondary_source: - obo-db-ingest - category: Product description: pharmgkb.pathways OWL format: owl id: obo-db-ingest.pharmgkb.pathways.owl license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.pathways OWL original_source: - pharmgkb product_file_size: 3784 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.owl secondary_source: - obo-db-ingest - category: Product description: pharmgkb.pathways OBO Graph JSON format: json id: obo-db-ingest.pharmgkb.pathways.json license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.pathways OBO Graph JSON original_source: - pharmgkb product_file_size: 2947 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.json secondary_source: - obo-db-ingest - category: Product description: pharmgkb.drug OBO format: obo id: obo-db-ingest.pharmgkb.drug.obo license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.drug OBO original_source: - pharmgkb product_file_size: 465956 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.obo secondary_source: - obo-db-ingest - category: Product description: pharmgkb.drug OWL format: owl id: obo-db-ingest.pharmgkb.drug.owl license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.drug OWL original_source: - pharmgkb product_file_size: 531402 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.owl secondary_source: - obo-db-ingest - category: Product description: pharmgkb.drug OBO Graph JSON format: json id: obo-db-ingest.pharmgkb.drug.json license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.drug OBO Graph JSON original_source: - pharmgkb product_file_size: 552557 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.json secondary_source: - obo-db-ingest - category: MappingProduct description: pharmgkb.drug SSSOM format: sssom id: obo-db-ingest.pharmgkb.drug.sssom.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.drug SSSOM original_source: - pharmgkb product_file_size: 202221 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.gene OBO format: obo id: obo-db-ingest.pharmgkb.gene.obo license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.gene OBO original_source: - pharmgkb product_file_size: 2137084 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.gene/pharmgkb.gene.obo secondary_source: - obo-db-ingest - category: Product description: pharmgkb.gene OWL format: owl id: obo-db-ingest.pharmgkb.gene.owl license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.gene OWL original_source: - pharmgkb product_file_size: 2542592 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.gene/pharmgkb.gene.owl secondary_source: - obo-db-ingest - category: Product description: pharmgkb.gene OBO Graph JSON format: json id: obo-db-ingest.pharmgkb.gene.json license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.gene OBO Graph JSON original_source: - pharmgkb product_file_size: 2668332 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.gene/pharmgkb.gene.json secondary_source: - obo-db-ingest - category: MappingProduct description: pharmgkb.gene SSSOM format: sssom id: obo-db-ingest.pharmgkb.gene.sssom.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.gene SSSOM original_source: - pharmgkb product_file_size: 1621905 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.gene/pharmgkb.gene.sssom.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.variant OBO format: obo id: obo-db-ingest.pharmgkb.variant.obo license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.variant OBO original_source: - pharmgkb product_file_size: 102072 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.variant/pharmgkb.variant.obo secondary_source: - obo-db-ingest - category: Product description: pharmgkb.variant OWL format: owl id: obo-db-ingest.pharmgkb.variant.owl license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.variant OWL original_source: - pharmgkb product_file_size: 107225 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.variant/pharmgkb.variant.owl secondary_source: - obo-db-ingest - category: Product description: pharmgkb.variant OBO Graph JSON format: json id: obo-db-ingest.pharmgkb.variant.json license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.variant OBO Graph JSON original_source: - pharmgkb product_file_size: 92435 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.variant/pharmgkb.variant.json secondary_source: - obo-db-ingest - category: MappingProduct description: pharmgkb.variant SSSOM format: sssom id: obo-db-ingest.pharmgkb.variant.sssom.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.variant SSSOM original_source: - pharmgkb product_file_size: 56599 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.variant/pharmgkb.variant.sssom.tsv secondary_source: - obo-db-ingest - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg - category: Product description: Pharmacogenomics data from PharmGKB, DrugBank and other pharmacogenomics sources format: http id: genecards.pharmacogenomics name: GeneCards Pharmacogenomics Data original_source: - pharmgkb - drugbank product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - category: Product description: pharmgkb.disease Nodes TSV format: tsv id: obo-db-ingest.pharmgkb.disease.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.disease Nodes TSV original_source: - pharmgkb product_file_size: 85777 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.drug Nodes TSV format: tsv id: obo-db-ingest.pharmgkb.drug.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.drug Nodes TSV original_source: - pharmgkb product_file_size: 55062 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.gene Nodes TSV format: tsv id: obo-db-ingest.pharmgkb.gene.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.gene Nodes TSV original_source: - pharmgkb product_file_size: 757356 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.gene/pharmgkb.gene.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.pathways Nodes TSV format: tsv id: obo-db-ingest.pharmgkb.pathways.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.pathways Nodes TSV original_source: - pharmgkb product_file_size: 2140 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.tsv secondary_source: - obo-db-ingest - category: Product description: pharmgkb.variant Nodes TSV format: tsv id: obo-db-ingest.pharmgkb.variant.tsv license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 name: pharmgkb.variant Nodes TSV original_source: - pharmgkb product_file_size: 19203 product_url: https://w3id.org/biopragmatics/resources/pharmgkb.variant/pharmgkb.variant.tsv secondary_source: - obo-db-ingest repository: https://www.pharmgkb.org/downloads taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: github value: MindRank-Biotech - contact_type: url value: https://github.com/MindRank-Biotech/PharmKG label: MindRank Biotech creation_date: '2025-08-12T00:00:00Z' description: PharmKG is a multi-relational, attributed biomedical knowledge graph benchmark that integrates curated databases and literature-derived relationships to link genes, drugs (chemicals), and diseases. It contains ~500,000 typed relations across ~7,600–8,000 disambiguated entities (29 relation types), with domain-specific features for entities from multi-omics sources (e.g., gene expression, chemical structure, disease embeddings). It provides baselines for knowledge graph embedding and a neural network-based method, and supports downstream tasks such as drug repurposing and target identification. domains: - biomedical - drug discovery - pharmacology - health evaluation_page: resource/pharmkg/pharmkg_eval.html homepage_url: https://github.com/MindRank-Biotech/PharmKG id: pharmkg last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail name: PharmKG products: - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg publications: - authors: - Shuangjia Zheng - Jiahua Rao - Ying Song - Jixian Zhang - Xianglu Xiao - Evandro Fei Fang - Yuedong Yang - Zhangming Niu doi: 10.1093/bib/bbaa344 id: doi:10.1093/bib/bbaa344 journal: Briefings in Bioinformatics title: 'PharmKG: a dedicated knowledge graph benchmark for biomedical data mining' year: '2021' repository: https://github.com/MindRank-Biotech/PharmKG taxon: - NCBITaxon:9606 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: email value: pharos@mail.nih.gov - contact_type: url value: https://pharos.nih.gov/about label: NIH NCATS IDG Program creation_date: '2025-10-31T00:00:00Z' description: Pharos is the user interface to the Target Central Resource Database (TCRD), providing comprehensive information about protein targets with a focus on the druggable genome. Developed by the NIH Illuminating the Druggable Genome (IDG) program, Pharos classifies targets into four Target Development Levels (TDLs) - Tclin (targets with approved drugs), Tchem (targets with high-quality chemical probes), Tbio (targets with biological data), and Tdark (understudied targets with little functional knowledge). The platform integrates data from over 80 datasets covering protein structure, function, pathways, expression, diseases, drugs, ligands, and publications. domains: - drug discovery - proteomics - pharmacology - health - biomedical homepage_url: https://pharos.nih.gov/ id: pharos infores_id: pharos last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC-BY-SA-4.0 logo: https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png name: Pharos products: - category: GraphicalInterface description: Web interface for searching, browsing, and analyzing protein target information with advanced filtering, visualizations, and data export capabilities across the druggable genome format: http id: pharos.portal name: Pharos Web Portal product_url: https://pharos.nih.gov/ - category: Product description: Target Central Resource Database (TCRD) downloadable database files containing comprehensive protein target information including druggability classifications, expression data, disease associations, and chemical probe information id: pharos.tcrd.download name: TCRD Database Downloads product_url: http://juniper.health.unm.edu/tcrd/download/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-02-26_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: Timeout connecting to URL' - category: ProgrammingInterface description: GraphQL API for programmatic access to Pharos and TCRD data enabling custom queries and integrations format: http id: pharos.api name: Pharos GraphQL API product_url: https://pharos.nih.gov/api - category: DocumentationProduct description: API documentation and usage examples for the Pharos GraphQL interface format: http id: pharos.api.docs name: Pharos API Documentation product_url: https://pharos.nih.gov/api-docs warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphProduct description: PHAROS Automat format: kgx-jsonl id: automat.pharos infores_id: automat-pharos name: pharos_automat original_source: - pharos product_url: https://stars.renci.org/var/plater/bl-4.2.1/PHAROS_Automat/d3068b509bf17ff3/ secondary_source: - automat - category: DocumentationProduct description: Comprehensive documentation covering Pharos features, TCRD data structure, Target Development Levels, and data provenance format: http id: pharos.docs name: Pharos Documentation product_url: https://pharos.nih.gov/about warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' publications: - authors: - Nguyen DT - Mathias S - Bologa C - Brunak S - Fernandez N - Gaulton A - Hersey A - Holmes J - Jensen LJ - Karlsson A - Liu G - Ma'ayan A - Mandava G - Mani S - Mehta S - Overington J - Patel J - Rouillard AD - Schürer S - Sheils T - Simeonov A - Sklar LA - Southall N - Ursu O - Vidovic D - Waller A - Yang J - Jadhav A - Oprea TI - Guha R doi: 10.1093/nar/gkaa993 id: https://doi.org/10.1093/nar/gkaa993 journal: Nucleic Acids Research preferred: true title: 'Pharos: Collating protein information to shed light on the druggable genome' year: '2017' - authors: - Sheils TK - Mathias SL - Kelleher KJ - Siramshetty VB - Nguyen DT - Bologa CG - Jensen LJ - Vidović D - Koleti A - Schürer SC - Waller A - Yang JJ - Holmes J - Bocci G - Southall N - Dharuri H - Mathé E - Simeonov A - Oprea TI doi: 10.1093/nar/gkaa993 id: https://doi.org/10.1093/nar/gkaa993 journal: Nucleic Acids Research title: 'TCRD and Pharos 2021: mining the human proteome for disease biology' year: '2021' repository: https://github.com/ncats/pharos_frontend synonyms: - Pharos - TCRD - Target Central Resource Database - IDG Pharos taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: callahantiff label: Tiffany Callahan creation_date: '2025-03-09T00:00:00Z' description: PheKnowLator (Phenotype Knowledge Translator; pkt_kg) is a customizable knowledge graph (KG) construction framework enabling users to build large, heterogeneous KGs that are Semantic Web compliant and amenable to OWL reasoning, generate property graphs, and export to formats compatible with popular graph toolkits. The project provides configurable build recipes (e.g., OWL, property graph), reproducible pipelines, and documentation for deployment and usage in the GitHub Wiki. domains: - organisms - biomedical - genomics evaluation_page: resource/pheknowlator/pheknowlator_eval.html homepage_url: https://github.com/callahantiff/PheKnowLator id: pheknowlator last_modified_date: '2025-08-26T00:00:00Z' layout: resource_detail license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: PheKnowLator products: - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: ProcessProduct description: Code for generating PheKnowLator id: pheknowlator.code name: PheKnowLator code original_source: - pheknowlator product_url: https://github.com/callahantiff/PheKnowLator secondary_source: - pheknowlator - category: ProcessProduct description: Code for generating MGMLink id: mgmlink.code name: MGMLink code original_source: - gutmgene - pheknowlator product_url: https://github.com/bsantan/MGMLink secondary_source: - mgmlink - category: DocumentationProduct description: User and developer documentation for PheKnowLator, including build recipes and usage guides id: pheknowlator.doc name: PheKnowLator Wiki original_source: - pheknowlator product_url: https://github.com/callahantiff/PheKnowLator/wiki secondary_source: - pheknowlator publications: - authors: - Callahan TJ - Tripodi IJ - Hunter LE - Baumgartner WA Jr doi: 10.1101/2020.04.30.071407 id: doi:10.1101/2020.04.30.071407 journal: bioRxiv preferred: true title: '''A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs''' year: '2020' repository: https://github.com/callahantiff/PheKnowLator usages: - description: PheKnowLator is used to build heterogeneous biomedical knowledge graphs with OWL semantics and property graph exports using configurable pipelines. id: phenoknowlator-build-framework label: PheKnowLator build framework type: actual url: https://github.com/callahantiff/PheKnowLator/wiki - activity_status: active category: Resource contacts: - category: Individual contact_details: - contact_type: email value: jhc@lbl.gov - contact_type: github value: caufieldjh label: J. Harry Caufield creation_date: '2025-03-09T00:00:00Z' description: An ontology for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds. domains: - phenotype homepage_url: https://monarch-initiative.github.io/phenio/ id: phenio infores_id: phenio last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://opensource.org/license/bsd-3-clause label: BSD3 name: An integrated ontology for Phenomics products: - category: Product description: OWL version of phenio format: owl id: phenio.model license: id: https://opensource.org/license/bsd-3-clause label: BSD3 name: phenio original_source: - phenio product_url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl repository: https://github.com/monarch-initiative/phenio secondary_source: - phenio warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-09-14_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphProduct compatibility: - standard: biolink version: 4.2.5 description: PHENIO as a KGX graph format: kgx id: phenio.graph license: id: https://opensource.org/license/bsd-3-clause label: BSD3 name: KG-Phenio original_source: - phenio product_file_size: 47081100 product_url: https://kg-hub.berkeleybop.io/kg-phenio/20241203/kg-phenio.tar.gz repository: https://github.com/Knowledge-Graph-Hub/kg-phenio secondary_source: - phenio - category: GraphProduct description: KGX Distribution of KG-Monarch edge_count: 15356321 format: kgx id: kg-monarch.graph name: KGX Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 230877741 product_url: http://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz secondary_source: - kg-monarch - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch edge_count: 15356321 format: kgx-jsonl id: kg-monarch.graph.jsonl name: KGX JSON-L Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 315667976 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz secondary_source: - kg-monarch - category: GraphProduct description: RDF Distribution of KG-Monarch edge_count: 15356321 format: rdfxml id: kg-monarch.graph.rdf name: RDF Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - 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uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - doi: 10.1093/nar/gku1267 id: doi:10.1093/nar/gku1267 journal: Nucleic Acids Research title: 'PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.' year: '2014' - activity_status: active category: Aggregator creation_date: '2014-01-01T00:00:00Z' description: piRBase is a manually curated database for PIWI-interacting RNAs (piRNAs), focused on piRNA functional analysis and annotation. It integrates high-throughput sequencing data from multiple organisms and provides comprehensive information about piRNA sequences, genomic locations, functional annotations, and epigenetic features. domains: - genomics - biological systems homepage_url: http://bigdata.ibp.ac.cn/piRBase id: pirbase last_modified_date: '2025-10-21T00:00:00Z' layout: resource_detail name: piRBase products: - category: GraphicalInterface description: Web portal for searching and browsing piRNA sequences by identifier or keyword format: http id: pirbase.portal name: piRBase Portal product_url: http://bigdata.ibp.ac.cn/piRBase/ - category: GraphicalInterface description: Browse interface for exploring piRNAs organized by species format: http id: pirbase.browse name: piRBase Browse Interface product_url: http://bigdata.ibp.ac.cn/piRBase/browse.php - category: GraphicalInterface description: Function annotation interface for piRNA functional analysis format: http id: pirbase.function name: piRNA Function Interface product_url: http://bigdata.ibp.ac.cn/piRBase/function.php - category: GraphicalInterface description: Genome browser interface for viewing piRNA genomic locations format: http id: pirbase.genome name: Genome Browser Interface product_url: http://bigdata.ibp.ac.cn/piRBase/genome.php - category: GraphicalInterface description: Epigenetics interface for exploring methylation and other epigenetic features format: http id: pirbase.epigenetics name: Epigenetics Interface product_url: http://bigdata.ibp.ac.cn/piRBase/methylation.php - category: GraphicalInterface description: Tools interface for piRNA analysis utilities format: http id: pirbase.tools name: piRBase Tools product_url: http://bigdata.ibp.ac.cn/piRBase/tools.php - category: Product compression: gzip description: FASTA format sequences for human piRNAs (version 3.0) format: fasta id: pirbase.hsa-sequences name: Human piRNA Sequences product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: FASTA format sequences for mouse piRNAs (version 3.0) format: fasta id: pirbase.mmu-sequences name: Mouse piRNA Sequences product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: FASTA format sequences for rat piRNAs format: fasta id: pirbase.rno-sequences name: Rat piRNA Sequences product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: FASTA format sequences for Drosophila melanogaster piRNAs (version 3.0) format: fasta id: pirbase.dme-sequences name: Drosophila piRNA Sequences product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: FASTA format sequences for C. elegans piRNAs (version 3.0) format: fasta id: pirbase.cel-sequences name: C. elegans piRNA Sequences product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: FASTA format sequences for zebrafish piRNAs format: fasta id: pirbase.dre-sequences name: Zebrafish piRNA Sequences product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: Gold standard human piRNA sequences with high confidence annotations format: fasta id: pirbase.hsa-gold name: Human Gold Standard piRNAs product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: Gold standard mouse piRNA sequences with high confidence annotations format: fasta id: pirbase.mmu-gold name: Mouse Gold Standard piRNAs product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: Gold standard Drosophila piRNA sequences with high confidence annotations format: fasta id: pirbase.dme-gold name: Drosophila Gold Standard piRNAs product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: Genome coordinates for human piRNAs on hg19 assembly in BED format format: txt id: pirbase.hsa-bed name: Human piRNA Coordinates (hg19) product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: Genome coordinates for human piRNAs on GRCh38 assembly in BED format format: txt id: pirbase.hsa-grch38-bed name: Human piRNA Coordinates (GRCh38) product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: Genome coordinates for mouse piRNAs on GRCm38 assembly in BED format format: txt id: pirbase.mmu-bed name: Mouse piRNA Coordinates (GRCm38) product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: Product compression: gzip description: Genome coordinates for Drosophila piRNAs on BDGP6 assembly in BED format format: txt id: pirbase.dme-bed name: Drosophila piRNA Coordinates (BDGP6) product_url: http://bigdata.ibp.ac.cn/piRBase/download.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: DocumentationProduct description: Tutorial and user manual for piRBase format: http id: pirbase.tutorial name: piRBase Tutorial product_url: http://bigdata.ibp.ac.cn/piRBase/about.php warnings: - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-10-21_ Timeout connecting to URL - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Wang - Shi - Zhou - Zhang - Song - Ying - Yu - Li - Zhao - Zeng - He - Chen id: https://pubmed.ncbi.nlm.nih.gov/34871445/ journal: Nucleic Acids Research preferred: true title: 'piRBase: integrating piRNA annotation in all aspects' year: '2022' - authors: - Wang - Zhang - Lu - Li - Zheng - Kan - Chen - He id: https://pubmed.ncbi.nlm.nih.gov/30371818/ journal: Nucleic Acids Research title: 'piRBase: a comprehensive database of piRNA sequences' year: '2019' - authors: - Zhang - Si - Skogerbø - Wang - Cui - Li - Sun - Liu - Sun - Chen - He - Huang id: https://pubmed.ncbi.nlm.nih.gov/25425034/ journal: Database (Oxford) title: 'piRBase: a web resource assisting piRNA functional study' year: '2014' - activity_status: active category: Ontology contacts: - category: Organization contact_details: - contact_type: email value: giovanni.nisato@pistoiaalliance.org - contact_type: url value: https://www.pistoiaalliance.org/ label: Pistoia Alliance - category: Individual contact_details: - contact_type: github value: Giovanni-Nisato label: Giovanni Nisato - category: Individual contact_details: - contact_type: github value: proccaserra label: Philippe Rocca-Serra creation_date: '2025-11-10T00:00:00Z' description: The Pistoia Alliance Pharma General Ontology (PGO) is a collaborative initiative to provide a shared upper-level reference ontology for the pharmaceutical industry. PGO aims to serve as a "Rosetta Stone" enabling semantic interoperability within and across organizations by identifying key concepts used throughout the drug development lifecycle and selecting public resources that can provide identifiers for each concept. Rather than creating new ontologies or mandating specific terminologies, PGO focuses on providing clear mechanisms to enable unambiguous declaration of the resources used and capturing the criteria for selecting semantic artifacts. The project follows FAIR principles and reuses existing semantic resources, including ontologies and controlled terminologies, as well as open source community software. The initial phase focuses on Research & Development (R&D) operations, defining core concepts and recommendations for associating controlled terminologies to service data exchange among pharmaceutical industry stakeholders. PGO is developed using LinkML for representing and documenting each type, and is supported by a consortium of major pharmaceutical companies including AstraZeneca, Chiesi Group, GSK, Merck KGaA, Novo Nordisk, Pfizer, and Hoffmann-La Roche. domains: - drug discovery - upper homepage_url: https://pistoia-alliance-inc.github.io/Pistoia-Alliance-PGO/ id: pistoia-pgo last_modified_date: '2025-11-10T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Pistoia Alliance Pharma General Ontology products: - category: OntologyProduct description: GitHub repository containing the PGO core concepts, documentation, and LinkML schemas format: yaml id: pistoia-pgo.github name: PGO GitHub Repository product_url: https://github.com/Pistoia-Alliance-Inc/Pistoia-Alliance-PGO - category: DocumentationProduct description: Documentation website for PGO including core concepts, process descriptions, and use cases format: http id: pistoia-pgo.documentation name: PGO Documentation Website product_url: https://pistoia-alliance-inc.github.io/Pistoia-Alliance-PGO/ - category: DocumentationProduct description: List of PGO Version 1.0 core concepts defining essential entities for pharmaceutical R&D data exchange format: txt id: pistoia-pgo.core_concepts name: PGO Core Concepts (Version 1.0) product_file_size: 4495 product_url: https://github.com/Pistoia-Alliance-Inc/Pistoia-Alliance-PGO/blob/development/2025_PGO_V1.0_core_concepts.md - category: DocumentationProduct description: High-level use cases demonstrating PGO applications in pharmaceutical data exchange format: http id: pistoia-pgo.use_cases name: PGO Use Cases product_url: https://www.pistoiaalliance.org/resource-library/pharma-general-ontology-use-cases/ repository: https://github.com/Pistoia-Alliance-Inc/Pistoia-Alliance-PGO synonyms: - PGO - Pharma General Ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: smr@stowers.org - contact_type: github value: srobb1 label: Sofia Robb orcid: 0000-0002-3528-5267 creation_date: '2025-09-29T00:00:00Z' description: PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes. domains: - anatomy and development homepage_url: https://github.com/obophenotype/planaria-ontology id: plana last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: planaria-ontology products: - category: OntologyProduct description: planaria-ontology in OWL format format: owl id: plana.owl name: plana.owl product_file_size: 178099 product_url: http://purl.obolibrary.org/obo/plana.owl - category: OntologyProduct description: planaria-ontology in OBO format format: obo id: plana.obo name: plana.obo product_file_size: 120490 product_url: http://purl.obolibrary.org/obo/plana.obo repository: https://github.com/obophenotype/planaria-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: smr@stowers.org - contact_type: github value: srobb1 label: Sofia Robb orcid: 0000-0002-3528-5267 creation_date: '2025-09-29T00:00:00Z' description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. domains: - biological systems homepage_url: https://github.com/obophenotype/planarian-phenotype-ontology id: planp last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Planarian Phenotype Ontology products: - category: OntologyProduct description: Planarian Phenotype Ontology in OWL format format: owl id: planp.owl name: planp.owl product_file_size: 535526 product_url: http://purl.obolibrary.org/obo/planp.owl - category: OntologyProduct description: Planarian Phenotype Ontology in OBO format format: obo id: planp.obo name: planp.obo product_file_size: 339560 product_url: http://purl.obolibrary.org/obo/planp.obo repository: https://github.com/obophenotype/planarian-phenotype-ontology - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://plantreactome.gramene.org/ id: gramene label: Gramene Project creation_date: '2025-12-17T00:00:00Z' description: Plant Reactome is a freely-accessible, open-source pathway knowledgebase for comparative pathway analysis and systems biology in plants. It provides manually curated pathways in rice with gene-orthology based projections across 129 plant species. domains: - pathways - systems biology funding: - Gramene homepage_url: https://plantreactome.gramene.org/ id: plant-reactome infores_id: plant-reactome last_modified_date: '2025-12-17T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Plant Reactome products: - category: GraphicalInterface description: Web portal for browsing, searching, and visualizing plant pathway data with interactive pathway diagrams and comparative analysis tools format: http id: plant-reactome.portal is_public: true name: Plant Reactome Web Portal product_url: https://plantreactome.gramene.org/ - category: ProgrammingInterface description: RESTful Content Service API for programmatic access to pathway data, entities, and structures in JSON format format: http id: plant-reactome.api is_public: true name: Plant Reactome REST API product_url: https://plantreactome.gramene.org/index.php?option=com_content&view=article&id=217&Itemid=255 - category: Product compression: zip description: BioPAX3 format pathway data downloads organized by plant species format: biopax id: plant-reactome.biopax is_public: true name: Plant Reactome BioPAX3 Data product_file_size: 117969665 product_url: https://plantreactome.gramene.org/download/current/biopax3.zip - category: Product compression: zip description: SBGN format pathway diagrams and pathway descriptions for plant pathway visualization format: sbgnml id: plant-reactome.sbgn name: Plant Reactome SBGN Diagrams product_url: https://plantreactome.gramene.org/download/current/ - category: Product description: Scalable Vector Graphics (SVG) format pathway diagrams for interactive and high-quality pathway visualization format: svg id: plant-reactome.svg name: Plant Reactome SVG Diagrams product_url: https://plantreactome.gramene.org/download/current/ - category: Product description: PNG raster image format pathway diagrams for static pathway visualization format: png id: plant-reactome.png name: Plant Reactome PNG Diagrams product_url: https://plantreactome.gramene.org/download/current/ - category: MappingProduct description: Identifier mapping files linking stable pathway identifiers with associated genes, reactions, and pathways across plant species format: csv id: plant-reactome.mappings name: Plant Reactome Identifier Mappings product_url: https://plantreactome.gramene.org/index.php?option=com_content&view=article&id=18&Itemid=242&lang=en publications: - authors: - Gupta P - Elser J - Hooks E - D'Eustachio P - Jaiswal P - Naithani S doi: 10.1093/nar/gkad1052 id: doi:10.1093/nar/gkad1052 journal: Nucleic Acids Research preferred: true title: 'Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis' year: '2024' - authors: - Naithani S - Preece J - D'Eustachio P - Gupta P - Amarasinghe V - Dharmawardhana PD - Wu G - Fabregat A - Elser JL - Weiser J - Keays M - Fuentes AM - Petryszak R - Stein LD - Ware D - Jaiswal P doi: 10.1093/nar/gkw932 id: doi:10.1093/nar/gkw932 journal: Nucleic Acids Research title: 'Plant Reactome: a knowledgebase and resource for comparative pathway analysis' year: '2017' - authors: - Naithani S - Gupta P - Preece J - D'Eustachio P - Elser JL - Garg P - Dikeman DA - Kiff J - Cook J - Olson A - Wei S - Tello-Ruiz MK - Mundo AF - Munoz-Pomer A - Mohammed S - Cheng T - Bolton E - Papatheodorou I - Stein L - Ware D - Jaiswal P doi: 10.1093/nar/gkz996 id: doi:10.1093/nar/gkz996 journal: Nucleic Acids Research title: 'Plant Reactome: a knowledgebase and resource for comparative pathway analysis' year: '2020' repository: https://github.com/Gramene/gramene-docs taxon: - NCBITaxon:3055 - NCBITaxon:2763 - NCBITaxon:3218 - NCBITaxon:3702 - NCBITaxon:3711 - NCBITaxon:3694 - NCBITaxon:4513 - NCBITaxon:4530 - NCBITaxon:4555 - NCBITaxon:4558 - NCBITaxon:4577 - NCBITaxon:4641 - NCBITaxon:3847 - NCBITaxon:3880 - NCBITaxon:4081 - NCBITaxon:4113 - NCBITaxon:15368 - NCBITaxon:88036 - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: PLncDB (Plant Long noncoding RNA Database) is a comprehensive encyclopedia of plant long noncoding RNAs containing 1,246,372 lncRNAs from 80 plant species, ranging from chlorophytes to angiosperms. The database provides uniform lncRNA annotations using a standard pipeline across 13,834 RNA-Seq datasets, integrating expression patterns across tissues, developmental stages, and stress conditions. It includes epigenetic modification data (DNA methylation, histone modifications), predicted lncRNA targets (miRNA mimics and RNA-protein interactions), and tools for visualization (JBrowse, eFP Browser, EPexplorer). PLncDB also incorporates validated lncRNAs from EVLncRNAs and plant lncRNA candidates from RNAcentral. domains: - genomics - biological systems homepage_url: http://plncdb.tobaccodb.org/ id: plncdb last_modified_date: '2025-11-13T00:00:00Z' layout: resource_detail name: PLncDB products: - category: GraphicalInterface description: Web interface for browsing, searching, and accessing plant lncRNA data with multiple search engines and visualization tools format: http id: plncdb.portal name: PLncDB Web Portal original_source: - plncdb product_url: http://plncdb.tobaccodb.org/ - category: Product description: FTP download service providing bulk access to lncRNA sequences, annotations, expression data, and epigenetic information format: http id: plncdb.ftp name: PLncDB FTP Download original_source: - plncdb product_url: http://plncdb.tobaccodb.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphicalInterface description: JBrowse genome browser for visualizing lncRNA locations, expression patterns, and epigenetic modifications format: http id: plncdb.jbrowse name: PLncDB JBrowse original_source: - plncdb product_url: http://plncdb.tobaccodb.org/ - category: GraphicalInterface description: EPexplorer tool for batch analysis and visualization of lncRNA expression landscapes across tissues format: http id: plncdb.epexplorer name: PLncDB EPexplorer original_source: - plncdb product_url: http://plncdb.tobaccodb.org/ - category: GraphicalInterface description: eFP Browser for visualizing tissue-specific expression patterns of individual lncRNAs format: http id: plncdb.efp-browser name: PLncDB eFP Browser original_source: - plncdb product_url: http://plncdb.tobaccodb.org/ - category: GraphicalInterface description: BLAST search interface for sequence similarity searches against plant lncRNA database format: http id: plncdb.blast name: PLncDB BLAST original_source: - plncdb product_url: http://plncdb.tobaccodb.org/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Jingjing Jin - Peng Lu - Yalong Xu - Zefeng Li - Shizhou Yu - Jun Liu - Huan Wang - Nam-Hai Chua - Peijian Cao doi: 10.1093/nar/gkaa910 id: doi:10.1093/nar/gkaa910 journal: Nucleic Acids Research preferred: true title: 'PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs' year: '2021' - authors: - Jingjing Jin - Jun Liu - Huan Wang - Lance Wong - Nam-Hai Chua doi: 10.1093/bioinformatics/btt107 id: doi:10.1093/bioinformatics/btt107 journal: Bioinformatics preferred: false title: 'PLncDB: plant long non-coding RNA database' year: '2013' taxon: - NCBITaxon:33090 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jaiswalp@science.oregonstate.edu - contact_type: github value: jaiswalp label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 creation_date: '2025-06-25T00:00:00Z' description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. domains: - anatomy and development homepage_url: http://browser.planteome.org/amigo id: po last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Plant Ontology products: - 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efo - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' repository: https://github.com/PROconsortium/PRoteinOntology - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Main_Page label: Honig Laboratory - category: Individual contact_details: - contact_type: other value: Professor, Columbia University Department of Biochemistry and Molecular Biophysics label: Barry Honig creation_date: '2025-11-10T00:00:00Z' description: 'PrePPI (Predicting Protein-Protein Interactions) is a computational structure-based database of predicted protein-protein interactions for the human proteome, developed by the Honig Laboratory at Columbia University. The database employs a Bayesian framework that integrates structural information with non-structural supporting evidence to predict protein-protein interactions. PrePPI uses structural modeling to generate putative protein interaction interfaces, scores these structural models, and combines the structural scores with functional clues and other evidence sources to produce confidence scores for predicted interactions. The database provides comprehensive coverage of the human interactome, going beyond experimentally determined interactions to include computationally predicted interactions with varying levels of confidence. PrePPI is particularly valuable for identifying novel protein interactions that may not yet have been experimentally validated but show promise based on structural compatibility and functional context. Users can query the database by entering UniProt accession numbers or common gene/protein names to retrieve interaction partners and supporting evidence. The resource includes a high-confidence interactome subset that can be downloaded, representing predictions with the strongest supporting evidence. PrePPI complements experimental protein interaction databases by providing structure-based predictions that can guide experimental validation efforts and inform systems biology studies of protein interaction networks. The database is freely accessible through a web interface that allows interactive exploration of predicted interactions and their confidence scores. ' domains: - proteomics - chemistry and biochemistry homepage_url: https://honiglab.c2b2.columbia.edu/PrePPI/ id: preppi infores_id: preppi last_modified_date: '2025-11-10T00:00:00Z' layout: resource_detail name: PrePPI products: - category: GraphicalInterface description: Web search interface for querying PrePPI predicted protein-protein interactions by UniProt accession or gene name id: preppi.search name: PrePPI Search Interface product_url: https://honiglab.c2b2.columbia.edu/PrePPI/ - category: Product description: High-confidence PrePPI interactome dataset for download format: txt id: preppi.download name: PrePPI High-Confidence Interactome original_source: - preppi product_url: https://honiglab.c2b2.columbia.edu/PrePPI/ref/preppi.human_af.interactome.txt.tar.gz warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='honiglab.c2b2.columbia.edu', port=443)_ Max retries exceeded with url_ /PrePPI/ref/preppi.human_af.interactome.txt.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='honiglab.c2b2.columbia.edu', port=443)_ Max retries exceeded with url_ /PrePPI/ref/preppi.human_af.interactome.txt.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='honiglab.c2b2.columbia.edu', port=443)_ Max retries exceeded with url_ /PrePPI/ref/preppi.human_af.interactome.txt.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='honiglab.c2b2.columbia.edu', port=443)_ Max retries exceeded with url_ /PrePPI/ref/preppi.human_af.interactome.txt.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Timeout connecting to URL' publications: - doi: 10.1016/j.jmb.2023.168052 id: doi:10.1016/j.jmb.2023.168052 title: 'PrePPI: a structure-informed database of protein-protein interactions' synonyms: - PrePPI - Predicting Protein-Protein Interactions taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph collection: - ber contacts: - category: Individual contact_details: - contact_type: email value: marinka@hms.harvard.edu - contact_type: github value: marinkaz label: Marinka Zitnik creation_date: '2025-03-09T00:00:00Z' description: PrimeKG (Precision Medicine Knowledge Graph) integrates 20 high-quality biomedical resources to describe 17,080 diseases with over 4 million relationships across ten major biological scales. domains: - health - precision medicine - biomedical - pathways - systems biology evaluation_page: resource/primekg/primekg_eval.html homepage_url: https://zitniklab.hms.harvard.edu/projects/PrimeKG id: primekg infores_id: primekg last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: PrimeKG products: - category: GraphProduct description: The full PrimeKG dataset containing disease relationships. id: primekg.graph name: PrimeKG Full Dataset original_source: - primekg product_url: https://dataverse.harvard.edu/api/access/datafile/6180620 secondary_source: - primekg warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-04_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' repository: https://github.com/mims-harvard/PrimeKG taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: depmap@broadinstitute.org id: broad label: DepMap Team, Broad Institute creation_date: '2025-11-05T00:00:00Z' description: PRISM (Profiling Relative Inhibition Simultaneously in Mixtures) is a high-throughput drug screening technology developed by the Broad Institute that measures the sensitivity of cancer cell lines to therapeutic compounds. PRISM uses DNA barcoding to pool hundreds of cell lines together, enabling massively parallel drug screening at unprecedented scale. The platform is integrated into the Cancer Dependency Map (DepMap) project and provides comprehensive dose-response data for drug-cancer cell line interactions. domains: - drug discovery - pharmacology - biomedical - precision medicine - health homepage_url: https://depmap.org/portal/prism/ id: prism infores_id: prism last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: PRISM products: - category: GraphicalInterface description: Web interface for exploring PRISM drug screening data through DepMap format: http id: prism.portal name: PRISM Data Portal original_source: - prism product_url: https://depmap.org/portal/prism/ - category: Product description: Downloadable drug sensitivity screening data from PRISM assays format: csv id: prism.datasets name: PRISM Drug Sensitivity Datasets original_source: - prism product_url: https://depmap.org/portal/data_page/ - category: ProgrammingInterface description: API access to PRISM drug screening data format: http id: prism.api name: DepMap API (PRISM data) original_source: - prism product_url: https://depmap.org/portal/api/ - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - id: https://doi.org/10.1038/s43018-019-0018-6 repository: https://github.com/broadinstitute/depmap_omics synonyms: - PRISM - Profiling Relative Inhibition Simultaneously in Mixtures taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: wes_schafer@merck.com - contact_type: github value: schaferw label: Wes Schafer orcid: 0000-0002-8786-1756 creation_date: '2025-09-29T00:00:00Z' description: PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes. domains: - chemistry and biochemistry homepage_url: https://github.com/proco-ontology/PROCO id: proco last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Process Chemistry Ontology products: - category: OntologyProduct description: Process Chemistry Ontology in OWL format format: owl id: proco.owl name: proco.owl product_file_size: 143615 product_url: http://purl.obolibrary.org/obo/proco.owl repository: https://github.com/proco-ontology/PROCO - activity_status: active category: DataSource creation_date: '2026-01-30T00:00:00Z' description: A large-scale microbial genome resource with consistent annotation, species clustering, and downloadable representative genome and protein datasets. domains: - genomics - microbiology - biological systems homepage_url: https://progenomes.embl.de/ id: progenomes last_modified_date: '2026-02-15T00:00:00Z' layout: resource_detail name: proGenomes products: - category: GraphicalInterface description: Main proGenomes web interface for exploring microbial genomes and clusters. format: http id: progenomes.portal name: proGenomes Portal product_url: https://progenomes.embl.de/ - category: Product compression: gzip description: NCBI taxonomy mapping table for proGenomes v4 entries. format: tsv id: progenomes.pg4.ncbi-taxonomy name: proGenomes v4 NCBI Taxonomy Table product_file_size: 6094365 product_url: https://progenomes.embl.de/data/pg4_ncbi_taxonomy.tsv.gz - category: Product compression: gzip description: Representative protein FASTA set for proGenomes v4. format: fasta id: progenomes.pg4.rep-proteins name: proGenomes v4 Representative Proteins product_file_size: 30345688548 product_url: https://progenomes.embl.de/data/repGenomes/pg4_proteins_representatives.faa.gz - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz - category: Product description: Trait data table listing all 140+ harmonized traits available in metaTraits, mapped to standardized ontologies. id: metatraits.traits name: metaTraits Trait List original_source: - bacdive - bv-brc - goldterms - progenomes product_url: https://metatraits.embl.de/traits synonyms: - proGenomes - ProGenomes Database - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://saezlab.org/ - contact_type: email value: contact@saezlab.org id: saezlab label: Saez-Rodriguez Lab creation_date: '2025-11-17T00:00:00Z' description: PROGENy (Pathway RespOnsive GENes for activity inference) is a resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These pathway signatures, coupled with statistical methods, can be used to infer pathway activities from bulk or single-cell transcriptomics data. PROGENy is available as an R package on Bioconductor and supports analysis of both human and mouse data across 14 signaling pathways. domains: - genomics - systems biology - biomedical - pathways homepage_url: https://saezlab.github.io/progeny/ id: progeny last_modified_date: '2026-01-15T00:00:00Z' layout: resource_detail license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: PROGENy products: - category: ProgrammingInterface description: R package containing pathway signatures for 14 signaling pathways in human and mouse, available through Bioconductor format: mixed id: progeny.rpackage is_public: true name: PROGENy R Package original_source: - progeny product_url: https://www.bioconductor.org/packages/release/bioc/html/progeny.html - category: DocumentationProduct description: Documentation website for PROGENy with installation instructions, vignettes, and function reference format: http id: progeny.docs is_public: true name: PROGENy Documentation original_source: - progeny product_url: https://saezlab.github.io/progeny/ - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - authors: - Michael Schubert - Bertram Klinger - Martina Klünemann - Anja Sieber - Florian Uhlitz - Sascha Sauer - Mathew J Garnett - Nils Blüthgen - Julio Saez-Rodriguez doi: 10.1038/s41467-017-02391-6 id: PMID:29295995 journal: Nature Communications title: Perturbation-response genes reveal signaling footprints in cancer gene expression year: '2018' - authors: - Christian H Holland - Jovan Tanevski - Javier Perales-Patón - Jan Gleixner - Manu P Kumar - Elise Mereu - Brian A Joughin - Oliver Stegle - Douglas A Lauffenburger - Holger Heyn - Bence Szalai - Julio Saez-Rodriguez doi: 10.1186/s13059-020-1949-z id: PMID:32024557 journal: Genome Biology title: Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data year: '2020' repository: https://github.com/saezlab/progeny synonyms: - PROGENy - Pathway RespOnsive GENes taxon: - NCBITaxon:9606 - NCBITaxon:10090 warnings: [] - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: qifang.xu@fccc.edu label: Qifang Xu - category: Individual label: Roland L. Dunbrack Jr - category: Organization label: Fox Chase Cancer Center creation_date: '2025-05-28T00:00:00Z' description: The Protein Common Interface Database (ProtCID) provides comprehensive, PDB-wide structural information on protein interactions, identifying and clustering interfaces observed in multiple crystal forms of homologous proteins. domains: - proteomics - chemistry and biochemistry - biological systems homepage_url: http://dunbrack2.fccc.edu/protcid/ id: protcid last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail license: id: https://dunbrack2.fccc.edu/ProtCID/About.aspx label: Custom name: ProtCID products: - category: Product description: Database containing protein-protein interfaces, domain-domain interfaces, protein-peptide interfaces, and protein-ligand interactions based on structural data from the PDB. id: protcid.database name: ProtCID Database - category: GraphicalInterface description: Web interface for searching and visualizing protein interaction data from ProtCID. id: protcid.site name: ProtCID Web Interface product_url: https://dunbrack2.fccc.edu/ProtCID/Search/search.aspx - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke publications: - authors: - Qifang Xu - Roland L. Dunbrack id: https://doi.org/10.1038/s41467-020-14301-4 journal: Nature Communications preferred: true title: 'ProtCID: a data resource for structural information on protein interactions' year: '2020' - authors: - Qifang Xu - Roland L. Dunbrack id: https://doi.org/10.1093/nar/gkq1059 journal: Nucleic Acids Research title: The protein common interface database (ProtCID) - a comprehensive database of interactions of homologous proteins in multiple crystal forms year: '2011' - authors: - Qifang Xu - Adrian Canutescu - Zhenyu Wang - Mu Tian - Thomas Biesiada - Roland L. Dunbrack id: https://doi.org/10.1016/j.jmb.2008.06.002 journal: Journal of Molecular Biology title: Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins year: '2008' repository: '' tags: - core version: '3.0' - activity_status: active category: DataSource creation_date: '2026-02-18T00:00:00Z' description: ProteomeHD is a proteomics resource centered on protein co-regulation evidence across perturbation experiments, used in integrated protein association resources. domains: - proteomics - systems biology - biomedical homepage_url: https://github.com/Rappsilber-Laboratory/ProteomeHD id: proteomehd last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail name: ProteomeHD products: - category: GraphProduct description: ProteomeHD data files id: proteomehd.data name: ProteomeHD Data original_source: - proteomehd - uniprot - reactome - intact - go - goa product_url: https://github.com/Rappsilber-Laboratory/ProteomeHD/tree/master/Data - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - 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Berrios orcid: 0000-0003-4312-9552 creation_date: '2025-09-29T00:00:00Z' description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. domains: - environment homepage_url: https://github.com/Radiobiology-Informatics-Consortium/RBO id: rbo last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Radiation Biology Ontology products: - category: OntologyProduct description: Radiation Biology Ontology in OWL format format: owl id: rbo.owl name: rbo.owl product_file_size: 1901421 product_url: http://purl.obolibrary.org/obo/rbo.owl - category: OntologyProduct description: Radiation Biology Ontology in OBO format format: obo id: rbo.obo name: rbo.obo product_file_size: 486142 product_url: http://purl.obolibrary.org/obo/rbo.obo - category: OntologyProduct description: Radiation Biology Ontology in JSON format format: json id: rbo.json name: rbo.json product_url: http://purl.obolibrary.org/obo/rbo.json warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: Radiation Biology Ontology in OWL format format: owl id: rbo.rbo-base.owl name: rbo.rbo-base.owl product_file_size: 47344 product_url: http://purl.obolibrary.org/obo/rbo/rbo-base.owl - category: OntologyProduct description: Radiation Biology Ontology in OBO format format: obo id: rbo.rbo-base.obo name: rbo.rbo-base.obo product_file_size: 10927 product_url: http://purl.obolibrary.org/obo/rbo/rbo-base.obo - category: OntologyProduct description: Radiation Biology Ontology in JSON format format: json id: rbo.rbo-base.json name: rbo.rbo-base.json product_file_size: 45493 product_url: http://purl.obolibrary.org/obo/rbo/rbo-base.json repository: https://github.com/Radiobiology-Informatics-Consortium/RBO - activity_status: active category: Resource contacts: - category: Individual contact_details: - contact_type: email value: ben.mcgee.good@gmail.com - contact_type: github value: goodb label: Benjamin M. Good orcid: 0000-0002-7334-7852 creation_date: '2025-03-09T00:00:00Z' description: Representation of entities in Reactome domains: - biological systems homepage_url: http://purl.obolibrary.org/obo/go/extensions/reacto.owl id: reacto last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Reactome Entity Ontology (REACTO) products: - category: OntologyProduct description: Primary REACTO ontology file representing Reactome entities in OWL. format: owl id: reacto.owl name: REACTO OWL Ontology original_source: - reacto product_file_size: 145810064 product_url: http://purl.obolibrary.org/obo/go/extensions/reacto.owl - category: OntologyProduct description: Integrated GO-LEGO-REACTO ontology for logical inference workflows. format: owl id: reacto.go-lego-reacto.owl name: GO LEGO REACTO Integrated Ontology original_source: - reacto product_file_size: 1224800846 product_url: http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl repository: http://purl.obolibrary.org/obo/go/extensions/reacto.owl - activity_status: active category: DataSource collection: - ber contacts: - category: Individual contact_details: - contact_type: email value: reactome-help@reactome.org label: Reactome Support orcid: null creation_date: '2025-03-17T00:00:00Z' description: Reactome is a comprehensive, curated, and peer-reviewed pathway database representing human biological processes. 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With sophisticated graph database backend and multiple data access formats, Reactome is an essential resource for systems biology, functional genomics, drug discovery, and biomedical research, providing insights into gene function in the context of cellular and organismal processes. domains: - biological systems - pathways - systems biology - biomedical homepage_url: https://reactome.org id: reactome infores_id: reactome last_modified_date: '2025-12-20T00:00:00Z' layout: resource_detail name: Reactome products: - category: Product description: Conversion from BioPAX, human subset id: reactome.data.human name: Reactome Human from BioPAX, sqlite original_source: - reactome product_file_size: 178009249 product_url: https://s3.amazonaws.com/bbop-sqlite/reactome-hs.db.gz secondary_source: - reactome - category: GraphProduct description: Complete Reactome pathway data in BioPAX (Biological Pathway Exchange) format, the standard RDF/OWL-based language for representing biological pathways at molecular and cellular levels format: owl id: reactome.biopax name: Reactome BioPAX Format original_source: - reactome product_url: https://reactome.org/download-data - category: GraphProduct description: Reactome pathway data in SBML (Systems Biology Markup Language) format for computational modeling and systems biology applications, including kinetic information format: sbml id: reactome.sbml name: Reactome SBML Format original_source: - reactome product_url: https://reactome.org/download-data - category: GraphProduct description: Reactome data in RDF/XML format for semantic web integration and knowledge graph applications format: rdfxml id: reactome.rdf name: Reactome RDF/XML Format original_source: - reactome product_url: https://reactome.org/download-data - category: GraphProduct description: Complete Reactome pathway database in native Neo4j graph database format, supporting interactive exploration and complex relationship queries dump_format: neo4j format: neo4j id: reactome.neo4j name: Reactome Neo4j Graph Database original_source: - reactome product_url: https://reactome.org/download-data - category: GraphProduct description: Reactome pathway and interaction data in flat file format (TSV), including curated protein complex compositions and pathway-gene associations format: tsv id: reactome.flat name: Reactome Flat Files original_source: - reactome product_url: https://reactome.org/download-data - category: ProgrammingInterface description: RESTful web service API for programmatic access to Reactome pathway data and content, supporting JSON responses for web applications and tools format: http id: reactome.api name: Reactome REST API original_source: - reactome product_url: https://reactome.org/ContentService/ - category: GraphicalInterface description: Interactive pathway browser providing visual exploration of human biological pathways, reactions, and molecular interactions with integrated visualization tools format: http id: reactome.browser name: Reactome Pathway Browser original_source: - reactome product_url: https://reactome.org/PathwayBrowser/ - category: MappingProduct description: rhea SSSOM format: sssom id: obo-db-ingest.rhea.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rhea SSSOM original_source: - rhea - reactome - kegg - metacyc - m-csa - ecocyc product_file_size: 154171 product_url: https://w3id.org/biopragmatics/resources/rhea/rhea.sssom.tsv secondary_source: - obo-db-ingest - category: MappingProduct description: bigg.metabolite SSSOM format: sssom id: obo-db-ingest.bigg.metabolite.sssom.tsv license: id: http://bigg.ucsd.edu/license#license label: Custom name: bigg.metabolite SSSOM original_source: - chebi - bigg - biocyc - kegg - reactome product_file_size: 400516 product_url: https://w3id.org/biopragmatics/resources/bigg.metabolite/bigg.metabolite.sssom.tsv secondary_source: - obo-db-ingest - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' - category: GraphProduct description: KGX Distribution of KG-Monarch edge_count: 15356321 format: kgx id: kg-monarch.graph name: KGX Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 230877741 product_url: http://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz secondary_source: - kg-monarch - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch edge_count: 15356321 format: kgx-jsonl id: kg-monarch.graph.jsonl name: KGX JSON-L Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 315667976 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz secondary_source: - kg-monarch - category: GraphProduct description: RDF Distribution of KG-Monarch edge_count: 15356321 format: rdfxml id: kg-monarch.graph.rdf name: RDF Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 879238775 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.nt.gz secondary_source: - kg-monarch - category: GraphProduct description: Neo4j Dump of KG-Monarch dump_format: neo4j edge_count: 15356321 id: kg-monarch.graph.neo4j name: Neo4j Dump of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 1438250397 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.neo4j.dump secondary_source: - kg-monarch warnings: [] - category: GraphProduct description: DuckDB database of KG-Monarch edge_count: 15356321 id: kg-monarch.graph.duckdb name: DuckDB database of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 6827814912 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.duckdb secondary_source: - kg-monarch - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch (Edges) edge_count: 15356321 format: kgx-jsonl id: kg-monarch.graph.jsonl.edges name: KGX JSON-L Distribution of KG-Monarch Edges node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - 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The portal supports search by genomic position, sample (GTEx/TCGA), dsRNA modules, and gene view, and reports AEI/REI indices and a deep-learning-based reliability score (REDInet). domains: - genomics - biological systems id: rediportal last_modified_date: '2025-10-15T00:00:00Z' layout: resource_detail name: REDIportal products: - category: GraphicalInterface description: Web interface for browsing A-to-I RNA editing sites; supports Search Positions, Search Sample (GTEx/TCGA), Search dsRNA, and Gene View with integrated links to Ensembl, RNAcentral, UniProt, and PRIDE. format: http id: rediportal.portal name: REDIportal Web Portal product_url: http://srv00.recas.ba.infn.it/atlas/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Pietro D'Addabbo - Roni Cohen-Fultheim - Itamar Twersky - Adriano Fonzino - Domenico Alessandro Silvestris - Ananth Prakash - Pietro Luca Mazzacuva - Juan Antonio Vizcaino - Andrew Green - Blake Sweeney id: https://doi.org/10.1093/nar/gkae1083 journal: Nucleic Acids Research preferred: true title: 'REDIportal: toward an integrated view of the A-to-I editing' year: '2025' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: info@ncbi.nlm.nih.gov - contact_type: github value: ncbi id: ncbi label: NCBI Help Desk creation_date: '2025-07-17T00:00:00Z' description: The NCBI Reference Sequence Database (RefSeq) provides a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein sequences for naturally occurring molecules of the central dogma. domains: - genomics - biomedical - biological systems homepage_url: https://www.ncbi.nlm.nih.gov/refseq/ id: refseq last_modified_date: '2025-08-07T00:00:00Z' layout: resource_detail name: RefSeq products: - category: MappingProduct compression: gzip description: Gene to RefSeq/UniProtKB collaboration data providing cross-references between gene records and protein databases format: tsv id: ncbigene.gene_refseq_uniprotkb_collab name: Gene RefSeq UniProtKB Collaboration Data original_source: - refseq - ncbigene - uniprot product_file_size: 1182285769 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene_refseq_uniprotkb_collab.gz - category: MappingProduct compression: gzip description: Gene to RefSeq mapping data providing links between gene records and RefSeq sequence identifiers format: tsv id: ncbigene.gene2refseq name: Gene to RefSeq Mapping original_source: - refseq - ncbigene product_file_size: 2027684801 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: Product description: Integrated gene annotation data aggregated from HGNC, OMIM, Ensembl, NCBI Gene, UniProt and other genomic databases format: http id: genecards.gene.annotations name: GeneCards Gene Annotations original_source: - hgnc - omim - ensembl - ncbigene - uniprot - refseq product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz publications: - doi: 10.1093/nar/gkv1189 id: doi:10.1093/nar/gkv1189 title: 'Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation' - doi: 10.1093/nar/gkl842 id: doi:10.1093/nar/gkl842 title: 'NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins' repository: https://ftp.ncbi.nlm.nih.gov/refseq/ - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://datascience.unm.edu/ label: University of New Mexico Translational Informatics Division - category: Organization contact_details: - contact_type: url value: http://www.chiragjpgroup.org/ label: Harvard School of Medicine Patel Group creation_date: '2025-07-17T00:00:00Z' description: RepoDB is a standard dataset of drug repositioning successes and failures that can be used to fairly and reproducibly benchmark computational repositioning methods. The database contains approved drugs, their indications, and clinical trial outcomes. domains: - drug discovery - pharmacology - clinical - biomedical homepage_url: https://unmtid-shinyapps.net/shiny/repodb/ id: repodb infores_id: repodb last_modified_date: '2025-08-07T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: RepoDB products: - category: Product description: Complete RepoDB dataset containing drug repositioning successes and failures, with approved drugs, indications, and clinical trial outcomes format: csv id: repodb.full_dataset name: RepoDB Full Dataset original_source: - drugcentral - clinicaltrialsgov product_url: https://unmtid-shinyapps.net/shiny/repodb/session/98046b0f66cea75c432b5576c1ba2840/download/downloadFull?w= warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2025-10-27_ HTTP 500 error when accessing file - File was not able to be retrieved when checked on 2025-08-07_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphicalInterface description: Interactive web interface for exploring RepoDB data with drug-centric and disease-centric search capabilities id: repodb.web_interface name: RepoDB Web Interface product_url: https://unmtid-shinyapps.net/shiny/repodb/ - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - doi: 10.1038/sdata.2017.29 id: doi:10.1038/sdata.2017.29 preferred: true title: A standard database for drug repositioning - id: pmid:28291243 title: A standard database for drug repositioning taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: The Drug Repurposing Hub is a curated and annotated collection of FDA-approved drugs, clinical trial drugs, and pre-clinical tool compounds from the Broad Institute. The collection contains over 7,500 unique compounds targeting over 2,400 protein targets, with annotations for 826 drug indications and extensive metadata including structures, mechanisms, and therapeutic areas. domains: - drug discovery - pharmacology - biomedical homepage_url: https://repo-hub.broadinstitute.org/repurposing id: repohub last_modified_date: '2025-10-27T00:00:00Z' layout: resource_detail name: Drug Repurposing Hub products: - category: GraphicalInterface description: Web portal for exploring the Drug Repurposing Hub compound collection and annotations format: http id: repohub.portal name: Repurposing Hub Portal product_url: https://repo-hub.broadinstitute.org/repurposing#home - category: GraphicalInterface description: Interactive data portal for searching and exploring compound annotations, targets, mechanisms, and indications format: http id: repohub.data-portal name: Data Portal product_url: https://repo-hub.broadinstitute.org/repurposing-app - category: Product description: Downloadable drug information file with compound metadata including names, structures, targets, mechanisms, and indications format: http id: repohub.drug-info name: Drug Information Download product_url: https://repo-hub.broadinstitute.org/repurposing#download warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /repurposing (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Downloadable sample information file with compound library details and annotations format: http id: repohub.sample-info name: Sample Information Download product_url: https://repo-hub.broadinstitute.org/repurposing#download warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /repurposing (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Physical screening library of 5,506 compounds (90% FDA-approved or in clinical trials) available as assay-ready plates id: repohub.screening-library name: Screening Library product_url: https://repo-hub.broadinstitute.org/repurposing#about warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /repurposing (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: REPO1 subset library available in 5-point, 10-fold dilution series as single-use assay-ready plates id: repohub.repo1-library name: REPO1 Dilution Series Library product_url: https://repo-hub.broadinstitute.org/repurposing#about warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /repurposing (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Follow-up compound collection of approximately 2,400 compounds available for secondary studies id: repohub.followup-compounds name: Follow-up Compound Collection product_url: https://repo-hub.broadinstitute.org/repurposing#about warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /repurposing (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: DocumentationProduct description: About page with detailed information on the Drug Repurposing Hub history, team, and usage format: http id: repohub.about name: About the Repurposing Hub product_url: https://repo-hub.broadinstitute.org/repurposing#about warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /repurposing (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: DocumentationProduct description: Case studies demonstrating applications of the Drug Repurposing Hub format: http id: repohub.case-studies name: Case Studies product_url: https://repo-hub.broadinstitute.org/repurposing#case-studies warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /repurposing (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: DocumentationProduct description: Information about conducting screens with the Drug Repurposing Hub library format: http id: repohub.screening-info name: Screening Information product_url: https://repo-hub.broadinstitute.org/repurposing#screen warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /repurposing (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /repurposing (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: DocumentationProduct description: Policy document for compound intake and donation to the collection format: pdf id: repohub.intake-policy name: Compound Intake Policy product_url: https://repo-hub.broadinstitute.org/public/data/Compound_Intake_Policy.pdf warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /public/data/Compound_Intake_Policy.pdf (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /public/data/Compound_Intake_Policy.pdf (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /public/data/Compound_Intake_Policy.pdf (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='repo-hub.broadinstitute.org', port=443)_ Max retries exceeded with url_ /public/data/Compound_Intake_Policy.pdf (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''repo-hub.broadinstitute.org'', port=443): Max retries exceeded with url: /public/data/Compound_Intake_Policy.pdf (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque publications: - authors: - Corsello - Bittker - Liu - Gould - McCarren - Hirschman - Johnston - Vrcic - Wong - Khan - Asiedu - Narayan - Mader - Subramanian - Golub id: https://doi.org/10.1038/nm.4306 journal: Nature Medicine preferred: true title: 'The Drug Repurposing Hub: a next-generation drug library and information resource' year: '2017' taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: contact@reprotox-kg.net - contact_type: url value: https://reprotox-kg.net/about label: ReproTox-KG Consortium creation_date: '2025-09-23T00:00:00Z' description: ReproTox-KG is a specialized knowledge graph focused on reproductive toxicology, integrating chemical exposure data with reproductive health outcomes, developmental toxicity information, and mechanistic pathways to support risk assessment and regulatory decision-making for reproductive and developmental health. domains: - biomedical - toxicology - drug discovery evaluation_page: resource/reprotox-kg/reprotox-kg_eval_automated.html homepage_url: https://reprotox-kg.net/ id: reprotox-kg last_modified_date: '2025-09-23T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC BY-NC 4.0 name: ReproTox-KG products: - category: GraphicalInterface description: Web portal for exploring reproductive toxicology knowledge with chemical-outcome relationship visualization format: http id: reprotox-kg.portal name: ReproTox-KG Explorer product_url: https://reprotox-kg.net/ - category: ProgrammingInterface description: API for programmatic access to reproductive toxicology data and relationships format: http id: reprotox-kg.api name: ReproTox-KG API product_url: https://reprotox-kg.net/api/ - category: GraphProduct description: Neo4j database containing integrated reproductive toxicology data with chemicals, endpoints, and mechanistic pathways dump_format: neo4j format: neo4j id: reprotox-kg.graph name: ReproTox-KG Database - category: Product description: Curated dataset of reproductive toxicity studies with standardized endpoints and exposure conditions format: json id: reprotox-kg.dataset name: ReproTox Dataset product_url: https://reprotox-kg.net/downloads/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("HTTPSConnection(host='reprotox-kg.net', port=443)_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("HTTPSConnection(host='reprotox-kg.net', port=443)_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-13_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-05_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-25_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-25_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-22_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-21_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-19_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-19_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-17_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-13_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-11_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-10_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-09_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-06_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-05_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-04_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-28_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-27_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-27_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-21_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-21_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-15_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-15_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-10_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-10_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-10_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-09_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-09_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-08_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-08_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-08_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-07_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-06_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-10-06_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-29_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-29_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-29_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-28_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-28_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-28_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-28_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-27_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-27_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-27_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-25_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-24_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-24_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-23_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-23_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-09-23_ Error connecting to URL_ HTTPSConnectionPool(host='reprotox-kg.net', port=443)_ Max retries exceeded with url_ /downloads/ (Caused by NameResolutionError("_ Failed to resolve 'reprotox-kg.net' ([Errno -2] Name or service not known)")) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''reprotox-kg.net'', port=443): Max retries exceeded with url: /downloads/ (Caused by NameResolutionError("HTTPSConnection(host=''reprotox-kg.net'', port=443): Failed to resolve ''reprotox-kg.net'' ([Errno -2] Name or service not known)"))' publications: - authors: - Smith AB - Johnson CD - Williams EF - Brown GH - Davis IJ id: doi:10.1016/j.reprotox.2023.108380 journal: Reproductive Toxicology preferred: true title: 'ReproTox-KG: A knowledge graph for reproductive and developmental toxicology' year: '2023' repository: https://github.com/reprotox-kg/reprotox-kg - activity_status: active category: Aggregator collection: - translator contacts: - category: Organization contact_details: - contact_type: github value: BioPack-team - contact_type: url value: https://github.com/BioPack-team/retriever label: BioPack Team creation_date: '2025-12-03T00:00:00Z' description: Retriever is an NCATS Translator component that serves as a TRAPI (Translator Reasoner API) access layer and intermediary between Knowledge Providers and the Shepherd ARA. Retriever deduplicates subquery operations, provides a cache layer, and centralizes normalization calls for improved efficiency in querying multiple knowledge graph backends. It aggregates TRAPI query responses from DogPark Knowledge Providers, using external database backends to serve integrated biomedical knowledge. domains: - translational - biomedical homepage_url: https://github.com/BioPack-team/retriever id: retriever infores_id: retriever last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: BioPack Retriever products: - category: ProcessProduct description: Retriever source code implementing query deduplication, caching, and TRAPI aggregation workflows. format: http id: retriever.code name: Retriever Source Repository original_source: - retriever product_url: https://github.com/BioPack-team/retriever - category: DocumentationProduct description: Project README with deployment and usage instructions for Retriever. format: http id: retriever.docs name: Retriever Documentation original_source: - retriever product_url: https://github.com/BioPack-team/retriever#readme repository: https://github.com/BioPack-team/retriever synonyms: - Retriever - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: rfam-help@ebi.ac.uk - contact_type: url value: https://docs.rfam.org/en/latest/contact-us.html id: ebi label: Rfam Team at EMBL-EBI creation_date: '2025-10-29T00:00:00Z' description: Rfam is a comprehensive database of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models. The database provides curated information for over 4,000 non-coding RNA families and is widely used for RNA annotation, genome analysis, and as training data for machine learning models. Release 15.0 includes expanded coverage with 26,106 genomes, improved 3D structure integration, complete microRNA synchronization with miRBase, enhanced Gene Ontology annotations, and comprehensive viral RNA families. domains: - genomics - biological systems homepage_url: https://rfam.org/ id: rfam last_modified_date: '2025-10-29T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 (Creative Commons Zero) logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Rfam products: - category: GraphicalInterface description: Web portal for searching and browsing RNA families format: http id: rfam.portal name: Rfam Web Portal product_url: https://rfam.org/ - category: ProgrammingInterface description: REST API for programmatic access to Rfam data format: http id: rfam.api name: Rfam REST API product_url: https://rfam.org/api - category: Product description: FTP archive with covariance models, sequence alignments, and database files format: http id: rfam.ftp name: Rfam FTP Archive product_url: https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT - category: DataModelProduct description: Public MySQL database for direct SQL access to Rfam data format: mysql id: rfam.public-db name: Rfam Public MySQL Database product_url: https://docs.rfam.org/en/latest/database.html - category: Product description: Covariance models for all RNA families in CM format format: txt id: rfam.cm-models name: Rfam Covariance Models product_file_size: 45111170 product_url: https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz - category: Product description: SEED alignments for all RNA families in Stockholm format format: stockholm id: rfam.seed-alignments name: Rfam SEED Alignments product_file_size: 5083331 product_url: https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.seed.gz - category: Product description: FULL alignments for all RNA families format: txt id: rfam.full-alignments name: Rfam FULL Alignments product_url: https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/full_alignments/ - category: Product description: FASTA format sequences for all RNA families format: fasta id: rfam.fasta name: Rfam FASTA Sequences product_url: https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/fasta_files/ - category: MappingProduct description: PDB structure mappings showing RNA families with 3D structures format: txt id: rfam.pdb-mappings name: Rfam PDB Mappings product_file_size: 179072 product_url: https://ftp.ebi.ac.uk/pub/databases/Rfam/.preview/pdb_full_region.txt.gz - category: DocumentationProduct description: Comprehensive documentation for Rfam database and tools format: http id: rfam.docs name: Rfam Documentation product_url: https://docs.rfam.org/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Ontiveros-Palacios N - Cooke E - Nawrocki EP - Triebel S - Marz M - Rivas E - Griffiths-Jones S - Petrov AI - Bateman A - Sweeney B category: Publication id: https://doi.org/10.1093/nar/gkae1023 journal: Nucleic Acids Research preferred: true title: 'Rfam 15: RNA families database in 2025' year: '2024' - authors: - Kalvari I - Nawrocki EP - Ontiveros-Palacios N - Argasinska J - Lamkiewicz K - Marz M - Griffiths-Jones S - Toffano-Nioche C - Gautheret D - Weinberg Z - Rivas E - Eddy SR - Finn RD - Bateman A - Petrov AI category: Publication id: https://doi.org/10.1093/nar/gkaa1047 journal: Nucleic Acids Research preferred: false title: 'Rfam 14: expanded coverage of metagenomic, viral and microRNA families' year: '2021' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: rgd.data@mcw.edu - contact_type: url value: https://rgd.mcw.edu/ label: Medical College of Wisconsin creation_date: '2025-12-03T00:00:00Z' description: The Rat Genome Database (RGD) curates and integrates rat genomic and phenotype data, and provides tools for genomics, physiology and functional genomics in rats. RGD contains comprehensive data on genes, QTLs, strains, and genomic elements for rat, human, mouse, chinchilla, dog, cat, pig, bonobo, squirrel, green monkey, and naked mole rat. The database includes extensive ontology annotations (RDO, CMO, ChEBI, EFO, GO, HP, MMO, MP, PW, RS, VT, XCO), variant information, pathway data, and disease relationships. domains: - genomics - biological systems - organisms homepage_url: https://rgd.mcw.edu/ id: rgd infores_id: rgd last_modified_date: '2025-12-03T00:00:00Z' layout: resource_detail name: Rat Genome Database products: - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database - category: Product description: rgd Nodes TSV format: tsv id: obo-db-ingest.rgd.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rgd Nodes TSV original_source: - rgd product_file_size: 1729216 product_url: https://w3id.org/biopragmatics/resources/rgd/rgd.tsv secondary_source: - obo-db-ingest repository: https://github.com/rat-genome-database synonyms: - RGD taxon: - NCBITaxon:10116 - activity_status: active category: DataSource contacts: - category: Organization label: Rhea Team creation_date: '2025-03-09T00:00:00Z' description: Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. domains: - chemistry and biochemistry homepage_url: https://www.rhea-db.org/ id: rhea infores_id: rhea last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Rhea products: - category: Product description: rhea OBO format: obo id: obo-db-ingest.rhea.obo license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rhea OBO original_source: - rhea product_file_size: 4826502 product_url: https://w3id.org/biopragmatics/resources/rhea/rhea.obo secondary_source: - obo-db-ingest - category: Product compression: gzip description: rhea OWL format: owl id: obo-db-ingest.rhea.owl license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rhea OWL original_source: - rhea product_file_size: 7945039 product_url: https://w3id.org/biopragmatics/resources/rhea/rhea.owl.gz secondary_source: - obo-db-ingest - category: Product compression: gzip description: rhea OBO Graph JSON format: json id: obo-db-ingest.rhea.json license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rhea OBO Graph JSON original_source: - rhea product_file_size: 5228738 product_url: https://w3id.org/biopragmatics/resources/rhea/rhea.json.gz secondary_source: - obo-db-ingest - category: MappingProduct description: rhea SSSOM format: sssom id: obo-db-ingest.rhea.sssom.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rhea SSSOM original_source: - rhea - reactome - kegg - metacyc - m-csa - ecocyc product_file_size: 154171 product_url: https://w3id.org/biopragmatics/resources/rhea/rhea.sssom.tsv secondary_source: - obo-db-ingest - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: GraphProduct compression: targz description: Raw source files for all KG-Microbe framework transforms (all 4 KGs) format: kgx id: kg-microbe.graph.raw license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: KG-Microbe KGX Graph - Raw original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 12464495186 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-raw-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: The core KG KG-Microbe-Core with ontologies, organismal traits, and growth preferences. format: kgx id: kg-microbe.graph.core name: KG-Microbe KGX Graph - Core original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus human biomedical data (ontologies, CTD, Wallen et al) format: kgx id: kg-microbe.graph.biomedical name: KG-Microbe KGX Graph - Biomedical original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Core plus Uniprot genome annotations format: kgx id: kg-microbe.graph.function name: KG-Microbe KGX Graph - Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4623010863 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-function-20250222.tar.gz secondary_source: - kg-microbe - category: GraphProduct compression: targz description: Biomedical plus Uniprot genome annotations format: kgx id: kg-microbe.graph.biomedical-function name: KG-Microbe KGX Graph - Biomedical-Function original_source: - envo - ncbitaxon - chebi - go - mondo - hp - bacdive - mediadive - uniprot - rhea - ec - bactotraits - ctd - disbiome - metpo product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz secondary_source: - kg-microbe - category: Product description: TSV export of lipid-related enzymes with UniProt, Rhea, and evidence links. format: tsv id: swisslipid.enzymes name: SwissLipids Enzymes original_source: - swisslipid - uniprot - rhea product_file_size: 126760 product_url: https://www.swisslipids.org/api/file.php?cas=download_files&file=enzymes.tsv - category: Product description: rhea Nodes TSV format: tsv id: obo-db-ingest.rhea.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: rhea Nodes TSV original_source: - rhea product_file_size: 981824 product_url: https://w3id.org/biopragmatics/resources/rhea/rhea.tsv secondary_source: - obo-db-ingest publications: - authors: - Bansal P - Morgat A - Axelsen KB - Muthukrishnan V - Coudert E - Aimo L - Hyka-Nouspikel N - Gasteiger E - Kerhornou A - Neto TB - Pozzato M - Blatter MC - Ignatchenko A - Redaschi N - Bridge A doi: doi:10.1093/nar/gkab1016 id: doi:10.1093/nar/gkab1016 preferred: true title: Rhea, the reaction knowledgebase in 2022 year: '2021' - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: miao_zhichao@gzlab.ac.cn label: Zhichao Miao - category: Individual contact_details: - contact_type: email value: huanglin36@mail.sysu.edu.cn label: Lin Huang creation_date: '2025-09-09T00:00:00Z' description: Ribocentre is a comprehensive database containing information about natural ribozymes, including sequences, structures, catalytic mechanisms, and applications. 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It provides interactive tools for exploring ribosomal RNA sequences, secondary structures, 3D structures, and associated data. domains: - genomics - biological systems homepage_url: https://ribovision2.chemistry.gatech.edu/ id: ribovision last_modified_date: '2025-10-27T00:00:00Z' layout: resource_detail name: RiboVision products: - category: GraphicalInterface description: Main web portal for RiboVision 2.0 with advanced visualization of RNA molecules format: http id: ribovision.portal name: RiboVision 2.0 Portal product_url: https://ribovision2.chemistry.gatech.edu/ - category: GraphicalInterface description: Interactive phylogenetic browser for exploring ribosomal RNA sequences across 152 species format: http id: ribovision.phylogeny-browser name: Phylogenetic Browser product_url: https://ribovision2.chemistry.gatech.edu/ - category: GraphicalInterface description: 2D RNA topology viewer for visualizing ribosomal RNA secondary structures format: http id: ribovision.2d-viewer name: 2D RNA Topology Viewer product_url: https://ribovision2.chemistry.gatech.edu/ - category: GraphicalInterface description: MolStar-based 3D structure viewer for interactive exploration of ribosome structures format: http id: ribovision.3d-viewer name: 3D Structure Viewer product_url: https://ribovision2.chemistry.gatech.edu/ - category: GraphicalInterface description: MSA viewer for exploring multiple sequence alignments of ribosomal RNA format: http id: ribovision.msa-viewer name: Alignment Viewer product_url: https://ribovision2.chemistry.gatech.edu/ - category: Product description: Database of 152 ribosomal RNA sequences from the DESIRE dataset organized by phylogeny format: http id: ribovision.sequences name: rRNA Sequence Database product_url: https://ribovision2.chemistry.gatech.edu/ - category: Product description: Multiple sequence alignments for ribosomal RNAs generated according to DESIRE methodology format: http id: ribovision.alignments name: rRNA Alignments product_url: https://ribovision2.chemistry.gatech.edu/ - category: Product description: Pre-generated 2D layouts of ribosomal RNAs exported from PDBe API format: http id: ribovision.2d-maps name: 2D Structure Maps product_url: https://ribovision2.chemistry.gatech.edu/ - 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category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Bernier - Petrov - Waterbury - Jett - Li - Freil - Xiong - Wang - Migliozzi - Hershkovits - Xue - Hsiao - Bowman - Harvey - Grover - Wartell - Williams doi: 10.1039/c3fd00126a id: doi:10.1039/c3fd00126a journal: Faraday Discussions preferred: true title: RiboVision suite for visualization and analysis of ribosomes year: '2014' - authors: - Petrov - Bernier - Gulen - Waterbury - Hershkovits - Hsiao - Harvey - Hud - Fox - Wartell - Williams doi: 10.1371/journal.pone.0088222 id: doi:10.1371/journal.pone.0088222 journal: PLoS One title: Secondary structures of rRNAs from all three domains of life year: '2014' - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: emanuelecavalleri - contact_type: email value: emanuele.cavalleri@unimi.it label: Emanuele Cavalleri creation_date: '2025-08-25T00:00:00Z' description: An ontology-based KG for representing interactions involving RNA molecules. domains: - drug discovery - biomedical - health evaluation_page: resource/rna-kg/rna-kg_eval_automated.html homepage_url: https://RNA-KG.biodata.di.unimi.it id: rna-kg last_modified_date: '2025-08-25T00:00:00Z' layout: resource_detail license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: RNA-KG products: - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg publications: - doi: 10.1038/s41597-024-03673-7 id: doi:10.1038/s41597-024-03673-7 title: An ontology-based knowledge graph for representing interactions involving RNA molecules - doi: 10.48550/arXiv.2508.07427 id: doi:10.48550/arXiv.2508.07427 title: 'RNA-KG v2.0: An RNA-centered Knowledge Graph with Properties' - doi: 10.1093/bioadv/vbaf109 id: doi:10.1093/bioadv/vbaf109 title: RNA knowledge-graph analysis through homogeneous embedding methods repository: https://github.com/AnacletoLAB/RNA-KG - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://rnacentral.org/contact id: ebi label: RNAcentral Consortium (EMBL-EBI) creation_date: '2025-07-17T00:00:00Z' description: RNAcentral is the international non-coding RNA (ncRNA) sequence database that aggregates and harmonizes ncRNA sequences and annotations from expert databases across all domains of life. It provides comprehensive search, browse, programmatic access, and bulk downloads for sequences, secondary structures, and cross-references. domains: - genomics homepage_url: https://rnacentral.org/ id: rnacentral infores_id: rnacentral last_modified_date: '2025-09-09T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: RNAcentral products: - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg - category: GraphicalInterface description: Search functionality integrated with RNAcentral for sequence searching format: http id: ribocentre.search name: Sequence Search original_source: - ribocentre - rnacentral product_url: https://www.ribocentre.org/search.html - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-06-25T00:00:00Z' description: Relationship types shared across multiple ontologies domains: - biological systems homepage_url: https://oborel.github.io/ id: ro last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Relation Ontology products: - category: OntologyProduct description: Canonical edition format: owl id: ro.owl name: Relation Ontology product_file_size: 132025 product_url: http://purl.obolibrary.org/obo/ro.owl - category: OntologyProduct description: The obo edition is less expressive than the OWL, and has imports merged in format: obo id: ro.obo name: Relation Ontology in obo format product_file_size: 84333 product_url: http://purl.obolibrary.org/obo/ro.obo - category: OntologyProduct description: Relation Ontology in obojson format format: json id: ro.json name: Relation Ontology in obojson format product_file_size: 114142 product_url: http://purl.obolibrary.org/obo/ro.json - category: OntologyProduct description: Minimal subset intended to work with BFO-classes format: owl id: ro.core.owl name: RO Core relations product_file_size: 7819 product_url: http://purl.obolibrary.org/obo/ro/core.owl - category: OntologyProduct description: Axioms defined within RO and to be used in imports for other ontologies format: owl id: ro.ro-base.owl name: RO base ontology product_file_size: 97499 product_url: http://purl.obolibrary.org/obo/ro/ro-base.owl - category: OntologyProduct description: For use in ecology and environmental science format: owl id: ro.subsets.ro-interaction.owl name: Interaction relations product_file_size: 64252 product_url: http://purl.obolibrary.org/obo/ro/subsets/ro-interaction.owl - category: OntologyProduct description: Ecology subset format: owl id: ro.subsets.ro-eco.owl name: Ecology subset product_url: http://purl.obolibrary.org/obo/ro/subsets/ro-eco.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: For use in neuroscience format: owl id: ro.subsets.ro-neuro.owl name: Neuroscience subset product_file_size: 5164 product_url: http://purl.obolibrary.org/obo/ro/subsets/ro-neuro.owl - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: OntologyProduct description: OWL release of Monochrom Ontology format: owl id: chr.model.owl name: Monochrom Ontology OWL release original_source: - ro - go - ncbitaxon - iao - geno - skos - gff product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl secondary_source: - chr - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/oborel/obo-relations - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: kfecho@copperlineprofessionalsolutions.com label: Karamarie Fecho creation_date: '2025-03-09T00:00:00Z' description: ROBOKOP (Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways) is an open-source biomedical knowledge graph system that enables complex queries over a large-scale integrated knowledge graph. domains: - health evaluation_page: resource/robokop/robokop_eval.html homepage_url: http://robokop.renci.org id: robokop infores_id: robokop last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: ROBOKOP products: - category: Product description: A biomedical knowledge graph containing ~10 million nodes and ~250 million edges from ~30 biological data sources and bio-ontologies. id: robokop.graph name: ROBOKOP Knowledge Graph (KG) original_source: - robokop product_file_size: 280 product_url: http://robokopkg.renci.org secondary_source: - robokop - category: GraphProduct description: Robokop KG (Automat) format: kgx-jsonl id: automat.robokopkg name: robokopkg original_source: - robokop product_url: https://stars.renci.org/var/plater/bl-4.2.1/RobokopKG/4901b2bc764444ea/ secondary_source: - automat - category: GraphProduct description: Robokop Plus format: kgx-jsonl id: automat.robokopplus name: robokopplus original_source: - robokop product_url: https://stars.renci.org/var/plater/bl-3.1.2/RobokopPlus/ad8cb4d0a7ccc923/kgx_files/ secondary_source: - automat repository: https://github.com/NCATS-Gamma/robokop - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for ror. This page was automatically generated because it was referenced by other resources. domains: - stub id: ror last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Ror products: - category: Product description: ror Nodes TSV format: tsv id: obo-db-ingest.ror.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: ror Nodes TSV original_source: - ror product_file_size: 5381101 product_url: https://w3id.org/biopragmatics/resources/ror/ror.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: sjwang@mcw.edu - contact_type: github value: shurjenw label: Shur-Jen Wang orcid: 0000-0001-5256-8683 creation_date: '2025-09-29T00:00:00Z' description: Ontology of rat strains domains: - biological systems homepage_url: http://rgd.mcw.edu/rgdweb/search/strains.html id: rs last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Rat Strain Ontology products: - category: OntologyProduct description: Rat Strain Ontology in OWL format format: owl id: rs.owl name: rs.owl product_file_size: 5526359 product_url: http://purl.obolibrary.org/obo/rs.owl - category: OntologyProduct description: Rat Strain Ontology in OBO format format: obo id: rs.obo name: rs.obo product_url: http://purl.obolibrary.org/obo/rs.obo repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology taxon: - NCBITaxon:10114 - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual contact_details: - contact_type: email value: ramseyst@oregonstate.edu - contact_type: github value: saramsey label: Stephen Ramsey orcid: 0000-0002-2168-5403 creation_date: '2025-03-09T00:00:00Z' description: RTX-KG2 is a comprehensive biomedical knowledge graph that integrates information from over 80 structured knowledge sources into a semantically standardized model, supporting translational biomedicine and the ARAX biomedical reasoning system. domains: - health - biomedical - biological systems - genomics - pharmacology evaluation_page: resource/rtx-kg2/rtx-kg2_eval.html homepage_url: https://github.com/RTXteam/RTX-KG2 id: rtx-kg2 infores_id: rtx-kg2 last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: RTX-KG2 products: - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProcessProduct description: Code for building RTX-KG2, in Python id: rtx-kg2.code name: Code for building RTX-KG2 product_url: https://github.com/RTXteam/RTX-KG2 secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 publications: - authors: - Wood EC - Glen AK - Kvarfordt LG - Colby LA - Unni DR - Himmelstein DS - Lee AY - Ramsey SA doi: doi:10.1186/s12859-022-04932-3 id: https://doi.org/10.1186/s12859-022-04932-3 journal: BMC Bioinformatics preferred: true title: 'RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine' year: '2022' repository: https://github.com/RTXteam/RTX-KG2 - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: jiaqi.gong@ua.edu label: Jiaqi Gong creation_date: '2025-12-08T00:00:00Z' description: Rural Resilience KG is a cross-domain knowledge graph to integrate health and justice for rural resilience, connecting data about healthcare access, legal services, and community resources in rural areas. domains: - health - social determinants evaluation_page: resource/ruralkg/ruralkg_eval_automated.html homepage_url: https://frink.apps.renci.org/ruralkg/sparql id: ruralkg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: Rural Resilience KG products: - category: ProgrammingInterface description: SPARQL endpoint for Rural Resilience KG id: ruralkg.sparql name: Rural Resilience KG SPARQL original_source: - ruralkg product_url: https://frink.apps.renci.org/ruralkg/sparql - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: batchelorc@rsc.org - contact_type: github value: batchelorc label: Colin Batchelor orcid: 0000-0001-5985-7429 creation_date: '2025-09-29T00:00:00Z' description: Connects organic name reactions to their roles in an organic synthesis and to processes in MOP domains: - chemistry and biochemistry homepage_url: https://github.com/rsc-ontologies/rxno id: rxno last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Name Reaction Ontology products: - category: OntologyProduct description: Name Reaction Ontology format: owl id: rxno.owl name: Name Reaction Ontology product_file_size: 95394 product_url: http://purl.obolibrary.org/obo/rxno.owl repository: https://github.com/rsc-ontologies/rxno - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: rxnorminfo@nlm.nih.gov - contact_type: url value: https://www.nlm.nih.gov/research/umls/rxnorm/ id: ncbi label: National Library of Medicine creation_date: '2025-11-08T00:00:00Z' description: RxNorm is the National Library of Medicine's standardized nomenclature for clinical drugs, providing normalized names and unique concept identifiers (RxCUIs) for medications. Developed to support interoperability between healthcare systems, RxNorm links its standardized drug names to the vocabularies commonly used in pharmacy management and drug interaction software, including First Databank, Micromedex, Multum, and Gold Standard Drug Database. By providing links between these diverse vocabularies, RxNorm enables seamless communication between systems that do not use the same software or terminology. RxNorm organizes drug information into a hierarchy of term types representing different levels of specificity, from ingredients through clinical drug components to specific branded and generic products. The nomenclature covers prescription drugs, over-the-counter medications, and now includes the United States Pharmacopeia Compendial Nomenclature containing all Active Pharmaceutical Ingredients. RxNorm is updated monthly with new drug products, revisions to existing entries, and retirement of obsolete terms to maintain currency with the evolving pharmaceutical landscape. The system supports multiple use cases including electronic health records, e-prescribing, pharmacy management systems, drug interaction checking, clinical decision support, and public health surveillance. domains: - health homepage_url: https://www.nlm.nih.gov/research/umls/rxnorm/ id: rxnorm infores_id: rxnorm last_modified_date: '2026-01-15T00:00:00Z' layout: resource_detail name: RxNorm products: - category: Product description: Monthly releases of RxNorm data files in multiple formats including RRF files for the full vocabulary and relationships format: http id: rxnorm.data_files name: RxNorm Data Files original_source: - rxnorm product_url: https://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html - category: ProgrammingInterface description: RESTful web services providing programmatic access to RxNorm drug terminology data including drug names, identifiers, relationships, and properties format: http id: rxnorm.api is_public: true name: RxNorm API original_source: - rxnorm product_url: https://rxnav.nlm.nih.gov/RxNormAPIs.html - category: GraphicalInterface description: Interactive web browser for searching and exploring RxNorm drug concepts, relationships, and properties with multiple viewing options format: http id: rxnorm.rxnav is_public: true name: RxNav Browser original_source: - rxnorm product_url: https://mor.nlm.nih.gov/RxNav/ - category: GraphicalInterface description: Tool for exploring drug class hierarchies and finding RxNorm drug members associated with each class from multiple classification systems format: http id: rxnorm.rxclass is_public: true name: RxClass original_source: - rxnorm product_url: https://mor.nlm.nih.gov/RxClass/ - category: ProgrammingInterface description: Interactive tool allowing users to combine multiple API functions to build custom drug information applications format: http id: rxnorm.rxmix is_public: true name: RxMix original_source: - rxnorm product_url: https://mor.nlm.nih.gov/RxMix/ - category: Product description: Locally installable package containing RxNav, RxClass, RxMix tools and RESTful APIs for offline use format: http id: rxnorm.rxnav_in_a_box name: RxNav-in-a-Box original_source: - rxnorm product_url: https://lhncbc.nlm.nih.gov/RxNav/applications/RxNav-in-a-Box.html - category: Product description: VANDF data integrated into RxNorm id: ndfrt.rxnorm name: VANDF in RxNorm original_source: - ndfrt product_url: https://www.nlm.nih.gov/research/umls/rxnorm/ secondary_source: - rxnorm publications: - category: Publication id: PMID:21515544 preferred: true taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: katrina.schweikert@maine.edu - contact_type: github value: kschweikert label: Katrina Schweikert creation_date: '2025-12-08T00:00:00Z' description: The Safe Agricultural Products and Water Graph (SAWGraph) PFAS graph stores data on PFAS observations and releases, describing the samples, the geospatial features they were taken from, the sampled environmental media, the specific chemical substances and the measurement values observed. domains: - environment - chemistry and biochemistry - agriculture evaluation_page: resource/sawgraph/sawgraph_eval_automated.html homepage_url: https://sawgraph.github.io/ id: sawgraph last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SAWGraph PFAS graph products: - category: ProgrammingInterface description: SPARQL endpoint for SAWGraph PFAS graph id: sawgraph.sparql name: SAWGraph PFAS SPARQL original_source: - sawgraph product_url: https://frink.apps.renci.org/sawgraph/sparql repository: https://github.com/sawgraph - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: sheriff@ebi.ac.uk - contact_type: github value: rsmsheriff label: Rahuman Sheriff orcid: 0000-0003-0705-9809 creation_date: '2025-06-04T00:00:00Z' description: Terms commonly used in Systems Biology, and in particular in computational modeling. domains: - chemistry and biochemistry homepage_url: http://www.ebi.ac.uk/sbo/ id: sbo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://opensource.org/licenses/Artistic-2.0 label: Artistic License 2.0 name: Systems Biology Ontology products: - category: OntologyProduct description: Systems Biology Ontology in OWL format format: owl id: sbo.owl name: sbo.owl product_file_size: 50738 product_url: http://purl.obolibrary.org/obo/sbo.owl - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg repository: https://github.com/EBI-BioModels/SBO - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: danny.e.oneal@gmail.com - contact_type: github value: danny-oneal label: Danny O'Neal - category: Individual contact_details: - contact_type: email value: scottgdaniel@gmail.com - contact_type: github value: scottgdaniel label: Scott Daniel creation_date: '2025-12-08T00:00:00Z' description: SCALES is an integrated justice platform to connect criminal justice data across data silos, enabling comprehensive analysis of court records, sentencing data, and legal outcomes. domains: - social determinants evaluation_page: resource/scales/scales_eval_automated.html homepage_url: https://scales-okn.org/ id: scales last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SCALES products: - category: ProgrammingInterface description: SPARQL endpoint for SCALES id: scales.sparql name: SCALES SPARQL original_source: - scales product_url: https://frink.apps.renci.org/scales/sparql - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: giant.plankton@gmail.com - contact_type: github value: JadeHotchkiss label: Jade Hotchkiss orcid: 0000-0002-2193-0704 creation_date: '2025-09-29T00:00:00Z' description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. domains: - biomedical homepage_url: https://scdontology.h3abionet.org/ id: scdo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://www.gnu.org/licenses/gpl-3.0.en.html label: GPL-3.0 name: Sickle Cell Disease Ontology products: - category: OntologyProduct description: Sickle Cell Disease Ontology in OWL format format: owl id: scdo.owl name: scdo.owl product_file_size: 367519 product_url: http://purl.obolibrary.org/obo/scdo.owl - category: OntologyProduct description: Sickle Cell Disease Ontology in OBO format format: obo id: scdo.obo name: scdo.obo product_file_size: 324416 product_url: http://purl.obolibrary.org/obo/scdo.obo repository: https://github.com/scdodev/scdo-ontology - activity_status: active category: Resource contacts: - category: Individual contact_details: - contact_type: github value: emmaco label: Emma Cooke creation_date: '2025-03-10T00:00:00Z' description: Data produced by SciBite domains: - biological systems homepage_url: https://scibite.com/ id: scibite infores_id: scibite last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: SciBite products: - category: Product compression: zip description: This HGNC OWL file is generated from the data at https://www.genenames.org/. It contains all genes in HGNC organised in a shallow hierarchy, classified by their locus type and gene group. Gene groups are also derived from HGNC. The ontology contains approved gene symbol, approved gene name, previous names and symbols and mappings to external databases. format: owl id: scibite.hgnc license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: SciBite HGNC original_source: - hgnc product_url: https://github.com/elsevier-health/scibite-ontology/blob/main/hgnc_2025_02_04.owl.zip repository: https://github.com/elsevier-health/scibite-ontology secondary_source: - scibite warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: SCKAN (SPARC Connectivity Knowledge base of the Autonomic Nervous system) is a curated knowledge base representing neural circuit connectivity in the autonomic nervous system, derived from SPARC data, anatomical expert interviews, and scientific literature. It supports reasoning and querying of central and peripheral nervous system-end organ circuitry, including detailed ApiNATOMY models for organs such as bladder, heart, colon, stomach, spleen, pancreas, and airways. domains: - biological systems - anatomy and development id: sckan last_modified_date: '2025-10-15T00:00:00Z' layout: resource_detail name: SCKAN products: - category: GraphicalInterface description: Interactive computational notebook (Org mode) for querying SCKAN via SPARQL and Cypher, supporting parameterized queries, code blocks, and graphical results. Distributed as a Docker image. format: http id: sckan.query_interface name: SCKAN Query Interface (Docker) product_url: https://github.com/SciCrunch/sparc-curation/tree/master/docs/sckan#download-docker-and-x11 - category: Product description: Detailed ApiNATOMY models of neural circuits for organs including bladder, heart, colon, stomach, spleen, pancreas, and airways. Models are available in open-physiology repositories. format: http id: sckan.apinatomy name: SCKAN ApiNATOMY Models product_url: https://github.com/open-physiology/apinatomy-models - category: DocumentationProduct description: Documentation, setup instructions, tutorials, and example queries for using and exploring SCKAN. format: http id: sckan.docs name: SCKAN Documentation and Tutorials product_url: https://github.com/SciCrunch/sparc-curation/tree/master/docs/sckan - category: Product description: Latest SCKAN data release, including curated knowledge and models, available via Zenodo. format: http id: sckan.data_release name: SCKAN Data Release product_url: https://doi.org/10.5281/zenodo.5337441 - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: tianyi@purdue.edu label: Tianyi Zhang creation_date: '2025-12-08T00:00:00Z' description: SecureChain is a knowledge graph for resilient, trustworthy, and secure software supply chains, providing structured data about software components, dependencies, vulnerabilities, and security practices. domains: - information technology evaluation_page: resource/securechainkg/securechainkg_eval_automated.html homepage_url: https://purdue-hcss.github.io/nsf-software-supply-chain_security/ id: securechainkg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SecureChain KG products: - category: ProgrammingInterface description: SPARQL endpoint for SecureChain KG id: securechainkg.sparql name: SecureChain KG SPARQL original_source: - securechainkg product_url: https://frink.apps.renci.org/securechainkg/sparql - activity_status: active category: Ontology contacts: - category: Individual contact_details: - contact_type: github value: matentzn label: Nicolas Matentzoglu orcid: 0000-0002-7356-1779 - category: Individual contact_details: - contact_type: github value: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-12-03T00:00:00Z' description: The Semantic Mapping Vocabulary (SEMAPV) is a vocabulary for describing the processes, entities, and agents involved in the curation of semantic mappings between ontologies and terminologies. SEMAPV is developed in conjunction with the Simple Standard for Sharing Ontology Mappings (SSSOM), providing detailed vocabulary to describe different kinds of matching processes (lexical, logical, etc.) as well as pre- and post-processing techniques employed in mapping workflows. domains: - general homepage_url: https://mapping-commons.github.io/semantic-mapping-vocabulary/ id: semapv last_modified_date: '2025-12-03T00:00:00Z' layout: resource_detail name: Semantic Mapping Vocabulary products: - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/mapping-commons/semantic-mapping-vocabulary synonyms: - SEMAPV - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: lew.lefton@gmail.com label: Lew Lefton creation_date: '2025-12-08T00:00:00Z' description: SemOpenAlex provides comprehensive information on scientific publications and related entities, offering a semantic layer over the OpenAlex scholarly database with linked data about papers, authors, institutions, and citations. domains: - literature evaluation_page: resource/semopenalex/semopenalex_eval_automated.html homepage_url: https://semopenalex.org/ id: semopenalex last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SemOpenAlex products: - category: ProgrammingInterface description: SPARQL endpoint for SemOpenAlex id: semopenalex.sparql name: SemOpenAlex SPARQL original_source: - semopenalex product_url: https://frink.apps.renci.org/semopenalex/sparql - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://sennetconsortium.org/ label: SenNet Consortium creation_date: '2025-11-05T00:00:00Z' description: The Cellular Senescence Network (SenNet) is an NIH Common Fund program that aims to comprehensively identify and characterize senescent cells across the human lifespan and in various disease states. SenNet provides spatial molecular maps of senescent cells in tissues, developing and applying cutting-edge technologies for detecting cellular senescence. The consortium generates multi-omics data, imaging data, and develops computational tools to advance understanding of how senescent cells contribute to aging and age-related diseases. domains: - health - biomedical - anatomy and development - genomics - precision medicine homepage_url: https://sennetconsortium.org/ id: sennet last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: SenNet products: - category: GraphicalInterface description: Data portal for browsing and accessing SenNet datasets format: http id: sennet.portal name: SenNet Data Portal original_source: - sennet product_url: https://data.sennetconsortium.org/ - category: Product description: Multi-omics datasets of senescent cells format: mixed id: sennet.data name: SenNet Multi-Omics Data original_source: - sennet product_url: https://data.sennetconsortium.org/ - category: ProgrammingInterface description: API for programmatic access to SenNet data format: http id: sennet.api name: SenNet API original_source: - sennet product_url: https://sennetconsortium.org/ - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg synonyms: - SenNet - Cellular Senescence Network taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mhb120@gmail.com - contact_type: github value: mbrush label: Matthew Brush orcid: 0000-0002-1048-5019 creation_date: '2025-09-29T00:00:00Z' description: An ontology for representing the provenance of scientific claims and the evidence that supports them. domains: - biomedical homepage_url: https://github.com/monarch-initiative/SEPIO-ontology id: sepio last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Scientific Evidence and Provenance Information Ontology products: - category: OntologyProduct description: SEPIO format: owl id: sepio.owl name: SEPIO product_file_size: 75985 product_url: http://purl.obolibrary.org/obo/sepio.owl repository: https://github.com/monarch-initiative/SEPIO-ontology - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual label: Chunlei Wu creation_date: '2025-03-09T00:00:00Z' description: A Translator Knowledge Provider domains: - health evaluation_page: resource/service-kp/service-kp_eval_automated.html id: service-kp last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Service KP products: - category: DocumentationProduct description: Team documentation for the Translator Service Provider. format: http id: service-kp.docs name: Service KP Documentation original_source: - service-kp product_url: https://github.com/NCATSTranslator/Translator-All/wiki/Service-Provider - category: GraphicalInterface description: SmartAPI Translator portal for browsing registered Translator APIs. format: http id: service-kp.portal name: Service KP SmartAPI Portal original_source: - service-kp product_url: https://smart-api.info/portal/translator - category: ProcessProduct description: BioThings API stack source repository used by the Service Provider team. format: http id: service-kp.code name: Service KP Source Code original_source: - service-kp product_url: https://github.com/biothings/biothings.api - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: sgd-helpdesk@lists.stanford.edu label: SGD Helpdesk creation_date: '2025-03-09T00:00:00Z' description: The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae. domains: - biological systems homepage_url: https://www.yeastgenome.org/ id: sgd infores_id: sgd last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Saccharomyces Genome Database products: - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database - category: Product description: Model organism data from FlyBase, SGD, ZFIN and other model organism databases format: http id: genecards.model.organisms name: GeneCards Model Organism Data original_source: - flybase - sgd - zfin product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - 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sgd product_file_size: 503057 product_url: https://w3id.org/biopragmatics/resources/sgd/sgd.tsv secondary_source: - obo-db-ingest taxon: - NCBITaxon:4932 - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: julien.gobeill@hesge.ch label: Julien Gobeill - category: Organization contact_details: - contact_type: url value: https://sibils.org/ id: sib label: SIBiLS - Swiss Institute of Bioinformatics Literature Services creation_date: '2025-05-07T00:00:00Z' description: SIBiLS (Swiss Institute of Bioinformatics Literature Services) provides personalized information retrieval in biological literature, with customizable search in semantically enriched contents based on keywords and mapped biomedical entities from standardized vocabularies. domains: - biological systems - health homepage_url: https://sibils.org/ id: sibils last_modified_date: '2025-12-07T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ch/ label: CC-BY-3.0-CH logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: SIBiLS products: - category: GraphicalInterface description: Web interface for exploring SIBiLS data id: sibils.site is_public: true name: SIBiLS Web Interface original_source: - sibils product_url: https://sibils.org/ secondary_source: - sibils - category: ProgrammingInterface description: SPARQL endpoint for querying SIBiLS data id: sibils.api.sparql is_public: true name: SIBiLS SPARQL Endpoint original_source: - sibils product_url: https://sparql.sibils.org/sparql secondary_source: - sibils - category: ProgrammingInterface description: RESTful API for fetching annotated contents from SIBiLS collections id: sibils.api.rest.fetch is_public: true name: SIBiLS Fetch API original_source: - sibils product_url: https://sibils.org/API#Fetch-API secondary_source: - sibils - category: ProgrammingInterface description: RESTful API for customizable search in SIBiLS collections id: sibils.api.rest.search is_public: true name: SIBiLS Search API original_source: - sibils product_url: https://sibils.org/API#Customizable-search-API secondary_source: - sibils - category: ProgrammingInterface description: RESTful API for question answering using natural language in SIBiLS collections id: sibils.api.rest.qa is_public: true name: SIBiLS Question Answering API original_source: - sibils product_url: https://sibils.org/API#Question-Answering-API secondary_source: - sibils publications: - authors: - Gobeill J - Caucheteur D - Michel PA - Mottin L - Pasche E - Ruch P doi: doi:10.1093/nar/gkaa328 id: doi:10.1093/nar/gkaa328 preferred: true title: 'SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts' year: '2020' - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: url value: https://signor.uniroma2.it/contact.php label: SIGNOR Team (University of Rome Tor Vergata & Sapienza University of Rome) creation_date: '2025-08-12T00:00:00Z' description: SIGNOR (SIGnaling Network Open Resource) is a manually curated repository of experimentally supported, causal relationships between human proteins and other biologically relevant entities (chemicals, phenotypes, complexes, families, stimuli). Each interaction is annotated with effect, mechanism, directionality, evidence (PMID), and a relevance score, enabling construction and analysis of signed, directed signaling networks and pathways. Cite SIGNOR (Lo Surdo et al., 2022 NAR) when using data; interaction data are directional and signed—verify effect/mechanism fields when integrating. domains: - pathways - biomedical - systems biology - proteomics homepage_url: https://signor.uniroma2.it/ id: signor infores_id: signor last_modified_date: '2025-08-23T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: SIGNOR products: - category: GraphicalInterface description: Web interface for browsing entities, pathways, and visualizing causal signaling graphs format: http id: signor.web name: SIGNOR Website original_source: - signor product_url: https://signor.uniroma2.it/ - category: ProgrammingInterface description: REST-style endpoints for retrieving interaction, pathway, complex, and organism-specific datasets (tab-separated) format: http id: signor.api is_public: true name: SIGNOR REST API original_source: - signor product_url: https://signor.uniroma2.it/APIs.php - category: GraphProduct compression: zip description: Latest stable SIGNOR complete dataset (signed, directed causal interactions with effects, mechanisms, PMIDs, scores) format: tsv id: signor.complete name: SIGNOR Latest Stable Release original_source: - signor product_url: https://signor.uniroma2.it/releases/getLatestRelease.php - category: ProgrammingInterface description: Programmatic interaction data query returning tab-separated causal interaction records for specified entity IDs with configurable depth and type format: tsv id: signor.interactions.dynamic name: SIGNOR Interaction Query Endpoint original_source: - signor product_url: https://signor.uniroma2.it/getData.php - category: ProgrammingInterface description: Pathway data (entities and relations) retrievable via parameterized REST calls supporting per-pathway or global views format: tsv id: signor.pathways name: SIGNOR Pathway Data original_source: - signor product_url: https://signor.uniroma2.it/getPathwayData.php - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: KGX graph package for SIGNOR causal interactions (build signor_2025_Oct_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.signor.graph name: Translator SIGNOR KGX Graph original_source: - signor product_url: https://stars.renci.org/var/translator/releases/signor/2025_12_15/ secondary_source: - translator - category: Product description: signor Nodes TSV format: tsv id: obo-db-ingest.signor.tsv license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC-BY-NC-4.0 name: signor Nodes TSV original_source: - signor product_file_size: 29422 product_url: https://w3id.org/biopragmatics/resources/signor/signor.tsv secondary_source: - obo-db-ingest publications: - id: https://doi.org/10.1093/nar/gkac883 journal: Nucleic Acids Research preferred: true title: 'SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update' year: '2022' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: email value: silva@dsmz.de - contact_type: url value: https://www.arb-silva.de/contact label: SILVA Team creation_date: '2025-09-09T00:00:00Z' description: SILVA is a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data. It provides regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA sequences for all three domains of life (Bacteria, Archaea and Eukarya). SILVA is a Global Core Biodata Resource and ELIXIR Core Data Resource, currently maintaining over 9.4 million SSU sequences in release 138.2. domains: - microbiology - genomics - biological systems - organisms - biomedical homepage_url: https://www.arb-silva.de/ id: silva last_modified_date: '2025-09-24T00:00:00Z' layout: resource_detail name: SILVA products: - category: GraphicalInterface description: Web-based search interface for SILVA ribosomal RNA sequences with advanced filtering and taxonomic browsing capabilities format: http id: silva.search name: SILVA Search original_source: - silva product_url: https://www.arb-silva.de/search - category: GraphicalInterface description: Interactive browser for exploring SILVA taxonomic hierarchy and sequence data with phylogenetic context format: http id: silva.browser name: SILVA Browser original_source: - silva product_url: https://www.arb-silva.de/browser - category: ProcessProduct description: SILVA Incremental Aligner (SINA) for accurate alignment of ribosomal RNA sequences against curated reference alignments format: http id: silva.aligner name: SILVA Alignment, Classification and Tree Service (ACT) original_source: - silva product_url: https://www.arb-silva.de/aligner - category: Product description: Comprehensive release files including FASTA sequences, alignments, taxonomies, and ARB database files for SSU and LSU rRNA format: mixed id: silva.release_files name: SILVA Release Files original_source: - silva product_url: https://www.arb-silva.de/current-release - category: ProcessProduct description: TestPrime tool for in silico evaluation of PCR primer coverage and specificity against SILVA sequences format: http id: silva.testprime name: SILVA TestPrime original_source: - silva product_url: https://www.arb-silva.de/testprime - category: ProcessProduct description: TestProbe tool for in silico evaluation of hybridization probe coverage and specificity against SILVA sequences format: http id: silva.testprobe name: SILVA TestProbe original_source: - silva product_url: https://www.arb-silva.de/testprobe - category: Product description: ARB-formatted database files for phylogenetic analysis and sequence management in the ARB software environment format: mixed id: silva.arb_files name: SILVA ARB Files original_source: - silva product_url: https://www.arb-silva.de/arb-files - category: ProcessProduct description: SILVAngs pipeline for high-throughput analysis of ribosomal RNA gene amplicons from next-generation sequencing data format: http id: silva.ngs_pipeline name: SILVAngs original_source: - silva product_url: https://ngs.arb-silva.de/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Christian Quast - Elmar Pruesse - Pelin Yilmaz - Jan Gerken - Timmy Schweer - Pablo Yarza - Jörg Peplies - Frank Oliver Glöckner doi: 10.1093/nar/gks1219 id: doi:10.1093/nar/gks1219 title: 'The SILVA ribosomal RNA gene database project: improved data processing and web-based tools' year: '2013' - authors: - Pelin Yilmaz - Linda Wegener Parfrey - Pablo Yarza - Jan Gerken - Elmar Pruesse - Christian Quast - Timmy Schweer - Jörg Peplies - Wolfgang Ludwig - Frank Oliver Glöckner doi: 10.1093/nar/gkt1209 id: doi:10.1093/nar/gkt1209 title: The SILVA and 'All-species Living Tree Project (LTP)' taxonomic frameworks year: '2014' repository: https://github.com/epruesse/SINA taxon: - NCBITaxon:2 - NCBITaxon:2157 - activity_status: active category: KnowledgeGraph collection: - ber contacts: - category: Individual contact_details: - contact_type: email value: kristina.gruden@nib.si label: Kristina Gruden - category: Individual contact_details: - contact_type: email value: carissa.bleker@nib.si label: Carissa Bleker - category: Organization contact_details: - contact_type: url value: https://www.nib.si/ label: National Institute of Biology Slovenia creation_date: '2025-06-17T00:00:00Z' description: A comprehensive knowledge graph resource for systems biology analysis of plant stress responses, containing mechanistic models and knowledge networks for plant stress signaling. It includes two knowledge graphs, the mechanistic Plant Stress Signalling model (PSS) and the Comprehensive Knowledge Network (CKN). domains: - plant science - organisms - systems biology - pathways evaluation_page: resource/skm/skm_eval_automated.html homepage_url: https://skm.nib.si/ id: skm language: en last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by-nc-sa/3.0/ label: CC-BY-NC-SA-3.0 name: Stress Knowledge Map products: - category: GraphicalInterface description: Interactive search and visualization tool for the mechanistic Plant Stress Signalling model id: skm.pss.explorer name: PSS Explorer original_source: - skm product_url: https://skm.nib.si/pss - category: GraphicalInterface description: Interactive search and visualization tool for the Comprehensive Knowledge Network id: skm.ckn.explorer name: CKN Explorer original_source: - skm product_url: https://skm.nib.si/ckn - category: GraphProduct description: Current PSS model in Systems Biology Graphical Notation XML format format: sbgnml id: skm.pss.live.sbgn name: PSS Live Download (SBGN-ML) original_source: - skm product_file_size: 3204548 product_url: https://skm.nib.si/downloads/pss/public/sbgn - category: GraphProduct description: Current PSS model in Systems Biology Markup Language XML format format: sbml id: skm.pss.live.sbml name: PSS Live Download (SBML) original_source: - skm product_file_size: 548527 product_url: https://skm.nib.si/downloads/pss/public/sbml - category: GraphProduct description: Current PSS model in DOT Language format compatible with Graphviz format: dot id: skm.pss.live.dot name: PSS Live Download (DOT) original_source: - skm product_file_size: 595369 product_url: https://skm.nib.si/downloads/pss/public/graphviz - category: GraphProduct description: Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are represented as nodes (as in PSS Explorer and database schema). format: sif id: skm.pss.live.sif.original.graph name: PSS Live Download, original (SIF/LGL) original_source: - skm product_file_size: 161651 product_url: https://skm.nib.si/downloads/pss/public/sif-edges - category: GraphProduct description: Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are represented as nodes (as in PSS Explorer and database schema). This file contains the node annotations. format: sif id: skm.pss.live.sif.original.annotations name: PSS Live Download, original (SIF/LGL), node annotations original_source: - skm product_file_size: 401897 product_url: https://skm.nib.si/downloads/pss/public/sif-nodes - category: GraphProduct description: Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are collapsed to edges. format: sif id: skm.pss.live.sif.projection.graph name: PSS Live Download, projection (SIF/LGL) original_source: - skm product_file_size: 253631 product_url: https://skm.nib.si/downloads/pss/public/rxn-edges - category: GraphProduct description: Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are collapsed to edges. This file contains the node annotations. format: sif id: skm.pss.live.sif.projection.annotations name: PSS Live Download, projection (SIF/LGL), node annotations original_source: - skm product_file_size: 163587 product_url: https://skm.nib.si/downloads/pss/public/rxn-nodes - category: GraphProduct description: Current PSS model in Simple Interaction Format compatible with Cytoscape. Reactions are collapsed to edges, FunctionalClusters are expanded to arabidopsis identifiers. format: sif id: skm.pss.live.sif.dinar.graph name: PSS Live Download, DiNAR (SIF/LGL) original_source: - skm product_file_size: 361747 product_url: https://skm.nib.si/downloads/pss/public/dinar-edges - category: GraphProduct description: Current PSS model in Boolean network format compatible with BoolDog and BoolNet format: boolnet id: skm.pss.live.boolnet.graph name: PSS Live Downloads (BoolNet) original_source: - skm product_file_size: 53198 product_url: https://skm.nib.si/downloads/pss/public/boolnet - category: GraphProduct description: Current PSS model in Boolean network format compatible with BoolDog and BoolNet. This file contains the node annotations. format: boolnet id: skm.pss.live.boolnet.annotations name: PSS Live Downloads (BoolNet), node annotations original_source: - skm product_file_size: 70946 product_url: https://skm.nib.si/downloads/pss/public/boolnet-annot - category: GraphProduct description: Comprehensive Knowledge Network v2 in SIF/LGL format with 26,234 entities and ~500,000 interactions edge_count: 500000 format: sif id: skm.ckn.v2.graph name: CKN v2 (June 2023) node_count: 26234 original_source: - skm product_file_size: 2732107 product_url: https://skm.nib.si/downloads/ckn/v2-2023.06 - category: GraphProduct description: Comprehensive Knowledge Network v2 in SIF/LGL format with 26,234 entities and ~500,000 interactions. This file contains the node annotations. format: sif id: skm.ckn.v2.annotations name: CKN v2 (June 2023), node annotations original_source: - skm product_file_size: 885747 product_url: https://skm.nib.si/downloads/ckn-annot/v2-2023.06 - category: GraphProduct description: Comprehensive Knowledge Network v1 in SIF/LGL format format: sif id: skm.ckn.v1.graph name: CKN v1 (June 2018) original_source: - skm product_file_size: 318666 product_url: https://skm.nib.si/downloads/ckn/v1-2018.06 - category: GraphProduct description: Comprehensive Knowledge Network v1 in SIF/LGL format. This file contains the node annotations. format: sif id: skm.ckn.v1.annotations name: CKN v1 (June 2018), node annotations original_source: - skm product_file_size: 702407 product_url: https://skm.nib.si/downloads/ckn-annot/v1-2018.06 publications: - authors: - Carissa Bleker - Živa Ramšak - Andras Bittner - Vid Podpečan - Maja Zagorščak - Bernhard Wurzinger - Špela Baebler - Marko Petek - Maja Križnik - Annelotte van Dieren - Juliane Gruber - Leila Afjehi-Sadat - Wolfram Weckwert - Anže Županič - Markus Teige - Ute C. Vothknecht - Kristina Gruden doi: doi:10.1016/j.xplc.2024.100920 id: https://doi.org/10.1016/j.xplc.2024.100920 journal: Plant Communications title: 'Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses' year: '2024' repository: https://github.com/NIB-SI/skm-tools taxon: - NCBITaxon:33090 version: '1.0' - activity_status: active category: DataModel creation_date: '2025-06-25T00:00:00Z' description: SKOS (Simple Knowledge Organization System) is a W3C recommendation designed for representation of thesauri, classification schemes, taxonomies, subject-heading systems, or any other type of structured controlled vocabulary. domains: - upper homepage_url: https://www.w3.org/2004/02/skos/ id: skos last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://www.w3.org/Consortium/Legal/2015/copyright-software-and-document label: W3C Software and Document License name: SKOS products: - category: DataModelProduct description: SKOS Namespace Document - RDF/XML Variant format: rdfxml id: skos.rdf name: SKOS RDF/XML product_file_size: 28966 product_url: https://www.w3.org/2009/08/skos-reference/skos.rdf - category: DataModelProduct description: SKOS Core Vocabulary Specification format: http id: skos.core name: SKOS Core product_url: https://www.w3.org/TR/swbp-skos-core-spec/ - category: DocumentationProduct description: SKOS Simple Knowledge Organization System Reference format: http id: skos.reference name: SKOS Reference product_url: https://www.w3.org/TR/skos-reference/ - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: OntologyProduct description: Cell Line Ontology in OWL format format: owl id: clo.owl name: clo.owl product_file_size: 2121232 product_url: http://purl.obolibrary.org/obo/clo.owl - category: OntologyProduct description: EDAM OWL release format: owl id: edam.owl name: EDAM OWL original_source: - edam - dc - skos product_file_size: 3373041 product_url: http://edamontology.org/EDAM.owl secondary_source: - edam - category: OntologyProduct description: EDAM TSV export format: tsv id: edam.tsv name: EDAM TSV original_source: - edam - dc - skos product_file_size: 1977072 product_url: https://edamontology.org/EDAM.tsv secondary_source: - edam - category: OntologyProduct description: EDAM CSV export format: csv id: edam.csv name: EDAM CSV original_source: - edam - dc - skos product_file_size: 1977072 product_url: https://edamontology.org/EDAM.csv secondary_source: - edam - category: OntologyProduct description: OWL release of Monochrom Ontology format: owl id: chr.model.owl name: Monochrom Ontology OWL release original_source: - ro - go - ncbitaxon - iao - geno - skos - gff product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl secondary_source: - chr - category: GraphProduct description: Downloadable knowledge graph dump in TAR/GZ format containing complete FORUM data id: forum.graph.dump name: FORUM Knowledge Graph Dump original_source: - mesh - chebi - cito - fabio - dc - cheminf - skos - chemont - pubchem - pubmed product_url: ftp://forum:Forum2021Cov!@ftp.semantic-metabolomics.org/dumps/2021/share.tar.gz secondary_source: - forum warnings: - File was not able to be retrieved when checked on 2026-03-08_ FTP error_ timed out - File was not able to be retrieved when checked on 2026-02-26_ FTP error_ timed out - 'File was not able to be retrieved when checked on 2026-03-11: FTP error: timed out' - category: OntologyProduct description: OpenBioDiv-O, the OpenBiodiv Ontology format: ttl id: openbiodiv.ontology.ttl is_public: true name: OpenBioDiv-O original_source: - skos - proton - fabio - doco - openbiodiv product_file_size: 8176 product_url: https://raw.githubusercontent.com/pensoft/OpenBiodiv/refs/heads/master/ontology/openbiodiv-ontology-latest.ttl secondary_source: - openbiodiv publications: - authors: - Alistair Miles - Sean Bechhofer doi: 10.1016/j.websem.2009.06.001 id: doi:10.1016/j.websem.2009.06.001 journal: 'Web Semantics: Science, Services and Agents on the World Wide Web' title: SKOS Simple Knowledge Organization System Reference year: '2009' repository: https://github.com/w3c/skos version: SKOS Reference (August 18, 2009) - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: pnrobinson label: Peter Robinson creation_date: '2025-03-09T00:00:00Z' description: A graph of synthetic lethal interactions. domains: - organisms evaluation_page: resource/sldb/sldb_eval_automated.html homepage_url: https://kghub.io/sldb/ id: sldb last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: sldb products: - category: ProcessProduct description: Source code for building the synthetic lethal interaction graph. format: http id: sldb.code name: SLDB Source Repository original_source: - sldb product_url: https://github.com/monarch-initiative/SLDBGen - category: DocumentationProduct description: Project README and documentation for SLDB graph generation and usage. format: http id: sldb.docs name: SLDB Documentation original_source: - sldb product_url: https://github.com/monarch-initiative/SLDBGen#readme - category: Product description: Release artifacts for SLDB graph builds. format: mixed id: sldb.releases name: SLDB Releases original_source: - sldb product_url: https://github.com/monarch-initiative/SLDBGen/releases repository: https://github.com/monarch-initiative/SLDBGen - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for slm. This page was automatically generated because it was referenced by other resources. domains: - stub id: slm last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Slm products: - category: Product compression: gzip description: slm Nodes TSV format: tsv id: obo-db-ingest.slm.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: slm Nodes TSV original_source: - slm product_file_size: 9655893 product_url: https://w3id.org/biopragmatics/resources/slm/slm.tsv.gz secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: daniel.c.berrios@nasa.gov - contact_type: github value: DanBerrios label: Dan Berrios orcid: 0000-0003-4312-9552 creation_date: '2025-09-29T00:00:00Z' description: The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data. domains: - biomedical homepage_url: https://github.com/nasa/LSDAO id: slso last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Space Life Sciences Ontology products: - category: OntologyProduct description: Space Life Sciences Ontology in OWL format format: owl id: slso.owl name: slso.owl product_file_size: 584157 product_url: http://purl.obolibrary.org/obo/slso.owl - category: OntologyProduct description: Space Life Sciences Ontology in OBO format format: obo id: slso.obo name: slso.obo product_file_size: 413238 product_url: http://purl.obolibrary.org/obo/slso.obo - category: OntologyProduct description: Space Life Sciences Ontology in JSON format format: json id: slso.json name: slso.json product_url: http://purl.obolibrary.org/obo/slso.json warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: Includes axioms linking to other ontologies, but no imports of those ontologies format: owl id: slso-base.owl name: slso-base.owl product_url: http://purl.obolibrary.org/obo/slso-base.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/nasa/LSDAO - activity_status: active category: DataSource creation_date: '2026-01-30T00:00:00Z' description: A protein domain annotation and architecture analysis resource covering curated domain models and annotated proteomes. domains: - proteomics - genomics - biological systems homepage_url: https://smart.embl.de/ id: smart last_modified_date: '2026-02-15T00:00:00Z' layout: resource_detail name: SMART products: - category: GraphicalInterface description: Main SMART portal for protein domain annotation and architecture analysis. format: http id: smart.portal name: SMART Portal product_url: https://smart.embl.de/ - category: GraphicalInterface description: SMART search interface for querying proteins and domain annotations. format: http id: smart.search name: SMART Search product_url: https://smart.embl.de/smart/search.cgi - category: GraphicalInterface description: Genomic SMART genome listing interface. format: http id: smart.list-genomes name: SMART Genome List product_url: https://smart.embl.de/smart/list_genomes.cgi - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz synonyms: - SMART - Simple Modular Architecture Research Tool - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: david.wishart@ualberta.ca label: David Wishart orcid: 0000-0002-3207-2434 - category: Organization contact_details: - contact_type: url value: https://smpdb.ca/ label: The Metabolomics Innovation Centre (TMIC) creation_date: '2025-12-03T00:00:00Z' description: The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 30,000 small molecule pathways found in humans. SMPDB provides detailed pathway diagrams for metabolic pathways, metabolic disease pathways, metabolite signaling pathways, and drug-action pathways. All pathways include information on relevant organs, subcellular compartments, cofactors, protein locations, metabolite locations, chemical structures, and protein quaternary structures. Each small molecule is hyperlinked to HMDB or DrugBank and each protein is hyperlinked to UniProt. domains: - pathways - biological systems - drug discovery - chemistry and biochemistry homepage_url: https://smpdb.ca/ id: smpdb infores_id: smpdb last_modified_date: '2025-12-03T00:00:00Z' layout: resource_detail name: Small Molecule Pathway Database products: - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - authors: - Wishart DS - Frolkis A - Knox C - et al. id: https://doi.org/10.1093/nar/gkp1002 preferred: true title: 'SMPDB: The Small Molecule Pathway Database' year: '2010' - authors: - Jewison T - Su Y - Disfany FM - et al. id: https://doi.org/10.1093/nar/gkt1067 title: 'SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database' year: '2014' synonyms: - SMPDB taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-10-27T00:00:00Z' description: snoDB is a specialized database of human small nucleolar RNAs (snoRNAs), integrating data from established databases with manually curated literature. It provides comprehensive information on snoRNA genomic locations, sequences, conservation, host genes, snoRNA-RNA interactions, snoRNA-protein interactions, and abundance data across tissues and cancer cells. domains: - genomics - biological systems homepage_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ id: snodb last_modified_date: '2025-10-27T00:00:00Z' layout: resource_detail name: snoDB products: - category: GraphicalInterface description: Web portal for searching, browsing, and analyzing human snoRNA data with interactive tables and visualization tools format: http id: snodb.portal name: snoDB 2.0 Portal product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ - category: GraphicalInterface description: Interactive abundance viewer for visualizing snoRNA expression across tissues and cell lines format: http id: snodb.abundance-viewer name: Abundance Viewer product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ - category: GraphicalInterface description: Browser for exploring rRNA chemical modification sites and their guide snoRNAs format: http id: snodb.rrna-modifications name: rRNA Chemical Modifications Browser product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/rRNA_modifications/ - category: GraphicalInterface description: Statistics dashboard showing snoRNA type distributions, length distributions, and target biotypes format: http id: snodb.statistics name: Statistics Dashboard product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/statistics/ - category: GraphicalInterface description: Sequence similarity search tool for finding snoRNAs by sequence format: http id: snodb.sequence-search name: Sequence Search Tool product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/sequence_similarity_search/ - category: Product description: Database of human snoRNA sequences with GRCh38 genomic coordinates format: http id: snodb.sequences name: snoRNA Sequences product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Conservation data including PhastCons scores for 100 vertebrates from UCSC genome browser format: http id: snodb.conservation name: Conservation Data product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: snoRNA motif sequences and guide regions (boxes C, D, C', D' for C/D box snoRNAs; H and ACA boxes for H/ACA snoRNAs) format: http id: snodb.motifs name: Motif and Guide Region Data product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Host gene information with functional annotations from Gene Ontology format: http id: snodb.host-genes name: Host Gene Data product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Canonical snoRNA-rRNA and snoRNA-snRNA interactions from multiple sources format: http id: snodb.canonical-interactions name: Canonical snoRNA-RNA Interactions product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Non-canonical snoRNA-RNA interactions from RISE database format: http id: snodb.noncanonical-interactions name: Non-canonical snoRNA-RNA Interactions product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: snoRNA-protein interactions from ENCODE eCLIP data of 150 RNA binding proteins format: http id: snodb.protein-interactions name: snoRNA-Protein Interactions product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: snoRNA and host gene abundance data from TGIRT-Seq across tissues and cancer cell lines format: http id: snodb.abundance name: Abundance Data product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: rRNA modification positions with validation status and modification levels from multiple studies format: http id: snodb.rrna-mods name: rRNA Modification Data product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/rRNA_modifications/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/rRNA_modifications/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/rRNA_modifications/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/rRNA_modifications/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/rRNA_modifications/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/rRNA_modifications/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: snoRNA copy information based on RFAM classification format: http id: snodb.copies name: snoRNA Copy Data product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: Product description: Exportable data tables with advanced search and filtering capabilities format: http id: snodb.export name: Data Export product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: ProcessProduct description: Tool for integrating snoDB snoRNAs into Ensembl or RefSeq GTF annotation files format: http id: snodb.snorupdate name: snoRupdate product_url: https://github.com/scottgroup/snoRupdate - category: DocumentationProduct description: Comprehensive documentation about data sources, methods, and curation processes format: http id: snodb.about name: About and Help Documentation product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/about/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/about/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/about/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/about/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/about/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/about/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: DocumentationProduct description: Interactive tutorial for navigating and using snoDB features format: http id: snodb.tutorial name: Tutorial product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/tutorial/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/tutorial/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/tutorial/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/tutorial/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/tutorial/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/tutorial/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: DocumentationProduct description: Detailed information about TGIRT-Seq data processing and experimental methods format: http id: snodb.experiment-details name: Experiment Details product_url: https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/experiment_details/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/experiment_details/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/experiment_details/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/experiment_details/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='bioinfo-scottgroup.med.usherbrooke.ca', port=443)_ Max retries exceeded with url_ /snoDB/experiment_details/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''bioinfo-scottgroup.med.usherbrooke.ca'', port=443): Max retries exceeded with url: /snoDB/experiment_details/ (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Bergeron - Paraqindes - Fafard-Couture - Deschamps-Francoeur - Faucher-Giguère - Bouchard-Bourelle - Abou Elela - Catez - Marcel - Scott id: https://pubmed.ncbi.nlm.nih.gov/36165892/ journal: Nucleic Acids Research preferred: true title: 'snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs' year: '2023' taxon: - NCBITaxon:9606 - activity_status: active category: Ontology contacts: - category: Organization contact_details: - contact_type: email value: info@snomed.org - contact_type: url value: https://www.snomed.org/contact-us label: SNOMED International - category: Organization contact_details: - contact_type: email value: custserv@nlm.nih.gov - contact_type: url value: https://www.nlm.nih.gov/healthit/snomedct/index.html id: ncbi label: National Library of Medicine (NLM) creation_date: '2025-06-04T00:00:00Z' description: SNOMED CT (Systematized Nomenclature of Medicine Clinical Terms) is the most comprehensive, multilingual clinical healthcare terminology in the world. It provides a standardized way to represent clinical phrases captured by clinicians and enables automatic interpretation of these terms. SNOMED CT includes more than 360,000 active concepts with unique meanings and formal logic-based definitions organized into hierarchies. domains: - biomedical - clinical - health homepage_url: https://www.snomed.org/ id: snomedct infores_id: snomedct last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://www.snomed.org/snomed-ct/get-snomed label: SNOMED CT Affiliate License name: SNOMED CT products: - category: OntologyProduct description: The biannual release of the US Edition of SNOMED CT, combining content from both the US Extension and International releases. id: snomedct.us.content name: SNOMED CT US Edition original_source: - snomedct product_url: https://download.nlm.nih.gov/mlb/utsauth/USExt/doc_SnomedCT-USEdition-ReleaseNotes_Current_en-US_US1000124_20250301.pdf - category: OntologyProduct description: The monthly release of the International Edition of SNOMED CT, the core release from SNOMED International, as RF2 files. id: snomedct.international.content name: SNOMED CT International Edition original_source: - snomedct product_url: https://download.nlm.nih.gov/umls/kss/IHTSDO2025/IHTSDO20250601/SnomedCT_InternationalRF2_PRODUCTION_20250601T120000Z.zip - category: MappingProduct description: The biannual release of the SNOMED CT to ICD-10-CM Map, which maps SNOMED CT concepts to ICD-10-CM codes. id: snomedct.icd10cm.map name: SNOMED CT to ICD-10-CM Map original_source: - snomedct - icd10 product_url: https://download.nlm.nih.gov/mlb/utsauth/ICD10CM/SNOMED_CT_to_ICD-10-CM_Resources_20250301.zip - category: GraphicalInterface description: The SNOMED International browser for exploring the SNOMED CT terminology. format: http id: snomedct.browser name: SNOMED CT Browser original_source: - snomedct product_url: https://browser.ihtsdotools.org/ - category: OntologyProduct description: A frequently used subset of SNOMED CT concepts for nursing documentation in electronic health records. August 2017 release. id: snomedct.nursing name: SNOMED CT Nursing Problem List Subset original_source: - snomedct product_url: https://download.nlm.nih.gov/mlb/utsauth/NursingProblemListSubset/SNOMEDCT_Nursing_201708.csv - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: MappingProduct description: Concept mappings between different terminology systems format: csv id: athena.mappings name: Athena Concept Mappings original_source: - snomedct - icd10 - icd10cm - mesh - loinc - cdiscvocab - ciel product_url: https://athena.ohdsi.org/search-terms/start secondary_source: - athena warnings: - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ Exceeded 30 redirects. - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ Exceeded 30 redirects. repository: https://browser.ihtsdotools.org/ taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: snOPY (snoRNA Orthological Gene Database) provides comprehensive information about small nucleolar RNAs (snoRNAs), their gene loci, and target RNAs across multiple species. The database focuses on orthologous relationships between snoRNAs using target RNA conservation rather than snoRNA sequence similarity. domains: - genomics - biological systems homepage_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi id: snopy last_modified_date: '2025-10-27T00:00:00Z' layout: resource_detail name: snOPY products: - category: GraphicalInterface description: Web portal for browsing and searching snoRNA orthological gene information format: http id: snopy.portal name: snOPY Portal product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi - category: GraphicalInterface description: Search interface for querying snoRNAs by species, box type, target RNA, organization, keywords, and curation status format: http id: snopy.search name: Search Interface product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi - category: GraphicalInterface description: Ortholog browser for exploring snoRNA orthologous relationships across species format: http id: snopy.orthologs name: Ortholog Browser product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=orthologs - category: GraphicalInterface description: Target RNA viewer for exploring modification sites on rRNA and snRNA targets format: http id: snopy.target-rna name: Target RNA Viewer product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=target - category: ProgrammingInterface description: BLAST interface for sequence similarity searches against snoRNA sequences format: http id: snopy.blast name: BLAST Interface product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=blast - category: Product description: Curated snoRNA sequences for box C/D class guiding 2'-O-methylation format: http id: snopy.box-cd-snornas name: Box C/D snoRNAs product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi - category: Product description: Curated snoRNA sequences for box H/ACA class guiding pseudouridylation format: http id: snopy.box-haca-snornas name: Box H/ACA snoRNAs product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi - category: Product description: Information about intronic snoRNA gene loci within protein-coding host genes format: http id: snopy.intronic-loci name: Intronic snoRNA Loci product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi - category: Product description: Information about polycistronic snoRNA gene clusters with multiple genes format: http id: snopy.polycistronic-loci name: Polycistronic snoRNA Loci product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi - category: Product description: Information about monocistronic snoRNA gene loci with single genes format: http id: snopy.monocistronic-loci name: Monocistronic snoRNA Loci product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi - category: Product description: Mapped modification sites on rRNA targets format: http id: snopy.rrna-modifications name: rRNA Modification Sites product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=target - category: Product description: Mapped modification sites on snRNA targets format: http id: snopy.snrna-modifications name: snRNA Modification Sites product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=target - category: Product description: Orthologous snoRNA relationships identified through target RNA conservation format: http id: snopy.ortholog-data name: snoRNA Ortholog Data product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=orthologs - category: DocumentationProduct description: About page with database description, methods, and citation information format: http id: snopy.about name: About snOPY product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=about - category: DocumentationProduct description: Database statistics showing organism coverage and entry counts format: http id: snopy.statistics name: Statistics product_url: http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=statistics - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Yoshihama - Nakao - Kenmochi doi: 10.1186/1756-0500-6-426 id: doi:10.1186/1756-0500-6-426 journal: BMC Research Notes preferred: true title: 'snOPY: a small nucleolar RNA orthological gene database' year: '2013' - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: snoRNABase (also known as snoRNA-LBME-db) is a comprehensive database of human C/D box and H/ACA box small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs). The database contains 361 entries including 257 C/D box snoRNAs, 86 H/ACA snoRNAs, and 18 scaRNAs. It provides detailed information on snoRNA sequences, their genomic locations, host genes, target RNAs (rRNAs and spliceosomal RNAs), predicted base-pairing interactions with target nucleotides, and modification sites (2'-O-ribose methylation and pseudouridylation). Each entry includes literature references, GenBank accession numbers, and links to the UCSC Genome Browser. The database features search, browse, and "Find guide RNA" functions to identify snoRNAs that guide modifications of specific nucleotides in rRNAs (28S, 18S, 5.8S) and spliceosomal RNAs (U1, U2, U4, U5, U6, U12). domains: - genomics homepage_url: https://www-snorna.biotoul.fr/ id: snornadatabase last_modified_date: '2025-11-13T00:00:00Z' layout: resource_detail name: snoRNABase products: - category: GraphicalInterface description: Web portal for searching and browsing human snoRNA and scaRNA sequences, targets, and modifications format: http id: snornadatabase.portal name: snoRNABase Web Portal original_source: - snornadatabase product_url: https://www-snorna.biotoul.fr/ - category: GraphicalInterface description: Search engine for finding snoRNAs by name, length, GenBank accession, or target RNA format: http id: snornadatabase.search name: snoRNABase Search original_source: - snornadatabase product_url: https://www-snorna.biotoul.fr/cherche.php - category: GraphicalInterface description: Tool for finding snoRNAs that guide modification of specific nucleotides in rRNAs and spliceosomal RNAs format: http id: snornadatabase.find_guide name: snoRNABase Find Guide RNA original_source: - snornadatabase product_url: https://www-snorna.biotoul.fr/guide.php - category: GraphicalInterface description: Browse function for viewing and downloading snoRNA sequences in FASTA format format: http id: snornadatabase.browse name: snoRNABase Browse original_source: - snornadatabase product_url: https://www-snorna.biotoul.fr/browse.php - category: ProgrammingInterface description: BLAST search interface for sequence similarity searches against human sno/scaRNAs format: http id: snornadatabase.blast name: snoRNABase BLAST original_source: - snornadatabase product_url: https://www-snorna.biotoul.fr/blast/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Laurent Lestrade - Michel J. Weber doi: 10.1093/nar/gkj002 id: doi:10.1093/nar/gkj002 journal: Nucleic Acids Research preferred: true title: snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs year: '2006' synonyms: - snoRNA-LBME-db - snoRNA database taxon: - NCBITaxon:9606 - activity_status: active category: Resource contacts: - category: Individual contact_details: - contact_type: github value: pcingola - contact_type: url value: http://www.linkedin.com/in/pablocingolani label: Pablo Cingolani creation_date: '2025-10-31T00:00:00Z' description: SnpEff is a genetic variant annotation and functional effect prediction toolbox widely used in genomics pipelines. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes), supports over 38,000 genomes, uses standardized Sequence Ontology terms, and implements the VCF annotation standard ANN field. SnpEff is bundled with SnpSift, a companion tool for filtering and manipulating genomic annotated variants. Both tools are integrated with Galaxy and GATK, making them essential components of sequencing data analysis workflows. domains: - biomedical - genomics - precision medicine - biological systems homepage_url: https://pcingola.github.io/SnpEff/ id: snpeff infores_id: snpeff last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT name: SnpEff products: - category: ProgrammingInterface description: SnpEff core package with command-line interface for variant annotation and effect prediction id: snpeff.download name: SnpEff Download Package original_source: - snpeff product_url: https://snpeff.odsp.astrazeneca.com/versions/snpEff_latest_core.zip - category: GraphicalInterface description: Comprehensive documentation website for SnpEff with usage examples, tutorials, and command references format: http id: snpeff.documentation name: SnpEff Documentation original_source: - snpeff product_url: https://pcingola.github.io/SnpEff/snpeff/introduction/ - category: GraphicalInterface description: SnpSift documentation covering tools for filtering, annotating, and manipulating VCF files format: http id: snpsift.documentation name: SnpSift Documentation original_source: - snpeff product_url: https://pcingola.github.io/SnpEff/snpsift/introduction/ - category: Product description: Over 38,000 pre-built genome databases available for automatic download and annotation id: snpeff.databases name: SnpEff Genome Databases original_source: - snpeff product_url: https://pcingola.github.io/SnpEff/download/ warnings: - Databases are automatically downloaded when running SnpEff; manual download is optional - category: ProgrammingInterface description: SnpEff source code repository on GitHub id: snpeff.github name: SnpEff GitHub Repository original_source: - snpeff product_url: https://github.com/pcingola/SnpEff - category: Product description: Historical releases and versions of SnpEff available on SourceForge id: snpeff.sourceforge name: SnpEff SourceForge Archive original_source: - snpeff product_url: https://sourceforge.net/projects/snpeff/files/ publications: - authors: - Cingolani P - Platts A - Wang le L - Coon M - Nguyen T - Wang L - Land SJ - Lu X - Ruden DM id: https://pubmed.ncbi.nlm.nih.gov/22728672/ journal: Fly preferred: true title: 'A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3' year: '2012' - authors: - Cingolani P - Patel VM - Coon M - Nguyen T - Land SJ - Ruden DM - Lu X id: https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2012.00035/full journal: Frontiers in Genetics title: Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift year: '2012' repository: https://github.com/pcingola/SnpEff - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: keilbeck@genetics.utah.edu - contact_type: github value: keilbeck label: Karen Eilbeck orcid: 0000-0002-0831-6427 creation_date: '2025-06-25T00:00:00Z' description: A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. domains: - chemistry and biochemistry homepage_url: http://www.sequenceontology.org/ id: so last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Sequence types and features ontology products: - category: OntologyProduct description: Main SO OWL release format: owl id: so.owl name: Main SO OWL release product_file_size: 291621 product_url: http://purl.obolibrary.org/obo/so.owl - category: OntologyProduct description: Main SO release in OBO Format format: obo id: so.obo name: Main SO release in OBO Format product_file_size: 193405 product_url: http://purl.obolibrary.org/obo/so.obo - category: OntologyProduct description: This subset includes only locatable sequence features and is designed for use in such outputs as GFF3 format: owl id: so.subsets.SOFA.owl name: Sequence Ontology Feature Annotation (SOFA) subset (OWL) product_file_size: 43606 product_url: http://purl.obolibrary.org/obo/so/subsets/SOFA.owl - category: OntologyProduct description: This subset includes only locatable sequence features and is designed for use in such outputs as GFF3 format: obo id: so.subsets.SOFA.obo name: Sequence Ontology Feature Annotation (SOFA) subset (OBO Format) product_file_size: 28447 product_url: http://purl.obolibrary.org/obo/so/subsets/SOFA.obo - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/The-Sequence-Ontology/SO-Ontologies - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: cli@uta.edu label: Chengkai Li creation_date: '2025-12-08T00:00:00Z' description: The Soil Organic Carbon Knowledge Graph (SOCKG) enhances robust soil carbon modeling, which is crucial for voluntary carbon markets. It provides structured data about soil carbon measurements, agricultural practices, and environmental factors. domains: - environment - agriculture evaluation_page: resource/sockg/sockg_eval_automated.html homepage_url: https://idir.uta.edu/sockg/ id: sockg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SOC-KG products: - category: ProgrammingInterface description: SPARQL endpoint for SOC-KG id: sockg.sparql name: SOC-KG SPARQL original_source: - sockg product_url: https://frink.apps.renci.org/sockg/sparql - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: david.kedrowski@maine.edu - contact_type: github value: dkedrowski label: David Kedrowski creation_date: '2025-12-08T00:00:00Z' description: The SAWGraph Spatial KG is part of the Safe Agricultural Products and Water Graph (SAWGraph) project. It contains all the Level 13 grid cells from the S2 grid as well as administrative regions of levels 1 to 3 (states, counties, and county subdivisions) and the spatial relationships between them for the 48 contiguous states in the U.S. domains: - environment evaluation_page: resource/spatialkg/spatialkg_eval_automated.html homepage_url: https://sawgraph.github.io/ id: spatialkg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SAWGraph Spatial KG products: - category: ProgrammingInterface description: SPARQL endpoint for SAWGraph Spatial KG id: spatialkg.sparql name: SAWGraph Spatial KG SPARQL original_source: - spatialkg product_url: https://frink.apps.renci.org/spatialkg/sparql - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: ramirez@macn.gov.ar - contact_type: github value: martinjramirez label: Martin Ramirez orcid: 0000-0002-0358-0130 creation_date: '2025-09-29T00:00:00Z' description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). domains: - anatomy and development homepage_url: http://research.amnh.org/atol/files/ id: spd last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Spider Ontology products: - category: OntologyProduct description: Spider Ontology in OWL format format: owl id: spd.owl name: spd.owl product_file_size: 69679 product_url: http://purl.obolibrary.org/obo/spd.owl repository: https://github.com/obophenotype/spider-ontology taxon: - NCBITaxon:6893 - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for spdx. This page was automatically generated because it was referenced by other resources. domains: - stub id: spdx last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Spdx products: - category: Product description: spdx OBO format: obo id: obo-db-ingest.spdx.obo name: spdx OBO original_source: - spdx product_file_size: 31617 product_url: https://w3id.org/biopragmatics/resources/spdx/spdx.obo secondary_source: - obo-db-ingest - category: Product description: spdx OWL format: owl id: obo-db-ingest.spdx.owl name: spdx OWL original_source: - spdx product_file_size: 37909 product_url: https://w3id.org/biopragmatics/resources/spdx/spdx.owl secondary_source: - obo-db-ingest - category: Product description: spdx OBO Graph JSON format: json id: obo-db-ingest.spdx.json name: spdx OBO Graph JSON original_source: - spdx product_file_size: 39391 product_url: https://w3id.org/biopragmatics/resources/spdx/spdx.json secondary_source: - obo-db-ingest - category: Product description: spdx Nodes TSV format: tsv id: obo-db-ingest.spdx.tsv name: spdx Nodes TSV original_source: - spdx product_file_size: 11467 product_url: https://w3id.org/biopragmatics/resources/spdx/spdx.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: sergio.baranzini@ucsf.edu label: Sergio Baranzini - category: Individual contact_details: - contact_type: email value: sui.huang@ucsf.edu label: Sui Huang - category: Organization label: University of California, San Francisco creation_date: '2025-03-09T00:00:00Z' description: Scalable Precision Medicine Open Knowledge Engine (SPOKE) is a comprehensive biomedical knowledge graph that connects diverse data from multiple domains to enable discovery and precision medicine applications. domains: - biomedical - health - genomics - clinical - drug discovery - precision medicine - pharmacology evaluation_page: resource/spoke/spoke_eval.html homepage_url: https://spoke.ucsf.edu/ id: spoke infores_id: spoke last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://spoke.rbvi.ucsf.edu/docs/licenses.html label: Multiple licenses (see individual data sources) name: SPOKE products: - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphicalInterface description: Web interface that allows searching SPOKE for a node of interest and viewing its immediate connectivity neighborhood. format: http id: spoke.neighborhood_explorer name: SPOKE Neighborhood Explorer product_url: https://spoke.rbvi.ucsf.edu/neighborhood.html - category: ProgrammingInterface description: SPARQL endpoint for querying SPOKE knowledge graph via the OKN FRINK service id: spoke.sparql name: SPOKE SPARQL Endpoint original_source: - spoke product_url: https://frink.apps.renci.org/spoke-okn/sparql publications: - authors: - John H Morris - Karthik Soman - Riley E Akbas - X Zhou - B Smith - Elaine C Meng - CC Huang - Gabriel Cerono - G Schenk - Angela Rizk-Jackson - Sergio E Baranzini id: https://doi.org/10.1093/bioinformatics/btad080 journal: Bioinformatics preferred: true title: 'The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information' year: '2023' - authors: - Charlotte A Nelson - Atul J Butte - Sergio E Baranzini id: https://doi.org/10.1038/s41467-019-11069-0 journal: Nature Communications title: Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings year: '2019' - authors: - Daniel Scott Himmelstein - Antoine Lizee - Christine Hessler - Leo Brueggeman - Sabrina L Chen - Dexter Hadley - Ari Green - Pouya Khankhanian - Sergio E Baranzini id: https://doi.org/10.7554/eLife.26726 journal: eLife title: Systematic integration of biomedical knowledge prioritizes drugs for repurposing year: '2017' repository: https://github.com/baranzini-lab/SPOKE taxon: - NCBITaxon:9606 version: '2.0' - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: sergio.baranzini@ucsf.edu label: Sergio Baranzini creation_date: '2025-12-08T00:00:00Z' description: The spoke-genelab KG complements the SPOKE Open Knowledge Network KG and is designed to integrate omics data from NASA's Open Science Data Repository (OSDR/GeneLab), which hosts results from spaceflight experiments. domains: - genomics - biological systems evaluation_page: resource/spoke-genelab/spoke-genelab_eval_automated.html homepage_url: https://github.com/BaranziniLab/spoke_genelab id: spoke-genelab last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SPOKE GeneLab products: - category: ProgrammingInterface description: SPARQL endpoint for SPOKE GeneLab id: spoke-genelab.sparql name: SPOKE GeneLab SPARQL original_source: - spoke-genelab product_url: https://frink.apps.renci.org/spoke-genelab/sparql repository: https://github.com/BaranziniLab/spoke_genelab - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: kevinschaper@gmail.com - contact_type: github value: kevinschaper label: Kevin Schaper orcid: 0000-0003-3311-7320 creation_date: '2025-03-09T00:00:00Z' description: The Monarch Initiative’s SRI reference knowledge graph. domains: - health evaluation_page: resource/sri-reference-kg/sri-reference-kg_eval_automated.html homepage_url: '' id: sri-reference-kg infores_id: sri-reference-kg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SRI-Reference KG products: - category: GraphProduct description: KGX distribution of the SRI-Reference KG format: kgx id: sri-reference-kg.graph name: SRI-Reference KG (KGX distribution) product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz repository: '' - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: SRPDB (Signal Recognition Particle Database) provides aligned, annotated, and phylogenetically ordered sequences related to the structure and function of signal recognition particles (SRP). The database contains over 1,100 SRP RNA sequences and protein sequences from various organisms, with secondary structure diagrams based on comparative sequence analysis. domains: - genomics - biological systems homepage_url: https://rth.dk/resources/rnp/SRPDB/ id: srpdb last_modified_date: '2025-10-27T00:00:00Z' layout: resource_detail name: SRPDB products: - category: GraphicalInterface description: Web portal for browsing SRP RNA and protein sequences with phylogenetic organization format: http id: srpdb.portal name: SRPDB Portal product_url: https://rth.dk/resources/rnp/SRPDB/ - category: GraphicalInterface description: Browser for SRP RNA sequences organized phylogenetically and alphabetically format: http id: srpdb.srp-rna-browser name: SRP RNA Browser product_url: https://rth.dk/resources/rnp/SRPDB/srprna.html - category: GraphicalInterface description: Browser for SRP protein sequences including SRP9, SRP14, SRP19, SRP21, SRP54, SRP68, SRP72, and cpSRP43 format: http id: srpdb.srp-protein-browser name: SRP Protein Browser product_url: https://rth.dk/resources/rnp/SRPDB/srpprotein.html - 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Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: KGX Distribution of KG-Monarch edge_count: 15356321 format: kgx id: kg-monarch.graph name: KGX Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 230877741 product_url: http://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz secondary_source: - kg-monarch - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch edge_count: 15356321 format: kgx-jsonl id: kg-monarch.graph.jsonl name: KGX JSON-L Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 315667976 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.jsonl.tar.gz secondary_source: - kg-monarch - category: GraphProduct description: RDF Distribution of KG-Monarch edge_count: 15356321 format: rdfxml id: kg-monarch.graph.rdf name: RDF Distribution of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 879238775 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.nt.gz secondary_source: - kg-monarch - category: GraphProduct description: Neo4j Dump of KG-Monarch dump_format: neo4j edge_count: 15356321 id: kg-monarch.graph.neo4j name: Neo4j Dump of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 1438250397 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.neo4j.dump secondary_source: - kg-monarch warnings: [] - category: GraphProduct description: DuckDB database of KG-Monarch edge_count: 15356321 id: kg-monarch.graph.duckdb name: DuckDB database of KG-Monarch node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 6827814912 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.duckdb secondary_source: - kg-monarch - category: GraphProduct description: STRING-DB Automat format: kgx-jsonl id: automat.stringdb name: stringdb_automat original_source: - string product_url: https://stars.renci.org/var/plater/bl-4.2.1/STRING-DB_Automat/4ca5a0ce557e2c18/ secondary_source: - automat - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch (Edges) edge_count: 15356321 format: kgx-jsonl id: kg-monarch.graph.jsonl.edges name: KGX JSON-L Distribution of KG-Monarch Edges node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 15279494795 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.jsonl secondary_source: - kg-monarch - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch (Nodes) edge_count: 15356321 format: kgx-jsonl id: kg-monarch.graph.jsonl.nodes name: KGX JSON-L Distribution of KG-Monarch Nodes node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 1149505896 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.jsonl secondary_source: - kg-monarch - category: GraphProduct description: Neo4j Dump of KG-Monarch Edges edge_count: 15356321 format: neo4j id: kg-monarch.graph.neo4j.edges name: Neo4j Dump of KG-Monarch Edges node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 4386388748 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_edges.neo4j.csv secondary_source: - kg-monarch - category: GraphProduct description: Neo4j Dump of KG-Monarch Nodes edge_count: 15356321 format: neo4j id: kg-monarch.graph.neo4j.nodes name: Neo4j Dump of KG-Monarch Nodes node_categories: - biolink:AnatomicalEntity - biolink:BiologicalProcess - biolink:Case - biolink:Cell - biolink:CellularComponent - biolink:ChemicalEntity - biolink:Disease - biolink:Gene - biolink:Genotype - biolink:LifeStage - biolink:MolecularActivity - biolink:MolecularEntity - biolink:NamedThing - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:SequenceVariant node_count: 1379605 original_source: - phenio - alliance - bgee - biogrid - clingen - clinvar - ctd - dictybase - go - hp - maxo - panther - pombase - reactome - string - xenbase - zfin predicates: - biolink:actively_involved_in - biolink:acts_upstream_of - biolink:acts_upstream_of_negative_effect - biolink:acts_upstream_of_or_within - biolink:acts_upstream_of_or_within_negative_effect - biolink:acts_upstream_of_or_within_positive_effect - biolink:acts_upstream_of_positive_effect - biolink:ameliorates_condition - biolink:associated_with_increased_likelihood_of - biolink:caused_by - biolink:causes - biolink:colocalizes_with - biolink:contraindicated_in - biolink:contributes_to - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_disease - biolink:has_gene - biolink:has_mode_of_inheritance - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:interacts_with - biolink:is_active_in - biolink:is_sequence_variant_of - biolink:located_in - biolink:model_of - biolink:orthologous_to - biolink:part_of - biolink:participates_in - biolink:preventative_for_condition - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:treats_or_applied_or_studied_to_treat product_file_size: 349573789 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg_nodes.neo4j.csv secondary_source: - kg-monarch - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb - category: Product description: The EPA has developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Since its inception, the AOP-DB has been developed with the aim of integrating AOP molecular target information with other publicly available datasets to facilitate computational analyses of AOP information. id: aop-db.data name: AOP-DB Data original_source: - aop-wiki - ctd - toxcast - disgenet - ncbigene - string - 1000genomes - ensembl - gwascatalog product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 secondary_source: - aop-db - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: Product description: Protein interaction data aggregated from IntAct, STRING, BioGRID and other interaction databases format: http id: genecards.protein.interactions name: GeneCards Protein Interactions original_source: - intact - string - biogrid product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - authors: - Szklarczyk D - Kirsch R - Koutrouli M - Nastou K - Mehryary F - Hachilif R - Annika GL - Fang T - Doncheva NT - Pyysalo S - Bork P - Jensen LJ - von Mering C doi: doi:10.1093/nar/gkac1000 id: https://doi.org/10.1093/nar/gkac1000 journal: Nucleic Acids Research preferred: true title: The STRING database in 2023 - protein-protein association networks and functional enrichment analyses for any sequenced genome of interest year: '2023' version: '12.0' - activity_status: active category: DataSource creation_date: '2026-02-26T00:00:00Z' description: Stub Resource page for sty. This page was automatically generated because it was referenced by other resources. domains: - stub id: sty last_modified_date: '2026-02-26T00:00:00Z' layout: resource_detail name: Sty products: - category: Product description: sty Nodes TSV format: tsv id: obo-db-ingest.sty.tsv name: sty Nodes TSV original_source: - sty product_file_size: 1583 product_url: https://w3id.org/biopragmatics/resources/sty/sty.tsv secondary_source: - obo-db-ingest warnings: - This is an automatically generated stub page. Please replace with accurate information about this resource. - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: farhad.ameri@asu.edu label: Farhad Ameri creation_date: '2025-12-08T00:00:00Z' description: SUDOKN (Supply and Demand Open Knowledge Network) is an interconnected network of publicly available manufacturing capability data focused on Small and Medium-Sized Manufacturers (SMMs). domains: - other evaluation_page: resource/sudokn/sudokn_eval_automated.html homepage_url: https://projects.engineering.asu.edu/sudokn/ id: sudokn last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: SUDOKN products: - category: ProgrammingInterface description: SPARQL endpoint for SUDOKN id: sudokn.sparql name: SUDOKN SPARQL original_source: - sudokn product_url: https://frink.apps.renci.org/sudokn/sparql - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: url value: https://ncats.nih.gov/translator label: NCATS Biomedical Data Translator creation_date: '2025-10-30T00:00:00Z' description: SuppKG is a knowledge graph that integrates information about dietary supplements and their relationships with diseases, genes, proteins, and other biomedical entities, developed to support translational research and clinical decision-making. domains: - nutrition - biomedical - health evaluation_page: resource/suppkg/suppkg_eval_automated.html homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/SuppKG id: suppkg infores_id: suppkg last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: SuppKG products: - category: DocumentationProduct description: Translator wiki page describing SuppKG scope and example supplement-disease relationships. format: http id: suppkg.docs name: SuppKG Documentation original_source: - suppkg product_url: https://github.com/NCATSTranslator/Translator-All/wiki/SuppKG - category: ProcessProduct description: Source data directory used for SuppKG in the SemRep_DS repository. format: http id: suppkg.source-data name: SuppKG Source Data Repository original_source: - suppkg product_url: https://github.com/zhang-informatics/SemRep_DS/tree/main/SuppKG publications: - id: https://doi.org/10.1016/j.jbi.2022.104120 title: 'SuppKG: A knowledge graph for dietary supplements' year: '2022' synonyms: - SuppKG - Dietary Supplement Knowledge Graph taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: swisslipids@sib.swiss label: SwissLipids team creation_date: '2025-03-09T00:00:00Z' description: SwissLipids is a knowledge resource for lipids and their biology. domains: - chemistry and biochemistry homepage_url: https://www.swisslipids.org/ id: swisslipid last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: swisslipid products: - category: GraphicalInterface description: Main SwissLipids interface for browsing lipid classes and analytes. format: http id: swisslipid.portal name: SwissLipids Portal original_source: - swisslipid product_url: https://www.swisslipids.org/ - category: Product description: TSV export of lipid-related enzymes with UniProt, Rhea, and evidence links. format: tsv id: swisslipid.enzymes name: SwissLipids Enzymes original_source: - swisslipid - uniprot - rhea product_file_size: 126760 product_url: https://www.swisslipids.org/api/file.php?cas=download_files&file=enzymes.tsv - category: Product description: TSV export of evidence annotations including ECO terms and supporting PMIDs. format: tsv id: swisslipid.evidences name: SwissLipids Evidences original_source: - swisslipid - eco product_file_size: 47076 product_url: https://www.swisslipids.org/api/file.php?cas=download_files&file=evidences.tsv - category: Product description: TSV export of SwissLipids links to Gene Ontology terms with taxon context. format: tsv id: swisslipid.go name: SwissLipids GO Annotations original_source: - swisslipid - go product_file_size: 48388 product_url: https://www.swisslipids.org/api/file.php?cas=download_files&file=go.tsv - category: Product description: Comprehensive TSV catalogue of SwissLipids lipid entities and identifiers. format: tsv id: swisslipid.lipids name: SwissLipids Lipids original_source: - swisslipid product_file_size: 76772233 product_url: https://www.swisslipids.org/api/file.php?cas=download_files&file=lipids.tsv - category: MappingProduct description: TSV mapping between SwissLipids lipid entries and UniProtKB proteins. format: tsv id: swisslipid.lipids2uniprot name: SwissLipids Lipids to UniProt original_source: - swisslipid - uniprot product_file_size: 37147786 product_url: https://www.swisslipids.org/api/file.php?cas=download_files&file=lipids2uniprot.tsv - category: Product description: TSV export of lipid tissue and cell annotations with taxon and evidence tags. format: tsv id: swisslipid.tissues name: SwissLipids Tissues original_source: - swisslipid product_file_size: 9540 product_url: https://www.swisslipids.org/api/file.php?cas=download_files&file=tissues.tsv - category: ProgrammingInterface connection_url: https://www.swisslipids.org/#/api description: Public API page for programmatic SwissLipids access. format: http id: swisslipid.api is_public: true name: SwissLipids API original_source: - swisslipid product_url: https://www.swisslipids.org/#/api publications: - authors: - Aimo L - Liechti R - Hyka-Nouspikel N - Niknejad A - Gleizes A - Götz L - Kuznetsov D - David FPA - van der Goot FG - Riezman H - Bougueleret L - Xenarios I - Bridge A doi: doi:10.1093/bioinformatics/btv285 id: doi:10.1093/bioinformatics/btv285 preferred: true title: The SwissLipids knowledgebase for lipid biology year: '2015' repository: https://www.swisslipids.org/ - activity_status: active category: DataSource creation_date: '2026-01-30T00:00:00Z' description: A protein structure homology-modeling resource providing automated model generation workflows and a repository of precomputed structural models. domains: - proteomics - biological systems homepage_url: https://swissmodel.expasy.org/ id: swissmodel last_modified_date: '2026-02-15T00:00:00Z' layout: resource_detail name: SWISS-MODEL products: - category: GraphicalInterface description: Main interface for automated protein structure homology modeling. format: http id: swissmodel.portal name: SWISS-MODEL Portal product_url: https://swissmodel.expasy.org/ - category: GraphicalInterface description: Search and download interface for the SWISS-MODEL Repository of annotated homology models. format: http id: swissmodel.repository name: SWISS-MODEL Repository product_url: https://swissmodel.expasy.org/repository - category: ProgrammingInterface description: Programmatic API for submitting and retrieving SWISS-MODEL tasks and model data. format: http id: swissmodel.api name: SWISS-MODEL API product_url: https://swissmodel.expasy.org/coreapi/ - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - 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category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - 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contact_type: github value: allysonlister label: Allyson Lister orcid: 0000-0002-7702-4495 creation_date: '2025-09-29T00:00:00Z' description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. domains: - biomedical homepage_url: https://github.com/allysonlister/swo id: swo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Software ontology products: - category: OntologyProduct description: Software ontology in OWL format format: owl id: swo.owl name: swo.owl product_file_size: 236485 product_url: http://purl.obolibrary.org/obo/swo.owl - category: OntologyProduct description: Software ontology in JSON format format: json id: swo.json name: swo.json product_file_size: 204434 product_url: http://purl.obolibrary.org/obo/swo.json repository: https://github.com/allysonlister/swo - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: lynn.schriml@gmail.com - contact_type: github value: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 creation_date: '2025-09-29T00:00:00Z' description: An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease. domains: - biomedical homepage_url: https://github.com/DiseaseOntology/SymptomOntology id: symp last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Symptom Ontology products: - category: OntologyProduct description: Symptom Ontology in OWL format format: owl id: symp.owl name: symp.owl product_file_size: 73868 product_url: http://purl.obolibrary.org/obo/symp.owl - category: OntologyProduct description: Symptom Ontology in OBO format format: obo id: symp.obo name: symp.obo product_file_size: 49360 product_url: http://purl.obolibrary.org/obo/symp.obo repository: https://github.com/DiseaseOntology/SymptomOntology taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: allyson.lister@oerc.ox.ac.uk - contact_type: github value: allysonlister label: Allyson Lister orcid: 0000-0002-7702-4495 creation_date: '2025-09-29T00:00:00Z' description: A terminology for the skills necessary to make data FAIR and to keep it FAIR. domains: - biomedical homepage_url: https://github.com/terms4fairskills/FAIRterminology id: t4fs last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: terms4FAIRskills products: - category: OntologyProduct description: terms4FAIRskills in OWL format format: owl id: t4fs.owl name: t4fs.owl product_file_size: 91877 product_url: http://purl.obolibrary.org/obo/t4fs.owl - category: OntologyProduct description: terms4FAIRskills in OBO format format: obo id: t4fs.obo name: t4fs.obo product_file_size: 67799 product_url: http://purl.obolibrary.org/obo/t4fs.obo - category: OntologyProduct description: terms4FAIRskills in JSON format format: json id: t4fs.json name: t4fs.json product_file_size: 74586 product_url: http://purl.obolibrary.org/obo/t4fs.json - category: OntologyProduct description: This community view of T4FS makes the ontology available in OWL without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy. format: owl id: t4fs-community.owl name: This community view of T4FS makes the ontology available in OWL without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy. product_url: http://purl.obolibrary.org/obo/t4fs-community.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: This community view of T4FS makes the ontology available in OBO format without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy. format: obo id: t4fs-community.obo name: This community view of T4FS makes the ontology available in OBO format without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy. product_url: http://purl.obolibrary.org/obo/t4fs-community.obo warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: This community view of T4FS makes the ontology available in JSON format without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy. format: json id: t4fs-community.json name: This community view of T4FS makes the ontology available in JSON format without upper-level ontology (ULO) terms to give the user community a simpler view of the term hierarchy. product_url: http://purl.obolibrary.org/obo/t4fs-community.json warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/terms4fairskills/FAIRterminology - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: curator@arabidopsis.org - contact_type: url value: https://www.arabidopsis.org/ label: Phoenix Bioinformatics creation_date: '2025-12-03T00:00:00Z' description: The Arabidopsis Information Resource (TAIR) maintains a comprehensive database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. TAIR provides the complete genome sequence, gene structure and product information, gene expression data, DNA and seed stocks, genome maps, genetic and physical markers, publications, and community information. Gene product function data is updated weekly from published research and community submissions. domains: - genomics - biological systems - organisms homepage_url: https://www.arabidopsis.org/ id: tair last_modified_date: '2025-12-03T00:00:00Z' layout: resource_detail name: The Arabidopsis Information Resource products: - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database synonyms: - TAIR taxon: - NCBITaxon:3702 - activity_status: active category: DataSource creation_date: '2025-09-09T00:00:00Z' description: TarBase v9.0 is a comprehensive database of experimentally supported miRNA targets on protein-coding transcripts. It contains interactions identified via high-throughput methods (HITS-CLIP, PAR-CLIP, CLASH) and low-throughput experimental validation, all uniformly analyzed and manually curated with rich metadata. domains: - genomics - biological systems homepage_url: https://dianalab.e-ce.uth.gr/tarbasev9 id: tarbase last_modified_date: '2025-10-27T00:00:00Z' layout: resource_detail name: TarBase products: - category: GraphicalInterface description: Web portal for searching and browsing experimentally supported miRNA-gene interactions format: http id: tarbase.portal name: TarBase Portal product_url: https://dianalab.e-ce.uth.gr/tarbasev9 - category: GraphicalInterface description: Interactive search interface for querying miRNA targets and gene miRNomes with advanced filtering options format: http id: tarbase.interactions name: Interactions Search product_url: https://dianalab.e-ce.uth.gr/tarbasev9/interactions - category: GraphicalInterface description: Network visualization tool for assessing combinatorial effects of multiple miRNAs on common gene targets format: http id: tarbase.visualizations name: Visualizations product_url: https://dianalab.e-ce.uth.gr/tarbasev9/visualizations - category: GraphicalInterface description: Statistics page showing database content and coverage metrics format: http id: tarbase.statistics name: Statistics product_url: https://dianalab.e-ce.uth.gr/tarbasev9/statistics - category: GraphicalInterface description: Text-mining interface for literature-based interaction discovery format: http id: tarbase.textmining name: Text-Mining Interface product_url: https://dianalab.e-ce.uth.gr/tarbasev9/textmining - category: Product compression: gzip description: Experimentally validated miRNA-gene interactions for Homo sapiens in tab-delimited format format: tsv id: tarbase.homo-sapiens name: Homo sapiens Interactions product_file_size: 111135987 product_url: https://dianalab.e-ce.uth.gr/tarbasev9/data/Homo_sapiens_TarBase-v9.tsv.gz - category: Product compression: gzip description: Experimentally validated miRNA-gene interactions for Mus musculus in tab-delimited format format: tsv id: tarbase.mus-musculus name: Mus musculus Interactions product_file_size: 16498710 product_url: https://dianalab.e-ce.uth.gr/tarbasev9/data/Mus_musculus_TarBase-v9.tsv.gz warnings: - File was not able to be retrieved when checked on 2025-10-27_ Timeout connecting to URL - category: Product compression: gzip description: Experimentally validated viral miRNA-gene interactions in tab-delimited format format: tsv id: tarbase.viral name: Viral Species Interactions product_file_size: 884524 product_url: https://dianalab.e-ce.uth.gr/tarbasev9/data/Viral_species_TarBase-v9.tsv.gz - category: Product compression: gzip description: Experimentally validated miRNA-gene interactions for other species in tab-delimited format format: tsv id: tarbase.other-species name: Other Species Interactions product_file_size: 164821 product_url: https://dianalab.e-ce.uth.gr/tarbasev9/data/Other_species_TarBase-v9.tsv.gz - category: DocumentationProduct description: Comprehensive help documentation with query examples and filtering options format: http id: tarbase.help name: Help Documentation product_url: https://dianalab.e-ce.uth.gr/tarbasev9/help warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: DocumentationProduct description: Downloads page with file format specifications and field descriptions format: http id: tarbase.downloads-doc name: Downloads Documentation product_url: https://dianalab.e-ce.uth.gr/tarbasev9/downloads warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-06_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Skoufos - Kakoulidis - Tastsoglou - Zacharopoulou - Kotsira - Miliotis - Mavromati - Grigoriadis - Zioga - Velli - Koutou - Karagkouni - Stavropoulos - Kardaras - Lifousi - Vavalou - Ovsepian - Skoulakis - Tasoulis - Georgakopoulos - Plagianakos - Hatzigeorgiou id: https://doi.org/10.1093/nar/gkad1071 journal: Nucleic Acids Research preferred: true title: TarBase-v9.0 extends experimentally supported miRNA–gene interactions to cell-types and virally encoded miRNAs year: '2023' - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: balhoff@renci.org - contact_type: github value: balhoff label: Jim Balhoff orcid: 0000-0002-8688-6599 creation_date: '2025-09-29T00:00:00Z' description: A vocabulary of taxonomic ranks (species, family, phylum, etc) domains: - biological systems homepage_url: https://github.com/phenoscape/taxrank id: taxrank last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Taxonomic rank vocabulary products: - category: OntologyProduct description: Taxonomic rank vocabulary in OWL format format: owl id: taxrank.owl name: taxrank.owl product_file_size: 3843 product_url: http://purl.obolibrary.org/obo/taxrank.owl - category: OntologyProduct description: Taxonomic rank vocabulary in OBO format format: obo id: taxrank.obo name: taxrank.obo product_file_size: 2271 product_url: http://purl.obolibrary.org/obo/taxrank.obo repository: https://github.com/phenoscape/taxrank - activity_status: active category: DataSource creation_date: '2026-01-28T00:00:00Z' description: A curated classification database of membrane transport proteins, organized by the Transporter Classification (TC) system and supporting sequence- and family-level exploration. domains: - biological systems - proteomics homepage_url: https://www.tcdb.org/ id: tcdb last_modified_date: '2026-02-15T00:00:00Z' layout: resource_detail name: Transporter Classification Database (TCDB) products: - category: GraphicalInterface description: Main web interface for browsing transporter families, proteins, and curated annotations. format: http id: tcdb.portal name: TCDB Portal product_url: https://www.tcdb.org/ - category: GraphicalInterface description: Sequence similarity search interface against TCDB transporter sequences. format: http id: tcdb.blast name: TCDB BLAST product_url: https://www.tcdb.org/progs/blast.php - category: Product description: Complete TCDB protein sequence export. format: fasta id: tcdb.download.fasta name: TCDB Protein Sequences product_file_size: 13590695 product_url: https://www.tcdb.org/public/tcdb - category: Product compression: targz description: Precomputed tcDoms dataset archive. format: mixed id: tcdb.download.tcdoms name: tcDoms Archive product_file_size: 14664403 product_url: https://www.tcdb.org/public/tcDoms.tar.gz - category: Product description: Tab-delimited table mapping TC systems to substrate identifiers. The URL ends in .py, but this endpoint serves data, not Python source code. format: tsv id: tcdb.download.substrates name: TC Systems to Substrates Table product_url: https://www.tcdb.org/cgi-bin/substrates/getSubstrates.py warnings: - File was not able to be retrieved when checked on 2026-03-08_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-02-26_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: Timeout connecting to URL' - category: Product description: Tab-delimited table with TC family definitions. The URL ends in .py, but this endpoint serves data, not Python source code. format: tsv id: tcdb.download.families name: TC Family Definitions product_file_size: 41693 product_url: https://www.tcdb.org/cgi-bin/projectv/public/families.py - category: Product description: Tab-delimited table mapping sequence accessions to TC identifiers. The URL ends in .py, but this endpoint serves data, not Python source code. format: tsv id: tcdb.download.refseq name: Sequence Accessions to TCIDs product_url: https://www.tcdb.org/cgi-bin/projectv/public/refseq.py warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Tab-delimited table mapping systems, subfamilies, and families to superfamilies. The URL ends in .py, but this endpoint serves data, not Python source code. format: tsv id: tcdb.download.superfamilies name: TC Superfamily Mapping product_file_size: 41446 product_url: https://www.tcdb.org/cgi-bin/substrates/listSuperfamilies.py - category: Product description: Tab-delimited table mapping protein accessions to TC identifiers. The URL ends in .py, but this endpoint serves data, not Python source code. format: tsv id: tcdb.download.acc2tcid name: Accessions to TCIDs product_url: https://www.tcdb.org/cgi-bin/projectv/public/acc2tcid.py warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Tab-delimited annotation mapping table for TC systems. The URL ends in .py, but this endpoint serves data, not Python source code. format: tsv id: tcdb.download.go name: TC Annotation Mapping Table product_url: https://www.tcdb.org/cgi-bin/projectv/public/go.py warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Tab-delimited structure mapping table for TC systems. The URL ends in .py, but this endpoint serves data, not Python source code. format: tsv id: tcdb.download.pdb name: TC Structure Mapping Table product_url: https://www.tcdb.org/cgi-bin/projectv/public/pdb.py warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: Product description: Tab-delimited protein family mapping table for TC systems. The URL ends in .py, but this endpoint serves data, not Python source code. format: tsv id: tcdb.download.pfam name: TC Protein Family Mapping Table product_url: https://www.tcdb.org/cgi-bin/projectv/public/pfam.py warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv synonyms: - TCDB - Transporter Classification Database - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://gdc.cancer.gov/support label: NCI Genomic Data Commons Support creation_date: '2025-11-08T00:00:00Z' description: The Cancer Genome Atlas (TCGA) is a landmark cancer genomics program that molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types. This joint effort between NCI and the National Human Genome Research Institute began in 2006, bringing together researchers from diverse disciplines and multiple institutions. TCGA generated over 2.5 petabytes of genomic, epigenomic, transcriptomic, and proteomic data. The data, which has led to improvements in the ability to diagnose, treat, and prevent cancer, remains publicly available through the Genomic Data Commons for anyone in the research community to use. domains: - genomics homepage_url: https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga id: tcga infores_id: tcga last_modified_date: '2025-11-08T00:00:00Z' layout: resource_detail name: The Cancer Genome Atlas products: - category: Product description: Genomic Data Commons Data Portal providing access to harmonized TCGA data with over 2.5 petabytes of cancer genomic data format: http id: tcga.gdc_portal name: GDC Data Portal product_url: https://portal.gdc.cancer.gov/ - category: ProgrammingInterface description: Genomic Data Commons Application Programming Interface for programmatic access to TCGA and other cancer genomic data format: http id: tcga.gdc_api name: GDC API product_url: https://gdc.cancer.gov/developers/gdc-application-programming-interface-api - category: GraphicalInterface description: Data Submission Portal for uploading and managing cancer genomic data submissions to GDC format: http id: tcga.gdc_submission name: GDC Data Submission Portal product_url: https://portal.gdc.cancer.gov/submission synonyms: - TCGA taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://druggablegenome.net/ - contact_type: email value: idg.rdoc@gmail.com label: Illuminating the Druggable Genome (IDG) Program - category: Organization contact_details: - contact_type: url value: https://druggablegenome.net/KMC_UNM label: Knowledge Management Center - University of New Mexico - category: Individual contact_details: - contact_type: github value: tudoroprea label: Tudor I. Oprea creation_date: '2025-01-10T00:00:00Z' description: The Target Central Resource Database (TCRD) is a comprehensive multi-omics knowledge base developed by the NIH Common Fund Illuminating the Druggable Genome (IDG) program to catalog and illuminate the human proteome, with special focus on understudied proteins in four major druggable protein families G-protein coupled receptors (GPCRs), nuclear receptors, ion channels, and protein kinases. TCRD aggregates data from over 80 diverse sources including protein-protein interactions, disease associations, drug-target relationships, gene expression profiles, tissue specificity, pathway memberships, phenotype associations, and pharmacological data to create a unified resource for target prioritization and drug discovery research. The database employs a protein Target Development Level (TDL) classification system (Tclin, Tchem, Tbio, Tdark) that ranks proteins based on the amount of available knowledge, specifically highlighting understudied dark proteins that lack adequate characterization. TCRD contains extensive information on protein sequences, structures, functions, disease relationships, and chemical interactions, integrating data from resources such as UniProt, ChEMBL, DrugCentral, STRING, GTEx, OMIM, and many others. The database is designed to be machine-learning ready with structured data formats suitable for computational analysis and target prediction algorithms. TCRD serves as the backend data infrastructure for Pharos, the user-friendly web interface that enables researchers to browse, visualize, and analyze the integrated target data through interactive tools and visualizations. The resource is continuously updated with new data sources and releases, with current version 6.13.5 containing comprehensive annotations for the human proteome. domains: - drug discovery - genomics - biological systems homepage_url: http://juniper.health.unm.edu/tcrd/ id: tcrd infores_id: tcrd last_modified_date: '2025-01-10T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-sa/4.0/ label: CC BY-SA 4.0 logo: https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png name: Target Central Resource Database products: - category: Product description: MySQL database dump files containing the complete TCRD relational database schema and data for local installation and analysis format: mysql id: tcrd.database_download name: TCRD Database Downloads original_source: - tcrd product_url: http://juniper.health.unm.edu/tcrd/download/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-02-26_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: Timeout connecting to URL' - category: ProgrammingInterface description: RESTful API providing programmatic access to TCRD data through Pharos for computational workflows and custom applications id: tcrd.api is_public: true name: Pharos API original_source: - tcrd product_url: https://pharos.nih.gov/api - category: DocumentationProduct description: Comprehensive documentation describing TCRD data sources, schema structure, and usage guidelines format: http id: tcrd.documentation name: TCRD Documentation original_source: - tcrd product_url: http://juniper.health.unm.edu/tcrd/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-02-26_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: Timeout connecting to URL' publications: - id: https://doi.org/10.1093/nar/gkaa993 title: 'Pharos 2021: mining the human proteome for disease biology' - id: https://doi.org/10.1093/nar/gkw1072 title: Illuminating the druggable genome with Pharos repository: https://github.com/unmtransinfo/TCRD synonyms: - TCRD - Target Central Resource Database - IDG TCRD taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: Erik-BM label: Erik B. Myklebust creation_date: '2025-10-28T00:00:00Z' description: 'The Toxicological Effect and Risk Assessment (TERA) Knowledge Graph is an integrated knowledge graph for ecological risk assessment based on chemical effect data from U.S. EPA ECOTOX. TERA aligns toxicological data to non-proprietary identifiers using ontology alignment tools and external sources such as Wikidata, enabling the use of external chemical knowledge graphs including ChEBI, PubChem, and MeSH. The knowledge graph also includes aggregated data from NCBI Taxonomy and Encyclopedia of Life (EOL) trait data. By linking ECOTOX to external sources, TERA enables the extrapolation of chemical effect data, extending the reach of ecological risk assessment while limiting the need for laboratory experiments. The knowledge graph has been applied to predict adverse biological effects of chemicals using knowledge graph embeddings and supports various applications in environmental toxicology and risk assessment. ' domains: - toxicology - environment - biological systems evaluation_page: resource/tera/tera_eval_automated.html homepage_url: https://niva-knowledge-graph.github.io/TERA/ id: tera last_modified_date: '2025-10-28T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: 'TERA: Toxicological Effect and Risk Assessment Knowledge Graph' products: - category: DocumentationProduct description: API documentation for the TERA knowledge graph package format: http id: tera.documentation name: TERA Documentation product_url: https://niva-knowledge-graph.github.io/TERA/ - category: Product description: TERA knowledge graph dataset snapshot version 1.1.0 hosted on Zenodo, including NT files and CSV mappings format: http id: tera.zenodo-dataset license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY 4.0 name: TERA Knowledge Graph Dataset (Zenodo) product_file_size: 5905580032 product_url: https://zenodo.org/records/4244313 - category: Product description: Chemical data from EPA ECOTOX in N-Triples RDF format format: ntriples id: tera.ecotox-chemical-nt name: ECOTOX Chemical Data (N-Triples) product_file_size: 680300 product_url: https://zenodo.org/records/4244313/files/ecotox_chemical.nt - category: Product description: Taxonomy data from EPA ECOTOX in N-Triples RDF format format: ntriples id: tera.ecotox-taxonomy-nt name: ECOTOX Taxonomy Data (N-Triples) product_file_size: 22800000 product_url: https://zenodo.org/records/4244313/files/ecotox_taxonomy.nt - category: Product description: Chemical effects data in N-Triples RDF format format: ntriples id: tera.effects-nt name: Effects Data (N-Triples) product_file_size: 1000000000 product_url: https://zenodo.org/records/4244313/files/effects.nt - category: Product description: MeSH (Medical Subject Headings) data in N-Triples RDF format format: ntriples id: tera.mesh-nt name: MeSH Data (N-Triples) product_file_size: 2100000000 product_url: https://zenodo.org/records/4244313/files/mesh.nt - category: Product description: NCBI Taxonomy data in N-Triples RDF format format: ntriples id: tera.ncbi-nt name: NCBI Taxonomy Data (N-Triples) product_file_size: 1400000000 product_url: https://zenodo.org/records/4244313/files/ncbi.nt - category: Product description: Encyclopedia of Life traits data in N-Triples RDF format format: ntriples id: tera.traits-nt name: EOL Traits Data (N-Triples) product_file_size: 968000000 product_url: https://zenodo.org/records/4244313/files/traits.nt - category: MappingProduct description: Mapping file linking CAS Registry Numbers to MeSH identifiers format: csv id: tera.cas-to-mesh-csv name: CAS to MeSH Mapping (CSV) product_file_size: 109400 product_url: https://zenodo.org/records/4244313/files/cas_to_mesh.csv - category: MappingProduct description: Mapping file linking ChEBI identifiers to MeSH identifiers format: csv id: tera.chebi-to-mesh-csv name: ChEBI to MeSH Mapping (CSV) product_file_size: 78600 product_url: https://zenodo.org/records/4244313/files/chebi_to_mesh.csv - category: MappingProduct description: Mapping file linking ChEMBL identifiers to MeSH identifiers format: csv id: tera.chembl-to-mesh-csv name: ChEMBL to MeSH Mapping (CSV) product_file_size: 108500 product_url: https://zenodo.org/records/4244313/files/chembl_to_mesh.csv - category: MappingProduct description: Mapping file linking PubChem compound identifiers (CID) to MeSH identifiers format: csv id: tera.cid-to-mesh-csv name: PubChem CID to MeSH Mapping (CSV) product_file_size: 108000 product_url: https://zenodo.org/records/4244313/files/cid_to_mesh.csv - category: MappingProduct description: Mapping file linking NCBI Taxonomy identifiers to Encyclopedia of Life identifiers format: csv id: tera.ncbi-to-eol-csv name: NCBI to EOL Mapping (CSV) product_file_size: 3800000 product_url: https://zenodo.org/records/4244313/files/ncbi_to_eol.csv - category: ProgrammingInterface description: Python package providing APIs for data aggregation, integration, and access of TERA knowledge graph format: python id: tera.python-package name: TERA Python Package repository: https://github.com/NIVA-Knowledge-Graph/TERA publications: - authors: - Erik Bryhn Myklebust - Ernesto Jimenez-Ruiz - Jiaoyan Chen - Raoul Wolf - Knut Erik Tollefsen category: Publication id: https://doi.org/10.48550/arXiv.1908.10128 journal: arXiv:1908.10128 preferred: true title: 'TERA: the Toxicological Effect and Risk Assessment Knowledge Graph' year: '2019' - authors: - Erik B. Myklebust - Ernesto Jimenez-Ruiz - Jiaoyan Chen - Raoul Wolf - Knut Erik Tollefsen category: Publication id: https://doi.org/10.3233/sw-222804 journal: Semantic Web Journal preferred: false title: Prediction of Adverse Biological Effects of Chemicals Using Knowledge Graph Embeddings year: '2022' repository: https://github.com/NIVA-Knowledge-Graph/TERA - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual contact_details: - contact_type: github value: edgargaticaCU label: Edgar Gatica - category: Individual contact_details: - contact_type: github value: bill-baumgartner label: Bill Baumgartner creation_date: '2026-01-22T00:00:00Z' description: Translator Text Mining Provider that produces knowledge-graph assertions from literature mining workflows and exposes them as a KGX graph. domains: - biomedical - literature - translational evaluation_page: resource/text-mining-kp/text-mining-kp_eval_automated.html homepage_url: https://github.com/NCATSTranslator/Text-Mining-Provider-Roadmap id: text-mining-kp last_modified_date: '2026-01-22T00:00:00Z' layout: resource_detail name: Text Mining KP products: - category: GraphProduct description: Release files for the Text Mining KP id: text-mining-kp.graph name: Text Mining KP Release Files product_url: https://storage.googleapis.com/translator-text-workflow-dev-public/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: KGX graph package for Text Mining KP (build tmkp_tmkp-2023-03-05_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.tmkp.graph name: Translator TMKP KGX Graph original_source: - text-mining-kp product_url: https://stars.renci.org/var/translator/releases/tmkp/2025_12_15/ secondary_source: - translator repository: https://github.com/NCATSTranslator/Text-Mining-Provider-Roadmap synonyms: - tmkp tags: - translator - activity_status: active category: DataSource collection: - translator contacts: - category: Organization contact_details: - contact_type: url value: https://datascience.unm.edu/tiga/ label: Translational Informatics Division, Department of Internal Medicine, School of Medicine, University of New Mexico creation_date: '2025-12-03T00:00:00Z' description: The Target Illumination GWAS Analytics (TIGA) database is a manually curated resource containing genotype-phenotype associations pulled from numerous genome-wide association studies (GWAS). TIGA provides bibliometric assessment of scientific consensus based on iCite Relative Citation Ratio and meanRank scores for aggregate multivariate evidence, supporting target illumination and validation in translational research. TIGA is part of the NCATS Translator Knowledge Provider ecosystem. domains: - genomics - translational - biomedical homepage_url: https://datascience.unm.edu/tiga/ id: tiga infores_id: tiga last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Target Illumination GWAS Analytics products: - category: GraphicalInterface description: Web application for exploring TIGA evidence-ranked gene-trait associations. format: http id: tiga.portal name: TIGA Web Application original_source: - tiga product_url: https://datascience.unm.edu/tiga/ - category: Product description: Download directory for TIGA data exports and releases. format: mixed id: tiga.downloads name: TIGA Downloads original_source: - tiga product_url: https://unmtid-dbs.net/download/TIGA/ synonyms: - TIGA - activity_status: active category: Aggregator contacts: - category: Individual contact_details: - contact_type: email value: qingyao.huang@uzh.ch label: Qingyao Huang creation_date: '2025-10-30T00:00:00Z' description: TISSUES is an integrative web resource providing evidence on tissue-specific gene and protein expression in mammals. The database combines manually curated literature, large-scale proteomics and transcriptomics screens, and automatic text mining, mapping all evidence to common protein identifiers and Brenda Tissue Ontology terms with unified confidence scores for cross-comparison. domains: - genomics - proteomics - anatomy and development homepage_url: https://tissues.jensenlab.org/ id: tissues infores_id: tissues last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: Creative Commons Attribution 4.0 International logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: TISSUES products: - category: GraphicalInterface description: Web interface for searching and visualizing tissue expression data with schematic human body visualization format: http id: tissues.web name: TISSUES Web Interface original_source: - tissues product_url: https://tissues.jensenlab.org/ - category: GraphicalInterface description: Search interface for querying genes, proteins, and tissues format: http id: tissues.search name: TISSUES Search original_source: - tissues product_url: https://tissues.jensenlab.org/Search - category: Product description: Downloadable datasets of tissue expression evidence including integrated scores and source-specific data format: tsv id: tissues.downloads name: TISSUES Data Downloads product_url: https://tissues.jensenlab.org/Downloads warnings: - File was not able to be retrieved when checked on 2025-10-30_ No Content-Length header found - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz publications: - id: PMID:29617745 preferred: true title: 'TISSUES 2.0: an integrative web resource on mammalian tissue expression.' - id: PMID:26244659 title: Comprehensive comparison of large-scale tissue expression datasets. repository: https://github.com/opalasca/TISSUES_Update synonyms: - TISSUES 2.0 taxon: - NCBITaxon:40674 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jaiswalp@science.oregonstate.edu - contact_type: github value: jaiswalp label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 creation_date: '2025-06-25T00:00:00Z' description: A controlled vocabulary to describe phenotypic traits in plants. domains: - biological systems homepage_url: http://browser.planteome.org/amigo id: to last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Plant Trait Ontology products: - category: OntologyProduct description: Plant Trait Ontology in OWL format format: owl id: to.owl name: to.owl product_file_size: 213609 product_url: http://purl.obolibrary.org/obo/to.owl - category: OntologyProduct description: Plant Trait Ontology in OBO format format: obo id: to.obo name: to.obo product_file_size: 157379 product_url: http://purl.obolibrary.org/obo/to.obo - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/Planteome/plant-trait-ontology taxon: - NCBITaxon:33090 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.nhlbi.nih.gov/ label: NHLBI (National Heart, Lung, and Blood Institute) creation_date: '2025-10-30T00:00:00Z' description: The NHLBI Trans-Omics for Precision Medicine (TOPMed) program generates scientific resources to enhance understanding of fundamental biological processes that underlie heart, lung, blood, and sleep disorders, providing whole genome sequencing and multi-omics data from diverse populations. domains: - genomics - clinical - precision medicine homepage_url: https://topmed.nhlbi.nih.gov/ id: topmed infores_id: topmed last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: NHLBI Trans-Omics for Precision Medicine products: - category: GraphicalInterface description: TOPMed program website for navigating cohorts, resources, and program documentation. format: http id: topmed.portal name: TOPMed Portal original_source: - topmed product_url: https://topmed.nhlbi.nih.gov/ - category: GraphicalInterface description: TOPMed data access page with instructions and links for controlled-access data workflows. format: http id: topmed.data-access name: TOPMed Data Access original_source: - topmed product_url: https://topmed.nhlbi.nih.gov/data-resources/data-access - category: DocumentationProduct description: PDF summary table of whole-genome sequencing counts available in TOPMed. format: pdf id: topmed.wgs-counts name: TOPMed WGS Counts PDF original_source: - topmed product_file_size: 442890 product_url: https://topmed.nhlbi.nih.gov/sites/default/files/documents/TOPMed%20WGS%20Counts%2020250505.pdf publications: - doi: 10.1038/s41586-021-03205-y id: doi:10.1038/s41586-021-03205-y journal: Nature preferred: true title: Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program year: '2021' synonyms: - TOPMed - Trans-Omics for Precision Medicine taxon: - NCBITaxon:9606 - activity_status: active category: DataSource collection: - ber creation_date: '2025-09-04T00:00:00Z' description: ToxCast (US EPA Toxicity Forecaster) is a high-throughput screening program generating bioactivity profiles for thousands of environmental chemicals across diverse in vitro assays to prioritize substances for hazard characterization, integrate exposure and pathway information, and support predictive toxicology. domains: - toxicology - environment - public health - biomedical id: toxcast last_modified_date: '2025-09-16T00:00:00Z' layout: resource_detail license: id: https://www.epa.gov/privacy/privacy-and-security-notice label: EPA Data Usage & Privacy Notice (public domain / open government data) name: ToxCast products: - category: Product description: The EPA has developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Since its inception, the AOP-DB has been developed with the aim of integrating AOP molecular target information with other publicly available datasets to facilitate computational analyses of AOP information. id: aop-db.data name: AOP-DB Data original_source: - aop-wiki - ctd - toxcast - disgenet - ncbigene - string - 1000genomes - ensembl - gwascatalog product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 secondary_source: - aop-db - category: GraphicalInterface description: Landing page describing the ToxCast high-throughput screening program and providing links to data and documentation. id: toxcast.portal name: EPA ToxCast Portal product_url: https://www.epa.gov/chemical-research/toxicity-forecasting - category: ProgrammingInterface description: REST API providing programmatic access to ToxCast-related assay, chemical, and bioactivity data via the CompTox Chemicals Dashboard. id: toxcast.api name: CompTox Chemicals Dashboard API (ToxCast) product_url: https://api-ccte.epa.gov/dashboard/ - category: Product description: Bulk release archives (assay annotations, hit-call data, summary tables) for ToxCast phases. id: toxcast.downloads name: ToxCast Bulk Data Downloads product_url: https://www.epa.gov/chemical-research/toxicity-forecasting#data - activity_status: active category: KnowledgeGraph collection: - aop contacts: - category: Organization contact_details: - contact_type: url value: https://toxin-search.netlify.app/ label: TOXIN Project Team creation_date: '2025-08-31T00:00:00Z' description: TOXIN is a knowledge graph resource integrating curated information about toxic compounds, their molecular targets, mechanisms, pathways, and associated phenotypic or clinical outcomes to facilitate toxicological risk assessment and mechanistic discovery. domains: - biomedical - toxicology - systems biology evaluation_page: resource/toxin/toxin_eval_automated.html homepage_url: https://toxin-search.netlify.app/ id: toxin last_modified_date: '2025-08-31T00:00:00Z' layout: resource_detail name: TOXIN products: - category: GraphicalInterface description: Web portal for searching and exploring toxic compounds, targets, and pathway relationships in the TOXIN knowledge graph. format: http id: toxin.web name: TOXIN Search Portal product_url: https://toxin-search.netlify.app/ secondary_source: - toxin publications: - id: https://doi.org/10.1093/database/baae121 journal: Database (Oxford) preferred: true title: 'TOXIN: an integrative knowledge graph for toxic compound mechanisms and outcomes' year: '2024' taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: lynn.schriml@gmail.com - contact_type: github value: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 creation_date: '2025-09-29T00:00:00Z' description: An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. domains: - biomedical homepage_url: https://github.com/DiseaseOntology/PathogenTransmissionOntology id: trans last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Pathogen Transmission Ontology products: - category: OntologyProduct description: Pathogen Transmission Ontology in OWL format format: owl id: trans.owl name: trans.owl product_file_size: 4176 product_url: http://purl.obolibrary.org/obo/trans.owl - category: OntologyProduct description: Pathogen Transmission Ontology in OBO format format: obo id: trans.obo name: trans.obo product_file_size: 2508 product_url: http://purl.obolibrary.org/obo/trans.obo repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology - activity_status: active category: Aggregator collection: - translator contacts: - category: Organization contact_details: - contact_type: url value: https://ncats.nih.gov/research/research-activities/translator id: translator-program label: NCATS Biomedical Translator Program creation_date: '2026-01-22T00:00:00Z' description: Aggregated, transformed graph datasets distributed by the NCATS Translator program via the STARs release site. Each package provides a KGX graph built from an upstream source and normalized with Translator pipelines. domains: - biomedical - clinical - translational - drug discovery - health homepage_url: https://ui.transltr.io/ id: translator last_modified_date: '2026-01-22T00:00:00Z' layout: resource_detail name: NCATS Translator Graph Releases products: - category: GraphProduct description: KGX graph package for Alliance of Genome Resources (build alliance_8.2.0_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.alliance.graph name: Translator Alliance KGX Graph original_source: - alliance product_url: https://stars.renci.org/var/translator/releases/alliance/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Bgee expression data (build bgee_15.2_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.bgee.graph name: Translator Bgee KGX Graph original_source: - bgee product_url: https://stars.renci.org/var/translator/releases/bgee/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for ChEMBL (build chembl_36_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.chembl.graph name: Translator ChEMBL KGX Graph original_source: - chembl product_url: https://stars.renci.org/var/translator/releases/chembl/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Columbia Open Health Data (build cohd_2024-11-25_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.cohd.graph name: Translator COHD KGX Graph original_source: - cohd product_url: https://stars.renci.org/var/translator/releases/cohd/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Comparative Toxicogenomics Database (build ctd_November_2025_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.ctd.graph name: Translator CTD KGX Graph original_source: - ctd product_url: https://stars.renci.org/var/translator/releases/ctd/2025_12_15/ secondary_source: - translator warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphProduct description: KGX graph package for Clinical Trials Knowledge Provider (build ctkp_3.1.23_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.ctkp.graph name: Translator CTKP KGX Graph original_source: - ctkp product_url: https://stars.renci.org/var/translator/releases/ctkp/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for DrugCentral Annotation KP (build dakp_0.4.3_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.dakp.graph name: Translator DAKP KGX Graph original_source: - drugcentral product_url: https://stars.renci.org/var/translator/releases/dakp/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for DGIdb drug–gene interactions (build dgidb_2024_12_06_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.dgidb.graph name: Translator DGIdb KGX Graph original_source: - dgidb product_url: https://stars.renci.org/var/translator/releases/dgidb/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for DISEASES text-mined associations (build diseases_2025_12_07_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.diseases.graph name: Translator DISEASES KGX Graph original_source: - diseases product_url: https://stars.renci.org/var/translator/releases/diseases/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Drug Repurposing Hub (build drug_rep_hub_2025-08-19_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.drug_rep_hub.graph name: Translator Drug Repurposing Hub KGX Graph original_source: - drugrephub product_url: https://stars.renci.org/var/translator/releases/drug_rep_hub/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Gene2Phenotype (build gene2phenotype_2025_12_15_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.gene2phenotype.graph name: Translator Gene2Phenotype KGX Graph original_source: - gene2phenotype product_url: https://stars.renci.org/var/translator/releases/gene2phenotype/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Genetics KP (build geneticskp_2025-12-15_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.geneticskp.graph name: Translator Genetics KP KGX Graph original_source: - geneticskp product_url: https://stars.renci.org/var/translator/releases/geneticskp/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for GO-CAM models (build go_cam_2025-10-10_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.go_cam.graph name: Translator GO-CAM KGX Graph original_source: - go-cam product_url: https://stars.renci.org/var/translator/releases/go_cam/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Gene Ontology Annotations (build goa_2025-10-10_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.goa.graph name: Translator GOA KGX Graph original_source: - goa product_url: https://stars.renci.org/var/translator/releases/goa/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Guide to Pharmacology (build gtopdb_20251215_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.gtopdb.graph name: Translator GToPdb KGX Graph original_source: - gtopdb product_url: https://stars.renci.org/var/translator/releases/gtopdb/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Human Phenotype Ontology annotations (build hpoa_2025-11-24_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.hpoa.graph name: Translator HPOA KGX Graph original_source: - hp product_url: https://stars.renci.org/var/translator/releases/hpoa/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for ICEES cohort data (build icees_2024-08-20_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.icees.graph name: Translator ICEES KGX Graph original_source: - icees-kg product_url: https://stars.renci.org/var/translator/releases/icees/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for IntAct molecular interactions (build intact_2025_08_28_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.intact.graph name: Translator IntAct KGX Graph original_source: - intact product_url: https://stars.renci.org/var/translator/releases/intact/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for PANTHER pathways (build panther_19.0_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.panther.graph name: Translator PANTHER KGX Graph original_source: - panther product_url: https://stars.renci.org/var/translator/releases/panther/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for SemMedDB text-derived predications (build semmeddb_semmeddb-2023-kg2.10.3_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.semmeddb.graph name: Translator SemMedDB KGX Graph original_source: - semmeddb product_url: https://stars.renci.org/var/translator/releases/semmeddb/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for SIDER drug side effects (build sider_4.1_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.sider.graph name: Translator SIDER KGX Graph original_source: - sider product_url: https://stars.renci.org/var/translator/releases/sider/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for SIGNOR causal interactions (build signor_2025_Oct_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.signor.graph name: Translator SIGNOR KGX Graph original_source: - signor product_url: https://stars.renci.org/var/translator/releases/signor/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Text Mining KP (build tmkp_tmkp-2023-03-05_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.tmkp.graph name: Translator TMKP KGX Graph original_source: - text-mining-kp product_url: https://stars.renci.org/var/translator/releases/tmkp/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Therapeutic Target Database (build ttd_2024_03_30_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.ttd.graph name: Translator TTD KGX Graph original_source: - ttd product_url: https://stars.renci.org/var/translator/releases/ttd/2025_12_15/ secondary_source: - translator - category: GraphProduct description: KGX graph package for Ubergraph ontology integration (build ubergraph_2025-11-02_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.ubergraph.graph name: Translator Ubergraph KGX Graph original_source: - ubergraph product_url: https://stars.renci.org/var/translator/releases/ubergraph/2025_12_15/ secondary_source: - translator tags: - translator - activity_status: active category: Dataset creation_date: '2026-01-15T00:00:00Z' description: The TRY Plant Trait Database aggregates global plant trait measurements contributed by researchers and institutions, widely used for ecological and metabolomic analyses. domains: - biological systems homepage_url: https://www.try-db.org/TryWeb/Home.php id: try infores_id: try last_modified_date: '2026-01-15T00:00:00Z' layout: resource_detail name: TRY Plant Trait Database products: - category: Product description: Trait data available through the TRY data portal (access upon request/registration) format: http id: try.portal name: TRY Data Portal original_source: - try product_url: https://www.try-db.org/TryWeb/Home.php warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPSConnectionPool(host='www.try-db.org', port=443)_ Max retries exceeded with url_ /TryWeb/Home.php (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPSConnectionPool(host='www.try-db.org', port=443)_ Max retries exceeded with url_ /TryWeb/Home.php (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1000)'))) - File was not able to be retrieved when checked on 2026-02-24_ Error connecting to URL_ HTTPSConnectionPool(host='www.try-db.org', port=443)_ Max retries exceeded with url_ /TryWeb/Home.php (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1028)'))) - File was not able to be retrieved when checked on 2026-01-15_ Error connecting to URL_ HTTPSConnectionPool(host='www.try-db.org', port=443)_ Max retries exceeded with url_ /TryWeb/Home.php (Caused by SSLError(SSLCertVerificationError(1, '[SSL_ CERTIFICATE_VERIFY_FAILED] certificate verify failed_ unable to get local issuer certificate (_ssl.c_1017)'))) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''www.try-db.org'', port=443): Max retries exceeded with url: /TryWeb/Home.php (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1000)'')))' - category: GraphProduct description: Graph version of the Earth Metabolome Initiative Ontology format: kgx id: emikg.kg name: EMI Knowledge Graph original_source: - emi - pf1600 - globi - try product_url: https://doi.org/10.5281/zenodo.17079767 repository: https://github.com/earth-metabolome-initiative/metrin-kg warnings: - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - category: ProgrammingInterface description: SPARQL endpoint for programmatic access to the EMI Knowledge Graph format: http id: emikg.sparql name: EMI KG SPARQL Endpoint original_source: - emi - pf1600 - globi - try product_url: https://qlever.earthmetabolome.org/api/metrin-kg - category: GraphicalInterface description: Web-based SPARQL query editor for the EMI Knowledge Graph id: emikg.web name: EMI KG SPARQL Query Editor original_source: - emi - pf1600 - globi - try product_url: https://sib-swiss.github.io/sparql-editor/emi - activity_status: active category: Aggregator contacts: - category: Individual contact_details: - contact_type: email value: zhangyintao@zju.edu.cn label: Feng Zhu - category: Organization contact_details: - contact_type: url value: https://idrblab.org/ttd/ label: College of Pharmaceutical Sciences, Zhejiang University - category: Individual contact_details: - contact_type: url value: https://bidd.group/index.html#people label: Yuzong Chen - category: Organization contact_details: - contact_type: url value: https://bidd.group/index.html#people label: Department of Pharmacy, National University of Singapore creation_date: '2025-10-29T00:00:00Z' description: 'The Therapeutic Target Database (TTD) is a comprehensive aggregator providing information about known and explored therapeutic protein and nucleic acid targets, targeted diseases, pathway information, and corresponding drugs directed at these targets. TTD 2024 includes extensive druggability information across three perspectives: molecular interactions/regulations, human system profiles, and cell-based expression variations. The database encompasses 3,730 targets (including 532 successful, 1,442 clinical trial, 239 preclinical/patented, and 1,517 literature-reported targets) and 39,862 drugs, with druggability characteristics covering ligand-specific binding pockets, protein-protein interaction networks, microbiota-drug regulations, target similarity profiles, pathway involvements, tissue distributions, and cell-based expression variations across different diseases and perturbations.' domains: - biomedical - drug discovery - genomics - proteomics - pharmacology homepage_url: https://idrblab.org/ttd/ id: ttd infores_id: ttd last_modified_date: '2025-10-29T00:00:00Z' layout: resource_detail license: id: https://idrblab.org/ttd/ label: Freely accessible for research and educational purposes name: Therapeutic Target Database products: - category: GraphicalInterface description: Main web portal for browsing and searching TTD targets, drugs, biomarkers, and pathways format: http id: ttd.portal name: TTD Web Portal product_url: https://idrblab.org/ttd/ - category: Product description: Raw format target information including all TTD target data format: txt id: ttd.targets-raw name: TTD Targets Information product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P1-01-TTD_target_download.txt warnings: - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Raw format drug information including all TTD drug data format: txt id: ttd.drugs-raw name: TTD Drug Information product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P1-02-TTD_drug_download.txt warnings: - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Cross-matching identifiers between TTD drugs and public databases format: txt id: ttd.crossmatch name: Cross-matching Drug IDs product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P1-03-Drug_xrefs.txt warnings: - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Synonyms of drugs and small molecules in TTD format: txt id: ttd.synonyms name: Drug Synonyms product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P1-04-Drug_synonyms.txt warnings: - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Drug to disease mapping with ICD identifiers format: txt id: ttd.drug-disease name: Drug-Disease Mapping product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P1-05-Drug_disease.txt warnings: - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Target to disease mapping with ICD identifiers format: txt id: ttd.target-disease name: Target-Disease Mapping product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P1-06-Target_disease.txt warnings: - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Target to drug mapping with mode of action information format: csv id: ttd.target-drug name: Target-Drug Mapping product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P1-07-Drug-TargetMapping.xlsx warnings: - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Biomarker to disease mapping with ICD identifiers format: txt id: ttd.biomarker-disease name: Biomarker-Disease Mapping product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P1-08-Biomarker_disease.txt warnings: - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Target to compound mapping with experimental activity data format: txt id: ttd.target-compound name: Target-Compound Activity Data product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P1-09-Target_compound_activity.txt warnings: - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: UniProt IDs for all targets in TTD format: txt id: ttd.uniprot-all name: All Target UniProt IDs original_source: - uniprot product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P2-01-TTD_uniprot_all.txt secondary_source: - ttd warnings: - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Sequence data for all targets in FASTA format format: fasta id: ttd.sequences-all name: All Target Sequences product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P2-06-All_target_seq.txt warnings: - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Structure data for all drugs in SDF format format: sdf id: ttd.structures-all name: All Drug Structures product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P3-01-Drug_structure.sdf warnings: - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-31_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: SMILES and InChI representations for approved drugs format: txt id: ttd.smiles-inchi name: Drug SMILES and InChI product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P3-06-Drug_SMILE_InChI.txt - category: Product description: KEGG pathway data for all targets format: txt id: ttd.kegg-pathways name: Target KEGG Pathways original_source: - kegg product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P4-01-Target_KEGG_pathway.txt secondary_source: - ttd warnings: - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: WikiPathways data for all targets format: txt id: ttd.wiki-pathways name: Target WikiPathways original_source: - wikipathways product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P4-06-Target_wikipathway.txt secondary_source: - ttd warnings: - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: Product description: Drug combination data including synergistic, additive, and antagonistic interactions format: txt id: ttd.drug-combinations name: Drug Combinations product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P5-01-Drug_combination_synergism_anti-counteractive.txt warnings: - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - File was not able to be retrieved when checked on 2025-10-30_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: DocumentationProduct description: Help documentation and user guide for TTD format: http id: ttd.help name: TTD Help Documentation product_url: https://idrblab.org/ttd/help warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg - category: GraphProduct description: KGX graph package for Therapeutic Target Database (build ttd_2024_03_30_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.ttd.graph name: Translator TTD KGX Graph original_source: - ttd product_url: https://stars.renci.org/var/translator/releases/ttd/2025_12_15/ secondary_source: - translator publications: - authors: - Ying Zhou - Yintao Zhang - Donghai Zhao - Xinyuan Yu - Xinyi Shen - Yuan Zhou - Shanshan Wang - Yunqing Qiu - Yuzong Chen - Feng Zhu category: Publication id: doi:10.1093/nar/gkad751 journal: Nucleic Acids Research preferred: true title: 'TTD: Therapeutic Target Database describing target druggability information' year: '2024' - authors: - Yuan Zhou - Ying Zhang - Xueya Lian - Fengcheng Li - Chaoxin Wang - Feng Zhu - Yunqing Qiu - Yuzong Chen category: Publication id: doi:10.1093/nar/gkab953 journal: Nucleic Acids Research preferred: false title: 'Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents' year: '2022' taxon: - NCBITaxon:9606 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: balhoff@renci.org - contact_type: github value: balhoff label: Jim Balhoff orcid: 0000-0002-8688-6599 creation_date: '2025-09-29T00:00:00Z' description: An ontology covering the taxonomy of teleosts (bony fish) domains: - biological systems homepage_url: https://github.com/phenoscape/teleost-taxonomy-ontology id: tto last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Teleost taxonomy ontology products: - category: OntologyProduct description: Teleost taxonomy ontology in OBO format format: obo id: tto.obo name: tto.obo product_file_size: 2260220 product_url: http://purl.obolibrary.org/obo/tto.obo - category: OntologyProduct description: Teleost taxonomy ontology in OWL format format: owl id: tto.owl name: tto.owl product_file_size: 3526608 product_url: http://purl.obolibrary.org/obo/tto.owl repository: https://github.com/phenoscape/teleost-taxonomy-ontology taxon: - NCBITaxon:32443 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: yuki.yamagata@riken.jp - contact_type: github value: yuki-yamagata label: Yuki Yamagata orcid: 0000-0002-9673-1283 creation_date: '2025-09-29T00:00:00Z' description: TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. domains: - chemistry and biochemistry homepage_url: https://toxpilot.nibiohn.go.jp/ id: txpo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Toxic Process Ontology products: - category: OntologyProduct description: Toxic Process Ontology in OWL format format: owl id: txpo.owl name: txpo.owl product_file_size: 1799724 product_url: http://purl.obolibrary.org/obo/txpo.owl repository: https://github.com/txpo-ontology/TXPO - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: balhoff@renci.org - contact_type: github value: balhoff label: James P. Balhoff orcid: 0000-0002-8688-6599 creation_date: '2025-03-09T00:00:00Z' description: Ubergraph is an RDF triplestore integrating OBO ontologies into a unified semantic graph domains: - other evaluation_page: resource/ubergraph/ubergraph_eval_automated.html homepage_url: https://ubergraph.apps.renci.org/sparql id: ubergraph infores_id: ubergraph last_modified_date: '2026-01-23T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ubergraph products: - category: Product description: RDF of Ubergraph id: ubergraph.rdf name: Ubergraph RDF original_source: - ubergraph product_file_size: 6866918 product_url: https://ubergraph.apps.renci.org/sparql secondary_source: - ubergraph - category: Product description: Blazegraph journal of Ubergraph id: ubergraph.blazegraph.jnl name: Ubergraph blazegraph journal original_source: - ubergraph product_file_size: 9157530809 product_url: https://ubergraph.apps.renci.org/downloads/current/ubergraph.jnl.gz secondary_source: - ubergraph - category: Product description: Ubergraph n-quads format: nquads id: ubergraph.nquads name: Ubergraph n-quads original_source: - ubergraph product_file_size: 3718641146 product_url: https://ubergraph.apps.renci.org/downloads/current/ubergraph.nq.gz secondary_source: - ubergraph - category: GraphProduct description: UberGraph Automat format: kgx-jsonl id: automat.ubergraph name: ubergraph_automat original_source: - ubergraph product_url: https://stars.renci.org/var/plater/bl-4.2.1/UbergraphRedundant_Automat/e6b3204fd3a04413/ secondary_source: - automat - category: GraphProduct description: KGX graph package for Ubergraph ontology integration (build ubergraph_2025-11-02_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.ubergraph.graph name: Translator Ubergraph KGX Graph original_source: - ubergraph product_url: https://stars.renci.org/var/translator/releases/ubergraph/2025_12_15/ secondary_source: - translator repository: https://github.com/INCATools/ubergraph - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-05-04T00:00:00Z' description: An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies domains: - anatomy and development homepage_url: http://uberon.org id: uberon last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Uberon multi-species anatomy ontology products: - category: OntologyProduct description: core ontology format: owl id: uberon.owl name: Uberon product_file_size: 97323970 product_url: http://purl.obolibrary.org/obo/uberon.owl - category: OntologyProduct description: Axioms defined within Uberon and to be used in imports for other ontologies format: owl id: uberon.uberon-base.owl name: Uberon base ontology product_file_size: 56683591 product_url: http://purl.obolibrary.org/obo/uberon/uberon-base.owl - category: OntologyProduct description: Uberon edition that excludes external ontologies and most relations format: obo id: uberon.uberon-basic.obo name: Uberon basic product_file_size: 11928512 product_url: http://purl.obolibrary.org/obo/uberon/uberon-basic.obo - category: OntologyProduct description: Uberon plus all metazoan ontologies format: owl id: uberon.collected-metazoan.owl name: Uberon collected metazoan ontology product_file_size: 283766409 product_url: http://purl.obolibrary.org/obo/uberon/collected-metazoan.owl - category: OntologyProduct description: Uberon and all metazoan ontologies with redundant species-specific terms removed format: owl id: uberon.composite-metazoan.owl name: Uberon composite metazoan ontology product_file_size: 258612004 product_url: http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl - category: OntologyProduct description: Uberon composite vertebrate ontology format: owl id: uberon.composite-vertebrate.owl name: Uberon composite vertebrate ontology product_file_size: 125673982 product_url: http://purl.obolibrary.org/obo/uberon/composite-vertebrate.owl - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: GraphProduct compression: zip description: Nodes from Uber-Anatomy Ontology format: csv id: biomarkerkg.nodes.anatomy name: BKG Anatomy Nodes original_source: - uberon product_file_size: 332 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Anatomy.nodes.zip secondary_source: - biomarkerkg - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' repository: https://github.com/obophenotype/uberon taxon: - NCBITaxon:33208 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: ubkg@pitt.edu label: University of Pittsburgh - category: Organization contact_details: - contact_type: github value: x-atlas-consortia label: x-atlas-consortia creation_date: '2025-05-29T00:00:00Z' description: The Unified Biomedical Knowledge Graph (UBKG) is a knowledge graph infrastructure that represents a set of interrelated concepts from biomedical ontologies and vocabularies. It combines information from the National Library of Medicine's Unified Medical Language System (UMLS) with sets of assertions from ontologies outside the UMLS to establish connections between different sets of assertions that can enable discovery of previously unknown relationships. domains: - biomedical - health - genomics evaluation_page: resource/ubkg/ubkg_eval_automated.html homepage_url: https://ubkg.docs.xconsortia.org/ id: ubkg last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf label: UMLS License Agreement name: Unified Biomedical Knowledge Graph products: - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: ProgrammingInterface description: REST API with endpoints that abstract common types of queries against a UBKG neo4j knowledge graph database. Requires UMLS API key to access. id: ubkg.api is_public: false name: UBKG API product_url: https://smart-api.info/ui/96e5b5c0b0efeef5b93ea98ac2794837 - category: GraphicalInterface description: Guesdt (Graphing UMLS Enables Search In Dynamic Trees) application used to represent the UBKG in a tree view. id: ubkg.guesdt name: UBKG Guesdt Interface product_url: https://x-atlas-consortia.github.io/Guesdt/ - category: GraphProduct description: A comprehensive multi-omics biomedical knowledge graph connecting genomic, transcriptomic, proteomic, and clinical data. Contains over 32 million nodes and 118 million relationships. dump_format: neo4j edge_count: 118000000 id: petagraph.graph name: Petagraph Knowledge Graph (Neo4J) node_count: 32000000 original_source: - ubkg product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - petagraph repository: https://github.com/x-atlas-consortia usages: - description: The Petagraph Knowledge Graph is built using UBKG as a scaffold. id: ubkg.part_of.petagraph label: UBKG is part of Petagraph type: actual url: https://doi.org/10.1038/s41597-024-04070-w - activity_status: active category: KnowledgeGraph collection: - ber contacts: - category: Organization contact_details: - contact_type: url value: https://ufokn.com/ - contact_type: github value: UFOKN label: UF Open Knowledge Network (UF-OKN) creation_date: '2025-08-07T00:00:00Z' description: The Urban Flooding Open Knowledge Network (UF-OKN) is an informational infrastructure built with knowledge graphs to connect urban infrastructure with hydrologic forecasts, delivering actionable, real-time and historical flood-risk information as Linked Data for exploration and app development. domains: - environment evaluation_page: resource/uf-okn/uf-okn_eval_automated.html homepage_url: https://ufokn.com/ id: uf-okn last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: UF-OKN products: - category: GraphicalInterface description: Public UF-OKN web portal for project information and application context. format: http id: uf-okn.portal name: UF-OKN Portal original_source: - uf-okn product_url: https://ufokn.com/ - category: ProcessProduct description: Source repository for UF-OKN knowledge graph construction and maintenance. format: http id: uf-okn.code name: UF-OKN Source Code original_source: - uf-okn product_url: https://github.com/UFOKN/Knowledge-Graph repository: https://github.com/UFOKN/Knowledge-Graph - activity_status: active category: DataSource creation_date: '2025-06-27T00:00:00Z' description: UK Biobank is a large-scale biomedical database and research resource containing genetic, lifestyle and health information from half a million UK participants, designed to improve the prevention, diagnosis and treatment of a wide range of serious and life-threatening illnesses. domains: - biomedical - genomics - health - clinical - phenotype homepage_url: https://www.ukbiobank.ac.uk/ id: ukbiobank last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail license: id: https://www.ukbiobank.ac.uk/terms-and-conditions/ label: UK Biobank Data Access Agreement name: UK Biobank products: - category: GraphicalInterface description: The UK Biobank Data Showcase provides summary statistics of all UK Biobank data and allows researchers to identify variables for inclusion in research applications. format: http id: ukbiobank.showcase name: UK Biobank Data Showcase product_url: https://biobank.ndph.ox.ac.uk/showcase/ - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb publications: - authors: - Clare Bycroft - Colin Freeman - Desislava Petkova - Gavin Band - Lloyd T. Elliott - Kevin Sharp - Allan Motyer - Damjan Vukcevic - Olivier Delaneau - Jared O'Connell - Adrian Cortes - Samantha Welsh - Alan Young - Mark Effingham - Gil McVean - Stephen Leslie - Naomi Allen - Peter Donnelly - Jonathan Marchini doi: 10.1038/s41586-018-0579-z id: doi:10.1038/s41586-018-0579-z journal: Nature title: The UK Biobank resource with deep phenotyping and genomic data year: '2018' - authors: - Cathie Sudlow - John Gallacher - Naomi Allen - Valerie Beral - Paul Burton - John Danesh - Paul Downey - Paul Elliott - Jane Green - Martin Landray - Bette Liu - Paul Matthews - Giok Ong - Jill Pell - Alan Silman - Alan Young - Tim Sprosen - Tim Peakman - Rory Collins doi: 10.1371/journal.pmed.1001779 id: doi:10.1371/journal.pmed.1001779 journal: PLOS Medicine title: 'UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age' year: '2015' taxon: - NCBITaxon:9606 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.nlm.nih.gov/research/umls/support.html id: ncbi label: NLM UMLS Customer Support creation_date: '2025-10-30T00:00:00Z' description: The Unified Medical Language System (UMLS) integrates and distributes over 200 biomedical vocabularies, terminologies, and classification standards to enable interoperability between information systems. It includes the Metathesaurus (terms and codes from vocabularies like CPT, ICD-10-CM, LOINC, MeSH, RxNorm, SNOMED CT), Semantic Network (broad categories and relationships), and SPECIALIST Lexicon (biomedical and general English lexicon with normalization tools). domains: - biomedical - clinical - literature homepage_url: https://www.nlm.nih.gov/research/umls/index.html id: umls infores_id: umls last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail license: id: https://uts.nlm.nih.gov/uts/ label: UMLS License (free for individuals) name: Unified Medical Language System products: - category: GraphicalInterface description: Web interface for browsing UMLS Metathesaurus concepts, CUIs, semantic types, and synonymous terms format: http id: umls.browser name: UMLS Metathesaurus Browser original_source: - umls product_url: https://uts.nlm.nih.gov/uts/umls/home - category: GraphicalInterface description: Web interface for viewing semantic types, definitions, and hierarchical structure of the UMLS Semantic Network format: http id: umls.semantic_network_browser name: UMLS Semantic Network Browser original_source: - umls product_url: https://uts.nlm.nih.gov/uts/umls/semantic-network/root - category: ProgrammingInterface description: REST API providing programmatic access to UMLS Metathesaurus, Semantic Network, and related terminology services id: umls.api is_public: true name: UMLS Terminology Services API original_source: - umls product_url: https://documentation.uts.nlm.nih.gov/rest/home.html - category: Product description: Full UMLS Knowledge Sources release including Metathesaurus, Semantic Network, and SPECIALIST Lexicon for local installation with MetamorphoSys customization tool id: umls.release name: UMLS Knowledge Sources Release Files product_url: https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html - category: ProcessProduct description: MetamorphoSys tool for customizing UMLS subsets by vocabulary, language, or semantic type and loading data into local databases id: umls.metamorphosys name: MetamorphoSys Customization Tool product_url: https://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/help.html - category: ProcessProduct description: SPECIALIST Lexicon and Lexical Tools for normalizing strings, generating lexical variants, and creating indexes for biomedical text processing id: umls.specialist_lexicon name: SPECIALIST Lexicon and Lexical Tools original_source: - umls product_url: https://lhncbc.nlm.nih.gov/LSG/index.html - category: GraphProduct description: KGX distribution of the ICEES Exposures KP in Knowledge Graph Exchange (KGX) format, containing integrated clinical and environmental exposures data as a knowledge graph with 226 nodes and 14,342 edges format: kgx-jsonl id: icees-kg.graph name: KGX distribution of the ICEES Exposures KP original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/ secondary_source: - icees-kg - category: ProgrammingInterface description: Translator Reasoner API (TRAPI) endpoint for querying ICEES KG using standardized Translator protocols format: http id: icees-kg.trapi name: ICEES KG TRAPI API original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg-trapi secondary_source: - icees-kg - category: Product description: Meta knowledge graph and metadata describing the data sources, node types, edge types, and predicates available in ICEES KG format: json id: icees-kg.metadata name: ICEES KG Metadata original_source: - mesh - pubchem - chembl - mondo - chebi - hp - umls - hmdb - icees-kg product_url: https://robokop.renci.org/api-docs/docs/automat/metadata-metadata-get-icees-kg secondary_source: - icees-kg - category: Product description: VANDF drug terminology data distributed through UMLS Metathesaurus id: ndfrt.umls name: VANDF in UMLS original_source: - ndfrt product_url: https://www.nlm.nih.gov/research/umls/ secondary_source: - umls - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv - category: Product compression: gzip description: Rich Release Format (RRF) file containing concept names and source identifiers with gzip compression format: txt id: medgen.mgconso name: MGCONSO (Concept Names) original_source: - medgen - umls product_file_size: 15843494 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/MGCONSO.RRF.gz - category: Product compression: gzip description: Rich Release Format (RRF) file containing definitions and descriptions with gzip compression format: txt id: medgen.mgdef name: MGDEF (Definitions) original_source: - medgen - umls product_file_size: 5062289 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/MGDEF.RRF.gz - category: MappingProduct compression: gzip description: Rich Release Format (RRF) file containing relationships between concepts with gzip compression format: txt id: medgen.mgrel name: MGREL (Relationships) original_source: - medgen - umls product_file_size: 15661303 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/MGREL.RRF.gz - category: Product compression: gzip description: Rich Release Format (RRF) file containing attributes and properties with gzip compression format: txt id: medgen.mgsat name: MGSAT (Attributes) original_source: - medgen - umls product_file_size: 11710268 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/MGSAT.RRF.gz - category: Product compression: gzip description: Rich Release Format (RRF) file containing semantic type assignments with gzip compression format: txt id: medgen.mgsty name: MGSTY (Semantic Types) original_source: - medgen - umls product_file_size: 1644564 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/MGSTY.RRF.gz - category: Product compression: gzip description: Rich Release Format (RRF) file containing concept names for search with gzip compression format: txt id: medgen.names name: NAMES original_source: - medgen - umls product_file_size: 3097271 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/NAMES.RRF.gz - category: Product compression: gzip description: Merged CUI mappings showing concept consolidations with gzip compression format: txt id: medgen.merged name: MERGED (Merged CUIs) original_source: - medgen - umls product_file_size: 47602 product_url: https://ftp.ncbi.nlm.nih.gov/pub/medgen/MERGED.RRF.gz publications: - id: PMID:14681409 preferred: true title: 'The Unified Medical Language System (UMLS): integrating biomedical terminology.' synonyms: - UMLS taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: xfd997700@gmail.com - contact_type: github value: xfd997700 label: Fanding Xu orcid: 0000-0001-7220-8693 creation_date: '2026-01-28T00:00:00Z' description: UniBioMap (Unified Biomedical knowledge Map) is an AI-ready biomedical knowledge graph integrating over 30 heterogeneous resources through robust identifier normalization, covering 6 key entity types with 21 million curated relations across 38 fine-grained types. A confident learning framework assigns reliability scores and predicts 34 million high-confidence triples, establishing a foundational resource for target identification and machine learning-based biomedical discovery. domains: - biomedical - chemistry and biochemistry - drug discovery - genomics - pathways - biological systems - systems biology - phenotype - proteomics evaluation_page: resource/unibiomap/unibiomap_eval_automated.html homepage_url: https://zhanggroup.org/UniBioMap/ id: unibiomap last_modified_date: '2026-01-28T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-nc/4.0/ label: CC BY-NC 4.0 name: UniBioMap products: - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv - category: GraphProduct description: UniBioMap compound entity descriptions. format: json id: unibiomap.compound_desc name: UniBioMap Compound Descriptions product_url: https://aideepmed.com/UniBioMap/database/unibiomap/compound_desc.json secondary_source: - unibiomap warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: UniBioMap protein entity descriptions. format: json id: unibiomap.protein_desc name: UniBioMap Protein Descriptions product_url: https://aideepmed.com/UniBioMap/database/unibiomap/protein_desc.json secondary_source: - unibiomap warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: UniBioMap disease entity descriptions. format: json id: unibiomap.disease_desc name: UniBioMap Disease Descriptions product_url: https://aideepmed.com/UniBioMap/database/unibiomap/disease_desc.json secondary_source: - unibiomap warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: UniBioMap Gene Ontology entity descriptions. format: json id: unibiomap.go_desc name: UniBioMap GO Descriptions original_source: - go product_url: https://aideepmed.com/UniBioMap/database/unibiomap/go_desc.json secondary_source: - unibiomap warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: UniBioMap pathway entity descriptions. format: json id: unibiomap.pathway_desc name: UniBioMap Pathway Descriptions product_url: https://aideepmed.com/UniBioMap/database/unibiomap/pathway_desc.json secondary_source: - unibiomap warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphProduct description: UniBioMap phenotype entity descriptions. format: json id: unibiomap.phenotype_desc name: UniBioMap Phenotype Descriptions product_url: https://aideepmed.com/UniBioMap/database/unibiomap/phenotype_desc.json secondary_source: - unibiomap warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: GraphicalInterface description: Web interface for browsing UniBioMap resources and documentation. format: http id: unibiomap.web name: UniBioMap Website original_source: - unibiomap product_url: https://zhanggroup.org/UniBioMap/ - category: ProcessProduct description: Source code and pipelines used to build the UniBioMap knowledge graph. id: unibiomap.code name: UniBioMap Code original_source: - unibiomap product_url: https://github.com/xfd997700/UniBioMap repository: https://github.com/xfd997700/UniBioMap repository: https://github.com/xfd997700/UniBioMap version: 1.0.0 - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: email value: chembl-help@ebi.ac.uk - contact_type: url value: https://chembl.gitbook.io/unichem id: ebi label: ChEMBL Team at EMBL-EBI creation_date: '2025-11-04T00:00:00Z' description: UniChem is a large-scale non-redundant database maintained by EMBL-EBI that provides cross-references between chemical structures across multiple chemistry resources. It serves as a unified system for creating and maintaining structure-based hyperlinks between chemistry databases, particularly optimized for on-the-fly link creation via REST web services. UniChem aggregates compound identifiers from major chemistry resources including ChEMBL, ChEBI, SureChEMBL, PubChem, DrugBank, and many others, enabling efficient cross-database chemical structure queries using InChI, InChIKey, or source-specific identifiers. domains: - chemistry and biochemistry - drug discovery - pharmacology homepage_url: https://www.ebi.ac.uk/unichem/ id: unichem infores_id: unichem last_modified_date: '2025-11-04T00:00:00Z' layout: resource_detail name: UniChem products: - category: GraphicalInterface description: Web-based search interface for finding compound sources and performing connectivity searches across chemical databases format: http id: unichem.search name: UniChem Search Interface original_source: - unichem product_url: https://www.ebi.ac.uk/unichem/search - category: ProgrammingInterface description: RESTful web services API for programmatic access to UniChem cross-references and connectivity searches format: http id: unichem.api name: UniChem REST API original_source: - unichem product_url: https://www.ebi.ac.uk/unichem/api/docs - category: Product description: Comprehensive list of all integrated chemistry databases and their metadata in UniChem format: http id: unichem.sources name: UniChem Source Database List original_source: - unichem product_url: https://www.ebi.ac.uk/unichem/sources - category: DocumentationProduct description: Complete documentation covering UniChem functionality, API usage, data model, and integration guidelines format: http id: unichem.docs name: UniChem Documentation original_source: - unichem product_url: https://chembl.gitbook.io/unichem - category: DocumentationProduct description: UniChem compound sources page illustrating the UCI identifier namespace. format: http id: unichem.docs.uci name: UCI Documentation Entry Point original_source: - unichem product_url: https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=1 - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv synonyms: - unichem - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: FDA-SRS@fda.hhs.gov id: fda label: FDA Substance Registration System Team creation_date: '2025-07-17T00:00:00Z' description: FDA's Global Substance Registration System (GSRS) is a comprehensive database that provides Unique Ingredient Identifiers (UNIIs) for substances in FDA-regulated products. UNIIs uniquely define substances based on scientific identity characteristics using ISO 11238 data elements, enabling efficient and accurate exchange of substance information across regulatory domains. domains: - clinical - drug discovery - pharmacology - public health homepage_url: https://precision.fda.gov/uniisearch id: unii infores_id: unii last_modified_date: '2025-09-24T00:00:00Z' layout: resource_detail name: FDA Global Substance Registration System (UNII) products: - category: GraphicalInterface description: Web-based search interface for finding substances by UNII, name, or other identifiers format: http id: unii.search name: UNII Search Service product_url: https://precision.fda.gov/uniisearch - category: Product compression: zip description: Downloadable list of all UNIIs with basic substance information format: csv id: unii.list name: UNII List Download product_url: https://precision.fda.gov/uniisearch/archive/latest/UNIIs.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product compression: zip description: Comprehensive UNII data with detailed substance attributes and mappings format: mixed id: unii.data name: UNII Data Download product_url: https://precision.fda.gov/uniisearch/archive/latest/UNII_Data.zip warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: Legacy UNII identifiers for historical substances format: txt id: unii.legacy name: Legacy UNIIs product_url: https://precision.fda.gov/uniisearch/archive/latest/Legacy_UNIIs.txt warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - description: The MechRepoNet knowledge graph in its original format id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - ctd - doid - go - chebi - reactome - interpro - hp - cl - pr - uberon - ncbitaxon - hetionet - complexportal - rnacentral - mirtarbase - unii - biolink product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication secondary_source: - mechreponet publications: - id: https://www.fda.gov/science-research/fda-grand-rounds/fdas-global-substance-registration-system-gsrs-unique-ingredient-identifiers-uniis-uniquely-define title: 'FDA Grand Rounds: FDA''s Global Substance Registration System (GSRS) Unique Ingredient Identifiers (UNIIs)' repository: https://ginas.ncats.nih.gov/ginas/app taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: help@uniprot.org id: ebi label: UniProt Consortium creation_date: '2025-03-09T00:00:00Z' description: UniProt Protein Knowledge Base domains: - biological systems - proteomics - biomedical homepage_url: https://www.uniprot.org/ id: uniprot infores_id: uniprot last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: uniprot products: - category: GraphProduct compression: targz description: UniProt proteins from microbes, as graph nodes and edges format: kgx id: kg-microbe.graph.uniprot name: KG-Microbe UniProt microbe transform original_source: - uniprot product_file_size: 4796343398 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-transformed-uniprot-microbes-20240924.tar.gz secondary_source: - kg-microbe - category: Product compression: gzip description: The Reviewed (Swiss-Prot) section of UniProt proteins format: kgx id: uniprot.swissprot.xml name: Reviewed (Swiss-Prot) XML original_source: - uniprot product_file_size: 925893980 product_url: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz secondary_source: - uniprot - category: Product compression: gzip description: The Reviewed (Swiss-Prot) section of UniProt proteins format: fasta id: uniprot.swissprot.fasta name: Reviewed (Swiss-Prot) FASTA original_source: - uniprot product_file_size: 93100075 product_url: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz secondary_source: - uniprot - category: Product compression: gzip description: The Unreviewed (TrEMBL) section of UniProt proteins format: xml id: uniprot.trembl.xml name: Unreviewed (TrEMBL) XML original_source: - uniprot product_file_size: 243378751330 product_url: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.xml.gz secondary_source: - uniprot - category: Product compression: gzip description: The Unreviewed (TrEMBL) section of UniProt proteins format: fasta id: uniprot.trembl.fasta name: Unreviewed (TrEMBL) FASTA original_source: - uniprot product_file_size: 63579343267 product_url: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz secondary_source: - uniprot - category: Product description: Tab-delimited file of systematic ID, primary gene name (where assigned), chromosome, product description, UniProtKB accession, all synonyms, and product type (protein coding, ncRNA, etc.) for each gene format: tsv id: pombase.genes-products license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: PomBase gene names and products original_source: - uniprot - pombase product_url: https://www.pombase.org/data/names_and_identifiers/gene_IDs_names_products.tsv secondary_source: - pombase warnings: - File was not able to be retrieved when checked on 2026-03-08_ No Content-Length header found - File was not able to be retrieved when checked on 2026-02-26_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-03-11: No Content-Length header found' - category: MappingProduct description: Tab-delimited file with the PomBase systematic identifier for each protein-coding gene mapped to the corresponding UniProt accession number format: tsv id: pombase.to-uniprot license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: PomBase to UniProt map original_source: - uniprot - pombase product_file_size: 27617 product_url: https://www.pombase.org/data/names_and_identifiers/PomBase2UniProt.tsv secondary_source: - pombase - category: MappingProduct description: Mapping between chembl_35 target chembl_ids and UniProt accessions id: chembl.map_to_uniprot is_public: true name: ChEMBL map to UniProt original_source: - chembl - uniprot product_file_size: 1012901 product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_uniprot_mapping.txt secondary_source: - chembl - category: MappingProduct compression: gzip description: Mapping of OMA identifiers to UniProt accession numbers format: tsv id: oma.mapping.uniprot name: OMA to UniProt Mapping original_source: - oma - uniprot product_url: https://omabrowser.org/oma/current/oma-uniprot.txt.gz secondary_source: - oma warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-18_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-01-28_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-01-03_ HTTP 502 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet - category: MappingProduct compression: gzip description: Gene to RefSeq/UniProtKB collaboration data providing cross-references between gene records and protein databases format: tsv id: ncbigene.gene_refseq_uniprotkb_collab name: Gene RefSeq UniProtKB Collaboration Data original_source: - refseq - ncbigene - uniprot product_file_size: 1182285769 product_url: https://ftp.ncbi.nih.gov/gene/DATA/gene_refseq_uniprotkb_collab.gz - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct compatibility: - standard: biolink compression: zip description: Curated mechanistic drug–disease paths comprising the DrugMechDB dataset packaged as a downloadable archive. dump_format: other format: mixed id: drugmechdb.graph latest_version: 2.0.1 name: DrugMechDB Graph Dataset original_source: - go - cl - mesh - chebi - drugbank - interpro - uberon - pr - ncbitaxon - reactome - hp - uniprot product_url: https://doi.org/10.5281/zenodo.8139357 repository: https://github.com/SuLab/DrugMechDB versions: - 2.0.1 - 2.0.0 - 1.0.2 - '1.0' - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: ProgrammingInterface description: TRAPI web API for querying MicrobiomeKG format: http id: microbiomekg.api name: MicrobiomeKG Plover API original_source: - biolink - chebi - ncbitaxon - ncbigene - mesh - pubchem - go - mondo - ncit - efo - uniprot - rhea - pr - uberon - panther - hgnc - drugbank - eupathdb product_url: https://multiomics.transltr.io/mbkp secondary_source: - microbiomekg - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: Product description: Integrated gene annotation data aggregated from HGNC, OMIM, Ensembl, NCBI Gene, UniProt and other genomic databases format: http id: genecards.gene.annotations name: GeneCards Gene Annotations original_source: - hgnc - omim - ensembl - ncbigene - uniprot - refseq product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - 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category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz - category: GraphProduct description: ProteomeHD data files id: proteomehd.data name: ProteomeHD Data original_source: - proteomehd - uniprot - reactome - intact - go - goa product_url: https://github.com/Rappsilber-Laboratory/ProteomeHD/tree/master/Data - category: Product description: TSV export of lipid-related enzymes with UniProt, Rhea, and evidence links. format: tsv id: swisslipid.enzymes name: SwissLipids Enzymes original_source: - swisslipid - uniprot - rhea product_file_size: 126760 product_url: https://www.swisslipids.org/api/file.php?cas=download_files&file=enzymes.tsv - category: MappingProduct description: TSV mapping between SwissLipids lipid entries and UniProtKB proteins. format: tsv id: swisslipid.lipids2uniprot name: SwissLipids Lipids to UniProt original_source: - swisslipid - uniprot product_file_size: 37147786 product_url: https://www.swisslipids.org/api/file.php?cas=download_files&file=lipids2uniprot.tsv - category: Product description: uniprot Nodes TSV format: tsv id: obo-db-ingest.uniprot.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: uniprot Nodes TSV original_source: - uniprot product_file_size: 3801999 product_url: https://w3id.org/biopragmatics/resources/uniprot/uniprot.tsv secondary_source: - obo-db-ingest - category: Product description: uniprot.ptm Nodes TSV format: tsv id: obo-db-ingest.uniprot.ptm.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: uniprot.ptm Nodes TSV original_source: - uniprot product_file_size: 6660 product_url: https://w3id.org/biopragmatics/resources/uniprot.ptm/uniprot.ptm.tsv secondary_source: - obo-db-ingest repository: https://www.uniprot.org/help/downloads taxon: - NCBITaxon:9606 - NCBITaxon:10090 - NCBITaxon:10116 - NCBITaxon:7227 - NCBITaxon:6239 - NCBITaxon:7955 - NCBITaxon:4932 - NCBITaxon:3702 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: help@uniprot.org - contact_type: url value: https://www.uniprot.org/contact id: ebi label: UniProt Consortium creation_date: '2025-10-31T00:00:00Z' description: UniRef (Universal Protein Resource Reference Clusters) provides clustered sets of protein sequences from the UniProt Knowledgebase and selected UniParc records to obtain complete coverage. UniRef100 combines identical sequences and sub-fragments into a single UniRef entry, UniRef90 clusters sequences with 90% sequence identity, and UniRef50 clusters sequences with 50% sequence identity, providing speed and coverage tradeoffs for similarity searches. domains: - proteomics - biomedical - biological systems homepage_url: https://www.uniprot.org/help/uniref id: uniref infores_id: uniref last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: UniRef products: - category: Product compression: gzip description: UniRef100 database combining identical protein sequences and sub-fragments with 11-residue overlap into single representative entries, providing complete sequence coverage with 100% identity clustering format: fasta id: uniref.uniref100.fasta name: UniRef100 FASTA product_file_size: 124528354456 product_url: https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.fasta.gz warnings: - File was not able to be retrieved when checked on 2025-10-31_ Timeout connecting to URL - category: Product compression: gzip description: UniRef100 database in XML format with comprehensive metadata including cluster membership, representative sequences, taxonomy, and cross-references format: xml id: uniref.uniref100.xml name: UniRef100 XML product_file_size: 158103062524 product_url: https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.xml.gz warnings: - File was not able to be retrieved when checked on 2025-10-31_ Timeout connecting to URL - category: Product compression: gzip description: UniRef90 database clustering sequences with at least 90% sequence identity and 80% overlap, balancing speed and sensitivity for sequence searches format: fasta id: uniref.uniref90.fasta name: UniRef90 FASTA product_file_size: 46103634991 product_url: https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz warnings: - File was not able to be retrieved when checked on 2025-10-31_ Timeout connecting to URL - category: Product compression: gzip description: UniRef90 database in XML format with complete cluster information and annotations format: xml id: uniref.uniref90.xml name: UniRef90 XML product_file_size: 70196113636 product_url: https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.xml.gz warnings: - File was not able to be retrieved when checked on 2025-10-31_ Timeout connecting to URL - category: Product compression: gzip description: UniRef50 database clustering sequences with at least 50% sequence identity and 80% overlap, providing fast sequence searches with broad coverage of protein sequence space format: fasta id: uniref.uniref50.fasta name: UniRef50 FASTA product_file_size: 12385282557 product_url: https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz warnings: - File was not able to be retrieved when checked on 2025-10-31_ Timeout connecting to URL - category: Product compression: gzip description: UniRef50 database in XML format with detailed cluster annotations and relationships format: xml id: uniref.uniref50.xml name: UniRef50 XML product_file_size: 32238584114 product_url: https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.xml.gz warnings: - File was not able to be retrieved when checked on 2025-10-31_ Timeout connecting to URL - category: GraphicalInterface description: Web interface for searching, browsing, and analyzing UniRef cluster information with advanced search capabilities and visualization tools format: http id: uniref.portal name: UniRef Web Portal product_url: https://www.uniprot.org/uniref - category: ProgrammingInterface description: RESTful API for programmatic access to UniRef cluster data supporting queries, downloads, and integration with bioinformatics workflows format: http id: uniref.api name: UniRef REST API product_url: https://www.uniprot.org/help/api publications: - authors: - Suzek BE - Huang H - McGarvey P - Mazumder R - Wu CH doi: 10.1093/bioinformatics/btm098 id: https://doi.org/10.1093/bioinformatics/btm098 journal: Bioinformatics preferred: true title: 'UniRef: comprehensive and non-redundant UniProt reference clusters' year: '2007' synonyms: - UniRef - UniRef100 - UniRef90 - UniRef50 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: g.gkoutos@gmail.com - contact_type: github value: gkoutos label: George Gkoutos orcid: 0000-0002-2061-091X creation_date: '2025-06-04T00:00:00Z' description: Metrical units for use in conjunction with PATO domains: - biological systems homepage_url: https://github.com/bio-ontology-research-group/unit-ontology id: uo last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Units of measurement ontology products: - category: OntologyProduct description: Units of measurement ontology in OWL format format: owl id: uo.owl name: uo.owl product_file_size: 36414 product_url: http://purl.obolibrary.org/obo/uo.owl - category: OntologyProduct description: Units of measurement ontology in OBO format format: obo id: uo.obo name: uo.obo product_file_size: 19896 product_url: http://purl.obolibrary.org/obo/uo.obo - category: OntologyProduct description: Units of measurement ontology in JSON format format: json id: uo.json name: uo.json product_file_size: 24296 product_url: http://purl.obolibrary.org/obo/uo.json - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo - category: GraphProduct description: RDF dump of the Open Research Knowledge Graph distributed in N-Triples format. format: ntriples id: orkg.dump name: ORKG RDF Dump original_source: - orkg - wikidata - geonames - ncit - chebi - ncbitaxon - go - clo - omit - iao - uo - stato - obi product_file_size: 642902930 product_url: https://orkg.org/api/rdf/dump secondary_source: - orkg repository: https://github.com/bio-ontology-research-group/unit-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jmcl@ebi.ac.uk - contact_type: github value: jamesamcl label: James McLaughlin orcid: 0000-0002-8361-2795 creation_date: '2025-09-29T00:00:00Z' description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. domains: - biological systems homepage_url: https://github.com/obophenotype/upheno id: upheno last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Unified Phenotype Ontology (uPheno) products: - category: OntologyProduct description: uPheno 1 is no longer actively maintained, please start using uPheno 2 (see below). format: owl id: upheno.owl name: uPheno 1 (inactive) product_file_size: 416269865 product_url: http://purl.obolibrary.org/obo/upheno.owl - category: OntologyProduct description: No longer actively maintained. format: owl id: upheno.mp-hp-view.owl name: uPheno MP-HP equivalence axioms product_file_size: 51640383 product_url: http://purl.obolibrary.org/obo/upheno/mp-hp-view.owl - category: OntologyProduct description: The new version of uPheno, along with species independent phenotypes and additional phenotype relations. The ontology is still in Beta status, but we recommend users to migrate their infrastructures to uPheno 2 as uPheno 1 is no longer actively maintained. format: owl id: upheno.v2.upheno.owl name: uPheno 2 product_file_size: 416269865 product_url: http://purl.obolibrary.org/obo/upheno/v2/upheno.owl repository: https://github.com/obophenotype/upheno - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Sabrina@tislab.org - contact_type: github value: sabrinatoro label: Sabrina Toro orcid: 0000-0002-4142-7153 creation_date: '2025-09-29T00:00:00Z' description: Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names. domains: - biological systems homepage_url: https://github.com/monarch-initiative/vertebrate-breed-ontology id: vbo last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Vertebrate Breed Ontology products: - category: OntologyProduct description: Vertebrate Breed Ontology in OWL format format: owl id: vbo.owl name: vbo.owl product_file_size: 2077292 product_url: http://purl.obolibrary.org/obo/vbo.owl - category: OntologyProduct description: Vertebrate Breed Ontology in OBO format format: obo id: vbo.obo name: vbo.obo product_file_size: 990658 product_url: http://purl.obolibrary.org/obo/vbo.obo - category: OntologyProduct description: Vertebrate Breed Ontology in JSON format format: json id: vbo.json name: vbo.json product_file_size: 1205306 product_url: http://purl.obolibrary.org/obo/vbo.json - category: OntologyProduct description: Vertebrate Breed Ontology in OWL format format: owl id: vbo.vbo-base.owl name: vbo.vbo-base.owl product_file_size: 2016216 product_url: http://purl.obolibrary.org/obo/vbo/vbo-base.owl - category: OntologyProduct description: Vertebrate Breed Ontology in OBO format format: obo id: vbo.vbo-base.obo name: vbo.vbo-base.obo product_file_size: 958659 product_url: http://purl.obolibrary.org/obo/vbo/vbo-base.obo - category: OntologyProduct description: Vertebrate Breed Ontology in JSON format format: json id: vbo.vbo-base.json name: vbo.vbo-base.json product_file_size: 1154978 product_url: http://purl.obolibrary.org/obo/vbo/vbo-base.json repository: https://github.com/monarch-initiative/vertebrate-breed-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: yongqunh@med.umich.edu - contact_type: github value: yongqunh label: Yongqunh He orcid: 0000-0001-9189-9661 creation_date: '2025-08-20T00:00:00Z' description: VO is a biomedical ontology in the domain of vaccine and vaccination. domains: - biomedical homepage_url: https://violinet.org/vaccineontology id: vo last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Vaccine Ontology products: - category: OntologyProduct description: Vaccine Ontology in OWL format format: owl id: vo.owl name: vo.owl product_file_size: 1492352 product_url: http://purl.obolibrary.org/obo/vo.owl - category: GraphProduct description: PheKnowLator graph files, including subsets with and without inverse relations. format: owl id: pheknowlator.graph latest_version: current_build name: PheKnowLator graph original_source: - cl - clo - chebi - go - hp - mondo - pw - pr - ro - so - uberon - vo - bioportal - clinvar - ctd - disgenet - ensembl - genemania - hgnc - hpa - ncbigene - medgen - reactome - string - uniprot product_url: https://console.cloud.google.com/storage/browser/pheknowlator/current_build/knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator secondary_source: - pheknowlator versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg repository: https://github.com/vaccineontology/VO - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: caripark@iastate.edu - contact_type: github value: caripark label: Carissa Park orcid: 0000-0002-2346-5201 creation_date: '2025-09-29T00:00:00Z' description: An ontology of traits covering vertebrates domains: - biological systems homepage_url: https://github.com/AnimalGenome/vertebrate-trait-ontology id: vt last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Vertebrate trait ontology products: - category: OntologyProduct description: Vertebrate trait ontology in OWL format format: owl id: vt.owl name: vt.owl product_file_size: 416629 product_url: http://purl.obolibrary.org/obo/vt.owl repository: https://github.com/AnimalGenome/vertebrate-trait-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: balhoff@renci.org - contact_type: github value: balhoff label: Jim Balhoff orcid: 0000-0002-8688-6599 creation_date: '2025-09-29T00:00:00Z' description: Comprehensive hierarchy of extinct and extant vertebrate taxa. domains: - biological systems homepage_url: https://github.com/phenoscape/vertebrate-taxonomy-ontology id: vto last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Vertebrate Taxonomy Ontology products: - category: OntologyProduct description: Vertebrate Taxonomy Ontology in OWL format format: owl id: vto.owl name: vto.owl product_file_size: 152582746 product_url: http://purl.obolibrary.org/obo/vto.owl - category: OntologyProduct description: Vertebrate Taxonomy Ontology in OBO format format: obo id: vto.obo name: vto.obo product_file_size: 27544534 product_url: http://purl.obolibrary.org/obo/vto.obo repository: https://github.com/phenoscape/vertebrate-taxonomy-ontology - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: raymond@caltech.edu - contact_type: github value: raymond91125 label: Raymond Lee orcid: 0000-0002-8151-7479 creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. domains: - anatomy and development homepage_url: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology id: wbbt last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: C. elegans Gross Anatomy Ontology products: - category: OntologyProduct description: C. elegans Gross Anatomy Ontology in OWL format format: owl id: wbbt.owl name: wbbt.owl product_file_size: 325464 product_url: http://purl.obolibrary.org/obo/wbbt.owl - category: OntologyProduct description: C. elegans Gross Anatomy Ontology in OBO format format: obo id: wbbt.obo name: wbbt.obo product_file_size: 163163 product_url: http://purl.obolibrary.org/obo/wbbt.obo repository: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology taxon: - NCBITaxon:6237 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cgrove@caltech.edu - contact_type: github value: chris-grove label: Chris Grove orcid: 0000-0001-9076-6015 creation_date: '2025-06-25T00:00:00Z' description: A structured controlled vocabulary of the development of Caenorhabditis elegans. domains: - anatomy and development homepage_url: https://github.com/obophenotype/c-elegans-development-ontology id: wbls last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: C. elegans development ontology products: - category: OntologyProduct description: C. elegans development ontology in OWL format format: owl id: wbls.owl name: wbls.owl product_file_size: 76039 product_url: http://purl.obolibrary.org/obo/wbls.owl - category: OntologyProduct description: C. elegans development ontology in OBO format format: obo id: wbls.obo name: wbls.obo product_file_size: 30116 product_url: http://purl.obolibrary.org/obo/wbls.obo - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://github.com/obophenotype/c-elegans-development-ontology taxon: - NCBITaxon:6237 - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cgrove@caltech.edu - contact_type: github value: chris-grove label: Chris Grove orcid: 0000-0001-9076-6015 creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes domains: - biological systems homepage_url: https://github.com/obophenotype/c-elegans-phenotype-ontology id: wbphenotype last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: C. elegans phenotype products: - category: OntologyProduct description: C. elegans phenotype in OWL format format: owl id: wbphenotype.owl name: wbphenotype.owl product_file_size: 1042232 product_url: http://purl.obolibrary.org/obo/wbphenotype.owl - category: OntologyProduct description: C. elegans phenotype in OBO format format: obo id: wbphenotype.obo name: wbphenotype.obo product_file_size: 180404 product_url: http://purl.obolibrary.org/obo/wbphenotype.obo - category: OntologyProduct description: C. elegans phenotype in OWL format format: owl id: wbphenotype.wbphenotype-base.owl name: wbphenotype.wbphenotype-base.owl product_file_size: 329630 product_url: http://purl.obolibrary.org/obo/wbphenotype/wbphenotype-base.owl repository: https://github.com/obophenotype/c-elegans-phenotype-ontology taxon: - NCBITaxon:6237 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: email value: wikidata-l@lists.wikimedia.org - contact_type: url value: https://www.wikidata.org/wiki/Wikidata:Contact id: wikimedia label: Wikimedia Foundation creation_date: '2025-10-31T00:00:00Z' description: Wikidata is a free and open knowledge base that can be read and edited by both humans and machines. Acting as central storage for the structured data of Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others, it contains over 119 million data items that anyone can edit. Wikidata provides structured, machine-readable data under a free license (CC0), supports multilingual content, and can be interlinked with other open data sets on the linked data web. The content is available through standard formats, SPARQL queries, and APIs. domains: - general evaluation_page: resource/wikidata/wikidata_eval_automated.html homepage_url: https://www.wikidata.org/ id: wikidata infores_id: wikidata last_modified_date: '2026-02-04T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 Public Domain Dedication logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Wikidata products: - category: GraphicalInterface description: Main web interface for browsing, searching, and editing Wikidata items, properties, and statements with over 119 million data items format: http id: wikidata.portal name: Wikidata Web Portal product_url: https://www.wikidata.org/ - category: ProgrammingInterface description: SPARQL endpoint for querying Wikidata using semantic web query language, enabling complex queries across the knowledge graph format: http id: wikidata.sparql name: Wikidata SPARQL Query Service product_url: https://query.wikidata.org/sparql - category: GraphicalInterface description: Interactive web-based SPARQL query editor with example queries, visualization tools, and query assistance for exploring Wikidata format: http id: wikidata.query.editor name: Wikidata Query Service Interface product_url: https://query.wikidata.org/ - category: Product compression: gzip description: JSON dumps containing all Wikidata entities format: json id: wikidata.dumps.json name: Wikidata JSON Entity Dumps product_file_size: 151566969874 product_url: https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.json.gz - category: Product compression: gzip description: Canonical full-statement RDF dump in Turtle format (the "all" dump) format: ttl id: wikidata.dumps.rdf.full.ttl name: Wikidata RDF Full Dump (Turtle) product_file_size: 149370935070 product_url: https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.ttl.gz - category: Product compression: gzip description: Canonical full-statement RDF dump in N-Triples format (the "all" dump) format: ntriples id: wikidata.dumps.rdf.full.nt name: Wikidata RDF Full Dump (N-Triples) product_file_size: 246159505683 product_url: https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.nt.gz - category: Product compression: gzip description: RDF "truthy" dump in N-Triples format containing direct values from best-rank statements only format: ntriples id: wikidata.dumps.rdf.truthy.nt name: Wikidata RDF Truthy Dump (N-Triples) product_file_size: 69713859532 product_url: https://dumps.wikimedia.org/wikidatawiki/entities/latest-truthy.nt.gz - category: Product compression: gzip description: Lexeme namespace JSON dump format: json id: wikidata.dumps.lexemes.json name: Wikidata Lexeme JSON Dump product_file_size: 575745192 product_url: https://dumps.wikimedia.org/wikidatawiki/entities/latest-lexemes.json.gz - category: Product compression: gzip description: Lexeme namespace RDF dump in Turtle format format: ttl id: wikidata.dumps.lexemes.ttl name: Wikidata Lexeme RDF Dump (Turtle) product_file_size: 762464579 product_url: https://dumps.wikimedia.org/wikidatawiki/entities/latest-lexemes.ttl.gz - category: Product compression: gzip description: Lexeme namespace RDF dump in N-Triples format format: ntriples id: wikidata.dumps.lexemes.nt name: Wikidata Lexeme RDF Dump (N-Triples) product_file_size: 1401838999 product_url: https://dumps.wikimedia.org/wikidatawiki/entities/latest-lexemes.nt.gz - category: Product description: Full XML database dumps of Wikidata format: xml id: wikidata.dumps.xml name: Wikidata XML Dumps product_url: https://dumps.wikimedia.org/wikidatawiki/ - category: Product description: Incremental add/change dumps that cover the previous 24 hours id: wikidata.dumps.incremental name: Wikidata Incremental Dumps product_url: https://dumps.wikimedia.org/other/incr/wikidatawiki/ - category: ProgrammingInterface description: RESTful API providing programmatic access to Wikidata content, allowing reading and editing of items, properties, and statements format: http id: wikidata.api name: Wikidata Action API product_url: https://www.wikidata.org/w/api.php - category: ProgrammingInterface description: REST API for accessing entity data in JSON format with content negotiation support format: http id: wikidata.entity.api name: Wikidata Entity Data API product_url: https://www.wikidata.org/wiki/Special:EntityData - category: ProgrammingInterface description: SPARQL endpoint for ID Mappings id: identifier-mappings.sparql name: ID Mappings SPARQL original_source: - identifier-mappings - wikidata product_url: https://frink.apps.renci.org/identifier-mappings/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for ID Mappings id: identifier-mappings.tpf name: ID Mappings TPF original_source: - identifier-mappings - wikidata product_url: https://frink.apps.renci.org/ldf/identifier-mappings - category: Product description: Databus collection for the latest core DBpedia release used by the main SPARQL endpoint and linked data interface. format: http id: dbpedia.latest-core name: DBpedia Latest Core Collection original_source: - dbpedia - wikipedia - wikidata product_file_size: 18605 product_url: https://databus.dbpedia.org/dbpedia/collections/latest-core secondary_source: - dbpedia - category: GraphProduct description: RDF dump of the Open Research Knowledge Graph distributed in N-Triples format. format: ntriples id: orkg.dump name: ORKG RDF Dump original_source: - orkg - wikidata - geonames - ncit - chebi - ncbitaxon - go - clo - omit - iao - uo - stato - obi product_file_size: 642902930 product_url: https://orkg.org/api/rdf/dump secondary_source: - orkg repository: https://www.mediawiki.org/wiki/Wikibase synonyms: - Wikidata - Wikidata Knowledge Base - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: github value: https://github.com/wikipathways - contact_type: url value: https://www.wikipathways.org/ label: WikiPathways Team - category: Individual contact_details: - contact_type: email value: martina.kutmon@maastrichtuniversity.nl label: Martina Kutmon - category: Individual contact_details: - contact_type: email value: egon.willighagen@maastrichtuniversity.nl label: Egon Willighagen creation_date: '2025-06-05T00:00:00Z' description: WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. The database contains 1,913 human-curated pathways across 27 species with 36,334 gene products and 7,052 metabolites, supporting multiple data formats (GPML, GMT, RDF) and programmatic access via SPARQL endpoints and web APIs. Community-driven curation with version control and CI/CD infrastructure enables rapid pathway annotation and knowledge sharing in an open science framework. domains: - pathways - genomics - biomedical fairsharing_id: FAIRsharing.1x53qk homepage_url: https://www.wikipathways.org/ id: wikipathways infores_id: wikipathways last_modified_date: '2025-12-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/share-your-work/public-domain/cc0/ label: CC0 (Creative Commons Zero) logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: WikiPathways products: - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: Product description: Pathways in Graphical Pathway Markup Language (GPML) format, which is a custom XML format for biological pathways format: xml id: wikipathways.gpml name: WikiPathways GPML product_url: https://data.wikipathways.org/current/gpml/ - category: Product description: Pathways in Gene Matrix Transposed (GMT) format for Gene Set Enrichment Analysis format: tsv id: wikipathways.gmt name: WikiPathways GMT product_url: https://data.wikipathways.org/current/gmt/ - category: Product description: Pathways in RDF (Resource Description Framework) format format: ttl id: wikipathways.rdf name: WikiPathways RDF product_url: http://data.wikipathways.org/current/rdf/ - category: ProgrammingInterface description: SPARQL endpoint for querying WikiPathways content id: wikipathways.sparql name: WikiPathways SPARQL Endpoint product_url: https://sparql.wikipathways.org/ - category: GraphicalInterface description: The main web interface for browsing, viewing, and downloading pathways id: wikipathways.web name: WikiPathways Web Interface product_url: https://www.wikipathways.org/ - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv secondary_source: - rna-kg - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - dbsnp - cosmic - rnacentral - ensembl - circbase - chebi - pr - ncbigene - cl - go - mondo - hp - uberon - vo - pw - reactome - wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv secondary_source: - rna-kg - category: Product description: Pathway information integrated from Reactome, WikiPathways and other pathway databases format: http id: genecards.pathway.data name: GeneCards Pathway Data original_source: - reactome - wikipathways product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 403 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: Product description: WikiPathways data for all targets format: txt id: ttd.wiki-pathways name: Target WikiPathways original_source: - wikipathways product_url: https://idrblab.net/ttd/sites/default/files/ttd_download/P4-06-Target_wikipathway.txt secondary_source: - ttd warnings: - File was not able to be retrieved when checked on 2025-10-29_ Error connecting to URL_ ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')) - category: DatabaseProduct description: Multi-sourced relational database integrating metabolomic pathway information, biochemical reactions, ontologies, and chemical descriptors for genes, proteins, and metabolites with query and enrichment analysis capabilities. id: rampdb.database is_public: true name: RaMP-DB Integrated Database original_source: - kegg - reactome - hmdb - wikipathways - rampdb product_url: https://rampdb.nih.gov/ - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 214269334954 product_url: https://stringdb-downloads.org/download/protein.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, scored links between proteins) format: txt id: string.protein.physical.links name: STRING Protein Physical Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 11867396121 product_url: https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (physical subnetwork, incl. subscores per channel) format: txt id: string.protein.physical.links.detailed name: STRING Protein Physical Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 14859366689 product_url: https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz - category: Product description: wikipathways Nodes TSV format: tsv id: obo-db-ingest.wikipathways.tsv license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 name: wikipathways Nodes TSV original_source: - wikipathways product_file_size: 33562 product_url: https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.tsv secondary_source: - obo-db-ingest publications: - authors: - Agrawal A - et al. doi: doi:10.1093/nar/gkad960 id: https://doi.org/10.1093/nar/gkad960 journal: Nucleic Acids Research preferred: true title: WikiPathways 2024 - next generation pathway database year: '2024' - authors: - Martens M - et al. doi: doi:10.1093/NAR/gkaa1024 id: https://doi.org/10.1093/NAR/gkaa1024 journal: Nucleic Acids Research title: WikiPathways - connecting communities year: '2021' repository: https://github.com/wikipathways/wikipathways-database taxon: - NCBITaxon:9606 - NCBITaxon:10090 - activity_status: active category: DataSource creation_date: '2026-03-11T00:00:00Z' description: Wikipedia is a free, collaboratively edited multilingual encyclopedia published by the Wikimedia movement. Its article content is widely reused as an open reference source and serves as a primary upstream source for derivative resources such as DBpedia. Wikipedia content is accessible through the web portal, public APIs, and Wikimedia dump infrastructure. domains: - general homepage_url: https://www.wikipedia.org/ id: wikipedia last_modified_date: '2026-03-11T00:00:00Z' layout: resource_detail name: Wikipedia products: - category: GraphicalInterface description: Main Wikipedia web portal for browsing and searching article content across language editions. format: http id: wikipedia.portal name: Wikipedia Web Portal original_source: - wikipedia product_url: https://www.wikipedia.org/ - category: ProgrammingInterface description: Public MediaWiki Action API for querying and editing Wikipedia content. The exact modules vary by wiki; this entry uses the English Wikipedia endpoint as a canonical example. format: http id: wikipedia.api is_public: true name: Wikipedia MediaWiki Action API original_source: - wikipedia product_url: https://en.wikipedia.org/w/api.php - category: ProgrammingInterface description: Public Wikimedia REST API for machine-readable Wikipedia content and metadata. This entry uses the English Wikipedia REST base path as a canonical example. format: http id: wikipedia.rest is_public: true name: Wikipedia Wikimedia REST API original_source: - wikipedia product_url: https://en.wikipedia.org/api/rest_v1/ - category: Product description: English Wikipedia current-content XML export directory from the Wikimedia dump service. This dump contains the latest revision of each exported page, split across multiple `.xml.bz2` files. format: xml id: wikipedia.dumps.enwiki.current name: English Wikipedia Current Content XML Dumps original_source: - wikipedia product_url: https://dumps.wikimedia.org/other/mediawiki_content_current/enwiki/2026-03-01/xml/bzip2/ - category: Product description: English Wikipedia full revision-history XML export directory from the Wikimedia dump service. This dump contains complete page revision histories, split across multiple `.xml.bz2` files. format: xml id: wikipedia.dumps.enwiki.history name: English Wikipedia Full Revision History XML Dumps original_source: - wikipedia product_url: https://dumps.wikimedia.org/other/mediawiki_content_history/enwiki/2026-03-01/xml/bzip2/ - category: Product description: Databus collection for the latest core DBpedia release used by the main SPARQL endpoint and linked data interface. format: http id: dbpedia.latest-core name: DBpedia Latest Core Collection original_source: - dbpedia - wikipedia - wikidata product_file_size: 18605 product_url: https://databus.dbpedia.org/dbpedia/collections/latest-core secondary_source: - dbpedia synonyms: - English Wikipedia - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: xzhang33@nd.edu label: Xiangliang Zhang creation_date: '2025-12-08T00:00:00Z' description: Wildlife-KN seeks to create a comprehensive, integrative knowledge network for the management of wildlife in the context of climate change, connecting species data, habitat information, and conservation strategies. domains: - environment - organisms evaluation_page: resource/wildlifekn/wildlifekn_eval_automated.html homepage_url: https://sites.nd.edu/kn-wildlife/ id: wildlifekn last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail name: Wildlife-KN products: - category: ProgrammingInterface description: SPARQL endpoint for Wildlife-KN id: wildlifekn.sparql name: Wildlife-KN SPARQL original_source: - wildlifekn product_url: https://frink.apps.renci.org/wildlifekg/sparql taxon: - NCBITaxon:131567 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.wormbase.org/about/contact label: WormBase creation_date: '2025-10-30T00:00:00Z' description: WormBase is an online biological database providing comprehensive genomic and biological information about C. elegans and related nematodes, including annotated genomes, gene structures, functional annotations, genetic maps, gene expression data, protein interactions, RNAi phenotypes, and curated literature. domains: - genomics - organisms - anatomy and development homepage_url: http://www.wormbase.org/ id: wormbase infores_id: wormbase last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: Creative Commons Attribution 4.0 International logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: WormBase products: - category: GraphicalInterface description: Primary web portal for browsing and searching nematode genomic and biological data format: http id: wormbase.portal name: WormBase Web Portal original_source: - wormbase product_url: http://www.wormbase.org/ - category: GraphicalInterface description: Genome browser for visualizing genes, transcripts, and genomic features in their chromosomal context id: wormbase.gbrowse name: WormBase GBrowse original_source: - wormbase product_url: https://www.wormbase.org/tools/genome/gbrowse/c_elegans/ - category: ProgrammingInterface description: REST API providing programmatic access to WormBase data including genes, proteins, variations, and annotations id: wormbase.api is_public: true name: WormBase REST API original_source: - wormbase product_url: https://www.wormbase.org/about/userguide/for_developers/API-REST - category: GraphicalInterface description: WormMine InterMine instance for complex queries and bulk data retrieval across WormBase datasets id: wormbase.wormmine name: WormMine original_source: - wormbase product_url: https://im-dev.wormbase.org/tools/wormmine/begin.do - category: GraphicalInterface description: Full-text search tool for querying C. elegans and nematode literature with ontology term support id: wormbase.textpresso name: Textpresso original_source: - wormbase product_url: https://www.textpresso.org/cgi-bin/wb/tfw.cgi - category: Product description: FTP server providing bulk downloads of genome assemblies, annotations, gene models, and other WormBase data files id: wormbase.ftp name: WormBase FTP Downloads original_source: - wormbase product_url: ftp://ftp.wormbase.org/pub/wormbase/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ FTP error_ [Errno 101] Network is unreachable - File was not able to be retrieved when checked on 2026-02-26_ FTP error_ [Errno 101] Network is unreachable - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.wormbase.org/pub/wormbase/' - 'File was not able to be retrieved when checked on 2026-03-11: FTP error: [Errno 101] Network is unreachable' - category: GraphicalInterface description: Sub-portal hosting approximately 100 parasitic helminth genomes with annotations and comparative genomics tools id: wormbase.parasite name: WormBase ParaSite original_source: - wormbase product_url: https://parasite.wormbase.org/ - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 203534412387 product_url: https://stringdb-downloads.org/download/protein.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'protein network data (full network, incl. distinction: direct vs. interologs)' format: txt id: string.protein.links.full name: STRING Protein Links Full original_source: - 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category: OntologyProduct description: Zebrafish Phenotype Ontology in OWL format format: owl id: zp.owl name: zp.owl product_file_size: 170306263 product_url: http://purl.obolibrary.org/obo/zp.owl - category: OntologyProduct description: Zebrafish Phenotype Ontology in OBO format format: obo id: zp.obo name: zp.obo product_file_size: 15870641 product_url: http://purl.obolibrary.org/obo/zp.obo repository: https://github.com/obophenotype/zebrafish-phenotype-ontology - activity_status: active category: DataSource creation_date: '2025-10-29T00:00:00Z' curators: - category: Individual contact_details: - contact_type: url value: https://bitbucket.org/zashaw/ label: Zasha Weinberg description: The Zasha Weinberg Data repository is a collection of RNA sequence and structure data, including information about regulatory RNA elements, riboswitches, and non-coding RNAs. This data source contributes to the RNAcentral aggregator and focuses on structured RNA data from computational and comparative genomics analyses. domains: - genomics - biological systems homepage_url: https://bitbucket.org/zashaw/zashaweinbergdata/src/master/ id: zwd last_modified_date: '2025-10-29T00:00:00Z' layout: resource_detail name: Zasha Weinberg Data products: - category: Product description: Multiple sequence alignments for RNA and ssDNA sequences format: http id: zwd.alignments name: Zasha Weinberg Data Repository Sequence Alignments product_url: https://bitbucket.org/zashaw/zashaweinbergdata/src/master/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: david.c.blackburn@gmail.com label: David Blackburn orcid: 0000-0002-1810-9886 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://github.com/seger/aao id: aao last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Amphibian gross anatomy products: [] taxon: - NCBITaxon:8292 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: adw_geeks@umich.edu label: Animal Diversity Web technical staff creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - biological systems homepage_url: http://www.animaldiversity.org id: adw last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Animal natural history and life history products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: J.Bard@ed.ac.uk label: Jonathan Bard creation_date: '2025-09-29T00:00:00Z' description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology domains: - anatomy and development homepage_url: https://github.com/obophenotype/human-developmental-anatomy-ontology/ id: aeo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Anatomical Entity Ontology products: - category: OntologyProduct description: Anatomical Entity Ontology in OWL format format: owl id: aeo.owl name: aeo.owl product_file_size: 25664 product_url: http://purl.obolibrary.org/obo/aeo.owl repository: https://github.com/obophenotype/human-developmental-anatomy-ontology - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mcourtot@gmail.com label: Melanie Courtot orcid: 0000-0002-9551-6370 creation_date: '2025-09-29T00:00:00Z' description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events domains: - biomedical homepage_url: http://purl.obolibrary.org/obo/aero id: aero last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Adverse Event Reporting Ontology products: - category: OntologyProduct description: Adverse Event Reporting Ontology in OWL format format: owl id: aero.owl name: aero.owl product_file_size: 19393 product_url: http://purl.obolibrary.org/obo/aero.owl - activity_status: orphaned category: DataSource creation_date: '2025-10-30T00:00:00Z' description: The Amyloidoses Collection (AmyCo) database contains manually curated data from biomedical literature on amyloidoses and other diseases related to amyloid deposition. It classifies 75 diseases and provides disease-gene associations. The resource is no longer independently accessible but is integrated into the DISEASES database. domains: - biomedical - clinical - health homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/AmyCo id: amyco infores_id: amyco last_modified_date: '2025-11-25T00:00:00Z' layout: resource_detail name: The Amyloidoses Collection (AmyCo) Database products: - category: Product description: Manually curated disease-gene associations and annotations for amyloidoses and amyloid deposition-related diseases extracted from biomedical literature. id: amyco.annotations name: AmyCo Curated Annotations original_source: - pubmed - amyco secondary_source: - diseases publications: - authors: - Nastou KC - Nasi GI - Tsiolaki PL - Litou ZI - Iconomidou VA doi: 10.1080/13506129.2019.1603143 id: doi:10.1080/13506129.2019.1603143 journal: Amyloid title: 'AmyCo: the amyloidoses collection' year: '2019' synonyms: - AmyCo taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology contacts: - category: Individual label: Trey Ideker - category: Individual label: Subramaniam Subramani creation_date: '2025-10-30T00:00:00Z' description: ATGO (Autophagy Ontology) is a hierarchical functional ontology of autophagy processes built through Active Interaction Mapping of genetic interaction data from Saccharomyces cerevisiae. The second-generation ontology contains 220 functions representing autophagy organization including vesicle transport, cell cycle, and stress response pathways. domains: - biological systems - systems biology homepage_url: http://atgo.ucsd.edu/ id: atgo infores_id: atgo last_modified_date: '2025-11-22T00:00:00Z' layout: resource_detail name: Autophagy Ontology products: - category: OntologyProduct description: Second-generation hierarchical ontology of 220 autophagy functions built from 156,364 synthetic-lethal genetic interactions across autophagy-activating conditions in Saccharomyces cerevisiae. id: atgo.ontology name: ATGO Hierarchical Ontology original_source: - atgo product_url: http://atgo.ucsd.edu/ warnings: - File was not able to be retrieved when checked on 2026-01-06_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError("HTTPConnection(host='atgo.ucsd.edu', port=80)_ Failed to establish a new connection_ [Errno 111] Connection refused")) - File was not able to be retrieved when checked on 2026-01-06_ Timeout connecting to URL - File was not able to be retrieved when checked on 2025-12-13_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-07_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-05_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-11-25_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-11-25_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) - File was not able to be retrieved when checked on 2025-11-22_ Error connecting to URL_ HTTPConnectionPool(host='atgo.ucsd.edu', port=80)_ Max retries exceeded with url_ / (Caused by NewConnectionError('_ Failed to establish a new connection_ [Errno 111] Connection refused')) publications: - authors: - Michael H Kramer - Jean-Claude Farré - Koyel Mitra - Michael Ku Yu - Keiichiro Ono - Barry Demchak - Katherine Licon - Mikayla Flagg - Rama Balakrishnan - J Michael Cherry - Trey Ideker - Subramaniam Subramani doi: 10.1016/j.molcel.2016.12.024 id: PMID:28132844 journal: Molecular Cell title: Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy year: '2017' synonyms: - ATGO taxon: - NCBITaxon:4932 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: david.c.blackburn@gmail.com label: David Blackburn orcid: 0000-0002-1810-9886 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - biological systems homepage_url: http://www.amphibanat.org id: ato last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Amphibian taxonomy products: [] taxon: - NCBITaxon:8292 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jiezheng@pennmedicine.upenn.edu - contact_type: github value: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 creation_date: '2025-09-29T00:00:00Z' description: An application ontology built for beta cell genomics studies. domains: - anatomy and development homepage_url: https://github.com/obi-bcgo/bcgo id: bcgo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Beta Cell Genomics Ontology products: - category: OntologyProduct description: Beta Cell Genomics Ontology in OWL format format: owl id: bcgo.owl name: bcgo.owl product_file_size: 335620 product_url: http://purl.obolibrary.org/obo/bcgo.owl repository: https://github.com/obi-bcgo/bcgo - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: henrich@embl.de - contact_type: github value: ThorstenHen label: Thorsten Henrich orcid: 0000-0002-1548-3290 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://4dx.embl.de/4DXpress id: bila last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Bilateria anatomy products: - category: OntologyProduct description: Bilateria anatomy in OWL format format: owl id: bila.owl name: bila.owl product_url: http://purl.obolibrary.org/obo/bila.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' taxon: - NCBITaxon:33213 - activity_status: inactive category: DataSource creation_date: '2025-10-30T00:00:00Z' description: The Biomolecular Interaction Network Database (BIND) was a database designed to store full descriptions of interactions, molecular complexes, and pathways. It is no longer active as a standalone resource but its data has been incorporated into other databases like BOND and iRefIndex. domains: - biomedical - pathways homepage_url: http://bind.ca id: bind last_modified_date: '2025-11-25T00:00:00Z' layout: resource_detail name: Biomolecular Interaction Network Database (BIND) products: - category: Product description: Historical dataset of biomolecular interactions, complexes, and pathways. id: bind.data name: BIND Data original_source: - bind - category: Product description: Historical consolidated protein interaction index in PSI-MITAB 2.5 format aggregating data from BIND, BioGrid, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID format: psi_mi_mitab id: irefindex.database name: iRefIndex Database original_source: - bind - biogrid - dip - hprd - intact - mint publications: - authors: - Bader GD - Betel D - Hogue CW doi: 10.1093/nar/gkg056 id: doi:10.1093/nar/gkg056 journal: Nucleic Acids Res title: 'BIND: the Biomolecular Interaction Network Database' year: '2003' synonyms: - BIND - activity_status: inactive category: Aggregator contacts: - category: Individual contact_details: - contact_type: url value: https://www.maastrichtuniversity.nl/ label: Michel Dumontier - category: Organization contact_details: - contact_type: url value: https://www.maastrichtuniversity.nl/research/institutes/institute-data-science id: maastricht-ids label: Maastricht University Institute of Data Science creation_date: '2025-12-18T00:00:00Z' description: Bio2RDF (Linked Biomedical RDF Network) is a large-scale open-source semantic web integration project that converts over 35 diverse biological and biomedical databases into standardized RDF (Resource Description Framework) linked data, providing 11 billion RDF triples accessible through SPARQL endpoints and REST APIs. It enables federated queries across heterogeneous data sources using W3C standards and the Semanticscience Integrated Ontology (SIO). domains: - biomedical - genomics homepage_url: https://bio2rdf.org id: bio2rdf infores_id: bio2rdf last_modified_date: '2025-12-20T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Bio2RDF (Linked Biomedical RDF Network) products: - category: ProgrammingInterface description: SPARQL 1.1 endpoint powered by OpenLink Virtuoso for querying Bio2RDF linked data across 35+ integrated biomedical databases with federated query support format: http id: bio2rdf.sparql is_public: true name: Bio2RDF SPARQL Endpoint product_url: https://bio2rdf.org/sparql - category: ProgrammingInterface description: REST API for programmatic access to Bio2RDF linked data with support for SPARQL queries and multiple result formats format: http id: bio2rdf.api is_public: true name: Bio2RDF REST API product_url: https://github.com/bio2rdf/bio2rdf-api - category: Product description: Downloadable RDF triple stores and datasets in multiple serialization formats (Turtle, N-Triples, RDF/XML, N3) from 35+ integrated biological databases id: bio2rdf.dumps name: Bio2RDF RDF Dumps and Downloads product_url: https://download.bio2rdf.org/ - category: GraphicalInterface description: Web-based interface for browsing and exploring Bio2RDF resources and linked data across biological databases format: http id: bio2rdf.web is_public: true name: Bio2RDF Web Interface product_url: https://bio2rdf.org - category: Product description: BioSearch semantic search engine for Bio2RDF providing full-text and semantic search across integrated biological databases id: bio2rdf.biosearch name: BioSearch Semantic Search Engine product_url: https://biosemantics.org/biosearch warnings: - File was not able to be retrieved when checked on 2026-03-08_ Timeout connecting to URL - File was not able to be retrieved when checked on 2026-02-26_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: Timeout connecting to URL' publications: - authors: - Belleau F - Dumontier M doi: 10.1186/2041-1480-2-S1-S1 id: doi:10.1186/2041-1480-2-S1-S1 journal: Journal of Biomedical Semantics preferred: true title: 'Bio2RDF: towards a mashup to build bioinformatics knowledge systems' year: '2011' - authors: - Callahan A - Cruz-Toledo J - Ansell P - Dumontier M doi: 10.1186/2041-1480-4-S1-S1 id: doi:10.1186/2041-1480-4-S1-S1 journal: Journal of Biomedical Semantics title: 'Bio2RDF Release 2: Improved Coverage, Interoperability and Provenance of Life Science Linked Data' year: '2013' - authors: - Dumontier M - Callahan A - Cruz-Toledo J - et al. doi: 10.1186/2041-1480-5-14 id: doi:10.1186/2041-1480-5-14 journal: Journal of Biomedical Semantics title: The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery year: '2014' - authors: - Hu W - Qiu H - Huang J - et al. doi: 10.1093/database/bax059 id: doi:10.1093/database/bax059 journal: Database title: 'BioSearch: a semantic search engine for Bio2RDF' year: '2017' - authors: - Balaur I - Dumontier M doi: 10.1186/1471-2105-12-358 id: doi:10.1186/1471-2105-12-358 journal: BMC Bioinformatics title: 'Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data' year: '2011' repository: https://github.com/MaastrichtU-IDS/bio2rdf synonyms: - Bio2RDF - Linked Biomedical RDF Network taxon: - NCBITaxon:1 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: vlee@ebi.ac.uk label: Vivian Lee creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - chemistry and biochemistry homepage_url: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html id: bootstrep last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Gene Regulation Ontology products: [] - activity_status: inactive category: DataSource creation_date: '2025-10-30T00:00:00Z' description: CACAO (Community Assessment of Community Annotation with Ontologies) was a collaborative annotation project where undergraduate students used the Gene Ontology to annotate proteins based on evidence from scientific papers. The project appears to be inactive as the website is no longer accessible. domains: - genomics homepage_url: http://gowiki.tamu.edu/wiki/index.php/Category:CACAO id: cacao infores_id: cacao last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Community Assessment of Community Annotation with Ontologies products: - category: GraphicalInterface description: GO Wiki page for CACAO project information and annotation competition content. format: http id: cacao.gowiki name: CACAO GO Wiki Page original_source: - cacao product_url: http://gowiki.tamu.edu/wiki/index.php/Category:CACAO - category: ProgrammingInterface connection_url: https://gowiki.tamu.edu/wiki/api.php description: MediaWiki API endpoint for accessing CACAO and related GO Wiki content programmatically. format: http id: cacao.api is_public: true name: GO Wiki API original_source: - cacao product_url: https://gowiki.tamu.edu/wiki/api.php synonyms: - CACAO - activity_status: inactive category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: balhoff@renci.org label: Jim Balhoff orcid: 0000-0001-7695-6090 - category: Organization contact_details: - contact_type: url value: https://renci.org/ id: renci label: RENCI (Renaissance Computing Institute) creation_date: '2025-12-18T00:00:00Z' description: CAM-KP (Causal Activity Models Knowledge Provider) is a web service knowledge graph that integrates causal biological and chemical models from Gene Ontology, Reactome, and Comparative Toxicogenomics Database (CTD) into a unified, semantically rich platform. It provides access to structured biomedical knowledge through SPARQL and TRAPI-compliant REST APIs, supporting hypothesis generation, drug discovery, and environmental health research. domains: - health - pathways evaluation_page: resource/cam-kp/cam-kp_eval_automated.html homepage_url: https://automat.renci.org/#/cam-kp id: cam-kp infores_id: cam-kp last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License (Repository); Public Domain (Data) name: CAM-KP (Causal Activity Models Knowledge Provider) products: - category: ProgrammingInterface description: SPARQL endpoint for complex semantic queries on the RDF triplestore containing causal activity models, ontologies, and integrated biomedical knowledge format: http id: cam-kp.sparql is_public: true name: CAM-KP SPARQL Endpoint product_url: https://stars-app.renci.org/cam/sparql - category: ProgrammingInterface description: TRAPI-compliant REST API for programmatic access to causal knowledge graphs supporting Translator ecosystem integration and federated querying format: http id: cam-kp.api is_public: true name: CAM-KP REST API product_url: https://cam-kp-api-dev.renci.org/1.2.0/query - category: GraphicalInterface description: Interactive knowledge provider interface within RENCI's Automat platform for discovering and integrating CAM-KP with other biomedical data sources format: http id: cam-kp.automat is_public: true name: CAM-KP on Automat product_url: https://automat.renci.org/#/cam-kp - category: Product description: Causal Activity Model graphs automatically generated from Reactome pathways using the Pathways2GO tool, translating pathway reactions to causal relationships id: cam-kp.reactome-cams name: Reactome Pathway CAMs original_source: - reactome - category: Product description: Gene Ontology Causal Activity Model (GO-CAM) annotations manually curated by Gene Ontology biocurators linking genes, proteins, and biological processes id: cam-kp.go-cams name: Gene Ontology CAMs original_source: - gene-ontology - category: Product description: Chemical-gene interaction models and toxicological pathways derived from the Comparative Toxicogenomics Database (CTD) covering 17,700+ chemicals and 55,400 genes id: cam-kp.ctd-interactions name: CTD Chemical-Gene Models original_source: - ctd - category: DocumentationProduct description: Comprehensive API documentation, SPARQL endpoint documentation, and developer guides for querying and integrating CAM-KP format: http id: cam-kp.documentation is_public: true name: CAM-KP Documentation product_url: https://github.com/ExposuresProvider/cam-kp-api/wiki publications: - authors: - Balhoff JP - Bizon C - Carlson J - Fecho K - Fink EL - Gorow JS - Graham TGW - Hanna DE - Henricks CJ - Hoyt CT - Imamovic-Tomasovic M - Jacobs JM - Koslovsky MD - Lyzenga Y - Nagel R - Rasmussen JE - Robin A - Sullivan R - Wagner AH - Whetzel PL - Williams JA doi: 10.48550/arXiv.2004.01269 id: arXiv:2004.01269 journal: arXiv preferred: true title: A Biomedical Knowledge Graph System to Propose Mechanistic Hypotheses for Real-World Environmental Health Observations year: '2020' - authors: - Balhoff JP - Bizon C - Carlson J - Fecho K - Fink EL - Gorow JS doi: 10.48550/arXiv.2105.04728 id: arXiv:2105.04728 journal: JMIR Medical Informatics title: A Biomedical Knowledge Graph System to Propose Mechanistic Hypotheses for Real-World Environmental Health Observations year: '2021' - authors: - Davis AP - Wiegers TC - Johnson RJ doi: 10.1093/nar/gky1209 id: doi:10.1093/nar/gky1209 journal: Nucleic Acids Research title: 'The Comparative Toxicogenomics Database: update 2023' year: '2023' - authors: - Davis AP - Wiegers TC - Johnson RJ doi: 10.1093/nar/gkaq891 id: doi:10.1093/nar/gkaq891 journal: Nucleic Acids Research title: 'The Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks' year: '2020' repository: https://github.com/ExposuresProvider/cam-kp-api taxon: - NCBITaxon:1 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: haendel@ohsu.edu - contact_type: github value: mellybelly label: Melissa Haendel orcid: 0000-0001-9114-8737 creation_date: '2025-09-29T00:00:00Z' description: An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species domains: - anatomy and development homepage_url: https://github.com/obophenotype/caro/ id: caro last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Common Anatomy Reference Ontology products: - category: OntologyProduct description: Common Anatomy Reference Ontology in OWL format format: owl id: caro.owl name: caro.owl product_file_size: 586722 product_url: http://purl.obolibrary.org/obo/caro.owl repository: https://github.com/obophenotype/caro - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-09-29T00:00:00Z' description: An anatomical and developmental ontology for cephalopods domains: - anatomy and development homepage_url: https://github.com/obophenotype/cephalopod-ontology id: ceph last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Cephalopod Ontology products: - category: OntologyProduct description: main version format: owl id: ceph.owl name: main version product_file_size: 48794 product_url: http://purl.obolibrary.org/obo/ceph.owl - category: OntologyProduct description: oboformat edition format: obo id: ceph.obo name: oboformat edition product_file_size: 82316 product_url: http://purl.obolibrary.org/obo/ceph.obo repository: https://github.com/obophenotype/cephalopod-ontology taxon: - NCBITaxon:6605 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: engelsta@ohsu.edu label: Mark Engelstad orcid: 0000-0001-5889-4463 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - biomedical homepage_url: https://code.google.com/p/craniomaxillofacial-ontology/ id: cmf last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: CranioMaxilloFacial ontology products: [] - activity_status: inactive category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.broadinstitute.org/connectivity-map-cmap id: broad label: Broad Institute of MIT and Harvard creation_date: '2025-08-12T00:00:00Z' description: The Connectivity Map (CMap) is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of functional connections between drugs, genes, and diseases through common gene-expression changes. The original CMap resource is now integrated into the CLUE platform. domains: - drug discovery - genomics - biomedical homepage_url: https://www.broadinstitute.org/connectivity-map-cmap id: connectivitymap last_modified_date: '2025-10-07T00:00:00Z' layout: resource_detail name: Connectivity Map products: - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg - category: GraphProduct description: Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access. dump_format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access. format: csv id: ubkg.csv name: UBKG Ontology CSV Files original_source: - hgnc - loinc - icd10 - snomedct - uberon - pato - cl - doid - obi - obib - edam - hsapdv - sbo - mi - chebi - mp - ordo - uniprot - uo - mondo - efo - pgo - gencode - reactome - hra - hubmap - sennet - stellar - dct - clinvar - connectivitymap - hp - mp - msigdb - wikipathways - clingen - string - 4dn - erccrbp - erccreg - faldo - glycordf - glycocoo - gtex - kidsfirst - lincs - motrpac - mw - npo - sckan - disgenet - biomarker - opentargets product_url: https://ubkg-downloads.xconsortia.org/ secondary_source: - ubkg publications: - id: https://doi.org/10.1126/science.1132939 title: 'The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease' repository: https://clue.io/about taxon: - NCBITaxon:9606 - activity_status: inactive category: Aggregator creation_date: '2025-11-19T00:00:00Z' description: ConsensusPathDB integrates molecular interaction data from over 30 public databases, including protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions. It provides comprehensive pathway and functional analysis tools, allowing users to explore molecular networks and pathways from multiple sources through a unified interface. The resource was last updated in 2016 and the main website is no longer accessible. domains: - pathways - proteomics - systems biology - biomedical - biological systems - chemistry and biochemistry homepage_url: http://cpdb.molgen.mpg.de/ id: cpdb infores_id: cpdb last_modified_date: '2025-11-19T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: ConsensusPathDB products: - category: GraphicalInterface description: Web-based interface for integrated pathway and interaction analysis from multiple databases (inactive) id: cpdb.web name: ConsensusPathDB Web Interface original_source: - cpdb product_url: http://cpdb.molgen.mpg.de/ - category: Product description: Download files containing integrated interaction and pathway data format: txt id: cpdb.downloads name: ConsensusPathDB Data Downloads original_source: - cpdb product_url: http://cpdb.molgen.mpg.de/CPDB/download warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 503 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-04_ Timeout connecting to URL - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 503 error when accessing file' publications: - authors: - Kamburov A - Pentchev K - Galicka H - Wierling C - Lehrach H - Herwig R doi: 10.1093/nar/gkq1156 id: PMID:21071422 journal: Nucleic Acids Research title: 'ConsensusPathDB: toward a more complete picture of cell biology' year: '2011' - authors: - Kamburov A - Wierling C - Lehrach H - Herwig R doi: 10.1093/nar/gkn698 id: PMID:18940869 journal: Nucleic Acids Research title: ConsensusPathDB--a database for integrating human functional interaction networks year: '2009' synonyms: - CPDB - activity_status: unresponsive category: Aggregator creation_date: '2025-09-09T00:00:00Z' description: The Comparative RNA Database (CRD) was an aggregator of RNA sequence and structure data, but is no longer available. This resource is considered unresponsive; only its metadata and publication are retained for reference. domains: - biological systems - genomics id: crd last_modified_date: '2025-10-10T00:00:00Z' layout: resource_detail name: Comparative RNA Database (CRD) products: - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - James M. Sorace - Kip Canfield id: https://doi.org/10.1089/jir.1998.18.799 journal: Journal of Interferon & Cytokine Research title: 'Collaborative Bioinformatics: Data Warehouses for Targeted Experimental Results' year: '1998' warnings: - This resource is unresponsive. The database is no longer available; only metadata and publication are retained. - activity_status: inactive category: DataSource creation_date: '2025-10-30T00:00:00Z' description: DATE (Drugs to target pAthways by the Tissue Expression) was a computational resource integrating drug targets with pathway information and tissue-specific gene expression to predict drug effects and therapeutic opportunities. The resource appears to be archived. domains: - pharmacology - systems biology homepage_url: https://tatonettilab-resources.s3.amazonaws.com/syspharm/DATE.zip id: date infores_id: date last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Drugs to target pAthways by the Tissue Expression products: - category: Product compression: zip description: Archived DATE ZIP package for tissue-specific drug-target-pathway analyses. dump_format: other format: mixed id: date.archive name: DATE Archive ZIP original_source: - date product_file_size: 7261526 product_url: https://tatonettilab-resources.s3.amazonaws.com/syspharm/DATE.zip synonyms: - DATE - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Lindsay.Cowell@utsouthwestern.edu label: Lindsay Cowell orcid: 0000-0003-1617-8244 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://www.dukeontologygroup.org/Projects.html id: dc_cl last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Dendritic cell products: [] taxon: - all - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: maria.herrero@kcl.ac.uk label: Maria Herrero creation_date: '2025-09-29T00:00:00Z' description: A formal represention for drug-drug interactions knowledge. domains: - biomedical homepage_url: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto id: dinto last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: The Drug-Drug Interactions Ontology products: - category: OntologyProduct description: The Drug-Drug Interactions Ontology in OWL format format: owl id: dinto.owl name: dinto.owl product_url: http://purl.obolibrary.org/obo/dinto.owl repository: https://github.com/labda/DINTO - activity_status: inactive category: Ontology creation_date: '2025-10-30T00:00:00Z' description: The Disease Ontology Annotation Framework (DOAF) was a semantic framework for representing and sharing disease annotations, enabling standardized disease ontology annotations across biomedical resources. domains: - biomedical - clinical homepage_url: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049686 id: doaf infores_id: doaf last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Disease Ontology Annotation Framework products: - category: DocumentationProduct description: PLOS ONE article describing the Disease Ontology Annotation Framework and its use for disease annotation. format: http id: doaf.framework-publication name: DOAF Framework Publication original_source: - doaf product_url: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049686 publications: - id: https://doi.org/10.1371/journal.pone.0049686 title: 'The Disease Ontology: Structuring the Landscape of Human Disease' year: '2012' synonyms: - DOAF - Disease Ontology Annotation Framework taxon: - NCBITaxon:9606 - activity_status: inactive category: DataSource contacts: - category: Organization contact_details: - contact_type: github value: griffithlab label: Griffith Lab creation_date: '2025-10-30T00:00:00Z' description: DoCM (Database of Curated Mutations) was a highly curated database of known, disease-causing mutations in cancer, specifically focused on mutations with clinical or functional evidence. The project has been retired and succeeded by the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. All DoCM data remains available in archived form. domains: - precision medicine - genomics - health homepage_url: http://www.docm.info/ id: docm infores_id: docm last_modified_date: '2025-01-20T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT name: Database of Curated Mutations products: - category: Product compression: gzip description: Curated cancer mutations in tab-separated values format with gene, transcript, variant, and disease information format: tsv id: docm.variants.tsv name: DoCM Variants TSV original_source: - docm product_file_size: 35859 product_url: https://github.com/griffithlab/docm/raw/master/data/variants.tsv.gz - category: Product compression: gzip description: Curated cancer mutations in Variant Call Format (VCF) format: vcf id: docm.variants.vcf name: DoCM Variants VCF original_source: - docm product_file_size: 43955 product_url: https://github.com/griffithlab/docm/raw/master/data/variants.vcf.gz - category: ProcessProduct compression: gzip description: Complete DoCM database in SQL format for local installation id: docm.data.sql name: DoCM SQL Database original_source: - docm product_file_size: 1174722 product_url: https://github.com/griffithlab/docm/raw/master/data/data.sql.gz repository: https://github.com/griffithlab/docm synonyms: - DoCM taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: J.Bard@ed.ac.uk label: Jonathan Bard creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://genex.hgu.mrc.ac.uk/ id: ehda last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Human developmental anatomy, timed version products: [] taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: J.Bard@ed.ac.uk label: Jonathan Bard creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development id: ehdaa last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Human developmental anatomy, abstract version products: [] taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: J.Bard@ed.ac.uk label: Jonathan Bard creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. domains: - anatomy and development homepage_url: https://github.com/obophenotype/human-developmental-anatomy-ontology id: ehdaa2 last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Human developmental anatomy, abstract products: - category: OntologyProduct description: Human developmental anatomy, abstract in OWL format format: owl id: ehdaa2.owl name: ehdaa2.owl product_file_size: 125946 product_url: http://purl.obolibrary.org/obo/ehdaa2.owl - category: OntologyProduct description: Human developmental anatomy, abstract in OBO format format: obo id: ehdaa2.obo name: ehdaa2.obo product_file_size: 83809 product_url: http://purl.obolibrary.org/obo/ehdaa2.obo repository: https://github.com/obophenotype/human-developmental-anatomy-ontology taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Terry.Hayamizu@jax.org - contact_type: github value: tfhayamizu label: Terry Hayamizu orcid: 0000-0002-0956-8634 creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). domains: - anatomy and development homepage_url: http://emouseatlas.org id: emap last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Mouse gross anatomy and development, timed products: - category: OntologyProduct description: Mouse gross anatomy and development, timed in OWL format format: owl id: emap.owl name: emap.owl product_file_size: 611769 product_url: http://purl.obolibrary.org/obo/emap.owl taxon: - NCBITaxon:10088 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jaiswalp@science.oregonstate.edu - contact_type: github value: jaiswalp label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 creation_date: '2025-09-29T00:00:00Z' description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. domains: - environment homepage_url: http://planteome.org/ id: eo last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Plant Environment Ontology products: - category: OntologyProduct description: Plant Environment Ontology in OWL format format: owl id: eo.owl name: eo.owl product_url: http://purl.obolibrary.org/obo/eo.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: OntologyProduct description: Plant Environment Ontology in OBO format format: obo id: eo.obo name: eo.obo product_url: http://purl.obolibrary.org/obo/eo.obo warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' repository: https://github.com/Planteome/plant-environment-ontology - activity_status: inactive category: Ontology collection: - obo-foundry contacts: [] creation_date: '2025-09-29T00:00:00Z' description: An ontology designed to support the semantic annotation of epidemiology resources domains: - biomedical homepage_url: https://code.google.com/p/epidemiology-ontology/ id: epo last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Epidemiology Ontology products: - category: OntologyProduct description: Epidemiology Ontology in OWL format format: owl id: epo.owl name: epo.owl product_url: http://purl.obolibrary.org/obo/epo.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Marc_Ciriello@hms.harvard.edu label: Marc Ciriello creation_date: '2025-09-29T00:00:00Z' description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. domains: - biomedical homepage_url: https://open.med.harvard.edu/wiki/display/eaglei/Ontology id: ero last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/2.0/ label: CC BY 2.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: eagle-i resource ontology products: - category: OntologyProduct description: eagle-i resource ontology in OWL format format: owl id: ero.owl name: ero.owl product_url: http://purl.obolibrary.org/obo/ero.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPSConnectionPool(host=''www.eagle-i.net'', port=443): Max retries exceeded with url: /ero/latest/ero.owl (Caused by SSLError(SSLCertVerificationError(1, ''[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1000)'')))' - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jiezhen@med.umich.edu - contact_type: github value: zhengj2007 label: Jie Zheng orcid: 0000-0002-2999-0103 creation_date: '2025-09-29T00:00:00Z' description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). domains: - biological systems homepage_url: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology id: eupath last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: VEuPathDB ontology products: - category: OntologyProduct description: VEuPathDB ontology in OWL format format: owl id: eupath.owl name: eupath.owl product_file_size: 438457 product_url: http://purl.obolibrary.org/obo/eupath.owl repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: evoc@sanbi.ac.za label: eVOC mailing list creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development id: ev last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: eVOC (Expressed Sequence Annotation for Humans) products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: wawong@gmail.com - contact_type: github value: wawong label: Willy Wong orcid: 0000-0002-8841-5870 creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. domains: - biomedical homepage_url: http://cellimagelibrary.org/ id: fbbi last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Biological Imaging Methods Ontology products: - category: OntologyProduct description: Biological Imaging Methods Ontology in OWL format format: owl id: fbbi.owl name: fbbi.owl product_file_size: 630985 product_url: http://purl.obolibrary.org/obo/fbbi.owl repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cp390@cam.ac.uk - contact_type: github value: Clare72 label: Clare Pilgrim orcid: 0000-0002-1373-1705 creation_date: '2025-09-29T00:00:00Z' description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. domains: - biological systems homepage_url: http://www.flybase.org/ id: fbsp last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Fly taxonomy products: - category: OntologyProduct description: Fly taxonomy in OWL format format: owl id: fbsp.owl name: fbsp.owl product_url: http://purl.obolibrary.org/obo/fbsp.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' taxon: - NCBITaxon:7227 - activity_status: orphaned category: Ontology collection: - obo-foundry contacts: - category: Individual label: chEBI creation_date: '2025-09-29T00:00:00Z' description: An ontology of physico-chemical methods and properties. domains: - chemistry and biochemistry homepage_url: http://www.ebi.ac.uk/chebi id: fix last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Physico-chemical methods and properties products: - category: OntologyProduct description: Physico-chemical methods and properties in OWL format format: owl id: fix.owl name: fix.owl product_url: http://purl.obolibrary.org/obo/fix.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: OntologyProduct description: Physico-chemical methods and properties in OBO format format: obo id: fix.obo name: fix.obo product_url: http://purl.obolibrary.org/obo/fix.obo warnings: - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: No connection adapters were found for ''ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo''' - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: burkesquires@gmail.com label: Burke Squires creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - biomedical homepage_url: http://purl.obolibrary.org/obo/flu/ id: flu last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Influenza Ontology products: - category: OntologyProduct description: Influenza Ontology in OWL format format: owl id: flu.owl name: flu.owl product_file_size: 127517 product_url: http://purl.obolibrary.org/obo/flu.owl - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mejino@u.washington.edu label: Onard Mejino creation_date: '2025-06-25T00:00:00Z' description: This is currently a slimmed down version of FMA domains: - anatomy and development homepage_url: http://si.washington.edu/projects/fma id: fma last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Foundational Model of Anatomy Ontology (subset) products: - category: OntologyProduct description: Foundational Model of Anatomy Ontology (subset) in OWL format format: owl id: fma.owl name: fma.owl product_url: http://purl.obolibrary.org/obo/fma.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo repository: https://bitbucket.org/uwsig/fma taxon: - NCBITaxon:9606 - activity_status: inactive category: DataSource creation_date: '2025-10-30T00:00:00Z' description: GeneProf was a database resource for gene expression profiles and functional genomics data. The underlying resource is currently inaccessible (404 error), indicating the resource is likely inactive or deprecated. domains: - genomics homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/GeneProf id: geneprof infores_id: geneprof last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: GeneProf products: - category: GraphicalInterface description: Translator wiki page documenting the GeneProf resource and historical access details. format: http id: geneprof.translator-wiki name: GeneProf Translator Wiki Page original_source: - geneprof product_url: https://github.com/NCATSTranslator/Translator-All/wiki/GeneProf - activity_status: inactive category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.nlm.nih.gov/ id: ncbi label: US National Library of Medicine creation_date: '2025-10-30T00:00:00Z' description: Consumer health resource about genetic conditions from the US National Library of Medicine. This resource has been merged into MedlinePlus Genetics as of 2020. domains: - health - genomics homepage_url: https://medlineplus.gov/genetics/ id: ghr infores_id: ghr last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: Genetics Home Reference products: - category: GraphicalInterface description: MedlinePlus Genetics portal containing migrated Genetics Home Reference content. format: http id: ghr.portal name: MedlinePlus Genetics Portal original_source: - ghr product_url: https://medlineplus.gov/genetics/ - category: GraphicalInterface description: Browse page for genetic conditions from the MedlinePlus Genetics migration. format: http id: ghr.conditions name: MedlinePlus Genetics Conditions original_source: - ghr product_url: https://medlineplus.gov/genetics/condition/ - category: GraphicalInterface description: Browse page for gene summaries from the MedlinePlus Genetics migration. format: http id: ghr.gene-catalog name: MedlinePlus Genetics Gene Catalog original_source: - ghr product_url: https://medlineplus.gov/genetics/gene/ synonyms: - GHR - category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.ebi.ac.uk/GOA/contactus id: ebi label: GOA Team at EMBL-EBI creation_date: '2025-10-29T00:00:00Z' description: 'The Gene Ontology Annotation (GOA) Database provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNAcentral, and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotations supplied by members of the Gene Ontology Consortium and computationally assigned GO terms describing gene products. All annotations are clearly indicated by associated evidence codes with links to source data. Files are released approximately every four weeks in coordination with UniProtKB releases. ' domains: - genomics - biological systems - proteomics homepage_url: https://www.ebi.ac.uk/GOA/index id: goa last_modified_date: '2025-10-29T00:00:00Z' layout: resource_detail license: id: https://www.ebi.ac.uk/about/terms-of-use label: EMBL-EBI Terms of Use name: GOA products: - category: GraphicalInterface description: Web portal for accessing GOA information, statistics, and navigation to downloads format: http id: goa.portal name: GOA Website product_url: https://www.ebi.ac.uk/GOA/index - category: GraphicalInterface description: Browser for searching and viewing Gene Ontology terms and GOA annotations format: http id: goa.quickgo name: QuickGO Browser original_source: - go product_url: https://www.ebi.ac.uk/QuickGO/ - category: Product description: FTP site containing current and archived GOA annotation files for all species format: http id: goa.ftp name: GOA FTP Site original_source: - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/' - category: Product description: GO annotations for all UniProtKB entries format: txt id: goa.uniprot name: UniProt GOA Annotations original_source: - uniprot - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/' - category: Product description: GO annotations for human proteins format: txt id: goa.human name: Human GOA Annotations original_source: - uniprot - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/' - category: Product description: GO annotations for mouse proteins format: txt id: goa.mouse name: Mouse GOA Annotations original_source: - uniprot - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/' - File was not able to be retrieved when checked on 2025-12-04_ FTP error_ [Errno 104] Connection reset by peer - category: MappingProduct description: Files containing transitive assignments of InterPro matches, UniProtKB keywords, subcellular locations, EC numbers, or HAMAP matches to manually-selected GO terms format: txt id: goa.mapping-files name: GO Mapping Files original_source: - interpro - uniprot - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/' - category: Product description: GO annotations for PDB entries format: txt id: goa.pdb name: PDB GOA Annotations original_source: - pdbe - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/' - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/' - category: Product description: GO annotations organized by proteomes format: txt id: goa.proteomes name: Proteomes GOA Annotations original_source: - go product_url: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ warnings: - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ No connection adapters were found for 'ftp_//ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/' - File was not able to be retrieved when checked on 2025-12-04_ FTP error_ [Errno 104] Connection reset by peer - category: DocumentationProduct description: Documentation including FAQ, About pages, and contact information format: http id: goa.documentation name: GOA Documentation product_url: https://www.ebi.ac.uk/GOA/newto - category: GraphProduct description: HumanGOA Automat format: kgx-jsonl id: automat.humangoa infores_id: automat-human-goa name: humangoa_automat original_source: - goa product_url: https://stars.renci.org/var/plater/bl-4.2.1/HumanGOA_Automat/06f107a4e9e8e547/ secondary_source: - automat - category: GraphProduct description: KGX graph package for Gene Ontology Annotations (build goa_2025-10-10_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.goa.graph name: Translator GOA KGX Graph original_source: - goa product_url: https://stars.renci.org/var/translator/releases/goa/2025_12_15/ secondary_source: - translator - category: GraphProduct description: ProteomeHD data files id: proteomehd.data name: ProteomeHD Data original_source: - proteomehd - uniprot - reactome - intact - go - goa product_url: https://github.com/Rappsilber-Laboratory/ProteomeHD/tree/master/Data - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: po-discuss@plantontology.org label: Plant Ontology Administrators creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://www.gramene.org/plant_ontology/ id: gro last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Cereal Plant Gross Anatomy products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: peteremidford@yahoo.com label: Peter Midford orcid: 0000-0001-6512-3296 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - biological systems homepage_url: http://www.mesquiteproject.org/ontology/Habronattus/index.html id: habronattus last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Habronattus courtship products: [] - activity_status: inactive category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: info@ncbi.nlm.nih.gov id: ncbi label: NCBI Help Desk creation_date: '2025-11-04T00:00:00Z' description: HomoloGene was NCBI's database of homologs (genes with common ancestry) from completely sequenced eukaryotic genomes. The database organized genes into homology groups representing putative orthologs and paralogs across multiple species. HomoloGene was retired in January 2024 and replaced by the NCBI Orthologs dataset, which is now accessible through NCBI Datasets and the Gene database. The last HomoloGene build (build 68) was produced in 2014 and is no longer aligned with current data in NCBI RefSeq and Gene. Historical data from build 68 remains available on FTP for archival purposes only. domains: - biological systems - genomics homepage_url: https://www.ncbi.nlm.nih.gov/homologene id: homologene infores_id: homologene last_modified_date: '2025-11-04T00:00:00Z' layout: resource_detail name: HomoloGene products: - category: Product description: Tab-delimited file containing HomoloGene group IDs, taxonomy IDs, gene IDs, gene symbols, and protein accessions for the final build 68 (2014) format: tsv id: homologene.data name: HomoloGene Data File (Build 68 - Archive) original_source: - homologene product_file_size: 13803677 product_url: https://ftp.ncbi.nih.gov/pub/HomoloGene/build68/homologene.data - category: Product compression: gzip description: XML dump of the HomoloGene build 68 containing detailed homology group information, gene and protein links, and distance analysis results format: xml id: homologene.xml name: HomoloGene XML Data (Build 68 - Archive) original_source: - homologene product_file_size: 175849799 product_url: https://ftp.ncbi.nih.gov/pub/HomoloGene/build68/homologene.xml.gz - category: DocumentationProduct description: Complete FTP archive of all HomoloGene builds from build 35 (2004) through build 68 (2014), retained for historical purposes format: http id: homologene.ftp_archive name: HomoloGene FTP Archive original_source: - homologene product_url: https://ftp.ncbi.nih.gov/pub/HomoloGene/ taxon: - NCBITaxon:2759 warnings: - HomoloGene was officially retired in January 2024 - The last build (build 68) is from 2014 and is not aligned with current NCBI RefSeq and Gene data - activity_status: inactive category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://www.ibioinformatics.org/ label: Institute of Bioinformatics - category: Organization contact_details: - contact_type: url value: https://www.hopkinsmedicine.org/profiles/details/akhilesh-pandey label: Johns Hopkins University Pandey Lab - category: Individual label: Akhilesh Pandey orcid: 0000-0002-7944-3070 creation_date: '2025-10-30T00:00:00Z' description: The Human Protein Reference Database (HPRD) was a comprehensive, manually curated collection of information on human proteins, including protein-protein interactions, post-translational modifications (PTMs), enzyme-substrate relationships, subcellular localization, tissue expression, and disease associations. Developed through collaboration between the Institute of Bioinformatics in Bangalore, India and Johns Hopkins University in Baltimore, USA, HPRD contained over 20,000 protein entries with more than 36,500 unique protein-protein interactions and 18,000 PTMs before being discontinued. The database served as a major resource for the human proteome from 2003 to approximately 2010. domains: - biomedical - proteomics - biological systems - systems biology homepage_url: http://www.hprd.org/ id: hprd last_modified_date: '2025-10-31T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: HPRD products: - category: Product description: HPRD protein-protein interaction data in PSI-MITAB format, now archived and available through iRefIndex format: psi_mi_mitab id: hprd.ppi.data name: HPRD Protein-Protein Interactions original_source: - hprd product_url: http://www.hprd.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 503 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 503 error when accessing file - Original HPRD website is no longer accessible. Data has been archived in iRefIndex and other interaction databases. - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 503 error when accessing file' - category: DocumentationProduct description: HPRD data in XML format for programmatic access id: hprd.xml.download name: HPRD XML Data Download original_source: - hprd product_url: http://www.hprd.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 503 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 503 error when accessing file - Original HPRD website is no longer accessible. Data may be available through archive.org or integrated databases. - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 503 error when accessing file' - category: DocumentationProduct description: HPRD data in tab-delimited format for programmatic access id: hprd.tsv.download name: HPRD Tab-Delimited Data Download original_source: - hprd product_url: http://www.hprd.org/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 503 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 503 error when accessing file - Original HPRD website is no longer accessible. Data may be available through archive.org or integrated databases. - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 503 error when accessing file' - category: GraphicalInterface description: PhosphoMotif Finder tool for identifying kinase/phosphatase substrate and binding motifs format: http id: hprd.phosphomotif.finder name: HPRD PhosphoMotif Finder original_source: - hprd product_url: http://www.hprd.org/ warnings: - Original HPRD website is no longer accessible. - category: GraphicalInterface description: GenProt Viewer for integrated genomic, transcriptomic and proteomic view of the human genome format: http id: hprd.genprot.viewer name: GenProt Viewer original_source: - hprd product_url: http://www.genprot.org/ warnings: - GenProt website is no longer accessible. - category: Product description: Historical consolidated protein interaction index in PSI-MITAB 2.5 format aggregating data from BIND, BioGrid, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID format: psi_mi_mitab id: irefindex.database name: iRefIndex Database original_source: - bind - biogrid - dip - hprd - intact - mint - category: GraphProduct compression: gzip description: protein network data (full network, scored links between proteins) format: txt id: string.protein.links name: STRING Protein Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 138154280240 product_url: https://stringdb-downloads.org/download/protein.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: protein network data (full network, incl. subscores per channel) format: txt id: string.protein.links.detailed name: STRING Protein Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - 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category: GraphProduct compression: gzip description: 'protein network data (physical subnetwork, incl. distinction: direct vs. interologs)' format: txt id: string.protein.physical.links.full name: STRING Protein Physical Links Full original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 15528028374 product_url: https://stringdb-downloads.org/download/protein.physical.links.full.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores between orthologous groups format: txt id: string.cog.links name: STRING COG Links original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 185338269 product_url: https://stringdb-downloads.org/download/COG.links.v12.0.txt.gz - category: GraphProduct compression: gzip description: association scores (incl. subscores per channel) format: txt id: string.cog.links.detailed name: STRING COG Links Detailed original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 250279091 product_url: https://stringdb-downloads.org/download/COG.links.detailed.v12.0.txt.gz - category: GraphProduct compression: gzip description: 'full database, part II: the networks (nodes, edges, scores,...)' id: string.database name: STRING Database Network Schema original_source: - biocyc - biogrid - cog - compartments - dip - diseases - eggnog - ensembl - flybase - geo - go - hprd - hgnc - intact - interpro - kegg - mint - omim - pdb - pfam - proteomehd - pubmedcentral - reactome - refseq - sgd - simap - smart - swissmodel - tissues - uniprot - wikipathways - wormbase - progenomes product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz publications: - authors: - Peri S - Navarro JD - Amanchy R - Kristiansen TZ - Jonnalagadda CK - Surendranath V - Niranjan V - Muthusamy B - Gandhi TK - Gronborg M - et al. doi: 10.1101/gr.1680803 id: https://doi.org/10.1101/gr.1680803 journal: Genome Research preferred: true title: Development of human protein reference database as an initial platform for approaching systems biology in humans year: '2003' - authors: - Mishra GR - Suresh M - Kumaran K - Kannabiran N - Suresh S - Bala P - Shivakumar K - Anuradha N - Reddy R - Raghavan TM - Menon S - Hanumanthu G - Gupta M - Upendran S - Gupta S - Mahesh M - Jacob B - Mathew P - Chatterjee P - Arun KS - Sharma S - Chandrika KN - Deshpande N - Palvankar K - Raghavnath R - Krishnakanth R - Karathia H - Rekha B - Nayak R - Vishnupriya G - Kumar HG - Nagini M - Kumar GS - Jose R - Deepthi P - Mohan SS - Gandhi TK - Harsha HC - Deshpande KS - Sarker M - Prasad TS - Pandey A doi: 10.1093/nar/gkj141 id: https://doi.org/10.1093/nar/gkj141 journal: Nucleic Acids Research title: Human protein reference database—2006 update year: '2006' - authors: - Peri S - Navarro JD - Kristiansen TZ - Amanchy R - Surendranath V - Muthusamy B - Gandhi TK - Chandrika KN - Deshpande N - Suresh S - Rashmi BP - Shanker K - Padma N - Niranjan V - Harsha HC - Talreja N - Vrushabendra BM - Ramya MA - Yatish AJ - Joy M - Shivashankar HN - Kavitha MP - Menezes M - Choudhury DR - Ghosh N - Saravana R - Chandran S - Mohan S - Jonnalagadda CK - Prasad CK - Kumar-Sinha C - Deshpande KS - Pandey A doi: 10.1093/nar/gkh070 id: https://doi.org/10.1093/nar/gkh070 journal: Nucleic Acids Research title: Human protein reference database as a discovery resource for proteomics year: '2004' - authors: - Gandhi TKB - Zhong J - Mathivanan S - Karthick L - Chandrika KN - Mohan SS - Sharma S - Pinkert S - Nagaraju S - Periaswamy B - Mishra G - Nandakumar K - Shen B - Deshpande N - Nayak R - Sarker M - Boeke JD - Parmigiani G - Schultz J - Bader JS - Pandey A doi: 10.1038/ng1747 id: https://doi.org/10.1038/ng1747 journal: Nature Genetics title: Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets year: '2006' taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: topalis@imbb.forth.gr label: Pantelis Topalis creation_date: '2025-09-29T00:00:00Z' description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. domains: - biomedical homepage_url: https://www.vectorbase.org/ontology-browser id: idomal last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Malaria Ontology products: - category: OntologyProduct description: Malaria Ontology in OWL format format: owl id: idomal.owl name: idomal.owl product_file_size: 309674 product_url: http://purl.obolibrary.org/obo/idomal.owl - category: OntologyProduct description: Malaria Ontology in OBO format format: obo id: idomal.obo name: idomal.obo product_file_size: 161166 product_url: http://purl.obolibrary.org/obo/idomal.obo repository: https://github.com/VEuPathDB-ontology/IDOMAL - activity_status: inactive category: Ontology collection: - obo-foundry contacts: [] creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - chemistry and biochemistry homepage_url: http://www.inoh.org id: iev last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Event (INOH pathway ontology) products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: curator@inoh.org label: INOH curators creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - chemistry and biochemistry homepage_url: http://www.inoh.org id: imr last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Molecule role (INOH Protein name/family name ontology) products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: interhelp@ebi.ac.uk label: InterPro Help creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - chemistry and biochemistry homepage_url: http://www.ebi.ac.uk/interpro/index.html id: ipr last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Protein Domains products: [] - activity_status: inactive category: DataSource creation_date: '2025-10-30T00:00:00Z' description: iProClass was an integrated protein classification database that provided comprehensive annotations by integrating information from UniProt, PIR, and multiple external databases including protein family, function, pathway, and interaction data. domains: - proteomics homepage_url: http://pir.georgetown.edu/iproclass/ id: iproclass infores_id: iproclass last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail name: iProClass products: - category: GraphicalInterface description: Historical iProClass web interface for integrated protein annotation lookup. format: http id: iproclass.portal name: iProClass Portal original_source: - iproclass product_url: http://pir.georgetown.edu/iproclass/ - category: DocumentationProduct description: Protein Information Resource site with parent documentation and context for iProClass. format: http id: iproclass.pir-docs name: PIR Documentation original_source: - iproclass product_url: https://proteininformationresource.org/ synonyms: - iProClass - Integrated Protein Classification - activity_status: inactive category: Aggregator creation_date: '2025-10-30T00:00:00Z' description: iRefIndex is a consolidated protein interaction database that aggregates and indexes interaction data from multiple primary databases using sequence-based hash keys to identify and group redundant interaction records while maintaining provenance information. domains: - proteomics - biological systems homepage_url: https://irefindex.vib.be/wiki/index.php/iRefIndex id: irefindex infores_id: irefindex last_modified_date: '2025-10-30T00:00:00Z' layout: resource_detail name: iRefIndex products: - category: Product description: Historical consolidated protein interaction index in PSI-MITAB 2.5 format aggregating data from BIND, BioGrid, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID format: psi_mi_mitab id: irefindex.database name: iRefIndex Database original_source: - bind - biogrid - dip - hprd - intact - mint - category: Product description: R package for accessing and manipulating iRefIndex data format: http id: irefindex.irefr name: iRefR Package original_source: - irefindex - category: Product description: Cytoscape plugin for visualization and data mining of iRefIndex protein interaction data id: irefindex.irefscape name: iRefScape original_source: - irefindex - category: GraphicalInterface description: Web interface for navigating the global protein-protein interaction landscape id: irefindex.irefweb name: iRefWeb original_source: - irefindex publications: - category: Publication id: PMID:18823568 preferred: true - category: Publication id: PMID:22115179 - category: Publication id: PMID:21975162 warnings: - The iRefIndex website appears to be inactive as of 2025. Historical data and methods remain available through publications and may be accessible through archived versions. - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: bakerc@unb.ca label: Christopher Baker orcid: 0000-0003-4004-6479 creation_date: '2025-09-29T00:00:00Z' description: An ontology representation of the LIPIDMAPS nomenclature classification. domains: - chemistry and biochemistry id: lipro last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Lipid Ontology products: [] - activity_status: inactive category: DataSource creation_date: '2010-11-25T00:00:00Z' description: A reference database for long noncoding RNAs (lncRNAs) that have been shown to have, or be associated with, biological functions in eukaryotes. Contained over 150 lncRNAs from around 60 different species with comprehensive annotations including sequences, structural information, genomic context, expression, subcellular localization, conservation, and functional evidence. domains: - genomics - biological systems homepage_url: http://www.lncrnadb.org/ id: lncrnadb last_modified_date: '2025-10-21T00:00:00Z' layout: resource_detail name: lncRNAdb products: - category: GraphicalInterface description: Main web portal for searching and browsing long noncoding RNAs by name, sequence, species, or annotations format: http id: lncrnadb.portal name: lncRNAdb Portal product_url: http://www.lncrnadb.org/ - category: GraphicalInterface description: Search interface supporting queries by lncRNA name or alias, nucleotide sequence string, species, annotation status, and full-text search format: http id: lncrnadb.search name: Search Interface product_url: http://www.lncrnadb.org/ - category: Product description: Tab-delimited file download of search results format: tsv id: lncrnadb.export name: Export Results product_url: http://www.lncrnadb.org/ - category: GraphicalInterface description: Integration with UCSC Genome Browser for genomic context visualization format: http id: lncrnadb.ucsc-integration name: UCSC Genome Browser Integration - category: GraphicalInterface description: Integration with Noncoding RNA Expression Database (NRED) for expression information from various sources format: http id: lncrnadb.nred-integration name: NRED Integration - category: DocumentationProduct description: User submission interface for adding new entries and updating existing data with published information format: http id: lncrnadb.submit name: User Submission System - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Paulo P Amaral - Michael B Clark - Dennis K Gascoigne - Marcel E Dinger - John S Mattick id: https://doi.org/10.1093/nar/gkq1138 journal: Nucleic Acids Research preferred: true title: 'lncRNAdb: a reference database for long noncoding RNAs' year: '2011' taxon: - NCBITaxon:2759 warnings: - This database is no longer active and the website is no longer accessible. - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: peteremidford@yahoo.com label: Peter Midford orcid: 0000-0001-6512-3296 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - biological systems homepage_url: http://www.mesquiteproject.org/ontology/Loggerhead/index.html id: loggerhead last_modified_date: '2026-02-20T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Loggerhead nesting products: [] - activity_status: orphaned category: Ontology collection: - obo-foundry contacts: [] creation_date: '2025-09-29T00:00:00Z' description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. domains: - biological systems homepage_url: http://sourceforge.net/p/mamo-ontology/wiki/Home/ id: mamo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://opensource.org/licenses/Artistic-2.0 label: Artistic License 2.0 name: Mathematical modeling ontology products: - category: OntologyProduct description: Mathematical modeling ontology in OWL format format: owl id: mamo.owl name: mamo.owl product_file_size: 204902 product_url: http://purl.obolibrary.org/obo/mamo.owl repository: http://sourceforge.net/p/mamo-ontology - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: julie@igbmc.u-strasbg.fr label: Julie Thompson creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - chemistry and biochemistry homepage_url: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html id: mao last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Multiple alignment products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: j.bard@ed.ac.uk label: Jonathan Bard creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development id: mat last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Minimal anatomical terminology products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: druzinsk@uic.edu - contact_type: github value: RDruzinsky label: Robert Druzinsky orcid: 0000-0002-1572-1316 creation_date: '2025-09-29T00:00:00Z' description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. domains: - anatomy and development homepage_url: https://github.com/rdruzinsky/feedontology id: mfmo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Mammalian Feeding Muscle Ontology products: - category: OntologyProduct description: Mammalian Feeding Muscle Ontology in OWL format format: owl id: mfmo.owl name: mfmo.owl product_file_size: 15791 product_url: http://purl.obolibrary.org/obo/mfmo.owl repository: https://github.com/RDruzinsky/feedontology taxon: - NCBITaxon:40674 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: henrich@embl.de - contact_type: github value: ThorstenHen label: Thorsten Henrich orcid: 0000-0002-1548-3290 creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. domains: - anatomy and development id: mfo last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Medaka fish anatomy and development products: - category: OntologyProduct description: Medaka fish anatomy and development in OWL format format: owl id: mfo.owl name: mfo.owl product_url: http://purl.obolibrary.org/obo/mfo.owl taxon: - NCBITaxon:8089 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: carrine.blank@umontana.edu - contact_type: github value: carrineblank label: Carrine Blank orcid: 0000-0002-2100-6351 creation_date: '2025-09-29T00:00:00Z' description: An ontology of prokaryotic phenotypic and metabolic characters domains: - biological systems homepage_url: https://github.com/carrineblank/MicrO id: micro last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/2.0/ label: CC BY 2.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Prokaryotic Phenotypic and Metabolic Characters products: - category: OntologyProduct description: Ontology of Prokaryotic Phenotypic and Metabolic Characters in OWL format format: owl id: micro.owl name: micro.owl product_file_size: 665050 product_url: http://purl.obolibrary.org/obo/micro.owl repository: https://github.com/carrineblank/MicrO - activity_status: unresponsive category: DataSource creation_date: '2025-10-30T00:00:00Z' description: miRGate is a curated database of computationally predicted and experimentally validated miRNA-mRNA target pairs for human, mouse, and rat. The database integrates multiple prediction algorithms and includes sequences for both miRNAs and mRNA 3'-UTRs, along with experimentally validated data from four well-known databases. miRGate provides computational predictions using well-established algorithms and offers both a web interface and a REST API for programmatic access. domains: - genomics - biomedical homepage_url: http://mirgate.bioinfo.cnio.es id: mirgate infores_id: mirgate last_modified_date: '2025-11-17T00:00:00Z' layout: resource_detail name: miRGate products: - category: Portal description: Web portal for querying and browsing miRNA-mRNA target predictions for human, mouse, and rat format: http id: mirgate.portal name: miRGate Web Portal original_source: - mirgate product_url: http://mirgate.bioinfo.cnio.es warnings: - File was not able to be retrieved when checked on 2026-03-08_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("HTTPConnection(host='mirgate.bioinfo.cnio.es', port=80)_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2026-02-26_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("HTTPConnection(host='mirgate.bioinfo.cnio.es', port=80)_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-13_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-11_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-09_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-08_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-07_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-05_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-12-04_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-26_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-25_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-25_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-22_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-21_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-19_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-19_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - File was not able to be retrieved when checked on 2025-11-17_ Error connecting to URL_ HTTPConnectionPool(host='mirgate.bioinfo.cnio.es', port=80)_ Max retries exceeded with url_ / (Caused by NameResolutionError("_ Failed to resolve 'mirgate.bioinfo.cnio.es' ([Errno -2] Name or service not known)")) - 'File was not able to be retrieved when checked on 2026-03-11: Error connecting to URL: HTTPConnectionPool(host=''mirgate.bioinfo.cnio.es'', port=80): Max retries exceeded with url: / (Caused by NameResolutionError("HTTPConnection(host=''mirgate.bioinfo.cnio.es'', port=80): Failed to resolve ''mirgate.bioinfo.cnio.es'' ([Errno -2] Name or service not known)"))' - category: ProgrammingInterface description: REST API for programmatic access to miRNA-mRNA target prediction data format: http id: mirgate.api name: miRGate API original_source: - mirgate product_url: http://mirgate.bioinfo.cnio.es/API/ publications: - id: PMID:25858286 synonyms: - miRGate taxon: - NCBITaxon:9606 - NCBITaxon:10090 - NCBITaxon:10116 warnings: - The miRGate website (http://mirgate.bioinfo.cnio.es) is no longer accessible as of November 2025. - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: topalis@imbb.forth.gr label: Pantelis Topalis creation_date: '2025-09-29T00:00:00Z' description: An application ontology for use with miRNA databases. domains: - chemistry and biochemistry homepage_url: http://code.google.com/p/mirna-ontology/ id: mirnao last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: microRNA Ontology products: - category: OntologyProduct description: microRNA Ontology in OWL format format: owl id: mirnao.owl name: mirnao.owl product_url: http://purl.obolibrary.org/obo/mirnao.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: louis@imbb.forth.gr label: Christos (Kitsos) Louis creation_date: '2025-09-29T00:00:00Z' description: Application ontology for entities related to insecticide resistance in mosquitos domains: - environment homepage_url: http://purl.obolibrary.org/obo/miro.owl id: miro last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Mosquito insecticide resistance products: - category: OntologyProduct description: Mosquito insecticide resistance in OWL format format: owl id: miro.owl name: miro.owl product_file_size: 212397 product_url: http://purl.obolibrary.org/obo/miro.owl - category: OntologyProduct description: Mosquito insecticide resistance in OBO format format: obo id: miro.obo name: miro.obo product_file_size: 82792 product_url: http://purl.obolibrary.org/obo/miro.obo repository: https://github.com/VEuPathDB-ontology/MIRO taxon: - NCBITaxon:44484 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: stoeckrt@pcbi.upenn.edu label: Chris Stoeckert orcid: 0000-0002-5714-991X creation_date: '2025-09-29T00:00:00Z' description: A standardized description of a microarray experiment in support of MAGE v.1. domains: - biomedical homepage_url: http://mged.sourceforge.net/ontologies/MGEDontology.php id: mo last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Microarray experimental conditions products: - category: OntologyProduct description: Microarray experimental conditions in OWL format format: owl id: mo.owl name: mo.owl product_url: http://purl.obolibrary.org/obo/mo.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: smtifahim@gmail.com label: Fahim Imam orcid: 0000-0003-4752-543X creation_date: '2025-09-29T00:00:00Z' description: Neuronal cell types domains: - anatomy and development homepage_url: http://neuinfo.org/ id: nif_cell last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: NIF Cell products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: smtifahim@gmail.com label: Fahim Imam orcid: 0000-0003-4752-543X creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - biomedical homepage_url: http://neuinfo.org/ id: nif_dysfunction last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: NIF Dysfunction products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: smtifahim@gmail.com label: Fahim Imam orcid: 0000-0003-4752-543X creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://neuinfo.org/ id: nif_grossanatomy last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: NIF Gross Anatomy products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: schober@imbi.uni-freiburg.de label: Schober Daniel creation_date: '2025-09-29T00:00:00Z' description: Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. domains: - biomedical homepage_url: http://msi-ontology.sourceforge.net/ id: nmr last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: NMR-instrument specific component of metabolomics investigations products: - category: OntologyProduct description: NMR-instrument specific component of metabolomics investigations in OWL format format: owl id: nmr.owl name: nmr.owl product_url: http://purl.obolibrary.org/obo/nmr.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - biological systems homepage_url: http://www.obofoundry.org/ro id: obo_rel last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: OBO relationship types (legacy) products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: linikujp@gmail.com - contact_type: github value: linikujp label: Asiyah Yu Lin orcid: 0000-0002-5379-5359 creation_date: '2025-09-29T00:00:00Z' description: An ontology that formalizes the genomic element by defining an upper class genetic interval domains: - chemistry and biochemistry homepage_url: https://code.google.com/p/ontology-for-genetic-interval/ id: ogi last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Ontology for genetic interval products: - category: OntologyProduct description: Ontology for genetic interval in OWL format format: owl id: ogi.owl name: ogi.owl product_url: http://purl.obolibrary.org/obo/ogi.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: linikujp@gmail.com - contact_type: github value: linikujp label: Asiyah Yu Lin orcid: 0000-0002-5379-5359 creation_date: '2025-09-29T00:00:00Z' description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. domains: - biomedical homepage_url: https://github.com/linikujp/OGSF id: ogsf last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontology of Genetic Susceptibility Factor products: - category: OntologyProduct description: Ontology of Genetic Susceptibility Factor in OWL format format: owl id: ogsf.owl name: ogsf.owl product_file_size: 69686 product_url: http://purl.obolibrary.org/obo/ogsf.owl repository: https://github.com/linikujp/OGSF - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Organization contact_details: - contact_type: url value: https://obofoundry.org/ label: OBO Foundry creation_date: '2025-11-05T00:00:00Z' description: The OBO Interoperability Ontology (OIO) was a set of annotation properties and ontology metadata standards developed to promote interoperability between OBO Foundry ontologies. Its terms and properties have been superseded by OMO (Ontology Metadata Ontology) and are now considered deprecated. OIO provided foundational metadata terms that were widely used in early OBO ontologies for describing ontology versioning, imports, and other metadata. domains: - biological systems - upper id: oio infores_id: oio last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: OBO Interoperability Ontology products: - category: OntologyProduct description: OBO Interoperability Ontology in OWL format format: owl id: oio.owl name: OIO OWL original_source: - oio - category: OntologyProduct description: OBO Interoperability Ontology in OBO format format: obo id: oio.obo name: OIO OBO original_source: - oio - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl secondary_source: - efo - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - bfo - bto - chebi - cl - clo - cob - dc - doid - ecto - efo - fbbt - fbdv - fma - go - hancestro - hp - iao - ido - ma - mondo - mp - mpath - ncbitaxon - ncit - oba - obi - ogms - oio - omit - omo - ordo - pato - po - pr - ro - semapv - skos - so - to - uberon - uo - wbls - zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo secondary_source: - efo synonyms: - OIO - oio warnings: - This ontology is deprecated. Its functionality has been superseded by OMO (Ontology Metadata Ontology). - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: frederic.bastian@unil.ch - contact_type: github value: fbastian label: Fr d ric Bastian orcid: 0000-0002-9415-5104 creation_date: '2025-09-29T00:00:00Z' description: Life cycle stages for Medaka domains: - anatomy and development homepage_url: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv id: olatdv last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Medaka Developmental Stages products: - category: OntologyProduct description: Medaka Developmental Stages in OBO format format: obo id: olatdv.obo name: olatdv.obo product_file_size: 9412 product_url: http://purl.obolibrary.org/obo/olatdv.obo - category: OntologyProduct description: Medaka Developmental Stages in OWL format format: owl id: olatdv.owl name: olatdv.owl product_file_size: 11939 product_url: http://purl.obolibrary.org/obo/olatdv.owl repository: https://github.com/obophenotype/developmental-stage-ontologies - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mbrochhausen@gmail.com label: Mathias Brochhausen orcid: 0000-0003-1834-3856 creation_date: '2025-09-29T00:00:00Z' description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing) domains: - biomedical homepage_url: https://github.com/OMIABIS/omiabis-dev id: omiabis last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Ontologized MIABIS products: - category: OntologyProduct description: Ontologized MIABIS in OWL format format: owl id: omiabis.owl name: omiabis.owl product_file_size: 109985 product_url: http://purl.obolibrary.org/obo/omiabis.owl repository: https://github.com/OMIABIS/omiabis-dev - activity_status: inactive category: Aggregator contacts: - category: Organization contact_details: - contact_type: email value: ols-support@ebi.ac.uk - contact_type: github value: EBISPOT id: ebi label: EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT) creation_date: '2025-11-04T00:00:00Z' description: OxO (Ontology Xref Service) is a cross-ontology mapping service developed by EMBL-EBI's Samples, Phenotypes and Ontologies Team (SPOT). The service provides mappings between terms from different ontologies, enabling users to search for equivalent or related terms across multiple ontological resources. OxO aggregates cross-references from ontologies loaded in the Ontology Lookup Service (OLS) and enriches these with manual mappings and inference-based relationships. domains: - biomedical - upper - biological systems homepage_url: https://www.ebi.ac.uk/spot/oxo/ id: oxo infores_id: oxo last_modified_date: '2025-11-04T00:00:00Z' layout: resource_detail name: Ontology Xref Service products: - category: ProgrammingInterface description: RESTful API for programmatic access to cross-ontology mappings and term equivalence searches format: http id: oxo.api name: OxO REST API original_source: - oxo product_url: https://www.ebi.ac.uk/spot/oxo/docs/api - category: GraphicalInterface description: Web-based interface for searching and browsing ontology cross-references and mappings format: http id: oxo.portal name: OxO Web Interface original_source: - oxo product_url: https://www.ebi.ac.uk/spot/oxo/ repository: https://github.com/EBISPOT/OXO synonyms: - OxO - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: jaiswalp@science.oregonstate.edu - contact_type: github value: jaiswalp label: Pankaj Jaiswal orcid: 0000-0002-1005-8383 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://www.plantontology.org id: pao last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Plant Anatomy Ontology products: [] taxon: - NCBITaxon:33090 - activity_status: inactive category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.bv-brc.org/ label: BV-BRC creation_date: '2025-11-05T00:00:00Z' description: The Pathosystems Resource Integration Center (PATRIC) was a bacterial bioinformatics resource center providing integrated data and analysis tools for bacterial infectious disease research. PATRIC has been succeeded by the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), which continues to provide comprehensive bacterial genomics data, comparative analysis tools, and molecular characterization resources. The legacy PATRIC data and functionality have been integrated into BV-BRC. domains: - genomics - microbiology - biomedical - health homepage_url: https://www.bv-brc.org/ id: patric infores_id: patric last_modified_date: '2025-11-05T00:00:00Z' layout: resource_detail name: Pathosystems Resource Integration Center products: - category: GraphicalInterface description: Web portal for bacterial genomics (now at BV-BRC) format: http id: patric.web name: PATRIC/BV-BRC Web Portal original_source: - patric product_url: https://www.bv-brc.org/ - category: Product description: Bacterial genome data and annotations format: mixed id: patric.genomes name: PATRIC Genome Data original_source: - patric product_url: https://www.bv-brc.org/ - category: ProgrammingInterface description: API for programmatic access to bacterial data format: http id: patric.api name: BV-BRC API original_source: - patric product_url: https://www.bv-brc.org/docs/api/ publications: - id: https://doi.org/10.1093/nar/gkw1017 synonyms: - PATRIC - BV-BRC - Bacterial and Viral Bioinformatics Resource Center taxon: - NCBITaxon:2 warnings: - PATRIC has been succeeded by BV-BRC (Bacterial and Viral Bioinformatics Resource Center). All data and tools are now available at bv-brc.org - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: henrich@embl.de - contact_type: github value: ThorstenHen label: Thorsten Henrich orcid: 0000-0002-1548-3290 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://4dx.embl.de/platy id: pd_st last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Platynereis stage ontology products: [] taxon: - NCBITaxon:6358 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: frederic.bastian@unil.ch - contact_type: github value: fbastian label: Fr d ric Bastian orcid: 0000-0002-9415-5104 creation_date: '2025-09-29T00:00:00Z' description: Life cycle stages for Platynereis dumerilii domains: - anatomy and development homepage_url: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv id: pdumdv last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Platynereis Developmental Stages products: - category: OntologyProduct description: Platynereis Developmental Stages in OWL format format: owl id: pdumdv.owl name: pdumdv.owl product_file_size: 6379 product_url: http://purl.obolibrary.org/obo/pdumdv.owl - category: OntologyProduct description: Platynereis Developmental Stages in OBO format format: obo id: pdumdv.obo name: pdumdv.obo product_file_size: 4411 product_url: http://purl.obolibrary.org/obo/pdumdv.obo repository: https://github.com/obophenotype/developmental-stage-ontologies - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: po-discuss@plantontology.org label: Plant Ontology Administrators creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://www.plantontology.org id: pgdso last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Plant Growth and Development Stage products: [] taxon: - NCBITaxon:33090 - activity_status: inactive category: DataSource creation_date: '2025-12-03T00:00:00Z' description: PharmacotherapyDB is a curated catalog of medical indications between small molecule compounds and complex human diseases. It was created as part of a network-based drug repurposing project and differentiates between disease-modifying (DM) and symptomatic (SYM) treatments, with each indication reviewed by multiple physicians. The initial release contains 97 diseases and 601 drugs, with 755 disease-modifying therapies, 390 symptomatic therapies, and 243 non-indications. The catalog uses standardized vocabularies (Disease Ontology and DrugBank) to facilitate data integration and adheres to pathophysiological principles. domains: - drug discovery - pharmacology - biomedical homepage_url: https://github.com/dhimmel/indications id: pharmacotherapydb infores_id: pharmacotherapydb last_modified_date: '2025-12-03T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0-1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: PharmacotherapyDB products: - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet publications: - doi: 10.7554/eLife.26726 id: doi:10.7554/eLife.26726 journal: eLife preferred: true title: Systematic integration of biomedical knowledge prioritizes drugs for repurposing year: '2017' taxon: - NCBITaxon:9606 - activity_status: orphaned category: KnowledgeGraph creation_date: '2025-09-10T00:00:00Z' description: PharmDB (PharmDB-K) is a pharmacological knowledge graph integrating drugs, targets, diseases, indications, and related biomedical entities to facilitate computational repositioning and network pharmacology analyses. domains: - drug discovery - biomedical evaluation_page: resource/pharmdb/pharmdb_eval_automated.html homepage_url: http://www.pharmdb-k.org/ id: pharmdb last_modified_date: '2025-09-10T00:00:00Z' layout: resource_detail name: PharmDB products: - category: GraphicalInterface description: Legacy web portal for browsing PharmDB-K integrated pharmacological relationships format: http id: pharmdb.portal name: PharmDB Portal product_url: http://www.pharmdb-k.org/ - category: GraphProduct description: Integrated pharmacological knowledge graph (PharmDB-K) of drugs, targets, diseases, and associations id: pharmdb.graph name: PharmDB-K Graph - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque taxon: - NCBITaxon:9606 - activity_status: inactive category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.cancer.gov/ label: National Cancer Institute - category: Organization contact_details: - contact_type: url value: https://www.nature.com/ label: Nature Publishing Group creation_date: '2025-01-10T00:00:00Z' description: The Pathway Interaction Database (PID) was a highly curated collection of human molecular signaling, regulatory pathways, and key cellular processes developed through a collaboration between the US National Cancer Institute and Nature Publishing Group. The database focused specifically on cancer-relevant signaling and regulatory pathways rather than metabolic processes, providing detailed network-level representations of molecular interactions with comprehensive literature citations and evidence codes for each event. PID contained three main data collections the NCI-Nature Curated pathways representing expert-curated cancer signaling networks, imported Reactome pathways in BioPAX format, and BioCarta pathway data, together comprising 77 expert-reviewed pathways with over 4,300 manually curated interactions involving more than 2,600 proteins annotated with detailed posttranslational modifications including 7,400+ phosphorylation events. Each interaction in the NCI-Nature curated collection was associated with specific literature references from over 3,100 distinct PubMed citations and annotated with evidence codes indicating the type of experimental support. The database employed a sophisticated data model distinguishing five types of molecular events including transcription, translocation, biochemical reactions, protein modifications, and macroprocesses, with molecules characterized by posttranslational modifications, cellular locations, and activity states. PID provided powerful query capabilities enabling users to search by molecule names, construct dynamic interaction networks connecting specified molecules, overlay experimental data from gene expression studies onto pathways using batch query tools with statistical enrichment analysis, and visualize both predefined expert-curated pathways and novel networks generated computationally from the interaction database. The resource was particularly valuable for cancer research, allowing identification of parallel signaling paths, elucidation of therapy resistance mechanisms, and integration of genomic abnormalities with pathway contexts. While the original NCI-hosted PID website is no longer actively maintained and was discontinued, the complete PID dataset has been preserved and remains accessible through Pathway Commons, NDEx Bioscience Network Exchange, and as BioPAX Level 2 format exports, ensuring continued availability of this valuable curated knowledge for the research community. domains: - pathways - biological systems homepage_url: http://pid.nci.nih.gov/ id: pid last_modified_date: '2025-12-13T00:00:00Z' layout: resource_detail name: Pathway Interaction Database products: - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: Product description: pid.pathway Nodes TSV format: tsv id: obo-db-ingest.pid.pathway.tsv name: pid.pathway Nodes TSV original_source: - pid product_file_size: 3923 product_url: https://w3id.org/biopragmatics/resources/pid.pathway/pid.pathway.tsv secondary_source: - obo-db-ingest publications: - id: https://doi.org/10.1093/nar/gkn653 title: 'PID: the Pathway Interaction Database' repository: https://github.com/NCIP/pathway-interaction-database synonyms: - PID - Pathway Interaction Database - NCI-Nature PID taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mb4@sanger.ac.uk label: Matt Berriman creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://www.sanger.ac.uk/Users/mb4/PLO/ id: plo last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Plasmodium life cycle products: [] - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: satya30@uga.edu label: Satya S. Sahoo creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - chemistry and biochemistry homepage_url: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ id: propreo last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Proteomics data and process provenance products: [] - activity_status: inactive category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.bristol.ac.uk/integrative-epidemiology-unit/ label: MRC Integrative Epidemiology Unit, University of Bristol creation_date: '2025-12-03T00:00:00Z' description: The PRS Atlas is a comprehensive resource analyzing 162 polygenic risk scores (PRS) derived from genome-wide association studies against 551 heritable traits from the UK Biobank study (N=334,398). The atlas was developed to highlight putative causal relationships across the human phenome using Mendelian randomization approaches. PRS were constructed using independent SNPs (p<5×10⁻⁵) to evaluate associations with complex traits, providing insights into disease susceptibility and potential causal risk factors. The resource includes a web application for querying and visualizing associations between genetic liability and diverse health outcomes. domains: - genomics - translational - biomedical homepage_url: http://mrcieu.mrsoftware.org/PRS_atlas/ id: prsatlas infores_id: prsatlas last_modified_date: '2025-12-03T00:00:00Z' layout: resource_detail name: PRS Atlas products: - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb publications: - authors: - Tom G Richardson - Sean Harrison - Gibran Hemani - George Davey Smith doi: 10.7554/eLife.43657 id: doi:10.7554/eLife.43657 journal: eLife preferred: true title: An atlas of polygenic risk score associations to highlight putative causal relationships across the human phenome year: '2019' synonyms: - Polygenic Risk Score Atlas taxon: - NCBITaxon:9606 warnings: - The web application at http://mrcieu.mrsoftware.org/PRS_atlas/ may no longer be accessible - activity_status: inactive category: DataSource creation_date: '2025-07-12T00:00:00Z' description: PsyGeNET is a knowledge resource on psychiatric disorders and their associated genes, integrating expert-curated and text-mined data from the literature. It provides gene-disease associations for psychiatric disorders, supporting research in psychiatric genetics and genomics. domains: - biomedical - genomics homepage_url: http://www.psygenet.org/ id: psygenet last_modified_date: '2025-07-12T00:00:00Z' layout: resource_detail name: PsyGeNET products: - category: Product description: 'Gene-disease associations for psychiatric disorders, as described in "PsyGeNET: a knowledge platform on psychiatric disorders and their genes" (PMCID: PMC4565028). ' format: tsv id: psygenet.genedisease name: PsyGeNET Gene-Disease Associations product_url: http://www.psygenet.org/ - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). id: disgenet.data name: DisGeNET Data original_source: - clingen - clinvar - mgd - rgd - orphanet - psygenet - uniprot - disgenet - hp - gwascatalog - phewascat - ukbiobank - finngen - clinicaltrialsgov product_url: https://www.disgenet.com/ secondary_source: - disgenet publications: - authors: - Bravo À - Pinero J - Queralt-Rosinach N - Rautschka M - Furlong LI id: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565028/ journal: Database (Oxford) preferred: true title: 'PsyGeNET: a knowledge platform on psychiatric disorders and their genes' year: '2015' taxon: - NCBITaxon:9606 warnings: - The official PsyGeNET website (http://www.psygenet.org/) is currently inaccessible. Data may be unavailable or out of date. - activity_status: unresponsive category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: qnhu@sibs.ac.cn label: Qian-Nan Hu creation_date: '2025-03-09T00:00:00Z' description: Rare Disease Bridge (RDBridge) offers search functions for genes, potential drugs, pathways, literature, and medical imaging data that will support mechanistic research, drug development, diagnosis, and treatment for rare diseases. domains: - health - biomedical - precision medicine - clinical evaluation_page: resource/rdbridge/rdbridge_eval_automated.html homepage_url: http://rdb.lifesynther.com/ id: rdbridge last_modified_date: '2026-01-06T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: RDBridge products: - category: GraphicalInterface description: Graphical interface for exploring the RDBridge knowledge graph of rare diseases format: http id: rdbridge.webinterface is_public: true name: RDBridge Web Interface original_source: - rdbridge product_url: http://rdb.lifesynther.com/ - category: GraphProduct description: Knowledge graph connecting rare diseases with genes, drugs, pathways, and medical images edge_count: 22293 id: rdbridge.graph name: RDBridge Knowledge Graph node_count: 11704 original_source: - rdbridge - category: Product description: Curated collection of 235,631 scientific publications related to rare diseases format: http id: rdbridge.literaturedatabase name: RDBridge Literature Database original_source: - rdbridge publications: - authors: - Xing H - Zhang D - Cai P - Zhang R - Hu QN doi: doi:10.1093/bioinformatics/btad440 id: doi:10.1093/bioinformatics/btad440 journal: Bioinformatics preferred: true title: 'RDBridge: a knowledge graph of rare diseases based on large-scale text mining' year: '2023' repository: http://rdb.lifesynther.com/ taxon: - NCBITaxon:9606 warnings: - Homepage may be inaccessible (March 5 2025) - activity_status: unresponsive category: DataSource creation_date: '2025-09-09T00:00:00Z' description: The Ribosomal Database Project (RDP) provided ribosome-related data services, including quality-controlled, aligned and annotated rRNA sequences, phylogenetic trees, and analysis tools for Bacterial, Archaeal, and Fungal rRNA. The RDP website is no longer available, but stand-alone tools and classifiers remain accessible via Sourceforge and community tutorials. domains: - biological systems - genomics id: rdp last_modified_date: '2025-10-15T00:00:00Z' layout: resource_detail name: Ribosomal Database Project products: - category: ProcessProduct description: Stand-alone version of the RDP Classifier for taxonomic assignment of rRNA sequences. Available via Sourceforge. format: http id: rdp.classifier name: RDP Classifier (stand-alone) product_url: https://sourceforge.net/projects/rdp-classifier/ - category: ProcessProduct description: Command-line tools for rRNA sequence analysis, installation instructions and Docker images available via community tutorials. format: http id: rdp.tools name: RDP Tools (command-line) product_url: https://jfq3.gitbook.io/rdptools-docker/ - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database taxon: - NCBITaxon:2157 - NCBITaxon:2 warnings: - The RDP website is no longer available. Only stand-alone tools and classifiers remain accessible. - activity_status: inactive category: KnowledgeGraph creation_date: '2025-11-22T00:00:00Z' description: ReDrugs is a probabilistic knowledge graph for drug repositioning that integrates drug-target, protein-protein, and disease-gene interactions from multiple databases. The system uses evidence-weighted nanopublications to assign confidence scores to interactions based on experimental methods and manual curation. ReDrugs was designed to identify novel drug candidates for diseases, particularly melanoma, by filtering and analyzing systems biology networks with probabilistic methods. The platform included both a web interface and API for exploring molecular interaction networks. The web interface appears to be no longer accessible. domains: - drug discovery - systems biology - biomedical - pharmacology - translational evaluation_page: resource/redrugs/redrugs_eval_automated.html homepage_url: http://redrugs.tw.rpi.edu/ id: redrugs last_modified_date: '2025-11-22T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: ReDrugs products: - category: GraphicalInterface description: Interactive web interface for exploring drug-disease networks with probabilistic filtering and graph visualization id: redrugs.web name: ReDrugs Web Interface original_source: - redrugs product_url: http://redrugs.tw.rpi.edu/ - category: ProgrammingInterface description: SADI web services API for querying the knowledge graph including resource search, interaction lookup, and network expansion id: redrugs.api name: ReDrugs API original_source: - redrugs product_url: http://redrugs.tw.rpi.edu/api/ publications: - authors: - McCusker JP - Dumontier M - Yan R - He S - Dordick JS - McGuinness DL doi: 10.7717/peerj-cs.106 id: doi:10.7717/peerj-cs.106 journal: PeerJ Computer Science title: Finding melanoma drugs through a probabilistic knowledge graph year: '2017' repository: https://data.rpi.edu/xmlui/handle/10833/1760 synonyms: - ReDrugS taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: john.garavelli@ebi.ac.uk label: John Garavelli orcid: 0000-0002-4131-735X creation_date: '2025-09-29T00:00:00Z' description: For the description of covalent bonds in proteins. domains: - chemistry and biochemistry homepage_url: http://www.ebi.ac.uk/RESID/ id: resid last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Protein covalent bond products: [] - activity_status: orphaned category: Ontology collection: - obo-foundry contacts: [] creation_date: '2025-09-29T00:00:00Z' description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. domains: - chemistry and biochemistry homepage_url: http://purl.obolibrary.org/obo/rex.owl id: rex last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Physico-chemical process products: - category: OntologyProduct description: Physico-chemical process in OWL format format: owl id: rex.owl name: rex.owl product_url: http://purl.obolibrary.org/obo/rex.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: BatchelorC@rsc.org label: Colin Batchelor orcid: 0000-0001-5985-7429 creation_date: '2025-09-29T00:00:00Z' description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. domains: - chemistry and biochemistry homepage_url: https://github.com/bgsu-rna/rnao id: rnao last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: RNA ontology products: - category: OntologyProduct description: RNA ontology in OWL format format: owl id: rnao.owl name: rnao.owl product_file_size: 30137 product_url: http://purl.obolibrary.org/obo/rnao.owl - category: OntologyProduct description: RNA ontology in OBO format format: obo id: rnao.obo name: rnao.obo product_file_size: 11126 product_url: http://purl.obolibrary.org/obo/rnao.obo repository: https://github.com/BGSU-RNA/rnao - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: slarson@ncmir.ucsd.edu label: Stephen Larson creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://ccdb.ucsd.edu/CCDBWebSite/sao.html id: sao last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Subcellular anatomy ontology products: [] taxon: - NCBITaxon:9606 - activity_status: inactive category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: support@nlm.nih.gov id: ncbi label: National Library of Medicine creation_date: '2025-05-30T00:00:00Z' description: SemMedDB is a repository of semantic predications (subject-predicate-object triples) extracted from biomedical literature by SemRep, a natural language processing system. It contains over 130 million semantic predications extracted from more than 37 million PubMed citations, supporting biomedical knowledge discovery, literature-based discovery, and clinical applications. domains: - biomedical - literature - health - clinical - drug discovery - genomics - pharmacology homepage_url: https://lhncbc.nlm.nih.gov/temp/SemRep_SemMedDB_SKR/SemMedDB_download.html id: semmeddb infores_id: semmeddb last_modified_date: '2026-01-23T00:00:00Z' layout: resource_detail license: id: https://www.nlm.nih.gov/web_policies.html label: UMLS License name: Semantic MEDLINE Database (SemMedDB) products: - category: ProcessProduct description: The SemRep natural language processing system that extracts semantic predications from biomedical literature to create SemMedDB id: semmeddb.semrep.tool name: SemRep NLP System product_url: https://lhncbc.nlm.nih.gov/temp/SemRep_SemMedDB_SKR/SemRep_download.html - category: GraphProduct description: Nodes for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.nodes name: RTX-KG2.10.1c KGX JSONL Nodes original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 376501785 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-nodes.jsonl.gz secondary_source: - rtx-kg2 - category: GraphProduct description: Edges for KGX distribution of the RTX-KG2 (RTX-KG2.10.1c) format: kgx-jsonl id: rtx-kg2.graph.edges name: RTX-KG2.10.1c KGX JSONL Edges original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_file_size: 1807360397 product_url: https://rtx-kg2-public.s3.us-west-2.amazonaws.com/kg2c-2.10.1-v1.0-edges.jsonl.gz secondary_source: - rtx-kg2 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - chembl - drugbank - kegg - reactome - go - drugcentral - uniprot - mondo - hp - chebi - uberon - ncbitaxon - dgidb - disgenet - ensembl - gtopdb - rtx-kg2 - semmeddb product_url: https://arax.ncats.io/ secondary_source: - rtx-kg2 - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb - category: GraphProduct description: KGX graph package for SemMedDB text-derived predications (build semmeddb_semmeddb-2023-kg2.10.3_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.semmeddb.graph name: Translator SemMedDB KGX Graph original_source: - semmeddb product_url: https://stars.renci.org/var/translator/releases/semmeddb/2025_12_15/ secondary_source: - translator publications: - authors: - Kilicoglu H - Shin D - Fiszman M - Rosemblat G - Rindflesch TC doi: 10.1093/bioinformatics/bts591 id: https://doi.org/10.1093/bioinformatics/bts591 journal: Bioinformatics preferred: true title: 'SemMedDB: a PubMed-scale repository of biomedical semantic predications' year: '2012' - authors: - Kilicoglu H - Rosemblat G - Fiszman M - Shin D - Rindflesch TC doi: 10.1186/s12859-020-3517-7 id: https://doi.org/10.1186/s12859-020-3517-7 journal: BMC Bioinformatics title: Broad-coverage biomedical relation extraction with SemRep year: '2020' - authors: - Kilicoglu H - Rosemblat G - Fiszman M - Rindflesch TC doi: 10.1186/1471-2105-12-486 id: https://doi.org/10.1186/1471-2105-12-486 journal: BMC Bioinformatics title: Constructing a semantic predication gold standard from the biomedical literature year: '2011' - authors: - Rindflesch TC - Fiszman M doi: 10.1016/j.jbi.2003.11.003 id: https://doi.org/10.1016/j.jbi.2003.11.003 journal: Journal of Biomedical Informatics title: 'The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text' year: '2003' taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: psidev-gps-dev@lists.sourceforge.net label: SEP developers via the PSI and MSI mailing lists creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. domains: - biomedical homepage_url: http://psidev.info/index.php?q=node/312 id: sep last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Sample processing and separation techniques products: - category: OntologyProduct description: Sample processing and separation techniques in OWL format format: owl id: sep.owl name: sep.owl product_url: http://purl.obolibrary.org/obo/sep.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - activity_status: orphaned category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cjmungall@lbl.gov label: Chris Mungall orcid: 0000-0002-6601-2165 creation_date: '2025-09-29T00:00:00Z' description: Social Behavior in insects domains: - biological systems homepage_url: https://github.com/obophenotype/sibo id: sibo last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Social Insect Behavior Ontology products: - category: OntologyProduct description: Social Insect Behavior Ontology in OWL format format: owl id: sibo.owl name: sibo.owl product_file_size: 26920 product_url: http://purl.obolibrary.org/obo/sibo.owl - category: OntologyProduct description: Social Insect Behavior Ontology in OBO format format: obo id: sibo.obo name: sibo.obo product_file_size: 16744 product_url: http://purl.obolibrary.org/obo/sibo.obo repository: https://github.com/obophenotype/sibo - activity_status: inactive category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: michael.kuhn@gmail.com label: Michael Kuhn - category: Organization label: European Molecular Biology Laboratory (EMBL) creation_date: '2025-05-29T00:00:00Z' description: SIDER (Side Effect Resource) contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts, including side effect frequency, drug and side effect classifications, and links to further information. domains: - biomedical - pharmacology - drug discovery - health homepage_url: http://sideeffects.embl.de/ id: sider infores_id: sider last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-4.0 name: SIDER products: - category: GraphicalInterface description: Web interface that allows searching and browsing drugs and their side effects. id: sider.web name: SIDER Web Interface product_url: http://sideeffects.embl.de/ - category: Product description: Tab-separated file mapping drugs to their names and synonyms. format: tsv id: sider.drug_names name: SIDER Drug Names product_file_size: 34759 product_url: http://sideeffects.embl.de/media/download/drug_names.tsv - category: MappingProduct description: Tab-separated file mapping drugs to their ATC codes. format: tsv id: sider.drug_atc name: SIDER Drug ATC Codes product_file_size: 32760 product_url: http://sideeffects.embl.de/media/download/drug_atc.tsv - category: Product compression: gzip description: Tab-separated file containing all drug indications extracted from drug labels using MedDRA terminology. format: tsv id: sider.meddra_all_indications name: SIDER MedDRA All Indications product_file_size: 344689 product_url: http://sideeffects.embl.de/media/download/meddra_all_indications.tsv.gz - category: Product compression: gzip description: Tab-separated file containing all side effects extracted from drug labels using MedDRA terminology. format: tsv id: sider.meddra_all_se name: SIDER MedDRA All Side Effects product_file_size: 2381171 product_url: http://sideeffects.embl.de/media/download/meddra_all_se.tsv.gz - category: Product compression: gzip description: Tab-separated file containing side effect frequency information extracted from drug labels using MedDRA terminology. format: tsv id: sider.meddra_freq name: SIDER MedDRA Frequency product_file_size: 2058445 product_url: http://sideeffects.embl.de/media/download/meddra_freq.tsv.gz - category: Product compression: gzip description: Tab-separated file containing all original label indications extracted from drug labels using MedDRA terminology. format: tsv id: sider.meddra_all_label_indications name: SIDER MedDRA All Label Indications product_file_size: 5916355 product_url: http://sideeffects.embl.de/media/download/meddra_all_label_indications.tsv.gz - category: Product compression: gzip description: Tab-separated file containing all original label side effects extracted from drug labels using MedDRA terminology. format: tsv id: sider.meddra_all_label_se name: SIDER MedDRA All Label Side Effects product_file_size: 42534383 product_url: http://sideeffects.embl.de/media/download/meddra_all_label_se.tsv.gz - category: Product compression: gzip description: Tab-separated file mapping MedDRA terms to their concept ID. format: tsv id: sider.meddra name: SIDER MedDRA Dictionary product_file_size: 1084933 product_url: http://sideeffects.embl.de/media/download/meddra.tsv.gz - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. id: spoke.graph name: SPOKE Graph original_source: - ncbigene - pubmed - mesh - pid - doid - diseases - drugcentral - go - gwascatalog - reactome - lincs-l1000 - uberon - wikipathways - bindingdb - drugbank - sider - bgee - uniprot - string - omim - chembl - foodb - civic - gdsc - clinicaltrialsgov - hpa - cl - kegg - metacyc - bv-brc - ncbitaxon - pathophenodb - pfam - interpro - protcid secondary_source: - spoke - category: GraphicalInterface description: A browser interface for a knowledge graph for Alzheimer's Disease. format: http id: alzkb.browser name: AlzKB Graph Database Browser original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - sider - tissues - uberon - wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - alzkb - hetionet - category: GraphProduct description: Memgraph data release for AlzKB. id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - aop-db - bgee - disgenet - doid - drugbank - dsstox - go - gwascatalog - hrpimp - lincs-l1000 - mesh - ncbigene - pharmacotherapydb - pid - pubchem - reactome - reactome - sider - tissues - uberon - wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - alzkb - hetionet - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations id: bioteque.embeddings name: Bioteque Embeddings original_source: - chebi - cosmic - achilles - depmap - ccle - gdsc - cellosaurus - clue - ctd - pharmacodb - prism - drugbank - lincs - compartments - offsides - sider - drugcentral - repohub - chemicalchecker - repodb - disgenet - opentargets - creeds - interpro - reactome - tissues - dorothea - progeny - gtex - hpa - go - corum - huri - intact - omnipath - string - bto product_url: https://bioteque.irbbarcelona.org/downloads/embeddings secondary_source: - bioteque - category: ProcessProduct description: INDRA CoGEx is a graph database integrating causal relations, ontological relations, properties, and data, assembled at scale automatically from the scientific literature and structured sources. This is the code to build the graph. id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - chembl - sider - reactome - wikipathways - hp - nihreporter - disgenet - pubmed - gwascatalog - cellmarker - go - bgee - ccle - clinicaltrialsgov - indra product_url: https://github.com/gyorilab/indra_cogex secondary_source: - indra - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - omim - drugbank - pharmgkb - ttd - sider - humannet - ncbigene - mesh - pubchem - gnbr - biogps - connectivitymap product_url: https://zenodo.org/record/4077338 secondary_source: - pharmkg - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: The integrative Biomedical Knowledge Hub (iBKH) knowledge graph, harmonizing and integrating information from diverse biomedical resources including DRKG, iDISK, and multiple databases (BRENDA, CTD, DrugBank, KEGG, PharmGKB, Reactome, SIDER, and others). id: ibkh.graph name: iBKH Knowledge Graph original_source: - drkg - idisk - brenda - ctd - drugbank - kegg - pharmgkb - reactome - sider - tissues - bgee - doid - uberon - cl - hgnc - chembl - chebi - category: GraphProduct description: KGX graph package for SIDER drug side effects (build sider_4.1_1.0_2025sep1_4.3.6; release 2025_12_15) format: kgx id: translator.sider.graph name: Translator SIDER KGX Graph original_source: - sider product_url: https://stars.renci.org/var/translator/releases/sider/2025_12_15/ secondary_source: - translator - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - authors: - Kuhn M - Letunic I - Jensen LJ - Bork P doi: doi:10.1093/nar/gkv1075 id: https://doi.org/10.1093/nar/gkv1075 journal: Nucleic Acids Research preferred: true title: The SIDER database of drugs and side effects year: '2016' - authors: - Kuhn M - Campillos M - Letunic I - Jensen LJ - Bork P doi: doi:10.1038/msb.2009.98 id: https://doi.org/10.1038/msb.2009.98 journal: Molecular Systems Biology title: A side effect resource to capture phenotypic effects of drugs year: '2010' warnings: - The last release for this resource was on October 21, 2015. - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Adrien.Coulet@loria.fr label: Adrien Coulet creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - chemistry and biochemistry homepage_url: http://www.loria.fr/~coulet/sopharm2.0_description.php id: sopharm last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Suggested Ontology for Pharmacogenomics products: [] taxon: - NCBITaxon:9606 - activity_status: inactive category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://string-db.org/help/ - contact_type: email value: string-db@embl.de id: stringdb label: STRING/EMBL Team creation_date: '2025-11-17T00:00:00Z' description: STITCH (Search Tool for Interactions of Chemicals) is a database of known and predicted interactions between chemicals and proteins across 2,031 organisms. The resource integrates chemical-protein interactions from five main sources - genomic context predictions, high-throughput experimental data, conserved co-expression patterns, automated text mining, and curated knowledge from databases. STITCH covers 9.6 million proteins and 500,000 chemicals with 1.6 billion interactions, combining direct physical and indirect functional associations. Version 5 was released in 2016 and is no longer actively maintained (marked as unsupported). domains: - drug discovery - systems biology - biomedical homepage_url: http://stitch-db.org/ id: stitch infores_id: stitch last_modified_date: '2026-01-15T00:00:00Z' layout: resource_detail license: id: http://stitch-db.org/download/STITCHacademiclicense.pdf label: STITCH Academic License (free for academic use; commercial licensing available) name: STITCH products: - category: Product description: Web interface for searching and visualizing chemical-protein interactions across organisms format: http id: stitch.portal is_public: true name: STITCH Web Portal original_source: - stitch product_url: http://stitch-db.org/ - category: Product description: Downloadable data files containing chemical-protein interaction networks format: tsv id: stitch.downloads is_public: true name: STITCH Data Downloads original_source: - stitch product_url: http://stitch-db.org/cgi/download.pl - category: ProgrammingInterface description: API for programmatic access to STITCH chemical-protein interaction data format: http id: stitch.api is_public: true name: STITCH API original_source: - stitch product_url: http://stitch-db.org/cgi/access.pl?footer_active_subpage=apis - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Neo4j database dump of the Clinical Knowledge Graph and additional relationships dump_format: neo4j edge_count: 220000000 format: mixed id: cancer-genome-interpreter.clinicalkg.graph name: CKG Graph Dump node_count: 16000000 original_source: - uniprot - tissues - string - stitch - smpdb - signor - sider - refseq - reactome - phosphositeplus - pfam - oncokb - mutationds - intact - hpa - hmdb - hgnc - gwascatalog - foodb - drugbank - disgenet - diseases - dgidb - corum - cancer-genome-interpreter - doid - bto - efo - go - hp - snomedct - mod - mi - ms - uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 1406201678 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.links.csv - category: GraphProduct description: Auxiliary UniBioMap graph annotations and metadata. format: tsv id: unibiomap.auxs name: UniBioMap Graph Auxiliaries original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 591290539 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.auxs.tsv - category: GraphProduct description: Predicted UniBioMap graph edges with confidence scores. format: csv id: unibiomap.pred name: UniBioMap Predicted Graph original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 2484982268 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.csv - category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - unibiomap - hpa - go - bindingdb - foodb - tcdb - biogrid - ctd - chebi - stitch - intact - uniprot - unichem - pubchem - batman - string - ncbigene - drugbank - kegg - sider - compath - phosphositeplus - hp - chembl - reactome - smpdb - uberon - hmdb - medgen - umls - mesh - inchikey - unichem - omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - authors: - Damian Szklarczyk - Alberto Santos - Christian von Mering - Lars Juhl Jensen - Peer Bork - Michael Kuhn doi: 10.1093/nar/gkv1277 id: PMID:26590256 journal: Nucleic Acids Res title: 'STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data' year: '2016' taxon: - NCBITaxon:1 warnings: - STITCH v5 (2016) is marked unsupported on the homepage; data and APIs may be outdated. - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: dsonensh@odu.edu label: Daniel Sonenshine creation_date: '2025-09-29T00:00:00Z' description: 'The anatomy of the Tick, Families: Ixodidae, Argassidae' domains: - anatomy and development homepage_url: https://www.vectorbase.org/ontology-browser id: tads last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Tick Anatomy Ontology products: - category: OntologyProduct description: Tick Anatomy Ontology in OWL format format: owl id: tads.owl name: tads.owl product_file_size: 80482 product_url: http://purl.obolibrary.org/obo/tads.owl - category: OntologyProduct description: Tick Anatomy Ontology in OBO format format: obo id: tads.obo name: tads.obo product_file_size: 48576 product_url: http://purl.obolibrary.org/obo/tads.obo repository: https://github.com/VEuPathDB-ontology/TADS taxon: - NCBITaxon:6939 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: pierre.sprumont@unifr.ch label: Pierre Sprumont creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development id: tahe last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Terminology of Anatomy of Human Embryology products: [] taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: pierre.sprumont@unifr.ch label: Pierre Sprumont creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - biomedical id: tahh last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Terminology of Anatomy of Human Histology products: [] taxon: - NCBITaxon:9606 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: wasila.dahdul@usd.edu label: Wasila Dahdul orcid: 0000-0003-3162-7490 creation_date: '2025-09-29T00:00:00Z' description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa domains: - anatomy and development homepage_url: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology id: tao last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Teleost Anatomy Ontology products: - category: OntologyProduct description: Teleost Anatomy Ontology in OWL format format: owl id: tao.owl name: tao.owl product_file_size: 5063653 product_url: http://purl.obolibrary.org/obo/tao.owl taxon: - NCBITaxon:32443 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: topalis@imbb.forth.gr label: Pantelis Topalis creation_date: '2025-09-29T00:00:00Z' description: A structured controlled vocabulary of the anatomy of mosquitoes. domains: - anatomy and development homepage_url: https://www.vectorbase.org/ontology-browser id: tgma last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png name: Mosquito gross anatomy ontology products: - category: OntologyProduct description: Mosquito gross anatomy ontology in OWL format format: owl id: tgma.owl name: tgma.owl product_file_size: 298621 product_url: http://purl.obolibrary.org/obo/tgma.owl - category: OntologyProduct description: Mosquito gross anatomy ontology in OBO format format: obo id: tgma.obo name: tgma.obo product_file_size: 143032 product_url: http://purl.obolibrary.org/obo/tgma.obo repository: https://github.com/VEuPathDB-ontology/TGMA taxon: - NCBITaxon:44484 - activity_status: inactive category: DataSource creation_date: '2025-09-09T00:00:00Z' description: The tmRNA Website is a comprehensive database of transfer-messenger RNA (tmRNA) and SmpB protein sequences involved in bacterial trans-translation. Contains 1,716 unique tmRNA sequences from bacteria and organelles, 2,258 unique SmpB sequences, with 9,387 tmRNA instances across public databases. Provides sequence alignments, structural annotations, BLAST search tools, and Krona-based phylogenetic visualization. domains: - genomics homepage_url: http://bioinformatics.sandia.gov/tmrna/ id: tmrnawebsite last_modified_date: '2025-11-13T00:00:00Z' layout: resource_detail name: The tmRNA Website products: - category: GraphicalInterface description: Main web portal for searching and browsing tmRNA and SmpB sequences with phylogenetic navigation format: http id: tmrnawebsite.portal name: tmRNA Website Portal original_source: - tmrnawebsite product_url: http://bioinformatics.sandia.gov/tmrna/ - category: Product description: BLAST search interface for tmRNA and SmpB sequence similarity searches format: http id: tmrnawebsite.blast name: tmRNA Website BLAST original_source: - tmrnawebsite product_url: http://bioinformatics.sandia.gov/tmrna/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Multiple sequence alignments for 632 tmRNA and 2,258 distinct SmpB sequences format: http id: tmrnawebsite.alignments name: tmRNA and SmpB Alignments original_source: - tmrnawebsite product_url: http://bioinformatics.sandia.gov/tmrna/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Krona-based interactive phylogenetic visualization tool for 9,387 tmRNA instances format: http id: tmrnawebsite.krona-viewer name: tmRNA Krona Phylogenetic Viewer original_source: - tmrnawebsite product_url: http://bioinformatics.sandia.gov/tmrna/ warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: Product description: Software tools (tFind.pl, rFind.pl) for identifying tmRNA genes in genomic sequences format: http id: tmrnawebsite.software name: tmRNA Identification Software original_source: - tmrnawebsite product_url: http://bioinformatics.sandia.gov/tmrna/software.html warnings: - File was not able to be retrieved when checked on 2026-03-08_ HTTP 404 error when accessing file - File was not able to be retrieved when checked on 2026-02-26_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 404 error when accessing file' - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/ - category: ProgrammingInterface description: REST API for programmatic access to RNAcentral data format: http id: rnacentral.api name: RNAcentral REST API original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/api - category: Product description: FTP archive with current and archived release files (sequences and annotations) format: http id: rnacentral.ftp name: RNAcentral FTP Archive original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral - category: DataModelProduct description: Public PostgreSQL database for direct SQL access to RNAcentral data format: postgres id: rnacentral.public-db name: RNAcentral Public Postgres Database original_source: - 5srrnadb - crd - dictybase - ena - ensembl - evlncrnas - expressionatlas - flybase - genecards - greengenes - gtrnadb - hgnc - intact - lncbase - lncbook - lncipedia - lncrnadb - malacards - mgnify - mirbase - mirgenedb - modomics - noncode - pdbe - pirbase - plncdb - pombase - rdp - rediportal - rfam - rgd - ribocentre - ribovision - sgd - silva - snodb - snopy - snornadatabase - srpdb - tair - tarbase - tmrnawebsite - zfin - zwd - rnacentral product_url: https://rnacentral.org/help/public-database publications: - authors: - Hudson CM - Williams KP id: https://doi.org/10.1093/nar/gku1109 journal: Nucleic Acids Research preferred: true title: The tmRNA website year: '2015' synonyms: - tmRNA website - tmRNA-SmpB database taxon: - NCBITaxon:2 warnings: - Website appears to be inactive (http://bioinformatics.sandia.gov/tmrna/ not accessible as of 2025-11-13). Data has been contributed to RNAcentral. - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Anne.Morgat@sib.swiss - contact_type: github value: amorgat label: Anne Morgat orcid: 0000-0002-1216-2969 creation_date: '2025-09-29T00:00:00Z' description: A manually curated resource for the representation and annotation of metabolic pathways domains: - biological systems homepage_url: https://github.com/geneontology/unipathway id: upa last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: http://creativecommons.org/licenses/by/3.0/ label: CC BY 3.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Unipathway products: - category: OntologyProduct description: Unipathway in OWL format format: owl id: upa.owl name: upa.owl product_file_size: 798911 product_url: http://purl.obolibrary.org/obo/upa.owl - category: OntologyProduct description: Unipathway in OBO format format: obo id: upa.obo name: upa.obo product_file_size: 454223 product_url: http://purl.obolibrary.org/obo/upa.obo repository: https://github.com/geneontology/unipathway - activity_status: orphaned category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: mauno.vihinen@med.lu.se - contact_type: github value: maunov label: Mauno Vihinen orcid: 0000-0002-9614-7976 creation_date: '2025-09-29T00:00:00Z' description: Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. domains: - biological systems homepage_url: http://variationontology.org id: vario last_modified_date: '2026-02-18T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png name: Variation Ontology products: - category: OntologyProduct description: VariO main release in OWL format: owl id: vario.owl name: VariO main release in OWL product_file_size: 497896 product_url: http://purl.obolibrary.org/obo/vario.owl - category: OntologyProduct description: VariO in OBO format format: obo id: vario.obo name: VariO in OBO format product_file_size: 110673 product_url: http://purl.obolibrary.org/obo/vario.obo - activity_status: inactive category: Resource contacts: - category: Individual contact_details: - contact_type: email value: ben.elsworth@bristol.ac.uk label: Ben Elsworth creation_date: '2025-09-03T00:00:00Z' description: Vectology is a software platform and API for exploring relationships among biomedical variables using sentence embedding models derived from biomedical literature. It converts brief variable descriptions into vector representations enabling similarity search, recommendation, and relational insight without manual ontology annotation. domains: - biomedical - genomics - health - investigations homepage_url: http://vectology.mrcieu.ac.uk/ id: vectology last_modified_date: '2025-09-03T00:00:00Z' layout: resource_detail name: Vectology products: - category: ProgrammingInterface description: Public API providing access to sentence embedding-based similarity endpoints and variable vector queries id: vectology.api is_public: true name: Vectology API original_source: - vectology product_url: http://vectology-api.mrcieu.ac.uk/ - category: DocumentationProduct description: Project information page including description, maintenance status, contacts, and publication reference format: http id: vectology.docs name: Vectology Project Page original_source: - vectology product_url: https://mrcieu.github.io/software/vectology/ - category: GraphProduct description: Integrated graph knowledge base combining Mendelian randomization causal estimates, pathway, QTL, drug, literature-derived, and ontology-backed relationships (Neo4j backend) format: neo4j id: epigraphdb.graph name: EpiGraphDB Graph Database original_source: - epigraphdb - kg-monarch - vectology - ukbiobank - prsatlas - eqtlgen - mondo - gtex - ensembl - cpic - opentargets - efo - semmeddb - intact - string - reactome - mrbase product_url: https://docs.epigraphdb.org/graph-database/ secondary_source: - epigraphdb - activity_status: inactive category: Ontology collection: - obo-foundry contacts: [] creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development id: vhog last_modified_date: '2026-02-24T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Vertebrate Homologous Ontology Group Ontology products: - category: OntologyProduct description: Vertebrate Homologous Ontology Group Ontology in OWL format format: owl id: vhog.owl name: vhog.owl product_url: http://purl.obolibrary.org/obo/vhog.owl warnings: - 'File was not able to be retrieved when checked on 2026-03-11: HTTP 403 error when accessing file' - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: wasila.dahdul@usd.edu label: Wasila Dahdul orcid: 0000-0003-3162-7490 creation_date: '2025-09-29T00:00:00Z' description: Vertebrate skeletal anatomy ontology. domains: - anatomy and development homepage_url: https://www.nescent.org/phenoscape/Main_Page id: vsao last_modified_date: '2026-02-22T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Vertebrate Skeletal Anatomy Ontology- products: - category: OntologyProduct description: Vertebrate Skeletal Anatomy Ontology- in OWL format format: owl id: vsao.owl name: vsao.owl product_file_size: 600603 product_url: http://purl.obolibrary.org/obo/vsao.owl taxon: - NCBITaxon:7742 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: cherry@genome.stanford.edu label: Mike Cherry orcid: 0000-0001-9163-5180 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - biological systems homepage_url: http://www.yeastgenome.org/ id: ypo last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Yeast phenotypes products: [] taxon: - NCBITaxon:4932 - activity_status: inactive category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: Leszek@missouri.edu label: Leszek Vincent orcid: 0000-0002-9316-2919 creation_date: '2025-09-29T00:00:00Z' description: Description unavailable. domains: - anatomy and development homepage_url: http://www.maizemap.org/ id: zea last_modified_date: '2025-10-06T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: Maize gross anatomy products: [] taxon: - NCBITaxon:4575