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. 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relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ publications: - authors: - Maciej Szymanski - Andrzej Zielezinski - Jan Barciszewski - Volker A. Erdmann - Wojciech M. Karlowski 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 - biomedical homepage_url: https://aact.ctti-clinicaltrials.org/ id: aact infores_id: aact last_modified_date: '2026-06-01T00:00:00Z' 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: aact - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: aact - relation_type: prov:hadPrimarySource source: clinicaltrialsgov product_url: https://aact.ctti-clinicaltrials.org/downloads - category: Product compression: zip description: Pipe-delimited text exports of the AACT database for import into databases or analysis tools format: csv id: aact.pipe_delimited name: AACT Pipe-Delimited Downloads original_source: - relation_type: prov:hadPrimarySource source: aact - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: aact product_url: https://aact.ctti-clinicaltrials.org/data_dictionary - 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: - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: aact product_url: https://aact.ctti-clinicaltrials.org/ - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for CTKP distributed via the NCATS Translator release site (release 2026_03_27; build ctkp_3.1.37_a99268cc_2025sep1_4.3.6; source version 3.1.37; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 438575 format: kgx-jsonl id: translator.ctkp.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator CTKP KGX Graph node_count: 41243 original_source: - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/ctkp/latest/ versions: - '2026_03_27' - ctkp_3.1.37_a99268cc_2025sep1_4.3.6 - category: GraphProduct description: Live TRAPI/BioThings metadata endpoint for the Multiomics BigGIM-DrugResponse KP, exposing the multiomics knowledge graph served by the Multiomics Provider (built from GTEx, TCGA, and drug-response data, with additional clinical-trials, drug-approval and knowledge-resource inputs). format: json id: multiomics-kp.graph name: Multiomics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: multiomics-kp - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcga - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: dailymed - relation_type: prov:hadPrimarySource source: faers product_url: https://biothings.transltr.io/biggim_drugresponse_kp/metadata secondary_source: - relation_type: prov:wasInfluencedBy source: aact - relation_type: prov:wasInfluencedBy source: biogrid - relation_type: prov:wasInfluencedBy source: huri - relation_type: prov:wasInfluencedBy source: cellmarker - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: ttd - relation_type: prov:wasInfluencedBy source: pubmed publications: - authors: - Asba Tasneem - Laura Aberle - Hari Ananth - Swati Chakraborty - Karen Chiswell - Brian J. McCourt - Ricardo Pietrobon doi: 10.1371/journal.pone.0033677 id: doi:10.1371/journal.pone.0033677 journal: PLOS ONE preferred: true title: The Database for Aggregate Analysis of ClinicalTrials.gov (AACT) and Subsequent Regrouping by Clinical Specialty year: '2012' 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 homepage_url: https://depmap.org/portal/achilles/ id: achilles last_modified_date: '2026-05-30T00:00:00Z' layout: resource_detail license: id: https://depmap.org/portal/terms/ label: DepMap Terms of Use name: Project Achilles products: - category: DocumentationProduct description: Project Achilles overview page on the DepMap portal describing screening methods, computational models, and release practices. format: http id: achilles.docs name: Project Achilles Overview original_source: - relation_type: prov:hadPrimarySource source: achilles product_url: https://depmap.org/portal/achilles/ warnings: [] - category: Product description: DepMap all-data downloads page where current Achilles and related dependency datasets are released. format: http id: achilles.downloads name: Project Achilles Data Releases original_source: - 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relation_type: prov:wasDerivedFrom source: wikipathways 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: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: yimingli99 label: Yiming Li creation_date: '2026-06-12T00:00:00Z' description: AcuKG is a comprehensive medical acupuncture knowledge graph that integrates acupuncture textbooks, official sources, clinical trials, biomedical literature, and ontology mappings to represent acupoints, anatomical locations, conditions, therapeutic indications, action targets, and evidence relationships. domains: - biomedical - clinical - anatomy and development homepage_url: https://github.com/yimingli99/AcuKG-Knowledge-graph-for-medical-acupuncture id: acukg last_modified_date: '2026-06-12T00:00:00Z' layout: resource_detail name: AcuKG products: - 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relation_type: prov:used source: mesh - relation_type: prov:used source: uberon - relation_type: prov:used source: snomedct product_url: https://github.com/yimingli99/AcuKG-Knowledge-graph-for-medical-acupuncture/tree/main/AcuKG_RDF - category: GraphProduct description: JSON representation of AcuKG relationship tables. edge_count: 11527 format: json id: acukg.json name: AcuKG JSON files node_count: 1839 original_source: - relation_type: prov:hadPrimarySource source: acukg - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:used source: mesh - relation_type: prov:used source: uberon - relation_type: prov:used source: snomedct product_url: https://github.com/yimingli99/AcuKG-Knowledge-graph-for-medical-acupuncture/tree/main/AcuKG_json publications: - authors: - Yiming Li - Xueqing Peng - Suyuan Peng - Jianfu Li - Donghong Pei - Qin Zhang - Yiwei Lu - Yan Hu - Fang Li - Li Zhou - Yongqun He - Cui Tao - Hua Xu - Na Hong doi: 10.1093/jamia/ocaf179 id: doi:10.1093/jamia/ocaf179 journal: Journal of the American Medical Informatics Association title: 'AcuKG: a comprehensive knowledge graph for medical acupuncture' year: '2026' repository: https://github.com/yimingli99/AcuKG-Knowledge-graph-for-medical-acupuncture 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). 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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 - biomedical homepage_url: https://datadryad.org/dataset/doi:10.5061/dryad.8q0s4 id: aeolus infores_id: aeolus last_modified_date: '2026-06-01T00:00:00Z' 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: 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 license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: AEOLUS Standardized FAERS Data original_source: - relation_type: prov:hadPrimarySource source: faers - relation_type: prov:hadPrimarySource source: aeolus product_url: https://datadryad.org/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 contacts: - category: Organization contact_details: - contact_type: url value: https://www.allotrope.org/ label: Allotrope Foundation creation_date: '2026-06-02T00:00:00Z' description: The Allotrope Foundation Ontology (AFO) is a suite of ontologies and controlled vocabularies from the Allotrope Foundation for representing laboratory analytical instruments, processes, materials, results, and related scientific data. domains: - chemistry and biochemistry - information technology homepage_url: https://www.allotrope.org/product-releases id: afo last_modified_date: '2026-06-02T00:00:00Z' 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: Allotrope Foundation Ontology products: - category: OntologyProduct description: Allotrope Foundation Ontology release information and access page for current AFO product releases. format: http id: afo.release latest_version: 2026/03 name: AFO Release Page original_source: - relation_type: prov:hadPrimarySource source: afo product_url: https://www.allotrope.org/product-releases - category: GraphicalInterface description: Ontobee browser page for the Allotrope Foundation Ontology. format: http id: afo.ontobee name: AFO Ontobee Browser original_source: - relation_type: prov:hadPrimarySource source: afo product_url: https://ontobee.org/ontology/AFO - category: GraphProduct description: RDF knowledge graph materialized by the MetaBoKG workflow from public metabolomics repository outputs, GNPS molecular-networking jobs, annotation evidence, sample metadata, and environmental and taxonomic context. The repository documents generated per-job Turtle files under mapping/kg and loading into Virtuoso named graphs. format: mixed id: metabokg.graph latest_version: arXiv v1 demonstration name: MetaboKG RDF Graph original_source: - relation_type: prov:hadPrimarySource source: metabokg - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubmedcentral - relation_type: prov:hadPrimarySource source: gnps - relation_type: prov:hadPrimarySource source: massive - relation_type: prov:hadPrimarySource source: redu product_url: https://github.com/HolobiomicsLab/MetaBoKG secondary_source: - relation_type: prov:used source: ms - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - relation_type: prov:used source: envo - relation_type: prov:used source: ncit - relation_type: prov:used source: uberon - relation_type: prov:used source: chmo - relation_type: prov:used source: sio - relation_type: prov:used source: prov-o - relation_type: prov:used source: dcat - relation_type: prov:used source: afo warnings: - No static public graph release or hosted endpoint was available in the GitHub repository when curated on 2026-06-02; the repository documents local Turtle materialization and Virtuoso loading. - category: DataModelProduct description: Turtle schema files defining MetaBoKG classes, properties, and ReDU class hierarchies used by the generated knowledge graph. format: ttl id: metabokg.schema license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: MetaBoKG RDF Schema original_source: - relation_type: prov:hadPrimarySource source: metabokg product_url: https://github.com/HolobiomicsLab/MetaBoKG/tree/main/Schema secondary_source: - relation_type: prov:wasInformedBy source: ms - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: envo - relation_type: prov:wasInformedBy source: ncit - relation_type: prov:wasInformedBy source: uberon - relation_type: prov:wasInformedBy source: chmo - relation_type: prov:wasInformedBy source: sio - relation_type: prov:wasInformedBy source: prov-o - relation_type: prov:wasInformedBy source: dcat - relation_type: prov:wasInformedBy source: afo synonyms: - AFO warnings: - Allotrope release packages may require access through Allotrope Foundation release pages rather than stable direct public ontology-file URLs. - 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 - organisms homepage_url: https://github.com/h3abionet/afpo id: afpo last_modified_date: '2026-06-27T00:00:00Z' 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) original_source: - relation_type: prov:hadPrimarySource source: afpo product_file_size: 96804 product_url: http://purl.obolibrary.org/obo/afpo.owl publications: [] repository: https://github.com/h3abionet/afpo - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.ars.usda.gov/ label: USDA Agricultural Research Service creation_date: '2026-07-01T00:00:00Z' description: The Agricultural Collaborative Research Outcomes System (AgCROS) is a USDA Agricultural Research Service "network of networks" that integrates multiple agricultural research databases into a single point of access. Its member networks include GRACEnet (Greenhouse gas Reduction through Agricultural Carbon Enhancement network), the Nutrient Uptake and Outcomes Network (NUOnet), Resilient Economic Agricultural Practices (REAP), the Long-Term Agroecosystem Research (LTAR) Network, and others. AgCROS holds field-level data on soil properties, greenhouse gas fluxes, crop yields, and management practices from long-term agricultural experiments, and serves as the primary upstream data source for the Soil Organic Carbon Knowledge Graph (SOCKG). domains: - agriculture - environment - general homepage_url: https://agcros-usdaars.opendata.arcgis.com/ id: agcros last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail license: id: '' label: U.S. Government Work (public domain) name: Agricultural Collaborative Research Outcomes System products: - category: GraphicalInterface description: The AgCROS open data portal, hosted on ArcGIS Hub, allows users to discover, analyze, and download data from the member research networks in formats including CSV, KML, Zip, GeoJSON, and GeoTIFF, along with GeoServices, WMS, and WFS API endpoints. format: http id: agcros.portal is_public: true name: AgCROS Open Data Portal original_source: - relation_type: prov:hadPrimarySource source: agcros product_url: https://agcros-usdaars.opendata.arcgis.com/ - category: GraphProduct description: The Soil Organic Carbon Knowledge Graph (SOCKG), an RDF knowledge graph integrating and mapping agricultural experimental data (soil properties, greenhouse gas fluxes, crop yields, and management practices) to support soil carbon modeling. Terminology is semantically aligned to the National Agricultural Library Thesaurus. format: rdfxml id: sockg.graph name: SOC-KG RDF Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: sockg - relation_type: prov:hadPrimarySource source: agcros product_url: https://idir.sockg.org/ secondary_source: - relation_type: prov:wasInfluencedBy source: nalt - activity_status: active category: Ontology collection: - obo-foundry - ber 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: '2026-06-13T00:00:00Z' 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: Agronomy Ontology products: - category: OntologyProduct description: Contains all AgrO terms and links to other relevant ontologies. format: owl id: agro.owl name: AgrO original_source: - relation_type: prov:hadPrimarySource source: agro product_file_size: 463598 product_url: http://purl.obolibrary.org/obo/agro.owl publications: - authors: - Medha Devare - Céline Aubert - Marie-Angélique Laporte - Léo Valette - Elizabeth Arnaud - Pier Luigi Buttigieg id: url:http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf journal: CEUR Workshop Proceedings title: 'Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics' year: '2016' - authors: - Medha Devare - Céline Aubert - Marie-Angélique Laporte - Léo Valette - Elizabeth Arnaud - Pier Luigi Buttigieg id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf journal: CEUR Workshop Proceedings title: 'Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.' year: '2016' 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. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology. domains: - anatomy and development homepage_url: https://github.com/insect-morphology/aism id: aism last_modified_date: '2026-06-27T00:00:00Z' 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 the Anatomy of the Insect SkeletoMuscular system (AISM) products: - category: OntologyProduct description: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) in OWL format format: owl id: aism.owl name: aism.owl original_source: - relation_type: prov:hadPrimarySource source: aism product_file_size: 1378303 product_url: http://purl.obolibrary.org/obo/aism.owl - category: OntologyProduct description: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) in OBO format format: obo id: aism.obo name: aism.obo original_source: - relation_type: prov:hadPrimarySource source: aism product_file_size: 896550 product_url: http://purl.obolibrary.org/obo/aism.obo - category: OntologyProduct description: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) in JSON format format: json id: aism.json name: aism.json original_source: - relation_type: prov:hadPrimarySource source: aism product_file_size: 929390 product_url: http://purl.obolibrary.org/obo/aism.json publications: - authors: - Girón JC - Tarasov S - González Montaña LA - Matentzoglu N - Smith AD - Koch M - Boudinot BE - Bouchard P - Burks R - Vogt L - Yoder M - Osumi-Sutherland D - Friedrich F - Beutel RG - Mikó I doi: 10.1093/sysbio/syad025 id: https://www.ncbi.nlm.nih.gov/pubmed/37094905 journal: Syst Biol preferred: true title: 'Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics' year: '2023' repository: https://github.com/insect-morphology/aism - 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: '2026-06-18T00:00:00Z' 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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'2026_03_06' - alliance_8.3.0_2023bb02_2025sep1_4.3.6 - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - 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Senior - Koray Kavukcuoglu - Pushmeet Kohli - Demis Hassabis doi: doi:10.1038/s41586-021-03819-2 id: doi:10.1038/s41586-021-03819-2 journal: Nature preferred: true title: Highly accurate protein structure prediction with AlphaFold year: '2021' - authors: - Mihaly Varadi - Stephen Anyango - Mandar Deshpande - Sreenath Nair - Cindy Natassia - Galabina Yordanova - David Yuan - Oana Stroe - Gemma Wood - Agata Laydon - Augustin Žídek - Tim Green - Kathryn Tunyasuvunakool - Stig Petersen - John Jumper - Ellen Clancy - Richard Green - Ankur Vora - Mira Lutfi - Michael Figurnov - Andrew Cowie - Nicole Hobbs - Pushmeet Kohli - Gerard Kleywegt - Ewan Birney - Demis Hassabis - Sameer Velankar doi: doi:10.1093/nar/gkab1061 id: doi:10.1093/nar/gkab1061 journal: Nucleic Acids Research title: 'AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models' year: '2022' repository: https://github.com/google-deepmind/alphafold - activity_status: active category: DataSource creation_date: '2026-06-15T00:00:00Z' description: AlphaMissense is a deep learning model from Google DeepMind that predicts the pathogenicity of missense variants across the human proteome. 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A practical projection of the full graph for human-centric biomedical use. 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biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 publications: - authors: - Jun Cheng - Guido Novati - Joshua Pan - Clare Bycroft - Akvilė Žemgulytė - Taylor Applebaum - Alexander Pritzel - Lai Hong Wong - Michal Zielinski - Tobias Sargeant - Rosalia G. Schneider - Andrew W. Senior - John Jumper - Demis Hassabis - Pushmeet Kohli - Žiga Avsec doi: doi:10.1126/science.adg7492 id: doi:10.1126/science.adg7492 journal: Science preferred: true title: Accurate proteome-wide missense variant effect prediction with AlphaMissense year: '2023' repository: https://github.com/google-deepmind/alphamissense taxon: - NCBITaxon:9606 - 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 - drug discovery - genomics evaluation_page: resource/alzkb/alzkb_eval_automated.html homepage_url: https://alzkb.ai/Home id: alzkb last_modified_date: '2026-06-22T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: alzkb - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dsstox - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hrpimp - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmacotherapydb - relation_type: prov:hadPrimarySource source: pid - 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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: DataSource contacts: - category: Organization contact_details: - contact_type: url value: http://www.aminode.org/ label: Aminode creation_date: '2026-06-17T00:00:00Z' description: Aminode performs evolutionary profiling of proteins and provides a user-friendly web tool for the routine and rapid inference of evolutionarily constrained regions (ECRs) in the human proteome, based on comparisons across many species. domains: - proteomics homepage_url: http://www.aminode.org/ id: aminode last_modified_date: '2026-06-17T00:00:00Z' layout: resource_detail name: Aminode products: - category: GraphicalInterface description: Web tool for inferring evolutionarily constrained regions in human proteins. format: http id: aminode.site is_public: true name: Aminode Website original_source: - relation_type: prov:hadPrimarySource source: aminode product_url: http://www.aminode.org/ - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: aminode - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: bitterdb - relation_type: prov:hadPrimarySource source: cdd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - 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relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ publications: - authors: - Kevin T. Chang - Junyan Guo - Alberto di Ronza - Marco Sardiello doi: 10.1038/s41598-018-19744-w id: https://doi.org/10.1038/s41598-018-19744-w journal: Scientific Reports preferred: true title: 'Aminode: Identification of Evolutionary Constraints in the Human Proteome' year: '2018' - 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: '2026-06-27T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: amphx 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 original_source: - relation_type: prov:hadPrimarySource source: amphx product_file_size: 8608 product_url: http://purl.obolibrary.org/obo/amphx.obo publications: - authors: - Stephanie Bertrand - João E. Carvalho - Delphine Dauga - Nicolas Matentzoglu - Vladimir Daric - Jr-Kai Yu - Michael Schubert - Hector Escrivá doi: 10.3389/fcell.2021.668025 id: https://pubmed.ncbi.nlm.nih.gov/33981708/ journal: Front Cell Dev Biol preferred: true title: The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX) year: '2021' repository: https://github.com/EBISPOT/amphx_ontology - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: url value: https://ncats.nih.gov/translator label: NCATS Translator creation_date: '2025-10-30T00:00:00Z' description: The Annotator Service is an NCATS Biomedical Data Translator service that provides detailed annotations for biomedical entities identified by CURIE. It aggregates metadata such as synonyms, descriptions, classifications, and cross-references from multiple knowledge sources (including BioThings services) to enhance entity understanding and interoperability across the Translator ecosystem. domains: - biomedical homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/Annotator-Service id: annotator infores_id: annotator last_modified_date: '2026-07-02T00:00:00Z' layout: resource_detail name: Annotator Service products: - category: GraphicalInterface description: Interactive Swagger UI for exploring and testing the Annotator Service REST API. format: http id: annotator.portal name: Translator Annotator API Documentation original_source: - relation_type: prov:hadPrimarySource source: annotator product_url: https://annotator.transltr.io/ - category: ProgrammingInterface connection_url: https://annotator.transltr.io description: Public HTTP REST API for CURIE-based biomedical entity annotation lookups (e.g. /curie/{curie}) in Translator, returning aggregated metadata as JSON. format: http id: annotator.api is_public: true name: Translator Annotator API original_source: - relation_type: prov:hadPrimarySource source: annotator product_url: https://annotator.transltr.io/openapi.json - activity_status: active category: Aggregator collection: - aop - ber 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: - toxicology - environment - pathways homepage_url: https://www.epa.gov/healthresearch/adverse-outcome-pathway-database-aop-db id: aop-db last_modified_date: '2026-06-22T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: aop-db product_url: https://www.epa.gov/healthresearch/adverse-outcome-pathway-database-aop-db - category: ProgrammingInterface connection_url: https://aopdb.rdf.bigcat-bioinformatics.org/ description: OpenRiskNet Virtuoso SPARQL endpoint loaded with RDF of the EPA AOP-DB for querying integrated AOP, gene, chemical, disease, tissue, pathway, orthology, ontology, and gene interaction relationships. format: http id: aop-db.sparql is_public: true name: AOP-DB SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: aop-wiki product_url: https://openrisknet.org/e-infrastructure/services/147/ - 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. format: http id: aop-db.data name: AOP-DB Data original_source: - relation_type: prov:hadPrimarySource source: 1000genomes - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: aop-wiki - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: toxcast product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 - category: DocumentationProduct description: The EPA Adverse Outcome Pathway Database (Aop-DB) Application User Manual format: pdf id: aop-db.manual name: Manual original_source: - relation_type: prov:hadPrimarySource 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 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-06-26: Error connecting to URL: (''Connection aborted.'', RemoteDisconnected(''Remote end closed connection without response''))' - 'File was not able to be retrieved when checked on 2026-06-22: Timeout connecting to URL' - 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')) - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - 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: - relation_type: prov:hadPrimarySource source: alzkb - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dsstox - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hrpimp - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmacotherapydb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - relation_type: prov:wasInfluencedBy source: hetionet - category: GraphProduct description: Memgraph data release for AlzKB. format: mixed id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - relation_type: prov:hadPrimarySource source: alzkb - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dsstox - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hrpimp - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmacotherapydb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - relation_type: prov:wasInfluencedBy source: hetionet publications: - authors: - Mortensen HM - Senn J - Levey T - Langley P - Williams AJ doi: 10.1038/s41597-021-00962-3 id: doi:10.1038/s41597-021-00962-3 journal: Scientific Data preferred: true title: The 2021 update of the EPA's adverse outcome pathway database year: '2021' - authors: - Pittman ME - Edwards SW - Ives C - Mortensen HM doi: 10.1016/j.taap.2018.02.006 id: doi:10.1016/j.taap.2018.02.006 journal: Toxicology and Applied Pharmacology title: 'AOP-DB: A database resource for the exploration of Adverse Outcome Pathways through integrated association networks' year: '2018' taxon: - NCBITaxon:9606 version: '2' - activity_status: active category: DataSource collection: - aop - ber 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: - toxicology - environment - pathways homepage_url: https://aopwiki.org/ id: aop-wiki last_modified_date: '2026-05-26T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: aop-wiki product_url: https://aopwiki.org/ - category: ProgrammingInterface connection_url: https://aopwiki-rdf.prod.openrisknet.org/ description: OpenRiskNet SPARQL endpoint loaded with RDF converted from AOP-Wiki quarterly XML dumps for querying AOPs, key events, key event relationships, and stressors. format: http id: aop-wiki.sparql is_public: true name: AOP-Wiki SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: aop-wiki product_url: https://openrisknet.org/e-infrastructure/services/133/ - 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 latest_version: '2026-04-01' name: AOP-Wiki Quarterly XML Snapshot original_source: - relation_type: prov:hadPrimarySource source: aop-wiki product_url: https://aopwiki.org/downloads - 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: - relation_type: prov:hadPrimarySource source: aop-wiki product_file_size: 9933339 product_url: https://aopwiki.org/downloads/aop-wiki-xml.gz - 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: - relation_type: prov:hadPrimarySource source: aop-wiki product_file_size: 238066 product_url: https://aopwiki.org/downloads/aop_ke_mie_ao.tsv - 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: - relation_type: prov:hadPrimarySource source: aop-wiki product_file_size: 189389 product_url: https://aopwiki.org/downloads/aop_ke_ker.tsv - 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: - relation_type: prov:hadPrimarySource source: aop-wiki product_file_size: 291132 product_url: https://aopwiki.org/downloads/aop_ke_ec.tsv - 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: - relation_type: prov:hadPrimarySource source: aop-wiki product_url: https://aopwiki.org/aops - 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 original_source: - relation_type: prov:hadPrimarySource source: aop-wiki product_url: https://aopwiki.org/handbooks/4 - 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. format: http id: aop-db.data name: AOP-DB Data original_source: - relation_type: prov:hadPrimarySource source: 1000genomes - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: aop-wiki - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: toxcast product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 - category: ProgrammingInterface connection_url: https://aopdb.rdf.bigcat-bioinformatics.org/ description: OpenRiskNet Virtuoso SPARQL endpoint loaded with RDF of the EPA AOP-DB for querying integrated AOP, gene, chemical, disease, tissue, pathway, orthology, ontology, and gene interaction relationships. format: http id: aop-db.sparql is_public: true name: AOP-DB SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: aop-wiki product_url: https://openrisknet.org/e-infrastructure/services/147/ - category: GraphProduct description: RDF knowledge graph (Turtle) repackaging AOP-Wiki data as an open knowledge graph format: ttl id: biobricks-aopwiki.graph name: BioBricks AOP-Wiki Graph original_source: - relation_type: prov:hadPrimarySource source: biobricks-aopwiki - relation_type: prov:wasDerivedFrom source: aop-wiki product_url: https://github.com/biobricks-ai/aopwikirdf-kg warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 404 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' taxon: - NCBITaxon:9606 version: '2.8' - 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 - phenotype homepage_url: http://www.yeastgenome.org/ id: apo last_modified_date: '2026-06-05T00:00:00Z' 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: Ascomycete phenotype ontology products: - category: OntologyProduct description: Ascomycete phenotype ontology in OWL format format: owl id: apo.owl name: apo.owl original_source: - relation_type: prov:hadPrimarySource source: apo 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 original_source: - relation_type: prov:hadPrimarySource source: apo product_file_size: 16797 product_url: http://purl.obolibrary.org/obo/apo.obo publications: - authors: - Costanzo MC - Skrzypek MS - Nash R - Wong E - Binkley G - Engel SR - Hitz B - Hong EL - Cherry JM - the Saccharomyces Genome Database Project doi: 10.1093/database/bap001 id: https://www.ncbi.nlm.nih.gov/pubmed/20157474 journal: Database (Oxford) title: New mutant phenotype data curation system in the Saccharomyces Genome Database year: '2009' 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: '2026-04-15T00:00:00Z' 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: Apollo Structured Vocabulary products: - category: OntologyProduct description: Apollo Structured Vocabulary in OWL format format: owl id: apollo_sv.owl name: apollo_sv.owl original_source: - relation_type: prov:hadPrimarySource source: apollo_sv product_file_size: 264551 product_url: http://purl.obolibrary.org/obo/apollo_sv.owl publications: - authors: - William R. Hogan - Michael M. Wagner - Mathias Brochhausen - John Levander - Shawn T. Brown - Nicholas Millett - Jay DePasse - Josh Hanna doi: 10.1186/s13326-016-0092-y id: https://doi.org/10.1186/s13326-016-0092-y journal: Journal of Biomedical Semantics title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation' year: '2016' 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 - information technology homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/ARAGORN id: aragorn infores_id: aragorn last_modified_date: '2026-06-01T00:00:00Z' layout: resource_detail license: id: https://opensource.org/license/mit/ label: MIT name: ARAGORN products: - category: ProgrammingInterface description: TRAPI-compliant API documentation for biomedical question answering format: http id: aragorn.api name: ARAGORN API original_source: - relation_type: prov:hadPrimarySource source: aragorn product_url: https://aragorn.renci.org/docs - category: GraphicalInterface description: Web interface for querying ARAGORN format: http id: aragorn.ui name: ARAGORN User Interface original_source: - relation_type: prov:hadPrimarySource 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 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: arax product_url: https://github.com/RTXteam/RTX/tree/master/code/ARAX/Examples publications: - authors: - Amy K Glen - Chunyu Ma - Luis Mendoza - Finn Womack - E C Wood - Meghamala Sinha - Liliana Acevedo - Lindsey G Kvarfordt - Ross C Peene - Shaopeng Liu - Andrew S Hoffman - Jared C Roach - Eric W Deutsch - Stephen A Ramsey - David Koslicki doi: 10.1093/bioinformatics/btad082 id: doi:10.1093/bioinformatics/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: DataSource 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: '2026-05-21T00:00:00Z' description: ARCHS4 is a Ma'ayan Lab resource for uniformly processed public RNA-seq data that provides gene and transcript count matrices, metadata search, and interactive exploration for large collections of human and mouse samples aggregated from GEO and SRA. domains: - biomedical - genomics homepage_url: https://archs4.org/ id: archs4 last_modified_date: '2026-06-01T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC BY-NC-SA 4.0 name: ARCHS4 products: - category: GraphicalInterface description: Web portal for metadata search, expression lookup, signature search, and interactive exploration of ARCHS4 sample and gene spaces format: http id: archs4.portal name: ARCHS4 Portal original_source: - relation_type: prov:hadPrimarySource source: archs4 product_url: https://archs4.org/ - category: DocumentationProduct description: ARCHS4 help page covering downloads, client packages, licensing, and citation information format: http id: archs4.help name: ARCHS4 Help original_source: - relation_type: prov:hadPrimarySource source: archs4 product_url: https://archs4.org/help - category: Product description: Latest human gene-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations format: hdf5 id: archs4.human.gene_counts name: ARCHS4 Human Gene Counts original_source: - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: geo - relation_type: prov:hadPrimarySource source: sra - relation_type: prov:wasDerivedFrom source: ensembl product_file_size: 61899310543 product_url: https://s3.dev.maayanlab.cloud/archs4/files/human_gene_v2.latest.h5 - category: Product description: Latest mouse gene-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations format: hdf5 id: archs4.mouse.gene_counts name: ARCHS4 Mouse Gene Counts original_source: - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: geo - relation_type: prov:hadPrimarySource source: sra - relation_type: prov:wasDerivedFrom source: ensembl product_file_size: 49065676268 product_url: https://s3.dev.maayanlab.cloud/archs4/files/mouse_gene_v2.latest.h5 - category: Product description: Latest human transcript-level ARCHS4 expression matrix in HDF5 format using Ensembl 107 annotations format: hdf5 id: archs4.human.transcript_counts name: ARCHS4 Human Transcript Counts original_source: - 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authors: - Lachmann A - Torre D - Keenan AB - Jagodnik KM - Lee HJ - Wang L - Silverstein MC - Ma'ayan A doi: 10.1038/s41467-018-03751-6 id: doi:10.1038/s41467-018-03751-6 journal: Nature Communications preferred: true title: Massive mining of publicly available RNA-seq data from human and mouse year: '2018' repository: https://github.com/MaayanLab/archs4 taxon: - NCBITaxon:9606 - NCBITaxon:10090 - 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. 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relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tcrd product_url: https://kg-hub.berkeleybop.io/kg-idg/current/kg-idg.tar.gz warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 404 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-01: HTTP 404 error. The kg-hub.berkeleybop.io host is being reorganized and KG-IDG downloads are pending relocation to a new home; no live download is currently available.' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' synonyms: - ATC - ATC/DDD - ATC/DDD Index - WHOCC ATC/DDD Index - activity_status: active category: Aggregator collection: - omop 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. Access to vocabulary selection and download workflows is mediated through the Athena web application rather than stable public download URLs. domains: - clinical - biomedical - information technology homepage_url: https://athena.ohdsi.org/ id: athena infores_id: athena last_modified_date: '2026-04-10T00:00:00Z' layout: resource_detail name: Athena products: - category: GraphicalInterface description: Web interface for searching and browsing standardized vocabularies; account login is required for download workflows format: http id: athena.web name: Athena Vocabulary Browser original_source: - relation_type: prov:hadPrimarySource source: athena product_url: https://athena.ohdsi.org/search-terms/start warnings: - Athena is an authenticated web application; access to vocabulary download workflows requires login. - category: Product description: Downloadable standardized vocabulary bundles for OMOP CDM assembled through the authenticated Athena web application format: csv id: athena.vocabularies name: Athena Vocabulary Downloads original_source: - relation_type: prov:hadPrimarySource source: athena - relation_type: prov:hadPrimarySource source: cdiscvocab - relation_type: prov:hadPrimarySource source: ciel - relation_type: prov:hadPrimarySource source: gemscript - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: medispan-gpi - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ndcd - relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: snomedct product_url: https://athena.ohdsi.org/vocabulary/list warnings: - Athena vocabulary downloads are prepared through the logged-in web application; stable direct public file URLs are not exposed. - category: MappingProduct description: Concept mappings between different terminology systems format: csv id: athena.mappings name: Athena Concept Mappings original_source: - relation_type: prov:hadPrimarySource source: athena - relation_type: prov:hadPrimarySource source: cdiscvocab - relation_type: prov:hadPrimarySource source: ciel - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: snomedct product_url: https://athena.ohdsi.org/search-terms/start warnings: - Athena mapping exports are accessed through the authenticated Athena web application; stable direct public file URLs are not exposed. - category: DataModelProduct description: OMOP Common Data Model specification and downloadable DDL artifacts maintained by the OHDSI community format: http id: ohdsi.omop_cdm name: OMOP Common Data Model original_source: - relation_type: prov:hadPrimarySource source: ohdsi product_url: https://ohdsi.github.io/CommonDataModel/ repository: https://github.com/OHDSI/CommonDataModel secondary_source: - relation_type: prov:wasInformedBy source: athena - category: GraphicalInterface description: Athena web application for searching OHDSI standardized vocabularies and preparing OMOP vocabulary downloads format: http id: ohdsi.athena name: OHDSI Athena Vocabulary Browser original_source: - relation_type: prov:hadPrimarySource source: athena - relation_type: prov:hadPrimarySource source: ohdsi product_url: https://athena.ohdsi.org/search-terms/start warnings: - Athena is an authenticated web application; access to vocabulary download workflows requires login. - category: Product description: Standardized vocabulary bundles for OMOP CDM assembled through the Athena authenticated web application format: csv id: ohdsi.athena_vocabularies name: OHDSI Standardized Vocabulary Downloads original_source: - relation_type: prov:hadPrimarySource source: athena - relation_type: prov:hadPrimarySource source: ohdsi product_url: https://athena.ohdsi.org/vocabulary/list warnings: - Athena vocabulary downloads are prepared through the logged-in web application; stable direct public file URLs are not exposed. synonyms: - Athena - OHDSI Athena taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.findhelp.org/ label: findhelp (formerly Aunt Bertha) creation_date: '2026-07-03T00:00:00Z' description: Aunt Bertha (now operating as findhelp) is a nationwide social care directory of free and reduced-cost health and human services, including food, housing, financial assistance, and other community programs. It provides structured records of service names, descriptions, contact information, locations, languages, cost, availability, hours, and service types. domains: - public health - general homepage_url: https://www.findhelp.org/ id: auntbertha last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: Aunt Bertha (findhelp) products: - category: GraphicalInterface description: Searchable web directory of free and reduced-cost social care services, including organizations, programs, locations, and hours. format: http id: auntbertha.site is_public: true name: findhelp Directory original_source: - relation_type: prov:hadPrimarySource source: auntbertha product_url: https://www.findhelp.org/ - category: GraphProduct description: DREAM-KG homelessness and social-services knowledge graph for the Philadelphia region, integrating social service directory records and provider reviews. Served via the DREAM-KG SPARQL and Triple Pattern Fragments endpoints. format: ttl id: dreamkg.graph is_public: true name: DREAM-KG Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: dreamkg - relation_type: prov:hadPrimarySource source: auntbertha - relation_type: prov:hadPrimarySource source: google-reviews product_url: https://dreamkg.com/ secondary_source: - relation_type: prov:wasInfluencedBy source: opendataphilly - 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: - biomedical 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: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: robokop product_url: https://stars.renci.org/var/plater/bl-4.2.1/RobokopKG/4901b2bc764444ea/ - category: GraphProduct description: Robokop Plus format: kgx-jsonl id: automat.robokopplus name: robokopplus original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: robokop product_url: https://stars.renci.org/var/plater/bl-3.1.2/RobokopPlus/ad8cb4d0a7ccc923/kgx_files/ - category: GraphProduct description: Biolink Automat format: kgx-jsonl id: automat.biolink name: biolink_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: biolink product_url: https://stars.renci.org/var/plater/bl-3.1.2/Biolink_Automat/329f8c92051c18d4/ - category: GraphProduct description: CTD Automat format: kgx-jsonl id: automat.ctd infores_id: automat-ctd name: ctd_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: ctd product_url: https://stars.renci.org/var/plater/bl-4.2.1/CTD_Automat/f92c663160ec5e36/ - category: GraphProduct description: DrugCentral Automat format: kgx-jsonl id: automat.drugcentral infores_id: automat-drug-central name: drugcentral_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: drugcentral product_url: https://stars.renci.org/var/plater/bl-4.2.1/DrugCentral_Automat/dec0617490b49c7a/ - category: GraphProduct description: GTEx Automat format: kgx-jsonl id: automat.gtex infores_id: automat-gtex name: gtex_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: gtex product_url: https://stars.renci.org/var/plater/bl-4.2.1/GTEx_Automat/a6448b9092bb81a1/ - category: GraphProduct description: GtoPdb Automat format: kgx-jsonl id: automat.gtopdb infores_id: automat-gtopdb name: gtopdb_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: gtopdb product_url: https://stars.renci.org/var/plater/bl-4.2.1/GtoPdb_Automat/0ea6074c824c2236/ - category: GraphProduct description: GWASCatalog Automat format: kgx-jsonl id: automat.gwascatalog infores_id: automat-gwas-catalog name: gwascatalog_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: gwascatalog product_url: https://stars.renci.org/var/plater/bl-4.2.1/GWASCatalog_Automat/e30aceb322a33462/ - category: GraphProduct description: Hetio Automat format: kgx-jsonl id: automat.hetio name: hetio_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: hetionet product_url: https://stars.renci.org/var/plater/bl-4.2.1/Hetio_Automat/85a5f53e63150e1e/ - category: GraphProduct description: HGNC Automat format: kgx-jsonl id: automat.hgnc infores_id: automat-hgnc name: hgnc_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: hgnc product_url: https://stars.renci.org/var/plater/bl-4.2.1/HGNC_Automat/dee31cfce74e5944/ - category: GraphProduct description: HMDB Automat format: kgx-jsonl id: automat.hmdb infores_id: automat-hmdb name: hmdb_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: hmdb product_url: https://stars.renci.org/var/plater/bl-4.2.1/HMDB_Automat/6715124699b6dbf0/ - category: GraphProduct description: HumanGOA Automat format: kgx-jsonl id: automat.humangoa infores_id: automat-human-goa name: humangoa_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: goa product_url: https://stars.renci.org/var/plater/bl-4.2.1/HumanGOA_Automat/06f107a4e9e8e547/ - category: GraphProduct description: IntAct Automat format: kgx-jsonl id: automat.intact infores_id: automat-intact name: intact_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: intact product_url: https://stars.renci.org/var/plater/bl-4.2.1/IntAct_Automat/e5b936f966a02c2c/ - category: GraphProduct description: PANTHER Automat format: kgx-jsonl id: automat.panther infores_id: automat-panther name: panther_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: panther product_url: https://stars.renci.org/var/plater/bl-4.2.1/PANTHER_Automat/c0189f14ba41da6c/ - category: GraphProduct description: PHAROS Automat format: kgx-jsonl id: automat.pharos infores_id: automat-pharos name: pharos_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: pharos product_url: https://stars.renci.org/var/plater/bl-4.2.1/PHAROS_Automat/d3068b509bf17ff3/ - category: GraphProduct description: STRING-DB Automat format: kgx-jsonl id: automat.stringdb name: stringdb_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: string product_url: https://stars.renci.org/var/plater/bl-4.2.1/STRING-DB_Automat/4ca5a0ce557e2c18/ - category: GraphProduct description: UberGraph Automat format: kgx-jsonl id: automat.ubergraph name: ubergraph_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://stars.renci.org/var/plater/bl-4.2.1/UbergraphRedundant_Automat/e6b3204fd3a04413/ repository: https://github.com/RobokopU24/ - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: email value: contact@bacdive.de id: dsmz-leibniz-institute-dsmz-german-collection-of-m label: BacDive 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: '2026-06-24T00:00:00Z' 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: BacDive products: - category: GraphicalInterface description: BacDive web interface for browsing, searching, and exploring standardized strain-level data for over 99,000 bacterial strains, including advanced search and the TAXplorer taxonomic exploration tool. format: http id: bacdive.portal name: BacDive Web Portal original_source: - relation_type: prov:hadPrimarySource source: bacdive product_url: https://bacdive.dsmz.de/ - category: ProgrammingInterface description: BacDive RESTful API for programmatic retrieval of strain data. Access requires free registration (publicly available credentials). format: http id: bacdive.api is_public: true name: BacDive API original_source: - relation_type: prov:hadPrimarySource source: bacdive product_url: https://api.bacdive.dsmz.de/ - category: ProgrammingInterface description: Example client packages and code for accessing the BacDive API from Python and R. format: http id: bacdive.client_examples is_public: true name: BacDive API Client Examples (Python/R) original_source: - relation_type: prov:hadPrimarySource source: bacdive product_url: https://api.bacdive.dsmz.de/client_examples - 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest - 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest - 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest - 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest - 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz - category: Product description: Trait data table listing all 140+ harmonized traits available in metaTraits, mapped to standardized ontologies. format: http id: metatraits.traits name: metaTraits Trait List original_source: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bv-brc - relation_type: prov:hadPrimarySource source: goldterms - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:hadPrimarySource source: progenomes product_url: https://metatraits.embl.de/traits - category: Product description: Family-level harmonized trait annotations aggregated for NCBI taxonomy in compressed TSV format. format: tsv id: metatraits.ncbi.family-summary name: metaTraits NCBI Family Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: ncbi - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 913932 product_url: https://www.bork.embl.de/~robbani/metatraits/ncbi_family_summary_no_predictions.tsv.gz - category: Product description: Genus-level harmonized trait annotations aggregated for NCBI taxonomy in compressed TSV format. format: tsv id: metatraits.ncbi.genus-summary name: metaTraits NCBI Genus Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: ncbi - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 2431808 product_url: https://www.bork.embl.de/~robbani/metatraits/ncbi_genus_summary_no_predictions.tsv.gz - category: Product description: Species-level harmonized trait annotations aggregated for NCBI taxonomy in compressed TSV format. format: tsv id: metatraits.ncbi.species-summary name: metaTraits NCBI Species Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: ncbi - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 6523019 product_url: https://www.bork.embl.de/~robbani/metatraits/ncbi_species_summary_no_predictions.tsv.gz - category: Product description: Family-level harmonized trait annotations aggregated for GTDB taxonomy in compressed TSV format. format: tsv id: metatraits.gtdb.family-summary name: metaTraits GTDB Family Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: gtdb - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 1513013 product_url: https://www.bork.embl.de/~robbani/metatraits/gtdb_family_summary_no_predictions.tsv.gz - category: Product description: Genus-level harmonized trait annotations aggregated for GTDB taxonomy in compressed TSV format. format: tsv id: metatraits.gtdb.genus-summary name: metaTraits GTDB Genus Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: gtdb - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 4965442 product_url: https://www.bork.embl.de/~robbani/metatraits/gtdb_genus_summary_no_predictions.tsv.gz - category: Product description: Species-level harmonized trait annotations aggregated for GTDB taxonomy in compressed TSV format. format: tsv id: metatraits.gtdb.species-summary name: metaTraits GTDB Species Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: gtdb - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 12570522 product_url: https://www.bork.embl.de/~robbani/metatraits/gtdb_species_summary_no_predictions.tsv.gz - category: GraphicalInterface description: MediaDive web portal for browsing, searching, comparing, and building microbial cultivation media recipes. format: http id: mediadive.portal name: MediaDive Web Portal original_source: - relation_type: prov:hadPrimarySource source: mediadive product_url: https://mediadive.dsmz.de/ secondary_source: - relation_type: prov:wasInformedBy source: bacdive - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - category: ProgrammingInterface description: MediaDive REST API documentation for programmatic retrieval of media, solutions, ingredients, strains, and related records. format: http id: mediadive.rest_api name: MediaDive REST API original_source: - relation_type: prov:hadPrimarySource source: mediadive product_url: https://mediadive.dsmz.de/doc/index.html secondary_source: - relation_type: prov:wasInformedBy source: bacdive - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - category: ProgrammingInterface description: MediaDive SPARQL endpoint for querying the DSMZ Digital Diversity RDF representation of MediaDive data. format: http id: mediadive.sparql name: MediaDive SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: mediadive product_url: https://sparql.dsmz.de/mediadive secondary_source: - relation_type: prov:wasInformedBy source: bacdive - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon publications: - authors: - Schober I - Koblitz J - Sardà Carbasse J - Ebeling C - Schmidt ML - Podstawka A - Gupta R - Ilangovan V - Chamanara J - Overmann J - Reimer LC doi: 10.1093/nar/gkae959 id: https://doi.org/10.1093/nar/gkae959 journal: Nucleic Acids Research preferred: true title: 'BacDive in 2025: the core database for prokaryotic strain data' year: '2025' repository: https://github.com/JKoblitz/bacdive-api taxon: - NCBITaxon:2 - activity_status: active category: DataSource collection: - ber 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: '2026-06-18T00:00:00Z' 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: BactoTraits products: - category: Product description: BactoTraits database with downloadable trait datasets format: http id: bactotraits.database is_public: true name: BactoTraits Database and Downloads original_source: - relation_type: prov:hadPrimarySource source: bactotraits 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 - 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authors: - Cébron A - Zeghal E - Usseglio-Polatera P - Meyer A - Bauda P - Lemmel F - Leyval C - Maunoury-Danger F doi: 10.1016/j.ecolind.2021.108047 id: https://doi.org/10.1016/j.ecolind.2021.108047 journal: Ecological Indicators preferred: true title: BactoTraits – A functional trait database to evaluate how natural and man-induced changes influence the assembly of bacterial communities year: '2021' synonyms: - BactoTraits - Bacterial Traits Database taxon: - NCBITaxon:2 - activity_status: active category: Ontology creation_date: '2026-06-15T00:00:00Z' description: The BioAssay Ontology (BAO) is a formal OWL-DL ontology that establishes common reference metadata terms and definitions for describing low- and high-throughput drug and probe screening assays and their results. It captures assay design, screening formats, detection technologies, perturbagens, biological targets, endpoints, and measured results, enabling integration, aggregation, retrieval, and analysis of bioassay data across resources such as PubChem and ChEMBL. BAO is modularized into reusable components covering biology, properties, and controlled vocabularies. domains: - drug discovery - pharmacology - biomedical homepage_url: http://bioassayontology.org/ id: bao last_modified_date: '2026-06-15T00:00:00Z' 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: BioAssay Ontology products: - category: OntologyProduct description: The complete BioAssay Ontology in OWL format, integrating the core ontology with its biology, properties, and vocabulary modules. format: owl id: bao.complete-owl name: BAO complete OWL original_source: - relation_type: prov:hadPrimarySource source: bao product_file_size: 39132 product_url: https://raw.githubusercontent.com/BioAssayOntology/BAO/master/bao_complete.owl - category: OntologyProduct description: The core BioAssay Ontology module in OWL format, containing the foundational BAO classes and relations. format: owl id: bao.core-owl name: BAO core OWL original_source: - 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A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - 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relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 publications: - authors: - Ubbo Visser - Saminda Abeyruwan - Uma Vempati - Robin P Smith - Vance Lemmon - Stephan C Schürer doi: doi:10.1186/1471-2105-12-257 id: doi:10.1186/1471-2105-12-257 journal: BMC Bioinformatics preferred: true title: 'BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results' year: '2011' - authors: - Saminda Abeyruwan - Uma D Vempati - Hande Küçük-McGinty - Ubbo Visser - Amar Koleti - Ahsan Mir - Kunie Sakurai - Caty Chung - Joshua A Bittker - Paul A Clemons - Steve Brudz - Anosha Siripala - Arturo J Morales - Martin Romacker - David Twomey - Svetlana Bureeva - Vance Lemmon - Stephan C Schürer doi: doi:10.1186/2041-1480-5-S1-S5 id: doi:10.1186/2041-1480-5-S1-S5 journal: Journal of Biomedical Semantics title: 'Evolving BioAssay Ontology (BAO): modularization, integration and applications' year: '2014' repository: https://github.com/BioAssayOntology/BAO - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: lidong.bprc@foxmail.com label: Dong Li - category: Individual contact_details: - contact_type: email value: liuzy1984@163.com label: Zhongyang Liu creation_date: '2026-02-18T00:00:00Z' description: BATMAN-TCM is a web resource and database for known and predicted interactions between traditional Chinese medicine ingredients and target proteins, supporting target prediction, enrichment analysis, and molecular-mechanism exploration for ingredients, herbs, and formulas. domains: - pharmacology - drug discovery - pathways homepage_url: http://bionet.ncpsb.org.cn/batman-tcm/ id: batman last_modified_date: '2026-06-01T00:00:00Z' layout: resource_detail name: BATMAN-TCM products: - category: GraphicalInterface description: Interactive BATMAN-TCM 2.0 web interface for querying traditional Chinese medicine ingredients, herbs, formulas, target proteins, and enriched pathways. format: http id: batman.web latest_version: '2.0' name: BATMAN-TCM Web Interface original_source: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - 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relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv publications: - authors: - Xiangren Kong - Chao Liu - Zuzhen Zhang - Meiqi Cheng - Zhijun Mei - Xiangdong Li - Peng Liu - Lihong Diao - Yajie Ma - Peng Jiang - Xiangya Kong - Shiyan Nie - Yingzi Guo - Ze Wang - Xinlei Zhang - Yan Wang - Liujun Tang - Shuzhen Guo - Zhongyang Liu - Dong Li doi: 10.1093/nar/gkad926 id: doi:10.1093/nar/gkad926 journal: Nucleic Acids Research preferred: true title: 'BATMAN-TCM 2.0: an enhanced integrative database for known and predicted interactions between traditional Chinese medicine ingredients and target proteins' year: '2024' - authors: - Zhongyang Liu - Feifei Guo - Yong Wang - Chun Li - Xinlei Zhang - Honglei Li - Lihong Diao - Jiangyong Gu - Wei Wang - Dong Li - Fuchu He doi: 10.1038/srep21146 id: doi:10.1038/srep21146 journal: Scientific Reports title: 'BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine' year: '2016' synonyms: - BATMAN - BATMAN-TCM - BATMAN-TCM 2.0 - Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine - activity_status: active category: Ontology collection: - obo-foundry - ber 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 - organisms homepage_url: https://github.com/BiodiversityOntologies/bco id: bco last_modified_date: '2026-06-05T00:00:00Z' 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: Biological Collections Ontology products: - 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Walls - John Deck - Robert Guralnick - Steve Baskauf - Reed Beaman - Stanley Blum - Shawn Bowers - Pier Luigi Buttigieg - Neil Davies - Dag Endresen - Maria Alejandra Gandolfo - Robert Hanner - Alyssa Janning - Leonard Krishtalka - Andréa Matsunaga - Peter Midford - Norman Morrison - Éamonn Ó. Tuama - Mark Schildhauer - Barry Smith - Brian J. Stucky - Andrea Thomer - John Wieczorek - Jamie Whitacre - John Wooley doi: 10.1371/journal.pone.0089606 id: https://doi.org/10.1371/journal.pone.0089606 journal: PLoS ONE title: 'Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies' year: '2014' 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 - general homepage_url: http://ifomis.org/bfo/ id: bfo infores_id: bfo last_modified_date: '2026-06-05T00:00:00Z' 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: Basic Formal Ontology products: - 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Gene Expression Database products: - category: GraphicalInterface description: Web interface for exploring Bgee data format: http id: bgee.site is_public: true name: Bgee Web Interface original_source: - relation_type: prov:hadPrimarySource source: bgee product_url: https://www.bgee.org/ - category: ProgrammingInterface description: SPARQL endpoint for querying Bgee RDF data format: http id: bgee.sparql is_public: true name: Bgee SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: bgee product_url: https://www.bgee.org/sparql/ - category: Product compression: zip description: Complete data dump of Bgee expression data for all species format: tsv id: bgee.expr_calls name: Bgee Expression Calls original_source: - relation_type: prov:hadPrimarySource source: bgee product_url: https://www.bgee.org/download/gene-expression-calls - category: Product compression: zip description: RDF version of the Bgee data for semantic web applications format: ttl id: bgee.rdf name: Bgee RDF Data original_source: - relation_type: prov:hadPrimarySource source: bgee product_file_size: 31556493880 product_url: https://www.bgee.org/ftp/current/rdf_easybgee.zip - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. format: http id: spoke.graph name: SPOKE Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: bv-brc - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: foodb - 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relation_type: prov:wasInfluencedBy source: 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. format: python id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: nihreporter - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: cellmarker - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: indra product_url: https://github.com/gyorilab/indra_cogex - 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relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: gtex product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ 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). format: mixed id: ibkh.graph name: iBKH Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drkg - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: ibkh - relation_type: prov:hadPrimarySource source: idisk - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for Bgee - Gene Expression Database distributed via the NCATS Translator release site (release 2026_03_06; build bgee_15.2_a4fc19df_2025sep1_4.3.6; source version 15.2; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 4654943 format: kgx-jsonl id: translator.bgee.graph latest_version: '2026_03_06' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Bgee KGX Graph node_count: 74689 original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/bgee/latest/ versions: - '2026_03_06' - bgee_15.2_a4fc19df_2025sep1_4.3.6 - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: ctd - 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A practical projection of the full graph for human-centric biomedical use. 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Moretti S - Tzivanopoulou M - Wollbrett J - Robinson-Rechavi M doi: 10.1093/nar/gkae1118 id: doi:10.1093/nar/gkae1118 journal: Nucleic Acids Research 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: 10.1093/nar/gkaa793 id: doi:10.1093/nar/gkaa793 journal: Nucleic Acids Research 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 - 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relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv publications: - authors: - King ZA - Lu JS - Dräger A - Miller PC - Federowicz S - Lerman JA - Ebrahim A - Palsson BO - Lewis NE doi: 10.1093/nar/gkv1049 id: doi:10.1093/nar/gkv1049 journal: Nucleic Acids Research 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 - contact_type: url value: https://www.bindingdb.org/rwd/bind/sendmail.jsp label: BindingDB - category: Organization contact_details: - contact_type: url value: https://pharmacy.ucsd.edu/ label: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego creation_date: '2025-06-04T00:00:00Z' description: BindingDB is a public, web-accessible database of measured binding affinities between small, drug-like molecules and protein targets, focusing on the interactions of proteins with small, drug-like molecules. It contains 3.0M data points for 1.3M compounds and 9.6K targets, serving as a crucial resource for drug discovery, pharmacology, and related fields. domains: - biomedical - drug discovery - chemistry and biochemistry - pharmacology fairsharing_id: FAIRsharing.3b36hk homepage_url: https://www.bindingdb.org/rwd/bind/index.jsp id: bindingdb infores_id: bindingdb last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: https://www.bindingdb.org/rwd/bind/info.jsp label: CC BY 4.0 name: BindingDB products: - category: Product compression: zip description: Full dataset containing all binding measurements in BindingDB with 2D compound structures format: sdf id: bindingdb.all_2d name: BindingDB All Data (2D structures) original_source: - relation_type: prov:hadPrimarySource source: bindingdb product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_All_2D_202507_sdf.zip - category: Product compression: zip description: Full dataset containing all binding measurements in BindingDB with 3D compound structures format: sdf id: bindingdb.all_3d name: BindingDB All Data (3D structures) original_source: - relation_type: prov:hadPrimarySource source: bindingdb product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_All_3D_202507_sdf.zip warnings: [] - category: Product compression: zip description: Full dataset containing all binding measurements in BindingDB in tab-separated values format format: tsv id: bindingdb.all_tsv name: BindingDB All Data (TSV) original_source: - relation_type: prov:hadPrimarySource source: bindingdb product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_All_202507_tsv.zip - category: Product compression: zip description: Data curated from articles by BindingDB with 2D compound structures format: sdf id: bindingdb.articles_2d name: BindingDB Articles Data (2D structures) original_source: - relation_type: prov:hadPrimarySource source: bindingdb product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_BindingDB_Articles_2D_202507_sdf.zip - category: Product compression: zip description: Data curated from articles by BindingDB with 3D compound structures format: sdf id: bindingdb.articles_3d name: BindingDB Articles Data (3D structures) original_source: - relation_type: prov:hadPrimarySource source: bindingdb product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_BindingDB_Articles_3D_202507_sdf.zip - category: Product compression: zip description: Data curated from articles by BindingDB in tab-separated values format format: tsv id: bindingdb.articles_tsv name: BindingDB Articles Data (TSV) original_source: - relation_type: prov:hadPrimarySource source: bindingdb product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_BindingDB_Articles_202507_tsv.zip - category: Product compression: zip description: Data in BindingDB drawn from ChEMBL with 2D compound structures format: sdf id: bindingdb.chembl_2d name: BindingDB ChEMBL Data (2D structures) original_source: - relation_type: prov:hadPrimarySource source: bindingdb product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_ChEMBL_2D_202507_sdf.zip warnings: [] - category: Product compression: zip description: Data in BindingDB drawn from ChEMBL with 3D compound structures format: sdf id: bindingdb.chembl_3d name: BindingDB ChEMBL Data (3D structures) original_source: - relation_type: prov:hadPrimarySource source: bindingdb product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_ChEMBL_3D_202507_sdf.zip warnings: [] - category: Product compression: zip description: Data in BindingDB drawn from ChEMBL in tab-separated values format format: tsv id: bindingdb.chembl_tsv name: BindingDB ChEMBL Data (TSV) original_source: - relation_type: prov:hadPrimarySource source: bindingdb product_url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?download_file=/rwd/bind/downloads/BindingDB_ChEMBL_202507_tsv.zip - 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relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: go-cam - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathbank - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: text-mining-kp - relation_type: prov:hadPrimarySource source: translator - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://kgx-storage.rtx.ai/releases/translator_kg/latest/ versions: - '2026_03_27' - 423af7989cac - category: GraphProduct compression: gzip description: PharMeBINet V2 JSON release published on February 6, 2024. format: json id: pharmebinet.json latest_version: v2 name: PharMeBINet JSON Release original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 1942958027 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_24_02_06.json.gz/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - 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category: GraphProduct compression: zip description: PharMeBINet V2 Neo4j database release published on February 6, 2024. format: neo4j id: pharmebinet.neo4j latest_version: v2 name: PharMeBINet Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 3847978577 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - 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category: GraphProduct compression: zip description: PharMeBINet V2 Neo4j dump release published on February 6, 2024. dump_format: neo4j format: neo4j id: pharmebinet.neo4j.dump latest_version: v2 name: PharMeBINet Neo4j Dump original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 3598325722 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_dump_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - 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relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://sugi.bio/biobtree/api/ - category: GraphProduct compatibility: - standard: biolink version: 4.2.1 compression: gzip description: Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - 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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - 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relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: bigg - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: ctrp - relation_type: prov:hadPrimarySource source: cmap - relation_type: prov:hadPrimarySource source: kinomescan - relation_type: prov:hadPrimarySource source: dsstoxdb - relation_type: prov:hadPrimarySource source: gelinea - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv - category: GraphProduct description: The SPOKE-OKN knowledge graph, an OKN-hosted RDF publication of the SPOKE biomedical and environmental health knowledge graph, served through FRINK query services. format: ttl id: spoke-okn.graph name: SPOKE-OKN Graph original_source: - relation_type: prov:hadPrimarySource source: spoke-okn - relation_type: prov:wasDerivedFrom source: spoke product_url: https://spoke.ucsf.edu secondary_source: - relation_type: prov:wasInfluencedBy source: bgee - relation_type: prov:wasInfluencedBy source: bindingdb - relation_type: prov:wasInfluencedBy source: bv-brc - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: civic - relation_type: prov:wasInfluencedBy source: cl - relation_type: prov:wasInfluencedBy source: clinicaltrialsgov - relation_type: prov:wasInfluencedBy source: diseases - relation_type: prov:wasInfluencedBy source: doid - relation_type: prov:wasInfluencedBy source: drugbank - relation_type: prov:wasInfluencedBy source: drugcentral - 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relation_type: prov:wasInfluencedBy source: sider - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikipathways - category: Product compression: gzip description: PubChem substance information in ASN.1 format format: xml id: pubchem.substances.asn name: PubChem Substances ASN original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/ASN/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways - category: Product compression: gzip description: PubChem substance information in SDF format format: sdf id: pubchem.substances.sdf name: PubChem Substances SDF original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways 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: Organization contact_details: - contact_type: url value: https://www.ai.sri.com/ label: SRI International, Artificial Intelligence Center creation_date: '2026-06-12T00:00:00Z' description: A knowledge base created from an introductory biology textbook domains: - biomedical homepage_url: https://www.ai.sri.com/~halo/public/exported-kb/biokb.html id: bio101 last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-nc-sa/3.0/ label: CC BY-NC-SA 3.0 name: KB Bio 101 products: - category: Product description: The full KB Bio 101 knowledge base exported from SRI's AURA system. It is offered as a downloadable archive in five logic serializations (first-order predicate logic, TPTP FOF, Answer Set Programming, SILK rule language, and OWL2), available as single-file or per-concept file versions. format: owl id: bio101.exported-kb license: id: https://creativecommons.org/licenses/by-nc-sa/3.0/ label: CC BY-NC-SA 3.0 name: KB Bio 101 Exported Knowledge Base original_source: - relation_type: prov:hadPrimarySource source: bio101 - relation_type: prov:wasDerivedFrom source: campbell-biology product_url: https://www.ai.sri.com/~halo/public/exported-kb/biokb.html publications: - authors: - Chaudhri VK - Cheng BH - Overholtzer A - Roschelle J - Spaulding A - Clark P - Greaves M - Gunning D doi: 10.1609/aimag.v34i3.2486 id: https://doi.org/10.1609/aimag.v34i3.2486 journal: AI Magazine preferred: true title: 'Inquire Biology: A Textbook that Answers Questions' year: '2013' - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: tom@insilica.co - contact_type: github value: tomlue label: Tom Luechtefeld - 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. 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: '2026-07-01T00:00:00Z' layout: resource_detail name: BioBricks AOP-Wiki products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks AOP-Wiki format: http id: biobricks-aopwiki.sparql name: BioBricks AOP-Wiki SPARQL original_source: - relation_type: prov:hadPrimarySource source: biobricks-aopwiki product_url: https://apps.okn.us/biobricks-aopwiki/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for BioBricks AOP-Wiki id: biobricks-aopwiki.tpf name: BioBricks AOP-Wiki TPF original_source: - relation_type: prov:hadPrimarySource source: biobricks-aopwiki product_url: https://apps.okn.us/ldf/biobricks-aopwiki - category: GraphProduct description: RDF knowledge graph (Turtle) repackaging AOP-Wiki data as an open knowledge graph format: ttl id: biobricks-aopwiki.graph name: BioBricks AOP-Wiki Graph original_source: - relation_type: prov:hadPrimarySource source: biobricks-aopwiki - relation_type: prov:wasDerivedFrom source: aop-wiki product_url: https://github.com/biobricks-ai/aopwikirdf-kg warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 404 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' 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 - contact_type: github value: tomlue label: Tom Luechtefeld - 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: '2026-07-01T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: BioBricks ICE products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks ICE format: http id: biobricks-ice.sparql name: BioBricks ICE SPARQL original_source: - relation_type: prov:hadPrimarySource source: biobricks-ice product_url: https://apps.okn.us/biobricks-ice/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for BioBricks ICE id: biobricks-ice.tpf name: BioBricks ICE TPF original_source: - relation_type: prov:hadPrimarySource source: biobricks-ice product_url: https://apps.okn.us/ldf/biobricks-ice - category: GraphProduct description: RDF knowledge graph repackaging ICE (Integrated Chemical Environment) cheminformatics and chemical safety data, built and published from the biobricks-okg repository. format: ttl id: biobricks-ice.graph name: BioBricks ICE Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: biobricks-ice - relation_type: prov:wasDerivedFrom source: ice product_url: https://github.com/biobricks-ai/biobricks-okg 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 - contact_type: github value: tomlue label: Tom Luechtefeld - 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. domains: - biomedical 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: '2026-07-01T00:00:00Z' layout: resource_detail name: BioBricks MeSH products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks MeSH format: http id: biobricks-mesh.sparql name: BioBricks MeSH SPARQL original_source: - relation_type: prov:hadPrimarySource source: biobricks-mesh product_url: https://apps.okn.us/biobricks-mesh/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for BioBricks MeSH id: biobricks-mesh.tpf name: BioBricks MeSH TPF original_source: - relation_type: prov:hadPrimarySource source: biobricks-mesh product_url: https://apps.okn.us/ldf/biobricks-mesh - category: GraphProduct description: RDF knowledge graph (Turtle) repackaging the MeSH biomedical vocabulary as an open knowledge graph format: ttl id: biobricks-mesh.graph name: BioBricks MeSH Graph original_source: - relation_type: prov:hadPrimarySource source: biobricks-mesh - relation_type: prov:wasDerivedFrom source: mesh product_url: https://github.com/biobricks-ai/mesh-kg warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 404 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' 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 - contact_type: github value: tomlue label: Tom Luechtefeld - 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. 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: '2026-07-01T00:00:00Z' layout: resource_detail name: BioBricks PubChem Annotations products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks PubChem Annotations format: http id: biobricks-pubchem-annotations.sparql name: BioBricks PubChem Annotations SPARQL original_source: - relation_type: prov:hadPrimarySource source: biobricks-pubchem-annotations product_url: https://apps.okn.us/biobricks-pubchem-annotations/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for BioBricks PubChem Annotations id: biobricks-pubchem-annotations.tpf name: BioBricks PubChem Annotations TPF original_source: - relation_type: prov:hadPrimarySource source: biobricks-pubchem-annotations product_url: https://apps.okn.us/ldf/biobricks-pubchem-annotations - category: GraphProduct description: RDF knowledge graph (Turtle) repackaging PubChem chemical annotations as an open knowledge graph format: ttl id: biobricks-pubchem-annotations.graph name: BioBricks PubChem Annotations Graph original_source: - relation_type: prov:hadPrimarySource source: biobricks-pubchem-annotations - relation_type: prov:wasDerivedFrom source: pubchem product_url: https://github.com/biobricks-ai/pubchem-annotations-kg 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 - contact_type: github value: tomlue label: Tom Luechtefeld - 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. 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: '2026-07-01T00:00:00Z' layout: resource_detail name: BioBricks Tox21 products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks Tox21 format: http id: biobricks-tox21.sparql name: BioBricks Tox21 SPARQL original_source: - relation_type: prov:hadPrimarySource source: biobricks-tox21 product_url: https://apps.okn.us/biobricks-tox21/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for BioBricks Tox21 id: biobricks-tox21.tpf name: BioBricks Tox21 TPF original_source: - relation_type: prov:hadPrimarySource source: biobricks-tox21 product_url: https://apps.okn.us/ldf/biobricks-tox21 - category: GraphProduct description: RDF knowledge graph repackaging EPA/NIH Tox21 high-throughput toxicology screening data, distributed via the biobricks-okg repository. format: ttl id: biobricks-tox21.graph name: BioBricks Tox21 Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: biobricks-tox21 - relation_type: prov:wasDerivedFrom source: tox21 product_url: https://github.com/biobricks-ai/biobricks-okg 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 - contact_type: github value: tomlue label: Tom Luechtefeld - 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. 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: '2026-07-01T00:00:00Z' layout: resource_detail name: BioBricks ToxCast products: - category: ProgrammingInterface description: SPARQL endpoint for BioBricks ToxCast format: http id: biobricks-toxcast.sparql name: BioBricks ToxCast SPARQL original_source: - relation_type: prov:hadPrimarySource source: biobricks-toxcast product_url: https://apps.okn.us/biobricks-toxcast/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for BioBricks ToxCast id: biobricks-toxcast.tpf name: BioBricks ToxCast TPF original_source: - relation_type: prov:hadPrimarySource source: biobricks-toxcast product_url: https://apps.okn.us/ldf/biobricks-toxcast - category: GraphProduct description: RDF knowledge graph (Turtle) repackaging EPA ToxCast high-throughput screening data as an open knowledge graph format: ttl id: biobricks-toxcast.graph name: BioBricks ToxCast Graph original_source: - relation_type: prov:hadPrimarySource source: biobricks-toxcast - relation_type: prov:wasDerivedFrom source: toxcast product_url: https://github.com/biobricks-ai/biobricks-okg repository: https://github.com/biobricks-ai/biobricks-okg - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: github value: tamerh label: Tamer Gur creation_date: '2026-06-15T00:00:00Z' description: BioBTree is a unified biomedical knowledge graph that integrates more than 70 primary data sources, including Ensembl, UniProt, PDB, ChEMBL, Reactome, and ClinVar, into a single queryable graph of cross-reference edges spanning genes, proteins, compounds, diseases, pathways, and clinical data. It lets users search, map, and traverse identifiers across databases with a chain-query syntax (for example, mapping a gene in Ensembl to UniProt proteins and on to PDB structures), and exposes the graph through a REST API, a Model Context Protocol (MCP) server, and a question-answering web interface for grounding LLM responses in structured biomedical data. domains: - biomedical - genomics - proteomics - pathways - drug discovery - clinical homepage_url: https://sugi.bio/biobtree/ id: biobtree last_modified_date: '2026-06-24T00:00:00Z' layout: resource_detail license: id: https://www.gnu.org/licenses/agpl-3.0.en.html label: AGPL-3.0 name: BioBTree products: - category: GraphProduct compatibility: - standard: biolink version: 4.2.1 compression: gzip description: Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - 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authors: - Tamer Gur doi: doi:10.12688/f1000research.17927.1 id: doi:10.12688/f1000research.17927.1 journal: F1000Research title: 'Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords' year: '2019' repository: https://github.com/tamerh/biobtree - 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. 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relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: progenomes - relation_type: prov:hadPrimarySource source: proteomehd - relation_type: prov:hadPrimarySource source: pubmedcentral - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: swissmodel - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wormbase product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz - 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: - relation_type: prov:hadPrimarySource source: imodulondb product_url: https://imodulondb.org/ secondary_source: - relation_type: prov:wasInformedBy source: biocyc - relation_type: prov:wasInformedBy source: string - 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: - relation_type: prov:hadPrimarySource source: imodulondb product_url: https://imodulondb.org/ secondary_source: - relation_type: prov:wasInformedBy source: biocyc - relation_type: prov:wasDerivedFrom source: sra - relation_type: prov:wasInformedBy source: string - category: GraphicalInterface description: Web interface for browsing and searching human metabolic pathways, genes, enzymes, reactions, and compounds within the BioCyc Pathway Tools environment. format: http id: humancyc.portal name: HumanCyc Web Portal original_source: - relation_type: prov:hadPrimarySource source: humancyc product_url: https://humancyc.org/ secondary_source: - relation_type: prov:wasInfluencedBy source: biocyc - category: Product description: Downloadable HumanCyc Pathway/Genome Database (PGDB) data, including pathways, reactions, enzymes, and compounds, available through the BioCyc download services. format: mixed id: humancyc.downloads name: HumanCyc Data Downloads original_source: - relation_type: prov:hadPrimarySource source: humancyc product_url: https://biocyc.org/download.shtml secondary_source: - relation_type: prov:wasInfluencedBy source: biocyc - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: aminode - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: bitterdb - relation_type: prov:hadPrimarySource source: cdd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: craft - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: ena - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: fabric - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: gard - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: geneorganizer - relation_type: prov:hadPrimarySource source: genomernai - relation_type: prov:hadPrimarySource source: glyconnect - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: gtrnadb - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: homologene - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hprd - relation_type: prov:hadPrimarySource source: humancyc - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: iid - relation_type: prov:hadPrimarySource source: imgt - relation_type: prov:hadPrimarySource source: innatedb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: lncbase - relation_type: prov:hadPrimarySource source: lncbook - relation_type: prov:hadPrimarySource source: lncipedia - relation_type: prov:hadPrimarySource source: lncrnadisease - relation_type: prov:hadPrimarySource source: malacards - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: medlineplus - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: mint - relation_type: prov:hadPrimarySource source: mirbase - relation_type: prov:hadPrimarySource source: mirgenedb - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: modomics - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: nextprot - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathwaycommons - relation_type: prov:hadPrimarySource source: paxdb - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pdbe - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pirsf - relation_type: prov:hadPrimarySource source: prosite - relation_type: prov:hadPrimarySource source: proteomicsdb - relation_type: prov:hadPrimarySource source: proteopedia - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubtator - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rfam - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: scop - relation_type: prov:hadPrimarySource source: sfld - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: silva - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: snodb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: snopy - relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 548527 product_url: https://skm.nib.si/downloads/pss/public/sbml - category: GraphProduct description: PSS model (v1.0.0, October 2023) in DOT Language format compatible with Graphviz. The live/current DOT export endpoint was retired upstream; this points to the latest published versioned DOT export. format: dot id: skm.pss.live.dot name: PSS Download (DOT, v1.0.0) original_source: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 405988 product_url: https://skm.nib.si/downloads/pss-version/v1.0.0/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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 2732107 product_url: https://skm.nib.si/downloads/ckn/v2-2023.06/edges - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 885747 product_url: https://skm.nib.si/downloads/ckn/v2-2023.06/nodes - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 318666 product_url: https://skm.nib.si/downloads/ckn/v1-2018.06/edges - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 702407 product_url: https://skm.nib.si/downloads/ckn/v1-2018.06/nodes publications: - authors: - Karp PD - Billington R - Caspi R - Fulcher CA - Latendresse M - Kothari A - Keseler IM - Krummenacker M - Midford PE - Ong Q - Ong WK - Paley SM - Subhraveti P doi: 10.1093/bib/bbx085 id: https://www.ncbi.nlm.nih.gov/pubmed/29447345 journal: Brief Bioinform preferred: true title: The BioCyc collection of microbial genomes and metabolic pathways year: '2019' taxon: - NCBITaxon:2759 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://biofactoid.org/ label: Bader Lab, University of Toronto (Pathway Commons) creation_date: '2026-06-03T00:00:00Z' description: Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of the molecular-level interactions between genes, gene products, and chemical compounds described in their publications. Author-sourced pathway knowledge is grounded to standard identifiers and made openly available in computable formats for reuse in pathway and network analysis. domains: - pathways - biological systems - systems biology homepage_url: https://biofactoid.org/ id: biofactoid last_modified_date: '2026-06-05T00:00:00Z' 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: Biofactoid products: - category: GraphicalInterface description: Web application where authors create a digital profile of their article's molecular interactions and browse shared pathway documents. format: http id: biofactoid.webapp name: Biofactoid Web Application original_source: - relation_type: prov:hadPrimarySource source: biofactoid product_url: https://biofactoid.org/ - category: Product description: Openly downloadable author-contributed pathway documents, exportable in Biofactoid's native JSON format as well as BioPAX and SBGNML standards. format: json id: biofactoid.documents name: Biofactoid Pathway Documents original_source: - relation_type: prov:hadPrimarySource source: biofactoid product_url: https://biofactoid.org/ - category: ProgrammingInterface description: Public API (documented via Swagger UI) for programmatic access to Biofactoid pathway documents. format: http id: biofactoid.api is_public: true name: Biofactoid API original_source: - relation_type: prov:hadPrimarySource source: biofactoid product_url: https://biofactoid.org/api - category: Product compression: gzip description: PC v14 integrated BioPAX Level 3 unified model containing normalized pathway data, molecular interactions, cross-database entity mappings, and metadata-derived content from 26 datasource rows. format: biopax id: pathwaycommons.biopax name: Integrated BioPAX Model original_source: - relation_type: prov:hadPrimarySource source: pathwaycommons product_file_size: 1700903742 product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/pc-biopax.owl.gz secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: unichem - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: humancyc - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: dip - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: intact - relation_type: prov:wasDerivedFrom source: bind - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: Product description: Download directory for Pathway Commons PC v14 integrated pathway and molecular interaction datasets, including BioPAX, SIF, GMT, TXT, and JSON-LD products. format: mixed id: pathwaycommons.downloads name: Pathway Commons Data Downloads original_source: - relation_type: prov:hadPrimarySource source: pathwaycommons product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/ secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: unichem - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: humancyc - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: dip - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: intact - relation_type: prov:wasDerivedFrom source: bind - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: Product compression: gzip description: PC v14 Simple Interaction Format network file representing binary pairwise molecular relationships integrated from Pathway Commons upstream datasource rows. format: sif id: pathwaycommons.sif name: SIF Network Format original_source: - 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relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: dip - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: intact - relation_type: prov:wasDerivedFrom source: bind - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid publications: - authors: - Jeffrey V Wong - Max Franz - Metin Can Siper - Dylan Fong - Funda Durupinar - Christian Dallago - Augustin Luna - John Giorgi - Igor Rodchenkov - Özgün Babur - John A Bachman - Benjamin M Gyori - Emek Demir - Gary D Bader - Chris Sander doi: 10.7554/eLife.68292 id: https://doi.org/10.7554/eLife.68292 journal: eLife title: 'Science Forum: Author-sourced capture of pathway knowledge in computable form using Biofactoid' year: '2021' repository: https://github.com/PathwayCommons/factoid synonyms: - Factoid tags: - biopragmatics - 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. 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relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ 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: '2026-06-18T00:00:00Z' 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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 original_source: - 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Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - 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relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - 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biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - category: GraphProduct compression: targz description: KGX Distribution of KG-Alzheimers format: kgx id: kg-alzheimers.graph name: KGX Distribution of KG-Alzheimers original_source: - relation_type: prov:hadPrimarySource source: kg-alzheimers - relation_type: prov:hadPrimarySource source: monarchinitiative - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: zfin - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: mesh product_file_size: 210868256 product_url: https://kg-hub.berkeleybop.io/kg-alzheimers/current/kg-alzheimers.tar.gz warnings: - File was not able to be retrieved when checked on 2026-07-01; no live download location was found (GitHub releases, kghub.io/current, and Zenodo all return 404 or have no published artifact). - category: GraphProduct description: KGX distribution of the SRI-Reference KG format: kgx id: sri-reference-kg.graph name: SRI-Reference KG (KGX distribution) original_source: - relation_type: prov:hadPrimarySource source: sri-reference-kg - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: wormbase - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: zfin - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bspo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ddanat - relation_type: prov:hadPrimarySource source: ddpheno - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: dpo - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: emapa - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: foodon - relation_type: prov:hadPrimarySource source: fypo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: nbo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: upheno - relation_type: prov:hadPrimarySource source: wbbt - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: wbphenotype - relation_type: prov:hadPrimarySource source: xao - relation_type: prov:hadPrimarySource source: xpo - relation_type: prov:hadPrimarySource source: zfa - relation_type: prov:hadPrimarySource source: zfs - relation_type: prov:hadPrimarySource source: zp - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: decipher - relation_type: prov:hadPrimarySource source: mmrrc - relation_type: prov:hadPrimarySource source: cureid - relation_type: prov:hadPrimarySource source: phenopacket-store product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz - category: GraphProduct description: Live TRAPI/BioThings metadata endpoint for the Multiomics BigGIM-DrugResponse KP, exposing the multiomics knowledge graph served by the Multiomics Provider (built from GTEx, TCGA, and drug-response data, with additional clinical-trials, drug-approval and knowledge-resource inputs). format: json id: multiomics-kp.graph name: Multiomics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: multiomics-kp - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcga - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: dailymed - relation_type: prov:hadPrimarySource source: faers product_url: https://biothings.transltr.io/biggim_drugresponse_kp/metadata secondary_source: - relation_type: prov:wasInfluencedBy source: aact - relation_type: prov:wasInfluencedBy source: biogrid - relation_type: prov:wasInfluencedBy source: huri - relation_type: prov:wasInfluencedBy source: cellmarker - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: ttd - relation_type: prov:wasInfluencedBy source: pubmed publications: - authors: - Rose Oughtred - Jennifer Rust - Christie Chang - Bobby‐Joe Breitkreutz - Chris Stark - Andrew Willems - Lorrie Boucher - Genie Leung - Nadine Kolas - Frederick Zhang - Sonam Dolma - Jasmin Coulombe‐Huntington - Andrew Chatr‐aryamontri - Kara Dolinski - Mike Tyers doi: 10.1002/pro.3978 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: '2021' - authors: - Rose Oughtred - Chris Stark - Bobby-Joe Breitkreutz - Jennifer Rust - Lorrie Boucher - Christie Chang - Nadine Kolas - Lara O’Donnell - Genie Leung - Rochelle McAdam - Frederick Zhang - Sonam Dolma - Andrew Willems - Jasmin Coulombe-Huntington - Andrew Chatr-aryamontri - Kara Dolinski - Mike Tyers doi: 10.1093/nar/gky1079 id: https://doi.org/10.1093/nar/gky1079 journal: Nucleic Acids Research title: 'The BioGRID interaction database: 2019 update' year: '2019' - authors: - C. Stark doi: 10.1093/nar/gkj109 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: - biomedical - public health evaluation_page: resource/biohealth/biohealth_eval_automated.html homepage_url: https://frink.renci.org/registry/kgs/biohealth/ id: biohealth last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail name: Bio-Health KG products: - category: ProgrammingInterface description: SPARQL endpoint for Bio-Health KG format: http id: biohealth.sparql name: Bio-Health KG SPARQL original_source: - relation_type: prov:hadPrimarySource source: biohealth product_url: https://apps.okn.us/biohealth/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for Bio-Health KG id: biohealth.tpf name: Bio-Health KG TPF original_source: - relation_type: prov:hadPrimarySource source: biohealth product_url: https://apps.okn.us/ldf/biohealth - 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: - general homepage_url: https://biolink.github.io/biolink-model/ id: biolink last_modified_date: '2026-06-27T00:00:00Z' 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: Biolink-Model products: - category: DocumentationProduct description: Biolink Model Documentation format: http id: biolink.docs name: Biolink Model Documentation original_source: - relation_type: prov:hadPrimarySource source: biolink product_url: https://biolink.github.io/biolink-model/ - 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: - relation_type: prov:hadPrimarySource source: biolink product_url: https://biolink.github.io/information-resource-registry/ - 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: - relation_type: prov:hadPrimarySource source: biolink product_file_size: 717005 product_url: https://w3id.org/biolink/biolink-model.owl.ttl 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: - relation_type: prov:hadPrimarySource source: biolink product_file_size: 138288 product_url: https://w3id.org/biolink/biolink-model.json 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: - relation_type: prov:hadPrimarySource source: biolink product_file_size: 18600 product_url: https://raw.githubusercontent.com/biolink/biolink-model/refs/heads/master/project/protobuf/biolink_model.proto 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: - relation_type: prov:hadPrimarySource source: biolink product_file_size: 161190 product_url: https://raw.githubusercontent.com/biolink/biolink-model/refs/heads/master/project/shacl/biolink_model.shacl.ttl 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: - relation_type: prov:hadPrimarySource source: biolink product_file_size: 17816 product_url: https://raw.githubusercontent.com/biolink/biolink-model/refs/heads/master/project/shex/biolink_model.shex 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: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: biolink product_url: https://stars.renci.org/var/plater/bl-3.1.2/Biolink_Automat/329f8c92051c18d4/ - 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: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: cpathkg - relation_type: prov:hadPrimarySource source: kg-monarch product_url: https://gitlab.c-path.org/c-pathontology/c-path-knowledge-graph-integration - description: The MechRepoNet knowledge graph in its original format format: mixed id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: complexportal - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: mechreponet - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: unii product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication - category: ProgrammingInterface description: Plover-hosted TRAPI web API for querying the Multiomics Microbiome knowledge graph format: http id: microbiomekg.api is_public: true name: MicrobiomeKG Plover TRAPI API original_source: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: eupathdb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: microbiomekg - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://multiomics.transltr.io/mbkp - category: Product description: Co-occurrence database generated from public PubMed abstracts with entity normalization for Biolink-relevant biomedical concepts format: mixed id: omnicorp.cooccurrence name: OmniCorp Co-occurrence Data original_source: - relation_type: prov:hadPrimarySource source: omnicorp - relation_type: prov:hadPrimarySource source: pubmed product_url: https://github.com/NCATSTranslator/Translator-All/wiki/OmniCorp secondary_source: - relation_type: prov:used source: biolink - category: ProgrammingInterface description: API behavior documented for adding co-occurrence counts and literature co-occurrence edges to TRAPI messages format: http id: omnicorp.api name: OmniCorp API original_source: - relation_type: prov:hadPrimarySource source: omnicorp - relation_type: prov:hadPrimarySource source: pubmed product_url: https://github.com/NCATSTranslator/Translator-All/wiki/OmniCorp secondary_source: - relation_type: prov:used source: biolink warnings: - The registry points to the Translator wiki documentation; checked RENCI OmniCorp service URLs were unavailable or had certificate issues on 2026-06-02. - category: ProgrammingInterface description: TRAPI 1.4 API for predicted drug treatments, drug-disease associations, similar entities, model metadata, and explanation endpoints format: http id: openpredict.api name: OpenPredict API original_source: - relation_type: prov:hadPrimarySource source: openpredict product_url: https://openpredict.semanticscience.org/docs secondary_source: - relation_type: prov:used source: biolink - relation_type: prov:used source: drugbank - relation_type: prov:used source: go - relation_type: prov:used source: hp - relation_type: prov:used source: kegg - relation_type: prov:used source: mesh - relation_type: prov:used source: omim 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: 10.1111/cts.13302 id: doi:10.1111/cts.13302 journal: Clinical and Translational Science 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://biomarkerkb.org/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: - biomedical - biological systems evaluation_page: resource/biomarker/biomarker_eval_automated.html homepage_url: https://biomarkerkb.org/ id: biomarker last_modified_date: '2026-07-14T00:00:00Z' 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: GraphicalInterface description: Public web portal for BiomarkerKB providing keyword search, filtering, data downloads, and interactive graph visualization of biomarker-condition associations. format: http id: biomarker.portal name: BiomarkerKB Web Portal original_source: - relation_type: prov:hadPrimarySource source: biomarker product_url: https://biomarkerkb.org/ - category: Product description: Downloadable BiomarkerKB datasets, including per-condition datasets and full data dumps of curated biomarker-condition associations in JSON format. format: json id: biomarker.downloads name: BiomarkerKB Data Downloads original_source: - relation_type: prov:hadPrimarySource source: biomarker product_url: https://data.biomarkerkb.org/ - category: ProgrammingInterface description: Backend REST API that powers the BiomarkerKB web portal and provides programmatic access to biomarker records and the biomarker ID assignment system. format: http id: biomarker.api is_public: true name: BiomarkerKB API original_source: - relation_type: prov:hadPrimarySource source: biomarker product_url: https://api.biomarkerkb.org/ - category: GraphProduct description: Neo4j knowledge graph built from curated BiomarkerKB data and integrated into the CFDE Unified Biomedical Knowledge Graph (UBKG). The initial release comprises over 300,000 nodes and 1.2 million edges. edge_count: 1200000 format: neo4j id: biomarker.kg name: BiomarkerKB Knowledge Graph node_count: 300000 original_source: - relation_type: prov:hadPrimarySource source: biomarker product_url: https://github.com/clinical-biomarkers/Knowledge-Graph secondary_source: - relation_type: prov:wasInfluencedBy source: ubkg - category: OntologyProduct description: The Ontology for Biomarkers of Clinical Interest (OBCI), which formally defines biomarkers for diseases, phenotypes, and effects used to structure BiomarkerKB. format: owl id: biomarker.obci name: Ontology for Biomarkers of Clinical Interest (OBCI) original_source: - relation_type: prov:hadPrimarySource source: biomarker product_url: https://github.com/clinical-biomarkers/OBCI - category: DataModelProduct description: The community-developed BiomarkerKB data model (data dictionary and derived JSON schema) that harmonizes biomarker knowledge across diverse biological data types, following the FDA-NIH BEST biomarker definition. format: json id: biomarker.datamodel name: BiomarkerKB Data Model original_source: - relation_type: prov:hadPrimarySource source: biomarker product_url: https://github.com/clinical-biomarkers/biomarker-partnership - 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ publications: - authors: - Daniall Masood - Mariia Kim - Jeet Vora - Robel Kahsay - Patrick McNeeley - Sean Kim - Sujeet Kulkarni - Darren A. Natale - Srinivasan Ramachandran - Shakti Gupta - Mano Maurya - Cristian G. Bologa - Thomas S. DeNapoli - Vincent T. Metzger - Praveen Kumar - Nasheath Ahmed - John Erol Evangelista - Sean C. Kelly - Jorge L. Sepulveda - Avi Ma'ayan - Jonathan Silverstein - Deanne M. Taylor - Daniel J. Crichton - Ashish Mahabal - Jeremy J. Yang - Christophe G. Lambert - Shankar Subramaniam - Mike Tiemeyer - Rene Ranzinger - Raja Mazumder doi: 10.64898/2026.01.26.701395 id: doi:10.64898/2026.01.26.701395 journal: bioRxiv preferred: true title: 'BiomarkerKB: An Integrated Knowledgebase Supporting Biomarker-Centric Exploration of Biomedical Data' year: '2026' repository: https://github.com/clinical-biomarkers - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: jeetvora@gwu.edu - contact_type: github value: jeet-vora label: Jeet Vora - category: Organization contact_details: - contact_type: email value: avi.maayan@mssm.edu label: MaayanLab creation_date: '2025-05-04T00:00:00Z' description: The BiomarkerKB knowledge graph is a structured network that connects biomarkers to diseases, drugs, biological entities, and evidence from the scientific literature. domains: - biomedical - biological systems evaluation_page: resource/biomarkerkg/biomarkerkg_eval_automated.html homepage_url: https://biomarkerkb.org/home/ id: biomarkerkg last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail name: BiomarkerKB KG products: - category: GraphicalInterface description: Web interface to explore and query the Biomarker Knowledge Graph format: http id: biomarkerkg.site name: BKG Explorer original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg product_url: https://bkg.dev.maayanlab.cloud/ - category: GraphProduct compression: zip description: Nodes from Uber-Anatomy Ontology format: csv id: biomarkerkg.nodes.anatomy name: BKG Anatomy Nodes original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: uberon product_file_size: 332 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Anatomy.nodes.zip - category: GraphProduct compression: zip description: Nodes from GlyGen Biomarker Database format: csv id: biomarkerkg.nodes.biomarker name: BKG Biomarker Nodes original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: glygen product_file_size: 1252064 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Biomarker.nodes.zip - category: GraphProduct compression: zip description: Nodes from PubChem Database format: csv id: biomarkerkg.nodes.compound name: BKG Compound Nodes original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: pubchem product_file_size: 871 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Compound.nodes.zip - category: GraphProduct compression: zip description: Nodes from Human Disease Ontology format: csv id: biomarkerkg.nodes.condition name: BKG Condition Nodes original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: doid product_file_size: 5501 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Condition.nodes.zip - category: GraphProduct compression: zip description: Nodes from OBCI format: csv id: biomarkerkg.nodes.role name: BKG Role Nodes original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: obci product_file_size: 276 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Role.nodes.zip - category: GraphProduct compression: zip description: Nodes from dbSNP format: csv id: biomarkerkg.nodes.variant name: BKG Variant Nodes original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: dbsnp product_file_size: 782975 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Variant.nodes.zip - 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: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: uberon product_file_size: 1229 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Anatomy.edges.zip - 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: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: pubchem product_file_size: 1333 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Compound.edges.zip - 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: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: doid product_file_size: 1204603 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Condition.edges.zip - category: GraphProduct compression: zip description: Biomarker to Role relationships (has_best_classification) format: csv id: biomarkerkg.edges.role name: BKG Role Edges original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: obci product_file_size: 355306 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Role.edges.zip - 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: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: dbsnp product_file_size: 1067491 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Variant.edges.zip - category: ProgrammingInterface description: SPARQL endpoint for BiomarkerKB KG id: biomarkerkg.sparql name: BiomarkerKB KG SPARQL original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg product_url: https://apps.okn.us/biomarkerkg/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for BiomarkerKB KG id: biomarkerkg.tpf name: BiomarkerKB KG TPF original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg product_url: https://apps.okn.us/ldf/biomarkerkg repository: https://github.com/MaayanLab/BiomarkerKG - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://hivelab.biochemistry.gwu.edu/ label: GW HIVE Lab creation_date: '2026-06-02T00:00:00Z' description: BioMuta is a cancer-associated single-nucleotide variation resource that integrates mutation records from cancer genomics sources into a unified dataset with protein and disease annotations. domains: - biomedical - genomics - precision medicine homepage_url: https://hivelab.biochemistry.gwu.edu/biomuta id: biomuta last_modified_date: '2026-06-03T00:00:00Z' layout: resource_detail name: BioMuta products: - category: GraphicalInterface description: Production BioMuta web interface hosted by the GW HIVE Lab for exploring cancer-associated mutation records. id: biomuta.portal name: BioMuta Web Portal original_source: - relation_type: prov:hadPrimarySource source: biomuta product_url: https://hivelab.biochemistry.gwu.edu/biomuta - category: Product description: Unified BioMuta cancer mutation dataset produced by combining mutation records from TCGA, ICGC, CIViC, and COSMIC into a common field structure. format: csv id: biomuta.dataset name: BioMuta Cancer Mutation Dataset original_source: - relation_type: prov:hadPrimarySource source: biomuta product_url: https://biomuta.readthedocs.io/en/latest/ secondary_source: - relation_type: prov:wasDerivedFrom source: civic - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: icgc - relation_type: prov:wasDerivedFrom source: tcga - category: ProcessProduct description: BioMuta v5 data release pipeline for downloading, converting, and combining cancer mutation source files into BioMuta datasets. id: biomuta.pipeline name: BioMuta Data Release Pipeline original_source: - relation_type: prov:hadPrimarySource source: biomuta product_url: https://biomuta.readthedocs.io/en/latest/ repository: https://github.com/GW-HIVE/biomuta - category: Product compression: zip description: Complete PTMD 2.0 PTM-disease association download in tab-delimited format format: tsv id: ptmd.total_pda name: PTMD Total PTM-Disease Associations original_source: - relation_type: prov:hadPrimarySource source: ptmd product_file_size: 4756362 product_url: https://ptmd.biocuckoo.cn/Download/Total.zip secondary_source: - relation_type: prov:wasDerivedFrom source: activedriverdb - relation_type: prov:wasDerivedFrom source: biomuta - relation_type: prov:wasDerivedFrom source: phosphositeplus publications: - authors: - Hayley M Dingerdissen - John Torcivia-Rodriguez - Yu Hu - Ting-Chia Chang - Raja Mazumder - Robel Kahsay doi: 10.1093/nar/gkx907 id: doi:10.1093/nar/gkx907 journal: Nucleic Acids Research preferred: true title: 'BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery' year: '2018' repository: https://github.com/GW-HIVE/biomuta taxon: - NCBITaxon:9606 - 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: - relation_type: prov:hadPrimarySource 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: Frontiers in Pharmacology 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 contacts: - category: Organization contact_details: - contact_type: email value: support@bioontology.org - contact_type: url value: https://www.bioontology.org/ label: National Center for Biomedical Ontology (NCBO), Stanford 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 - general homepage_url: https://bioportal.bioontology.org/ 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 original_source: - relation_type: prov:hadPrimarySource source: bioportal 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 original_source: - relation_type: prov:hadPrimarySource source: bioportal 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: - 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relation_type: prov:wasInfluencedBy source: bioportal - category: GraphicalInterface description: NCBO BioPortal entry for browsing and exploring the GlycoRDF ontology format: http id: glycordf.bioportal name: GlycoRDF BioPortal Entry original_source: - relation_type: prov:hadPrimarySource source: glycordf product_url: https://bioportal.bioontology.org/ontologies/GLYCORDF secondary_source: - relation_type: prov:wasInfluencedBy source: bioportal publications: - authors: - Jennifer Vendetti - Nomi L Harris - Michael V Dorf - Alex Skrenchuk - J Harry Caufield - Rafael S Gonçalves - John B Graybeal - Harshad Hegde - Timothy Redmond - Christopher J Mungall - Mark A Musen 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' repository: https://github.com/ncbo 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: - biomedical evaluation_page: resource/bioteque/bioteque_eval.html homepage_url: https://bioteque.irbbarcelona.org/ id: bioteque last_modified_date: '2026-06-22T00:00:00Z' layout: resource_detail name: Bioteque products: - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - 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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: - relation_type: prov:hadPrimarySource source: bioteque product_url: https://gitlabsbnb.irbbarcelona.org/bioteque/bioteque - category: ProcessProduct description: BQsupports is a tool to uncover biomedical evidence behind experimental paired data. id: bioteque.bqsupports name: BQsupports original_source: - relation_type: prov:hadPrimarySource source: bioteque product_url: https://bioteque.irbbarcelona.org/bqsupports publications: - authors: - Adrià Fernández-Torras - Miquel Duran-Frigola - Martino Bertoni - Martina Locatelli - Patrick Aloy doi: 10.1038/s41467-022-33026-0 id: doi:10.1038/s41467-022-33026-0 journal: Nature Communications 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: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://biothings.io/ label: BioThings creation_date: '2026-06-02T00:00:00Z' description: BioThings is an ecosystem and Python SDK for building high-performance biomedical annotation APIs from one or more data sources. domains: - biomedical - information technology homepage_url: https://biothings.io/ id: biothings last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/Apache-2.0 label: Apache-2.0 name: BioThings products: - category: GraphicalInterface description: BioThings homepage describing the BioThings API ecosystem, major public APIs, SDK, Studio, and related community resources. format: http id: biothings.portal name: BioThings Homepage original_source: - relation_type: prov:hadPrimarySource source: biothings product_url: https://biothings.io/ - category: Product description: Python-based BioThings SDK for aggregating biomedical annotations and exposing them as high-performance APIs. id: biothings.sdk name: BioThings SDK original_source: - 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relation_type: prov:hadPrimarySource source: gtrx product_url: https://biothings.ncats.io/gtrx secondary_source: - relation_type: prov:wasDerivedFrom source: biothings publications: - authors: - Sebastien Lelong - Xinghua Zhou - Cyrus Afrasiabi - Zhongchao Qian - Chunlei Wu doi: 10.1093/bioinformatics/btac017 id: doi:10.1093/bioinformatics/btac017 journal: Bioinformatics preferred: true title: 'BioThings SDK: a toolkit for building high-performance data APIs in biomedical research' year: '2022' repository: https://github.com/biothings/biothings.api - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://bitterdb.agri.huji.ac.il/dbbitter.php label: BitterDB - The Hebrew University of Jerusalem creation_date: '2026-06-17T00:00:00Z' description: BitterDB is a database of bitter-tasting compounds and their associated bitter taste receptors. It compiles bitter molecules reported in the literature together with the human and other species' bitter taste receptors (T2Rs) they activate, supporting research in chemoreception and ligand-receptor pharmacology. domains: - chemistry and biochemistry - pharmacology homepage_url: https://bitterdb.agri.huji.ac.il/dbbitter.php id: bitterdb last_modified_date: '2026-06-17T00:00:00Z' layout: resource_detail name: BitterDB products: - category: GraphicalInterface description: Web interface for browsing and searching bitter compounds and bitter taste receptors. format: http id: bitterdb.site is_public: true name: BitterDB Website original_source: - relation_type: prov:hadPrimarySource source: bitterdb product_url: https://bitterdb.agri.huji.ac.il/dbbitter.php - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - 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relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ publications: - authors: - Ayana Dagan-Wiener - Antonella Di Pizio - Ido Nissim - Malkeet S Bahia - Nitzan Dubovski - Eitan Margulis - Masha Y Niv doi: 10.1093/nar/gky974 id: https://doi.org/10.1093/nar/gky974 journal: Nucleic Acids Research preferred: true title: 'BitterDB: taste ligands and receptors database in 2019' year: '2019' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.airfire.org/ label: USFS AirFire / Pacific Wildland Fire Sciences Laboratory creation_date: '2026-06-18T00:00:00Z' description: BlueSky is the U.S. Forest Service AirFire team's wildfire smoke modeling framework (NOT the social network of the same name). It chains together fire information, fuel loading, consumption, emissions, plume rise, and meteorological dispersion models to predict where smoke from wildland fires will travel and how it affects ground-level air quality. AirFire operates BlueSky Daily Runs that produce routine smoke forecasts, distributed through the AirFire tools portal for fire and air-quality decision support. It is developed and maintained by the USFS Pacific Northwest Research Station's Pacific Wildland Fire Sciences Laboratory. domains: - environment - public health - information technology homepage_url: https://www.airfire.org/ id: bluesky last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: BlueSky Smoke Modeling Framework products: - category: GraphicalInterface description: AirFire Tools portal providing access to BlueSky Daily Run smoke forecasts, the BlueSky Daily Run Viewer, the BlueSky Playground, and related smoke and fire products. format: http id: bluesky.portal name: AirFire Tools Portal original_source: - relation_type: prov:hadPrimarySource source: bluesky product_url: https://tools.airfire.org/ - category: DocumentationProduct description: Source code and documentation for the BlueSky Pipeline, the BlueSky smoke modeling framework rearchitected as a pipeable collection of standalone modules for fire emissions, plume rise, and smoke dispersion. format: http id: bluesky.code name: BlueSky Pipeline Repository original_source: - relation_type: prov:hadPrimarySource source: bluesky product_url: https://github.com/pnwairfire/bluesky - 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 original_source: - relation_type: prov:hadPrimarySource source: knowwheregraph - relation_type: prov:wasDerivedFrom source: wikidata - relation_type: prov:hadPrimarySource source: bluesky - relation_type: prov:hadPrimarySource source: cdc-places - relation_type: prov:hadPrimarySource source: cdc-svi - relation_type: prov:hadPrimarySource source: cropland-data-layer - relation_type: prov:hadPrimarySource source: epa-aqs - relation_type: prov:hadPrimarySource source: gadm - relation_type: prov:hadPrimarySource source: gnis - relation_type: prov:hadPrimarySource source: hifld - relation_type: prov:hadPrimarySource source: mtbs - relation_type: prov:hadPrimarySource source: nhpn - relation_type: prov:hadPrimarySource source: nifc - relation_type: prov:hadPrimarySource source: noaa-hms - relation_type: prov:hadPrimarySource source: noaa-ncei - relation_type: prov:hadPrimarySource source: openfema - relation_type: prov:hadPrimarySource source: reliefweb - relation_type: prov:hadPrimarySource source: ssurgo - relation_type: prov:hadPrimarySource source: us-census - relation_type: prov:hadPrimarySource source: usdm - relation_type: prov:hadPrimarySource source: usgs-comcat product_url: https://knowwheregraph.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: 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: '2026-06-27T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: bmont product_file_size: 167585 product_url: http://purl.obolibrary.org/obo/BMONT.owl publications: [] 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: '2026-06-01T00:00:00Z' 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: brenda product_url: https://www.brenda-enzymes.org/download.php - category: DocumentationProduct description: BRENDA help and tutorial resources covering support, usage guidance, FAQs, and tutorial videos. format: http id: brenda.docs name: BRENDA Help and Tutorials original_source: - relation_type: prov:hadPrimarySource source: brenda product_url: https://www.brenda-enzymes.org/help.php warnings: [] - 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). format: mixed id: ibkh.graph name: iBKH Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drkg - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: ibkh - relation_type: prov:hadPrimarySource source: idisk - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - 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relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://sugi.bio/biobtree/api/ - category: GraphProduct compatibility: - standard: biolink version: 4.2.1 compression: gzip description: Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 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 Res title: 'BRENDA in 2026: a Global Core Biodata Resource for functional enzyme and metabolic data within the DSMZ Digital Diversity' year: '2026' - 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 Res title: 'BRENDA, the ELIXIR core data resource in 2021: new developments and updates' year: '2021' taxon: - NCBITaxon:131567 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://bridge2ai.org/ label: Bridge2AI Consortium creation_date: '2026-07-01T00:00:00Z' description: Bridge to Artificial Intelligence (Bridge2AI) is an NIH Common Fund program that generates new flagship biomedical and behavioral data sets that are ethically sourced, trustworthy, well-defined, and accessible for widespread use by researchers applying artificial intelligence and machine learning. The program produces AI/ML-ready data across multiple domains, together with standards, tools, and best practices for creating and using such data, and disseminates the resulting data, models, and ethical frameworks to the broader research community. domains: - biomedical - clinical - information technology homepage_url: https://bridge2ai.org/ id: bridge2ai last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail name: Bridge to Artificial Intelligence (Bridge2AI) products: - category: GraphicalInterface description: Main Bridge2AI program portal providing access to program information, generated AI/ML-ready data sets, standards, and tools format: http id: bridge2ai.portal name: Bridge2AI Portal original_source: - relation_type: prov:hadPrimarySource source: bridge2ai product_url: https://bridge2ai.org/ - category: GraphProduct description: Statistically inferred genomic evidence graph connecting genes, gene sets, inferred disease mechanisms, and human phenotypes. Gene sets are derived from eleven NIH Common Fund programs (GlyGen, GTEx, IDG, IMPC/KOMP2, LINCS, MoTrPAC, Bridge2AI, HuBMAP, Metabolomics Workbench, SenNet, and SPARC) and phenotype-gene set relationships are computed with PIGEAN (Priors Inferred from GEne ANnotations). format: http id: digcfdekg.graph name: CFDE REVEAL Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: digcfdekg - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: impc - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: bridge2ai - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: sparc product_url: https://cfdeknowledge.org/r/cfde_reveal secondary_source: - relation_type: prov:wasInfluencedBy source: hubmap - category: GraphProduct description: The CM4AI Talent Knowledge Graph connecting Bridge2AI and CM4AI researchers, projects, publications, datasets, and bio-entities. format: ttl id: cm4ai_talent_kg.graph name: CM4AI Talent Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: cm4ai_talent_kg - relation_type: prov:hadPrimarySource source: pubmed-knowledge-graph - relation_type: prov:hadPrimarySource source: semantic-scholar product_url: https://cm4aikg.vercel.app/ secondary_source: - relation_type: prov:wasInfluencedBy source: orcid - relation_type: prov:wasInfluencedBy source: bridge2ai publications: - authors: - Timothy Clark - Harry Caufield - Jillian A Parker - Sadnan Al Manir - Edilberto Amorim - James Eddy - Nayoon Gim - Brian Gow - Wesley Goar - Jan N Hansen - Nomi Harris - Henning Hermjakob - Marcin Joachimiak - Gianna Jordan - In-Hee Lee - Shannon K McWeeney - Camille Nebeker - Milen Nikolov - Sarah J Ratcliffe - Justin Reese - Jamie Shaffer - Nathan Sheffield - Gloria Sheynkman - James Stevenson - Jake Y Chen - Chris Mungall - Alex Wagner - Sek Won Kong - Satrajit S Ghosh - Bhavesh Patel - Andrew Williams - Monica C Munoz-Torres doi: 10.1101/2024.10.23.619844 id: https://www.ncbi.nlm.nih.gov/pubmed/39484409 journal: bioRxiv preferred: true title: 'AI-readiness for Biomedical Data: Bridge2AI Recommendations' year: '2024' repository: https://github.com/bridge2ai synonyms: - Bridge2AI - Bridge to Artificial Intelligence - 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 infores_id: bspo last_modified_date: '2026-06-18T00:00:00Z' 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: - 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relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: decipher - relation_type: prov:hadPrimarySource source: mmrrc - relation_type: prov:hadPrimarySource source: cureid - relation_type: prov:hadPrimarySource source: phenopacket-store product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz publications: - authors: - Dahdul WM - Cui H - Mabee PM - Mungall CJ - Osumi-Sutherland D - Walls RL - Haendel MA doi: 10.1186/2041-1480-5-34 id: https://www.ncbi.nlm.nih.gov/pubmed/25140222 journal: J Biomed Semantics title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.' year: '2014' 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: '2026-04-15T00:00:00Z' 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: BRENDA tissue / enzyme source products: - category: OntologyProduct description: BRENDA tissue / enzyme source in OWL format format: owl id: bto.owl name: bto.owl original_source: - relation_type: prov:hadPrimarySource source: bto 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 original_source: - 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relation_type: prov:wasInfluencedBy source: kegg - relation_type: prov:wasInfluencedBy source: lincs-l1000 - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: metacyc - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: ncbitaxon - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pathophenodb - relation_type: prov:wasInfluencedBy source: pfam - relation_type: prov:wasInfluencedBy source: pid - relation_type: prov:wasInfluencedBy source: protcid - relation_type: prov:wasInfluencedBy source: pubmed - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: sider - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikipathways 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: 10.1093/nar/gkac1003 id: https://pubmed.ncbi.nlm.nih.gov/36350631/ journal: Nucleic Acids Res preferred: true title: 'Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR' year: '2023' repository: https://github.com/BV-BRC taxon: - NCBITaxon:2 - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.cabi.org/ label: CABI creation_date: '2026-07-03T00:00:00Z' description: The CABI Invasive Species Compendium (ISC) is an encyclopedic reference resource covering invasive species that threaten agriculture, biodiversity, and the environment. It brings together datasheets, distribution data, host and pathway information, images, and a bibliographic database, and is published by CABI as part of the CABI Compendium on the CABI Digital Library. domains: - organisms - environment - agriculture homepage_url: https://www.cabidigitallibrary.org/product/qi id: cabi-isc last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail license: id: https://www.cabidigitallibrary.org/terms-and-conditions label: CABI Digital Library Terms and Conditions (proprietary / subscription) name: CABI Invasive Species Compendium products: - category: GraphicalInterface description: Web portal for the CABI Invasive Species Compendium providing species datasheets, distribution and host information, and bibliographic references on invasive species. format: http id: cabi-isc.portal name: CABI Invasive Species Compendium Portal original_source: - relation_type: prov:hadPrimarySource source: cabi-isc product_url: https://www.cabidigitallibrary.org/product/qi - category: GraphProduct description: The Wildlife-KN knowledge graph, an integrative RDF network of managed species and their habitats, environmental factors, and climate context, built to support wildlife management under climate change. It is served as Linked Data through the Wildlife-KN SPARQL and Triple Pattern Fragments endpoints. format: ttl id: wildlifekn.graph name: Wildlife-KN Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: wildlifekn - relation_type: prov:hadPrimarySource source: usgs - relation_type: prov:hadPrimarySource source: edrr-invasive-catalog - relation_type: prov:hadPrimarySource source: gbif - relation_type: prov:hadPrimarySource source: worldclim - relation_type: prov:hadPrimarySource source: iucn-red-list - relation_type: prov:hadPrimarySource source: cabi-isc product_url: https://apps.okn.us/ldf/wildlifekn - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.pearson.com/en-us/subject-catalog/p/campbell-biology/P200000007019 label: Pearson Education creation_date: '2026-07-03T00:00:00Z' description: Campbell Biology (by Reece, Urry, Cain, Wasserman, Minorsky, and Jackson; published by Pearson) is a widely used undergraduate introductory biology textbook. It is the source text encoded by SRI International's AURA / Project Halo effort to produce the KB Bio 101 knowledge base. domains: - general - biomedical homepage_url: https://openlibrary.org/isbn/9780134093413 id: campbell-biology last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail license: id: https://www.pearson.com/en-us/legal-information/terms-of-use.html label: Pearson — proprietary / all rights reserved name: Campbell Biology products: - category: Product description: Bibliographic catalog record for the Campbell Biology textbook. format: http id: campbell-biology.openlibrary name: Campbell Biology (Open Library record) original_source: - relation_type: prov:hadPrimarySource source: campbell-biology product_url: https://openlibrary.org/isbn/9780134093413 - category: Product description: The full KB Bio 101 knowledge base exported from SRI's AURA system. It is offered as a downloadable archive in five logic serializations (first-order predicate logic, TPTP FOF, Answer Set Programming, SILK rule language, and OWL2), available as single-file or per-concept file versions. format: owl id: bio101.exported-kb license: id: https://creativecommons.org/licenses/by-nc-sa/3.0/ label: CC BY-NC-SA 3.0 name: KB Bio 101 Exported Knowledge Base original_source: - relation_type: prov:hadPrimarySource source: bio101 - relation_type: prov:wasDerivedFrom source: campbell-biology product_url: https://www.ai.sri.com/~halo/public/exported-kb/biokb.html - 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 original_source: - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter 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 original_source: - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter 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: - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: clinicalkg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Graph database dump and additional relationship files for the Clinical Knowledge Graph. format: neo4j id: ckg.graph latest_version: '1' license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: CKG Graph Database Dump original_source: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: ckg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: 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 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: '2026-06-18T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: cancer-registry-kg - relation_type: prov:hadPrimarySource source: louisiana-tumor-registry - relation_type: prov:hadPrimarySource source: naaccr product_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC8324069/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ HTTP 405 error when accessing file - File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 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: - relation_type: prov:hadPrimarySource source: cancer-registry-kg - relation_type: prov:hadPrimarySource source: kentucky-cancer-registry - relation_type: prov:hadPrimarySource source: naaccr product_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC8324069/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ HTTP 405 error when accessing file - File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 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: - relation_type: prov:hadPrimarySource source: cancer-registry-kg - relation_type: prov:hadPrimarySource source: us-census - relation_type: prov:hadPrimarySource source: rural-urban-continuum-codes product_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC8324069/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ HTTP 405 error when accessing file - File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: doi:10.1109/JBHI.2020.2990797 journal: IEEE Journal of Biomedical and Health Informatics preferred: true title: Knowledge Graph-Enabled Cancer Data Analytics year: '2020' synonyms: - Cancer Registry KG - Cancer Registry Knowledge Graph taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: github value: ImperialCollegeLondon - contact_type: url value: https://www.imperial.ac.uk/ label: Imperial College London creation_date: '2026-06-12T00:00:00Z' description: CardioKG is a multimodal cardiovascular disease knowledge graph that integrates computer vision-derived cardiovascular phenotypes from biomedical imaging with biomedical database content to model gene, disease, phenotype, pathway, and drug relationships for gene-disease prediction, druggability assessment, and drug repurposing. domains: - biomedical - clinical - medical imaging - precision medicine homepage_url: https://github.com/ImperialCollegeLondon/cardioKG id: cardiokg last_modified_date: '2026-06-12T00:00:00Z' layout: resource_detail license: id: https://opensource.org/license/mit/ label: MIT License name: CardioKG products: - category: GraphProduct description: Neo4j construction artifacts for CardioKG, including Cypher scripts to create graph nodes and add edges. dump_format: neo4j format: neo4j id: cardiokg.neo4j name: CardioKG Neo4j graph construction scripts original_source: - relation_type: prov:hadPrimarySource source: cardiokg - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:used source: mesh - relation_type: prov:used source: mondo - relation_type: prov:used source: reactome - relation_type: prov:used source: kegg - relation_type: prov:used source: uniprot - relation_type: prov:used source: string - relation_type: prov:used source: opentargets product_url: https://github.com/ImperialCollegeLondon/cardioKG/tree/main/Building%20KG - category: Product description: CardioKG supporting data tables for anatomy and cardiac magnetic resonance anatomy mappings. format: csv id: cardiokg.data name: CardioKG supporting data tables original_source: - relation_type: prov:hadPrimarySource source: cardiokg - relation_type: prov:hadPrimarySource source: ukbiobank product_url: https://github.com/ImperialCollegeLondon/cardioKG/tree/main/Data - category: Product description: Generated CardioKG embeddings for gene-disease and medication-disease association prediction tasks. id: cardiokg.embeddings name: CardioKG generated embeddings original_source: - relation_type: prov:hadPrimarySource source: cardiokg product_url: https://github.com/ImperialCollegeLondon/cardioKG/tree/main/Generated_embeddings - category: ProcessProduct description: Analysis notebooks and scripts for CardioKG graph construction, PageRank importance analysis, gene-disease association prediction, and drug repurposing. id: cardiokg.workflow name: CardioKG analysis workflow original_source: - relation_type: prov:hadPrimarySource source: cardiokg product_url: https://github.com/ImperialCollegeLondon/cardioKG - category: Product compression: zip description: Archived CardioKG repository release on Zenodo. id: cardiokg.zenodo-archive name: CardioKG Zenodo archive original_source: - relation_type: prov:hadPrimarySource source: cardiokg product_url: https://doi.org/10.5281/zenodo.16025953 publications: - authors: - Khaled Rjoob - Kathryn A. McGurk - Sean L. Zheng - Lara Curran - Mahmoud Ibrahim - Lingyao Zeng - Vladislav Kim - Shamin Tahasildar - Soodeh Kalaie - Deva S. Senevirathne - Parisa Gifani - Vladimir Losev - Jin Zheng - Wenjia Bai - Antonio de Marvao - James S. Ware - Christian Bender - Declan P. O'Regan doi: 10.1038/s44161-025-00757-4 id: doi:10.1038/s44161-025-00757-4 journal: Nature Cardiovascular Research title: A multimodal vision knowledge graph of cardiovascular disease year: '2025' repository: https://github.com/ImperialCollegeLondon/cardioKG taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://crates.io/policies label: Rust Foundation creation_date: '2026-07-03T00:00:00Z' description: crates.io is the official package registry for the Rust ecosystem, hosting metadata and distributable artifacts (crates) for Rust libraries. domains: - information technology homepage_url: https://crates.io/ id: cargo last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: crates.io (Cargo) products: - category: GraphicalInterface description: Web interface and public registry for browsing and retrieving Rust crates format: http id: cargo.website name: crates.io website original_source: - relation_type: prov:hadPrimarySource source: cargo product_url: https://crates.io/ - category: GraphProduct description: SecureChain knowledge graph of software supply-chain components, versions, dependencies, and vulnerabilities, served as RDF/Turtle via the project's SPARQL and Triple Pattern Fragments endpoints. format: ttl id: securechainkg.graph name: SecureChain KG Graph original_source: - relation_type: prov:hadPrimarySource source: securechainkg - relation_type: prov:hadPrimarySource source: npm - relation_type: prov:hadPrimarySource source: pypi - relation_type: prov:hadPrimarySource source: maven-central - relation_type: prov:hadPrimarySource source: nuget - relation_type: prov:hadPrimarySource source: rubygems - relation_type: prov:hadPrimarySource source: cargo - relation_type: prov:hadPrimarySource source: osv product_url: https://purdue-hcss.github.io/nsf-software-supply-chain_security/ - activity_status: active category: KnowledgeGraph collection: - ber 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: - organisms 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: '2026-06-12T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: catalogue-of-life 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 original_source: - relation_type: prov:hadPrimarySource source: catalogue-of-life 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 original_source: - relation_type: prov:hadPrimarySource source: catalogue-of-life - relation_type: prov:hadPrimarySource source: itis - relation_type: prov:hadPrimarySource source: gbif 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 original_source: - relation_type: prov:hadPrimarySource source: catalogue-of-life - relation_type: prov:hadPrimarySource source: itis - relation_type: prov:hadPrimarySource source: gbif product_url: https://www.catalogueoflife.org/data/download warnings: - Automated checks may return HTTP 418 due to anti-bot challenge on catalogueoflife.org download pages; URL is retained as the canonical human-access endpoint. - 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 original_source: - relation_type: prov:hadPrimarySource source: catalogue-of-life product_url: https://www.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 original_source: - relation_type: prov:hadPrimarySource source: catalogue-of-life product_url: https://api.catalogueoflife.org/ - category: GraphicalInterface description: Web interface for browsing, querying, and visualizing ecological networks format: http id: mangal.portal name: mangal.io Web Portal original_source: - relation_type: prov:hadPrimarySource source: mangal product_url: https://mangal.io/ secondary_source: - relation_type: prov:used source: catalogue-of-life - relation_type: prov:used source: gbif - relation_type: prov:used source: itis - 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 original_source: - relation_type: prov:hadPrimarySource source: mangal product_url: https://mangal.io/api/v2/ secondary_source: - relation_type: prov:used source: catalogue-of-life - relation_type: prov:used source: gbif - relation_type: prov:used source: itis - category: DocumentationProduct description: API documentation, user guides, and data model specification format: http id: mangal.docs name: mangal.io Documentation original_source: - relation_type: prov:hadPrimarySource source: mangal product_url: https://mangal.io/documentation - category: ProcessProduct description: R package for retrieving and exploring data from the Mangal ecological interactions database format: http id: mangal.rmangal name: rmangal R Client original_source: - relation_type: prov:hadPrimarySource source: mangal product_url: https://docs.ropensci.org/rmangal/ secondary_source: - relation_type: prov:used source: catalogue-of-life - relation_type: prov:used source: gbif - relation_type: prov:used source: itis publications: - authors: - Olaf Bánki doi: 10.3897/biss.6.94040 id: doi:10.3897/biss.6.94040 journal: Biodiversity Information Science and Standards title: 'Catalogue of Life: From a list to a service' year: '2022' - 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: Ontology contacts: - category: Organization contact_details: - contact_type: url value: https://cns.iu.edu/ label: Indiana University Cyberinfrastructure for Network Science Center (CNS) creation_date: '2026-06-18T00:00:00Z' description: The Common Coordinate Framework (CCF) Ontology is the spatial and semantic framework that underpins the Human Reference Atlas (HRA) developed within the NIH Human BioMolecular Atlas Program (HuBMAP). It encodes the relationships among anatomical structures, cell types, and biomarkers captured in the ASCT+B (Anatomical Structures, Cell Types, plus Biomarkers) tables, linking them to established ontologies such as Uberon, FMA, and Cell Ontology. The CCF also provides a spatial component that supports 3D spatial registration of tissue samples to reference organs via the CCF Registration User Interface, giving each sample a defined location in a common coordinate system. Together these clinical, semantic, and spatial layers serve as a primary upstream source for the HRA Knowledge Graph (HRA-KG). domains: - anatomy and development - biomedical homepage_url: https://humanatlas.io/ccf-ontology id: ccf last_modified_date: '2026-06-18T00:00:00Z' 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 Coordinate Framework Ontology products: - category: OntologyProduct description: The Common Coordinate Framework (CCF) Ontology in OWL (RDF/XML) format, integrating ASCT+B anatomical structures, cell types, and biomarkers with the CCF spatial model for the Human Reference Atlas. format: owl id: ccf.owl name: CCF Ontology (OWL) original_source: - relation_type: prov:hadPrimarySource source: ccf product_file_size: 44683831 product_url: https://cdn.humanatlas.io/digital-objects/graph/ccf/latest/assets/ccf.owl - 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: - relation_type: prov:hadPrimarySource source: hra-kg - relation_type: prov:hadPrimarySource source: ccf - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: fma - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hravs - relation_type: prov:hadPrimarySource source: lmha - relation_type: prov:hadPrimarySource source: pcl - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: vccf product_file_size: 204030087 product_url: https://cdn.humanatlas.io/digital-objects/collection/hra/v2.2/graph.ttl - 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: - relation_type: prov:hadPrimarySource source: hra-kg - relation_type: prov:hadPrimarySource source: ccf - 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relation_type: prov:hadPrimarySource source: lmha - relation_type: prov:hadPrimarySource source: pcl - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: vccf product_file_size: 291382102 product_url: https://cdn.humanatlas.io/digital-objects/collection/hra/v2.2/graph.nt - 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: - relation_type: prov:hadPrimarySource source: hra-kg - relation_type: prov:hadPrimarySource source: ccf - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: fma - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hravs - relation_type: prov:hadPrimarySource source: lmha - relation_type: prov:hadPrimarySource source: pcl - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: vccf product_file_size: 376981902 product_url: https://cdn.humanatlas.io/digital-objects/collection/hra/v2.2/graph.nq publications: - authors: - Börner K - Teichmann SA - Quardokus EM - Gee JC doi: 10.1038/s41556-021-00788-6 id: https://pubmed.ncbi.nlm.nih.gov/34750582 journal: Nat Cell Biol preferred: true title: Anatomical structures, cell types and biomarkers of the Human Reference Atlas year: '2021' - 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: - biomedical homepage_url: https://sites.broadinstitute.org/ccle/ id: ccle last_modified_date: '2026-06-18T00:00:00Z' 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: CCLE products: - category: DocumentationProduct description: CCLE project site describing the Cancer Cell Line Encyclopedia collaboration, motivations, and project phases. format: http id: ccle.docs name: CCLE Project Site original_source: - relation_type: prov:hadPrimarySource source: ccle product_url: https://sites.broadinstitute.org/ccle/ - category: Product description: CCLE datasets page linking processed genetic, transcriptomic, proteomic, and metabolomic releases and related DepMap resources. format: http id: ccle.datasets name: CCLE Datasets original_source: - relation_type: prov:hadPrimarySource source: ccle product_url: https://sites.broadinstitute.org/ccle/datasets - 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: - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 19324 product_url: https://w3id.org/biopragmatics/resources/ccle/ccle.obo - 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relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways publications: - authors: - Barretina J - Caponigro G - Stransky N - Venkatesan K - Margolin AA doi: 10.1038/nature11003 id: https://www.ncbi.nlm.nih.gov/pubmed/22460905 journal: Nature preferred: true title: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity year: '2012' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.encodeproject.org/help/contacts/ label: ENCODE Data Coordination Center (DCC) creation_date: '2026-06-18T00:00:00Z' description: The ENCODE Registry of candidate cis-Regulatory Elements (cCREs) is a curated annotation of regulatory regions in the human and mouse genomes derived from ENCODE and Roadmap Epigenomics data. Each cCRE is classified by its biochemical signature, including promoter-like, enhancer-like, and CTCF-bound elements based on DNase hypersensitivity, H3K4me3, H3K27ac, and CTCF ChIP-seq signals. 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Thompson - Arlin Stoltzfus doi: 10.4137/EBO.S2320 id: https://doi.org/10.4137/EBO.S2320 journal: Evolutionary Bioinformatics title: Initial Implementation of a Comparative Data Analysis Ontology year: '2009' repository: https://github.com/evoinfo/cdao - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.cdc.gov/ label: Centers for Disease Control and Prevention (CDC) creation_date: '2026-06-18T00:00:00Z' description: CDC PLACES (Population Level Analysis and Community Estimates) provides model-based small-area estimates of chronic disease risk factors, health outcomes, prevention practices, and health status measures for the United States. Estimates are produced at the county, place, census tract, and ZIP Code Tabulation Area levels, allowing local health departments and planners to assess and compare community health where direct survey data are sparse. 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CDC PLACES is an upstream source for KnowWhereGraph. domains: - public health - clinical - phenotype homepage_url: https://www.cdc.gov/places/ id: cdc-places last_modified_date: '2026-06-27T00:00:00Z' layout: resource_detail license: id: https://www.usa.gov/government-works label: U.S. Government Work (public domain) name: CDC PLACES products: - category: GraphicalInterface description: CDC PLACES portal providing interactive maps, data visualizations, and access to model-based small-area estimates of health measures for US counties, places, census tracts, and ZIP Code Tabulation Areas. format: http id: cdc-places.portal name: CDC PLACES Portal original_source: - relation_type: prov:hadPrimarySource source: cdc-places product_url: https://www.cdc.gov/places/ - category: Product description: CDC PLACES datasets published on the data.cdc.gov open data platform, providing downloadable model-based estimates of health measures by county, place, census tract, and ZIP Code Tabulation Area as CSV, JSON, and other file formats accessible via the Socrata Open Data API. format: http id: cdc-places.datasets name: CDC PLACES Open Datasets original_source: - relation_type: prov:hadPrimarySource source: cdc-places product_url: https://data.cdc.gov/browse?category=500+Cities+%26+Places - 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 original_source: - relation_type: prov:hadPrimarySource source: knowwheregraph - relation_type: prov:wasDerivedFrom source: wikidata - relation_type: prov:hadPrimarySource source: bluesky - relation_type: prov:hadPrimarySource source: cdc-places - relation_type: prov:hadPrimarySource source: cdc-svi - relation_type: prov:hadPrimarySource source: cropland-data-layer - relation_type: prov:hadPrimarySource source: epa-aqs - relation_type: prov:hadPrimarySource source: gadm - relation_type: prov:hadPrimarySource source: gnis - relation_type: prov:hadPrimarySource source: hifld - relation_type: prov:hadPrimarySource source: mtbs - relation_type: prov:hadPrimarySource source: nhpn - relation_type: prov:hadPrimarySource source: nifc - relation_type: prov:hadPrimarySource source: noaa-hms - relation_type: prov:hadPrimarySource source: noaa-ncei - relation_type: prov:hadPrimarySource source: openfema - relation_type: prov:hadPrimarySource source: reliefweb - relation_type: prov:hadPrimarySource source: ssurgo - relation_type: prov:hadPrimarySource source: us-census - relation_type: prov:hadPrimarySource source: usdm - relation_type: prov:hadPrimarySource source: usgs-comcat product_url: https://knowwheregraph.org/ publications: - authors: - Greenlund KJ - Lu H - Wang Y - Matthews KA - LeClercq JM - Lee B - Carlson SA doi: 10.5888/pcd19.210459 id: https://www.ncbi.nlm.nih.gov/pubmed/35709356 journal: Prev Chronic Dis preferred: true title: 'PLACES: Local Data for Better Health' year: '2022' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.atsdr.cdc.gov/place-health/php/svi/ label: CDC/ATSDR Geospatial Research, Analysis, and Services Program (GRASP) creation_date: '2026-06-18T00:00:00Z' description: The CDC/ATSDR Social Vulnerability Index (SVI) measures the relative social vulnerability of U.S. communities to disasters and public-health emergencies at the census-tract and county level. 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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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: athena - relation_type: prov:hadPrimarySource source: cdiscvocab - relation_type: prov:hadPrimarySource source: ciel - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: snomedct product_url: https://athena.ohdsi.org/search-terms/start warnings: - Athena mapping exports are accessed through the authenticated Athena web application; stable direct public file URLs are not exposed. - category: Product description: Downloadable standardized vocabulary bundles for OMOP CDM assembled through the authenticated Athena web application format: csv id: athena.vocabularies name: Athena Vocabulary Downloads original_source: - relation_type: prov:hadPrimarySource source: athena - relation_type: prov:hadPrimarySource source: cdiscvocab - relation_type: prov:hadPrimarySource source: ciel - relation_type: prov:hadPrimarySource source: gemscript - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: medispan-gpi - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ndcd - relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: snomedct product_url: https://athena.ohdsi.org/vocabulary/list warnings: - Athena vocabulary downloads are prepared through the logged-in web application; stable direct public file URLs are not exposed. 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 - nutrition homepage_url: https://cdno.info/ id: cdno last_modified_date: '2026-06-05T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: cdno 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 original_source: - relation_type: prov:hadPrimarySource source: cdno product_file_size: 331277 product_url: http://purl.obolibrary.org/obo/cdno.obo publications: - authors: - Liliana Andrés-Hernández - Kai Blumberg - Ramona L. Walls - Damion Dooley - Ramil Mauleon - Matthew Lange - Magalie Weber - Lauren Chan - Adnan Malik - Anders Møller - Jayne Ireland - Lucia Segovia - Xuhuiqun Zhang - Britt Burton-Freeman - Paul Magelli - Andrew Schriever - Shavawn M. Forester - Lei Liu - Graham J. King doi: 10.3389/fnut.2022.928837 id: https://doi.org/10.3389/fnut.2022.928837 journal: Frontiers in Nutrition title: Establishing a Common Nutritional Vocabulary - From Food Production to Diet year: '2022' repository: https://github.com/CompositionalDietaryNutritionOntology/cdno - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://cebs.niehs.nih.gov/ label: NIEHS - category: Organization contact_details: - contact_type: email value: CEBS-support@mail.nih.gov label: CEBS Support 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 - public health homepage_url: https://cebs.niehs.nih.gov/ id: cebs infores_id: cebs last_modified_date: '2026-06-01T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: cebs product_url: https://cebs.niehs.nih.gov/cebs/search - category: Product description: Toxicology study data from NTP and other programs format: mixed id: cebs.data name: CEBS Study Data original_source: - relation_type: prov:hadPrimarySource source: cebs product_url: https://cebs.niehs.nih.gov/cebs/ - category: ProgrammingInterface connection_url: https://manticore.niehs.nih.gov/cebsapi/v1 description: Programmatic API access to CEBS data, documented by the CEBS API user help format: http id: cebs.api name: CEBS API original_source: - relation_type: prov:hadPrimarySource source: cebs product_url: https://tools.niehs.nih.gov/cebs3/support/assets/docs/CEBS_API-User-Help.pdf - category: DocumentationProduct description: CEBS citation guidance for referencing the database and study URLs format: pdf id: cebs.citation-guide name: Citing CEBS original_source: - relation_type: prov:hadPrimarySource source: cebs product_file_size: 152093 product_url: https://cebs.niehs.nih.gov/cebs/support/download/Citing-CEBS.pdf publications: - authors: - Cari Martini - Ying Frances Liu - Hui Gong - Nicole Sayers - German Segura - Jennifer Fostel doi: 10.1093/nar/gkab981 id: doi:10.1093/nar/gkab981 journal: Nucleic Acids Research preferred: true title: 'CEBS update: curated toxicology database with enhanced tools for data integration' year: '2022' - authors: - Isabel A. Lea - Hui Gong - Anand Paleja - Asif Rashid - Jennifer Fostel doi: 10.1093/nar/gkw1077 id: doi:10.1093/nar/gkw1077 journal: Nucleic Acids Research title: 'CEBS: a comprehensive annotated database of toxicological data' year: '2017' 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 - category: Organization contact_details: - contact_type: url value: https://bio-bigdata.hrbmu.edu.cn/CellMarker/ label: College of Bioinformatics Science and Technology, Harbin Medical University 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. CellMarker 2.0 provides a manually curated collection of 26,915 markers across 2,578 cell types and 656 tissues, resulting in 83,361 tissue-cell type-marker entries, and includes integrated web tools for single-cell data analysis. domains: - biomedical - genomics - biological systems - organisms homepage_url: https://bio-bigdata.hrbmu.edu.cn/CellMarker/ id: cellmarker infores_id: cellmarker last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail name: CellMarker products: - category: Product description: Human CellMarker 2.0 marker dataset in spreadsheet format format: mixed id: cellmarker.human name: Human Cell Markers original_source: - relation_type: prov:hadPrimarySource source: cellmarker product_file_size: 7982475 product_url: http://117.50.127.228/CellMarker/CellMarker_download_files/file/Cell_marker_Human.xlsx - category: Product description: Mouse CellMarker 2.0 marker dataset in spreadsheet format format: mixed id: cellmarker.mouse name: Mouse Cell Markers original_source: - relation_type: prov:hadPrimarySource source: cellmarker product_file_size: 3740448 product_url: http://117.50.127.228/CellMarker/CellMarker_download_files/file/Cell_marker_Mouse.xlsx - category: Product description: CellMarker 2.0 marker dataset derived from single-cell sequencing studies in human and mouse format: mixed id: cellmarker.singlecell name: Single Cell Markers original_source: - relation_type: prov:hadPrimarySource source: cellmarker product_file_size: 6005874 product_url: http://117.50.127.228/CellMarker/CellMarker_download_files/file/Cell_marker_Seq.xlsx - category: Product description: Combined CellMarker 2.0 marker dataset for human and mouse in spreadsheet format format: mixed id: cellmarker.all name: All Cell Markers original_source: - relation_type: prov:hadPrimarySource source: cellmarker product_file_size: 10010437 product_url: http://117.50.127.228/CellMarker/CellMarker_download_files/file/Cell_marker_All.xlsx - category: GraphicalInterface description: CellMarker 2.0 annotation tool for assigning cell types using curated marker genes format: http id: cellmarker.act name: Cell Annotation Tool original_source: - relation_type: prov:hadPrimarySource source: cellmarker product_url: http://117.50.127.228/CellMarker/CellMarker_annotation.jsp - 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. format: python id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: nihreporter - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: cellmarker - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: indra product_url: https://github.com/gyorilab/indra_cogex - category: Product description: Harmonizome 3.0 processed dataset downloads, including dataset-specific association files and knowledge graph serialization downloads. format: mixed id: harmonizome.downloads name: Harmonizome Downloads original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://maayanlab.cloud/Harmonizome/download secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct description: Neo4j knowledge graph serialization of Harmonizome processed datasets, including genes, attributes, resources, datasets, and gene-attribute associations. dump_format: neo4j format: neo4j id: harmonizome.kg-neo4j latest_version: '3.0' name: Harmonizome Knowledge Graph Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://harmonizome-kg.maayanlab.cloud/ secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct description: Live TRAPI/BioThings metadata endpoint for the Multiomics BigGIM-DrugResponse KP, exposing the multiomics knowledge graph served by the Multiomics Provider (built from GTEx, TCGA, and drug-response data, with additional clinical-trials, drug-approval and knowledge-resource inputs). format: json id: multiomics-kp.graph name: Multiomics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: multiomics-kp - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcga - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: dailymed - relation_type: prov:hadPrimarySource source: faers product_url: https://biothings.transltr.io/biggim_drugresponse_kp/metadata secondary_source: - relation_type: prov:wasInfluencedBy source: aact - relation_type: prov:wasInfluencedBy source: biogrid - relation_type: prov:wasInfluencedBy source: huri - relation_type: prov:wasInfluencedBy source: cellmarker - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: ttd - relation_type: prov:wasInfluencedBy source: pubmed publications: - authors: - Hu C - Li T - Xu Y - Zhang X - Li F - Bai J - Chen J - Jiang W - Yang K - Ou Q - Li X - Zhang Y doi: 10.1093/nar/gkac947 id: doi:10.1093/nar/gkac947 journal: Nucleic Acids Research preferred: true title: 'CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data' year: '2023' - 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 title: CellMarker - a manually curated resource of cell markers in human and mouse year: '2019' 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 - biomedical homepage_url: https://www.cellosaurus.org/ id: cellosaurus last_modified_date: '2026-06-18T00:00:00Z' 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: 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: - relation_type: prov:hadPrimarySource source: cellosaurus product_url: https://www.cellosaurus.org/ - category: Product description: Complete Cellosaurus data in flat text format format: tsv id: cellosaurus.txt name: Cellosaurus Text original_source: - relation_type: prov:hadPrimarySource source: cellosaurus product_file_size: 117036445 product_url: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt - category: Product description: Cellosaurus data in XML format format: xml id: cellosaurus.xml name: Cellosaurus XML original_source: - relation_type: prov:hadPrimarySource source: cellosaurus product_file_size: 634465764 product_url: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.xml - category: MappingProduct description: Cellosaurus cross-references in tab-delimited format format: tsv id: cellosaurus.xrefs name: Cellosaurus Cross-references original_source: - relation_type: prov:hadPrimarySource source: cellosaurus product_file_size: 37328 product_url: https://ftp.expasy.org/databases/cellosaurus/cellosaurus_xrefs.txt - category: ProgrammingInterface description: RESTful API for programmatic access to Cellosaurus data format: http id: cellosaurus.api.rest is_public: true name: Cellosaurus API original_source: - relation_type: prov:hadPrimarySource source: cellosaurus product_url: https://api.cellosaurus.org/ - category: ProgrammingInterface description: SPARQL endpoint for querying Cellosaurus RDF data format: http id: cellosaurus.api.sparql is_public: true name: Cellosaurus SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: cellosaurus product_url: https://api.cellosaurus.org/sparql-editor - category: ProcessProduct description: CLASTR tool for STR similarity search across cell lines format: javascript id: cellosaurus.clastr name: CLASTR STR Similarity Search original_source: - relation_type: prov:hadPrimarySource source: cellosaurus product_url: https://www.cellosaurus.org/str-search/ - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: bioteque - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: cellosaurus - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chemicalchecker - relation_type: prov:hadPrimarySource source: clue - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: creeds - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: dorothea - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: huri - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: offsides - relation_type: prov:hadPrimarySource source: omnipath - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: pharmacodb - relation_type: prov:hadPrimarySource source: prism - relation_type: prov:hadPrimarySource source: progeny - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: repodb - relation_type: prov:hadPrimarySource source: repohub - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues product_url: https://bioteque.irbbarcelona.org/downloads/embeddings publications: - authors: - Bairoch A doi: 10.7171/jbt.18-2902-002 id: doi:10.7171/jbt.18-2902-002 journal: 'Journal of Biomolecular Techniques : JBT' 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: DataSource creation_date: '2026-06-15T00:00:00Z' description: CellPhoneDB is a publicly available repository of manually curated human receptors, ligands and their interactions, paired with a statistical tool to infer cell-cell communication from single-cell transcriptomics data. It accounts for the subunit architecture of both ligands and receptors, accurately representing heteromeric complexes, and predicts enriched signaling between cell types based on the combined expression of interacting partners. domains: - systems biology - biological systems - immunology homepage_url: https://www.cellphonedb.org/ id: cellphonedb last_modified_date: '2026-06-15T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT name: CellPhoneDB products: - category: MappingProduct description: Curated database of human receptors, ligands and their interactions, including heteromeric complex composition, distributed as downloadable files for use with the CellPhoneDB analysis package. format: csv id: cellphonedb.database name: CellPhoneDB Interactions Database original_source: - relation_type: prov:hadPrimarySource source: cellphonedb product_url: https://www.cellphonedb.org/downloads warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 404 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' - category: ProcessProduct description: Python package that interrogates single-cell transcriptomics data against the CellPhoneDB database to statistically infer enriched ligand-receptor interactions between cell types. format: python id: cellphonedb.package name: CellPhoneDB Python Package original_source: - relation_type: prov:hadPrimarySource source: cellphonedb product_url: https://github.com/ventolab/CellphoneDB - category: GraphicalInterface description: Web interface for browsing and searching CellPhoneDB receptors, ligands and their curated interactions. format: http id: cellphonedb.web name: CellPhoneDB Web Interface original_source: - relation_type: prov:hadPrimarySource source: cellphonedb product_url: https://www.cellphonedb.org/ - category: DocumentationProduct description: Source code, tutorials, and documentation for the CellPhoneDB database and analysis package. format: http id: cellphonedb.docs name: CellPhoneDB Repository and Documentation original_source: - relation_type: prov:hadPrimarySource source: cellphonedb product_url: https://github.com/ventolab/CellphoneDB - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - 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Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 publications: - authors: - Mirjana Efremova - Miquel Vento-Tormo - Sarah A. Teichmann - Roser Vento-Tormo doi: doi:10.1038/s41596-020-0292-x id: doi:10.1038/s41596-020-0292-x journal: Nature Protocols preferred: true title: 'CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes' year: '2020' repository: https://github.com/ventolab/CellphoneDB - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: cellxgene@chanzuckerberg.com - contact_type: url value: https://cellxgene.cziscience.com/ label: Chan Zuckerberg Initiative creation_date: '2026-05-28T00:00:00Z' description: CZ CELLxGENE is a platform for finding, downloading, exploring, and analyzing single-cell datasets through a public data portal, integrated analysis interfaces, and the CELLxGENE Census programmatic access layer. domains: - biomedical - genomics homepage_url: https://cellxgene.cziscience.com/ id: cellxgene last_modified_date: '2026-06-18T00:00:00Z' 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: CZ CELLxGENE products: - category: GraphicalInterface description: Main CZ CELLxGENE Discover portal for browsing public single-cell collections, datasets, gene expression views, and analysis tools. format: http id: cellxgene.portal name: CZ CELLxGENE Discover original_source: - relation_type: prov:hadPrimarySource source: cellxgene product_url: https://cellxgene.cziscience.com/ - category: GraphicalInterface description: Search and download interface for public curated collections and datasets available through CZ CELLxGENE Discover. format: http id: cellxgene.datasets name: CZ CELLxGENE Datasets Browser original_source: - relation_type: prov:hadPrimarySource source: cellxgene product_url: https://cellxgene.cziscience.com/datasets - category: ProgrammingInterface description: Documentation and entry point for the CELLxGENE Census API and data object used to query standardized single-cell expression data in R and Python. format: http id: cellxgene.census is_public: true name: CZ CELLxGENE Census original_source: - relation_type: prov:hadPrimarySource source: cellxgene product_url: https://chanzuckerberg.github.io/cellxgene-census/ - category: DocumentationProduct description: Official documentation for CZ CELLxGENE Discover, Explorer, Gene Expression, and Annotate workflows. format: http id: cellxgene.docs name: CZ CELLxGENE Documentation original_source: - relation_type: prov:hadPrimarySource source: cellxgene product_url: https://cellxgene.cziscience.com/docs - 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: - relation_type: prov:hadPrimarySource source: cl-kg - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cellxgene product_url: https://cellular-semantics.sanger.ac.uk/browser/ - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - 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standard: biolink version: 4.2.1 compression: gzip description: Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - category: GraphProduct description: The NLM-CKN knowledge graph of cellular phenotypes. It is built from triple assertions (subject-predicate-object) that link single-cell genomics experimental data (from the CELLxGENE Census) and computationally derived NS-Forest marker genes to the Cell Ontology and other reference ontologies, augmented with literature-derived assertions from text mining/NLP. The graph is produced by the NLM-CKN ETL pipeline as an ArangoDB archive and served via the web application at https://nlm-ckn.org. format: http id: nlm-ckn.graph name: nlm-ckn-graph original_source: - relation_type: prov:hadPrimarySource source: nlm-ckn - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: pubmed product_url: https://nlm-ckn.org secondary_source: - relation_type: prov:wasInfluencedBy source: cl - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: pato - relation_type: prov:wasInfluencedBy source: mondo - relation_type: prov:wasInfluencedBy source: hsapdv publications: - authors: - Shibla Abdulla - Brian Aevermann - CZI Cell Science Program doi: 10.1093/nar/gkae1142 id: https://doi.org/10.1093/nar/gkae1142 journal: Nucleic Acids Research preferred: true title: 'CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data' year: '2025' repository: https://github.com/chanzuckerberg/single-cell-data-portal - 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: - biomedical 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: '2026-05-27T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: cfde-ddkg - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: umls 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: - relation_type: prov:hadPrimarySource source: cfde-ddkg - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: umls 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://gse.cfde.cloud/ id: cfde-gse last_modified_date: '2026-06-22T00:00:00Z' 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: 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 original_source: - relation_type: prov:hadPrimarySource source: cfde-gse product_url: https://gse.cfde.cloud/ - 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 original_source: - relation_type: prov:hadPrimarySource source: cfde-gse product_url: https://gse.cfde.cloud/api/ - category: GraphicalInterface description: Interactive graph traversal interface for exploring connections between genes and CFDE program-specific signatures format: http id: cfde-gse.connection-explorer name: CFDE-GSE Connection Explorer original_source: - relation_type: prov:hadPrimarySource source: cfde-gse product_url: https://gse.cfde.cloud/ConnectionExplorer - 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 original_source: - relation_type: prov:hadPrimarySource source: cfde-gse - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: motrpac - category: Product description: Standardized gene set collections from Common Fund programs in GMT format format: txt id: cfde-gse.genesets name: CFDE Gene Set Collections original_source: - relation_type: prov:hadPrimarySource source: cfde-gse - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: motrpac product_url: https://gse.cfde.cloud/downloads/ - category: Product description: Downloadable node metadata CSV snapshots from the CFDE-GSE downloads page (for example, Gene.nodes.csv and program-specific node tables) format: csv id: cfde-gse.nodes-csv name: CFDE-GSE Node CSV Snapshot original_source: - relation_type: prov:hadPrimarySource source: cfde-gse product_file_size: 2119955 product_url: https://s3.amazonaws.com/maayan-kg/cfde-kg/042123/Gene.nodes.csv - category: Product description: Downloadable edge/triple CSV snapshots from the CFDE-GSE downloads page using source.relation.target edge files format: csv id: cfde-gse.edges-csv name: CFDE-GSE Edge CSV Snapshot original_source: - relation_type: prov:hadPrimarySource source: cfde-gse product_file_size: 7307504 product_url: https://s3.amazonaws.com/maayan-kg/cfde-kg/042123/KOMP2_Mouse_Phenotypes_2022.KOMP2_Mouse_Phenotype.Gene.edges.csv publications: - authors: - Clarke DJB - Jeon M - Stein DJ - Moiseyev N - Kropiwnicki E - Ben-Moshe NB - Barupal DK - Ma'ayan A id: doi:10.1038/s41467-022-28631-3 journal: Nature Communications preferred: true title: Cross-program analysis of the CFDE gene sets reveals common biological themes year: '2022' repository: https://github.com/MaayanLab/CFDE-KG - 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: https://birdgenenames.org/index.jsp id: cgnc last_modified_date: '2026-05-30T00:00:00Z' layout: resource_detail name: CGNC products: - category: GraphicalInterface description: Official Chicken Gene Nomenclature Consortium portal for searching gene symbols, guidelines, downloads, and curation resources. format: http id: cgnc.portal name: CGNC Portal original_source: - relation_type: prov:hadPrimarySource source: cgnc product_url: https://birdgenenames.org/index.jsp - category: Product description: CGNC public downloads page for standardized chicken gene nomenclature data and related consortium resources. format: http id: cgnc.genes name: CGNC Genes original_source: - relation_type: prov:hadPrimarySource source: cgnc product_url: https://birdgenenames.org/downloads.jsp - 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: - relation_type: prov:hadPrimarySource source: cgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 683991 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.obo - 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: - relation_type: prov:hadPrimarySource source: cgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 911421 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.owl - 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: - relation_type: prov:hadPrimarySource source: cgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 861880 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.json - 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: - relation_type: prov:hadPrimarySource source: cgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 258292 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.sssom.tsv - 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: - relation_type: prov:hadPrimarySource source: cgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 406670 product_url: https://w3id.org/biopragmatics/resources/cgnc/cgnc.tsv 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 journal: BMC Genomics title: The Chicken Gene Nomenclature Committee report year: '2009' - activity_status: active category: DataSource 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: '2026-05-21T00:00:00Z' description: ChEA is a family of transcription factor enrichment resources developed by the Ma'ayan Lab, spanning the original ChIP Enrichment Analysis database and later ChEA2 and ChEA3 releases that assemble transcription factor target gene sets from ChIP-X experiments and other orthogonal omics data. domains: - biomedical - genomics - systems biology homepage_url: https://maayanlab.cloud/chea3/ id: chea last_modified_date: '2026-06-01T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC BY-NC-SA 4.0 name: ChEA products: - category: GraphicalInterface description: Public ChEA3 web interface for transcription factor enrichment analysis and result visualization format: http id: chea.portal name: ChEA Explorer original_source: - relation_type: prov:hadPrimarySource source: chea product_url: https://maayanlab.cloud/chea3/ - category: ProgrammingInterface connection_url: https://maayanlab.cloud/chea3/api/enrich/ description: ChEA3 enrichment API for submitting gene sets and retrieving transcription factor ranking results format: http id: chea.api name: ChEA API original_source: - relation_type: prov:hadPrimarySource source: chea product_url: https://maayanlab.cloud/chea3/api/enrich/ - category: Product description: Download catalog for ChEA3 transcription factor target libraries and benchmark datasets format: http id: chea.libraries name: ChEA Library Downloads original_source: - relation_type: prov:hadPrimarySource source: chea - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: remap - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: geo - relation_type: prov:hadPrimarySource source: tcga product_url: https://maayanlab.cloud/chea3/index.html#content4-13 - category: Product description: Docker image for running the ChEA3 web application locally format: mixed id: chea.docker name: ChEA3 Docker Image original_source: - relation_type: prov:hadPrimarySource source: chea product_url: https://hub.docker.com/r/maayanlab/chea3 warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: GraphicalInterface description: Interactive ChEA3 web interface for transcription factor enrichment analysis, result tables, and network visualizations format: http id: chea-kg.portal name: ChEA-KG Explorer original_source: - relation_type: prov:hadPrimarySource source: chea-kg product_url: https://maayanlab.cloud/chea-kg/ secondary_source: - relation_type: prov:wasInfluencedBy source: chea - category: ProgrammingInterface description: ChEA3 API endpoint for submitting gene sets and retrieving transcription factor enrichment results as JSON format: http id: chea-kg.api name: ChEA-KG API original_source: - relation_type: prov:hadPrimarySource source: chea-kg product_url: https://maayanlab.cloud/chea3/api/enrich/ secondary_source: - relation_type: prov:wasInfluencedBy source: chea - category: GraphProduct description: Neo4j knowledge graph integrating transcription factor target libraries, coexpression networks, and benchmark datasets used by the ChEA3 resource dump_format: neo4j format: neo4j id: chea-kg.graph name: ChEA-KG Database original_source: - relation_type: prov:hadPrimarySource source: chea-kg - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: remap - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: geo - relation_type: prov:hadPrimarySource source: tcga secondary_source: - relation_type: prov:wasInfluencedBy source: chea - category: Product description: Download catalog for ChEA3 transcription factor target libraries, benchmark datasets, and additional supporting libraries format: http id: chea-kg.libraries name: ChEA-KG Library Downloads original_source: - relation_type: prov:hadPrimarySource source: chea-kg - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: remap - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: geo - relation_type: prov:hadPrimarySource source: tcga product_url: https://maayanlab.cloud/chea3/index.html#content4-13 secondary_source: - relation_type: prov:wasInfluencedBy source: chea - category: Product description: Harmonizome 3.0 processed dataset downloads, including dataset-specific association files and knowledge graph serialization downloads. format: mixed id: harmonizome.downloads name: Harmonizome Downloads original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://maayanlab.cloud/Harmonizome/download secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - 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relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct description: Neo4j knowledge graph serialization of Harmonizome processed datasets, including genes, attributes, resources, datasets, and gene-attribute associations. dump_format: neo4j format: neo4j id: harmonizome.kg-neo4j latest_version: '3.0' name: Harmonizome Knowledge Graph Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://harmonizome-kg.maayanlab.cloud/ secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways publications: - authors: - Lachmann A - Xu H - Krishnan J - Berger SI - Mazloom AR - Ma'ayan A doi: 10.1093/bioinformatics/btq466 id: doi:10.1093/bioinformatics/btq466 journal: Bioinformatics title: 'ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments' year: '2010' - authors: - Keenan AB - Torre D - Lachmann A - Leong AK - Wojciechowicz ML - Utti V - Jagodnik KM - Kropiwnicki E - Wang Z - Ma'ayan A doi: 10.1093/nar/gkz446 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/chea3web - 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 Ma'ayan Lab transcription factor knowledge graph and web resource associated with the ChEA3 platform, integrating transcription factor target gene libraries, coexpression networks, benchmarking datasets, and interactive query results for transcription factor enrichment analysis. 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: '2026-05-21T00:00:00Z' layout: resource_detail license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC BY-NC-SA 4.0 name: ChEA-KG products: - category: GraphicalInterface description: Interactive ChEA3 web interface for transcription factor enrichment analysis, result tables, and network visualizations format: http id: chea-kg.portal name: ChEA-KG Explorer original_source: - relation_type: prov:hadPrimarySource source: chea-kg product_url: https://maayanlab.cloud/chea-kg/ secondary_source: - relation_type: prov:wasInfluencedBy source: chea - category: ProgrammingInterface description: ChEA3 API endpoint for submitting gene sets and retrieving transcription factor enrichment results as JSON format: http id: chea-kg.api name: ChEA-KG API original_source: - relation_type: prov:hadPrimarySource source: chea-kg product_url: https://maayanlab.cloud/chea3/api/enrich/ secondary_source: - relation_type: prov:wasInfluencedBy source: chea - category: GraphProduct description: Neo4j knowledge graph integrating transcription factor target libraries, coexpression networks, and benchmark datasets used by the ChEA3 resource dump_format: neo4j format: neo4j id: chea-kg.graph name: ChEA-KG Database original_source: - relation_type: prov:hadPrimarySource source: chea-kg - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: remap - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: geo - relation_type: prov:hadPrimarySource source: tcga secondary_source: - relation_type: prov:wasInfluencedBy source: chea - category: Product description: Download catalog for ChEA3 transcription factor target libraries, benchmark datasets, and additional supporting libraries format: http id: chea-kg.libraries name: ChEA-KG Library Downloads original_source: - relation_type: prov:hadPrimarySource source: chea-kg - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: remap - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: geo - relation_type: prov:hadPrimarySource source: tcga product_url: https://maayanlab.cloud/chea3/index.html#content4-13 secondary_source: - relation_type: prov:wasInfluencedBy source: chea publications: - authors: - Keenan AB - Torre D - Lachmann A - Leong AK - Wojciechowicz ML - Utti V - Jagodnik KM - Kropiwnicki E - Wang Z - Ma'ayan A doi: 10.1093/nar/gkz446 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 - category: Organization contact_details: - contact_type: url value: https://www.ebi.ac.uk/ id: ebi label: EMBL-EBI 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 infores_id: chebi last_modified_date: '2026-07-01T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: chebi 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 original_source: - relation_type: prov:hadPrimarySource source: chebi 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 original_source: - relation_type: prov:hadPrimarySource source: chebi product_file_size: 506456231 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 original_source: - relation_type: prov:hadPrimarySource source: chebi product_file_size: 62947851 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 original_source: - relation_type: prov:hadPrimarySource source: chebi 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 original_source: - relation_type: prov:hadPrimarySource source: chebi 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - 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relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphicalInterface description: MediaDive web portal for browsing, searching, comparing, and building microbial cultivation media recipes. format: http id: mediadive.portal name: MediaDive Web Portal original_source: - relation_type: prov:hadPrimarySource source: mediadive product_url: https://mediadive.dsmz.de/ secondary_source: - relation_type: prov:wasInformedBy source: bacdive - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - category: ProgrammingInterface description: MediaDive REST API documentation for programmatic retrieval of media, solutions, ingredients, strains, and related records. format: http id: mediadive.rest_api name: MediaDive REST API original_source: - relation_type: prov:hadPrimarySource source: mediadive product_url: https://mediadive.dsmz.de/doc/index.html secondary_source: - relation_type: prov:wasInformedBy source: bacdive - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - category: ProgrammingInterface description: MediaDive SPARQL endpoint for querying the DSMZ Digital Diversity RDF representation of MediaDive data. format: http id: mediadive.sparql name: MediaDive SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: mediadive product_url: https://sparql.dsmz.de/mediadive secondary_source: - relation_type: prov:wasInformedBy source: bacdive - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - category: Product compression: gzip description: PC v14 integrated BioPAX Level 3 unified model containing normalized pathway data, molecular interactions, cross-database entity mappings, and metadata-derived content from 26 datasource rows. format: biopax id: pathwaycommons.biopax name: Integrated BioPAX Model original_source: - relation_type: prov:hadPrimarySource source: pathwaycommons product_file_size: 1700903742 product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/pc-biopax.owl.gz secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: unichem - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: humancyc - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: dip - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: intact - relation_type: prov:wasDerivedFrom source: bind - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: GraphProduct description: RDF knowledge graph materialized by the MetaBoKG workflow from public metabolomics repository outputs, GNPS molecular-networking jobs, annotation evidence, sample metadata, and environmental and taxonomic context. The repository documents generated per-job Turtle files under mapping/kg and loading into Virtuoso named graphs. format: mixed id: metabokg.graph latest_version: arXiv v1 demonstration name: MetaboKG RDF Graph original_source: - relation_type: prov:hadPrimarySource source: metabokg - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubmedcentral - relation_type: prov:hadPrimarySource source: gnps - relation_type: prov:hadPrimarySource source: massive - relation_type: prov:hadPrimarySource source: redu product_url: https://github.com/HolobiomicsLab/MetaBoKG secondary_source: - relation_type: prov:used source: ms - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - relation_type: prov:used source: envo - relation_type: prov:used source: ncit - relation_type: prov:used source: uberon - relation_type: prov:used source: chmo - relation_type: prov:used source: sio - relation_type: prov:used source: prov-o - relation_type: prov:used source: dcat - relation_type: prov:used source: afo warnings: - No static public graph release or hosted endpoint was available in the GitHub repository when curated on 2026-06-02; the repository documents local Turtle materialization and Virtuoso loading. - category: DataModelProduct description: Turtle schema files defining MetaBoKG classes, properties, and ReDU class hierarchies used by the generated knowledge graph. format: ttl id: metabokg.schema license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: MetaBoKG RDF Schema original_source: - relation_type: prov:hadPrimarySource source: metabokg product_url: https://github.com/HolobiomicsLab/MetaBoKG/tree/main/Schema secondary_source: - relation_type: prov:wasInformedBy source: ms - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: envo - relation_type: prov:wasInformedBy source: ncit - relation_type: prov:wasInformedBy source: uberon - relation_type: prov:wasInformedBy source: chmo - relation_type: prov:wasInformedBy source: sio - relation_type: prov:wasInformedBy source: prov-o - relation_type: prov:wasInformedBy source: dcat - relation_type: prov:wasInformedBy source: afo - category: Product description: Download directory for Pathway Commons PC v14 integrated pathway and molecular interaction datasets, including BioPAX, SIF, GMT, TXT, and JSON-LD products. format: mixed id: pathwaycommons.downloads name: Pathway Commons Data Downloads original_source: - relation_type: prov:hadPrimarySource source: pathwaycommons product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/ secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: unichem - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: phosphositeplus - 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relation_type: prov:hadPrimarySource source: pathwaycommons product_file_size: 9810179 product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/pc-hgnc.sif.gz secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: unichem - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: humancyc - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: dip - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: intact - relation_type: prov:wasDerivedFrom source: bind - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: Product compression: gzip description: PC v14 Gene Matrix Transposed gene sets for pathway enrichment analysis, derived from the integrated Pathway Commons pathway archive. format: tsv id: pathwaycommons.gmt name: GMT Gene Set Format original_source: - relation_type: prov:hadPrimarySource source: pathwaycommons product_file_size: 262513 product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/pc-hgnc.gmt.gz secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - 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relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: Product compression: gzip description: PC v14 tab-delimited extended SIF node and edge file using HGNC-oriented identifiers for integrated Pathway Commons interactions. format: txt id: pathwaycommons.txt name: Extended SIF TXT Format original_source: - relation_type: prov:hadPrimarySource source: pathwaycommons product_file_size: 115608500 product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/pc-hgnc.txt.gz secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: unichem - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: humancyc - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: dip - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: intact - relation_type: prov:wasDerivedFrom source: bind - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: GraphicalInterface description: Web interface that allows searching, browsing, and exploring food compounds and their properties. format: http id: foodb.web name: FooDB Web Interface original_source: - 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relation_type: prov:hadPrimarySource source: foodb product_file_size: 180900659 product_url: https://foodb.ca/public/system/downloads/foodb_2020_4_7_mysql.tar.gz secondary_source: - relation_type: prov:wasInformedBy source: hmdb - relation_type: prov:wasInformedBy source: pubchem - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: kegg - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: pubmed - relation_type: prov:wasInformedBy source: itis - relation_type: prov:wasInformedBy source: wikipedia - relation_type: prov:wasInformedBy source: wikispecies - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - relation_type: prov:hadPrimarySource source: biobtree - 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relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://sugi.bio/biobtree/api/ - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: aminode - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: bitterdb - relation_type: prov:hadPrimarySource source: cdd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: craft - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: ena - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: fabric - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: gard - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: geneorganizer - relation_type: prov:hadPrimarySource source: genomernai - relation_type: prov:hadPrimarySource source: glyconnect - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: gtrnadb - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: homologene - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hprd - relation_type: prov:hadPrimarySource source: humancyc - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: iid - relation_type: prov:hadPrimarySource source: imgt - relation_type: prov:hadPrimarySource source: innatedb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: lncbase - relation_type: prov:hadPrimarySource source: lncbook - relation_type: prov:hadPrimarySource source: lncipedia - relation_type: prov:hadPrimarySource source: lncrnadisease - relation_type: prov:hadPrimarySource source: malacards - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: medlineplus - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: mint - relation_type: prov:hadPrimarySource source: mirbase - relation_type: prov:hadPrimarySource source: mirgenedb - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: modomics - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: nextprot - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathwaycommons - relation_type: prov:hadPrimarySource source: paxdb - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pdbe - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pirsf - relation_type: prov:hadPrimarySource source: prosite - relation_type: prov:hadPrimarySource source: proteomicsdb - relation_type: prov:hadPrimarySource source: proteopedia - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubtator - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rfam - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: scop - relation_type: prov:hadPrimarySource source: sfld - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: silva - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: snodb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: snopy - relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ - category: GraphProduct compatibility: - standard: biolink version: 4.2.1 compression: gzip description: Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - category: GraphProduct description: Public SPARQL endpoint (OpenLink Virtuoso) providing query access to the complete FORUM knowledge graph. The former credentialed FTP tarball dump (2021) is no longer published; the SPARQL endpoint is the current canonical access point for the full RDF graph. format: http id: forum.graph.dump name: FORUM Knowledge Graph SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cheminf - relation_type: prov:hadPrimarySource source: chemont - relation_type: prov:hadPrimarySource source: cito - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: fabio - relation_type: prov:hadPrimarySource source: forum - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: skos product_url: https://forum.semantic-metabolomics.fr/sparql - category: GraphProduct compression: targz description: KGX Distribution of KG-Alzheimers format: kgx id: kg-alzheimers.graph name: KGX Distribution of KG-Alzheimers original_source: - relation_type: prov:hadPrimarySource source: kg-alzheimers - relation_type: prov:hadPrimarySource source: monarchinitiative - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: zfin - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: mesh product_file_size: 210868256 product_url: https://kg-hub.berkeleybop.io/kg-alzheimers/current/kg-alzheimers.tar.gz warnings: - File was not able to be retrieved when checked on 2026-07-01; no live download location was found (GitHub releases, kghub.io/current, and Zenodo all return 404 or have no published artifact). - 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: - relation_type: prov:hadPrimarySource source: kg-covid-19 - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cord-19 - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: uniprot product_url: https://kghub.io/kg-covid-19/ warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 404 error when accessing file' - 'Download offline as of 2026-07-01: the KG-Hub reorganization has taken this file offline. The kghub.io and kg-hub.berkeleybop.io hosts return HTTP 404 for all kg-covid-19 artifacts (current and dated) and the kg-hub-public-data S3 objects return HTTP 403. No replacement public download URL is available.' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' - category: GraphProduct description: KGX Distribution of KG-IDG format: kgx id: kg-idg.graph name: KGX Distribution of KG-IDG original_source: - relation_type: prov:hadPrimarySource source: kg-idg - relation_type: prov:hadPrimarySource source: atc - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ogms - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tcrd product_url: https://kg-hub.berkeleybop.io/kg-idg/current/kg-idg.tar.gz warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 404 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-01: HTTP 404 error. The kg-hub.berkeleybop.io host is being reorganized and KG-IDG downloads are pending relocation to a new home; no live download is currently available.' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' - 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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: bigg - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: ctrp - relation_type: prov:hadPrimarySource source: cmap - relation_type: prov:hadPrimarySource source: kinomescan - relation_type: prov:hadPrimarySource source: dsstoxdb - relation_type: prov:hadPrimarySource source: gelinea - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 3676906360 product_url: https://molepro.s3.amazonaws.com/nodes.tsv - 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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: hmdb - 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relation_type: prov:hadPrimarySource source: cmap - relation_type: prov:hadPrimarySource source: kinomescan - relation_type: prov:hadPrimarySource source: dsstoxdb - relation_type: prov:hadPrimarySource source: gelinea - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv - category: GraphProduct description: Merged KG with ontology-grounded KG and literature-based graph as TSV file format: tsv id: np-kg.graph.tsv name: NP-KG TSV original_source: - relation_type: prov:hadPrimarySource source: np-kg - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: dideo - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: indra - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: oae - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pheknowlator - relation_type: prov:hadPrimarySource source: pmc - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semrep - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon product_file_size: 1074149258 product_url: https://zenodo.org/records/12536780/files/NP-KG_v3.0.0.tsv?download=1 - category: GraphProduct description: Merged KG with ontology-grounded KG and literature-based graph as NetworkX multidigraph object dump_format: gpickle format: mixed id: np-kg.graph.networkx name: NP-KG gpickle original_source: - relation_type: prov:hadPrimarySource source: np-kg - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: dideo - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: indra - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: oae - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pheknowlator - relation_type: prov:hadPrimarySource source: pmc - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semrep - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon product_file_size: 936065236 product_url: https://zenodo.org/records/12536780/files/NP-KG_v3.0.0.gpickle?download=1 - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 548527 product_url: https://skm.nib.si/downloads/pss/public/sbml - category: GraphProduct description: PSS model (v1.0.0, October 2023) in DOT Language format compatible with Graphviz. The live/current DOT export endpoint was retired upstream; this points to the latest published versioned DOT export. format: dot id: skm.pss.live.dot name: PSS Download (DOT, v1.0.0) original_source: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 405988 product_url: https://skm.nib.si/downloads/pss-version/v1.0.0/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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 2732107 product_url: https://skm.nib.si/downloads/ckn/v2-2023.06/edges - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 885747 product_url: https://skm.nib.si/downloads/ckn/v2-2023.06/nodes - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 318666 product_url: https://skm.nib.si/downloads/ckn/v1-2018.06/edges - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 702407 product_url: https://skm.nib.si/downloads/ckn/v1-2018.06/nodes - category: GraphProduct description: KGX distribution of the SRI-Reference KG format: kgx id: sri-reference-kg.graph name: SRI-Reference KG (KGX distribution) original_source: - relation_type: prov:hadPrimarySource source: sri-reference-kg - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: wormbase - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: zfin - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bspo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ddanat - relation_type: prov:hadPrimarySource source: ddpheno - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: dpo - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: emapa - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: foodon - relation_type: prov:hadPrimarySource source: fypo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: nbo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: upheno - relation_type: prov:hadPrimarySource source: wbbt - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: wbphenotype - relation_type: prov:hadPrimarySource source: xao - relation_type: prov:hadPrimarySource source: xpo - relation_type: prov:hadPrimarySource source: zfa - relation_type: prov:hadPrimarySource source: zfs - relation_type: prov:hadPrimarySource source: zp - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: decipher - relation_type: prov:hadPrimarySource source: mmrrc - relation_type: prov:hadPrimarySource source: cureid - relation_type: prov:hadPrimarySource source: phenopacket-store product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz - category: GraphProduct description: UniBioMap compound entity descriptions. format: json id: unibiomap.compound_desc name: UniBioMap Compound Descriptions original_source: - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: unibiomap product_url: https://aideepmed.com/UniBioMap/database/unibiomap/compound_desc.json warnings: - File was not able to be retrieved when checked on 2026-03-30_ No Content-Length header found - category: GraphProduct description: Integrated rare-disease knowledge graph produced by the RD-Clust workflow, connecting rare diseases to genes, phenotypes, Gene Ontology terms, drugs/ligands, and pathway interactions. Distributed as the processed disease ontograph within the RD-Clust repository. format: http id: ncatsgardkg.graph name: NCATS GARD Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: ncatsgardkg - relation_type: prov:hadPrimarySource source: gard product_url: https://github.com/ncats/RD-Clust/tree/main/data/processed secondary_source: - relation_type: prov:wasInfluencedBy source: hp - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: mondo - relation_type: prov:wasInfluencedBy source: orphanet - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: pharos - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: chebi - relation_type: prov:wasInfluencedBy source: pubchem - relation_type: prov:wasInfluencedBy source: pathwaycommons - category: Product compression: gzip description: PubChem substance information in ASN.1 format format: xml id: pubchem.substances.asn name: PubChem Substances ASN original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/ASN/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways - category: Product compression: gzip description: PubChem substance information in SDF format format: sdf id: pubchem.substances.sdf name: PubChem Substances SDF original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways publications: - authors: - Adnan Malik - Muhammad Arsalan - Carlos Moreno - Juan Mosquera - Eloy Félix - Tevfik Kizilören - Venkatesh Muthukrishnan - Barbara Zdrazil - Andrew R Leach - Noel M O’Boyle doi: 10.1093/nar/gkaf1271 id: https://doi.org/10.1093/nar/gkaf1271 journal: Nucleic Acids Research title: 'ChEBI: re-engineered for a sustainable future' year: '2026' - authors: - Hastings J - Owen G - Dekker A - Ennis M - Kale N - Muthukrishnan V - Turner S - Swainston N - Mendes P - Steinbeck C doi: 10.1093/nar/gkv1031 id: https://www.ncbi.nlm.nih.gov/pubmed/26467479 journal: Nucleic Acids Res title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.' year: '2016' 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: '2026-06-27T00:00:00Z' 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 format: http id: chembl.site is_public: true name: ChEMBL Web Interface original_source: - relation_type: prov:hadPrimarySource source: chembl product_url: https://www.ebi.ac.uk/chembl/ - category: ProgrammingInterface description: RESTful API for accessing ChEMBL data programmatically format: http id: chembl.api is_public: true name: ChEMBL API original_source: - relation_type: prov:hadPrimarySource source: chembl product_url: https://www.ebi.ac.uk/chembl/api/data/docs - category: Product compression: gzip description: PostgreSQL database dump of the complete ChEMBL database format: postgres id: chembl.postgres name: ChEMBL PostgreSQL original_source: - relation_type: prov:hadPrimarySource source: chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ - category: Product compression: gzip description: MySQL database dump of the complete ChEMBL database format: mysql id: chembl.mysql name: ChEMBL MySQL original_source: - relation_type: prov:hadPrimarySource source: chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ - category: Product compression: gzip description: SQLite database file containing the complete ChEMBL database format: sqlite id: chembl.sqlite name: ChEMBL SQLite original_source: - relation_type: prov:hadPrimarySource source: chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ - category: Product compression: gzip description: Structure data files for all chemical compounds in ChEMBL format: sdf id: chembl.sdf name: ChEMBL SDF original_source: - relation_type: prov:hadPrimarySource source: chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/ - category: Product compression: gzip description: RDF version of the ChEMBL database format: ttl id: chembl.rdf name: ChEMBL RDF original_source: - relation_type: prov:hadPrimarySource source: chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/latest/ - category: Product compression: gzip description: RDF (Turtle) download of the ChEMBL data via the EBI ChEMBL-RDF FTP archive. The former EBI RDF Platform SPARQL endpoint has been retired, so ChEMBL RDF is now distributed as downloadable Turtle dumps. format: ttl id: chembl.sparql is_public: true name: ChEMBL RDF Download original_source: - relation_type: prov:hadPrimarySource source: chembl product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/latest/ - category: MappingProduct description: Mapping between chembl_35 target chembl_ids and UniProt accessions format: txt id: chembl.map_to_uniprot is_public: true name: ChEMBL map to UniProt original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: uniprot product_file_size: 1012901 product_url: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_uniprot_mapping.txt - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. format: http id: spoke.graph name: SPOKE Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: bv-brc - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: pathophenodb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: protcid - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: spoke - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://spoke.ucsf.edu/data-tools - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j format: http id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb product_url: https://arax.ncats.io/ - 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. format: python id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: nihreporter - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: cellmarker - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: indra product_url: https://github.com/gyorilab/indra_cogex - 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: - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: icees-kg product_url: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/ - 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: - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: translator product_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg-trapi - 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: - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: translator product_url: https://robokop.renci.org/api-docs/docs/automat/metadata-metadata-get-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). format: mixed id: ibkh.graph name: iBKH Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drkg - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: ibkh - relation_type: prov:hadPrimarySource source: idisk - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for ChEMBL distributed via the NCATS Translator release site (release 2026_03_06; build chembl_36_76533eea_2025sep1_4.3.6; source version 36; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 267871 format: kgx-jsonl id: translator.chembl.graph latest_version: '2026_03_06' license: id: https://opensource.org/license/mit/ label: MIT name: Translator ChEMBL KGX Graph node_count: 153369 original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/chembl/latest/ versions: - '2026_03_06' - chembl_36_76533eea_2025sep1_4.3.6 - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: batman - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: compath - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: batman - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: compath - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: batman - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: compath - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: batman - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: compath - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 411222 product_url: https://w3id.org/biopragmatics/resources/chembl.compound/chembl.compound.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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 260194 product_url: https://w3id.org/biopragmatics/resources/chembl.target/chembl.target.tsv - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: go-cam - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathbank - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: text-mining-kp - relation_type: prov:hadPrimarySource source: translator - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://kgx-storage.rtx.ai/releases/translator_kg/latest/ versions: - '2026_03_27' - 423af7989cac - 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: - relation_type: prov:hadPrimarySource source: tcrd product_url: https://unmtid-dbs.net/download/TCRD/ secondary_source: - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: gtex - relation_type: prov:wasInfluencedBy source: omim warnings: - File was not able to be retrieved when checked on 2026-03-30_ Timeout connecting to URL - category: ProgrammingInterface description: RESTful API providing programmatic access to TCRD data through Pharos for computational workflows and custom applications format: http id: tcrd.api is_public: true name: Pharos API original_source: - relation_type: prov:hadPrimarySource source: tcrd product_url: https://pharos.nih.gov/api secondary_source: - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: gtex - relation_type: prov:wasInfluencedBy source: omim - category: DocumentationProduct description: Comprehensive documentation describing TCRD data sources, schema structure, and usage guidelines format: http id: tcrd.documentation name: TCRD Documentation original_source: - relation_type: prov:hadPrimarySource source: tcrd product_url: https://unmtid-dbs.net/download/TCRD/ secondary_source: - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: gtex - relation_type: prov:wasInfluencedBy source: omim warnings: - File was not able to be retrieved when checked on 2026-03-30_ Timeout connecting to URL - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - 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relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://sugi.bio/biobtree/api/ - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - 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A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - 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biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - 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: - relation_type: prov:hadPrimarySource source: kg-covid-19 - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - 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The kghub.io and kg-hub.berkeleybop.io hosts return HTTP 404 for all kg-covid-19 artifacts (current and dated) and the kg-hub-public-data S3 objects return HTTP 403. No replacement public download URL is available.' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' - 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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - 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relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 3676906360 product_url: https://molepro.s3.amazonaws.com/nodes.tsv - 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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: pharos - 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relation_type: prov:hadPrimarySource source: dsstoxdb - relation_type: prov:hadPrimarySource source: gelinea - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv - category: GraphProduct description: Integrated pharmacological knowledge graph (PharmDB-K) of drugs, targets, diseases, and associations format: http id: pharmdb.graph name: PharmDB-K Graph original_source: - relation_type: prov:hadPrimarySource source: pharmdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dip - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: mint - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: dcdb - relation_type: prov:hadPrimarySource source: gad - relation_type: prov:hadPrimarySource source: matador - relation_type: prov:hadPrimarySource source: t3db - relation_type: prov:hadPrimarySource source: wipo-tkp - category: GraphProduct description: RDF knowledge graph of the Experimental Natural Products Knowledge Graph, integrating experimental LC-MS/MS spectra and GNPS-based annotations, ISDB-LOTUS structural annotations, taxonomic and bioactivity metadata, cross-linked to Wikidata and served from the public GraphDB/SPARQL endpoint. format: ttl id: kg-enp.graph license: id: https://creativecommons.org/publicdomain/zero/1.0/legalcode label: CC0-1.0 name: ENPKG RDF Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: kg-enp - 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Distributed as the processed disease ontograph within the RD-Clust repository. format: http id: ncatsgardkg.graph name: NCATS GARD Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: ncatsgardkg - relation_type: prov:hadPrimarySource source: gard product_url: https://github.com/ncats/RD-Clust/tree/main/data/processed secondary_source: - relation_type: prov:wasInfluencedBy source: hp - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: mondo - relation_type: prov:wasInfluencedBy source: orphanet - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: pharos - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: chebi - relation_type: prov:wasInfluencedBy source: pubchem - relation_type: prov:wasInfluencedBy source: pathwaycommons - category: GraphProduct description: The SPOKE-OKN knowledge graph, an OKN-hosted RDF publication of the SPOKE biomedical and environmental health knowledge graph, served through FRINK query services. format: ttl id: spoke-okn.graph name: SPOKE-OKN Graph original_source: - 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relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways - category: Product compression: gzip description: PubChem substance information in SDF format format: sdf id: pubchem.substances.sdf name: PubChem Substances SDF original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways 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: 10.1093/nar/gkad1004 id: doi:10.1093/nar/gkad1004 journal: Nucleic Acids Research preferred: true title: 'The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods' year: '2024' 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: https://chemicalchecker.com/ id: chemicalchecker last_modified_date: '2026-06-18T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: chemicalchecker product_url: https://chemicalchecker.com/downloads/root warnings: [] - category: ProcessProduct description: Software tool for producing bioactivity signature vectors. format: python id: chemicalchecker.signaturizer name: Signaturizer original_source: - relation_type: prov:hadPrimarySource source: chemicalchecker product_url: https://github.com/sbnb-irb/signaturizer - category: ProgrammingInterface description: Programmatic interface for Chemical Checker data. format: http id: chemicalchecker.api name: Chemical Checker RESTful API original_source: - relation_type: prov:hadPrimarySource source: chemicalchecker product_url: https://chemicalchecker.com/api/db/getSignature/ - category: DocumentationProduct description: Main Chemical Checker portal for searching molecules, browsing statistics, help, and downloads. format: http id: chemicalchecker.portal name: Chemical Checker Portal original_source: - relation_type: prov:hadPrimarySource source: chemicalchecker product_url: https://chemicalchecker.com/ warnings: [] - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: bioteque - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: cellosaurus - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chemicalchecker - relation_type: prov:hadPrimarySource source: clue - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: creeds - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: dorothea - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: huri - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: offsides - relation_type: prov:hadPrimarySource source: omnipath - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: pharmacodb - relation_type: prov:hadPrimarySource source: prism - relation_type: prov:hadPrimarySource source: progeny - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: repodb - relation_type: prov:hadPrimarySource source: repohub - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues product_url: https://bioteque.irbbarcelona.org/downloads/embeddings publications: - authors: - Duran-Frigola M - Pauls E - Guitart-Pla O - Bertoni M - Alcalde V - Amat D - Juan-Blanco T - Aloy P doi: 10.1038/s41587-020-0502-7 id: https://www.ncbi.nlm.nih.gov/pubmed/32440005 journal: Nat Biotechnol preferred: true title: Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker year: '2020' 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: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: cheminf product_file_size: 22830 product_url: http://purl.obolibrary.org/obo/cheminf.owl - category: GraphProduct description: Public SPARQL endpoint (OpenLink Virtuoso) providing query access to the complete FORUM knowledge graph. The former credentialed FTP tarball dump (2021) is no longer published; the SPARQL endpoint is the current canonical access point for the full RDF graph. format: http id: forum.graph.dump name: FORUM Knowledge Graph SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cheminf - relation_type: prov:hadPrimarySource source: chemont - relation_type: prov:hadPrimarySource source: cito - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: fabio - relation_type: prov:hadPrimarySource source: forum - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: skos product_url: https://forum.semantic-metabolomics.fr/sparql publications: - authors: - Hastings J - Chepelev L - Willighagen E - Adams N - Steinbeck C - Dumontier M doi: 10.1371/journal.pone.0025513 id: https://www.ncbi.nlm.nih.gov/pubmed/21991315 journal: PLoS One title: 'The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web' year: '2011' 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: '2026-06-18T00:00:00Z' layout: resource_detail name: ChemOnt products: - category: GraphicalInterface description: ClassyFire web interface for chemical classification and ontology exploration format: http id: chemont.classyfire name: ClassyFire Web Interface original_source: - relation_type: prov:hadPrimarySource source: chemont 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 original_source: - relation_type: prov:hadPrimarySource source: chemont product_file_size: 307900 product_url: http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip - category: GraphProduct description: Public SPARQL endpoint (OpenLink Virtuoso) providing query access to the complete FORUM knowledge graph. The former credentialed FTP tarball dump (2021) is no longer published; the SPARQL endpoint is the current canonical access point for the full RDF graph. format: http id: forum.graph.dump name: FORUM Knowledge Graph SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cheminf - relation_type: prov:hadPrimarySource source: chemont - relation_type: prov:hadPrimarySource source: cito - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: fabio - relation_type: prov:hadPrimarySource source: forum - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: skos product_url: https://forum.semantic-metabolomics.fr/sparql publications: - authors: - Djoumbou Feunang Y - Eisner R - Knox C - Chepelev L - Hastings J - Owen G - Fahy E - Steinbeck C - Subramanian S - Bolton E - Greiner R - Wishart DS doi: 10.1186/s13321-016-0174-y id: https://www.ncbi.nlm.nih.gov/pubmed/27867422 journal: J Cheminform preferred: true title: 'ClassyFire: automated chemical classification with a comprehensive, computable taxonomy' year: '2016' 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: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: chiro 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 original_source: - relation_type: prov:hadPrimarySource source: chiro product_file_size: 3337 product_url: http://purl.obolibrary.org/obo/chiro.obo publications: - authors: - Charles Tapley Hoyt - Christopher Mungall - Nicole Vasilevsky - Daniel Domingo-Fernández - Matthew Healy - Viswa Colluru doi: 10.26434/chemrxiv.12591221 id: https://doi.org/10.26434/chemrxiv.12591221 title: Extension of Roles in the ChEBI Ontology year: '2020' 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: '2026-06-27T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: chmo product_file_size: 460248 product_url: http://purl.obolibrary.org/obo/chmo.owl - category: GraphProduct description: RDF knowledge graph materialized by the MetaBoKG workflow from public metabolomics repository outputs, GNPS molecular-networking jobs, annotation evidence, sample metadata, and environmental and taxonomic context. The repository documents generated per-job Turtle files under mapping/kg and loading into Virtuoso named graphs. format: mixed id: metabokg.graph latest_version: arXiv v1 demonstration name: MetaboKG RDF Graph original_source: - relation_type: prov:hadPrimarySource source: metabokg - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubmedcentral - relation_type: prov:hadPrimarySource source: gnps - relation_type: prov:hadPrimarySource source: massive - relation_type: prov:hadPrimarySource source: redu product_url: https://github.com/HolobiomicsLab/MetaBoKG secondary_source: - relation_type: prov:used source: ms - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - relation_type: prov:used source: envo - relation_type: prov:used source: ncit - relation_type: prov:used source: uberon - relation_type: prov:used source: chmo - relation_type: prov:used source: sio - relation_type: prov:used source: prov-o - relation_type: prov:used source: dcat - relation_type: prov:used source: afo warnings: - No static public graph release or hosted endpoint was available in the GitHub repository when curated on 2026-06-02; the repository documents local Turtle materialization and Virtuoso loading. - category: DataModelProduct description: Turtle schema files defining MetaBoKG classes, properties, and ReDU class hierarchies used by the generated knowledge graph. format: ttl id: metabokg.schema license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: MetaBoKG RDF Schema original_source: - relation_type: prov:hadPrimarySource source: metabokg product_url: https://github.com/HolobiomicsLab/MetaBoKG/tree/main/Schema secondary_source: - relation_type: prov:wasInformedBy source: ms - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: envo - relation_type: prov:wasInformedBy source: ncit - relation_type: prov:wasInformedBy source: uberon - relation_type: prov:wasInformedBy source: chmo - relation_type: prov:wasInformedBy source: sio - relation_type: prov:wasInformedBy source: prov-o - relation_type: prov:wasInformedBy source: dcat - relation_type: prov:wasInformedBy source: afo publications: [] 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: - relation_type: prov:hadPrimarySource source: chr - relation_type: prov:hadPrimarySource source: geno - relation_type: prov:hadPrimarySource source: gff - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: skos product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl 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: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: cido product_file_size: 2511321 product_url: http://purl.obolibrary.org/obo/cido.owl publications: - authors: - He Y - Yu H - Huffman A - Lin AY - Natale DA - Beverley J - Zheng L - Perl Y - Wang Z - Liu Y - Ong E - Wang Y - Huang P - Tran L - Du J - Shah Z - Shah E - Desai R - Huang HH - Tian Y - Merrell E - Duncan WD - Arabandi S - Schriml LM - Zheng J - Masci AM - Wang L - Liu H - Smaili FZ - Hoehndorf R - Pendlington ZM - Roncaglia P - Ye X - Xie J - Tang YW - Yang X - Peng S - Zhang L - Chen L - Hur J - Omenn GS - Athey B - Smith B doi: 10.1186/s13326-022-00279-z id: https://www.ncbi.nlm.nih.gov/pubmed/36271389 journal: J Biomed Semantics title: 'A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology' year: '2022' repository: https://github.com/cido-ontology/cido - activity_status: active category: Aggregator collection: - omop 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 - biomedical - information technology homepage_url: https://openconceptlab.org/project/ciel/ id: ciel last_modified_date: '2026-04-10T00:00:00Z' 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: 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: athena - relation_type: prov:hadPrimarySource source: cdiscvocab - relation_type: prov:hadPrimarySource source: ciel - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: snomedct product_url: https://athena.ohdsi.org/search-terms/start warnings: - Athena mapping exports are accessed through the authenticated Athena web application; stable direct public file URLs are not exposed. - category: Product description: Downloadable standardized vocabulary bundles for OMOP CDM assembled through the authenticated Athena web application format: csv id: athena.vocabularies name: Athena Vocabulary Downloads original_source: - relation_type: prov:hadPrimarySource source: athena - relation_type: prov:hadPrimarySource source: cdiscvocab - relation_type: prov:hadPrimarySource source: ciel - relation_type: prov:hadPrimarySource source: gemscript - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: medispan-gpi - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ndcd - relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: snomedct product_url: https://athena.ohdsi.org/vocabulary/list warnings: - Athena vocabulary downloads are prepared through the logged-in web application; stable direct public file URLs are not exposed. 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 - information technology homepage_url: https://github.com/BgeeDB/confidence-information-ontology id: cio last_modified_date: '2026-06-05T00:00:00Z' 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: Confidence Information Ontology products: - category: OntologyProduct description: Confidence Information Ontology in OWL format format: owl id: cio.owl name: cio.owl original_source: - relation_type: prov:hadPrimarySource source: cio 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 original_source: - relation_type: prov:hadPrimarySource source: cio product_file_size: 3960 product_url: http://purl.obolibrary.org/obo/cio.obo publications: - authors: - Bastian FB - Chibucos MC - Gaudet P - Giglio M - Holliday GL - Huang H - Lewis SE - Niknejad A - Orchard S - Poux S - Skunca N - Robinson-Rechavi M doi: 10.1093/database/bav043 id: https://www.ncbi.nlm.nih.gov/pubmed/25957950 journal: Database (Oxford) title: 'The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations' year: '2015' 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 homepage_url: https://www.circbase.org/ id: circbase last_modified_date: '2026-06-01T00:00:00Z' layout: resource_detail license: id: http://www.circbase.org/ label: circBase site terms (dataset-specific; cite original studies) name: circBase products: - 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relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pathophenodb - relation_type: prov:wasInfluencedBy source: pfam - relation_type: prov:wasInfluencedBy source: pid - relation_type: prov:wasInfluencedBy source: protcid - relation_type: prov:wasInfluencedBy source: pubmed - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: sider - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikipathways 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: KnowledgeGraph creation_date: '2026-04-06T00:00:00Z' description: Clinical Knowledge Graph (CKG) is an open-source biomedical knowledge graph platform that integrates proteomics data, clinical data, biomedical databases, and literature to support clinically meaningful querying, analysis, and hypothesis generation. CKG has been integrated into the BioCypher framework while its original repository, documentation, and graph database dump remain available. domains: - clinical - biomedical - precision medicine - proteomics homepage_url: https://ckg.readthedocs.io/ id: ckg last_modified_date: '2026-06-01T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: Clinical Knowledge Graph products: - category: GraphProduct description: Graph database dump and additional relationship files for the Clinical Knowledge Graph. format: neo4j id: ckg.graph latest_version: '1' license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: CKG Graph Database Dump original_source: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: ckg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: DocumentationProduct description: Project documentation for installing, building, and querying the Clinical Knowledge Graph. format: http id: ckg.docs name: CKG Documentation original_source: - relation_type: prov:hadPrimarySource source: ckg product_url: https://ckg.readthedocs.io/ publications: - authors: - Alberto Santos - Ana R. Colaço - Annelaura B. Nielsen - Lili Niu - Maximilian Strauss - Philipp E. Geyer - Fabian Coscia - Nicolai J. Wewer Albrechtsen - Filip Mundt - Lars Juhl Jensen - Matthias Mann doi: 10.1038/s41587-021-01145-6 id: doi:10.1038/s41587-021-01145-6 journal: Nature Biotechnology preferred: true title: A knowledge graph to interpret clinical proteomics data year: '2022' repository: https://github.com/MannLabs/CKG 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 infores_id: cl last_modified_date: '2026-06-18T00:00:00Z' 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: 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 original_source: - relation_type: prov:hadPrimarySource source: cl product_file_size: 65879178 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 original_source: - relation_type: prov:hadPrimarySource source: cl product_file_size: 17326417 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 original_source: - relation_type: prov:hadPrimarySource source: cl product_file_size: 39845315 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 original_source: - relation_type: prov:hadPrimarySource source: cl product_file_size: 9533929 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) original_source: - relation_type: prov:hadPrimarySource source: cl product_file_size: 3346117 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) original_source: - relation_type: prov:hadPrimarySource source: cl product_file_size: 6060633 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 original_source: - relation_type: prov:hadPrimarySource source: cl product_file_size: 12575443 product_url: http://purl.obolibrary.org/obo/cl/cl-base.owl - category: OntologyProduct description: complete CL but with no imports or external axioms format: obo id: cl.cl-base.obo name: CL base module (OBO version) original_source: - relation_type: prov:hadPrimarySource source: cl product_file_size: 3755296 product_url: http://purl.obolibrary.org/obo/cl/cl-base.obo - category: OntologyProduct description: complete CL but with no imports or external axioms format: json id: cl.cl-base.json name: CL base module (OBOGraph-JSON version) original_source: - relation_type: prov:hadPrimarySource source: cl product_file_size: 7755251 product_url: http://purl.obolibrary.org/obo/cl/cl-base.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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. format: http id: spoke.graph name: SPOKE Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: bv-brc - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: pathophenodb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: protcid - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: spoke - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://spoke.ucsf.edu/data-tools - 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). format: mixed id: ibkh.graph name: iBKH Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drkg - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: ibkh - relation_type: prov:hadPrimarySource source: idisk - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - description: The MechRepoNet knowledge graph in its original format format: mixed id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: complexportal - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: mechreponet - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: unii product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication - 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: - relation_type: prov:hadPrimarySource source: bioportal - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: genemania - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pheknowlator - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vo 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 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: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: circbase - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rna-kg - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: vo - relation_type: prov:hadPrimarySource source: wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: circbase - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rna-kg - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: vo - relation_type: prov:hadPrimarySource source: wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: circbase - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rna-kg - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: vo - relation_type: prov:hadPrimarySource source: wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: cob - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: ecto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: fbbt - 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A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - 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The graph is produced by the NLM-CKN ETL pipeline as an ArangoDB archive and served via the web application at https://nlm-ckn.org. format: http id: nlm-ckn.graph name: nlm-ckn-graph original_source: - relation_type: prov:hadPrimarySource source: nlm-ckn - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: pubmed product_url: https://nlm-ckn.org secondary_source: - relation_type: prov:wasInfluencedBy source: cl - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: pato - relation_type: prov:wasInfluencedBy source: mondo - relation_type: prov:wasInfluencedBy source: hsapdv - category: GraphProduct description: The SPOKE-OKN knowledge graph, an OKN-hosted RDF publication of the SPOKE biomedical and environmental health knowledge graph, served through FRINK query services. format: ttl id: spoke-okn.graph name: SPOKE-OKN Graph original_source: - relation_type: prov:hadPrimarySource source: spoke-okn - relation_type: prov:wasDerivedFrom source: spoke product_url: https://spoke.ucsf.edu secondary_source: - relation_type: prov:wasInfluencedBy source: bgee - relation_type: prov:wasInfluencedBy source: bindingdb - relation_type: prov:wasInfluencedBy source: bv-brc - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: civic - relation_type: prov:wasInfluencedBy source: cl - relation_type: prov:wasInfluencedBy source: clinicaltrialsgov - relation_type: prov:wasInfluencedBy source: diseases - relation_type: prov:wasInfluencedBy source: doid - relation_type: prov:wasInfluencedBy source: drugbank - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: foodb - relation_type: prov:wasInfluencedBy source: gdsc - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: gwascatalog - relation_type: prov:wasInfluencedBy source: hpa - relation_type: prov:wasInfluencedBy source: interpro - relation_type: prov:wasInfluencedBy source: kegg - relation_type: prov:wasInfluencedBy source: lincs-l1000 - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: metacyc - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: ncbitaxon - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pathophenodb - relation_type: prov:wasInfluencedBy source: pfam - relation_type: prov:wasInfluencedBy source: pid - relation_type: prov:wasInfluencedBy source: protcid - relation_type: prov:wasInfluencedBy source: pubmed - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: sider - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikipathways publications: - authors: - Diehl AD - Meehan TF - Bradford YM - Brush MH - Dahdul WM - Dougall DS - He Y - Osumi-Sutherland D - Ruttenberg A - Sarntivijai S - Van Slyke CE - Vasilevsky NA - Haendel MA - Blake JA - Mungall CJ doi: 10.1186/s13326-016-0088-7 id: https://www.ncbi.nlm.nih.gov/pubmed/27377652 journal: J Biomed Semantics title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.' year: '2016' 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: '2026-05-27T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: cl-kg - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cellxgene product_url: https://cellular-semantics.sanger.ac.uk/browser/ 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: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: clao 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 original_source: - relation_type: prov:hadPrimarySource source: clao product_file_size: 74344 product_url: http://purl.obolibrary.org/obo/clao.obo publications: [] repository: https://github.com/luis-gonzalez-m/Collembola - activity_status: active category: KnowledgeGraph collection: - okn - ber contacts: - category: Individual contact_details: - contact_type: email value: climatepub4kg@tuprd.onmicrosoft.com - contact_type: github value: aayushacharya label: Aayush Acharya - 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. domains: - environment - information technology evaluation_page: resource/climatemodelskg/climatemodelskg_eval_automated.html homepage_url: https://frink.renci.org/registry/kgs/climatepub4-kg/ id: climatemodelskg last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: Climate Models KG products: - category: ProgrammingInterface description: SPARQL endpoint for Climate Models KG format: http id: climatemodelskg.sparql name: Climate Models KG SPARQL original_source: - relation_type: prov:hadPrimarySource source: climatemodelskg product_url: https://apps.okn.us/climatemodelskg/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for Climate Models KG id: climatemodelskg.tpf name: Climate Models KG TPF original_source: - relation_type: prov:hadPrimarySource source: climatemodelskg product_url: https://apps.okn.us/ldf/climatemodelskg - category: GraphProduct description: RDF/Turtle knowledge graph integrating climate model and dataset metadata (from ESGF, CMIP controlled vocabularies, and the NASA GCMD keyword taxonomy) with entities and relationships extracted from climate-science publications. Served through the FRINK federation and the SPARQL and TPF endpoints. format: ttl id: climatemodelskg.graph name: Climate Models KG Graph original_source: - relation_type: prov:hadPrimarySource source: climatemodelskg - relation_type: prov:hadPrimarySource source: esgf - relation_type: prov:hadPrimarySource source: cmip - relation_type: prov:hadPrimarySource source: gcmd product_url: https://frink.renci.org/registry/kgs/climatepub4-kg/ - 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 homepage_url: https://clinicalgenome.org/ id: clingen infores_id: clingen last_modified_date: '2026-06-27T00:00:00Z' 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: 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. These curations classify evidence as Definitive, Strong, Moderate, Limited, No Reported Evidence, or Disputed. format: csv id: clingen.gene-disease name: Gene-Disease Validity Curations original_source: - relation_type: prov:hadPrimarySource source: clingen product_url: https://search.clinicalgenome.org/kb/gene-validity - category: Product description: ClinGen Dosage Sensitivity curations evaluate whether genes and genomic regions are sensitive to copy number variation. These curations determine if haploinsufficiency (loss of one copy) or triplosensitivity (gain of one copy) of a gene/region causes disease. format: tsv id: clingen.dosage name: Dosage Sensitivity Curations original_source: - relation_type: prov:hadPrimarySource source: clingen product_url: https://search.clinicalgenome.org/kb/gene-dosage - category: Product description: ClinGen Clinical Actionability evaluations assess the clinical actions available to manage risk for patients with specific genetic disorders. 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 original_source: - relation_type: prov:hadPrimarySource source: clingen 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 original_source: - relation_type: prov:hadPrimarySource source: clingen 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. format: http id: clingen.evrepo.api name: ClinGen Evidence Repository API original_source: - relation_type: prov:hadPrimarySource source: clingen product_url: https://erepo.clinicalgenome.org/evrepo/api/summary/ - 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. format: http id: clingen.web.interface name: ClinGen Search Interface original_source: - relation_type: prov:hadPrimarySource source: clingen 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 original_source: - relation_type: prov:hadPrimarySource source: clingen 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - category: GraphProduct description: Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. 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relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/geneticskp/latest/ versions: - '2026_03_27' - geneticskp_2026-03-27_1f1ad62b_2025sep1_4.3.6 - 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 original_source: - relation_type: prov:hadPrimarySource source: litvar product_url: https://www.ncbi.nlm.nih.gov/research/litvar2/ secondary_source: - relation_type: prov:wasInformedBy source: clingen - relation_type: prov:wasInformedBy source: clinvar - relation_type: prov:wasInformedBy source: dbsnp - relation_type: prov:wasDerivedFrom source: pmc - relation_type: prov:wasDerivedFrom source: pubmed - relation_type: prov:used source: pubtator - 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 original_source: - 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relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: decipher - relation_type: prov:hadPrimarySource source: mmrrc - relation_type: prov:hadPrimarySource source: cureid - relation_type: prov:hadPrimarySource source: phenopacket-store product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz - category: GraphProduct description: TRAPI knowledge graph served by the Genetics KP, exposing gene/disease and gene/phenotype associations computed from large-scale human genetics data (e.g. Genebass exome association statistics aggregated with methods such as MAGMA and the HuGE calculator) and integrated curated gene-condition resources. The linked endpoint returns the meta knowledge graph describing the served node and edge types. format: json id: genetics-kp.graph name: Genetics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: genetics-kp - relation_type: prov:hadPrimarySource source: genebass product_file_size: 3538 product_url: https://genetics-kp.transltr.io/genetics_provider/trapi/v1.5/meta_knowledge_graph secondary_source: - relation_type: prov:wasInfluencedBy source: gencc - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: clingen publications: - authors: - Rehm HL - Berg JS - Brooks LD - Bustamante CD - Evans JP - Landrum MJ - Ledbetter DH - et al. 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: - Erica F. Andersen - ClinGen Consortium 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: '2025' 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: - biomedical - clinical - information technology - 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 license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC BY-NC-SA 4.0 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: clinical-data-kp product_url: https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Data-Provider publications: - authors: - Casey N. Ta - Michel Dumontier - George Hripcsak - Nicholas P. Tatonetti - Chunhua Weng doi: 10.1038/sdata.2018.273 id: https://www.ncbi.nlm.nih.gov/pubmed/30480666 journal: Scientific Data preferred: true title: Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records year: '2018' repository: https://github.com/WengLab-InformaticsResearch/cohd_api 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 evaluation_page: resource/clinicalkg/clinicalkg_eval.html homepage_url: https://ckg.readthedocs.io/ id: clinicalkg last_modified_date: '2026-05-30T00:00:00Z' layout: resource_detail license: id: https://opensource.org/licenses/MIT label: MIT License name: Clinical Knowledge Graph (CKG) products: - category: DocumentationProduct description: Project documentation for installation, graph building, querying, reporting, and API usage. format: http id: clinicalkg.docs name: CKG Documentation original_source: - relation_type: prov:hadPrimarySource source: clinicalkg product_url: https://ckg.readthedocs.io/ - 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: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: clinicalkg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: 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 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 - biomedical - public health - drug discovery - precision medicine fairsharing_id: FAIRsharing.mewhad homepage_url: https://clinicaltrials.gov/ id: clinicaltrialsgov infores_id: clinicaltrials last_modified_date: '2026-06-18T00:00:00Z' 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: aact 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: - relation_type: prov:hadPrimarySource 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. format: http id: spoke.graph name: SPOKE Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: bv-brc - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: pathophenodb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: protcid - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: spoke - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://spoke.ucsf.edu/data-tools - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). format: http id: disgenet.data name: DisGeNET Data original_source: - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: mgd - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: psygenet - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: phewascat - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: finngen - relation_type: prov:hadPrimarySource source: clinicaltrialsgov product_url: https://www.disgenet.com/ - 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. format: python id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: nihreporter - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: cellmarker - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: indra product_url: https://github.com/gyorilab/indra_cogex - category: Product description: Complete RepoDB dataset containing drug repositioning successes and failures, with approved drugs, indications, and clinical trial outcomes. Distributed as full.csv via the figshare deposit "repoDB (Final Database)" (DOI 10.6084/m9.figshare.3811674). format: csv id: repodb.full_dataset name: RepoDB Full Dataset original_source: - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: repodb product_file_size: 1029743 product_url: https://ndownloader.figshare.com/files/7341422 - category: Product description: Clinical trial information from ClinicalTrials.gov format: http id: genecards.clinical.trials name: GeneCards Clinical Trials original_source: - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: genecards product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ 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: - relation_type: prov:hadPrimarySource source: aact - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: aact - relation_type: prov:hadPrimarySource source: clinicaltrialsgov product_url: https://aact.ctti-clinicaltrials.org/downloads - category: Product compression: gzip description: clinicaltrials OBO format: obo id: obo-db-ingest.clinicaltrialsgov.obo license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials OBO original_source: - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: obo-db-ingest 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.clinicaltrialsgov.owl license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials OWL original_source: - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: obo-db-ingest 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.clinicaltrialsgov.json license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials OBO Graph JSON original_source: - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: obo-db-ingest 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.clinicaltrialsgov.sssom.tsv license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials SSSOM original_source: - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: obo-db-ingest 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.clinicaltrialsgov.tsv license: id: https://clinicaltrials.gov/about-site/terms-conditions#availability label: Custom name: clinicaltrials Nodes TSV original_source: - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 19140027 product_url: https://w3id.org/biopragmatics/resources/clinicaltrials/clinicaltrials.tsv - category: Product description: Raw format target information including all TTD target data format: txt id: ttd.targets-raw name: TTD Targets Information original_source: - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: pubmed 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')) - category: Product description: Drug to disease mapping with ICD identifiers format: txt id: ttd.drug-disease name: Drug-Disease Mapping original_source: - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: pubmed 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')) - category: Product description: Target to disease mapping with ICD identifiers format: txt id: ttd.target-disease name: Target-Disease Mapping original_source: - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: pubmed 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')) - category: Product description: Target to drug mapping with mode of action information format: csv id: ttd.target-drug name: Target-Drug Mapping original_source: - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: pubmed 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')) - category: Product description: Biomarker to disease mapping with ICD identifiers format: txt id: ttd.biomarker-disease name: Biomarker-Disease Mapping original_source: - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: pubmed 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')) - category: Product description: Target to compound mapping with experimental activity data format: txt id: ttd.target-compound name: Target-Compound Activity Data original_source: - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: pubmed 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')) - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for CTKP distributed via the NCATS Translator release site (release 2026_03_27; build ctkp_3.1.37_a99268cc_2025sep1_4.3.6; source version 3.1.37; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 438575 format: kgx-jsonl id: translator.ctkp.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator CTKP KGX Graph node_count: 41243 original_source: - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/ctkp/latest/ versions: - '2026_03_27' - ctkp_3.1.37_a99268cc_2025sep1_4.3.6 - category: Product compression: zip description: Pipe-delimited text exports of the AACT database for import into databases or analysis tools format: csv id: aact.pipe_delimited name: AACT Pipe-Delimited Downloads original_source: - relation_type: prov:hadPrimarySource source: aact - relation_type: prov:hadPrimarySource source: clinicaltrialsgov product_url: https://aact.ctti-clinicaltrials.org/downloads - category: Product description: Alzheimer's disease case study drug repurposing predictions format: csv id: kg-predict.ad_predictions name: AD Drug Predictions original_source: - relation_type: prov:hadPrimarySource source: kg-predict product_file_size: 44034 product_url: http://nlp.case.edu/public/data/GPKG-Predict/case_study_predict_results.csv secondary_source: - relation_type: prov:wasInformedBy source: clinicaltrialsgov - category: Product description: Alzheimer's disease National Clinical Trial evidence file used with the KG-Predict case study format: csv id: kg-predict.ad_nct_evidence name: AD National Clinical Trial Evidence original_source: - relation_type: prov:hadPrimarySource source: kg-predict product_file_size: 1789 product_url: http://nlp.case.edu/public/data/GPKG-Predict/ad_nct_evidence.csv secondary_source: - relation_type: prov:wasDerivedFrom source: clinicaltrialsgov - category: GraphProduct description: Source CSV tables for AcuKG, including acupoint therapeutic actions, indications, anatomy relationships, clinical trial links, and PubMed links. edge_count: 11527 format: csv id: acukg.csv name: AcuKG CSV tables node_count: 1839 original_source: - relation_type: prov:hadPrimarySource source: acukg - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:used source: mesh - relation_type: prov:used source: uberon - relation_type: prov:used source: snomedct product_url: https://github.com/yimingli99/AcuKG-Knowledge-graph-for-medical-acupuncture/tree/main/AcuKG - category: GraphProduct description: RDF Turtle representation of AcuKG relationship tables. edge_count: 11527 format: ttl id: acukg.rdf name: AcuKG RDF Turtle files node_count: 1839 original_source: - relation_type: prov:hadPrimarySource source: acukg - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:used source: mesh - relation_type: prov:used source: uberon - relation_type: prov:used source: snomedct product_url: https://github.com/yimingli99/AcuKG-Knowledge-graph-for-medical-acupuncture/tree/main/AcuKG_RDF - category: GraphProduct description: JSON representation of AcuKG relationship tables. edge_count: 11527 format: json id: acukg.json name: AcuKG JSON files node_count: 1839 original_source: - relation_type: prov:hadPrimarySource source: acukg - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:used source: mesh - relation_type: prov:used source: uberon - relation_type: prov:used source: snomedct product_url: https://github.com/yimingli99/AcuKG-Knowledge-graph-for-medical-acupuncture/tree/main/AcuKG_json - category: GraphProduct description: Multilayer epilepsy knowledge graph generated by the myAURA data processing workflow from biomedical, clinical, literature, and patient-centered data sources. format: mixed id: myaura.graph name: myAURA epilepsy knowledge graph original_source: - relation_type: prov:hadPrimarySource source: myaura - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: web-of-science product_url: https://github.com/cns-iu/myaura - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - 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A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - 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biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - category: GraphProduct description: The SPOKE-OKN knowledge graph, an OKN-hosted RDF publication of the SPOKE biomedical and environmental health knowledge graph, served through FRINK query services. format: ttl id: spoke-okn.graph name: SPOKE-OKN Graph original_source: - relation_type: prov:hadPrimarySource source: spoke-okn - 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relation_type: prov:wasInfluencedBy source: kegg - relation_type: prov:wasInfluencedBy source: lincs-l1000 - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: metacyc - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: ncbitaxon - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pathophenodb - relation_type: prov:wasInfluencedBy source: pfam - relation_type: prov:wasInfluencedBy source: pid - relation_type: prov:wasInfluencedBy source: protcid - relation_type: prov:wasInfluencedBy source: pubmed - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: sider - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikipathways - category: GraphProduct description: Live TRAPI/BioThings metadata endpoint for the Multiomics BigGIM-DrugResponse KP, exposing the multiomics knowledge graph served by the Multiomics Provider (built from GTEx, TCGA, and drug-response data, with additional clinical-trials, drug-approval and knowledge-resource inputs). format: json id: multiomics-kp.graph name: Multiomics KP Knowledge Graph original_source: - 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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 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 original_source: - relation_type: prov:hadPrimarySource source: clinvar 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) original_source: - relation_type: prov:hadPrimarySource source: clinvar 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) original_source: - relation_type: prov:hadPrimarySource source: clinvar 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 original_source: - relation_type: prov:hadPrimarySource source: clinvar 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) original_source: - relation_type: prov:hadPrimarySource source: clinvar 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 original_source: - relation_type: prov:hadPrimarySource source: clinvar 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. 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relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/geneticskp/latest/ versions: - '2026_03_27' - geneticskp_2026-03-27_1f1ad62b_2025sep1_4.3.6 - 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 original_source: - relation_type: prov:hadPrimarySource source: litvar product_url: https://www.ncbi.nlm.nih.gov/research/litvar2/ secondary_source: - relation_type: prov:wasInformedBy source: clingen - relation_type: prov:wasInformedBy source: clinvar - relation_type: prov:wasInformedBy source: dbsnp - relation_type: prov:wasDerivedFrom source: pmc - relation_type: prov:wasDerivedFrom source: pubmed - relation_type: prov:used source: pubtator - 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 original_source: - relation_type: prov:hadPrimarySource source: litvar product_url: https://www.ncbi.nlm.nih.gov/research/litvar2-api/ secondary_source: - relation_type: prov:wasInformedBy source: clingen - relation_type: prov:wasInformedBy source: clinvar - relation_type: prov:wasInformedBy source: dbsnp - relation_type: prov:wasDerivedFrom source: pmc - relation_type: prov:wasDerivedFrom source: pubmed - relation_type: prov:used source: pubtator - category: Product compression: zip description: Bulk downloadable ActiveDriverDB datasets, including cancer, disease, and population mutations affecting PTM sites and kinase-target site-specific networks. id: activedriverdb.downloads name: ActiveDriverDB Downloads original_source: - relation_type: prov:hadPrimarySource source: activedriverdb product_url: https://activedriverdb.org/download/ secondary_source: - relation_type: prov:wasDerivedFrom source: 1000genomes - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: tcga - category: Product description: Harmonizome 3.0 processed dataset downloads, including dataset-specific association files and knowledge graph serialization downloads. format: mixed id: harmonizome.downloads name: Harmonizome Downloads original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://maayanlab.cloud/Harmonizome/download secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct description: Neo4j knowledge graph serialization of Harmonizome processed datasets, including genes, attributes, resources, datasets, and gene-attribute associations. dump_format: neo4j format: neo4j id: harmonizome.kg-neo4j latest_version: '3.0' name: Harmonizome Knowledge Graph Neo4j Database original_source: - 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A practical projection of the full graph for human-centric biomedical use. 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relation_type: prov:wasInfluencedBy source: wikipathways - category: Product compression: gzip description: PubChem substance information in SDF format format: sdf id: pubchem.substances.sdf name: PubChem Substances SDF original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - 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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: '2026-04-15T00:00:00Z' 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: - 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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 format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: bioteque - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: cellosaurus - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chemicalchecker - relation_type: prov:hadPrimarySource source: clue - relation_type: prov:hadPrimarySource source: compartments - 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anatomy and development homepage_url: https://github.com/EBISPOT/clyh_ontology id: clyh last_modified_date: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: clyh 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 original_source: - relation_type: prov:hadPrimarySource source: clyh product_file_size: 9651 product_url: http://purl.obolibrary.org/obo/clyh.obo publications: [] 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: '2026-07-02T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: cm4ai_talent_kg product_url: https://cm4aikg.vercel.app/ - category: GraphProduct description: The CM4AI Talent Knowledge Graph connecting Bridge2AI and CM4AI researchers, projects, publications, datasets, and bio-entities. format: ttl id: cm4ai_talent_kg.graph name: CM4AI Talent Knowledge Graph original_source: - 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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: '2026-06-01T00:00:00Z' 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 format: http id: cmap.clue name: CLUE Platform original_source: - relation_type: prov:hadPrimarySource source: cmap product_url: https://clue.io/ secondary_source: - relation_type: prov:wasInfluencedBy source: lincs - 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relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv publications: - authors: - Aravind Subramanian - Rajiv Narayan - Steven M. Corsello - David D. Peck - Ted E. Natoli - Xiaodong Lu - Joshua Gould - John F. Davis - Andrew A. Tubelli - Jacob K. Asiedu - David L. Lahr - Jodi E. Hirschman - Zihan Liu - Melanie Donahue - Bina Julian - Mariya Khan - David Wadden - Ian C. Smith - Daniel Lam - Arthur Liberzon - Courtney Toder - Mukta Bagul - Marek Orzechowski - Oana M. Enache - Federica Piccioni - Sarah A. Johnson - Nicholas J. Lyons - Alice H. Berger - Alykhan F. Shamji - Angela N. Brooks - Anita Vrcic - Corey Flynn - Jacqueline Rosains - David Y. Takeda - Roger Hu - Desiree Davison - Justin Lamb - Kristin Ardlie - Larson Hogstrom - Peyton Greenside - Nathanael S. Gray - Paul A. Clemons - Serena Silver - Xiaoyun Wu - Wen-Ning Zhao - Willis Read-Button - Xiaohua Wu - Stephen J. Haggarty - Lucienne V. Ronco - Jesse S. Boehm - Stuart L. Schreiber - John G. Doench - Joshua A. Bittker - David E. Root - Bang Wong - Todd R. Golub doi: 10.1016/j.cell.2017.10.049 id: https://doi.org/10.1016/j.cell.2017.10.049 journal: Cell title: 'A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles' year: '2017' repository: https://github.com/cmap synonyms: - CMap - Connectivity Map - LINCS L1000 taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2026-05-29T00:00:00Z' description: CMAUP is a database of collective molecular activities of useful plants, linking plant ingredients to targets, phenotypes, diseases, pathways, and traditional uses to support natural product and medicinal plant research. domains: - biomedical - drug discovery - pharmacology - chemistry and biochemistry id: cmaup last_modified_date: '2026-05-30T00:00:00Z' layout: resource_detail name: CMAUP products: - category: DocumentationProduct description: Nucleic Acids Research database article describing CMAUP, its data model, and its coverage of useful plants, ingredients, targets, pathways, and phenotypes. format: http id: cmaup.publication name: CMAUP Database Publication original_source: - relation_type: prov:hadPrimarySource source: cmaup product_url: https://academic.oup.com/nar/article/47/D1/D1118/5144144 warnings: [] - category: GraphProduct description: The OREGANO knowledge graph dataset integrating drug, protein, gene, and disease information for drug repositioning. format: http id: oregano.graph name: OREGANO Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: oregano product_url: https://gitub.u-bordeaux.fr/erias/oregano/-/tree/master/Data_OREGANO/Graphs secondary_source: - relation_type: prov:wasDerivedFrom source: cmaup - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: npass - relation_type: prov:wasDerivedFrom source: orphanet - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: umls - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: bio2rdf publications: - authors: - Xian Zeng - Peng Zhang - Yali Wang - Chu Qin - Shangying Chen - Weidong He - Lin Tao - Ying Tan - Dan Gao - Bohua Wang - Zhe Chen - Weiping Chen - Yu Yang Jiang - Yu Zong Chen doi: 10.1093/nar/gky965 id: https://doi.org/10.1093/nar/gky965 journal: Nucleic Acids Research preferred: true title: 'CMAUP: a database of collective molecular activities of useful plants' year: '2019' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://github.com/WCRP-CMIP label: World Climate Research Programme (WCRP) CMIP Panel creation_date: '2026-07-03T00:00:00Z' description: The Coupled Model Intercomparison Project (CMIP) is a coordinated climate modeling framework organized under the World Climate Research Programme (WCRP). Its CMIP6 Controlled Vocabularies (CMIP6CV) define the standardized identifiers used across CMIP, including source_id (models), experiment_id (experiments), activity_id (MIP activities), and institution_id, published as machine-readable files. domains: - environment - information technology - general homepage_url: https://github.com/WCRP-CMIP/CMIP6_CVs id: cmip last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: Coupled Model Intercomparison Project (CMIP) products: - category: Product description: The CMIP6 Controlled Vocabularies (CMIP6CV) are machine-readable JSON files defining standardized CMIP identifiers such as source_id, experiment_id, activity_id, and institution_id. format: json id: cmip.cmip6cvs name: CMIP6 Controlled Vocabularies original_source: - relation_type: prov:hadPrimarySource source: cmip product_url: https://github.com/WCRP-CMIP/CMIP6_CVs - category: GraphProduct description: RDF/Turtle knowledge graph integrating climate model and dataset metadata (from ESGF, CMIP controlled vocabularies, and the NASA GCMD keyword taxonomy) with entities and relationships extracted from climate-science publications. Served through the FRINK federation and the SPARQL and TPF endpoints. format: ttl id: climatemodelskg.graph name: Climate Models KG Graph original_source: - relation_type: prov:hadPrimarySource source: climatemodelskg - relation_type: prov:hadPrimarySource source: esgf - relation_type: prov:hadPrimarySource source: cmip - relation_type: prov:hadPrimarySource source: gcmd product_url: https://frink.renci.org/registry/kgs/climatepub4-kg/ - 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: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: cmo product_file_size: 9415213 product_url: http://purl.obolibrary.org/obo/cmo.owl - category: OntologyProduct description: Clinical measurement ontology in OBO format format: obo id: cmo.obo name: cmo.obo original_source: - relation_type: prov:hadPrimarySource source: cmo product_file_size: 2583137 product_url: http://purl.obolibrary.org/obo/cmo.obo publications: - authors: - Shimoyama M - Nigam R - McIntosh LS - Nagarajan R - Rice T - Rao DC - Dwinell MR doi: 10.3389/fgene.2012.00087 id: https://www.ncbi.nlm.nih.gov/pubmed/22654893 journal: Front Genet title: Three ontologies to define phenotype measurement data. year: '2012' - authors: - Smith JR - Park CA - Nigam R - Laulederkind SJ - Hayman GT - Wang SJ - Lowry TF - Petri V - Pons JD - Tutaj M - Liu W - Worthey EA - Shimoyama M - Dwinell MR doi: 10.1186/2041-1480-4-26 id: https://www.ncbi.nlm.nih.gov/pubmed/24103152 journal: J Biomed Semantics title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' year: '2013' repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology - 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Vera Alvarez R - Landsman D - Koonin EV doi: 10.1093/nar/gkaa1018 id: https://www.ncbi.nlm.nih.gov/pubmed/33167031 journal: Nucleic Acids Res preferred: true title: 'COG database update: focus on microbial diversity, model organisms, and widespread pathogens' year: '2021' 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 - biomedical - public health - precision medicine homepage_url: https://cohd-api.ci.transltr.io/ id: cohd infores_id: cohd last_modified_date: '2026-06-02T00:00:00Z' layout: resource_detail name: Columbia Open Health Data (COHD) products: - category: ProgrammingInterface connection_url: https://cohd-api.ci.transltr.io/api 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: - relation_type: prov:hadPrimarySource source: cohd product_url: https://cohd-api.ci.transltr.io/ - category: GraphicalInterface description: Interactive web interface for exploring clinical concept frequencies and associations format: http id: cohd.portal name: COHD Web Interface original_source: - relation_type: prov:hadPrimarySource source: cohd product_url: https://cohd-api.ci.transltr.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: - relation_type: prov:hadPrimarySource 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: COHD about page describing the datasets, privacy-preserving counts, OMOP standard concepts, and collaborating groups format: http id: cohd.docs name: COHD Documentation original_source: - relation_type: prov:hadPrimarySource source: cohd product_url: https://cohd-api.ci.transltr.io/about.html - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for Columbia Open Health Data (COHD) distributed via the NCATS Translator release site (release 2026_03_12; build cohd_2024-11-25_75f200bb_2025sep1_4.3.6; source version 2024-11-25; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 84 format: kgx-jsonl id: translator.cohd.graph latest_version: '2026_03_12' license: id: https://opensource.org/license/mit/ label: MIT name: Translator COHD KGX Graph node_count: 86 original_source: - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/cohd/latest/ versions: - '2026_03_12' - cohd_2024-11-25_75f200bb_2025sep1_4.3.6 - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: go-cam - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathbank - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: text-mining-kp - relation_type: prov:hadPrimarySource source: translator - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://kgx-storage.rtx.ai/releases/translator_kg/latest/ versions: - '2026_03_27' - 423af7989cac publications: - authors: - Casey N. Ta - Michel Dumontier - George Hripcsak - Nicholas P. Tatonetti - Chunhua Weng doi: 10.1038/sdata.2018.273 id: doi:10.1038/sdata.2018.273 journal: Scientific Data preferred: true title: Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records year: '2018' 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: '2026-06-27T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: colao 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 original_source: - relation_type: prov:hadPrimarySource source: colao product_file_size: 83585 product_url: http://purl.obolibrary.org/obo/colao.obo publications: [] repository: https://github.com/insect-morphology/colao - activity_status: active category: DataSource creation_date: '2026-06-15T00:00:00Z' description: CollecTRI is a comprehensive collection of signed transcription factor (TF)-target gene regulatory interactions compiled from 12 different resources. It provides high-confidence regulons with expanded TF coverage and the sign (activation or repression) of each interaction, enabling accurate estimation of transcription factor activities from gene expression data. The regulons are distributed through the decoupler ecosystem and OmniPath for downstream enrichment and footprint analysis. domains: - systems biology - genomics - pathways homepage_url: https://github.com/saezlab/CollecTRI id: collectri last_modified_date: '2026-06-15T00:00:00Z' layout: resource_detail license: id: https://www.gnu.org/licenses/gpl-3.0.en.html label: GPL-3.0 name: CollecTRI products: - category: MappingProduct description: The CollecTRI gene regulatory network of signed transcription factor-target gene interactions, compiled from 12 resources, provided as a table of TF-target regulons with the sign (weight) of each interaction. format: csv id: collectri.regulons name: CollecTRI Regulons original_source: - relation_type: prov:hadPrimarySource source: collectri product_url: https://github.com/saezlab/CollecTRI - category: ProcessProduct description: Programmatic access to the CollecTRI regulons through the decoupler Python package, which retrieves the signed TF-target network for downstream transcription factor activity estimation. format: python id: collectri.decoupler name: CollecTRI via decoupler original_source: - relation_type: prov:hadPrimarySource source: collectri product_url: https://decoupler-py.readthedocs.io/ - category: DocumentationProduct description: Source code, construction scripts, benchmarking and case-study notebooks, and usage documentation for CollecTRI. format: http id: collectri.docs name: CollecTRI Repository and Documentation original_source: - relation_type: prov:hadPrimarySource source: collectri product_url: https://github.com/saezlab/CollecTRI - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - 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A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - 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biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 publications: - authors: - Sophia Müller-Dott - Eirini Tsirvouli - Miguel Vazquez - Ricardo O Ramirez Flores - Pau Badia-i-Mompel - Robin Fallegger - Dénes Türei - Astrid Lægreid - Julio Saez-Rodriguez doi: doi:10.1093/nar/gkad841 id: doi:10.1093/nar/gkad841 journal: Nucleic Acids Research preferred: true title: Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities year: '2023' repository: https://github.com/saezlab/CollecTRI - 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relation_type: prov:hadPrimarySource source: complexportal 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 original_source: - relation_type: prov:hadPrimarySource source: complexportal 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 original_source: - relation_type: prov:hadPrimarySource source: complexportal 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 original_source: - relation_type: prov:hadPrimarySource source: complexportal 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: complexportal product_url: https://www.ebi.ac.uk/complexportal/documentation - description: The MechRepoNet knowledge graph in its original format format: mixed id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: complexportal - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: mechreponet - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: unii product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication - 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: - relation_type: prov:hadPrimarySource source: complexportal - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 654220 product_url: https://w3id.org/biopragmatics/resources/complexportal/complexportal.tsv - 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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa product_url: https://ftp.ebi.ac.uk/pub/databases/GO/goa/ secondary_source: - relation_type: prov:wasInformedBy source: uniprot - relation_type: prov:wasInformedBy source: rnacentral - relation_type: prov:wasInformedBy source: complexportal 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' 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: - biomedical 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: '2026-07-01T00:00:00Z' layout: resource_detail license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: Connections Hypothesis KP products: - category: GraphProduct description: Bayesian-network knowledge graph served by the Connections Hypothesis Provider over the Translator TRAPI interface. Inference is computed over a breast cancer dataset from The Cancer Genome Atlas (TCGA), supporting queries relating genetic, therapeutic, and patient clinical features to patient survival. format: http id: connections-hypothesis-kp.graph name: Connections Hypothesis KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: connections-hypothesis-kp - relation_type: prov:hadPrimarySource source: tcga product_url: https://smart-api.info/registry?q=412af63e15b73e5a30778aac84ce313f - 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: connections-hypothesis-kp product_url: https://smart-api.info/registry?q=412af63e15b73e5a30778aac84ce313f - 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: '2026-06-12T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: corum product_url: https://mips.helmholtz-muenchen.de/corum/download/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ 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 2026-03-30_ 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 2026-02-04_ 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)'))) - 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 original_source: - relation_type: prov:hadPrimarySource source: corum product_url: https://mips.helmholtz-muenchen.de/corum/download/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ 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 2026-03-30_ 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 2026-02-04_ 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)'))) - 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 original_source: - relation_type: prov:hadPrimarySource source: corum product_url: https://mips.helmholtz-muenchen.de/corum/download/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ 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 2026-03-30_ 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 2026-02-04_ 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)'))) - 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 original_source: - relation_type: prov:hadPrimarySource source: corum product_url: https://mips.helmholtz-muenchen.de/corum/download/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ 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 2026-03-30_ 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 2026-02-04_ 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)'))) - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: bioteque - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: cellosaurus - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chemicalchecker - 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authors: - Madalina 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. 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The hosted service it ran (redrugs.tw.rpi.edu) is no longer available. format: python id: redrugs.source name: ReDrugs Source Code original_source: - relation_type: prov:hadPrimarySource source: redrugs - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: irefindex - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: cosmic product_url: https://github.com/dlmcguinness/redrugs - category: GraphProduct description: KGX nodes file for JensenLab DISEASES KG format: kgx-jsonl id: kg-jensenlab-diseases.nodes.kgx name: DISEASES KGX nodes original_source: - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: medlineplus 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 original_source: - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: medlineplus 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 original_source: - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: medlineplus product_file_size: 132 product_url: https://github.com/biothings/pending.api/blob/translator-output/plugins/DISEASES/DISEASES_trapi_edges.jsonl publications: - authors: - Tate JG - Bamford S - Jubb HC - Sondka Z - Beare DM - Bindal N - Boutselakis H - Cole CG - Creatore C - Dawson E - Fish P - Harsha B - Hathaway C - Jupe SC - Kok CY - Noble K - Ponting L - Ramshaw CC - Rye CE - Speedy HE - Stefancsik R - Thompson SL - Wang S - Ward S - Campbell PJ - Forbes SA doi: 10.1093/nar/gky1015 id: https://www.ncbi.nlm.nih.gov/pubmed/30371878 journal: Nucleic Acids Res preferred: true title: 'COSMIC: the Catalogue Of Somatic Mutations In Cancer' year: '2019' 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: - biomedical evaluation_page: resource/cpathkg/cpathkg_eval_automated.html homepage_url: https://gitlab.c-path.org/c-pathontology/c-path-knowledge-graph-integration 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: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: cpathkg - relation_type: prov:hadPrimarySource source: kg-monarch product_url: https://gitlab.c-path.org/c-pathontology/c-path-knowledge-graph-integration 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 journal: JAMIA Open title: Increased discoverability of rare disease datasets through knowledge graph integration year: '2024' repository: https://gitlab.c-path.org/c-pathontology/c-path-knowledge-graph-integration - activity_status: active 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 frames-based site remains reachable and reports Release 35 for the human instance, dated June 5, 2021. 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: '2026-06-27T00:00:00Z' layout: resource_detail license: id: http://cpdb.molgen.mpg.de/ label: Free for academic use; commercial users must contact the developers (integrated interaction data inherits the license terms of the contributing source databases) name: ConsensusPathDB products: - category: GraphicalInterface description: Web-based interface for integrated pathway and interaction analysis from multiple databases format: http id: cpdb.web name: ConsensusPathDB Web Interface original_source: - relation_type: prov:hadPrimarySource source: cpdb product_url: http://cpdb.molgen.mpg.de/ - category: Product description: Download and access page for ConsensusPathDB data and service assets format: http id: cpdb.downloads name: ConsensusPathDB Data Downloads original_source: - relation_type: prov:hadPrimarySource source: cpdb product_url: http://cpdb.molgen.mpg.de/download warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: ProgrammingInterface description: SOAP web service description for ConsensusPathDB programmatic access format: xml id: cpdb.wsdl name: ConsensusPathDB SOAP WSDL original_source: - relation_type: prov:hadPrimarySource source: cpdb product_url: http://cpdb.molgen.mpg.de/download/CPDB.wsdl - 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: - relation_type: prov:hadPrimarySource source: rdbridge - relation_type: prov:hadPrimarySource source: pmc - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: cpdb publications: - authors: - Atanas Kamburov - Konstantin Pentchev - Hanna Galicka - Christoph Wierling - Hans Lehrach - Ralf Herwig doi: 10.1093/nar/gkq1156 id: doi:10.1093/nar/gkq1156 journal: Nucleic Acids Research preferred: true title: 'ConsensusPathDB: toward a more complete picture of cell biology' year: '2011' - authors: - Atanas Kamburov - Christoph Wierling - Hans Lehrach - Ralf Herwig doi: 10.1093/nar/gkn698 id: doi:10.1093/nar/gkn698 journal: Nucleic Acids Research title: ConsensusPathDB--a database for integrating human functional interaction networks year: '2009' synonyms: - CPDB - CPDB-human - ConsensusPathDB-human taxon: - NCBITaxon:9606 - NCBITaxon:10090 - NCBITaxon:4932 - 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 - clinical - drug discovery homepage_url: https://cpicpgx.org/ id: cpic last_modified_date: '2026-06-18T00:00:00Z' 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: 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: - relation_type: prov:hadPrimarySource source: cpic product_url: https://cpicpgx.org/ - category: DocumentationProduct description: Peer-reviewed, evidence-based, updatable pharmacogenetic clinical practice guidelines translating genotype into prescribing recommendations format: http id: cpic.guidelines is_public: true name: CPIC Clinical Practice Guidelines original_source: - relation_type: prov:hadPrimarySource source: cpic product_url: https://cpicpgx.org/guidelines/ - category: Product description: Curated gene–drug pair tables linking pharmacogenes with affected medications and guideline recommendations format: http id: cpic.genes_drugs is_public: true name: CPIC Genes-Drugs Tables original_source: - relation_type: prov:hadPrimarySource source: cpic product_url: https://cpicpgx.org/genes-drugs/ - category: Product description: Allele function and diplotype-to-phenotype tables standardized for clinical pharmacogenetic test result interpretation format: http id: cpic.alleles is_public: true name: CPIC Allele & Diplotype Function Tables original_source: - relation_type: prov:hadPrimarySource source: cpic product_url: https://cpicpgx.org/alleles/ - category: ProgrammingInterface connection_url: https://api.cpicpgx.org/ description: Structured data (database and API) for CPIC guideline-derived gene–drug relationships, allele function, and standardized terms format: json id: cpic.api is_public: true name: CPIC Database & API original_source: - 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K Bretonnel Cohen - Karin Verspoor - Judith A Blake - Lawrence E Hunter doi: 10.1186/1471-2105-13-161 id: https://doi.org/10.1186/1471-2105-13-161 journal: BMC Bioinformatics preferred: true title: Concept annotation in the CRAFT corpus year: '2012' repository: https://github.com/UCDenver-ccp/CRAFT - activity_status: active category: Ontology contacts: - category: Organization contact_details: - contact_type: url value: https://credit.niso.org/ label: National Information Standards Organization creation_date: '2026-02-26T00:00:00Z' description: CRediT (Contributor Roles Taxonomy) is a controlled vocabulary of contributor roles used to describe how individuals contributed to research and scholarly outputs. 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relation_type: prov:hadPrimarySource source: credit - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 136 product_url: https://w3id.org/biopragmatics/resources/credit/credit.sssom.tsv - category: Product description: credit Nodes TSV format: tsv id: obo-db-ingest.credit.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: credit Nodes TSV original_source: - relation_type: prov:hadPrimarySource source: credit - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 1046 product_url: https://w3id.org/biopragmatics/resources/credit/credit.tsv publications: - authors: - Brand A - Allen L - Altman M - Hlava M - Scott J doi: 10.1087/20150211 id: https://doi.org/10.1087/20150211 journal: Learned Publishing preferred: true title: 'Beyond authorship: attribution, contribution, collaboration, and credit' year: '2015' - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: avi.maayan@mssm.edu - contact_type: github value: MaayanLab label: Avi Ma'ayan orcid: 0000-0002-6628-6249 creation_date: '2025-07-08T00:00:00Z' description: CREEDS (CRowd Extracted Expression of Differential Signatures) is a database of crowdsourced gene expression signatures for drug, genetic, and disease perturbations. domains: - pharmacology - genomics id: creeds last_modified_date: '2026-06-18T00:00:00Z' 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: CREEDS products: - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: bioteque - relation_type: prov:hadPrimarySource source: bto - 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relation_type: prov:hadPrimarySource source: creeds product_file_size: 58276121 product_url: https://maayanlab.cloud/CREEDS/download/single_gene_perturbations-v1.0.json - category: Product description: Manual gene expression signatures derived from disease signatures format: json id: creeds.manual_disease_signatures name: CREEDS Manual Disease Signatures original_source: - relation_type: prov:hadPrimarySource source: creeds product_file_size: 16865407 product_url: https://maayanlab.cloud/CREEDS/download/disease_signatures-v1.0.json - category: Product description: Manual gene expression signatures derived single drug perturbations format: json id: creeds.manual_single_drug name: CREEDS Manual Single Drug Perturbations original_source: - relation_type: prov:hadPrimarySource source: creeds product_file_size: 17836091 product_url: https://maayanlab.cloud/CREEDS/download/single_drug_perturbations-v1.0.json - category: Product description: DrugMatrix single drug perturbations format: json id: creeds.drugmatrix name: CREEDS DrugMatrix single drug perturbations original_source: - relation_type: prov:hadPrimarySource source: creeds product_file_size: 86943390 product_url: https://maayanlab.cloud/CREEDS/download/single_drug_perturbations-DM.json - category: Product description: Automatic gene expression signatures derived from single gene perturbations format: json id: creeds.automatic_single_gene name: CREEDS Automatic Single Gene Perturbations original_source: - relation_type: prov:hadPrimarySource source: creeds product_file_size: 175552254 product_url: https://maayanlab.cloud/CREEDS/download/single_gene_perturbations-p1.0.json - category: Product description: Automatic gene expression signatures derived from disease signatures format: json id: creeds.automatic_disease_signatures name: CREEDS Automatic Disease Signatures original_source: - relation_type: prov:hadPrimarySource source: creeds product_file_size: 29173111 product_url: https://maayanlab.cloud/CREEDS/download/disease_signatures-p1.0.json - category: Product description: Automatic gene expression signatures derived from single drug perturbations format: json id: creeds.automatic_single_drug name: CREEDS Automatic Single Drug Perturbations original_source: - relation_type: prov:hadPrimarySource source: creeds product_file_size: 87060413 product_url: https://maayanlab.cloud/CREEDS/download/single_drug_perturbations-p1.0.json - category: GraphicalInterface description: Web interface for exploring CREEDS gene expression signatures format: http id: creeds.web_interface name: CREEDS Web Interface original_source: - relation_type: prov:hadPrimarySource source: creeds product_url: https://maayanlab.cloud/CREEDS/ publications: - authors: - Zichen Wang - Caroline D. Monteiro - Kathleen M. Jagodnik - Nicolas F. Fernandez - Gregory W. Gundersen - Andrew D. Rouillard - Sherry L. Jenkins - Axel S. Feldmann - Kevin S. Hu - Michael G. McDermott - Qiaonan Duan - Neil R. Clark - Matthew R. Jones - Yan Kou - Troy Goff - Holly Woodland - Fabio M R. Amaral - Gregory L. Szeto - Oliver Fuchs - Sophia M. Schüssler-Fiorenza Rose - Shvetank Sharma - Uwe Schwartz - Xabier Bengoetxea Bausela - Maciej Szymkiewicz - Vasileios Maroulis - Anton Salykin - Carolina M. Barra - Candice D. Kruth - Nicholas J. Bongio - Vaibhav Mathur - Radmila D Todoric - Udi E. Rubin - Apostolos Malatras - Carl T. Fulp - John A. Galindo - Ruta Motiejunaite - Christoph Jüschke - Philip C. Dishuck - Katharina Lahl - Mohieddin Jafari - Sara Aibar - Apostolos Zaravinos - Linda H. Steenhuizen - Lindsey R. Allison - Pablo Gamallo - Fernando de Andres Segura - Tyler Dae Devlin - Vicente Pérez-García - Avi Ma’ayan doi: 10.1038/ncomms12846 id: doi:10.1038/ncomms12846 journal: Nature Communications title: Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd year: '2016' - activity_status: active category: Ontology collection: - obo-foundry contacts: - category: Individual contact_details: - contact_type: email value: whimar@ohsu.edu - contact_type: github value: marijane label: Marijane White orcid: 0000-0001-5059-4132 creation_date: '2025-09-29T00:00:00Z' description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. domains: - biomedical - information technology homepage_url: https://github.com/data2health/contributor-role-ontology id: cro last_modified_date: '2026-06-27T00:00:00Z' 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: Contributor Role Ontology products: - category: OntologyProduct description: CRO format: owl id: cro.owl name: CRO original_source: - relation_type: prov:hadPrimarySource source: cro product_file_size: 12414 product_url: http://purl.obolibrary.org/obo/cro.owl publications: - authors: - Violeta Ilik - Michael Conlon - Graham Triggs - Marijane White - Muhammad Javed - Matthew Brush - Karen Gutzman - Shahim Essaid - Paul Friedman - Simon Porter - Martin Szomszor - Melissa Anne Haendel - David Eichmann - Kristi L. Holmes doi: 10.3389/frma.2017.00012 id: https://doi.org/10.3389/frma.2017.00012 journal: Frontiers in Research Metrics and Analytics preferred: true title: 'OpenVIVO: Transparency in Scholarship' year: '2018' repository: https://github.com/data2health/contributor-role-ontology - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: url value: https://www.nass.usda.gov/Research_and_Science/Cropland/SARS1a.php label: USDA National Agricultural Statistics Service creation_date: '2026-06-18T00:00:00Z' description: The Cropland Data Layer (CDL) is an annual, georeferenced, crop-specific land cover raster map covering the conterminous United States, produced by the USDA National Agricultural Statistics Service (NASS). It is generated from satellite imagery and extensive agricultural ground reference data, classifying each 30-meter pixel into crop types and other land cover categories. The CDL serves as an upstream source for KnowWhereGraph and supports agricultural monitoring, acreage estimation, and land use analysis. domains: - agriculture - environment - general homepage_url: https://www.nass.usda.gov/Research_and_Science/Cropland/SARS1a.php id: cropland-data-layer last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: '' label: US federal government public domain name: Cropland Data Layer products: - category: GraphicalInterface description: CroplandCROS web mapping application for interactive viewing, querying, and exporting Cropland Data Layer crop-type raster data. format: http id: cropland-data-layer.croplandcros name: CroplandCROS Viewer original_source: - relation_type: prov:hadPrimarySource source: cropland-data-layer product_url: https://croplandcros.scinet.usda.gov/ - 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 original_source: - relation_type: prov:hadPrimarySource source: knowwheregraph - relation_type: prov:wasDerivedFrom source: wikidata - relation_type: prov:hadPrimarySource source: bluesky - relation_type: prov:hadPrimarySource source: cdc-places - relation_type: prov:hadPrimarySource source: cdc-svi - relation_type: prov:hadPrimarySource source: cropland-data-layer - relation_type: prov:hadPrimarySource source: epa-aqs - relation_type: prov:hadPrimarySource source: gadm - relation_type: prov:hadPrimarySource source: gnis - relation_type: prov:hadPrimarySource source: hifld - relation_type: prov:hadPrimarySource source: mtbs - relation_type: prov:hadPrimarySource source: nhpn - relation_type: prov:hadPrimarySource source: nifc - relation_type: prov:hadPrimarySource source: noaa-hms - relation_type: prov:hadPrimarySource source: noaa-ncei - relation_type: prov:hadPrimarySource source: openfema - relation_type: prov:hadPrimarySource source: reliefweb - relation_type: prov:hadPrimarySource source: ssurgo - relation_type: prov:hadPrimarySource source: us-census - relation_type: prov:hadPrimarySource source: usdm - relation_type: prov:hadPrimarySource source: usgs-comcat product_url: https://knowwheregraph.org/ - category: GraphProduct description: The SAWGraph PFAS knowledge graph, integrating PFAS observations and releases with the samples, geospatial features, environmental media, and chemical substances they describe. The RDF (Turtle) graph is constructed from federal and state PFAS datasets and geospatial reference data, and is served through the SAWGraph SPARQL and Triple Pattern Fragments endpoints. format: ttl id: sawgraph.graph name: SAWGraph PFAS Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: sawgraph - relation_type: prov:hadPrimarySource source: epa-sdwis - relation_type: prov:hadPrimarySource source: epa-ucmr - relation_type: prov:hadPrimarySource source: water-quality-portal - relation_type: prov:hadPrimarySource source: epa-ghg - relation_type: prov:hadPrimarySource source: epa-frs - relation_type: prov:hadPrimarySource source: maine-egad product_url: https://github.com/SAWGraph/pfas-kg secondary_source: - relation_type: prov:wasInfluencedBy source: epa-echo - relation_type: prov:wasInfluencedBy source: usgs-nhd - relation_type: prov:wasInfluencedBy source: us-census - relation_type: prov:wasInfluencedBy source: knowwheregraph - relation_type: prov:wasInfluencedBy source: ssurgo - 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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. format: http id: aop-db.data name: AOP-DB Data original_source: - relation_type: prov:hadPrimarySource source: 1000genomes - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: aop-wiki - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: toxcast product_url: https://catalog.data.gov/dataset/adverse-outcome-pathway-database-aop-db-version-2 - 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). format: mixed id: ibkh.graph name: iBKH Knowledge Graph original_source: - 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Function original_source: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest - 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz - 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 format: http id: cam-kp.ctd-interactions name: CTD Chemical-Gene Models original_source: - relation_type: prov:hadPrimarySource source: cam-kp - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for CTD distributed via the NCATS Translator release site (release 2026_03_27; build ctd_February_2026_b588520f_2025sep1_4.3.6; source version February_2026; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 4175538 format: kgx-jsonl id: translator.ctd.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator CTD KGX Graph node_count: 86425 original_source: - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/ctd/latest/ versions: - '2026_03_27' - ctd_February_2026_b588520f_2025sep1_4.3.6 - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: batman - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: compath - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - 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relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - 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relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - 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relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: text-mining-kp - relation_type: prov:hadPrimarySource source: translator - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://kgx-storage.rtx.ai/releases/translator_kg/latest/ versions: - '2026_03_27' - 423af7989cac - category: GraphProduct description: The OREGANO knowledge graph dataset integrating drug, protein, gene, and disease information for drug repositioning. format: http id: oregano.graph name: OREGANO Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: oregano product_url: https://gitub.u-bordeaux.fr/erias/oregano/-/tree/master/Data_OREGANO/Graphs secondary_source: - relation_type: prov:wasDerivedFrom source: cmaup - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: hp - 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Davis AP - Wiegers TC - Sciaky D - Barkalow F - Strong M - Wyatt B - Wiegers J - McMorran R - Abrar S - Mattingly CJ doi: 10.1093/nar/gkae883 id: https://doi.org/10.1093/nar/gkae883 journal: Nucleic Acids Research preferred: true title: 'Comparative Toxicogenomics Database''s 20th anniversary: update 2025' year: '2025' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: NCICCGenomics@mail.nih.gov - contact_type: url value: https://www.cancer.gov/ccg/research/functional-genomics/ctd2 label: National Cancer Institute Center for Cancer Genomics creation_date: '2026-06-02T00:00:00Z' description: The Cancer Target Discovery and Development Network is an NCI functional genomics initiative that releases cancer target discovery, validation, perturbation, and screening data for precision oncology research. domains: - biomedical - genomics - precision medicine - drug discovery homepage_url: https://www.cancer.gov/ccg/research/functional-genomics/ctd2 id: ctd2 last_modified_date: '2026-06-27T00:00:00Z' layout: resource_detail name: Cancer Target Discovery and Development Network products: - 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NCI has consolidated CTD2 data access into the Index of NCI Studies / Study Catalog (https://studycatalog.cancer.gov), reachable via the CTD2 Data Portal product. No live replacement for the dashboard application itself was found. - category: DocumentationProduct description: NCI guidance for accessing, using, and acknowledging CTD2 Network data and associated raw and analyzed datasets. id: ctd2.usage-guide name: Using CTD2 Data original_source: - relation_type: prov:hadPrimarySource source: ctd2 product_url: https://www.cancer.gov/ccg/research/functional-genomics/ctd2/using-ctd2-data - 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 original_source: - relation_type: prov:hadPrimarySource source: depmap product_url: https://depmap.org/portal/data_page/ secondary_source: - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: prism - relation_type: prov:wasDerivedFrom source: ctd2 publications: - authors: - Bulent Aksoy - Vlado Dancik - Kenneth Smith - Jessica Mazerik - Zhou Ji - Benjamin Gross doi: 10.1093/database/bax054 id: doi:10.1093/database/bax054 journal: Database preferred: true title: 'CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network' year: '2017' synonyms: - CTD2 - CTD^2 - CTD² - 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: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: cteno product_file_size: 15458 product_url: http://purl.obolibrary.org/obo/cteno.owl publications: [] repository: https://github.com/obophenotype/ctenophore-ontology taxon: - NCBITaxon:10197 - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual contact_details: - contact_type: github value: gglusman label: Gwênlyn Glusman 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 - biomedical evaluation_page: resource/ctkp/ctkp_eval_automated.html homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Trials-KP id: ctkp last_modified_date: '2026-05-30T00:00:00Z' layout: resource_detail name: Clinical Trials KP products: - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for CTKP distributed via the NCATS Translator release site (release 2026_03_27; build ctkp_3.1.37_a99268cc_2025sep1_4.3.6; source version 3.1.37; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 438575 format: kgx-jsonl id: translator.ctkp.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator CTKP KGX Graph node_count: 41243 original_source: - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/ctkp/latest/ versions: - '2026_03_27' - ctkp_3.1.37_a99268cc_2025sep1_4.3.6 - 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: - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: translator product_url: https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Trials-KP - category: DocumentationProduct description: SmartAPI registry entry for the Multiomics Clinical Trials KP TRAPI 1.5 endpoint. format: http id: ctkp.smartapi name: Clinical Trials KP SmartAPI Registration original_source: - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: translator product_url: https://smart-api.info/registry?q=e51073371d7049b9643e1edbdd61bcbd - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; 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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: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: cto product_file_size: 96492 product_url: http://purl.obolibrary.org/obo/cto.owl publications: [] 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. 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relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv publications: - authors: - Matthew G Rees - Brinton Seashore-Ludlow - Jaime H Cheah - Drew J Adams - Edmund V Price - Shubhroz Gill - Sarah Javaid - Matthew E Coletti - Victor L Jones - Nicole E Bodycombe - Christian K Soule - Benjamin Alexander - Ava Li - Philip Montgomery - Joanne D Kotz - C Suk-Yee Hon - Benito Munoz - Ted Liefeld - Vlado Dančík - Daniel A Haber - Clary B Clish - Joshua A Bittker - Michelle Palmer - Bridget K Wagner - Paul A Clemons - Alykhan F Shamji - Stuart L Schreiber doi: 10.1038/nchembio.1986 id: https://doi.org/10.1038/nchembio.1986 journal: Nature Chemical Biology title: Correlating chemical sensitivity and basal gene expression reveals mechanism of action year: '2016' - authors: - Brinton Seashore-Ludlow - Matthew G. Rees - Jaime H. Cheah - Murat Cokol - Edmund V. Price - Matthew E. Coletti - Victor Jones - Nicole E. Bodycombe - Christian K. Soule - Joshua Gould - Benjamin Alexander - Ava Li - Philip Montgomery - Mathias J. Wawer - Nurdan Kuru - Joanne D. Kotz - C. Suk-Yee Hon - Benito Munoz - Ted Liefeld - Vlado Dančík - Joshua A. Bittker - Michelle Palmer - James E. Bradner - Alykhan F. Shamji - Paul A. Clemons - Stuart L. Schreiber doi: 10.1158/2159-8290.CD-15-0235 id: https://doi.org/10.1158/2159-8290.CD-15-0235 journal: Cancer Discovery title: Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset year: '2015' - authors: - Amrita Basu - Nicole E. Bodycombe - Jaime H. Cheah - Edmund V. Price - Ke Liu - Giannina I. Schaefer - Richard Y. Ebright - Michelle L. Stewart - Daisuke Ito - Stephanie Wang - Abigail L. Bracha - Ted Liefeld - Mathias Wawer - Joshua C. Gilbert - Andrew J. Wilson - Nicolas Stransky - Gregory V. Kryukov - Vlado Dancik - Jordi Barretina - Levi A. Garraway - C. Suk-Yee Hon - Benito Munoz - Joshua A. Bittker - Brent R. Stockwell - Dineo Khabele - Andrew M. Stern - Paul A. Clemons - Alykhan F. Shamji - Stuart L. Schreiber doi: 10.1016/j.cell.2013.08.003 id: https://doi.org/10.1016/j.cell.2013.08.003 journal: Cell title: An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules year: '2013' synonyms: - CTRP - Cancer Therapeutics Response Portal taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://ncats.nih.gov/ label: National Center for Advancing Translational Sciences (NCATS) creation_date: '2026-06-18T00:00:00Z' description: CURE ID is a crowdsourcing platform and mobile/web app developed by the U.S. National Center for Advancing Translational Sciences (NCATS) at NIH in collaboration with the U.S. Food and Drug Administration (FDA). It allows clinicians around the world to report and share real-world clinical experiences treating difficult-to-treat and rare diseases, with an emphasis on novel uses of existing (off-label) drugs. The collected case reports and treatment outcomes form a repository intended to surface promising therapies and inform clinical research. CURE ID serves as an upstream ingest source for the Monarch/SRI Reference Knowledge Graph. domains: - clinical - drug discovery - public health homepage_url: https://cure.ncats.io/ id: cureid last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: CURE ID products: - category: GraphicalInterface description: Web application for exploring and contributing crowdsourced real-world clinical treatment cases for difficult-to-treat and rare diseases, including off-label drug use. format: http id: cureid.app name: CURE ID Web App original_source: - relation_type: prov:hadPrimarySource source: cureid product_url: https://cure.ncats.io/ - category: GraphicalInterface description: Browseable interface for exploring diseases, treatments, and submitted clinical case reports within the CURE ID platform. format: http id: cureid.explore name: CURE ID Explore original_source: - relation_type: prov:hadPrimarySource source: cureid product_url: https://cure.ncats.io/explore - category: DocumentationProduct description: About page describing the CURE ID initiative, its NCATS/FDA partnership, and how clinicians can participate. id: cureid.about name: CURE ID About original_source: - relation_type: prov:hadPrimarySource source: cureid product_url: https://cure.ncats.io/about warnings: [] - category: GraphProduct description: KGX distribution of the SRI-Reference KG format: kgx id: sri-reference-kg.graph name: SRI-Reference KG (KGX distribution) original_source: - relation_type: prov:hadPrimarySource source: sri-reference-kg - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: goa - 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relation_type: prov:hadPrimarySource source: cureid - relation_type: prov:hadPrimarySource source: phenopacket-store product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz - 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: '2026-04-15T00:00:00Z' 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: Cardiovascular Disease Ontology products: - category: OntologyProduct description: Cardiovascular Disease Ontology in OWL format format: owl id: cvdo.owl name: cvdo.owl original_source: - relation_type: prov:hadPrimarySource source: cvdo product_file_size: 105498 product_url: http://purl.obolibrary.org/obo/cvdo.owl publications: [] repository: https://github.com/OpenLHS/CVDO - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: iisinfo@cdc.gov - contact_type: url value: https://www.cdc.gov/iis/code-sets/index.html label: CDC IIS Helpdesk creation_date: '2026-02-26T00:00:00Z' description: CVX is the vaccine administered code set maintained by the Centers for Disease Control and Prevention for Immunization Information Systems (IIS). It provides identifiers for vaccine products and historical vaccine administrations used in immunization records, exchange standards, and public health reporting. domains: - clinical - biomedical - public health homepage_url: https://www2.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx id: cvx last_modified_date: '2026-05-30T00:00:00Z' layout: resource_detail name: Vaccine Administered Code Set (CVX) products: - category: DocumentationProduct description: CDC IIS code-set hub with release notes, related code mappings, and additional access options for vaccine coding resources. format: http id: cvx.docs name: CDC Vaccine Code Sets Documentation original_source: - relation_type: prov:hadPrimarySource source: cvx product_url: https://www.cdc.gov/iis/code-sets/index.html - category: Product description: cvx Nodes TSV format: tsv id: obo-db-ingest.cvx.tsv name: cvx Nodes TSV original_source: - relation_type: prov:hadPrimarySource source: cvx - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 6401 product_url: https://w3id.org/biopragmatics/resources/cvx/cvx.tsv - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://cytoscape.org/ label: Cytoscape Consortium creation_date: '2026-06-02T00:00:00Z' description: Cytoscape is an open-source platform for visualizing, analyzing, and integrating complex networks with biological and other attribute data. domains: - biomedical - biological systems - information technology - pathways homepage_url: https://cytoscape.org/ id: cytoscape last_modified_date: '2026-06-03T00:00:00Z' layout: resource_detail license: id: https://www.gnu.org/licenses/lgpl-2.1.html label: LGPL-2.1 name: Cytoscape products: - category: GraphicalInterface description: Cross-platform Cytoscape desktop application for complex network visualization, molecular interaction analysis, and integration of network attribute data. id: cytoscape.desktop name: Cytoscape Desktop original_source: - relation_type: prov:hadPrimarySource source: cytoscape product_url: https://cytoscape.org/download.html repository: https://github.com/cytoscape/cytoscape - category: GraphicalInterface description: Cytoscape App Store for discovering and installing Cytoscape apps that extend analysis, visualization, and data integration workflows. id: cytoscape.app-store name: Cytoscape App Store original_source: - relation_type: prov:hadPrimarySource source: cytoscape product_url: https://apps.cytoscape.org/ - category: ProgrammingInterface description: CyREST-powered Cytoscape Automation interface for executing reproducible Cytoscape workflows from external tools such as Python, R, and Jupyter. id: cytoscape.automation-api is_public: true name: Cytoscape Automation API original_source: - relation_type: prov:hadPrimarySource source: cytoscape product_url: https://apps.cytoscape.org/apps/cyrest - category: Product description: Open-source Cytoscape app that brings GeneMANIA gene function prediction, downloadable data sets, command-line tools, and Cytoscape Automation support to desktop network analysis workflows format: http id: genemania.cytoscape-app latest_version: 3.5.3 name: GeneMANIA Cytoscape App original_source: - relation_type: prov:hadPrimarySource source: genemania product_url: https://apps.cytoscape.org/apps/genemania repository: https://github.com/GeneMANIA/genemania secondary_source: - relation_type: prov:wasInfluencedBy source: cytoscape publications: - authors: - Paul Shannon - Andrew Markiel - Owen Ozier - Nitin S Baliga - Jonathan T Wang - Daniel Ramage doi: 10.1101/gr.1239303 id: doi:10.1101/gr.1239303 journal: Genome Research preferred: true title: 'Cytoscape: a software environment for integrated models of biomolecular interaction networks' year: '2003' repository: https://github.com/cytoscape/cytoscape - 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: - biomedical homepage_url: https://dailymed.nlm.nih.gov/dailymed/ id: dailymed infores_id: dailymed last_modified_date: '2026-06-01T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: dailymed product_url: https://dailymed.nlm.nih.gov/dailymed/ - category: ProgrammingInterface connection_url: https://dailymed.nlm.nih.gov/dailymed/services/v2/ 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 original_source: - relation_type: prov:hadPrimarySource source: dailymed 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 original_source: - relation_type: prov:hadPrimarySource source: dailymed product_url: https://dailymed.nlm.nih.gov/dailymed/spl-resources-all-drug-labels.cfm secondary_source: - relation_type: prov:wasInformedBy source: rxnorm - relation_type: prov:wasInformedBy source: unii - relation_type: prov:wasInformedBy source: ndcd - 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 original_source: - relation_type: prov:hadPrimarySource source: dailymed 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 original_source: - relation_type: prov:hadPrimarySource source: dailymed product_url: https://dailymed.nlm.nih.gov/dailymed/rss-updates.cfm - category: Product compression: zip description: Current MED-RT DTS release archive from the NCI EVS MED-RT distribution. id: med-rt.core_dts name: Core MED-RT DTS Archive original_source: - relation_type: prov:hadPrimarySource source: med-rt product_file_size: 2479793 product_url: https://evs.nci.nih.gov/ftp1/MED-RT/Core_MEDRT_DTS.zip secondary_source: - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasInformedBy source: dailymed - relation_type: prov:wasInformedBy source: mesh - relation_type: prov:wasInformedBy source: rxnorm - relation_type: prov:wasInformedBy source: snomedct - relation_type: prov:wasInformedBy source: umls - category: Product compression: zip description: Current MED-RT XML release archive from the NCI EVS MED-RT distribution. format: xml id: med-rt.core_xml name: Core MED-RT XML Archive original_source: - relation_type: prov:hadPrimarySource source: med-rt product_file_size: 2558768 product_url: https://evs.nci.nih.gov/ftp1/MED-RT/Core_MEDRT_XML.zip secondary_source: - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasInformedBy source: dailymed - relation_type: prov:wasInformedBy source: mesh - relation_type: prov:wasInformedBy source: rxnorm - relation_type: prov:wasInformedBy source: snomedct - relation_type: prov:wasInformedBy source: umls - category: Product compression: zip description: Structured Product Labeling subset archive from the current MED-RT distribution. id: med-rt.core_spl name: Core MED-RT SPL Archive original_source: - relation_type: prov:hadPrimarySource source: med-rt product_file_size: 40677 product_url: https://evs.nci.nih.gov/ftp1/MED-RT/Core_MEDRT_SPL.zip secondary_source: - relation_type: prov:wasInformedBy source: dailymed - relation_type: prov:wasInformedBy source: rxnorm - relation_type: prov:wasInformedBy source: umls - category: ProcessProduct description: Active GitHub repository for MeDI/medic medicines, diseases, indications, and contraindications data and processing code format: http id: medi.github name: medic GitHub Repository original_source: - relation_type: prov:hadPrimarySource source: medi product_url: https://github.com/marcello-deluca/medic secondary_source: - relation_type: prov:wasInformedBy source: dailymed - relation_type: prov:wasInformedBy source: mondo - category: Product description: Matrix indication list spreadsheet from the medic v1.0.1 release id: medi.matrix_indication_list latest_version: v1.0.1 name: Matrix Indication List original_source: - relation_type: prov:hadPrimarySource source: medi product_file_size: 2173559 product_url: https://github.com/marcello-deluca/medic/releases/download/v1.0.1/matrix_indication_list.xlsx secondary_source: - relation_type: prov:wasDerivedFrom source: dailymed - relation_type: prov:used source: mondo - category: Product description: Flexible drug list CSV from the medic v1.0.1 release format: csv id: medi.drug_list_flexible latest_version: v1.0.1 name: MeDI Flexible Drug List original_source: - relation_type: prov:hadPrimarySource source: medi product_file_size: 4428523 product_url: https://github.com/marcello-deluca/medic/releases/download/v1.0.1/drug_list_flexible.csv secondary_source: - relation_type: prov:wasDerivedFrom source: dailymed - relation_type: prov:wasInformedBy source: rxnorm - category: Product description: Stringent drug list CSV from the medic v1.0.1 release format: csv id: medi.drug_list_stringent latest_version: v1.0.1 name: MeDI Stringent Drug List original_source: - relation_type: prov:hadPrimarySource source: medi product_file_size: 3672087 product_url: https://github.com/marcello-deluca/medic/releases/download/v1.0.1/drug_list_stringent.csv secondary_source: - relation_type: prov:wasDerivedFrom source: dailymed - relation_type: prov:wasInformedBy source: rxnorm - category: Product description: LabeledIn indication corpus described in the source publication, containing human-reviewed drug-disease treatment relationships with links back to source drug labels. format: http id: labeledin.indications name: LabeledIn Drug Indication Corpus original_source: - relation_type: prov:hadPrimarySource source: labeledin product_url: https://doi.org/10.1016/j.jbi.2014.08.004 secondary_source: - relation_type: prov:wasDerivedFrom source: dailymed - relation_type: prov:used source: rxnorm - category: GraphProduct description: Live TRAPI/BioThings metadata endpoint for the Multiomics BigGIM-DrugResponse KP, exposing the multiomics knowledge graph served by the Multiomics Provider (built from GTEx, TCGA, and drug-response data, with additional clinical-trials, drug-approval and knowledge-resource inputs). format: json id: multiomics-kp.graph name: Multiomics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: multiomics-kp - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcga - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: dailymed - relation_type: prov:hadPrimarySource source: faers product_url: https://biothings.transltr.io/biggim_drugresponse_kp/metadata secondary_source: - relation_type: prov:wasInfluencedBy source: aact - relation_type: prov:wasInfluencedBy source: biogrid - relation_type: prov:wasInfluencedBy source: huri - relation_type: prov:wasInfluencedBy source: cellmarker - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: ttd - relation_type: prov:wasInfluencedBy source: pubmed 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: '2026-06-27T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: darkkinasekb product_url: https://darkkinome.org - category: Browser description: Expression browser data and source code showing tissue-specific expression of dark kinases using GTEx RNA-seq and Human Proteome Map data with kinome-wide comparisons. The hosted Shiny application formerly at expression.darkkinome.org has been retired; the underlying data and code remain available in this GitHub repository. format: http id: darkkinasekb.expression name: DKK Expression Browser original_source: - relation_type: prov:hadPrimarySource source: darkkinasekb product_url: https://github.com/IDG-Kinase/kinase_expression - 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: darkkinasekb product_url: https://www.synapse.org/#!Synapse:syn18360482/files/ - category: GraphicalInterface description: Interactive Shiny web interface for exploring and visualizing human kinase-substrate interactions format: http id: kinace.portal name: KiNet Web Portal original_source: - relation_type: prov:hadPrimarySource source: kinace product_url: https://kinet.kinametrix.com/ secondary_source: - relation_type: prov:wasDerivedFrom source: coralkinome - relation_type: prov:wasDerivedFrom source: darkkinasekb - relation_type: prov:wasDerivedFrom source: epsd - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: kinhub - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: uniprot publications: - authors: - Berginski ME - Moret N - Liu C - Goldfarb D - Sorger PK - Gomez SM doi: 10.1093/nar/gkaa853 id: PMID:33079988 journal: Nucleic Acids Res title: 'The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases.' year: '2021' 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 evaluation_page: resource/dbpedia/dbpedia_eval_automated.html homepage_url: https://www.dbpedia.org/ id: dbpedia last_modified_date: '2026-05-30T00:00:00Z' 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: dbpedia product_url: http://dbpedia.org/sparql - category: GraphProduct 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: - relation_type: prov:hadPrimarySource source: dbpedia - relation_type: prov:wasDerivedFrom source: wikipedia - relation_type: prov:wasDerivedFrom source: wikidata product_file_size: 18605 product_url: https://databus.dbpedia.org/dbpedia/collections/latest-core - category: OntologyProduct description: DBpedia ontology T-box download used to define the cross-domain schema and mappings applied during DBpedia extraction releases. format: owl id: dbpedia.ontology name: DBpedia Ontology original_source: - relation_type: prov:hadPrimarySource source: dbpedia product_file_size: 3289 product_url: http://archivo.dbpedia.org/download?o=http%3A//dbpedia.org/ontology/&f=owl publications: - authors: - Soren Auer - Christian Bizer - Georgi Kobilarov - Jens Lehmann - Richard Cyganiak - Zachary Ives doi: 10.1007/978-3-540-76298-0_52 id: https://doi.org/10.1007/978-3-540-76298-0_52 journal: Lecture Notes in Computer Science preferred: true title: 'DBpedia: A Nucleus for a Web of Open Data' year: '2007' - authors: - Christian Bizer - Jens Lehmann - Georgi Kobilarov - Soren Auer - Christian Becker - Richard Cyganiak - Sebastian Hellmann doi: 10.1016/j.websem.2009.07.002 id: https://doi.org/10.1016/j.websem.2009.07.002 journal: Journal of Web Semantics title: DBpedia - A crystallization point for the Web of Data year: '2009' repository: https://github.com/dbpedia/extraction-framework synonyms: - DBpedia - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://biomics.lab.nycu.edu.tw/dbPTM/ label: dbPTM Team creation_date: '2026-06-02T00:00:00Z' description: dbPTM is an integrated protein post-translational modification resource that curates experimentally verified PTM sites, literature evidence, proteomic datasets, regulatory networks, and disease-associated PTM annotations. domains: - biomedical - proteomics - biological systems homepage_url: https://biomics.lab.nycu.edu.tw/dbPTM/ id: dbptm last_modified_date: '2026-06-03T00:00:00Z' layout: resource_detail name: dbPTM products: - category: GraphicalInterface description: dbPTM 2025 web portal for searching proteins, browsing PTM general information, and analyzing disease-associated PTMs, PTM crosstalk, drug-binding-associated PTM sites, and kinase activity profiles. id: dbptm.portal name: dbPTM Web Portal original_source: - relation_type: prov:hadPrimarySource source: dbptm product_url: https://biomics.lab.nycu.edu.tw/dbPTM/ - category: Product description: dbPTM downloads for experimental and putative PTM sites, benchmark datasets, and cancer proteomics datasets, with PTM records mapped to UniProtKB protein entries and linked to literature evidence. format: tsv id: dbptm.downloads name: dbPTM Download Datasets original_source: - relation_type: prov:hadPrimarySource source: dbptm product_url: https://biomics.lab.nycu.edu.tw/dbPTM/download.php secondary_source: - relation_type: prov:wasDerivedFrom source: pubmed - relation_type: prov:wasDerivedFrom source: uniprot - category: GraphProduct description: Current iPTMnet PTM record table with PTM type, source, UniProt protein, organism, site, enzyme, relation identifiers, and publication evidence. format: tsv id: iptmnet.ptm license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC BY-NC-SA 4.0 name: iPTMnet PTM Table original_source: - relation_type: prov:hadPrimarySource source: iptmnet product_file_size: 44116546 product_url: https://research.bioinformatics.udel.edu/iptmnet_data/files/current/ptm.txt secondary_source: - relation_type: prov:wasDerivedFrom source: dbptm - relation_type: prov:wasDerivedFrom source: dbsno - relation_type: prov:wasDerivedFrom source: efip - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: nextprot - relation_type: prov:wasDerivedFrom source: p3db - relation_type: prov:wasDerivedFrom source: phosphoelm - relation_type: prov:wasDerivedFrom source: phosphogrid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: phosphat - relation_type: prov:wasDerivedFrom source: pombase - relation_type: prov:wasDerivedFrom source: pubtator - relation_type: prov:wasDerivedFrom source: rlims-p - relation_type: prov:wasDerivedFrom source: signor - relation_type: prov:wasDerivedFrom source: uniprot publications: - authors: - Chia-Ru Chung - Yun Tang - Yen-Peng Chiu - Shangfu Li - Wen-Kai Hsieh - Tzong-Yi Lee doi: 10.1093/nar/gkae1005 id: doi:10.1093/nar/gkae1005 journal: Nucleic Acids Research preferred: true title: 'dbPTM 2025 update: comprehensive integration of PTMs and proteomic data for advanced insights into cancer research' year: '2025' taxon: - NCBITaxon:9606 - NCBITaxon:10090 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://biomics.lab.nycu.edu.tw/dbSNO/index.php label: dbSNO Team creation_date: '2026-06-02T00:00:00Z' description: dbSNO is a protein S-nitrosylation database that curates experimentally verified S-nitrosylated proteins and cysteine sites with structural, functional, disease, and regulatory network annotations. domains: - biomedical - proteomics - biological systems homepage_url: https://biomics.lab.nycu.edu.tw/dbSNO/index.php id: dbsno last_modified_date: '2026-06-27T00:00:00Z' layout: resource_detail name: dbSNO products: - category: GraphicalInterface description: dbSNO 3.0 web portal for searching, browsing, and analyzing S-nitrosylated proteins, SNO sites, disease associations, SNO regulatory networks, and structural environments. format: http id: dbsno.portal name: dbSNO Web Portal original_source: - relation_type: prov:hadPrimarySource source: dbsno product_url: https://biomics.lab.nycu.edu.tw/dbSNO/index.php - category: Product description: Tab-delimited dbSNO 3.0 S-nitrosylation dataset containing UniProt identifiers, organisms, positions, and sequence context for manually curated and experimentally identified S-nitrosylated peptides. format: tsv id: dbsno.downloads name: dbSNO Download Dataset original_source: - relation_type: prov:hadPrimarySource source: dbsno product_url: https://biomics.lab.nycu.edu.tw/dbSNO/download.php secondary_source: - relation_type: prov:wasDerivedFrom source: pubmed - relation_type: prov:wasDerivedFrom source: uniprot warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 500 error when accessing file' - 'File was not able to be retrieved when checked on 2026-06-27: HTTP 500 error when accessing file. The dbSNO 3.0 download page (download.php) renders its page shell but the server errors before emitting download links; the rest of the site (index.php, statistics.php) is live (200).' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 500 error when accessing file' - category: GraphProduct description: Current iPTMnet PTM record table with PTM type, source, UniProt protein, organism, site, enzyme, relation identifiers, and publication evidence. format: tsv id: iptmnet.ptm license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC BY-NC-SA 4.0 name: iPTMnet PTM Table original_source: - relation_type: prov:hadPrimarySource source: iptmnet product_file_size: 44116546 product_url: https://research.bioinformatics.udel.edu/iptmnet_data/files/current/ptm.txt secondary_source: - relation_type: prov:wasDerivedFrom source: dbptm - relation_type: prov:wasDerivedFrom source: dbsno - relation_type: prov:wasDerivedFrom source: efip - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: nextprot - relation_type: prov:wasDerivedFrom source: p3db - relation_type: prov:wasDerivedFrom source: phosphoelm - relation_type: prov:wasDerivedFrom source: phosphogrid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: phosphat - relation_type: prov:wasDerivedFrom source: pombase - relation_type: prov:wasDerivedFrom source: pubtator - relation_type: prov:wasDerivedFrom source: rlims-p - relation_type: prov:wasDerivedFrom source: signor - relation_type: prov:wasDerivedFrom source: uniprot publications: - authors: - Yi-Ju Chen - Cheng-Tsung Lu - Min-Gang Su - Kai-Yao Huang - Wei-Chieh Ching - Hsiao-Hsiang Yang - Yen-Chen Liao - Yu-Ju Chen - Tzong-Yi Lee doi: 10.1093/nar/gku1176 id: doi:10.1093/nar/gku1176 journal: Nucleic Acids Research preferred: true title: 'dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation' year: '2015' taxon: - NCBITaxon:9606 - NCBITaxon:10090 - 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 - biomedical homepage_url: https://www.ncbi.nlm.nih.gov/snp/ id: dbsnp infores_id: dbsnp last_modified_date: '2026-06-18T00:00:00Z' 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 format: http id: dbsnp.site is_public: true name: dbSNP Web Interface original_source: - relation_type: prov:hadPrimarySource source: dbsnp product_url: https://www.ncbi.nlm.nih.gov/snp/ - category: ProgrammingInterface description: Programmatic access to dbSNP data via the NCBI E-utilities API format: http id: dbsnp.api is_public: true name: dbSNP E-utilities API original_source: - relation_type: prov:hadPrimarySource source: dbsnp product_url: https://www.ncbi.nlm.nih.gov/books/NBK25500/ - category: Product compression: gzip description: JSON format files with dbSNP RefSNP data format: json id: dbsnp.json name: dbSNP JSON Files original_source: - relation_type: prov:hadPrimarySource source: dbsnp product_url: https://ftp.ncbi.nih.gov/snp/latest_release/JSON/ - category: ProgrammingInterface description: NCBI Variation Services API for accessing and manipulating variant data format: http id: dbsnp.variation.api is_public: true name: NCBI Variation Services API original_source: - relation_type: prov:hadPrimarySource source: dbsnp product_url: https://api.ncbi.nlm.nih.gov/variation/v0/ - category: GraphProduct compression: zip description: Nodes from dbSNP format: csv id: biomarkerkg.nodes.variant name: BKG Variant Nodes original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: dbsnp product_file_size: 782975 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Variant.nodes.zip - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: circbase - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - 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T. Sherry doi: 10.1093/nar/29.1.308 id: doi:10.1093/nar/29.1.308 journal: Nucleic Acids Research title: 'dbSNP: the NCBI database of genetic variation' year: '2001' - authors: - Lon Phan - Hua Zhang - Qiang Wang - Ricardo Villamarin - Tim Hefferon - Aravinthan Ramanathan - Brandi Kattman doi: 10.1093/nar/gkae977 id: doi:10.1093/nar/gkae977 journal: Nucleic Acids Research preferred: true title: 'The evolution of dbSNP: 25 years of impact in genomic research' year: '2025' repository: https://github.com/ncbi/dbsnp taxon: - NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://asntech.org/dbsuper/ label: dbSUPER creation_date: '2026-06-17T00:00:00Z' description: dbSUPER is an integrated and interactive database of super-enhancers in mouse and human genomes. 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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: '2026-06-18T00:00:00Z' 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: 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 original_source: - relation_type: prov:hadPrimarySource source: dc 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 original_source: - relation_type: prov:hadPrimarySource source: dc 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 original_source: - relation_type: prov:hadPrimarySource source: dc 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 original_source: - relation_type: prov:hadPrimarySource source: dc 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 original_source: - relation_type: prov:hadPrimarySource source: dc 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 original_source: - relation_type: prov:hadPrimarySource source: dc 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 original_source: - relation_type: prov:hadPrimarySource source: dc 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: - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: cob - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: ecto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: fma - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hancestro - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: ido - relation_type: prov:hadPrimarySource source: ma - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: ogms - relation_type: prov:hadPrimarySource source: oio - relation_type: prov:hadPrimarySource source: omit - relation_type: prov:hadPrimarySource source: omo - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semapv - relation_type: prov:hadPrimarySource source: skos - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: cob - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: ecto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: fma - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hancestro - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: ido - relation_type: prov:hadPrimarySource source: ma - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: ogms - relation_type: prov:hadPrimarySource source: oio - relation_type: prov:hadPrimarySource source: omit - relation_type: prov:hadPrimarySource source: omo - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semapv - relation_type: prov:hadPrimarySource source: skos - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo - category: GraphProduct description: Public SPARQL endpoint (OpenLink Virtuoso) providing query access to the complete FORUM knowledge graph. The former credentialed FTP tarball dump (2021) is no longer published; the SPARQL endpoint is the current canonical access point for the full RDF graph. format: http id: forum.graph.dump name: FORUM Knowledge Graph SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cheminf - relation_type: prov:hadPrimarySource source: chemont - relation_type: prov:hadPrimarySource source: cito - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: fabio - relation_type: prov:hadPrimarySource source: forum - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: skos product_url: https://forum.semantic-metabolomics.fr/sparql - category: OntologyProduct description: EDAM OWL release format: owl id: edam.owl name: EDAM OWL original_source: - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: skos product_file_size: 3373041 product_url: http://edamontology.org/EDAM.owl - category: OntologyProduct description: EDAM TSV export format: tsv id: edam.tsv name: EDAM TSV original_source: - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: skos product_file_size: 1977072 product_url: https://edamontology.org/EDAM.tsv - category: OntologyProduct description: EDAM CSV export format: csv id: edam.csv name: EDAM CSV original_source: - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: skos product_file_size: 1977072 product_url: https://edamontology.org/EDAM.csv 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: DataModel contacts: - category: Organization contact_details: - contact_type: url value: https://www.w3.org/ label: World Wide Web Consortium creation_date: '2026-06-02T00:00:00Z' description: The Data Catalog Vocabulary (DCAT) is a W3C RDF vocabulary designed to support interoperability between data catalogs published on the Web. domains: - information technology - general homepage_url: https://www.w3.org/TR/vocab-dcat-3/ id: dcat last_modified_date: '2026-06-02T00:00:00Z' layout: resource_detail name: Data Catalog Vocabulary products: - category: DataModelProduct description: Turtle serialization of the W3C Data Catalog Vocabulary namespace. id: dcat.ttl latest_version: '3' name: DCAT Turtle Vocabulary original_source: - relation_type: prov:hadPrimarySource source: dcat product_file_size: 200345 product_url: https://www.w3.org/ns/dcat.ttl - category: DocumentationProduct description: W3C Recommendation for Data Catalog Vocabulary version 3. format: http id: dcat.spec latest_version: '3' name: DCAT Version 3 Specification original_source: - relation_type: prov:hadPrimarySource source: dcat product_url: https://www.w3.org/TR/vocab-dcat-3/ - category: GraphProduct description: RDF knowledge graph materialized by the MetaBoKG workflow from public metabolomics repository outputs, GNPS molecular-networking jobs, annotation evidence, sample metadata, and environmental and taxonomic context. The repository documents generated per-job Turtle files under mapping/kg and loading into Virtuoso named graphs. format: mixed id: metabokg.graph latest_version: arXiv v1 demonstration name: MetaboKG RDF Graph original_source: - relation_type: prov:hadPrimarySource source: metabokg - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubmedcentral - relation_type: prov:hadPrimarySource source: gnps - relation_type: prov:hadPrimarySource source: massive - relation_type: prov:hadPrimarySource source: redu product_url: https://github.com/HolobiomicsLab/MetaBoKG secondary_source: - relation_type: prov:used source: ms - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - relation_type: prov:used source: envo - relation_type: prov:used source: ncit - relation_type: prov:used source: uberon - relation_type: prov:used source: chmo - relation_type: prov:used source: sio - relation_type: prov:used source: prov-o - relation_type: prov:used source: dcat - relation_type: prov:used source: afo warnings: - No static public graph release or hosted endpoint was available in the GitHub repository when curated on 2026-06-02; the repository documents local Turtle materialization and Virtuoso loading. - category: DataModelProduct description: Turtle schema files defining MetaBoKG classes, properties, and ReDU class hierarchies used by the generated knowledge graph. format: ttl id: metabokg.schema license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: MetaBoKG RDF Schema original_source: - relation_type: prov:hadPrimarySource source: metabokg product_url: https://github.com/HolobiomicsLab/MetaBoKG/tree/main/Schema secondary_source: - relation_type: prov:wasInformedBy source: ms - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: envo - relation_type: prov:wasInformedBy source: ncit - relation_type: prov:wasInformedBy source: uberon - relation_type: prov:wasInformedBy source: chmo - relation_type: prov:wasInformedBy source: sio - relation_type: prov:wasInformedBy source: prov-o - relation_type: prov:wasInformedBy source: dcat - relation_type: prov:wasInformedBy source: afo publications: - authors: - Riccardo Albertoni - David Browning - Simon Cox - Alejandra Gonzalez Beltran - Andrea Perego - Peter Winstanley id: https://www.w3.org/TR/vocab-dcat-3/ journal: W3C Recommendation preferred: true title: Data Catalog Vocabulary (DCAT) - Version 3 year: '2024' synonyms: - DCAT - 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: - information technology - literature homepage_url: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ id: dct last_modified_date: '2026-05-30T00:00:00Z' 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: Dublin Core Terms products: - category: DocumentationProduct description: Authoritative DCMI specification for Dublin Core metadata terms in the /terms/ namespace, including properties, classes, encoding schemes, and usage notes. format: http id: dct.spec name: Dublin Core Terms Specification original_source: - relation_type: prov:hadPrimarySource source: dct product_url: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ - category: DataModelProduct description: RDF vocabulary endpoint for Dublin Core terms in the /terms/ namespace. format: rdfxml id: dct.rdf name: Dublin Core Terms RDF Vocabulary original_source: - relation_type: prov:hadPrimarySource source: dct product_url: http://purl.org/dc/terms/ - 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ synonyms: - DCT - DCMI Terms - Dublin Core - Dublin Core Metadata Initiative - 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 infores_id: dda last_modified_date: '2026-06-27T00:00:00Z' 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: Dictyostelium discoideum anatomy products: - category: OntologyProduct description: Dictyostelium discoideum anatomy in OWL format format: owl id: ddanat.owl name: ddanat.owl original_source: - relation_type: prov:hadPrimarySource source: ddanat 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 original_source: - relation_type: prov:hadPrimarySource source: ddanat product_file_size: 8493 product_url: http://purl.obolibrary.org/obo/ddanat.obo - category: GraphProduct description: KGX distribution of the SRI-Reference KG format: kgx id: sri-reference-kg.graph name: SRI-Reference KG (KGX distribution) original_source: - relation_type: prov:hadPrimarySource source: sri-reference-kg - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: wormbase - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: zfin - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bspo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ddanat - relation_type: prov:hadPrimarySource source: ddpheno - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: dpo - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: emapa - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: foodon - relation_type: prov:hadPrimarySource source: fypo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: nbo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: upheno - relation_type: prov:hadPrimarySource source: wbbt - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: wbphenotype - relation_type: prov:hadPrimarySource source: xao - relation_type: prov:hadPrimarySource source: xpo - relation_type: prov:hadPrimarySource source: zfa - relation_type: prov:hadPrimarySource source: zfs - relation_type: prov:hadPrimarySource source: zp - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: decipher - relation_type: prov:hadPrimarySource source: mmrrc - relation_type: prov:hadPrimarySource source: cureid - relation_type: prov:hadPrimarySource source: phenopacket-store product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz publications: - authors: - Gaudet P - Williams JG - Fey P - Chisholm RL doi: 10.1186/1471-2164-9-130 id: https://www.ncbi.nlm.nih.gov/pubmed/18366659 journal: BMC Genomics title: An anatomy ontology to represent biological knowledge in Dictyostelium discoideum year: '2008' 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 homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/ddinter id: ddinter infores_id: ddinter last_modified_date: '2026-06-18T00:00:00Z' 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: - 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authors: - Xiong G - Yang Z - Yi J - Wang N - Wang L - Zhu H - Wu C - Lu A - Chen X - Liu S - Hou T - Cao D doi: 10.1093/nar/gkab880 id: https://www.ncbi.nlm.nih.gov/pubmed/34634800 journal: Nucleic Acids Res preferred: true title: 'DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety' year: '2022' 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 infores_id: ddpheno last_modified_date: '2026-06-18T00:00:00Z' 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: - 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It links genomic variants to associated phenotypes (using Human Phenotype Ontology terms) to support interpretation of variant pathogenicity and clinical diagnosis. DECIPHER integrates Ensembl genome resources and an international consortium of clinical genetics centers. It is an upstream data source for the SRI-Reference Knowledge Graph and the Monarch Initiative. domains: - genomics - clinical - phenotype - precision medicine homepage_url: https://www.deciphergenomics.org/ id: decipher last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: DECIPHER products: - category: GraphicalInterface description: DECIPHER web interface for browsing genomic variants, syndromes, and associated phenotypes in patients with rare developmental disorders. format: http id: decipher.web name: DECIPHER web platform original_source: - relation_type: prov:hadPrimarySource source: decipher product_url: https://www.deciphergenomics.org/ - category: Product description: DECIPHER downloadable datasets, including aggregated patient variant and phenotype data and supporting genomic annotation files. format: http id: decipher.downloads name: DECIPHER downloadable data original_source: - relation_type: prov:hadPrimarySource source: decipher product_url: https://www.deciphergenomics.org/about/downloads/data - 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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 contacts: - category: Organization contact_details: - contact_type: url value: http://dgv.tcag.ca/dgv/app/contact label: The Centre for Applied Genomics, The Hospital for Sick Children creation_date: '2026-06-17T00:00:00Z' description: The Database of Genomic Variants (DGV) provides a curated catalogue of structural variation in the genomes of control individuals from healthy populations. 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MacDonald - Robert Ziman - Ryan K. C. Yuen - Lars Feuk - Stephen W. Scherer doi: 10.1093/nar/gkt958 id: https://doi.org/10.1093/nar/gkt958 journal: Nucleic Acids Research preferred: true title: 'The Database of Genomic Variants: a curated collection of structural variation in the human genome' year: '2014' - 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. It provides genomic, phenotypic, and molecular data including gene annotations, protein sequences, expression data, phenotypes, literature, and community annotations. 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authors: - Basu S - Fey P - Pandit Y - Dodson R - Kibbe WA - Chisholm RL doi: 10.1093/nar/gks1064 id: https://www.ncbi.nlm.nih.gov/pubmed/23172289 journal: Nucleic Acids Res preferred: true title: 'dictyBase 2013: integrating multiple Dictyostelid species' year: '2013' 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: '2026-06-27T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: dideo product_file_size: 88427 product_url: http://purl.obolibrary.org/obo/dideo.owl - category: GraphProduct description: Merged KG with ontology-grounded KG and literature-based graph as TSV file format: tsv id: np-kg.graph.tsv name: NP-KG TSV original_source: - relation_type: prov:hadPrimarySource source: np-kg - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: dideo - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: indra - relation_type: prov:hadPrimarySource source: mondo - 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relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: dideo - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: indra - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: oae - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pheknowlator - relation_type: prov:hadPrimarySource source: pmc - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semrep - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon product_file_size: 936065236 product_url: https://zenodo.org/records/12536780/files/NP-KG_v3.0.0.gpickle?download=1 publications: - authors: - John Judkins - Jessica Tay-Sontheimer - Richard D. Boyce - Mathias Brochhausen doi: 10.1186/s13326-018-0183-z id: https://pubmed.ncbi.nlm.nih.gov/29743102 journal: J Biomed Semantics preferred: true title: Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse year: '2018' repository: https://github.com/DIDEO/DIDEO - activity_status: active category: KnowledgeGraph collection: - okn contacts: - category: Individual contact_details: - contact_type: email value: flannick@broadinstitute.org - contact_type: github value: flannick label: Jason Flannick - category: Individual contact_details: - contact_type: email value: burtt@broadinstitute.org label: Noel Burtt creation_date: '2026-05-09T00:00:00Z' description: The CFDE REVEAL Knowledge Graph is a statistically inferred genomic evidence graph to integrate and disseminate knowledge within the Common Fund Data Ecosystem (CFDE). domains: - biomedical - genomics - systems biology evaluation_page: resource/digcfdekg/digcfdekg_eval_automated.html homepage_url: https://cfdeknowledge.org/ id: digcfdekg last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail name: CFDE REVEAL Knowledge Graph products: - category: GraphicalInterface description: CFDE Knowledge Center web application for natural-language exploration of mechanistic leads, evidence, and hypothesis-generation workflows backed by the CFDE REVEAL graph. format: http id: digcfdekg.portal name: CFDE REVEAL Portal original_source: - relation_type: prov:hadPrimarySource source: digcfdekg product_url: https://cfdeknowledge.org/r/cfde_reveal - category: GraphProduct description: Statistically inferred genomic evidence graph connecting genes, gene sets, inferred disease mechanisms, and human phenotypes. Gene sets are derived from eleven NIH Common Fund programs (GlyGen, GTEx, IDG, IMPC/KOMP2, LINCS, MoTrPAC, Bridge2AI, HuBMAP, Metabolomics Workbench, SenNet, and SPARC) and phenotype-gene set relationships are computed with PIGEAN (Priors Inferred from GEne ANnotations). format: http id: digcfdekg.graph name: CFDE REVEAL Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: digcfdekg - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: impc - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: bridge2ai - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: sparc product_url: https://cfdeknowledge.org/r/cfde_reveal secondary_source: - relation_type: prov:wasInfluencedBy source: hubmap - 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: '2026-06-18T00:00:00Z' layout: resource_detail license: id: https://dip.doe-mbi.ucla.edu/dip/Download.cgi label: DIP Terms of Use 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 format: http id: dip.search name: DIP Search Interface original_source: - relation_type: prov:hadPrimarySource source: dip 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 original_source: - 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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: - relation_type: prov:hadPrimarySource source: bind - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: dip - relation_type: prov:hadPrimarySource source: hprd - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: irefindex - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: cog - 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relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: GraphProduct description: Integrated pharmacological knowledge graph (PharmDB-K) of drugs, targets, diseases, and associations format: http id: pharmdb.graph name: PharmDB-K Graph original_source: - relation_type: prov:hadPrimarySource source: pharmdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dip - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: mint - 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Xenarios doi: 10.1093/nar/30.1.303 id: https://doi.org/10.1093/nar/30.1.303 journal: Nucleic Acids Research title: 'DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions' year: '2002' - authors: - L. Salwinski doi: 10.1093/nar/gkh086 id: https://doi.org/10.1093/nar/gkh086 journal: Nucleic Acids Research title: 'The Database of Interacting Proteins: 2004 update' year: '2004' - authors: - Sandra Orchard - Samuel Kerrien - Sara Abbani - Bruno Aranda - Jignesh Bhate - Shelby Bidwell - Alan Bridge - Leonardo Briganti - Fiona S L Brinkman - Gianni Cesareni - Andrew Chatr-aryamontri - Emilie Chautard - Carol Chen - Marine Dumousseau - Johannes Goll - Robert E W Hancock - Linda I Hannick - Igor Jurisica - Jyoti Khadake - David J Lynn - Usha Mahadevan - Livia Perfetto - Arathi Raghunath - Sylvie Ricard-Blum - Bernd Roechert - Lukasz Salwinski - Volker Stümpflen - Mike Tyers - Peter Uetz - Ioannis Xenarios - Henning Hermjakob doi: 10.1038/nmeth.1931 id: https://doi.org/10.1038/nmeth.1931 journal: Nature Methods title: 'Protein interaction data curation: The International Molecular Exchange (IMEx) consortium' year: '2012' 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: - 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relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz publications: - authors: - Yorick Janssens - Joachim Nielandt - Antoon Bronselaer - Nathan Debunne - Frederick Verbeke - Evelien Wynendaele - Filip Van Immerseel - Yves-Paul Vandewynckel - Guy De Tre - Bart De Spiegeleer doi: 10.1186/s12866-018-1197-5 id: doi:10.1186/s12866-018-1197-5 journal: BMC Microbiology preferred: true title: 'Disbiome database: linking the microbiome to disease' year: '2018' 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: '2026-04-15T00:00:00Z' 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: Disease Drivers Ontology products: - category: OntologyProduct description: Disease Drivers Ontology in OWL format format: owl id: disdriv.owl name: disdriv.owl original_source: - relation_type: prov:hadPrimarySource source: disdriv product_file_size: 13991 product_url: http://purl.obolibrary.org/obo/disdriv.owl publications: [] 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. 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relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ - category: GraphProduct description: KGX nodes file for JensenLab DISEASES KG format: kgx-jsonl id: kg-jensenlab-diseases.nodes.kgx name: DISEASES KGX nodes original_source: - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: medlineplus 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 original_source: - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: medlineplus 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 original_source: - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: medlineplus product_file_size: 132 product_url: https://github.com/biothings/pending.api/blob/translator-output/plugins/DISEASES/DISEASES_trapi_edges.jsonl - category: GraphProduct description: The SPOKE-OKN knowledge graph, an OKN-hosted RDF publication of the SPOKE biomedical and environmental health knowledge graph, served through FRINK query services. format: ttl id: spoke-okn.graph name: SPOKE-OKN Graph original_source: - relation_type: prov:hadPrimarySource source: spoke-okn - relation_type: prov:wasDerivedFrom source: spoke product_url: https://spoke.ucsf.edu secondary_source: - relation_type: prov:wasInfluencedBy source: bgee - relation_type: prov:wasInfluencedBy source: bindingdb - relation_type: prov:wasInfluencedBy source: bv-brc - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: civic - relation_type: prov:wasInfluencedBy source: cl - relation_type: prov:wasInfluencedBy source: clinicaltrialsgov - relation_type: prov:wasInfluencedBy source: diseases - relation_type: prov:wasInfluencedBy source: doid - relation_type: prov:wasInfluencedBy source: drugbank - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: foodb - relation_type: prov:wasInfluencedBy source: gdsc - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: gwascatalog - relation_type: prov:wasInfluencedBy source: hpa - relation_type: prov:wasInfluencedBy source: interpro - relation_type: prov:wasInfluencedBy source: kegg - relation_type: prov:wasInfluencedBy source: lincs-l1000 - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: metacyc - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: ncbitaxon - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pathophenodb - relation_type: prov:wasInfluencedBy source: pfam - relation_type: prov:wasInfluencedBy source: pid - relation_type: prov:wasInfluencedBy source: protcid - relation_type: prov:wasInfluencedBy source: pubmed - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: sider - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikipathways publications: - authors: - Wright AJ - Orlic-Milacic M - Rothfels K - Weiser J - Trinh QM - Jassal B - Haw RA - Stein LD doi: 10.1093/database/baac009 id: PMID:35348650 journal: Database (Oxford) preferred: true title: Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase. year: '2022' - authors: - Pletscher-Frankild S - Pallejà A - Tsafou K - Binder JX - Jensen LJ doi: 10.1016/j.ymeth.2014.11.020 id: PMID:25484339 journal: Methods title: 'DISEASES: text mining and data integration of disease-gene associations.' year: '2015' 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 - drug discovery homepage_url: https://www.disgenet.com/ id: disgenet infores_id: disgenet last_modified_date: '2026-06-22T00:00:00Z' 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). format: http id: disgenet.data name: DisGeNET Data original_source: - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: mgd - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: psygenet - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: phewascat - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: finngen - relation_type: prov:hadPrimarySource source: clinicaltrialsgov product_url: https://www.disgenet.com/ - category: ProgrammingInterface description: API access to DisGeNET data (requires registration and subscription). format: http id: disgenet.api name: DisGeNET API original_source: - relation_type: prov:hadPrimarySource source: disgenet product_url: https://www.disgenet.com/ - category: GraphicalInterface description: Browser for DisGeNET data (requires registration and subscription). format: http id: disgenet.browser name: DisGeNET Browser original_source: - relation_type: prov:hadPrimarySource source: disgenet product_url: https://www.disgenet.com/search?view=ALL&idents=ALL&source=ALL&tab=GDA - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j format: http id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb product_url: https://arax.ncats.io/ - 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: - relation_type: prov:hadPrimarySource source: alzkb - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dsstox - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hrpimp - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmacotherapydb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - relation_type: prov:wasInfluencedBy source: hetionet - category: GraphProduct description: Memgraph data release for AlzKB. format: mixed id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - relation_type: prov:hadPrimarySource source: alzkb - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dsstox - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hrpimp - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmacotherapydb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - relation_type: prov:wasInfluencedBy source: 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: bioteque - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: cellosaurus - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chemicalchecker - relation_type: prov:hadPrimarySource source: clue - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: creeds - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: dorothea - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: huri - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: offsides - relation_type: prov:hadPrimarySource source: omnipath - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: pharmacodb - relation_type: prov:hadPrimarySource source: prism - relation_type: prov:hadPrimarySource source: progeny - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: repodb - relation_type: prov:hadPrimarySource source: repohub - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues product_url: https://bioteque.irbbarcelona.org/downloads/embeddings - 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. format: python id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: nihreporter - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: cellmarker - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: indra product_url: https://github.com/gyorilab/indra_cogex - 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: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: clinicalkg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - 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category: Product description: Harmonizome 3.0 processed dataset downloads, including dataset-specific association files and knowledge graph serialization downloads. format: mixed id: harmonizome.downloads name: Harmonizome Downloads original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://maayanlab.cloud/Harmonizome/download secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct description: Neo4j knowledge graph serialization of Harmonizome processed datasets, including genes, attributes, resources, datasets, and gene-attribute associations. dump_format: neo4j format: neo4j id: harmonizome.kg-neo4j latest_version: '3.0' name: Harmonizome Knowledge Graph Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://harmonizome-kg.maayanlab.cloud/ secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct description: Neo4j construction artifacts for CardioKG, including Cypher scripts to create graph nodes and add edges. dump_format: neo4j format: neo4j id: cardiokg.neo4j name: CardioKG Neo4j graph construction scripts original_source: - relation_type: prov:hadPrimarySource source: cardiokg - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:used source: mesh - relation_type: prov:used source: mondo - relation_type: prov:used source: reactome - relation_type: prov:used source: kegg - relation_type: prov:used source: uniprot - relation_type: prov:used source: string - relation_type: prov:used source: opentargets product_url: https://github.com/ImperialCollegeLondon/cardioKG/tree/main/Building%20KG - category: GraphProduct description: The full PrimeKG dataset containing disease relationships. format: csv id: primekg.graph name: PrimeKG Full Dataset original_source: - relation_type: prov:hadPrimarySource source: primekg - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: umls product_url: https://dataverse.harvard.edu/api/access/datafile/6180620 warnings: - File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-04_ Timeout connecting to URL 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: '2019' 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: '2026-06-01T00:00:00Z' 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: disprot product_url: https://www.disprot.org/download secondary_source: - relation_type: prov:wasInformedBy source: uniprot - relation_type: prov:wasInformedBy source: interpro - relation_type: prov:wasInformedBy source: go - relation_type: prov:wasInformedBy source: eco - category: ProgrammingInterface connection_url: https://www.disprot.org/api/search description: RESTful API for programmatic access to DisProt data format: json id: disprot.api is_public: true name: DisProt API original_source: - relation_type: prov:hadPrimarySource source: disprot product_url: https://www.disprot.org/api - category: GraphicalInterface description: Deposition system for submitting experimental data on intrinsically disordered proteins format: http id: disprot.deposition name: DisProt Deposition System original_source: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: disprot product_file_size: 50945 product_url: https://www.disprot.org/assets/data/IDPO_v0.3.0.owl secondary_source: - relation_type: prov:wasInformedBy source: go - relation_type: prov:wasInformedBy source: eco publications: - authors: - Aspromonte MC - Nugnes MV - Quaglia F - Bouharoua A - DisProt Consortium - Tosatto SCE - Piovesan D doi: 10.1093/nar/gkad928 id: PMID:37904585 journal: Nucleic Acids Res preferred: true title: 'DisProt in 2024: improving function annotation of intrinsically disordered proteins.' year: '2024' - authors: - Quaglia F - Mészáros B - Salladini E - Hatos A - Pancsa R - Chemes LB - Pajkos M - Lazar T - Peña-Díaz S - Santos J - Ács V - Farahi N - Fichó E - Aspromonte MC - Bassot C - Chasapi A - Davey NE - Davidović R - Dobson L - Elofsson A - Erdős G - Gaudet P - Giglio M - Glavina J - Iserte J - Iglesias V - Kálmán Z - Lambrughi M - Leonardi E - Longhi S - Macedo-Ribeiro S - Maiani E - Marchetti J - Marino-Buslje C - Mészáros A - Monzon AM - Minervini G - Nadendla S - Nilsson JF - Novotný M - Ouzounis CA - Palopoli N - Papaleo E - Pereira PJB - Pozzati G - Promponas VJ - Pujols J - Rocha ACS - Salas M - Sawicki LR - Schad E - Shenoy A - Szaniszló T - Tsirigos KD - Veljkovic N - Parisi G - Ventura S - Dosztányi Z - Tompa P - Tosatto SCE - Piovesan D doi: 10.1093/nar/gkab1082 id: PMID:34850135 journal: Nucleic Acids Res title: 'DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.' year: '2022' - authors: - Hatos A - Hajdu-Soltész B - Monzon AM - Palopoli N - Álvarez L - Aykac-Fas B - Bassot C - Benítez GI - Bevilacqua M - Chasapi A - Chemes L - Davey NE - Davidović R - Dunker AK - Elofsson A - Gobeill J - Foutel NSG - Sudha G - Guharoy M - Horvath T - Iglesias V - Kajava AV - Kovacs OP - Lamb J - Lambrughi M - Lazar T - Leclercq JY - Leonardi E - Macedo-Ribeiro S - Macossay-Castillo M - Maiani E - Manso JA - Marino-Buslje C - Martínez-Pérez E - Mészáros B - Mičetić I - Minervini G - Murvai N - Necci M - Ouzounis CA - Pajkos M - Paladin L - Pancsa R - Papaleo E - Parisi G - Pasche E - Barbosa Pereira PJ - Promponas VJ - Pujols J - Quaglia F - Ruch P - Salvatore M - Schad E - Szabo B - Szaniszló T - Tamana S - Tantos A - Veljkovic N - Ventura S - Vranken W - Dosztányi Z - Tompa P - Tosatto SCE - Piovesan D doi: 10.1093/nar/gkz975 id: PMID:31713636 journal: Nucleic Acids Res title: 'DisProt: intrinsic protein disorder annotation in 2020.' year: '2020' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://digital.nhs.uk/services/terminology-and-classifications/dm-d label: NHS England creation_date: '2026-06-02T00:00:00Z' description: The NHS dictionary of medicines and devices is the national clinical vocabulary for identifying medicines and medical devices used across the NHS and for exchanging medicines information between clinical systems. domains: - clinical - biomedical - pharmacology homepage_url: https://digital.nhs.uk/services/terminology-and-classifications/dm-d id: dmd last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail name: NHS dictionary of medicines and devices products: - category: GraphicalInterface description: Official NHSBSA browser for searching and viewing dm+d medicines and device concepts. format: http id: dmd.browser name: dm+d Browser original_source: - relation_type: prov:hadPrimarySource source: dmd product_url: https://services.nhsbsa.nhs.uk/dmd-browser/ - category: ProgrammingInterface description: NHS Terminology Server access route recommended by NHS England for integrating dm+d terminology into healthcare IT systems. format: http id: dmd.terminology-server is_public: true name: dm+d Terminology Server Access original_source: - relation_type: prov:hadPrimarySource source: dmd product_url: https://digital.nhs.uk/services/terminology-and-classifications/dm-d - category: Product description: Raw dm+d data files distributed as XML for system implementation and terminology integration. format: xml id: dmd.raw-files name: dm+d Raw Data Files original_source: - relation_type: prov:hadPrimarySource source: dmd product_url: https://digital.nhs.uk/services/terminology-and-classifications/dm-d warnings: [] - category: DocumentationProduct description: Vision help documentation describing Gemscript as the integrated drug dictionary used in Vision 3 prescribing workflows format: http id: gemscript.documentation name: Gemscript Vision Help Documentation original_source: - relation_type: prov:hadPrimarySource source: gemscript product_url: https://help.visionhealth.co.uk/Vision_Consultation_Manager_Help_Centre/Content/ConMgr/Gemscript/Gemscript_Drug_Dictionary.htm secondary_source: - relation_type: prov:wasInformedBy source: dmd - category: DocumentationProduct description: Monthly Gemscript bulletin summarizing additions, deletions, name changes, and drug class changes in the active dictionary format: pdf id: gemscript.bulletin latest_version: 2026 May v.01 name: Gemscript Monthly Bulletin original_source: - relation_type: prov:hadPrimarySource source: gemscript product_file_size: 173789 product_url: https://help.visionhealth.co.uk/PDFs/Dictionaries/Gemscript/Gemscript_Bulletin_May_2026.pdf secondary_source: - relation_type: prov:wasInformedBy source: dmd synonyms: - dm+d - dmd - Dictionary of Medicines and Devices - 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: '2026-06-27T00:00:00Z' 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) original_source: - relation_type: prov:hadPrimarySource source: doco 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: - relation_type: prov:hadPrimarySource source: skos - relation_type: prov:hadPrimarySource source: proton - relation_type: prov:hadPrimarySource source: fabio - relation_type: prov:hadPrimarySource source: doco - relation_type: prov:hadPrimarySource source: openbiodiv product_file_size: 8176 product_url: https://raw.githubusercontent.com/pensoft/OpenBiodiv/refs/heads/master/ontology/openbiodiv-ontology-latest.ttl publications: - authors: - Alexandru Constantin - Silvio Peroni - Steve Pettifer - David Shotton - Fabio Vitali doi: 10.3233/SW-150177 id: https://doi.org/10.3233/SW-150177 journal: Semantic Web preferred: true title: The Document Components Ontology (DoCO) year: '2016' 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: '2026-06-18T00:00:00Z' 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: 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. original_source: - relation_type: prov:hadPrimarySource source: doid product_file_size: 2118169 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. original_source: - relation_type: prov:hadPrimarySource source: doid product_file_size: 1376460 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.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: - 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relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - relation_type: prov:wasInfluencedBy source: hetionet - category: GraphProduct description: Memgraph data release for AlzKB. format: mixed id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - relation_type: prov:hadPrimarySource source: alzkb - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dsstox - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hrpimp - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmacotherapydb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - relation_type: prov:wasInfluencedBy source: hetionet - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. format: http id: spoke.graph name: SPOKE Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: bv-brc - 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Mappings from MONDO identifiers to other namespaces. format: sssom id: mondo.sssom name: MONDO SSSOM original_source: - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo product_file_size: 1437457 product_url: https://raw.githubusercontent.com/monarch-initiative/mondo/refs/heads/master/src/ontology/mappings/mondo.sssom.tsv - 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 format: http id: cam-kp.ctd-interactions name: CTD Chemical-Gene Models original_source: - relation_type: prov:hadPrimarySource source: cam-kp - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - category: GraphicalInterface description: Browser for complete Hetionet v1.0 graph database in Neo4j format: http id: hetionet.neo4j name: Hetionet v1.0 Neo4j Database original_source: - 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authors: - Schriml LM - Munro JB - Schor M - Olley D - McCracken C - Felix V - Baron JA - Jackson R - Bello SM - Bearer C - Lichenstein R - Bisordi K - Dialo NC - Giglio M - Greene C doi: 10.1093/nar/gkab1063 id: https://www.ncbi.nlm.nih.gov/pubmed/34755882 journal: Nucleic Acids Res title: The Human Disease Ontology 2022 update year: '2022' 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: '2026-06-18T00:00:00Z' layout: resource_detail license: id: https://github.com/saezlab/dorothea/blob/master/LICENSE label: GPL-3.0 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 original_source: - relation_type: prov:hadPrimarySource source: dorothea - relation_type: prov:hadPrimarySource source: remap - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hocomoco - relation_type: prov:hadPrimarySource source: oreganno - relation_type: prov:hadPrimarySource source: trrust - relation_type: prov:hadPrimarySource source: tfacts - relation_type: prov:hadPrimarySource source: tred product_url: https://github.com/saezlab/dorothea/releases/tag/v1.0.0 - category: ProcessProduct description: Bioconductor R data package containing human and mouse regulons for TF activity inference format: http id: dorothea.r-package name: DoRothEA R Package original_source: - relation_type: prov:hadPrimarySource source: dorothea product_url: https://bioconductor.org/packages/release/data/experiment/html/dorothea.html - category: DocumentationProduct description: Project documentation, usage examples, and methodological notes format: http id: dorothea.docs name: DoRothEA Documentation original_source: - relation_type: prov:hadPrimarySource source: dorothea 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 format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: bioteque - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: cellosaurus - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chemicalchecker - relation_type: prov:hadPrimarySource source: clue - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: creeds - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: dorothea - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: huri - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: offsides - relation_type: prov:hadPrimarySource source: omnipath - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: pharmacodb - relation_type: prov:hadPrimarySource source: prism - relation_type: prov:hadPrimarySource source: progeny - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: repodb - relation_type: prov:hadPrimarySource source: repohub - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues product_url: https://bioteque.irbbarcelona.org/downloads/embeddings publications: - authors: - Luz Garcia-Alonso - Christian H. Holland - Mahmoud M. Ibrahim - Denes Turei - Julio Saez-Rodriguez doi: 10.1101/gr.240663.118 id: doi:10.1101/gr.240663.118 journal: Genome Research preferred: true title: Benchmark and integration of resources for the estimation of human transcription factor activities year: '2019' - authors: - Sophia Müller-Dott - Eirini Tsirvouli - Miguel Vázquez - Ricardo O. Ramirez Flores - Pau Badia-i-Mompel - Robin Fallegger - Astrid Lægreid - Julio Saez-Rodriguez 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' repository: https://github.com/saezlab/dorothea/ taxon: - NCBITaxon:9606 - NCBITaxon:10090 - 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 - phenotype homepage_url: http://purl.obolibrary.org/obo/fbcv id: dpo last_modified_date: '2026-06-05T00:00:00Z' 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: Drosophila Phenotype Ontology products: - 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relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: nbo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: upheno - relation_type: prov:hadPrimarySource source: wbbt - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: wbphenotype - relation_type: prov:hadPrimarySource source: xao - relation_type: prov:hadPrimarySource source: xpo - relation_type: prov:hadPrimarySource source: zfa - relation_type: prov:hadPrimarySource source: zfs - relation_type: prov:hadPrimarySource source: zp - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: decipher - relation_type: prov:hadPrimarySource source: mmrrc - relation_type: prov:hadPrimarySource source: cureid - relation_type: prov:hadPrimarySource source: phenopacket-store product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz publications: - authors: - Osumi-Sutherland D - Marygold SJ - Millburn GH - McQuilton PA - Ponting L - Stefancsik R - Falls K - Brown NH - Gkoutos GV doi: 10.1186/2041-1480-4-30 id: https://www.ncbi.nlm.nih.gov/pubmed/24138933 journal: J Biomed Semantics title: The Drosophila phenotype ontology. year: '2013' 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 - contact_type: github value: yuzhouguangc label: Yuzhou Chen - category: Individual contact_details: - contact_type: email value: yuzhou.chen@temple.edu label: Yuzhou Chen creation_date: '2025-12-08T00:00:00Z' description: Develop Dynamic, REsponsive, Adaptive, and Multifaceted Knowledge Graphs to Address Homelessness With Explainable AI domains: - public health - biomedical evaluation_page: resource/dreamkg/dreamkg_eval_automated.html homepage_url: https://dreamkg.com/ id: dreamkg last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: DREAM-KG products: - category: ProgrammingInterface description: SPARQL endpoint for DREAM-KG format: http id: dreamkg.sparql name: DREAM-KG SPARQL original_source: - relation_type: prov:hadPrimarySource source: dreamkg product_url: https://apps.okn.us/dreamkg/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for DREAM-KG id: dreamkg.tpf name: DREAM-KG TPF original_source: - relation_type: prov:hadPrimarySource source: dreamkg product_url: https://apps.okn.us/ldf/dreamkg - category: GraphProduct description: DREAM-KG homelessness and social-services knowledge graph for the Philadelphia region, integrating social service directory records and provider reviews. Served via the DREAM-KG SPARQL and Triple Pattern Fragments endpoints. format: ttl id: dreamkg.graph is_public: true name: DREAM-KG Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: dreamkg - relation_type: prov:hadPrimarySource source: auntbertha - relation_type: prov:hadPrimarySource source: google-reviews product_url: https://dreamkg.com/ secondary_source: - relation_type: prov:wasInfluencedBy source: opendataphilly - 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: - biomedical evaluation_page: resource/drkg/drkg_eval_automated.html homepage_url: https://github.com/gnn4dr/DRKG id: drkg last_modified_date: '2026-06-22T00:00:00Z' 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. format: mixed id: drkg.graph name: DRKG graph original_source: - relation_type: prov:hadPrimarySource source: drkg - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: gnbr - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: string product_file_size: 216650245 product_url: https://dgl-data.s3-us-west-2.amazonaws.com/dataset/DRKG/drkg.tar.gz - 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). format: mixed id: ibkh.graph name: iBKH Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drkg - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: ibkh - relation_type: prov:hadPrimarySource source: idisk - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon 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: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: dron product_file_size: 701717829 product_url: http://purl.obolibrary.org/obo/dron.owl publications: - authors: - William R. Hogan - Josh Hanna - Amanda Hicks - Samira Amirova - Baxter Bramblett - Matthew Diller - Rodel Enderez - Timothy Modzelewski - Mirela Vasconcelos - Chris Delcher doi: 10.1186/s13326-017-0121-5 id: https://doi.org/10.1186/s13326-017-0121-5 journal: Journal of Biomedical Semantics title: 'Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request' year: '2017' 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: - biomedical - pharmacology - drug discovery evaluation_page: resource/drug-approvals-kp/drug-approvals-kp_eval_automated.html id: drug-approvals-kp last_modified_date: '2026-05-28T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo product_file_size: 701451 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_nodes_v0.3.9.tsv - 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: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo product_file_size: 31052966 product_url: https://db.systemsbiology.net/gestalt/KG/drug_approvals_kg_edges_v0.3.9.tsv - category: ProcessProduct description: Code for the Drug Approvals KP id: drug-approvals-kp.code name: Drug Approvals KP code original_source: - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: translator product_url: https://github.com/multiomicsKP/drug_approvals_kp - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for Drug Approvals KP distributed via the NCATS Translator release site (release 2026_03_19; build dakp_0.5.3_c3f74ab4_2025sep1_4.3.6; source version 0.5.3; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 73999 format: kgx-jsonl id: translator.dakp.graph latest_version: '2026_03_19' license: id: https://opensource.org/license/mit/ label: MIT name: Translator DAKP KGX Graph node_count: 3783 original_source: - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/dakp/latest/ versions: - '2026_03_19' - dakp_0.5.3_c3f74ab4_2025sep1_4.3.6 - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: go-cam - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathbank - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: text-mining-kp - relation_type: prov:hadPrimarySource source: translator - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://kgx-storage.rtx.ai/releases/translator_kg/latest/ versions: - '2026_03_27' - 423af7989cac 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: - biomedical - chemistry and biochemistry - pharmacology - genomics - proteomics homepage_url: https://www.drugbank.com/ id: drugbank infores_id: drugbank last_modified_date: '2026-06-22T00:00:00Z' 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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 format: http id: drugbank.clinical.api is_public: true name: DrugBank Clinical API original_source: - relation_type: prov:hadPrimarySource 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. format: http id: spoke.graph name: SPOKE Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: bv-brc - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - 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relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://spoke.ucsf.edu/data-tools - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - 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relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - relation_type: prov:wasInfluencedBy source: hetionet - category: GraphProduct description: Memgraph data release for AlzKB. format: mixed id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - relation_type: prov:hadPrimarySource source: alzkb - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dsstox - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hrpimp - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmacotherapydb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - relation_type: prov:wasInfluencedBy source: hetionet - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: bioteque - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: cellosaurus - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chemicalchecker - relation_type: prov:hadPrimarySource source: clue - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: creeds - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: dorothea - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: huri - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: offsides - relation_type: prov:hadPrimarySource source: omnipath - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: pharmacodb - relation_type: prov:hadPrimarySource source: prism - relation_type: prov:hadPrimarySource source: progeny - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: repodb - relation_type: prov:hadPrimarySource source: repohub - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues product_url: https://bioteque.irbbarcelona.org/downloads/embeddings - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 format: mixed id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: gnbr - relation_type: prov:hadPrimarySource source: humannet - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pharmkg - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: ttd product_url: https://zenodo.org/record/4077338 - 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: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: clinicalkg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugmechdb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: 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: Plover-hosted TRAPI web API for querying the Multiomics Microbiome knowledge graph format: http id: microbiomekg.api is_public: true name: MicrobiomeKG Plover TRAPI API original_source: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: eupathdb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: microbiomekg - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://multiomics.transltr.io/mbkp - 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: - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: pharmgkb product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ 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). format: mixed id: ibkh.graph name: iBKH Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drkg - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: ibkh - relation_type: prov:hadPrimarySource source: idisk - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - category: GraphProduct description: Core UniBioMap graph edges file. format: csv id: unibiomap.links name: UniBioMap Graph Links original_source: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: batman - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: compath - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: batman - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: compath - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: batman - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: compath - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: batman - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: compath - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: omim product_file_size: 6303875907 product_url: https://aideepmed.com/UniBioMap/database/unibiomap/unibiomap.pred.full.csv - category: GraphProduct description: Graph database dump and additional relationship files for the Clinical Knowledge Graph. format: neo4j id: ckg.graph latest_version: '1' license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: CKG Graph Database Dump original_source: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: ckg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct compression: targz description: DRKG graph files, including a TSV of triples, embeddings, ID mappings, and a glossary of relation types. format: mixed id: drkg.graph name: DRKG graph original_source: - relation_type: prov:hadPrimarySource source: drkg - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: gnbr - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: string product_file_size: 216650245 product_url: https://dgl-data.s3-us-west-2.amazonaws.com/dataset/DRKG/drkg.tar.gz - category: GraphicalInterface description: Browser for complete Hetionet v1.0 graph database in Neo4j format: http id: hetionet.neo4j name: Hetionet v1.0 Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 format: neo4j id: hetionet.data.neo4j name: Hetionet v1.0 Neo4j original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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) original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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) original_source: - relation_type: prov:hadPrimarySource source: hetionet - 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relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: Product description: Download directory for Pathway Commons PC v14 integrated pathway and molecular interaction datasets, including BioPAX, SIF, GMT, TXT, and JSON-LD products. format: mixed id: pathwaycommons.downloads name: Pathway Commons Data Downloads original_source: - relation_type: prov:hadPrimarySource source: pathwaycommons product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/ secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: unichem - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: humancyc - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: dip - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: intact - relation_type: prov:wasDerivedFrom source: bind - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: Product compression: gzip description: PC v14 Simple Interaction Format network file representing binary pairwise molecular relationships integrated from Pathway Commons upstream datasource rows. format: sif id: pathwaycommons.sif name: SIF Network Format original_source: - relation_type: prov:hadPrimarySource source: pathwaycommons product_file_size: 9810179 product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/pc-hgnc.sif.gz secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: unichem - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: humancyc - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: dip - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: intact - relation_type: prov:wasDerivedFrom source: bind - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: Product compression: gzip description: PC v14 Gene Matrix Transposed gene sets for pathway enrichment analysis, derived from the integrated Pathway Commons pathway archive. format: tsv id: pathwaycommons.gmt name: GMT Gene Set Format original_source: - relation_type: prov:hadPrimarySource source: pathwaycommons product_file_size: 262513 product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/pc-hgnc.gmt.gz secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: unichem - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: humancyc - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: dip - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: intact - relation_type: prov:wasDerivedFrom source: bind - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: Product compression: gzip description: PC v14 tab-delimited extended SIF node and edge file using HGNC-oriented identifiers for integrated Pathway Commons interactions. format: txt id: pathwaycommons.txt name: Extended SIF TXT Format original_source: - relation_type: prov:hadPrimarySource source: pathwaycommons product_file_size: 115608500 product_url: https://download.baderlab.org/PathwayCommons/PC2/v14/pc-hgnc.txt.gz secondary_source: - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: unichem - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: humancyc - relation_type: prov:wasDerivedFrom source: hprd - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: dip - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: intact - relation_type: prov:wasDerivedFrom source: bind - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: reconx - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: inoh - relation_type: prov:wasDerivedFrom source: netpath - relation_type: prov:wasDerivedFrom source: pathbank - relation_type: prov:wasDerivedFrom source: innatedb - relation_type: prov:wasDerivedFrom source: biofactoid - category: ProcessProduct description: PREDICT computational method for large-scale prediction of drug indications using drug-drug and disease-disease similarity measures and known drug-disease associations. format: http id: predict.method name: PREDICT Drug-Indication Inference Method original_source: - relation_type: prov:hadPrimarySource source: predict product_url: https://www.embopress.org/doi/abs/10.1038/msb.2011.26 secondary_source: - relation_type: prov:used source: drugbank - relation_type: prov:used source: mesh - relation_type: prov:used source: omim warnings: [] - category: Product description: Supporting information for the PREDICT study, including supplementary tables and data supporting the drug-disease association gold standard and prediction analyses. format: mixed id: predict.supporting-information name: PREDICT Supporting Information original_source: - relation_type: prov:hadPrimarySource source: predict product_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC3159979/ secondary_source: - relation_type: prov:used source: drugbank - relation_type: prov:used source: mesh - relation_type: prov:used source: omim - category: GraphProduct description: Neo4j construction artifacts for CardioKG, including Cypher scripts to create graph nodes and add edges. dump_format: neo4j format: neo4j id: cardiokg.neo4j name: CardioKG Neo4j graph construction scripts original_source: - relation_type: prov:hadPrimarySource source: cardiokg - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:used source: mesh - relation_type: prov:used source: mondo - relation_type: prov:used source: reactome - relation_type: prov:used source: kegg - relation_type: prov:used source: uniprot - relation_type: prov:used source: string - relation_type: prov:used source: opentargets product_url: https://github.com/ImperialCollegeLondon/cardioKG/tree/main/Building%20KG - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: aminode - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: bitterdb - relation_type: prov:hadPrimarySource source: cdd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: craft - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: ena - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: fabric - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: gard - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: geneorganizer - relation_type: prov:hadPrimarySource source: genomernai - relation_type: prov:hadPrimarySource source: glyconnect - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: gtrnadb - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: homologene - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hprd - relation_type: prov:hadPrimarySource source: humancyc - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: iid - relation_type: prov:hadPrimarySource source: imgt - relation_type: prov:hadPrimarySource source: innatedb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: lncbase - relation_type: prov:hadPrimarySource source: lncbook - relation_type: prov:hadPrimarySource source: lncipedia - relation_type: prov:hadPrimarySource source: lncrnadisease - relation_type: prov:hadPrimarySource source: malacards - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: medlineplus - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: mint - relation_type: prov:hadPrimarySource source: mirbase - relation_type: prov:hadPrimarySource source: mirgenedb - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: modomics - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: nextprot - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathwaycommons - relation_type: prov:hadPrimarySource source: paxdb - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pdbe - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pirsf - relation_type: prov:hadPrimarySource source: prosite - relation_type: prov:hadPrimarySource source: proteomicsdb - relation_type: prov:hadPrimarySource source: proteopedia - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubtator - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rfam - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: scop - relation_type: prov:hadPrimarySource source: sfld - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: silva - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: snodb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: snopy - relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ - category: Product description: ReDrugS source code (TurboGears/SADI web application and probabilistic nanopublication pipeline). The hosted service it ran (redrugs.tw.rpi.edu) is no longer available. format: python id: redrugs.source name: ReDrugs Source Code original_source: - relation_type: prov:hadPrimarySource source: redrugs - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: irefindex - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: cosmic product_url: https://github.com/dlmcguinness/redrugs - category: GraphProduct description: GP_KG.txt edge_count: 1246726 format: txt id: gp-kg.graph name: GP-KG node_count: 61146 original_source: - relation_type: prov:hadPrimarySource source: gp-kg - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: mgi - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: goa - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: umls - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: faers - relation_type: prov:wasDerivedFrom source: phenomebrowser - relation_type: prov:wasDerivedFrom source: treatkb product_file_size: 48397035 product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt - 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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: bigg - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: ctrp - relation_type: prov:hadPrimarySource source: cmap - relation_type: prov:hadPrimarySource source: kinomescan - relation_type: prov:hadPrimarySource source: dsstoxdb - relation_type: prov:hadPrimarySource source: gelinea - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 3676906360 product_url: https://molepro.s3.amazonaws.com/nodes.tsv - 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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: bigg - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: ctrp - relation_type: prov:hadPrimarySource source: cmap - relation_type: prov:hadPrimarySource source: kinomescan - relation_type: prov:hadPrimarySource source: dsstoxdb - relation_type: prov:hadPrimarySource source: gelinea - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv - category: GraphProduct description: Merged KG with ontology-grounded KG and literature-based graph as TSV file format: tsv id: np-kg.graph.tsv name: NP-KG TSV original_source: - relation_type: prov:hadPrimarySource source: np-kg - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: dideo - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: indra - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: oae - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pheknowlator - relation_type: prov:hadPrimarySource source: pmc - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semrep - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon product_file_size: 1074149258 product_url: https://zenodo.org/records/12536780/files/NP-KG_v3.0.0.tsv?download=1 - category: GraphProduct description: Merged KG with ontology-grounded KG and literature-based graph as NetworkX multidigraph object dump_format: gpickle format: mixed id: np-kg.graph.networkx name: NP-KG gpickle original_source: - relation_type: prov:hadPrimarySource source: np-kg - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: dideo - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: indra - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: oae - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pheknowlator - relation_type: prov:hadPrimarySource source: pmc - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semrep - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon product_file_size: 936065236 product_url: https://zenodo.org/records/12536780/files/NP-KG_v3.0.0.gpickle?download=1 - category: GraphProduct description: Integrated pharmacological knowledge graph (PharmDB-K) of drugs, targets, diseases, and associations format: http id: pharmdb.graph name: PharmDB-K Graph original_source: - relation_type: prov:hadPrimarySource source: pharmdb - relation_type: prov:hadPrimarySource source: chembl - 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relation_type: prov:hadPrimarySource source: spoke-okn - relation_type: prov:wasDerivedFrom source: spoke product_url: https://spoke.ucsf.edu secondary_source: - relation_type: prov:wasInfluencedBy source: bgee - relation_type: prov:wasInfluencedBy source: bindingdb - relation_type: prov:wasInfluencedBy source: bv-brc - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: civic - relation_type: prov:wasInfluencedBy source: cl - relation_type: prov:wasInfluencedBy source: clinicaltrialsgov - relation_type: prov:wasInfluencedBy source: diseases - relation_type: prov:wasInfluencedBy source: doid - relation_type: prov:wasInfluencedBy source: drugbank - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: foodb - relation_type: prov:wasInfluencedBy source: gdsc - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: gwascatalog - relation_type: prov:wasInfluencedBy source: hpa - 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category: Product compression: gzip description: PubChem substance information in ASN.1 format format: xml id: pubchem.substances.asn name: PubChem Substances ASN original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/ASN/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways - category: Product compression: gzip description: PubChem substance information in SDF format format: sdf id: pubchem.substances.sdf name: PubChem Substances SDF original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways publications: - authors: - Craig Knox - Mike Wilson - Christen M Klinger - Mark Franklin - Eponine Oler - Alex Wilson - Allison Pon - Jordan Cox - Na Eun (Lucy) Chin - Seth A Strawbridge - Marysol Garcia-Patino - Ray Kruger - Aadhavya Sivakumaran - Selena Sanford - Rahil Doshi - Nitya Khetarpal - Omolola Fatokun - Daphnee Doucet - Ashley Zubkowski - Dorsa Yahya Rayat - Hayley Jackson - Karxena Harford - Afia Anjum - Mahi Zakir - Fei Wang - Siyang Tian - Brian Lee - Jaanus Liigand - Harrison Peters - Ruo Qi (Rachel) Wang - Tue Nguyen - Denise So - Matthew Sharp - Rodolfo da Silva - Cyrella Gabriel - Joshua Scantlebury - Marissa Jasinski - David Ackerman - Timothy Jewison - Tanvir Sajed - Vasuk Gautam - David S Wishart doi: 10.1093/nar/gkad976 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' - authors: - David S Wishart - Yannick D Feunang - An C Guo - Elvis J Lo - Ana Marcu - Jason R Grant - Tanvir Sajed - Daniel Johnson - Carin Li - Zinat Sayeeda - Nazanin Assempour - Ithayavani Iynkkaran - Yifeng Liu - Adam Maciejewski - Nicola Gale - Alex Wilson - Lucy Chin - Ryan Cummings - Diana Le - Allison Pon - Craig Knox - Michael Wilson doi: 10.1093/nar/gkx1037 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: - biomedical 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: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: drugcentral product_url: https://stars.renci.org/var/plater/bl-4.2.1/DrugCentral_Automat/dec0617490b49c7a/ - 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: - relation_type: prov:hadPrimarySource source: drugcentral product_file_size: 1400714190 product_url: https://unmtid-dbs.net/download/drugcentral.dump.11012023.sql.gz - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. format: http id: spoke.graph name: SPOKE Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - 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relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j format: http id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb product_url: https://arax.ncats.io/ - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: bioteque - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: cellosaurus - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chemicalchecker - relation_type: prov:hadPrimarySource source: clue - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: creeds - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: dorothea - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: huri - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: offsides - relation_type: prov:hadPrimarySource source: omnipath - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: pharmacodb - relation_type: prov:hadPrimarySource source: prism - relation_type: prov:hadPrimarySource source: progeny - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: repodb - relation_type: prov:hadPrimarySource source: repohub - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues product_url: https://bioteque.irbbarcelona.org/downloads/embeddings - 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: - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: mechreponet - relation_type: prov:hadPrimarySource source: mind - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh product_url: https://zenodo.org/records/8117748/files/train.txt warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-06-13: Timeout connecting to URL' - File was not able to be retrieved when checked on 2026-03-30_ 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 2026-07-15: 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: - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: mechreponet - relation_type: prov:hadPrimarySource source: mind - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh product_url: https://zenodo.org/records/8117748/files/test.txt warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-06-13: Timeout connecting to URL' - File was not able to be retrieved when checked on 2026-03-30_ 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 2026-07-15: 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: - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: mechreponet - relation_type: prov:hadPrimarySource source: mind - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh product_url: https://zenodo.org/records/8117748/files/valid.txt warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-06-13: Timeout connecting to URL' - File was not able to be retrieved when checked on 2026-03-30_ 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 2026-07-15: 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: - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: mechreponet - relation_type: prov:hadPrimarySource source: mind - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh product_file_size: 5629618 product_url: https://zenodo.org/records/8117748/files/entities.dict - 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: - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: mechreponet - relation_type: prov:hadPrimarySource source: mind - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh product_file_size: 1648 product_url: https://zenodo.org/records/8117748/files/relations.dict - category: Product description: Complete RepoDB dataset containing drug repositioning successes and failures, with approved drugs, indications, and clinical trial outcomes. Distributed as full.csv via the figshare deposit "repoDB (Final Database)" (DOI 10.6084/m9.figshare.3811674). format: csv id: repodb.full_dataset name: RepoDB Full Dataset original_source: - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: repodb product_file_size: 1029743 product_url: https://ndownloader.figshare.com/files/7341422 - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for Drug Approvals KP distributed via the NCATS Translator release site (release 2026_03_19; build dakp_0.5.3_c3f74ab4_2025sep1_4.3.6; source version 0.5.3; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 73999 format: kgx-jsonl id: translator.dakp.graph latest_version: '2026_03_19' license: id: https://opensource.org/license/mit/ label: MIT name: Translator DAKP KGX Graph node_count: 3783 original_source: - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/dakp/latest/ versions: - '2026_03_19' - dakp_0.5.3_c3f74ab4_2025sep1_4.3.6 - 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: - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 407590 product_url: https://w3id.org/biopragmatics/resources/drugcentral/drugcentral.tsv - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for DrugCentral distributed via the NCATS Translator release site (release 2026_03_19; build drugcentral_2023_11_01_82890f34_2025sep1_4.3.6; source version 2023_11_01; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 36494 format: kgx-jsonl id: translator.drugcentral.graph latest_version: '2026_03_19' license: id: https://opensource.org/license/mit/ label: MIT name: Translator DrugCentral KGX Graph node_count: 5493 original_source: - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/drugcentral/latest/ versions: - '2026_03_19' - drugcentral_2023_11_01_82890f34_2025sep1_4.3.6 - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: go-cam - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathbank - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: text-mining-kp - relation_type: prov:hadPrimarySource source: translator - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://kgx-storage.rtx.ai/releases/translator_kg/latest/ versions: - '2026_03_27' - 423af7989cac - category: GraphicalInterface description: Browser for complete Hetionet v1.0 graph database in Neo4j format: http id: hetionet.neo4j name: Hetionet v1.0 Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 format: neo4j id: hetionet.data.neo4j name: Hetionet v1.0 Neo4j original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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) original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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) original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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: hetionet.hetnetpy name: hetnetpy original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral product_url: https://het.io/search - category: GraphProduct compression: gzip description: PharMeBINet V2 JSON release published on February 6, 2024. format: json id: pharmebinet.json latest_version: v2 name: PharMeBINet JSON Release original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 1942958027 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_24_02_06.json.gz/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct compression: zip description: PharMeBINet V2 TSV release published on February 6, 2024. format: tsv id: pharmebinet.tsv latest_version: v2 name: PharMeBINet TSV Release original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 1922614551 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_tsv_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct compression: zip description: PharMeBINet V2 GraphML release published on February 6, 2024. format: mixed id: pharmebinet.graphml latest_version: v2 name: PharMeBINet GraphML Release original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 2027519087 product_url: https://zenodo.org/api/records/17814889/files/PharMeBiNet_graphml_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct compression: zip description: PharMeBINet V2 Neo4j database release published on February 6, 2024. format: neo4j id: pharmebinet.neo4j latest_version: v2 name: PharMeBINet Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 3847978577 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct compression: zip description: PharMeBINet V2 Neo4j dump release published on February 6, 2024. dump_format: neo4j format: neo4j id: pharmebinet.neo4j.dump latest_version: v2 name: PharMeBINet Neo4j Dump original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 3598325722 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_dump_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - 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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: - relation_type: prov:hadPrimarySource source: tcrd product_url: https://unmtid-dbs.net/download/TCRD/ secondary_source: - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: gtex - relation_type: prov:wasInfluencedBy source: omim warnings: - File was not able to be retrieved when checked on 2026-03-30_ Timeout connecting to URL - category: ProgrammingInterface description: RESTful API providing programmatic access to TCRD data through Pharos for computational workflows and custom applications format: http id: tcrd.api is_public: true name: Pharos API original_source: - 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No replacement public download URL is available.' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' - category: GraphProduct description: KGX Distribution of KG-IDG format: kgx id: kg-idg.graph name: KGX Distribution of KG-IDG original_source: - relation_type: prov:hadPrimarySource source: kg-idg - relation_type: prov:hadPrimarySource source: atc - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ogms - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tcrd product_url: https://kg-hub.berkeleybop.io/kg-idg/current/kg-idg.tar.gz warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 404 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-01: HTTP 404 error. The kg-hub.berkeleybop.io host is being reorganized and KG-IDG downloads are pending relocation to a new home; no live download is currently available.' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' - 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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: tcrd - 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category: GraphProduct description: Live TRAPI/BioThings metadata endpoint for the Multiomics BigGIM-DrugResponse KP, exposing the multiomics knowledge graph served by the Multiomics Provider (built from GTEx, TCGA, and drug-response data, with additional clinical-trials, drug-approval and knowledge-resource inputs). format: json id: multiomics-kp.graph name: Multiomics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: multiomics-kp - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcga - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: dailymed - relation_type: prov:hadPrimarySource source: faers product_url: https://biothings.transltr.io/biggim_drugresponse_kp/metadata secondary_source: - relation_type: prov:wasInfluencedBy source: aact - relation_type: prov:wasInfluencedBy source: biogrid - relation_type: prov:wasInfluencedBy source: huri - relation_type: prov:wasInfluencedBy source: cellmarker - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: ttd - relation_type: prov:wasInfluencedBy source: pubmed - category: Product compression: gzip description: PubChem substance information in ASN.1 format format: xml id: pubchem.substances.asn name: PubChem Substances ASN original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/ASN/ secondary_source: - 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relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways publications: - authors: - Ursu O - Holmes J - Knockel J - Bologa CG - Yang JJ - Mathias SL - Nelson SJ - Oprea TI doi: 10.1093/nar/gkw993 id: doi:10.1093/nar/gkw993 journal: Nucleic Acids Research 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: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugmechdb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: 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 original_source: - relation_type: prov:hadPrimarySource source: drugmechdb product_url: https://sulab.github.io/DrugMechDB/ publications: - authors: - Adriana Carolina Gonzalez-Cavazos - Anna Tanska - Michael Mayers - Denise Carvalho-Silva - Brindha Sridharan - Patrick A. Rewers - Umasri Sankarlal - Lakshmanan Jagannathan - Andrew I. Su 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 infores_id: drug-repurposing-hub last_modified_date: '2026-06-27T00:00:00Z' 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 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 original_source: - relation_type: prov:hadPrimarySource source: drugrephub product_file_size: 661900 product_url: https://repo-hub.broadinstitute.org/public/data/repo-drug-annotation-20200324.txt warnings: - 'File was not able to be retrieved with default certificate verification when checked on 2026-06-01: SSL certificate verification failed; file responded with HTTP 200 when checked without local certificate verification' - 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 original_source: - relation_type: prov:hadPrimarySource source: drugrephub product_file_size: 4072927 product_url: https://repo-hub.broadinstitute.org/public/data/repo-sample-annotation-20240610.txt secondary_source: - relation_type: prov:wasInformedBy source: pubchem warnings: - 'File was not able to be retrieved with default certificate verification when checked on 2026-06-01: SSL certificate verification failed; file responded with HTTP 200 when checked without local certificate verification' - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for Drug Repurposing Hub distributed via the NCATS Translator release site (release 2026_03_06; build drug_rep_hub_2025-08-19_99c18ef1_2025sep1_4.3.6; source version 2025-08-19; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 19389 format: kgx-jsonl id: translator.drug_rep_hub.graph latest_version: '2026_03_06' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Drug Repurposing Hub KGX Graph node_count: 8842 original_source: - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/drug_rep_hub/latest/ versions: - '2026_03_06' - drug_rep_hub_2025-08-19_99c18ef1_2025sep1_4.3.6 - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - 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relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: bigg - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: ctrp - relation_type: prov:hadPrimarySource source: cmap - relation_type: prov:hadPrimarySource source: kinomescan - relation_type: prov:hadPrimarySource source: dsstoxdb - relation_type: prov:hadPrimarySource source: gelinea - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv publications: - authors: - Steven M Corsello - Joshua A Bittker - Zihan Liu - Joshua Gould - Patrick McCarren - Jodi E Hirschman - Stephen E Johnston - Anita Vrcic - Bang Wong - Mariya Khan - Jacob Asiedu - Rajiv Narayan - Christopher C Mader - Aravind Subramanian - Todd R Golub doi: 10.1038/nm.4306 id: doi:10.1038/nm.4306 journal: Nature Medicine preferred: true title: 'The Drug Repurposing Hub: a next-generation drug library and information resource' year: '2017' - 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 homepage_url: https://www.epa.gov/comptox-tools/distributed-structure-searchable-toxicity-dsstox-database id: dsstox last_modified_date: '2026-06-27T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: dsstox 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 original_source: - relation_type: prov:hadPrimarySource source: dsstox product_url: https://comptox.epa.gov/dashboard - category: ProgrammingInterface description: Public API for programmatic access to DSSTox data format: http id: dsstox.api is_public: true name: CompTox API original_source: - relation_type: prov:hadPrimarySource source: dsstox product_url: https://comptox.epa.gov/ctx-api/docs/chemical.html - category: DocumentationProduct description: Documentation for the DSSTox database format: docx id: dsstox.description name: DSSToxDB Description original_source: - relation_type: prov:hadPrimarySource source: dsstox 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 2026-07-10: HTTP 404 error when accessing file' - File was not able to be retrieved when checked on 2026-03-30_ HTTP 404 error when accessing file - 'File was not able to be retrieved when checked on 2026-07-15: 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: - relation_type: prov:hadPrimarySource source: alzkb - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - 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relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - relation_type: prov:wasInfluencedBy source: 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/comptox-tools/distributed-structure-searchable-toxicity-dsstox-database id: dsstoxdb infores_id: dsstoxdb last_modified_date: '2026-06-18T00:00:00Z' 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: - relation_type: prov:hadPrimarySource 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 latest_version: 10.23645/epacomptox.5588566.v8 license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 name: DSSTox Data Downloads original_source: - 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authors: - Grulke CM - Williams AJ - Thillanadarajah I - Richard AM doi: 10.1016/j.comtox.2019.100096 id: https://pubmed.ncbi.nlm.nih.gov/33426407 journal: Comput Toxicol preferred: true title: 'EPA''s DSSTox database: History of development of a curated chemistry resource supporting computational toxicology research' year: '2019' - 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 - information technology homepage_url: https://github.com/EBISPOT/DUO id: duo last_modified_date: '2026-06-18T00:00:00Z' 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: - 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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://github.com/Knowledge-Graph-Hub/eco-kg id: eco-kg last_modified_date: '2026-06-18T00:00:00Z' 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: 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: - relation_type: prov:hadPrimarySource source: eco-kg - relation_type: prov:hadPrimarySource source: eol-traitbank - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: maizegdb - relation_type: prov:hadPrimarySource source: planteome - relation_type: prov:hadPrimarySource source: rapdb product_url: https://github.com/Knowledge-Graph-Hub/eco-kg repository: https://github.com/Knowledge-Graph-Hub/eco-kg tags: - core taxon: - NCBITaxon:33090 - activity_status: active category: Ontology collection: - obo-foundry - ber 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: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: ecocore 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 original_source: - relation_type: prov:hadPrimarySource source: ecocore product_file_size: 834439 product_url: http://purl.obolibrary.org/obo/ecocore.obo publications: [] 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: '2026-06-18T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: ecocyc - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: m-csa - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: obo-db-ingest - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rhea product_file_size: 154171 product_url: https://w3id.org/biopragmatics/resources/rhea/rhea.sssom.tsv - category: GraphicalInterface description: Web interface for EcoCyc database format: http id: ecocyc.web name: EcoCyc Web Interface original_source: - relation_type: prov:hadPrimarySource 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 format: http id: ecocyc.api is_public: true name: EcoCyc Web Services original_source: - relation_type: prov:hadPrimarySource source: ecocyc product_url: https://ecocyc.org/web-services.shtml - category: ProcessProduct description: Metabolic model for E. coli K-12 derived from EcoCyc format: http id: ecocyc.metabolic_model name: EcoCyc Metabolic Model original_source: - relation_type: prov:hadPrimarySource source: ecocyc product_url: http://www.biomedcentral.com/1752-0509/8/79 publications: - authors: - Keseler IM - Gama-Castro S - Mackie A - Billington R - Bonavides-Martínez C - Caspi R - Kothari A - Krummenacker M - Midford PE - Muñiz-Rascado L - Ong WK - Paley S - Santos-Zavaleta A - Subhraveti P - Tierrafría VH - Wolfe AJ - Collado-Vides J - Paulsen IT - Karp PD doi: 10.3389/fmicb.2021.711077 id: https://www.ncbi.nlm.nih.gov/pubmed/34394059 journal: Front Microbiol preferred: true title: The EcoCyc Database in 2021 year: '2021' 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: https://github.com/bioepic-data/ecosim-ontology id: ecosim last_modified_date: '2026-06-27T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: ecosim repository: https://github.com/bioepic-data/ecosim-ontology - activity_status: active category: Ontology collection: - obo-foundry - ber 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 infores_id: ecto last_modified_date: '2026-04-15T00:00:00Z' 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: 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 original_source: - relation_type: prov:hadPrimarySource source: ecto 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 original_source: - relation_type: prov:hadPrimarySource source: ecto 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 original_source: - relation_type: prov:hadPrimarySource source: ecto 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 original_source: - relation_type: prov:hadPrimarySource source: ecto 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 original_source: - relation_type: prov:hadPrimarySource source: ecto 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 original_source: - relation_type: prov:hadPrimarySource source: ecto 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: - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: cob - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: ecto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: fma - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hancestro - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: ido - relation_type: prov:hadPrimarySource source: ma - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: ogms - relation_type: prov:hadPrimarySource source: oio - relation_type: prov:hadPrimarySource source: omit - relation_type: prov:hadPrimarySource source: omo - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semapv - relation_type: prov:hadPrimarySource source: skos - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: cob - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: ecto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: fma - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hancestro - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: ido - relation_type: prov:hadPrimarySource source: ma - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: ogms - relation_type: prov:hadPrimarySource source: oio - relation_type: prov:hadPrimarySource source: omit - relation_type: prov:hadPrimarySource source: omo - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semapv - relation_type: prov:hadPrimarySource source: skos - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo publications: [] 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: - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: skos product_file_size: 3373041 product_url: http://edamontology.org/EDAM.owl - category: OntologyProduct description: EDAM TSV export format: tsv id: edam.tsv name: EDAM TSV original_source: - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: skos product_file_size: 1977072 product_url: https://edamontology.org/EDAM.tsv - category: OntologyProduct description: EDAM CSV export format: csv id: edam.csv name: EDAM CSV original_source: - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: skos product_file_size: 1977072 product_url: https://edamontology.org/EDAM.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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ 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: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.usgs.gov/ label: U.S. Geological Survey (USGS) creation_date: '2026-07-03T00:00:00Z' description: The Catalog of U.S. Federal Early Detection/Rapid Response (EDRR) Invasive Species Databases and Tools catalogs and describes existing online, federally supported databases and tools relevant to a potential national early detection and rapid response invasive species framework. It is published as a USGS data release on ScienceBase. domains: - organisms - environment homepage_url: https://www.sciencebase.gov/catalog/item/5bf87027e4b045bfcae2ece6 id: edrr-invasive-catalog last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: Catalog of U.S. Federal Early Detection/Rapid Response Invasive Species Databases and Tools products: - category: Product description: USGS ScienceBase data release containing the catalog of U.S. federal early detection/rapid response invasive species databases and tools, distributed as tabular spreadsheet data with metadata. id: edrr-invasive-catalog.dataset name: EDRR Invasive Species Databases and Tools Catalog (Version 2.0) original_source: - relation_type: prov:hadPrimarySource source: edrr-invasive-catalog product_url: https://www.sciencebase.gov/catalog/item/5bf87027e4b045bfcae2ece6 warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: GraphProduct description: The Wildlife-KN knowledge graph, an integrative RDF network of managed species and their habitats, environmental factors, and climate context, built to support wildlife management under climate change. It is served as Linked Data through the Wildlife-KN SPARQL and Triple Pattern Fragments endpoints. format: ttl id: wildlifekn.graph name: Wildlife-KN Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: wildlifekn - relation_type: prov:hadPrimarySource source: usgs - relation_type: prov:hadPrimarySource source: edrr-invasive-catalog - relation_type: prov:hadPrimarySource source: gbif - relation_type: prov:hadPrimarySource source: worldclim - relation_type: prov:hadPrimarySource source: iucn-red-list - relation_type: prov:hadPrimarySource source: cabi-isc product_url: https://apps.okn.us/ldf/wildlifekn publications: - authors: - Simpson A - Morisette JT - Fuller P - Reaser J - Guala GF doi: 10.5066/P9CNVBYR id: doi:10.5066/P9CNVBYR title: 'Catalog of U.S. Federal Early Detection/Rapid Response Invasive Species Databases and Tools: Version 2.0' year: '2019' - activity_status: active category: DataModel contacts: - category: Organization contact_details: - contact_type: url value: https://effas.com/about-us/ label: EFFAS (European Federation of Financial Analysts Societies) creation_date: '2026-06-18T00:00:00Z' description: KPIs for ESG is a standardized framework of Key Performance Indicators for Environmental, Social, and Governance (ESG) reporting, published by EFFAS (the European Federation of Financial Analysts Societies) together with DVFA (the German Society of Investment Professionals). The current "KPIs for ESG 3.0" edition defines sector-specific ESG indicators aligned with the Dow Jones Industry Classification Benchmark (ICB), intended for integration of ESG data into corporate performance reporting. It provides the controlled KPI vocabulary used by EmeraldGraph/EmeraldMind. domains: - environment - general - public health homepage_url: https://effas.com/ id: effas-kpi last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: EFFAS KPIs for ESG products: - category: DocumentationProduct description: Official "KPIs for ESG 3.0" framework document (PDF) defining the ESG Key Performance Indicator vocabulary. format: pdf id: effas-kpi.document name: KPIs for ESG 3.0 (Final) original_source: - relation_type: prov:hadPrimarySource source: effas-kpi product_file_size: 1275425 product_url: https://effas.com/wp-content/uploads/2021/09/KPIs_for_ESG_3_0_Final.pdf - category: GraphicalInterface description: EFFAS announcement and landing page for the KPIs for ESG 3.0 exposure draft and framework. format: http id: effas-kpi.landing name: EFFAS/DVFA KPIs for ESG 3.0 Page original_source: - relation_type: prov:hadPrimarySource source: effas-kpi product_url: https://effas.com/download/effas-dvfa-launch-exposure-draft-kpis-for-esg-3-0/ - category: GraphProduct description: Pre-built EmeraldGraph JSON export containing sustainability-related triples extracted from corporate ESG reports. edge_count: 59921 format: json id: emeraldgraph.graph-json name: EmeraldGraph JSON export original_source: - relation_type: prov:hadPrimarySource source: emeraldgraph - relation_type: prov:hadPrimarySource source: effas-kpi - relation_type: prov:hadPrimarySource source: greenclaims product_file_size: 2283928 product_url: https://github.com/ai4greenwashing/EmeraldMind/blob/main/graph_latest.json - 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 - 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: - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: cob - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: ecto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: fma - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hancestro - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: ido - relation_type: prov:hadPrimarySource source: ma - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: ogms - relation_type: prov:hadPrimarySource source: oio - relation_type: prov:hadPrimarySource source: omit - relation_type: prov:hadPrimarySource source: omo - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semapv - relation_type: prov:hadPrimarySource source: skos - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: zfa product_file_size: 240665663 product_url: https://www.ebi.ac.uk/efo/efo.owl - category: OntologyProduct description: The latest release of EFO in OBO format format: obo id: efo.obo name: EFO OBO original_source: - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: cob - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: ecto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: fma - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hancestro - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: ido - relation_type: prov:hadPrimarySource source: ma - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: ogms - relation_type: prov:hadPrimarySource source: oio - relation_type: prov:hadPrimarySource source: omit - relation_type: prov:hadPrimarySource source: omo - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semapv - relation_type: prov:hadPrimarySource source: skos - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo - category: GraphicalInterface description: Browse EFO with EBI's Ontology Lookup Service (OLS) format: http id: efo.ols name: EFO in OLS original_source: - relation_type: prov:hadPrimarySource source: efo product_url: https://www.ebi.ac.uk/ols/ontologies/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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.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: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: clinicalkg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: 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 original_source: - relation_type: prov:hadPrimarySource source: clo product_file_size: 2121232 product_url: http://purl.obolibrary.org/obo/clo.owl - category: ProgrammingInterface description: Plover-hosted TRAPI web API for querying the Multiomics Microbiome knowledge graph format: http id: microbiomekg.api is_public: true name: MicrobiomeKG Plover TRAPI API original_source: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: eupathdb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: microbiomekg - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://multiomics.transltr.io/mbkp - 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: - relation_type: prov:hadPrimarySource source: epigraphdb - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: vectology - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: prsatlas - relation_type: prov:hadPrimarySource source: eqtlgen - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: cpic - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: mrbase product_url: https://docs.epigraphdb.org/graph-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: - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Graph database dump and additional relationship files for the Clinical Knowledge Graph. format: neo4j id: ckg.graph latest_version: '1' license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: CKG Graph Database Dump original_source: - 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relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 1942958027 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_24_02_06.json.gz/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - 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A practical projection of the full graph for human-centric biomedical use. 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relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: progenomes - relation_type: prov:hadPrimarySource source: proteomehd - relation_type: prov:hadPrimarySource source: pubmedcentral - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: swissmodel - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wormbase product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz publications: - authors: - Hernández-Plaza A - Szklarczyk D - Botas J - Cantalapiedra CP - Giner-Lamia J - Mende DR - Kirsch R - Rattei T - Letunic I - Jensen LJ - Bork P - von Mering C - Huerta-Cepas J doi: 10.1093/nar/gkac1022 id: https://www.ncbi.nlm.nih.gov/pubmed/36399505 journal: Nucleic Acids Res preferred: true title: 'eggNOG 6.0: enabling comparative genomics across 12,535 organisms' year: '2023' synonyms: - eggNOG - 'Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups' - activity_status: active category: KnowledgeGraph contacts: - category: Individual contact_details: - contact_type: email value: sergio.consoli@ec.europa.eu label: Sergio Consoli orcid: 0000-0001-7357-5858 creation_date: '2026-04-22T00:00:00Z' description: eKG is an epidemiological knowledge graph extracted from the World Health Organization Disease Outbreak News corpus using an ensemble of large language models and published through the European Commission Joint Research Centre Data Catalogue. domains: - biomedical - public health evaluation_page: resource/ekg/ekg_eval_automated.html homepage_url: https://data.jrc.ec.europa.eu/dataset/89056048-7f5d-4d7c-96ad-f99d1c0f6601 id: ekg last_modified_date: '2026-06-27T00:00:00Z' 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: eKG products: - 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It uses NLP (including the TERMite engine) and expert curation to extract and quality-control relationships from full-text scientific literature and other sources, and offers interactive visualization (e.g., Sankey diagrams) and filtering to support discovery and decision-making in drug research and biology. domains: - biomedical - drug discovery - literature evaluation_page: resource/embiology/embiology_eval.html homepage_url: https://www.embiology.com/ id: embiology infores_id: embiology last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: https://www.elsevier.com/legal/elsevier-website-terms-and-conditions label: Elsevier Website Terms and Conditions name: EmBiology products: - category: GraphicalInterface description: Web interface for exploring biological relationships in EmBiology format: http id: embiology.web name: EmBiology Web Interface original_source: - relation_type: prov:hadPrimarySource source: embiology product_url: https://www.embiology.com/ taxon: - NCBITaxon:9606 - activity_status: active category: KnowledgeGraph contacts: - category: Organization contact_details: - contact_type: github value: ai4greenwashing - contact_type: url value: https://github.com/ai4greenwashing label: ai4greenwashing creation_date: '2026-06-12T00:00:00Z' description: EmeraldGraph is the domain-specific knowledge graph used by EmeraldMind, a knowledge graph-augmented framework for greenwashing detection. 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relation_type: prov:hadPrimarySource source: ccre - relation_type: prov:hadPrimarySource source: fire - relation_type: prov:hadPrimarySource source: motifmap product_url: https://available-inventions.umich.edu/product/genomickb-a-knowledgebase-for-the-human-genome publications: - authors: - The ENCODE Project Consortium doi: 10.1038/nature11247 id: doi:10.1038/nature11247 journal: Nature preferred: true title: An integrated encyclopedia of DNA elements in the human genome year: '2012' repository: https://github.com/ENCODE-DCC/encoded taxon: - NCBITaxon:9606 - NCBITaxon:10090 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: http://www.licpathway.net/ENdb/Contact.php - contact_type: email value: lcqbio@163.com label: School of Medical Informatics, Daqing Campus, Harbin Medical University creation_date: '2026-06-18T00:00:00Z' description: ENdb is a manually curated database of experimentally validated enhancers for human and mouse, compiled from published literature. Each entry links an enhancer to its experimentally supported target gene(s) and includes detailed regulatory annotations such as the validation experiment type, associated transcription factors, disease and tissue/cell-line context, and references to the supporting publications. The database provides browse, search, genome browser, and bulk download interfaces, and serves as an upstream primary source for integrated resources including GenomicKB. domains: - genomics - systems biology - biomedical homepage_url: http://www.licpathway.net/ENdb/ id: endb last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: ENdb products: - category: GraphicalInterface description: Web interface for browsing manually curated, experimentally validated enhancers and their target genes and regulatory annotations in ENdb. id: endb.browse name: ENdb Browse original_source: - relation_type: prov:hadPrimarySource source: endb product_url: http://www.licpathway.net/ENdb/Browse.php - category: Product description: Bulk download of the ENdb dataset of experimentally supported enhancer-target gene records and associated regulatory metadata. id: endb.download name: ENdb Download original_source: - relation_type: prov:hadPrimarySource source: endb product_url: http://www.licpathway.net/ENdb/Download.php - category: GraphProduct description: GenomicKB 1.0 Neo4j Database Dump (Requires license) dump_format: neo4j format: http id: genomickb.graph name: GenomicKB Graph Dump original_source: - relation_type: prov:hadPrimarySource source: genomickb - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: dbvar - relation_type: prov:hadPrimarySource source: endb - relation_type: prov:hadPrimarySource source: enhanceratlas - relation_type: prov:hadPrimarySource source: ccre - relation_type: prov:hadPrimarySource source: fire - relation_type: prov:hadPrimarySource source: motifmap product_url: https://available-inventions.umich.edu/product/genomickb-a-knowledgebase-for-the-human-genome publications: - authors: - Xuefeng Bai - Shanshan Shi - Bo Ai - Yong Jiang - Yuejuan Liu - Xiaole Han - Mingcong Xu - Qi Pan - Fan Wang - Qiuyu Wang - Jian Zhang - Xuecang Li - Chenchen Feng - Yanyu Li - Yuezhu Wang - Yiwei Song - Ke Feng - Chunquan Li doi: 10.1093/nar/gkz973 id: https://pubmed.ncbi.nlm.nih.gov/31665430 journal: Nucleic Acids Res preferred: true title: 'ENdb: a manually curated database of experimentally supported enhancers for human and mouse' year: '2020' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: http://www.enhanceratlas.org/ label: Qian Lab, Johns Hopkins University School of Medicine creation_date: '2026-06-18T00:00:00Z' description: EnhancerAtlas is a genome-wide atlas of enhancer annotations spanning a large number of human and animal cell and tissue types. The resource integrates diverse high-throughput experimental datasets (including histone modifications, DNase-seq, transcription factor binding, and other epigenomic signals) to predict consensus enhancer regions and infer enhancer-target gene interactions. EnhancerAtlas 2.0 provides enhancer annotations for 586 tissue and cell types across nine species, making it a comprehensive reference for regulatory genomics. It serves as an upstream data source for the GenomicKB knowledge graph. domains: - genomics - systems biology - biological systems homepage_url: http://www.enhanceratlas.org/ id: enhanceratlas last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: EnhancerAtlas products: - category: DataProduct description: Downloadable enhancer annotation datasets covering 586 tissue and cell types across nine species, including predicted enhancer regions and enhancer-target gene interactions, available in BED and related tabular formats. id: enhanceratlas.download name: EnhancerAtlas 2.0 Download original_source: - relation_type: prov:hadPrimarySource source: enhanceratlas product_url: http://www.singlecelldb.com/downloadv2.php - category: GraphicalInterface description: A web-based browser for exploring and visualizing enhancer annotations by species, tissue, and cell type within the EnhancerAtlas resource. id: enhanceratlas.browse name: EnhancerAtlas 2.0 Browser original_source: - relation_type: prov:hadPrimarySource source: enhanceratlas product_url: http://www.singlecelldb.com/browse.php - category: GraphProduct description: GenomicKB 1.0 Neo4j Database Dump (Requires license) dump_format: neo4j format: http id: genomickb.graph name: GenomicKB Graph Dump original_source: - relation_type: prov:hadPrimarySource source: genomickb - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: dbvar - relation_type: prov:hadPrimarySource source: endb - relation_type: prov:hadPrimarySource source: enhanceratlas - relation_type: prov:hadPrimarySource source: ccre - relation_type: prov:hadPrimarySource source: fire - relation_type: prov:hadPrimarySource source: motifmap product_url: https://available-inventions.umich.edu/product/genomickb-a-knowledgebase-for-the-human-genome publications: - authors: - Gao T - Qian J doi: 10.1093/nar/gkz980 id: https://pubmed.ncbi.nlm.nih.gov/31740966/ journal: Nucleic Acids Res preferred: true title: 'EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species' year: '2020' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://labs.icahn.mssm.edu/maayanlab/ label: Ma'ayan Laboratory creation_date: '2026-05-21T00:00:00Z' description: Enrichr is a Ma'ayan Lab web-based gene set enrichment analysis resource that accepts gene lists and related inputs, tests them against hundreds of curated and crowd-sourced gene set libraries, and provides ranked enrichment results, visualizations, and programmatic access. domains: - biomedical - genomics - systems biology homepage_url: https://maayanlab.cloud/Enrichr/ id: enrichr last_modified_date: '2026-06-02T00:00:00Z' 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 products: - category: GraphicalInterface description: Main Enrichr web interface for submitting gene sets, exploring enrichment results, browsing libraries, and viewing interactive visualizations format: http id: enrichr.portal name: Enrichr Web Portal original_source: - 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relation_type: prov:hadPrimarySource source: enrichr-kg - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: go product_file_size: 35177347 product_url: https://s3.amazonaws.com/maayan-kg/enrichr-kg/current/GO_Biological_Process_2021.GO_BP.Gene.edges.csv publications: - authors: - Chen EY - Tan CM - Kou Y - Duan Q - Wang Z - Meirelles GV - Clark NR - Ma'ayan A doi: 10.1186/1471-2105-14-128 id: doi:10.1186/1471-2105-14-128 journal: BMC Bioinformatics preferred: true title: 'Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool' year: '2013' - authors: - Kuleshov MV - Jones MR - Rouillard AD - Fernandez NF - Duan Q - Wang Z - Koplev S - Jenkins SL - Jagodnik KM - Lachmann A - McDermott MG - Monteiro CD - Ma'ayan A doi: 10.1093/nar/gkw377 id: doi:10.1093/nar/gkw377 journal: Nucleic Acids Research preferred: false title: 'Enrichr: a comprehensive gene set enrichment analysis web server 2016 update' year: '2016' repository: https://github.com/MaayanLab/enrichr_issues taxon: - NCBITaxon:9606 - 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 Ma'ayan Lab knowledge graph and enrichment web resource built from Enrichr gene set libraries, connecting genes to pathways, diseases, drugs, cell types, ontologies, and other functional annotations for graph-based exploration and enrichment analysis. 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: '2026-06-27T00:00:00Z' 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: - 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Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - category: GraphProduct description: GenomicKB 1.0 Neo4j Database Dump (Requires license) dump_format: neo4j format: http id: genomickb.graph name: GenomicKB Graph Dump original_source: - relation_type: prov:hadPrimarySource source: genomickb - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: dbvar - relation_type: prov:hadPrimarySource source: endb - relation_type: prov:hadPrimarySource source: enhanceratlas - relation_type: prov:hadPrimarySource source: ccre - relation_type: prov:hadPrimarySource source: fire - relation_type: prov:hadPrimarySource source: motifmap product_url: https://available-inventions.umich.edu/product/genomickb-a-knowledgebase-for-the-human-genome - category: GraphProduct description: KGX nodes file for JensenLab DISEASES KG format: kgx-jsonl id: kg-jensenlab-diseases.nodes.kgx name: DISEASES KGX nodes original_source: - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: medlineplus 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 original_source: - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: medlineplus 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 original_source: - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: medlineplus product_file_size: 132 product_url: https://github.com/biothings/pending.api/blob/translator-output/plugins/DISEASES/DISEASES_trapi_edges.jsonl 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/search/ id: entrez infores_id: entrez last_modified_date: '2026-06-01T00:00:00Z' layout: resource_detail name: Entrez products: - category: ProgrammingInterface connection_url: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ description: E-utilities API for programmatic access to Entrez databases format: json id: entrez.eutils name: Entrez E-utilities original_source: - relation_type: prov:hadPrimarySource source: entrez product_url: https://www.ncbi.nlm.nih.gov/books/NBK25501/ secondary_source: - relation_type: prov:wasInformedBy source: pubmed - relation_type: prov:wasInformedBy source: ncbigene - relation_type: prov:wasInformedBy source: ncbitaxon - category: GraphicalInterface description: Web-based search interface for Entrez databases format: http id: entrez.web name: Entrez Web Interface original_source: - relation_type: prov:hadPrimarySource source: entrez product_url: https://www.ncbi.nlm.nih.gov/search/ - category: ProgrammingInterface description: Entrez Direct command-line tools for Unix systems format: mixed id: entrez.edirect name: Entrez Direct (EDirect) original_source: - relation_type: prov:hadPrimarySource 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 - ber 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: '2026-04-15T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: envo 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 original_source: - relation_type: prov:hadPrimarySource source: envo 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 original_source: - relation_type: prov:hadPrimarySource source: envo 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 original_source: - relation_type: prov:hadPrimarySource source: 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 original_source: - relation_type: prov:hadPrimarySource source: envo 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 original_source: - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest - 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest - 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest - 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_url: https://github.com/Knowledge-Graph-Hub/kg-microbe/releases/latest - 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: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bactotraits - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disbiome - relation_type: prov:hadPrimarySource source: ec - relation_type: prov:hadPrimarySource source: envo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-microbe - relation_type: prov:hadPrimarySource source: mediadive - relation_type: prov:hadPrimarySource source: metpo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uniprot product_file_size: 4640682152 product_url: https://portal.nersc.gov/project/m4689/KGMicrobe-biomedical-function-20250222.tar.gz - category: GraphProduct description: RDF knowledge graph materialized by the MetaBoKG workflow from public metabolomics repository outputs, GNPS molecular-networking jobs, annotation evidence, sample metadata, and environmental and taxonomic context. The repository documents generated per-job Turtle files under mapping/kg and loading into Virtuoso named graphs. format: mixed id: metabokg.graph latest_version: arXiv v1 demonstration name: MetaboKG RDF Graph original_source: - relation_type: prov:hadPrimarySource source: metabokg - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubmedcentral - relation_type: prov:hadPrimarySource source: gnps - relation_type: prov:hadPrimarySource source: massive - relation_type: prov:hadPrimarySource source: redu product_url: https://github.com/HolobiomicsLab/MetaBoKG secondary_source: - relation_type: prov:used source: ms - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - relation_type: prov:used source: envo - relation_type: prov:used source: ncit - relation_type: prov:used source: uberon - relation_type: prov:used source: chmo - relation_type: prov:used source: sio - relation_type: prov:used source: prov-o - relation_type: prov:used source: dcat - relation_type: prov:used source: afo warnings: - No static public graph release or hosted endpoint was available in the GitHub repository when curated on 2026-06-02; the repository documents local Turtle materialization and Virtuoso loading. - category: DataModelProduct description: Turtle schema files defining MetaBoKG classes, properties, and ReDU class hierarchies used by the generated knowledge graph. format: ttl id: metabokg.schema license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: MetaBoKG RDF Schema original_source: - relation_type: prov:hadPrimarySource source: metabokg product_url: https://github.com/HolobiomicsLab/MetaBoKG/tree/main/Schema secondary_source: - relation_type: prov:wasInformedBy source: ms - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: envo - relation_type: prov:wasInformedBy source: ncit - relation_type: prov:wasInformedBy source: uberon - relation_type: prov:wasInformedBy source: chmo - relation_type: prov:wasInformedBy source: sio - relation_type: prov:wasInformedBy source: prov-o - relation_type: prov:wasInformedBy source: dcat - relation_type: prov:wasInformedBy source: afo publications: - authors: - Pier Buttigieg - Norman Morrison - Barry Smith - Christopher J Mungall - Suzanna E Lewis doi: 10.1186/2041-1480-4-43 id: https://doi.org/10.1186/2041-1480-4-43 journal: Journal of Biomedical Semantics title: 'The environment ontology: contextualising biological and biomedical entities' year: '2013' - authors: - Pier Luigi Buttigieg - Evangelos Pafilis - Suzanna E. Lewis - Mark P. Schildhauer - Ramona L. Walls - Christopher J. Mungall doi: 10.1186/s13326-016-0097-6 id: https://doi.org/10.1186/s13326-016-0097-6 journal: Journal of Biomedical Semantics title: 'The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation' year: '2016' 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: - organisms - phenotype homepage_url: https://eol.org/traitbank id: eol-traitbank infores_id: eol-traitbank last_modified_date: '2026-06-27T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: eol-traitbank product_url: https://eol.org/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 original_source: - relation_type: prov:hadPrimarySource source: eol-traitbank 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 original_source: - relation_type: prov:hadPrimarySource source: eol-traitbank 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 original_source: - relation_type: prov:hadPrimarySource source: eol-traitbank 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 original_source: - relation_type: prov:hadPrimarySource source: eol-traitbank 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 original_source: - relation_type: prov:hadPrimarySource source: eol-traitbank product_url: https://eol.org/docs/what-is-eol/data-services warnings: - 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)'))) - 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: - relation_type: prov:hadPrimarySource source: eco-kg - relation_type: prov:hadPrimarySource source: eol-traitbank - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: maizegdb - relation_type: prov:hadPrimarySource source: planteome - relation_type: prov:hadPrimarySource source: rapdb product_url: https://github.com/Knowledge-Graph-Hub/eco-kg publications: - authors: - Cynthia S. Parr - Katja S. Schulz - Jennifer Hammock - Nathan Wilson - Patrick Leary - Jeremy Rice - Robert J. Corrigan doi: 10.3233/SW-150190 id: doi:10.3233/SW-150190 journal: Semantic Web preferred: true title: 'TraitBank: Practical semantics for organism attribute data' year: '2016' - authors: - Cynthia S. Parr - Nathan Wilson - Patrick Leary - Katja Schulz - Kristen Lans - Lisa Walley - Jennifer Hammock - Anthony Goddard - Jeremy Rice - Marie Studer - Jeffrey Holmes - Robert Corrigan, Jr. doi: 10.3897/bdj.2.e1079 id: doi:10.3897/bdj.2.e1079 journal: Biodiversity Data Journal 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: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: url value: https://www.epa.gov/aqs label: US Environmental Protection Agency creation_date: '2026-06-18T00:00:00Z' description: The Air Quality System (AQS) is the US Environmental Protection Agency's repository of ambient air-quality monitoring data, assembled to support air quality assessments, area designations, modeling for permit review, and reports to Congress mandated by the Clean Air Act. It holds pollutant measurements from thousands of monitoring stations operated by EPA, state, local, and tribal agencies, along with meteorological data, station location information, and quality-assurance records. AQS data are exposed programmatically through a public REST API that returns JSON. AQS is an upstream data source for the KnowWhereGraph. domains: - environment - public health homepage_url: https://www.epa.gov/aqs id: epa-aqs last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: '' label: US federal government public domain name: EPA Air Quality System (AQS) products: - category: GraphicalInterface description: The AQS landing page describing the Air Quality System repository and providing access to data, tools, and documentation. format: http id: epa-aqs.landing name: EPA Air Quality System (AQS) landing page original_source: - relation_type: prov:hadPrimarySource source: epa-aqs product_url: https://www.epa.gov/aqs - category: ProgrammingInterface description: The AQS Data API, a public REST web service returning JSON for programmatic access to ambient air-quality sample data, monitor metadata, and quality-assurance records. format: http id: epa-aqs.api name: AQS Data API original_source: - relation_type: prov:hadPrimarySource source: epa-aqs product_url: https://aqs.epa.gov/aqsweb/documents/data_api.html - 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 original_source: - relation_type: prov:hadPrimarySource source: knowwheregraph - relation_type: prov:wasDerivedFrom source: wikidata - relation_type: prov:hadPrimarySource source: bluesky - relation_type: prov:hadPrimarySource source: cdc-places - relation_type: prov:hadPrimarySource source: cdc-svi - relation_type: prov:hadPrimarySource source: cropland-data-layer - relation_type: prov:hadPrimarySource source: epa-aqs - relation_type: prov:hadPrimarySource source: gadm - relation_type: prov:hadPrimarySource source: gnis - relation_type: prov:hadPrimarySource source: hifld - relation_type: prov:hadPrimarySource source: mtbs - relation_type: prov:hadPrimarySource source: nhpn - relation_type: prov:hadPrimarySource source: nifc - relation_type: prov:hadPrimarySource source: noaa-hms - relation_type: prov:hadPrimarySource source: noaa-ncei - relation_type: prov:hadPrimarySource source: openfema - relation_type: prov:hadPrimarySource source: reliefweb - relation_type: prov:hadPrimarySource source: ssurgo - relation_type: prov:hadPrimarySource source: us-census - relation_type: prov:hadPrimarySource source: usdm - relation_type: prov:hadPrimarySource source: usgs-comcat product_url: https://knowwheregraph.org/ - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://echo.epa.gov/ label: US Environmental Protection Agency creation_date: '2026-07-01T00:00:00Z' description: EPA Enforcement and Compliance History Online (ECHO) is a US Environmental Protection Agency web resource that provides access to compliance and enforcement information for regulated facilities, along with integrated environmental data downloads. ECHO hosts the PFAS Analytic Tools, which aggregate per- and polyfluoroalkyl substance (PFAS) information from multiple EPA programs, including drinking water sampling, clean water discharge monitoring, facility registry records, and greenhouse gas reporting, into downloadable, filterable datasets. SAWGraph obtains several of its federal PFAS datasets through the ECHO PFAS Analytic Tools download interface. domains: - environment - public health - chemistry and biochemistry homepage_url: https://echo.epa.gov/ id: epa-echo last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail license: id: '' label: US federal government public domain name: EPA Enforcement and Compliance History Online (ECHO) products: - category: GraphicalInterface description: The ECHO landing page providing access to facility compliance and enforcement information, data downloads, and analytic tools. format: http id: epa-echo.landing name: EPA ECHO landing page original_source: - relation_type: prov:hadPrimarySource source: epa-echo product_url: https://echo.epa.gov/ - category: GraphicalInterface description: The ECHO PFAS Analytic Tools, which aggregate PFAS data from multiple EPA programs into downloadable, filterable datasets by state and program. format: http id: epa-echo.pfas-tools name: EPA PFAS Analytic Tools original_source: - relation_type: prov:hadPrimarySource source: epa-echo product_url: https://echo.epa.gov/trends/pfas-tools - category: GraphProduct description: The SAWGraph PFAS knowledge graph, integrating PFAS observations and releases with the samples, geospatial features, environmental media, and chemical substances they describe. The RDF (Turtle) graph is constructed from federal and state PFAS datasets and geospatial reference data, and is served through the SAWGraph SPARQL and Triple Pattern Fragments endpoints. format: ttl id: sawgraph.graph name: SAWGraph PFAS Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: sawgraph - relation_type: prov:hadPrimarySource source: epa-sdwis - relation_type: prov:hadPrimarySource source: epa-ucmr - relation_type: prov:hadPrimarySource source: water-quality-portal - relation_type: prov:hadPrimarySource source: epa-ghg - relation_type: prov:hadPrimarySource source: epa-frs - relation_type: prov:hadPrimarySource source: maine-egad product_url: https://github.com/SAWGraph/pfas-kg secondary_source: - relation_type: prov:wasInfluencedBy source: epa-echo - relation_type: prov:wasInfluencedBy source: usgs-nhd - relation_type: prov:wasInfluencedBy source: us-census - relation_type: prov:wasInfluencedBy source: knowwheregraph - relation_type: prov:wasInfluencedBy source: ssurgo - relation_type: prov:wasInfluencedBy source: cropland-data-layer - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.epa.gov/frs label: US Environmental Protection Agency creation_date: '2026-07-01T00:00:00Z' description: The Facility Registry Service (FRS) is the US Environmental Protection Agency's centrally managed database that identifies facilities, sites, and places subject to environmental regulation or of environmental interest. Each facility is assigned a unique FRS identifier and described with location, industry classification (NAICS and SIC codes), and links to EPA program records. SAWGraph uses FRS as a primary source for the facilities associated with PFAS releases and for their industry classifications, integrated through the SAWGraph Facilities and Industries Ontology (FIO). domains: - environment - general homepage_url: https://www.epa.gov/frs id: epa-frs last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail license: id: '' label: US federal government public domain name: EPA Facility Registry Service (FRS) products: - category: GraphicalInterface description: EPA landing page for the Facility Registry Service describing the centrally managed database of regulated facilities and how to access it. format: http id: epa-frs.landing name: EPA FRS landing page original_source: - relation_type: prov:hadPrimarySource source: epa-frs product_url: https://www.epa.gov/frs - category: ProgrammingInterface description: EPA page describing FRS geospatial data downloads and services for facility location and identification records. format: http id: epa-frs.data name: EPA FRS data downloads original_source: - relation_type: prov:hadPrimarySource source: epa-frs product_url: https://www.epa.gov/frs/geospatial-data-download-service - category: GraphProduct description: The SAWGraph PFAS knowledge graph, integrating PFAS observations and releases with the samples, geospatial features, environmental media, and chemical substances they describe. The RDF (Turtle) graph is constructed from federal and state PFAS datasets and geospatial reference data, and is served through the SAWGraph SPARQL and Triple Pattern Fragments endpoints. format: ttl id: sawgraph.graph name: SAWGraph PFAS Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: sawgraph - relation_type: prov:hadPrimarySource source: epa-sdwis - relation_type: prov:hadPrimarySource source: epa-ucmr - relation_type: prov:hadPrimarySource source: water-quality-portal - relation_type: prov:hadPrimarySource source: epa-ghg - relation_type: prov:hadPrimarySource source: epa-frs - relation_type: prov:hadPrimarySource source: maine-egad product_url: https://github.com/SAWGraph/pfas-kg secondary_source: - relation_type: prov:wasInfluencedBy source: epa-echo - relation_type: prov:wasInfluencedBy source: usgs-nhd - relation_type: prov:wasInfluencedBy source: us-census - relation_type: prov:wasInfluencedBy source: knowwheregraph - relation_type: prov:wasInfluencedBy source: ssurgo - relation_type: prov:wasInfluencedBy source: cropland-data-layer - category: GraphProduct description: The SAWGraph Facilities and Industries Ontology (FIO) / Facility Registry Service (FRS) knowledge graph, an RDF (Turtle) graph representing US facilities from EPA's Facility Registry Service together with their NAICS and SIC industry classifications and spatial locations. It is served through the SAWGraph FRS SPARQL and Triple Pattern Fragments endpoints. format: ttl id: fiokg.graph name: SAWGraph FRS Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: fiokg - relation_type: prov:wasDerivedFrom source: sawgraph - relation_type: prov:hadPrimarySource source: epa-frs product_url: https://github.com/SAWGraph/fio secondary_source: - relation_type: prov:wasInfluencedBy source: naics - relation_type: prov:wasInfluencedBy source: sic - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.epa.gov/ghgreporting label: US Environmental Protection Agency creation_date: '2026-07-01T00:00:00Z' description: The US Environmental Protection Agency's Greenhouse Gas Reporting Program (GHGRP) collects annual greenhouse gas data from large emitting facilities, suppliers, and other sources across the United States. It includes fluorinated greenhouse gas emissions and supplies, some of which involve per- and polyfluoroalkyl substances (PFAS) and related fluorinated chemistry, reported by facility with location, chemical identity, and emission amounts. SAWGraph uses GHGRP facility emission data, obtained through the EPA PFAS Analytic Tools, as a primary source for PFAS-related releases from industrial facilities. domains: - environment - chemistry and biochemistry homepage_url: https://www.epa.gov/ghgreporting id: epa-ghg last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail license: id: '' label: US federal government public domain name: EPA Greenhouse Gas Reporting Program (GHGRP) products: - category: GraphicalInterface description: EPA landing page for the Greenhouse Gas Reporting Program, describing reported emissions data, tools, and downloads. format: http id: epa-ghg.landing name: EPA GHGRP landing page original_source: - relation_type: prov:hadPrimarySource source: epa-ghg product_url: https://www.epa.gov/ghgreporting - category: GraphicalInterface description: EPA page providing fluorinated greenhouse gas emissions and supplies data reported to the GHGRP. format: http id: epa-ghg.fgas name: Fluorinated GHG Emissions and Supplies original_source: - relation_type: prov:hadPrimarySource source: epa-ghg product_url: https://www.epa.gov/ghgreporting/fluorinated-greenhouse-gas-emissions-and-supplies-reported-ghgrp - category: GraphProduct description: The SAWGraph PFAS knowledge graph, integrating PFAS observations and releases with the samples, geospatial features, environmental media, and chemical substances they describe. The RDF (Turtle) graph is constructed from federal and state PFAS datasets and geospatial reference data, and is served through the SAWGraph SPARQL and Triple Pattern Fragments endpoints. format: ttl id: sawgraph.graph name: SAWGraph PFAS Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: sawgraph - relation_type: prov:hadPrimarySource source: epa-sdwis - relation_type: prov:hadPrimarySource source: epa-ucmr - relation_type: prov:hadPrimarySource source: water-quality-portal - relation_type: prov:hadPrimarySource source: epa-ghg - relation_type: prov:hadPrimarySource source: epa-frs - relation_type: prov:hadPrimarySource source: maine-egad product_url: https://github.com/SAWGraph/pfas-kg secondary_source: - relation_type: prov:wasInfluencedBy source: epa-echo - relation_type: prov:wasInfluencedBy source: usgs-nhd - relation_type: prov:wasInfluencedBy source: us-census - relation_type: prov:wasInfluencedBy source: knowwheregraph - relation_type: prov:wasInfluencedBy source: ssurgo - relation_type: prov:wasInfluencedBy source: cropland-data-layer - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.epa.gov/ground-water-and-drinking-water/safe-drinking-water-information-system-sdwis-federal-reporting label: US Environmental Protection Agency creation_date: '2026-07-01T00:00:00Z' description: The Safe Drinking Water Information System (SDWIS) is the US Environmental Protection Agency's national database of public water system information collected under the Safe Drinking Water Act. It records public water systems, their sampling points, monitoring results, and violations, including per- and polyfluoroalkyl substance (PFAS) sampling reported by states and EPA. SDWIS PFAS results are distributed through the EPA PFAS Analytic Tools and SDWIS Federal Reports interfaces. SAWGraph uses SDWIS drinking water PFAS data as a primary source for PFAS occurrence in public water systems. domains: - environment - public health - chemistry and biochemistry homepage_url: https://www.epa.gov/ground-water-and-drinking-water/safe-drinking-water-information-system-sdwis-federal-reporting id: epa-sdwis last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail license: id: '' label: US federal government public domain name: EPA Safe Drinking Water Information System (SDWIS) products: - category: GraphicalInterface description: EPA overview page describing SDWIS federal reporting, the national database of public water system information collected under the Safe Drinking Water Act. format: http id: epa-sdwis.landing name: EPA SDWIS federal reporting landing page original_source: - relation_type: prov:hadPrimarySource source: epa-sdwis product_url: https://www.epa.gov/ground-water-and-drinking-water/safe-drinking-water-information-system-sdwis-federal-reporting - category: GraphicalInterface description: The SDWIS Federal Reports Search interface for querying public water system, sampling, and violation data. format: http id: epa-sdwis.reports name: SDWIS Federal Reports Search original_source: - relation_type: prov:hadPrimarySource source: epa-sdwis product_url: https://sdwis.epa.gov/ords/sfdw_pub/r/sfdw/sdwis_fed_reports_public/200 - category: GraphProduct description: The SAWGraph PFAS knowledge graph, integrating PFAS observations and releases with the samples, geospatial features, environmental media, and chemical substances they describe. The RDF (Turtle) graph is constructed from federal and state PFAS datasets and geospatial reference data, and is served through the SAWGraph SPARQL and Triple Pattern Fragments endpoints. format: ttl id: sawgraph.graph name: SAWGraph PFAS Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: sawgraph - relation_type: prov:hadPrimarySource source: epa-sdwis - relation_type: prov:hadPrimarySource source: epa-ucmr - relation_type: prov:hadPrimarySource source: water-quality-portal - relation_type: prov:hadPrimarySource source: epa-ghg - relation_type: prov:hadPrimarySource source: epa-frs - relation_type: prov:hadPrimarySource source: maine-egad product_url: https://github.com/SAWGraph/pfas-kg secondary_source: - relation_type: prov:wasInfluencedBy source: epa-echo - relation_type: prov:wasInfluencedBy source: usgs-nhd - relation_type: prov:wasInfluencedBy source: us-census - relation_type: prov:wasInfluencedBy source: knowwheregraph - relation_type: prov:wasInfluencedBy source: ssurgo - relation_type: prov:wasInfluencedBy source: cropland-data-layer - category: GraphProduct description: The Geoconnex knowledge graph, an open community-contributed RDF graph linking U.S. hydrologic features via persistent identifiers. It integrates USGS reference features (NHDPlus High Resolution hydrologic units, Watershed Boundary Dataset subwatersheds, reference stream gages, and national aquifers) with community-contributed feature registries, and is served through the Geoconnex SPARQL and Triple Pattern Fragments endpoints. format: ttl id: geoconnex.graph name: GEOCONNEX Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: geoconnex - relation_type: prov:hadPrimarySource source: usgs-nhd - relation_type: prov:hadPrimarySource source: usgs-nwis product_url: https://github.com/internetofwater/geoconnex.us secondary_source: - relation_type: prov:wasInfluencedBy source: epa-sdwis - relation_type: prov:wasInfluencedBy source: us-census - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.epa.gov/ label: U.S. Environmental Protection Agency creation_date: '2026-06-02T00:00:00Z' description: EPA Substance Registry Services is the U.S. Environmental Protection Agency's central system for information about substances tracked or regulated by EPA or other sources, including chemicals, biological organisms, and substance lists. domains: - environment - chemistry and biochemistry homepage_url: https://cdxapps.epa.gov/oms-substance-registry-services/about-srs id: epa-srs last_modified_date: '2026-06-03T00:00:00Z' layout: resource_detail license: id: https://edg.epa.gov/epa_data_license.html label: EPA Standard Open Data License name: EPA Substance Registry Services products: - category: GraphicalInterface description: Public EPA Substance Registry Services search interface for looking up substances tracked or regulated by EPA programs and other sources. format: http id: epa-srs.search name: EPA SRS Search original_source: - relation_type: prov:hadPrimarySource source: epa-srs product_url: https://cdxapps.epa.gov/oms-substance-registry-services/search - category: DocumentationProduct description: EPA overview page explaining Substance Registry Services as the central EPA system for substance information and program-list membership. format: http id: epa-srs.about name: About EPA Substance Registry Services original_source: - relation_type: prov:hadPrimarySource source: epa-srs product_url: https://cdxapps.epa.gov/oms-substance-registry-services/about-srs - category: ProgrammingInterface description: EPA SRS widget service for embedding a Substance Registry Services search box in external web pages. format: http id: epa-srs.widget is_public: true name: EPA SRS Widget original_source: - relation_type: prov:hadPrimarySource source: epa-srs product_url: https://www.epa.gov/developers/data-data-products-substance-registry-services-widget - 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 latest_version: 10.23645/epacomptox.5588566.v8 license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 name: DSSTox Data Downloads original_source: - relation_type: prov:hadPrimarySource source: dsstoxdb product_url: https://epa.figshare.com/articles/dataset/Chemistry_Dashboard_Data_DSSTox_Identifiers_Mapped_to_CAS_Numbers_and_Names/5588566 secondary_source: - relation_type: prov:wasInformedBy source: epa-srs - relation_type: prov:wasInformedBy source: chemid - relation_type: prov:wasInformedBy source: pubchem synonyms: - EPA SRS - Substance Registry Services - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.epa.gov/dwucmr label: US Environmental Protection Agency creation_date: '2026-07-01T00:00:00Z' description: The Unregulated Contaminant Monitoring Rule (UCMR) program directs the US Environmental Protection Agency to collect nationally representative occurrence data for contaminants that are not yet regulated in public drinking water systems. The fifth cycle (UCMR 5) requires monitoring for 29 per- and polyfluoroalkyl substances (PFAS) and lithium, producing sampling results reported by public water systems across the United States. SAWGraph uses UCMR PFAS monitoring results as a primary source for PFAS occurrence in drinking water. domains: - environment - public health - chemistry and biochemistry homepage_url: https://www.epa.gov/dwucmr id: epa-ucmr last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail license: id: '' label: US federal government public domain name: EPA Unregulated Contaminant Monitoring Rule (UCMR) products: - category: GraphicalInterface description: EPA landing page for the Unregulated Contaminant Monitoring Rule program, describing monitoring cycles, contaminant lists, and access to occurrence data. format: http id: epa-ucmr.landing name: EPA UCMR landing page original_source: - relation_type: prov:hadPrimarySource source: epa-ucmr product_url: https://www.epa.gov/dwucmr - category: GraphProduct description: The SAWGraph PFAS knowledge graph, integrating PFAS observations and releases with the samples, geospatial features, environmental media, and chemical substances they describe. The RDF (Turtle) graph is constructed from federal and state PFAS datasets and geospatial reference data, and is served through the SAWGraph SPARQL and Triple Pattern Fragments endpoints. format: ttl id: sawgraph.graph name: SAWGraph PFAS Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: sawgraph - relation_type: prov:hadPrimarySource source: epa-sdwis - relation_type: prov:hadPrimarySource source: epa-ucmr - relation_type: prov:hadPrimarySource source: water-quality-portal - relation_type: prov:hadPrimarySource source: epa-ghg - relation_type: prov:hadPrimarySource source: epa-frs - relation_type: prov:hadPrimarySource source: maine-egad product_url: https://github.com/SAWGraph/pfas-kg secondary_source: - relation_type: prov:wasInfluencedBy source: epa-echo - relation_type: prov:wasInfluencedBy source: usgs-nhd - relation_type: prov:wasInfluencedBy source: us-census - relation_type: prov:wasInfluencedBy source: knowwheregraph - relation_type: prov:wasInfluencedBy source: ssurgo - relation_type: prov:wasInfluencedBy source: cropland-data-layer - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://epd.expasy.org/epd/ label: Swiss Institute of Bioinformatics creation_date: '2026-06-17T00:00:00Z' description: The Eukaryotic Promoter Database (EPD) is an annotated, non-redundant collection of experimentally validated eukaryotic POL II promoters. Its EPDnew components provide high-quality, automatically derived promoter collections for selected organisms, with tools for promoter analysis. domains: - genomics - systems biology homepage_url: https://epd.expasy.org/epd/ id: epd last_modified_date: '2026-06-17T00:00:00Z' layout: resource_detail name: Eukaryotic Promoter Database products: - category: GraphicalInterface description: Web interface for browsing and searching experimentally validated eukaryotic promoters. format: http id: epd.site is_public: true name: EPD Website original_source: - relation_type: prov:hadPrimarySource source: epd product_url: https://epd.expasy.org/epd/ - category: Product description: FTP archive of EPDnew promoter collections and annotation files. format: mixed id: epd.downloads name: EPD Downloads original_source: - relation_type: prov:hadPrimarySource source: epd product_url: https://epd.expasy.org/ftp/epdnew/ - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - 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It supports systematic causal inference, data mining, and exploration through a web application, API, R package, and curated graph knowledge base. domains: - biomedical - genomics - general evaluation_page: resource/epigraphdb/epigraphdb_eval_automated.html homepage_url: https://epigraphdb.org/ id: epigraphdb last_modified_date: '2026-06-01T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: epigraphdb product_url: https://epigraphdb.org/ - category: ProgrammingInterface connection_url: https://api.epigraphdb.org/ description: Public REST API for programmatic access to EpiGraphDB graph entities, relationships, causal estimates, and metadata format: json id: epigraphdb.api is_public: true name: EpiGraphDB REST API original_source: - 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relation_type: prov:hadPrimarySource source: epigraphdb - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: vectology - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: prsatlas - relation_type: prov:hadPrimarySource source: eqtlgen - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: cpic - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: mrbase product_url: https://docs.epigraphdb.org/graph-database/ - 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: - relation_type: prov:hadPrimarySource source: epigraphdb product_url: https://docs.epigraphdb.org/ publications: - authors: - Yi Liu - Benjamin Elsworth - Pau Erola - Valeriia Haberland - Gibran Hemani - Matt Lyon - Jie Zheng - Oliver Lloyd - Marina Vabistsevits - Tom R Gaunt doi: 10.1093/bioinformatics/btaa961 id: doi:10.1093/bioinformatics/btaa961 journal: Bioinformatics preferred: true title: 'EpiGraphDB: a database and data mining platform for health data science' year: '2021' repository: https://github.com/MRCIEU/epigraphdb - 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: '2026-06-27T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: epio product_file_size: 415175 product_url: http://purl.obolibrary.org/obo/epio.owl publications: [] 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: '2026-06-01T00:00:00Z' layout: resource_detail name: Eukaryotic Phosphorylation Site Database 2.0 products: - category: GraphicalInterface 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: - relation_type: prov:hadPrimarySource source: epsd product_url: https://epsd.biocuckoo.cn - category: GraphicalInterface 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: - relation_type: prov:hadPrimarySource source: epsd product_url: https://epsd.biocuckoo.cn - category: GraphicalInterface 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: - relation_type: prov:hadPrimarySource source: epsd product_url: https://epsd.biocuckoo.cn - category: Product 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: - relation_type: prov:hadPrimarySource source: epsd product_url: https://epsd.biocuckoo.cn/Download.php secondary_source: - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: iptmnet - category: GraphicalInterface description: Interactive Shiny web interface for exploring and visualizing human kinase-substrate interactions format: http id: kinace.portal name: KiNet Web Portal original_source: - relation_type: prov:hadPrimarySource source: kinace product_url: https://kinet.kinametrix.com/ secondary_source: - relation_type: prov:wasDerivedFrom source: coralkinome - relation_type: prov:wasDerivedFrom source: darkkinasekb - relation_type: prov:wasDerivedFrom source: epsd - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: kinhub - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: uniprot - category: GraphProduct description: CSV download of the full KiNet human kinase-substrate interaction dataset with source database, evidence, and PMID reference fields format: csv id: kinace.interactions name: KiNet Full Interaction Dataset original_source: - relation_type: prov:hadPrimarySource source: kinace product_file_size: 5180792 product_url: https://raw.githubusercontent.com/GauravPandeyLab/KiNet/master/data/ksi_source_full_dataset.csv secondary_source: - relation_type: prov:wasDerivedFrom source: epsd - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: phosphositeplus publications: - authors: - Miaomiao Chen - Yujie Gou - Ming Lei - Leming Xiao - Miaoying Zhao - Xinhe Huang - Dan Liu - Zihao Feng - Di Peng - Yu Xue doi: 10.1093/gpbjnl/qzaf057 id: doi:10.1093/gpbjnl/qzaf057 journal: Genomics, Proteomics & Bioinformatics preferred: true title: 'EPSD 2.0: An Updated Database of Protein Phosphorylation Sites Across Eukaryotic Species' year: '2025' - authors: - Shaofeng Lin - Chenwei Wang - Jiaqi Zhou - Ying Shi - Chen Ruan - Yiran Tu - Lan Yao - Di Peng - Yu Xue doi: 10.1093/bib/bbz169 id: doi:10.1093/bib/bbz169 journal: Briefings in Bioinformatics title: 'EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes' year: '2021' 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 original_source: - relation_type: prov:hadPrimarySource source: eqtlgen 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 original_source: - relation_type: prov:hadPrimarySource source: eqtlgen 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 original_source: - relation_type: prov:hadPrimarySource source: eqtlgen 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 original_source: - relation_type: prov:hadPrimarySource source: eqtlgen 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 original_source: - relation_type: prov:hadPrimarySource source: eqtlgen 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 original_source: - relation_type: prov:hadPrimarySource source: eqtlgen 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 original_source: - relation_type: prov:hadPrimarySource source: eqtlgen 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 original_source: - relation_type: prov:hadPrimarySource source: eqtlgen 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 original_source: - relation_type: prov:hadPrimarySource source: eqtlgen 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: - relation_type: prov:hadPrimarySource source: epigraphdb - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: vectology - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: prsatlas - relation_type: prov:hadPrimarySource source: eqtlgen - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: cpic - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: mrbase product_url: https://docs.epigraphdb.org/graph-database/ publications: - authors: - Võsa U - Claringbould A - Westra HJ - Bonder MJ - Deelen P - Zeng B - Franke L doi: 10.1038/s41588-021-00913-z 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 - biomedical - phenotype - precision medicine homepage_url: http://119.3.41.228/eram/ id: eram infores_id: eram last_modified_date: '2026-06-27T00:00:00Z' layout: resource_detail license: id: http://119.3.41.228/eram/download.php label: Free of charge for non-profit (academic) institutions 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: - relation_type: prov:hadPrimarySource source: eram product_url: http://119.3.41.228/eram/ secondary_source: - relation_type: prov:wasInformedBy source: omim - relation_type: prov:wasInformedBy source: umls - relation_type: prov:wasInformedBy source: doid - relation_type: prov:wasInformedBy source: mesh - relation_type: prov:wasInformedBy source: orphanet - relation_type: prov:wasInformedBy source: hp - relation_type: prov:wasInformedBy source: mp - 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: - relation_type: prov:hadPrimarySource source: eram product_url: http://119.3.41.228/eram/download.php secondary_source: - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: umls - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: mesh - relation_type: prov:wasDerivedFrom source: orphanet - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: mp 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: doi:10.1093/nar/gkx1062 journal: Nucleic Acids Research preferred: true 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://esgf.llnl.gov/ label: Earth System Grid Federation creation_date: '2026-07-03T00:00:00Z' description: The Earth System Grid Federation (ESGF) is an international, distributed data infrastructure that archives and serves climate model output and observational data, including the CMIP model ensembles. ESGF exposes dataset metadata such as source_id, experiment_id, variable_id, and activity_id through federated search nodes and APIs, enabling discovery and download of climate simulation datasets. domains: - environment - information technology - general homepage_url: https://esgf.llnl.gov/ id: esgf last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: Earth System Grid Federation (ESGF) products: - category: ProgrammingInterface description: The ESGF search interface (MetaGrid / AIMS) provides discovery and access to climate dataset metadata across the federation, including CMIP model output indexed by source_id, experiment_id, variable_id, and activity_id. format: http id: esgf.search name: ESGF Search original_source: - relation_type: prov:hadPrimarySource source: esgf product_url: https://aims2.llnl.gov/search - category: GraphProduct description: RDF/Turtle knowledge graph integrating climate model and dataset metadata (from ESGF, CMIP controlled vocabularies, and the NASA GCMD keyword taxonomy) with entities and relationships extracted from climate-science publications. Served through the FRINK federation and the SPARQL and TPF endpoints. format: ttl id: climatemodelskg.graph name: Climate Models KG Graph original_source: - relation_type: prov:hadPrimarySource source: climatemodelskg - relation_type: prov:hadPrimarySource source: esgf - relation_type: prov:hadPrimarySource source: cmip - relation_type: prov:hadPrimarySource source: gcmd product_url: https://frink.renci.org/registry/kgs/climatepub4-kg/ - 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: '2026-06-27T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: eupathdb 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 original_source: - relation_type: prov:hadPrimarySource source: eupathdb 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 original_source: - relation_type: prov:hadPrimarySource source: eupathdb 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 original_source: - relation_type: prov:hadPrimarySource source: eupathdb product_url: https://veupathdb.org/veupathdb/app/workspace/strategies - category: GraphicalInterface description: Map-based visualization tool (PopBio Map) within VectorBase for field-collected data including insecticide resistance, population abundance, and pathogen infection status. Successor to the standalone MapVEu tool, now folded into VectorBase (part of VEuPathDB). format: http id: eupathdb.mapveu name: VectorBase PopBio Map (formerly MapVEu) original_source: - relation_type: prov:hadPrimarySource source: eupathdb product_url: https://vectorbase.org/vectorbase/app/popbio-map - 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 original_source: - relation_type: prov:hadPrimarySource source: eupathdb product_url: https://veupathdb.org/veupathdb/app/static-content/landing.html - category: ProgrammingInterface description: Plover-hosted TRAPI web API for querying the Multiomics Microbiome knowledge graph format: http id: microbiomekg.api is_public: true name: MicrobiomeKG Plover TRAPI API original_source: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: eupathdb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: microbiomekg - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://multiomics.transltr.io/mbkp publications: - authors: - Aurrecoechea C - Barreto A - Brestelli J - Brunk BP - Cade S - Doherty R - Fischer S - Gajria B - Gao X - Gingle A doi: 10.1093/nar/gks1113 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 original_source: - relation_type: prov:hadPrimarySource source: evlncrnas 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 original_source: - relation_type: prov:hadPrimarySource source: evlncrnas 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 original_source: - relation_type: prov:hadPrimarySource source: evlncrnas 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 original_source: - relation_type: prov:hadPrimarySource source: evlncrnas 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 original_source: - relation_type: prov:hadPrimarySource source: evlncrnas product_url: https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/#/structures - 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relation_type: prov:hadPrimarySource source: exmo product_url: http://purl.obolibrary.org/obo/exmo.owl publications: - authors: - Liu X - Yang Y - Zong H - Zhang K - Jiang M - Yu C - Chen Y - Bao T - Li D - Wang J - Tang T - Ren S - Ruso JM - Shen B doi: 10.1038/s41597-024-04217-9 id: https://www.ncbi.nlm.nih.gov/pubmed/39695140 journal: Sci Data title: Core reference ontology for individualized exercise prescription year: '2024' 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: '2026-06-18T00:00:00Z' 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: - 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relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://sugi.bio/biobtree/api/ - category: GraphProduct compatibility: - standard: biolink version: 4.2.1 compression: gzip description: Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - 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relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - 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: - relation_type: prov:hadPrimarySource source: eco-kg - relation_type: prov:hadPrimarySource source: eol-traitbank - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: maizegdb - relation_type: prov:hadPrimarySource source: planteome - relation_type: prov:hadPrimarySource source: rapdb product_url: https://github.com/Knowledge-Graph-Hub/eco-kg 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: '2019' 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: '2026-06-18T00:00:00Z' layout: resource_detail name: FABIO products: - category: OntologyProduct description: FABIO ontology in Turtle RDF format format: ttl id: fabio.ttl name: FABIO Turtle File original_source: - relation_type: prov:hadPrimarySource source: fabio product_file_size: 140152 product_url: http://purl.org/spar/fabio.ttl - category: DocumentationProduct description: FABIO ontology documentation, specification, and usage guidelines format: http id: fabio.documentation name: FABIO Documentation original_source: - relation_type: prov:hadPrimarySource source: fabio product_url: https://sparontologies.github.io/fabio/current/fabio.html - category: GraphProduct description: Public SPARQL endpoint (OpenLink Virtuoso) providing query access to the complete FORUM knowledge graph. The former credentialed FTP tarball dump (2021) is no longer published; the SPARQL endpoint is the current canonical access point for the full RDF graph. format: http id: forum.graph.dump name: FORUM Knowledge Graph SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cheminf - relation_type: prov:hadPrimarySource source: chemont - relation_type: prov:hadPrimarySource source: cito - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: fabio - relation_type: prov:hadPrimarySource source: forum - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: skos product_url: https://forum.semantic-metabolomics.fr/sparql - category: OntologyProduct description: OpenBioDiv-O, the OpenBiodiv Ontology format: ttl id: openbiodiv.ontology.ttl is_public: true name: OpenBioDiv-O original_source: - relation_type: prov:hadPrimarySource source: skos - relation_type: prov:hadPrimarySource source: proton - relation_type: prov:hadPrimarySource source: fabio - relation_type: prov:hadPrimarySource source: doco - relation_type: prov:hadPrimarySource source: openbiodiv product_file_size: 8176 product_url: https://raw.githubusercontent.com/pensoft/OpenBiodiv/refs/heads/master/ontology/openbiodiv-ontology-latest.ttl publications: - authors: - Peroni S - Shotton D doi: 10.1016/j.websem.2012.08.001 id: https://doi.org/10.1016/j.websem.2012.08.001 journal: Journal of Web Semantics preferred: true title: 'FaBiO and CiTO: ontologies for describing bibliographic resources and citations' year: '2012' repository: https://github.com/SPAROntologies/fabio - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://fabric-cancer.huji.ac.il/ label: FABRIC Cancer Portal - The Hebrew University of Jerusalem creation_date: '2026-06-17T00:00:00Z' description: The FABRIC (Functional Alteration Bias Recovery In Coding regions) Cancer Portal is a catalogue of human protein-coding genes ranked by the strength of positive selection acting on them in cancer. It quantifies, for each gene, the bias toward functional alteration of its protein across large somatic mutation datasets. domains: - genomics - biomedical homepage_url: https://fabric-cancer.huji.ac.il/ id: fabric last_modified_date: '2026-06-17T00:00:00Z' layout: resource_detail name: FABRIC Cancer Portal products: - category: GraphicalInterface description: Web portal for browsing genes ranked by protein functional alteration bias in cancer. format: http id: fabric.site is_public: true name: FABRIC Cancer Portal original_source: - relation_type: prov:hadPrimarySource source: fabric product_url: https://fabric-cancer.huji.ac.il/ - category: GraphicalInterface description: Browsable table of genes with their cancer functional alteration bias scores and statistics. format: http id: fabric.genes is_public: true name: FABRIC Gene Rankings original_source: - relation_type: prov:hadPrimarySource source: fabric product_url: https://fabric-cancer.huji.ac.il/genes - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - 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relation_type: prov:hadPrimarySource source: proteopedia - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubtator - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rfam - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: scop - relation_type: prov:hadPrimarySource source: sfld - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: silva - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: snodb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: snopy - relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ publications: - authors: - Nadav Brandes - Nathan Linial - Michal Linial doi: 10.1093/nar/gkz546 id: https://doi.org/10.1093/nar/gkz546 journal: Nucleic Acids Research preferred: true title: Quantifying gene selection in cancer through protein functional alteration bias year: '2019' - 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 Monitoring System (AEMS), formerly 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. AEMS/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: '2026-06-02T00:00:00Z' 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: - relation_type: prov:hadPrimarySource 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 latest_version: 2026Q1 name: FAERS Quarterly Data Files (ASCII) original_source: - relation_type: prov:hadPrimarySource source: faers product_url: https://fis.fda.gov/extensions/FPD-QDE-FAERS/FPD-QDE-FAERS.html secondary_source: - relation_type: prov:wasInformedBy source: meddra - 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 latest_version: 2026Q1 name: FAERS Quarterly Data Files (XML) original_source: - relation_type: prov:hadPrimarySource source: faers product_url: https://fis.fda.gov/extensions/FPD-QDE-FAERS/FPD-QDE-FAERS.html secondary_source: - relation_type: prov:wasInformedBy source: meddra - 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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 license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 name: AEOLUS Standardized FAERS Data original_source: - relation_type: prov:hadPrimarySource source: faers - relation_type: prov:hadPrimarySource source: aeolus product_url: https://datadryad.org/dataset/doi:10.5061/dryad.8q0s4 - category: GraphProduct description: GP-KG tab-delimited knowledge graph containing 1,246,726 associations between 61,146 entities from multiple genotypic and phenotypic databases format: tsv id: kg-predict.gpkg name: GP-KG Knowledge Graph Data original_source: - relation_type: prov:hadPrimarySource source: kg-predict product_file_size: 48397035 product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt secondary_source: - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: faers - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: mgi - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: string - relation_type: prov:wasDerivedFrom source: umls - category: GraphProduct description: GP_KG.txt edge_count: 1246726 format: txt id: gp-kg.graph name: GP-KG node_count: 61146 original_source: - relation_type: prov:hadPrimarySource source: gp-kg - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: mgi - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: goa - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: umls - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: faers - relation_type: prov:wasDerivedFrom source: phenomebrowser - relation_type: prov:wasDerivedFrom source: treatkb product_file_size: 48397035 product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt - category: GraphProduct description: Live TRAPI/BioThings metadata endpoint for the Multiomics BigGIM-DrugResponse KP, exposing the multiomics knowledge graph served by the Multiomics Provider (built from GTEx, TCGA, and drug-response data, with additional clinical-trials, drug-approval and knowledge-resource inputs). format: json id: multiomics-kp.graph name: Multiomics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: multiomics-kp - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcga - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: dailymed - relation_type: prov:hadPrimarySource source: faers product_url: https://biothings.transltr.io/biggim_drugresponse_kp/metadata secondary_source: - relation_type: prov:wasInfluencedBy source: aact - relation_type: prov:wasInfluencedBy source: biogrid - relation_type: prov:wasInfluencedBy source: huri - relation_type: prov:wasInfluencedBy source: cellmarker - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: ttd - relation_type: prov:wasInfluencedBy source: pubmed synonyms: - AEMS - FDA Adverse Event Monitoring System - FAERS - FDA Adverse Event Reporting System 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ repository: https://github.com/OBioFoundry/FALDO synonyms: - Feature Annotation Location Description Ontology - activity_status: active category: DataSource creation_date: '2026-06-15T00:00:00Z' description: FANTOM5 (Functional Annotation of the Mammalian Genome 5) is a RIKEN-led international project that built a promoter-level mammalian expression atlas using Cap Analysis of Gene Expression (CAGE). It maps transcription start sites and quantifies promoter and enhancer activity across a broad collection of human and mouse primary cells, tissues, and cell lines. The resource provides genome-wide catalogues of CAGE peaks (promoters) and transcribed enhancers together with their expression profiles, supporting studies of gene regulation and cell-type-specific transcription. domains: - genomics - systems biology - anatomy and development homepage_url: https://fantom.gsc.riken.jp/5/ id: fantom5 last_modified_date: '2026-06-15T00:00:00Z' 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: FANTOM5 products: - category: Product description: Downloadable data files for the FANTOM5 promoter-level expression atlas, including CAGE peaks (promoters), transcribed enhancers, and associated expression matrices for human and mouse genome assemblies. format: tsv id: fantom5.atlas name: FANTOM5 Expression Atlas Data Files original_source: - relation_type: prov:hadPrimarySource source: fantom5 product_url: https://fantom.gsc.riken.jp/5/datafiles/ - category: GraphicalInterface description: SSTAR (Semantic catalogue of Samples, Transcription initiation, And Regulations) is the FANTOM5 web interface for browsing samples, CAGE peaks, co-expression clusters, and transcription factor annotations. format: http id: fantom5.sstar name: FANTOM5 SSTAR Browser original_source: - relation_type: prov:hadPrimarySource source: fantom5 product_url: https://fantom.gsc.riken.jp/5/sstar/ - category: GraphicalInterface description: ZENBU is the interactive data integration and visualization system used to explore FANTOM5 promoter, enhancer, and time-course expression data in genomic context. format: http id: fantom5.zenbu name: FANTOM5 ZENBU Browser original_source: - relation_type: prov:hadPrimarySource source: fantom5 product_url: https://fantom.gsc.riken.jp/zenbu/ - category: DocumentationProduct description: FANTOM5 project website with documentation, data access guidelines, tool descriptions, and citation information for the promoter-level mammalian expression atlas. format: http id: fantom5.docs name: FANTOM5 Project Website original_source: - relation_type: prov:hadPrimarySource source: fantom5 product_url: https://fantom.gsc.riken.jp/5/ - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://sugi.bio/biobtree/api/ - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: aminode - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: bitterdb - relation_type: prov:hadPrimarySource source: cdd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: craft - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: ena - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: fabric - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: gard - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: geneorganizer - relation_type: prov:hadPrimarySource source: genomernai - relation_type: prov:hadPrimarySource source: glyconnect - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: gtrnadb - 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Ellinor - Mark Daly - Krishna G. Aragam - Connie R. Bezzina doi: 10.1038/s41588-024-01975-5 id: doi:10.1038/s41588-024-01975-5 journal: Nature Genetics title: Genome-wide association study reveals mechanisms underlying dilated cardiomyopathy and myocardial resilience year: '2024' - authors: - Vilma Lammi - Tomoko Nakanishi - Samuel E. Jones - Shea J. Andrews - Juha Karjalainen - Beatriz Cortés - Heath E. O’Brien - Ana Ochoa-Guzman - Brian E. Fulton-Howard - Martin Broberg - Hele H. Haapaniemi - Masahiro Kanai - Matti Pirinen - Axel Schmidt - Ruth E. Mitchell - Abdou Mousas - Massimo Mangino - Alicia Huerta-Chagoya - Nasa Sinnott-Armstrong - Elizabeth T. Cirulli - Marc Vaudel - Alex S. F. Kwong - Amit K. Maiti - Minttu M. Marttila - Daniel C. Posner - Alexis A. Rodriguez - Chiara Batini - Francesca Minnai - Anna R. Dearman - C. A. Robert Warmerdam - Celia B. Sequeros - Thomas W. Winkler - Daniel M. Jordan - Raimonds Rešcenko - Lorenzo Miano - Jacqueline M. Lane - Ryan K. 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Ollila doi: 10.1038/s41588-025-02100-w id: doi:10.1038/s41588-025-02100-w journal: Nature Genetics 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 FRS (Facility Registry Service) KG is the part of the SAWGraph project that stores data about facilities from EPA's Facility Registry service (FRS) together with their NAICS industry classification and the spatial location. domains: - environment - agriculture evaluation_page: resource/fiokg/fiokg_eval_automated.html homepage_url: https://sawgraph.github.io/ id: fiokg last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: SAWGraph FRS KG products: - category: ProgrammingInterface description: SPARQL endpoint for SAWGraph FRS KG format: http id: fiokg.sparql name: SAWGraph FRS KG SPARQL original_source: - relation_type: prov:hadPrimarySource source: fiokg product_url: https://apps.okn.us/fiokg/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for SAWGraph FRS KG id: fiokg.tpf name: SAWGraph FRS KG TPF original_source: - relation_type: prov:hadPrimarySource source: fiokg product_url: https://apps.okn.us/ldf/fiokg - category: GraphProduct description: The SAWGraph Facilities and Industries Ontology (FIO) / Facility Registry Service (FRS) knowledge graph, an RDF (Turtle) graph representing US facilities from EPA's Facility Registry Service together with their NAICS and SIC industry classifications and spatial locations. 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Öztürk-Çolak A - Marygold SJ - Antonazzo G - Attrill H - Goutte-Gattat D - Jenkins VK - Matthews BB - Millburn G - dos Santos G - Tabone CJ doi: 10.1093/genetics/iyad211 id: https://www.ncbi.nlm.nih.gov/pubmed/38301657 journal: Genetics preferred: true title: 'FlyBase: updates to the Drosophila genes and genomes database' year: '2024' 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 - nutrition homepage_url: https://github.com/pcastellanoescuder/FoodBiomarkerOntology id: fobi last_modified_date: '2026-06-05T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: fobi product_file_size: 118923 product_url: http://purl.obolibrary.org/obo/fobi.owl publications: - authors: - Castellano-Escuder P - González-Domínguez R - Wishart DS - Andrés-Lacueva C - Sánchez-Pla A doi: 10.1093/databa/baaa033 id: https://www.ncbi.nlm.nih.gov/pubmed/32556148 journal: Database (Oxford) title: 'FOBI: an ontology to represent food intake data and associate it with metabolomic data' year: '2020' - authors: - Castellano-Escuder P - Andrés-Lacueva C - Sánchez-Pla A doi: 10.1093/bioinformatics/btab626 id: https://www.ncbi.nlm.nih.gov/pubmed/34601570 journal: Bioinformatics title: 'The fobitools framework: the first steps towards food enrichment analysis' year: '2021' 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) - 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: '2025-05-29T00:00:00Z' description: The Food Database (FooDB) is the world's largest and most comprehensive resource on food constituents, chemistry, and biology. 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'File was not able to be retrieved when checked on 2026-07-02: Timeout connecting to URL' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: Product description: FooDB downloads page listing the available bulk data archives, spectra, peak lists, and supplementary files (including NMR Free Induction Decay data). 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category: Product compression: zip description: Experimental MS-MS peak lists from FooDB. format: mixed id: foodb.data.experimental_msms_peak_lists name: FooDB Experimental MS-MS Peak Lists original_source: - relation_type: prov:hadPrimarySource source: foodb product_url: https://foodb.ca/public/system/downloads/foodb_experimental_msms_peak_lists.zip warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-02: Timeout connecting to URL' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: Product compression: zip description: Predicted MS-MS peak lists from FooDB. format: mixed id: foodb.data.predicted_msms_peak_lists name: FooDB Predicted MS-MS Peak Lists original_source: - relation_type: prov:hadPrimarySource source: foodb product_url: https://foodb.ca/public/system/downloads/foodb_predicted_msms_peak_lists.zip warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-02: Timeout connecting to URL' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: Product compression: zip description: NMR peak lists from FooDB. format: mixed id: foodb.data.nmr_peak_lists name: FooDB NMR Peak Lists original_source: - relation_type: prov:hadPrimarySource source: foodb product_url: https://foodb.ca/public/system/downloads/foodb_nmr_peak_lists.zip warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-02: Timeout connecting to URL' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. format: http id: spoke.graph name: SPOKE Graph original_source: - 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relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: The SPOKE-OKN knowledge graph, an OKN-hosted RDF publication of the SPOKE biomedical and environmental health knowledge graph, served through FRINK query services. format: ttl id: spoke-okn.graph name: SPOKE-OKN Graph original_source: - relation_type: prov:hadPrimarySource source: spoke-okn - relation_type: prov:wasDerivedFrom source: spoke product_url: https://spoke.ucsf.edu secondary_source: - relation_type: prov:wasInfluencedBy source: bgee - relation_type: prov:wasInfluencedBy source: bindingdb - relation_type: prov:wasInfluencedBy source: bv-brc - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: civic - relation_type: prov:wasInfluencedBy source: cl - relation_type: prov:wasInfluencedBy source: clinicaltrialsgov - relation_type: prov:wasInfluencedBy source: diseases - relation_type: prov:wasInfluencedBy source: doid - relation_type: prov:wasInfluencedBy source: drugbank - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: foodb - relation_type: prov:wasInfluencedBy source: gdsc - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: gwascatalog - relation_type: prov:wasInfluencedBy source: hpa - relation_type: prov:wasInfluencedBy source: interpro - relation_type: prov:wasInfluencedBy source: kegg - relation_type: prov:wasInfluencedBy source: lincs-l1000 - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: metacyc - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: ncbitaxon - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pathophenodb - relation_type: prov:wasInfluencedBy source: pfam - relation_type: prov:wasInfluencedBy source: pid - relation_type: prov:wasInfluencedBy source: protcid - relation_type: prov:wasInfluencedBy source: pubmed - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: sider - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikipathways 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: 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 doi: 10.1093/nar/gkx1089 id: https://doi.org/10.1093/nar/gkx1089 journal: Nucleic Acids Research title: HMDB 4.0 - The Human Metabolome Database for 2018 year: '2018' 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 - nutrition homepage_url: https://foodon.org/ id: foodon infores_id: foodon last_modified_date: '2026-06-18T00:00:00Z' 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: 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 original_source: - relation_type: prov:hadPrimarySource source: foodon 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 2026-07-10: HTTP 404 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' - category: GraphProduct compression: gzip description: PharMeBINet V2 JSON release published on February 6, 2024. format: json id: pharmebinet.json latest_version: v2 name: PharMeBINet JSON Release original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 1942958027 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_24_02_06.json.gz/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - 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relation_type: prov:hadPrimarySource source: phenopacket-store product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz publications: - authors: - Dooley DM - Griffiths EJ - Gosal GS - Buttigieg PL - Hoehndorf R - Lange MC - Schriml LM - Brinkman FSL - Hsiao WWL doi: 10.1038/s41538-018-0032-6 id: https://www.ncbi.nlm.nih.gov/pubmed/31304272 journal: NPJ Sci Food title: 'FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration' year: '2018' 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. 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The former credentialed FTP tarball dump (2021) is no longer published; the SPARQL endpoint is the current canonical access point for the full RDF graph. format: http id: forum.graph.dump name: FORUM Knowledge Graph SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cheminf - relation_type: prov:hadPrimarySource source: chemont - relation_type: prov:hadPrimarySource source: cito - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: fabio - relation_type: prov:hadPrimarySource source: forum - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: skos product_url: https://forum.semantic-metabolomics.fr/sparql 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. 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Traits are defined in the Ontology of Biological Attributes (OBA). domains: - biological systems - phenotype homepage_url: https://github.com/futres/fovt id: fovt last_modified_date: '2026-06-05T00:00:00Z' 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: 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 original_source: - relation_type: prov:hadPrimarySource source: fovt product_file_size: 2587818 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 original_source: - relation_type: prov:hadPrimarySource source: fovt product_file_size: 1628339 product_url: http://purl.obolibrary.org/obo/fovt.obo - 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relation_type: prov:hadPrimarySource source: fypo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: nbo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: upheno - relation_type: prov:hadPrimarySource source: wbbt - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: wbphenotype - relation_type: prov:hadPrimarySource source: xao - relation_type: prov:hadPrimarySource source: xpo - relation_type: prov:hadPrimarySource source: zfa - relation_type: prov:hadPrimarySource source: zfs - relation_type: prov:hadPrimarySource source: zp - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: decipher - relation_type: prov:hadPrimarySource source: mmrrc - relation_type: prov:hadPrimarySource source: cureid - relation_type: prov:hadPrimarySource source: phenopacket-store product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz publications: - authors: - Harris MA - Lock A - Bähler J - Oliver SG - Wood V doi: 10.1093/bioinformatics/btt266 id: https://www.ncbi.nlm.nih.gov/pubmed/23658422 journal: Bioinformatics title: 'FYPO: The Fission Yeast Phenotype Ontology.' year: '2013' repository: https://github.com/pombase/fypo taxon: - NCBITaxon:4896 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://gadm.org/about.html label: GADM creation_date: '2026-06-18T00:00:00Z' description: GADM (Database of Global Administrative Areas) provides maps and spatial data of administrative boundaries for all countries and their sub-divisions. The current version (4.1) delimits over 400,000 administrative areas across multiple levels, from countries down to local divisions. The polygons are distributed for download by country or for the entire world in several geospatial formats. GADM is used as an upstream source of administrative boundary data by projects such as KnowWhereGraph. domains: - environment - general - information technology homepage_url: https://gadm.org/ id: gadm last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: '' label: GADM license (free for academic/non-commercial use) name: GADM products: - category: Product description: Download page for GADM administrative boundary spatial data by country, the recommended approach for obtaining GADM polygons. id: gadm.download_country name: GADM Data Download (by country) original_source: - relation_type: prov:hadPrimarySource source: gadm product_url: https://gadm.org/download_country.html - category: Product description: Download page for GADM administrative boundary spatial data covering the entire world. id: gadm.download_world name: GADM Data Download (world) original_source: - relation_type: prov:hadPrimarySource source: gadm product_url: https://gadm.org/download_world.html - category: DocumentationProduct description: Metadata documentation describing the GADM data, its structure, and administrative levels. id: gadm.metadata name: GADM Metadata original_source: - relation_type: prov:hadPrimarySource source: gadm product_url: https://gadm.org/metadata.html - 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 original_source: - relation_type: prov:hadPrimarySource source: knowwheregraph - relation_type: prov:wasDerivedFrom source: wikidata - relation_type: prov:hadPrimarySource source: bluesky - relation_type: prov:hadPrimarySource source: cdc-places - relation_type: prov:hadPrimarySource source: cdc-svi - relation_type: prov:hadPrimarySource source: cropland-data-layer - relation_type: prov:hadPrimarySource source: epa-aqs - relation_type: prov:hadPrimarySource source: gadm - relation_type: prov:hadPrimarySource source: gnis - relation_type: prov:hadPrimarySource source: hifld - relation_type: prov:hadPrimarySource source: mtbs - relation_type: prov:hadPrimarySource source: nhpn - relation_type: prov:hadPrimarySource source: nifc - relation_type: prov:hadPrimarySource source: noaa-hms - relation_type: prov:hadPrimarySource source: noaa-ncei - relation_type: prov:hadPrimarySource source: openfema - relation_type: prov:hadPrimarySource source: reliefweb - relation_type: prov:hadPrimarySource source: ssurgo - relation_type: prov:hadPrimarySource source: us-census - relation_type: prov:hadPrimarySource source: usdm - relation_type: prov:hadPrimarySource source: usgs-comcat product_url: https://knowwheregraph.org/ synonyms: - Database of Global Administrative Areas - 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 - phenotype homepage_url: https://adeans.github.io/gallont/ id: gallont last_modified_date: '2026-06-27T00:00:00Z' 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: Plant Gall Ontology products: - category: OntologyProduct description: Plant Gall Ontology in OWL format format: owl id: gallont.owl name: gallont.owl original_source: - relation_type: prov:hadPrimarySource source: gallont product_file_size: 91521 product_url: http://purl.obolibrary.org/obo/gallont.owl - category: OntologyProduct description: Plant Gall Ontology in OBO format format: obo id: gallont.obo name: gallont.obo original_source: - relation_type: prov:hadPrimarySource source: gallont product_file_size: 60631 product_url: http://purl.obolibrary.org/obo/gallont.obo publications: [] repository: https://github.com/adeans/gallont - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://contact.rarediseases.info.nih.gov/Gard/s/?language=en_US label: GARD Information Specialists creation_date: '2026-02-26T00:00:00Z' description: The Genetic and Rare Diseases Information Center provides free, reliable, and easy-to-understand information and resources about rare and genetic diseases. domains: - biomedical homepage_url: https://rarediseases.info.nih.gov/ id: gard last_modified_date: '2026-05-30T00:00:00Z' layout: resource_detail name: Genetic and Rare Diseases Information Center products: - category: DocumentationProduct description: Public GARD website for disease summaries, support resources, and contact-center access. format: http id: gard.portal name: GARD Web Portal original_source: - relation_type: prov:hadPrimarySource source: gard product_url: https://rarediseases.info.nih.gov/ - category: Product description: gard Nodes TSV format: tsv id: obo-db-ingest.gard.tsv name: gard Nodes TSV original_source: - relation_type: prov:hadPrimarySource source: gard - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 314439 product_url: https://w3id.org/biopragmatics/resources/gard/gard.tsv - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: aminode - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: bitterdb - relation_type: prov:hadPrimarySource source: cdd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: craft - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: ena - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: fabric - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: gard - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: geneorganizer - relation_type: prov:hadPrimarySource source: genomernai - relation_type: prov:hadPrimarySource source: glyconnect - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: gtrnadb - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: homologene - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hprd - relation_type: prov:hadPrimarySource source: humancyc - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: iid - relation_type: prov:hadPrimarySource source: imgt - relation_type: prov:hadPrimarySource source: innatedb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: lncbase - relation_type: prov:hadPrimarySource source: lncbook - relation_type: prov:hadPrimarySource source: lncipedia - relation_type: prov:hadPrimarySource source: lncrnadisease - relation_type: prov:hadPrimarySource source: malacards - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: medlineplus - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: mint - relation_type: prov:hadPrimarySource source: mirbase - relation_type: prov:hadPrimarySource source: mirgenedb - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: modomics - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: nextprot - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathwaycommons - relation_type: prov:hadPrimarySource source: paxdb - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pdbe - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pirsf - relation_type: prov:hadPrimarySource source: prosite - relation_type: prov:hadPrimarySource source: proteomicsdb - relation_type: prov:hadPrimarySource source: proteopedia - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubtator - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rfam - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: scop - relation_type: prov:hadPrimarySource source: sfld - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: silva - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: snodb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: snopy - relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ - category: GraphProduct description: Integrated rare-disease knowledge graph produced by the RD-Clust workflow, connecting rare diseases to genes, phenotypes, Gene Ontology terms, drugs/ligands, and pathway interactions. Distributed as the processed disease ontograph within the RD-Clust repository. format: http id: ncatsgardkg.graph name: NCATS GARD Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: ncatsgardkg - relation_type: prov:hadPrimarySource source: gard product_url: https://github.com/ncats/RD-Clust/tree/main/data/processed secondary_source: - relation_type: prov:wasInfluencedBy source: hp - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: mondo - relation_type: prov:wasInfluencedBy source: orphanet - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: pharos - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: chebi - relation_type: prov:wasInfluencedBy source: pubchem - relation_type: prov:wasInfluencedBy source: pathwaycommons - 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: '2026-04-15T00:00:00Z' 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: Gazetteer products: - category: OntologyProduct description: Gazetteer in OWL format format: owl id: gaz.owl name: gaz.owl original_source: - relation_type: prov:hadPrimarySource source: gaz 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 original_source: - relation_type: prov:hadPrimarySource source: gaz 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 original_source: - relation_type: prov:hadPrimarySource source: gaz product_file_size: 42847 product_url: http://purl.obolibrary.org/obo/gaz/gaz-countries.owl publications: [] repository: https://github.com/EnvironmentOntology/gaz - activity_status: active category: DataSource collection: - ber 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: - organisms - environment homepage_url: https://www.gbif.org/ id: gbif infores_id: gbif last_modified_date: '2026-06-18T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: gbif 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 original_source: - relation_type: prov:hadPrimarySource source: gbif 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 original_source: - relation_type: prov:hadPrimarySource source: gbif product_url: https://api.gbif.org/v2/map/ - 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 original_source: - relation_type: prov:hadPrimarySource source: gbif product_url: https://www.gbif.org/occurrence/download warnings: - File was not able to be retrieved when checked on 2026-03-30_ 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 original_source: - relation_type: prov:hadPrimarySource source: gbif product_url: https://www.gbif.org/occurrence/download warnings: - File was not able to be retrieved when checked on 2026-03-30_ 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 original_source: - relation_type: prov:hadPrimarySource source: gbif 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) original_source: - relation_type: prov:hadPrimarySource source: gbif product_url: https://www.gbif.org/ipt warnings: - File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 error when accessing file - 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 original_source: - relation_type: prov:hadPrimarySource source: catalogue-of-life - relation_type: prov:hadPrimarySource source: itis - relation_type: prov:hadPrimarySource source: gbif 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 original_source: - relation_type: prov:hadPrimarySource source: catalogue-of-life - relation_type: prov:hadPrimarySource source: itis - relation_type: prov:hadPrimarySource source: gbif product_url: https://www.catalogueoflife.org/data/download warnings: - Automated checks may return HTTP 418 due to anti-bot challenge on catalogueoflife.org download pages; URL is retained as the canonical human-access endpoint. - category: GraphicalInterface description: Web interface for browsing, querying, and visualizing ecological networks format: http id: mangal.portal name: mangal.io Web Portal original_source: - relation_type: prov:hadPrimarySource source: mangal product_url: https://mangal.io/ secondary_source: - relation_type: prov:used source: catalogue-of-life - relation_type: prov:used source: gbif - relation_type: prov:used source: itis - 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 original_source: - relation_type: prov:hadPrimarySource source: mangal product_url: https://mangal.io/api/v2/ secondary_source: - relation_type: prov:used source: catalogue-of-life - relation_type: prov:used source: gbif - relation_type: prov:used source: itis - category: DocumentationProduct description: API documentation, user guides, and data model specification format: http id: mangal.docs name: mangal.io Documentation original_source: - relation_type: prov:hadPrimarySource source: mangal product_url: https://mangal.io/documentation - 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 original_source: - relation_type: prov:hadPrimarySource source: openbiodiv - relation_type: prov:hadPrimarySource source: gbif 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 original_source: - relation_type: prov:hadPrimarySource source: openbiodiv - relation_type: prov:hadPrimarySource source: gbif 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 original_source: - relation_type: prov:hadPrimarySource source: openbiodiv - relation_type: prov:hadPrimarySource source: gbif product_url: https://graph.openbiodiv.net/webapi - category: ProcessProduct description: R package for retrieving and exploring data from the Mangal ecological interactions database format: http id: mangal.rmangal name: rmangal R Client original_source: - relation_type: prov:hadPrimarySource source: mangal product_url: https://docs.ropensci.org/rmangal/ secondary_source: - relation_type: prov:used source: catalogue-of-life - relation_type: prov:used source: gbif - relation_type: prov:used source: itis - category: GraphProduct description: The Wildlife-KN knowledge graph, an integrative RDF network of managed species and their habitats, environmental factors, and climate context, built to support wildlife management under climate change. It is served as Linked Data through the Wildlife-KN SPARQL and Triple Pattern Fragments endpoints. format: ttl id: wildlifekn.graph name: Wildlife-KN Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: wildlifekn - relation_type: prov:hadPrimarySource source: usgs - relation_type: prov:hadPrimarySource source: edrr-invasive-catalog - relation_type: prov:hadPrimarySource source: gbif - relation_type: prov:hadPrimarySource source: worldclim - relation_type: prov:hadPrimarySource source: iucn-red-list - relation_type: prov:hadPrimarySource source: cabi-isc product_url: https://apps.okn.us/ldf/wildlifekn 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://gcmd.earthdata.nasa.gov/ label: NASA Earth Science Data Systems (GCMD) creation_date: '2026-07-03T00:00:00Z' description: The Global Change Master Directory (GCMD) Keywords are NASA's hierarchical controlled vocabulary of Earth science keywords, covering science topics, instruments, platforms, data centers, locations, and related concepts. GCMD Keywords are widely used to describe and discover Earth science datasets and serve as the taxonomic backbone for climate metadata. domains: - environment - information technology - general homepage_url: https://gcmd.earthdata.nasa.gov/ id: gcmd last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: NASA Global Change Master Directory (GCMD) Keywords products: - _replace_warnings: true category: Product description: The GCMD Keyword Viewer provides browsable access to NASA's hierarchical Earth science controlled vocabulary, including science keywords, instruments, platforms, providers, and locations. format: http id: gcmd.keywords name: GCMD Keyword Viewer original_source: - relation_type: prov:hadPrimarySource source: gcmd product_url: https://gcmd.earthdata.nasa.gov/KeywordViewer/ warnings: [] - category: GraphProduct description: RDF/Turtle knowledge graph integrating climate model and dataset metadata (from ESGF, CMIP controlled vocabularies, and the NASA GCMD keyword taxonomy) with entities and relationships extracted from climate-science publications. Served through the FRINK federation and the SPARQL and TPF endpoints. format: ttl id: climatemodelskg.graph name: Climate Models KG Graph original_source: - relation_type: prov:hadPrimarySource source: climatemodelskg - relation_type: prov:hadPrimarySource source: esgf - relation_type: prov:hadPrimarySource source: cmip - relation_type: prov:hadPrimarySource source: gcmd product_url: https://frink.renci.org/registry/kgs/climatepub4-kg/ - 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: gdc product_url: https://gdc.cancer.gov/access-data/gdc-data-transfer-tool publications: - authors: - Mark A. Jensen - Vincent Ferretti - Robert L. Grossman - Louis M. Staudt 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.sanger.ac.uk/tool/gdsc-genomics-drug-sensitivity-cancer/ 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 - drug discovery - genomics - pharmacology homepage_url: https://www.sanger.ac.uk/tool/gdsc-genomics-drug-sensitivity-cancer/ id: gdsc infores_id: gdsc last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: https://www.sanger.ac.uk/tool/gdsc-genomics-drug-sensitivity-cancer/ 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: - relation_type: prov:hadPrimarySource source: gdsc product_url: https://www.sanger.ac.uk/tool/gdsc-genomics-drug-sensitivity-cancer/ - category: GraphProduct description: The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources. format: http id: spoke.graph name: SPOKE Graph original_source: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: bv-brc - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: pathophenodb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: protcid - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: spoke - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://spoke.ucsf.edu/data-tools - category: Product description: Network embeddings of the Bioteque graph that represent biological entities and their associations format: mixed id: bioteque.embeddings name: Bioteque Embeddings original_source: - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: bioteque - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: cellosaurus - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chemicalchecker - relation_type: prov:hadPrimarySource source: clue - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: creeds - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: dorothea - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: huri - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: offsides - relation_type: prov:hadPrimarySource source: omnipath - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: pharmacodb - relation_type: prov:hadPrimarySource source: prism - relation_type: prov:hadPrimarySource source: progeny - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: repodb - relation_type: prov:hadPrimarySource source: repohub - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues product_url: https://bioteque.irbbarcelona.org/downloads/embeddings - category: GraphicalInterface description: Primary web portal for searching and browsing cancer pharmacogenomics data across multiple integrated datasets with interactive dose-response curve visualization format: http id: pharmacodb.portal name: PharmacoDB Web Application original_source: - relation_type: prov:hadPrimarySource source: pharmacodb product_url: https://pharmacodb.ca/ secondary_source: - relation_type: prov:wasInfluencedBy source: ccle - relation_type: prov:wasInfluencedBy source: gdsc - relation_type: prov:wasInfluencedBy source: ctrp - category: ProgrammingInterface description: GraphQL API providing programmatic access to cell lines, compounds, tissues, datasets, experiments, and intersections data format: http id: pharmacodb.api is_public: true name: PharmacoDB API original_source: - relation_type: prov:hadPrimarySource source: pharmacodb product_url: https://pharmacodb.ca/graphql secondary_source: - relation_type: prov:wasInfluencedBy source: ccle - relation_type: prov:wasInfluencedBy source: gdsc - relation_type: prov:wasInfluencedBy source: ctrp - 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: - relation_type: prov:hadPrimarySource source: pharmacodb product_url: https://pharmacodb.ca/documentation secondary_source: - relation_type: prov:wasInfluencedBy source: ccle - relation_type: prov:wasInfluencedBy source: gdsc - relation_type: prov:wasInfluencedBy source: ctrp - 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 original_source: - relation_type: prov:hadPrimarySource source: depmap product_url: https://depmap.org/portal/data_page/ secondary_source: - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: prism - relation_type: prov:wasDerivedFrom source: ctd2 - category: Product description: Harmonizome 3.0 processed dataset downloads, including dataset-specific association files and knowledge graph serialization downloads. format: mixed id: harmonizome.downloads name: Harmonizome Downloads original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://maayanlab.cloud/Harmonizome/download secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct description: Neo4j knowledge graph serialization of Harmonizome processed datasets, including genes, attributes, resources, datasets, and gene-attribute associations. dump_format: neo4j format: neo4j id: harmonizome.kg-neo4j latest_version: '3.0' name: Harmonizome Knowledge Graph Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://harmonizome-kg.maayanlab.cloud/ secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct description: The SPOKE-OKN knowledge graph, an OKN-hosted RDF publication of the SPOKE biomedical and environmental health knowledge graph, served through FRINK query services. format: ttl id: spoke-okn.graph name: SPOKE-OKN Graph original_source: - relation_type: prov:hadPrimarySource source: spoke-okn - relation_type: prov:wasDerivedFrom source: spoke product_url: https://spoke.ucsf.edu secondary_source: - relation_type: prov:wasInfluencedBy source: bgee - relation_type: prov:wasInfluencedBy source: bindingdb - relation_type: prov:wasInfluencedBy source: bv-brc - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: civic - relation_type: prov:wasInfluencedBy source: cl - relation_type: prov:wasInfluencedBy source: clinicaltrialsgov - relation_type: prov:wasInfluencedBy source: diseases - relation_type: prov:wasInfluencedBy source: doid - relation_type: prov:wasInfluencedBy source: drugbank - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: foodb - relation_type: prov:wasInfluencedBy source: gdsc - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: gwascatalog - relation_type: prov:wasInfluencedBy source: hpa - relation_type: prov:wasInfluencedBy source: interpro - relation_type: prov:wasInfluencedBy source: kegg - relation_type: prov:wasInfluencedBy source: lincs-l1000 - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: metacyc - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: ncbitaxon - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pathophenodb - relation_type: prov:wasInfluencedBy source: pfam - relation_type: prov:wasInfluencedBy source: pid - relation_type: prov:wasInfluencedBy source: protcid - relation_type: prov:wasInfluencedBy source: pubmed - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: sider - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikipathways - category: GraphProduct description: Live TRAPI/BioThings metadata endpoint for the Multiomics BigGIM-DrugResponse KP, exposing the multiomics knowledge graph served by the Multiomics Provider (built from GTEx, TCGA, and drug-response data, with additional clinical-trials, drug-approval and knowledge-resource inputs). format: json id: multiomics-kp.graph name: Multiomics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: multiomics-kp - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcga - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: dailymed - relation_type: prov:hadPrimarySource source: faers product_url: https://biothings.transltr.io/biggim_drugresponse_kp/metadata secondary_source: - relation_type: prov:wasInfluencedBy source: aact - relation_type: prov:wasInfluencedBy source: biogrid - relation_type: prov:wasInfluencedBy source: huri - relation_type: prov:wasInfluencedBy source: cellmarker - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: ttd - relation_type: prov:wasInfluencedBy source: pubmed 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: '2012' - 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 doi: 10.1016/j.cell.2016.06.017 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 doi: 10.1038/nature11005 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 - organisms homepage_url: https://github.com/IHCC-cohorts/GECKO id: gecko last_modified_date: '2026-06-05T00:00:00Z' 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: Genomics Cohorts Knowledge Ontology products: - category: OntologyProduct description: Genomics Cohorts Knowledge Ontology in OWL format format: owl id: gecko.owl name: gecko.owl original_source: - relation_type: prov:hadPrimarySource source: gecko product_file_size: 18443 product_url: http://purl.obolibrary.org/obo/gecko.owl publications: [] 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: - relation_type: prov:hadPrimarySource source: gelinea product_url: https://github.com/broadinstitute/GeLiNEA - 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: - 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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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: chebi - 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relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv 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 collection: - omop creation_date: '2026-04-10T00:00:00Z' description: Gemscript is a medication and device terminology used primarily within the UK's Vision 3 general practice software. Maintained by RESIP UK and integrated with dm+d-aligned descriptions, Gemscript provides unique internal drug identifiers and associated prescribing metadata used to select, classify, and manage medicines and appliances in active clinical workflows. Although Gemscript remains in active operational use, its distribution appears to occur through Vision update channels rather than a single public bulk-download site. domains: - clinical - biomedical - pharmacology homepage_url: https://help.visionhealth.co.uk/Vision_Consultation_Manager_Help_Centre/Content/ConMgr/Gemscript/Gemscript_Drug_Dictionary.htm id: gemscript last_modified_date: '2026-06-01T00:00:00Z' layout: resource_detail name: Gemscript products: - category: DocumentationProduct description: Vision help documentation describing Gemscript as the integrated drug dictionary used in Vision 3 prescribing workflows format: http id: gemscript.documentation name: Gemscript Vision Help Documentation original_source: - relation_type: prov:hadPrimarySource source: gemscript product_url: https://help.visionhealth.co.uk/Vision_Consultation_Manager_Help_Centre/Content/ConMgr/Gemscript/Gemscript_Drug_Dictionary.htm secondary_source: - relation_type: prov:wasInformedBy source: dmd - category: DocumentationProduct description: Monthly Gemscript bulletin summarizing additions, deletions, name changes, and drug class changes in the active dictionary format: pdf id: gemscript.bulletin latest_version: 2026 May v.01 name: Gemscript Monthly Bulletin original_source: - relation_type: prov:hadPrimarySource source: gemscript product_file_size: 173789 product_url: https://help.visionhealth.co.uk/PDFs/Dictionaries/Gemscript/Gemscript_Bulletin_May_2026.pdf secondary_source: - relation_type: prov:wasInformedBy source: dmd - category: Product description: Downloadable standardized vocabulary bundles for OMOP CDM assembled through the authenticated Athena web application format: csv id: athena.vocabularies name: Athena Vocabulary Downloads original_source: - relation_type: prov:hadPrimarySource source: athena - relation_type: prov:hadPrimarySource source: cdiscvocab - relation_type: prov:hadPrimarySource source: ciel - relation_type: prov:hadPrimarySource source: gemscript - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: medispan-gpi - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ndcd - relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: snomedct product_url: https://athena.ohdsi.org/vocabulary/list warnings: - Athena vocabulary downloads are prepared through the logged-in web application; stable direct public file URLs are not exposed. synonyms: - Gemscript Drug Dictionary - GemscriptDrug taxon: - NCBITaxon:9606 - 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 - biomedical homepage_url: http://genomics.senescence.info/genes/ id: genage infores_id: genage last_modified_date: '2026-06-12T00:00:00Z' 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: genage product_url: https://genomics.senescence.info/genes/models.html publications: - authors: - João Pedro de Magalhães - Zoya Abidi - Gabriel Arantes dos Santos - Roberto A Avelar - Diogo Barardo - Kasit Chatsirisupachai - Peter Clark - Evandro A De-Souza - Emily J Johnson - Inês Lopes - Guy Novoa - Ludovic Senez - Angelo Talay - Daniel Thornton - Paul Ka Po To 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: - João Pedro de Magalhães - Olivier Toussaint doi: 10.1016/j.febslet.2004.07.006 id: doi:10.1016/j.febslet.2004.07.006 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. 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relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 3598325722 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_dump_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - 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relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for Genetics KP distributed via the NCATS Translator release site (release 2026_03_27; build geneticskp_2026-03-27_1f1ad62b_2025sep1_4.3.6; source version 2026-03-27; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 653544 format: kgx-jsonl id: translator.geneticskp.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Genetics KP KGX Graph node_count: 28023 original_source: - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/geneticskp/latest/ versions: - '2026_03_27' - geneticskp_2026-03-27_1f1ad62b_2025sep1_4.3.6 - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://sugi.bio/biobtree/api/ - category: GraphProduct compatibility: - standard: biolink version: 4.2.1 compression: gzip description: Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - category: GraphProduct description: TRAPI knowledge graph served by the Genetics KP, exposing gene/disease and gene/phenotype associations computed from large-scale human genetics data (e.g. Genebass exome association statistics aggregated with methods such as MAGMA and the HuGE calculator) and integrated curated gene-condition resources. The linked endpoint returns the meta knowledge graph describing the served node and edge types. format: json id: genetics-kp.graph name: Genetics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: genetics-kp - relation_type: prov:hadPrimarySource source: genebass product_file_size: 3538 product_url: https://genetics-kp.transltr.io/genetics_provider/trapi/v1.5/meta_knowledge_graph secondary_source: - relation_type: prov:wasInfluencedBy source: gencc - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: clingen 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: '2026-06-02T00:00:00Z' layout: resource_detail name: GENCODE products: - category: Product description: Current comprehensive GENCODE gene annotations for the human GRCh38.p14 genome assembly in GTF format format: gff id: gencode.human.gtf latest_version: v49 name: GENCODE Human Annotations GTF original_source: - relation_type: prov:hadPrimarySource source: gencode product_file_size: 93374019 product_url: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_49/gencode.v49.annotation.gtf.gz secondary_source: - relation_type: prov:wasDerivedFrom source: ensembl - relation_type: prov:wasInformedBy source: hgnc - relation_type: prov:wasInformedBy source: ncbigene - category: Product description: Current comprehensive GENCODE gene annotations for the mouse GRCm39 genome assembly in GTF format format: gff id: gencode.mouse.gtf latest_version: M38 name: GENCODE Mouse Annotations GTF original_source: - relation_type: prov:hadPrimarySource source: gencode product_file_size: 37627563 product_url: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M38/gencode.vM38.annotation.gtf.gz secondary_source: - relation_type: prov:wasDerivedFrom source: ensembl - relation_type: prov:wasInformedBy source: mgi - relation_type: prov:wasInformedBy source: ncbigene - category: Product description: GENCODE Primary transcript set capturing minimal transcripts at protein coding genes format: gff id: gencode.primary latest_version: current name: GENCODE Primary Transcripts original_source: - relation_type: prov:hadPrimarySource 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - 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relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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 original_source: - 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relation_type: prov:wasInformedBy source: ensembl - relation_type: prov:wasInformedBy source: hgnc - category: Product description: Current HuRI PSI-MI formatted interaction file with detailed experimental information and isoform-specific ORF, transcript, and protein identifiers format: psi_mi_mitab id: hrpimp.huri.psi latest_version: HuRI name: HuRI PSI-MI Interaction Data original_source: - relation_type: prov:hadPrimarySource source: hrpimp - relation_type: prov:hadPrimarySource source: huri product_file_size: 169848924 product_url: https://www.interactome-atlas.org/data/HuRI.psi secondary_source: - relation_type: prov:wasInformedBy source: gencode - relation_type: prov:wasInformedBy source: ensembl - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - 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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 - biomedical - nutrition - biological systems homepage_url: https://hagr.ageing-map.org/diet/ id: gendr infores_id: gendr last_modified_date: '2026-06-12T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: gendr product_url: https://hagr.ageing-map.org/diet/ - category: Product description: Downloadable dataset of dietary restriction-related genes format: csv id: gendr.data latest_version: Build 4 name: GenDR Data Download original_source: - relation_type: prov:hadPrimarySource source: gendr product_file_size: 8209 product_url: https://hagr.ageing-map.org/diet/dataset.zip secondary_source: - relation_type: prov:wasInformedBy source: pubmed - relation_type: prov:wasInformedBy source: ncbigene - category: Product description: Excel spreadsheet of dietary-restriction gene expression signatures from the HAGR meta-analysis of dietary restriction in mammals format: http id: gendr.expression-signatures name: GenDR Dietary Restriction Expression Signatures original_source: - relation_type: prov:hadPrimarySource source: gendr product_file_size: 49152 product_url: https://hagr.ageing-map.org/diet/TableS2.xls secondary_source: - relation_type: prov:wasInformedBy source: pubmed publications: - authors: - João Pedro de Magalhães - Zoya Abidi - Gabriel Arantes dos Santos - Roberto A Avelar - Diogo Barardo - Kasit Chatsirisupachai - Peter Clark - Evandro A De-Souza - Emily J Johnson - Inês Lopes - Guy Novoa - Ludovic Senez - Angelo Talay - Daniel Thornton - Paul Ka Po To 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' synonyms: - GenDR - gendr taxon: - NCBITaxon:2759 - 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: '2026-03-30T00:00:00Z' description: Selected studies from the Gene Expression Atlas (https://www.ebi.ac.uk/gxa/home). domains: - biomedical - genomics evaluation_page: resource/gene-expression-atlas-okn/gene-expression-atlas-okn_eval_automated.html homepage_url: https://www.ebi.ac.uk/gxa/home id: gene-expression-atlas-okn last_modified_date: '2026-07-02T00:00:00Z' layout: resource_detail name: Gene Expression Atlas products: - category: GraphProduct description: RDF graph of the Gene Expression Atlas OKN knowledge graph, served via the FRINK federated knowledge network. format: ttl id: gene-expression-atlas-okn.graph name: Gene Expression Atlas OKN Graph original_source: - relation_type: prov:hadPrimarySource source: gene-expression-atlas-okn - relation_type: prov:wasDerivedFrom source: expression-atlas product_url: https://frink.apps.renci.org/gene-expression-atlas-okn - category: ProgrammingInterface description: SPARQL endpoint for Gene Expression Atlas format: http id: gene-expression-atlas-okn.sparql name: Gene Expression Atlas SPARQL original_source: - relation_type: prov:hadPrimarySource source: gene-expression-atlas-okn product_url: https://apps.okn.us/gene-expression-atlas-okn/sparql - category: ProgrammingInterface description: Triple Pattern Fragments endpoint for Gene Expression Atlas format: http id: gene-expression-atlas-okn.tpf name: Gene Expression Atlas TPF original_source: - relation_type: prov:hadPrimarySource source: gene-expression-atlas-okn product_url: https://apps.okn.us/ldf/gene-expression-atlas-okn - activity_status: active category: Aggregator contacts: - category: Organization contact_details: - contact_type: email value: geo@ncbi.nlm.nih.gov - contact_type: url value: https://www.ncbi.nlm.nih.gov/geo/ label: NCBI Gene Expression Omnibus creation_date: '2026-07-01T00:00:00Z' description: The Gene Expression Omnibus (GEO) is a public functional genomics data repository maintained by the NCBI at the U.S. National Library of Medicine. It archives and freely distributes high-throughput gene expression and other functional genomics datasets, including the single-cell and single-nucleus studies of human pancreatic islets that PanKbase identified and reprocessed. domains: - biomedical - genomics homepage_url: https://www.ncbi.nlm.nih.gov/geo/ id: gene-expression-omnibus last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail name: Gene Expression Omnibus (GEO) products: - category: DataSource description: Web portal for searching, browsing, and downloading functional genomics datasets archived in the Gene Expression Omnibus. format: http id: gene-expression-omnibus.portal name: GEO Portal original_source: - relation_type: prov:hadPrimarySource source: gene-expression-omnibus product_url: https://www.ncbi.nlm.nih.gov/geo/ - category: GraphProduct description: Pancreas-focused knowledge graph integrating genes, SNPs, pancreatic expression QTLs, and donor-derived islet datasets harmonized within PanKbase. format: http id: pankgraph.graph name: PanKgraph Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: pankgraph - relation_type: prov:wasDerivedFrom source: pankbase - relation_type: prov:hadPrimarySource source: hpap - relation_type: prov:hadPrimarySource source: iidp - relation_type: prov:hadPrimarySource source: prodo product_url: https://pankgraph.org/ secondary_source: - relation_type: prov:wasInfluencedBy source: gene-expression-omnibus - category: GraphProduct description: RDF (Turtle) knowledge graph of the NIAID Data Ecosystem, harmonizing dataset and computational-tool metadata harvested from NIAID-funded and globally-relevant infectious and immune-mediated disease repositories. Served through the Proto-OKN FRINK federated SPARQL platform. format: ttl id: nde.graph name: NIAID Data Ecosystem KG (graph) original_source: - relation_type: prov:hadPrimarySource source: nde - relation_type: prov:hadPrimarySource source: immport - relation_type: prov:hadPrimarySource source: vdjserver product_url: https://frink.apps.renci.org/nde secondary_source: - relation_type: prov:wasInfluencedBy source: gene-expression-omnibus - relation_type: prov:wasInfluencedBy source: sra - relation_type: prov:wasInfluencedBy source: omicsdi - relation_type: prov:wasInfluencedBy source: hubmap - relation_type: prov:wasInfluencedBy source: massive - relation_type: prov:wasInfluencedBy source: pdb - relation_type: prov:wasInfluencedBy source: lincs - activity_status: active category: DataSource contacts: - category: Individual contact_details: - contact_type: email value: hvf21@cam.ac.uk label: Helen V. Firth - category: Individual contact_details: - contact_type: email value: seh@ebi.ac.uk label: Sarah E. Hunt 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 - biomedical homepage_url: https://www.ebi.ac.uk/gene2phenotype/ id: gene2phenotype infores_id: gene2phenotype last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: https://www.ebi.ac.uk/about/terms-of-use/ label: EMBL-EBI Terms of Use name: Gene2Phenotype products: - category: GraphicalInterface description: Main interface for searching curated gene-disease evidence and panels. format: http id: gene2phenotype.portal name: Gene2Phenotype Portal original_source: - relation_type: prov:hadPrimarySource source: gene2phenotype 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 original_source: - relation_type: prov:hadPrimarySource source: gene2phenotype 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 original_source: - relation_type: prov:hadPrimarySource source: gene2phenotype product_url: https://www.ebi.ac.uk/gene2phenotype/api/schema/ - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for Gene2Phenotype distributed via the NCATS Translator release site (release 2026_03_27; build gene2phenotype_2026_03_27_4773272d_2025sep1_4.3.6; source version 2026_03_27; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 3022 format: kgx-jsonl id: translator.gene2phenotype.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Gene2Phenotype KGX Graph node_count: 5424 original_source: - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/gene2phenotype/latest/ versions: - '2026_03_27' - gene2phenotype_2026_03_27_4773272d_2025sep1_4.3.6 - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: go-cam - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathbank - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: text-mining-kp - relation_type: prov:hadPrimarySource source: translator - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://kgx-storage.rtx.ai/releases/translator_kg/latest/ versions: - '2026_03_27' - 423af7989cac - category: GraphProduct description: KGX nodes file for EBI Gene2Phenotype KG format: kgx-jsonl id: kg-ebi-gene2pheno.nodes.kgx name: EBI gene2pheno KGX nodes original_source: - relation_type: prov:hadPrimarySource source: kg-ebi-gene2pheno - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: orphanet 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 original_source: - relation_type: prov:hadPrimarySource source: kg-ebi-gene2pheno - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: orphanet 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 original_source: - relation_type: prov:hadPrimarySource source: kg-ebi-gene2pheno - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: orphanet product_file_size: 142045 product_url: https://github.com/biothings/pending.api/blob/translator-output/plugins/ebi_gene2phenotype/EBIgene2pheno_trapi_edges.jsonl publications: - authors: - T. Michael Yates - Morad Ansari - Louise Thompson - Sarah E. Hunt - Elena Cibrian Uhalte - Rachel J. Hobson - Joseph A. Marsh - Caroline F. Wright - Helen V. Firth doi: 10.1186/s13073-024-01398-1 id: https://www.ncbi.nlm.nih.gov/pubmed/39506859 journal: Genome Medicine preferred: true title: Curating genomic disease-gene relationships with Gene2Phenotype (G2P) year: '2024' - authors: - Anja Thormann - Mihail Halachev - William McLaren - David J. Moore - Victoria Svinti - Archie Campbell - Shona M. Kerr - Marc Tischkowitz - Sarah E. Hunt - Malcolm G. Dunlop - Matthew E. Hurles - Caroline F. Wright - Helen V. Firth - Fiona Cunningham - David R. FitzPatrick doi: 10.1038/s41467-019-10016-3 id: https://www.ncbi.nlm.nih.gov/pubmed/31147538 journal: Nature Communications title: Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP year: '2019' 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: - relation_type: prov:hadPrimarySource source: genebass product_url: https://app.genebass.org/ - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for Genetics KP distributed via the NCATS Translator release site (release 2026_03_27; build geneticskp_2026-03-27_1f1ad62b_2025sep1_4.3.6; source version 2026-03-27; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 653544 format: kgx-jsonl id: translator.geneticskp.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Genetics KP KGX Graph node_count: 28023 original_source: - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/geneticskp/latest/ versions: - '2026_03_27' - geneticskp_2026-03-27_1f1ad62b_2025sep1_4.3.6 - category: GraphProduct description: TRAPI knowledge graph served by the Genetics KP, exposing gene/disease and gene/phenotype associations computed from large-scale human genetics data (e.g. Genebass exome association statistics aggregated with methods such as MAGMA and the HuGE calculator) and integrated curated gene-condition resources. The linked endpoint returns the meta knowledge graph describing the served node and edge types. format: json id: genetics-kp.graph name: Genetics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: genetics-kp - relation_type: prov:hadPrimarySource source: genebass product_file_size: 3538 product_url: https://genetics-kp.transltr.io/genetics_provider/trapi/v1.5/meta_knowledge_graph secondary_source: - relation_type: prov:wasInfluencedBy source: gencc - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: clingen publications: - authors: - Konrad J. Karczewski - Matthew Solomonson - Katherine R. Chao - Julia K. Goodrich - Grace Tiao - Wenhan Lu - Bridget M. Riley-Gillis - Ellen A. Tsai - Hye In Kim - Xiuwen Zheng - Fedik Rahimov - Sahar Esmaeeli - A. Jason Grundstad - Mark Reppell - Jeff Waring - Howard Jacob - David Sexton - Paola G. Bronson - Xing Chen - Xinli Hu - Jacqueline I. Goldstein - Daniel King - Christopher Vittal - Timothy Poterba - Duncan S. Palmer - Claire Churchhouse - Daniel P. Howrigan - Wei Zhou - Nicholas A. Watts - Kevin Nguyen - Huy Nguyen - Cara Mason - Christopher Farnham - Charlotte Tolonen - Laura D. Gauthier - Namrata Gupta - Daniel G. MacArthur - Heidi L. Rehm - Cotton Seed - Anthony A. Philippakis - Mark J. Daly - J. Wade Davis - Heiko Runz - Melissa R. Miller - Benjamin M. Neale 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. 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relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vo 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 versions: - v1.0.0 - v2.0.0 - v2.1.0 - v3.0.2 - v4.0.0 - current_build publications: - authors: - David Warde-Farley - Sylva L. Donaldson - Ovi Comes - Khalid Zuberi - Rashad Badrawi - Pauline Chao - Max Franz - Chris Grouios - Farzana Kazi - Christian Tannus Lopes - Anson Maitland - Sara Mostafavi - Jason Montojo - Quentin Shao - George Wright - Gary D. Bader - Quaid Morris 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' repository: https://github.com/GeneMANIA/genemania synonyms: - GeneMANIA - GeneMANIA prediction server 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: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://geneorganizer.huji.ac.il/ label: Gene ORGANizer - The Hebrew University of Jerusalem creation_date: '2026-06-17T00:00:00Z' description: Gene ORGANizer is a tool and database that links genes to the body parts and organs they affect. It contains curated associations between human genes and the anatomical components in which their phenotypes manifest, supporting analysis of the physiological effects of genes. domains: - genomics - anatomy and development homepage_url: https://geneorganizer.huji.ac.il/ id: geneorganizer last_modified_date: '2026-06-17T00:00:00Z' layout: resource_detail name: Gene ORGANizer products: - category: GraphicalInterface description: Web tool for exploring associations between genes and the organs and body parts they affect. format: http id: geneorganizer.site is_public: true name: Gene ORGANizer Website original_source: - relation_type: prov:hadPrimarySource source: geneorganizer product_url: https://geneorganizer.huji.ac.il/ - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: aminode - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: bitterdb - relation_type: prov:hadPrimarySource source: cdd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: craft - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: ena - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: fabric - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: gard - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: geneorganizer - relation_type: prov:hadPrimarySource source: genomernai - relation_type: prov:hadPrimarySource source: glyconnect - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: gtrnadb - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: homologene - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hprd - relation_type: prov:hadPrimarySource source: humancyc - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: iid - relation_type: prov:hadPrimarySource source: imgt - relation_type: prov:hadPrimarySource source: innatedb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: lncbase - relation_type: prov:hadPrimarySource source: lncbook - relation_type: prov:hadPrimarySource source: lncipedia - relation_type: prov:hadPrimarySource source: lncrnadisease - relation_type: prov:hadPrimarySource source: malacards - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: medlineplus - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: mint - relation_type: prov:hadPrimarySource source: mirbase - relation_type: prov:hadPrimarySource source: mirgenedb - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: modomics - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: nextprot - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathwaycommons - relation_type: prov:hadPrimarySource source: paxdb - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pdbe - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pirsf - relation_type: prov:hadPrimarySource source: prosite - relation_type: prov:hadPrimarySource source: proteomicsdb - relation_type: prov:hadPrimarySource source: proteopedia - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubtator - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rfam - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: scop - relation_type: prov:hadPrimarySource source: sfld - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: silva - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: snodb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: snopy - relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ publications: - authors: - David Gokhman - Guy Kelman - Adir Amartely - Guy Gershon - Shira Tsur - Liran Carmel doi: 10.1093/nar/gkx302 id: https://doi.org/10.1093/nar/gkx302 journal: Nucleic Acids Research preferred: true title: 'Gene ORGANizer: linking genes to the organs they affect' year: '2017' - 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 infores_id: genepio last_modified_date: '2026-06-18T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: genepio product_file_size: 732830 product_url: http://purl.obolibrary.org/obo/genepio.owl publications: [] 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: - biomedical evaluation_page: resource/genetics-kp/genetics-kp_eval_automated.html id: genetics-kp infores_id: genetics-data-provider last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: Genetics KP products: - category: GraphProduct description: TRAPI knowledge graph served by the Genetics KP, exposing gene/disease and gene/phenotype associations computed from large-scale human genetics data (e.g. Genebass exome association statistics aggregated with methods such as MAGMA and the HuGE calculator) and integrated curated gene-condition resources. The linked endpoint returns the meta knowledge graph describing the served node and edge types. format: json id: genetics-kp.graph name: Genetics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: genetics-kp - relation_type: prov:hadPrimarySource source: genebass product_file_size: 3538 product_url: https://genetics-kp.transltr.io/genetics_provider/trapi/v1.5/meta_knowledge_graph secondary_source: - relation_type: prov:wasInfluencedBy source: gencc - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: clingen - 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: genetics-kp product_url: https://github.com/broadinstitute/genetics-kp-dev - activity_status: active category: KnowledgeGraph collection: - translator contacts: - category: Individual contact_details: - contact_type: email value: mduby@broadinstitute.org label: Marc Duby - category: Individual label: Jason Flannick - category: Individual label: Noel Burt 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 - biomedical evaluation_page: resource/geneticskp/geneticskp_eval_automated.html homepage_url: https://github.com/NCATSTranslator/Translator-All/wiki/Genetics-Knowledge-Provider id: geneticskp infores_id: genetics-data-provider last_modified_date: '2026-06-27T00:00:00Z' layout: resource_detail name: Genetics KP products: - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for Genetics KP distributed via the NCATS Translator release site (release 2026_03_27; build geneticskp_2026-03-27_1f1ad62b_2025sep1_4.3.6; source version 2026-03-27; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 653544 format: kgx-jsonl id: translator.geneticskp.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Genetics KP KGX Graph node_count: 28023 original_source: - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/geneticskp/latest/ versions: - '2026_03_27' - geneticskp_2026-03-27_1f1ad62b_2025sep1_4.3.6 - category: DocumentationProduct description: Translator wiki overview for Genetics KP, including team contacts, public API entrypoint, upstream data resources, and method references. format: http id: geneticskp.docs name: Genetics KP Documentation original_source: - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: translator product_url: https://github.com/NCATSTranslator/Translator-All/wiki/Genetics-Knowledge-Provider - category: ProgrammingInterface description: Translator Reasoner API endpoint for Genetics KP. format: http id: geneticskp.trapi name: Genetics KP TRAPI Endpoint original_source: - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: translator product_url: https://genetics-kp.transltr.io/genetics_provider/trapi/v1.5/ - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: go-cam - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathbank - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: text-mining-kp - relation_type: prov:hadPrimarySource source: translator - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://kgx-storage.rtx.ai/releases/translator_kg/latest/ versions: - '2026_03_27' - 423af7989cac 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: '2026-04-15T00:00:00Z' 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: Genotype Ontology products: - category: OntologyProduct description: GENO format: owl id: geno.owl name: GENO original_source: - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: chr - relation_type: prov:hadPrimarySource source: geno - relation_type: prov:hadPrimarySource source: gff - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: skos product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl publications: [] repository: https://github.com/monarch-initiative/GENO-ontology - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: http://www.genomernai.org/ label: GenomeRNAi creation_date: '2026-06-17T00:00:00Z' description: GenomeRNAi is a database containing phenotypes from cell-based and in vivo RNA interference (RNAi) screens in Drosophila and Homo sapiens. It also provides a curated resource of RNAi reagents and their predicted specificity and efficiency. domains: - genomics - organisms homepage_url: http://www.genomernai.org/ id: genomernai last_modified_date: '2026-06-17T00:00:00Z' layout: resource_detail name: GenomeRNAi products: - category: GraphicalInterface description: Web interface for browsing and searching RNAi phenotypes and reagents. format: http id: genomernai.site is_public: true name: GenomeRNAi Website original_source: - relation_type: prov:hadPrimarySource source: genomernai product_url: http://www.genomernai.org/ - category: Product description: Bulk downloads of RNAi phenotype and reagent datasets. format: mixed id: genomernai.downloads name: GenomeRNAi Downloads original_source: - relation_type: prov:hadPrimarySource source: genomernai product_url: http://www.genomernai.org/Download - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - 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relation_type: prov:hadPrimarySource source: genomernai - relation_type: prov:hadPrimarySource source: glyconnect - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: gtrnadb - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: homologene - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hprd - relation_type: prov:hadPrimarySource source: humancyc - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: iid - relation_type: prov:hadPrimarySource source: imgt - 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relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ publications: - authors: - Esther E. Schmidt - Oliver Pelz - Svetlana Buhlmann - Grainne Kerr - Thomas Horn - Michael Boutros doi: 10.1093/nar/gks1170 id: https://doi.org/10.1093/nar/gks1170 journal: Nucleic Acids Research preferred: true title: 'GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update' year: '2013' - 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: '2026-06-27T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: genomickb product_url: https://gkb.dcmb.med.umich.edu/search - category: GraphProduct description: GenomicKB 1.0 Neo4j Database Dump (Requires license) dump_format: neo4j format: http id: genomickb.graph name: GenomicKB Graph Dump original_source: - relation_type: prov:hadPrimarySource source: genomickb - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: dbvar - relation_type: prov:hadPrimarySource source: endb - relation_type: prov:hadPrimarySource source: enhanceratlas - relation_type: prov:hadPrimarySource source: ccre - relation_type: prov:hadPrimarySource source: fire - relation_type: prov:hadPrimarySource source: motifmap product_url: https://available-inventions.umich.edu/product/genomickb-a-knowledgebase-for-the-human-genome - activity_status: active category: KnowledgeGraph collection: - ber 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: '2026-06-22T00:00:00Z' 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. format: kgx id: genophenoenvo-kg.data name: GenoPhenoEnvo KG Data original_source: - relation_type: prov:hadPrimarySource source: genophenoenvo-kg - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: peco - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: interpro 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: - relation_type: prov:hadPrimarySource 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. 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Swetnam - Harshad Hegde - Justin Reese - Justin Elser - Pankaj Jaiswal doi: 10.3389/frai.2023.1201002 id: PMID:37384147 journal: Front Artif Intell 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: '2026-05-31T00:00:00Z' 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: Geographical Entity Ontology products: - category: OntologyProduct description: Geographical Entity Ontology in OWL format format: owl id: geo.owl name: geo.owl original_source: - 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It integrates USGS reference features (NHDPlus High Resolution hydrologic units, Watershed Boundary Dataset subwatersheds, reference stream gages, and national aquifers) with community-contributed feature registries, and is served through the Geoconnex SPARQL and Triple Pattern Fragments endpoints. format: ttl id: geoconnex.graph name: GEOCONNEX Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: geoconnex - relation_type: prov:hadPrimarySource source: usgs-nhd - relation_type: prov:hadPrimarySource source: usgs-nwis product_url: https://github.com/internetofwater/geoconnex.us secondary_source: - relation_type: prov:wasInfluencedBy source: epa-sdwis - relation_type: prov:wasInfluencedBy source: us-census repository: https://github.com/internetofwater/geoconnex.us - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: email value: info@geonames.org label: GeoNames creation_date: '2026-02-26T00:00:00Z' description: GeoNames is a geographical database covering all countries and providing over eleven million place names through downloads and web services. domains: - environment - general homepage_url: https://www.geonames.org/ id: geonames last_modified_date: '2026-05-30T00:00:00Z' 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: GeoNames products: - category: DocumentationProduct description: GeoNames feature class and feature code vocabulary for classifying geographic entities. format: http id: geonames.feature-codes name: GeoNames Feature Codes original_source: - relation_type: prov:hadPrimarySource source: geonames product_url: https://www.geonames.org/export/codes.html - category: DocumentationProduct description: GeoNames download and webservice overview for daily data extracts, postal code datasets, and usage conditions. format: http id: geonames.export name: GeoNames Download and Webservice Overview original_source: - relation_type: prov:hadPrimarySource source: geonames product_url: https://www.geonames.org/export/ - category: ProgrammingInterface description: GeoNames web service overview covering search, country, postal code, hierarchy, and nearby-place APIs. format: http id: geonames.api name: GeoNames Web Services original_source: - relation_type: prov:hadPrimarySource source: geonames product_url: https://www.geonames.org/export/ws-overview.html - 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: - relation_type: prov:hadPrimarySource source: geonames - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 549884 product_url: https://w3id.org/biopragmatics/resources/geonames/geonames.tsv - 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: - relation_type: prov:hadPrimarySource source: orkg - relation_type: prov:hadPrimarySource source: wikidata - relation_type: prov:hadPrimarySource source: geonames - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: omit - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: stato - relation_type: prov:hadPrimarySource source: obi product_file_size: 642902930 product_url: https://orkg.org/files/rdf-dumps/rdf-export-orkg.nt - category: GraphProduct description: RDF/XML serialization of the eKG epidemiological knowledge graph format: rdfxml id: ekg.rdf name: eKG RDF original_source: - relation_type: prov:hadPrimarySource source: ekg product_file_size: 3853565 product_url: https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/ETOHA/ETOHA-OPEN/epidemicIE-DONs.rdf secondary_source: - 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relation_type: prov:wasDerivedFrom source: who - relation_type: prov:wasInformedBy source: bioportal - relation_type: prov:wasInformedBy source: geonames - category: GraphicalInterface description: JRC Data Catalogue dataset landing page for browsing and downloading eKG (the former Virtuoso faceted browser at api-vast.jrc.service.ec.europa.eu/fct/ has been retired) format: http id: ekg.browser name: eKG Data Catalogue Page original_source: - relation_type: prov:hadPrimarySource source: ekg product_url: https://data.jrc.ec.europa.eu/dataset/89056048-7f5d-4d7c-96ad-f99d1c0f6601 secondary_source: - relation_type: prov:wasDerivedFrom source: who - relation_type: prov:wasInformedBy source: bioportal - relation_type: prov:wasInformedBy source: geonames - category: Product description: geonames.feature Nodes TSV format: tsv id: obo-db-ingest.geonames.feature.tsv license: id: https://creativecommons.org/licenses/by/4.0/ label: CC-BY-4.0 name: geonames.feature Nodes TSV original_source: - relation_type: prov:hadPrimarySource source: geonames.feature - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 20951 product_url: https://w3id.org/biopragmatics/resources/geonames.feature/geonames.feature.tsv - 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 original_source: - 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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.org/ id: glkb last_modified_date: '2026-06-01T00:00:00Z' layout: resource_detail name: GLKB products: - category: GraphicalInterface description: Graphical interface for GLKB format: http id: glkb.site name: GLKB Site original_source: - relation_type: prov:hadPrimarySource source: glkb product_url: https://glkb.org/ secondary_source: - relation_type: prov:wasInfluencedBy source: pubmed 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: '2024' - 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: '2026-06-18T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: globi 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 original_source: - relation_type: prov:hadPrimarySource source: globi 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 original_source: - relation_type: prov:hadPrimarySource source: globi 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) original_source: - relation_type: prov:hadPrimarySource source: globi product_file_size: 3044531169 product_url: https://zenodo.org/record/14640564/files/interactions.tsv.gz - 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relation_type: prov:hadPrimarySource source: globi 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 original_source: - relation_type: prov:hadPrimarySource source: globi product_url: https://api.globalbioticinteractions.org/interactionFields?type=json warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - File was not able to be retrieved when checked on 2026-03-30_ No Content-Length header found - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: Product description: Field (column) definitions CSV endpoint format: csv id: globi.fields.csv name: interactionFields.csv original_source: - relation_type: prov:hadPrimarySource source: globi 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 original_source: - relation_type: prov:hadPrimarySource source: globi 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) original_source: - relation_type: prov:hadPrimarySource source: globi 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 original_source: - relation_type: prov:hadPrimarySource source: globi 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: - relation_type: prov:hadPrimarySource source: emi - relation_type: prov:hadPrimarySource source: emikg - relation_type: prov:hadPrimarySource source: globi - relation_type: prov:hadPrimarySource source: pf1600 - relation_type: prov:hadPrimarySource source: try product_url: https://doi.org/10.5281/zenodo.17079767 repository: https://github.com/earth-metabolome-initiative/metrin-kg warnings: [] - 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: - relation_type: prov:hadPrimarySource source: emi - relation_type: prov:hadPrimarySource source: emikg - relation_type: prov:hadPrimarySource source: globi - relation_type: prov:hadPrimarySource source: pf1600 - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: emi - relation_type: prov:hadPrimarySource source: emikg - relation_type: prov:hadPrimarySource source: globi - relation_type: prov:hadPrimarySource source: pf1600 - relation_type: prov:hadPrimarySource source: try product_url: https://sib-swiss.github.io/sparql-editor/emi publications: - authors: - Jorrit H. Poelen - James D. Simons - Chris J. Mungall 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: '2026-06-02T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_file_size: 29233 product_url: https://raw.githubusercontent.com/glycoinfo/GlycoCoO/master/ontology/glycocoo.owl secondary_source: - relation_type: prov:wasDerivedFrom source: glycordf - category: GraphicalInterface description: NCBO BioPortal entry for browsing and exploring the GlycoCoO ontology format: http id: glycocoo.bioportal name: GlycoCoO BioPortal Entry original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_url: https://bioportal.bioontology.org/ontologies/GLYCOCOO secondary_source: - relation_type: prov:wasInfluencedBy source: bioportal - category: DocumentationProduct description: GitHub Wiki with developer information, database providers, and prefix documentation format: http id: glycocoo.wiki name: GlycoCoO Wiki Documentation original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_url: https://github.com/glycoinfo/GlycoCoO/wiki secondary_source: - relation_type: prov:wasInformedBy source: glycordf - 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 original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_url: https://github.com/glycoinfo/GlycoCoO/tree/master/RDF_Sample secondary_source: - relation_type: prov:wasDerivedFrom source: glycordf - relation_type: prov:wasInformedBy source: unicarbkb - relation_type: prov:wasInformedBy source: glyconnect - relation_type: prov:wasInformedBy source: glyconavi - category: Product description: Example SPARQL queries for querying glycoconjugate data across federated endpoints format: http id: glycocoo.sparql-examples name: GlycoCoO SPARQL Query Examples original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_file_size: 2467 product_url: https://github.com/glycoinfo/GlycoCoO/blob/master/SPARQL_Query.md secondary_source: - relation_type: prov:wasInformedBy source: 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ 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 doi: 10.1093/glycob/cwab013 id: doi: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: url value: https://glyconavi.org/ label: GlycoNAVI creation_date: '2026-06-02T00:00:00Z' description: GlycoNAVI is an integrated glycoscience portal that provides searchable glycan structures, glycoproteins, glycosylation sites, glycan-related genes, disease annotations, glycan tools, and GlyCosmos-linked data resources. domains: - chemistry and biochemistry - biomedical - proteomics homepage_url: https://glyconavi.org/ id: glyconavi last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail name: GlycoNAVI products: - category: GraphicalInterface description: GlycoNAVI integrated portal for glycoscience research, including glycan structures, glycoproteins, glycosylation sites, glycan-related genes, diseases, and glycan analysis tools. id: glyconavi.portal name: GlycoNAVI Portal original_source: - relation_type: prov:hadPrimarySource source: glyconavi product_url: https://glyconavi.org/ - category: Product description: GlycoNAVI glycan structure table with GlyTouCan identifiers and WURCS strings, available through browser views and JSON, CSV, and TSV downloads. format: mixed id: glyconavi.glycans name: GlycoNAVI Glycans original_source: - relation_type: prov:hadPrimarySource source: glyconavi product_url: https://glyconavi.org/Glycans secondary_source: - relation_type: prov:wasInformedBy source: glytoucan - 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 original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_url: https://github.com/glycoinfo/GlycoCoO/tree/master/RDF_Sample secondary_source: - relation_type: prov:wasDerivedFrom source: glycordf - relation_type: prov:wasInformedBy source: unicarbkb - relation_type: prov:wasInformedBy source: glyconnect - relation_type: prov:wasInformedBy source: glyconavi synonyms: - Glyco-Database Information Search - 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: '2026-06-27T00:00:00Z' 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 format: http id: glyconnect.site is_public: true name: GlyConnect Web Interface original_source: - relation_type: prov:hadPrimarySource source: glyconnect product_url: https://glyconnect.expasy.org/ - category: ProgrammingInterface description: RESTful API for accessing GlyConnect data format: http id: glyconnect.api.rest is_public: true name: GlyConnect RESTful API original_source: - relation_type: prov:hadPrimarySource source: glyconnect product_url: https://glyconnect.expasy.org/api/docs - category: ProgrammingInterface description: SPARQL endpoint for querying GlyConnect RDF data format: http id: glyconnect.api.sparql is_public: true name: GlyConnect SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: glyconnect product_url: https://glyconnect.expasy.org/rdf - category: Product description: Compositions dataset containing glycan compositions format: csv id: glyconnect.compositions name: GlyConnect Glycan Compositions original_source: - relation_type: prov:hadPrimarySource source: glyconnect product_url: https://glyconnect.expasy.org/downloads/compositions/ - category: Product description: Immunoglobulins dataset containing glycans commonly found on immunoglobulins format: csv id: glyconnect.immunoglobulins name: GlyConnect Immunoglobulins Dataset original_source: - relation_type: prov:hadPrimarySource source: glyconnect product_url: https://glyconnect.expasy.org/downloads/Immunoglobulins/ - 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 original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_url: https://github.com/glycoinfo/GlycoCoO/tree/master/RDF_Sample secondary_source: - relation_type: prov:wasDerivedFrom source: glycordf - relation_type: prov:wasInformedBy source: unicarbkb - relation_type: prov:wasInformedBy source: glyconnect - relation_type: prov:wasInformedBy source: glyconavi - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: aminode - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: bitterdb - relation_type: prov:hadPrimarySource source: cdd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - 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relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: gard - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: geneorganizer - relation_type: prov:hadPrimarySource source: genomernai - relation_type: prov:hadPrimarySource source: glyconnect - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: gtrnadb - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: homologene - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hprd - relation_type: prov:hadPrimarySource source: humancyc - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: iid - relation_type: prov:hadPrimarySource source: imgt - relation_type: prov:hadPrimarySource source: innatedb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: lncbase - relation_type: prov:hadPrimarySource source: lncbook - relation_type: prov:hadPrimarySource source: lncipedia - relation_type: prov:hadPrimarySource source: lncrnadisease - relation_type: prov:hadPrimarySource source: malacards - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: medlineplus - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: mint - relation_type: prov:hadPrimarySource source: mirbase - relation_type: prov:hadPrimarySource source: mirgenedb - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: modomics - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: nextprot - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathwaycommons - relation_type: prov:hadPrimarySource source: paxdb - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pdbe - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pirsf - relation_type: prov:hadPrimarySource source: prosite - relation_type: prov:hadPrimarySource source: proteomicsdb - relation_type: prov:hadPrimarySource source: proteopedia - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubtator - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rfam - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: scop - relation_type: prov:hadPrimarySource source: sfld - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: silva - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: snodb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: snopy - relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ publications: - authors: - Alocci D - Mariethoz J - Gastaldello A - Gasteiger E - Karlsson NG - Kolarich D - Packer NH - Lisacek F doi: 10.1021/acs.jproteome.8b00766 id: doi:10.1021/acs.jproteome.8b00766 journal: Journal of Proteome Research 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' 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: https://www.glycoinfo.org/GlycoRDF/ id: glycordf last_modified_date: '2026-06-02T00:00:00Z' 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) original_source: - relation_type: prov:hadPrimarySource source: glycordf product_file_size: 389060 product_url: https://raw.githubusercontent.com/glycoinfo/GlycoRDF/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 original_source: - relation_type: prov:hadPrimarySource source: glycordf product_url: https://bioportal.bioontology.org/ontologies/GLYCORDF secondary_source: - relation_type: prov:wasInfluencedBy source: bioportal - category: DocumentationProduct description: Comprehensive documentation of the GlycoRDF ontology classes, predicates, and usage examples format: doc id: glycordf.documentation name: GlycoRDF Documentation original_source: - relation_type: prov:hadPrimarySource source: glycordf product_file_size: 62492 product_url: https://raw.githubusercontent.com/glycoinfo/GlycoRDF/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 original_source: - relation_type: prov:hadPrimarySource source: glycordf product_url: https://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 original_source: - relation_type: prov:hadPrimarySource source: glycordf 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 original_source: - relation_type: prov:hadPrimarySource source: glycordf product_url: https://github.com/glycoinfo/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 original_source: - relation_type: prov:hadPrimarySource source: glycordf 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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 original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_file_size: 29233 product_url: https://raw.githubusercontent.com/glycoinfo/GlycoCoO/master/ontology/glycocoo.owl secondary_source: - relation_type: prov:wasDerivedFrom source: glycordf - category: DocumentationProduct description: GitHub Wiki with developer information, database providers, and prefix documentation format: http id: glycocoo.wiki name: GlycoCoO Wiki Documentation original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_url: https://github.com/glycoinfo/GlycoCoO/wiki secondary_source: - relation_type: prov:wasInformedBy source: glycordf - 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 original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_url: https://github.com/glycoinfo/GlycoCoO/tree/master/RDF_Sample secondary_source: - relation_type: prov:wasDerivedFrom source: glycordf - relation_type: prov:wasInformedBy source: unicarbkb - relation_type: prov:wasInformedBy source: glyconnect - relation_type: prov:wasInformedBy source: glyconavi - category: Product description: Example SPARQL queries for querying glycoconjugate data across federated endpoints format: http id: glycocoo.sparql-examples name: GlycoCoO SPARQL Query Examples original_source: - relation_type: prov:hadPrimarySource source: glycocoo product_file_size: 2467 product_url: https://github.com/glycoinfo/GlycoCoO/blob/master/SPARQL_Query.md secondary_source: - relation_type: prov:wasInformedBy source: glycordf 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 doi: 10.1093/bioinformatics/btu732 id: doi: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 doi: 10.1186/2041-1480-4-39 id: doi: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: '2026-06-18T00:00:00Z' 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: GlyGen products: - category: GraphicalInterface description: Web interface for exploring GlyGen data format: http id: glygen.site is_public: true name: GlyGen Website original_source: - relation_type: prov:hadPrimarySource source: glygen product_url: https://glygen.org/ - category: ProgrammingInterface description: RESTful API for accessing GlyGen data format: http id: glygen.api is_public: true name: GlyGen API original_source: - relation_type: prov:hadPrimarySource source: glygen product_url: https://api.glygen.org/ - category: GraphicalInterface description: Interface for searching GlyGen protein and glycan data format: csv id: glygen.data.site name: GlyGen Data Downloads original_source: - relation_type: prov:hadPrimarySource source: glygen product_url: https://data.glygen.org/ - category: GraphProduct compression: zip description: Nodes from GlyGen Biomarker Database format: csv id: biomarkerkg.nodes.biomarker name: BKG Biomarker Nodes original_source: - relation_type: prov:hadPrimarySource source: biomarkerkg - relation_type: prov:hadPrimarySource source: glygen product_file_size: 1252064 product_url: https://s3.amazonaws.com/maayan-kg/biomarker-kg/Biomarker.nodes.zip - category: GraphProduct description: GlyGen amino acid nodes used in ProKN format: csv id: prokn.glygen.aminoacid.nodes name: ProKN GlyGen AminoAcid Nodes original_source: - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: prokn product_file_size: 853 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_PROTEOFORM.AminoAcid.nodes.csv - category: GraphProduct description: GlyGen glycoprotein glycosylated site edges format: csv id: prokn.glygen.glycoprotein.glycosylated_at.glycosylationsite.edges name: ProKN GlyGen Glycosylated Site Edges original_source: - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: prokn product_file_size: 14046942 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_PROTEOFORM.Glycoprotein.GLYCOSYLATED_AT.GlycosylationSite.edges.csv - category: GraphProduct description: GlyGen glycoprotein evidence edges format: csv id: prokn.glygen.glycoprotein.has_evidence.glycoproteinevidence.edges name: ProKN GlyGen Evidence Edges original_source: - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: prokn product_file_size: 33863751 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_PROTEOFORM.Glycoprotein.HAS_EVIDENCE.GlycoproteinEvidence.edges.csv - category: GraphProduct description: GlyGen glycoprotein PRO entry edges format: csv id: prokn.glygen.glycoprotein.has_pro_entry.gpid2pro.edges name: ProKN GlyGen PRO Entry Edges original_source: - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: prokn product_file_size: 15557656 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_PROTEOFORM.Glycoprotein.HAS_PRO_ENTRY.GPID2PRO.edges.csv - category: GraphProduct description: GlyGen glycoprotein isoform sequence edges format: csv id: prokn.glygen.glycoprotein.sequence.isoform.edges name: ProKN GlyGen Isoform Sequence Edges original_source: - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: prokn product_file_size: 7097575 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_PROTEOFORM.Glycoprotein.SEQUENCE.Isoform.edges.csv - category: GraphProduct description: GlyGen glycoprotein protein sequence edges format: csv id: prokn.glygen.glycoprotein.sequence.protein.edges name: ProKN GlyGen Protein Sequence Edges original_source: - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: prokn product_file_size: 7773165 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_PROTEOFORM.Glycoprotein.SEQUENCE.Protein.edges.csv - category: GraphProduct description: GlyGen glycoprotein evidence citation edges format: csv id: prokn.glygen.glycoproteinevidence.citation.glycoproteincitation.edges name: ProKN GlyGen Evidence Citation Edges original_source: - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: prokn product_file_size: 571669 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_PROTEOFORM.GlycoproteinEvidence.CITATION.GlycoproteinCitation.edges.csv - category: GraphProduct description: GlyGen glycosylation enzyme protein edges format: csv id: prokn.glygen.glycosylation.has_enzyme_protein.protein.edges name: ProKN GlyGen Enzyme Protein Edges original_source: - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: prokn product_file_size: 23734 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_GLYCANS.Glycosylation.HAS_ENZYME_PROTEIN.Protein.edges.csv - category: GraphProduct description: GlyGen glycosylation site saccharide edges format: csv id: prokn.glygen.glycosylationsite.has_saccharide.glytoucan.edges name: ProKN GlyGen Saccharide Edges original_source: - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: prokn product_file_size: 11352916 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_PROTEOFORM.GlycosylationSite.HAS_SACCHARIDE.Glytoucan.edges.csv - 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Gene sets are derived from eleven NIH Common Fund programs (GlyGen, GTEx, IDG, IMPC/KOMP2, LINCS, MoTrPAC, Bridge2AI, HuBMAP, Metabolomics Workbench, SenNet, and SPARC) and phenotype-gene set relationships are computed with PIGEAN (Priors Inferred from GEne ANnotations). format: http id: digcfdekg.graph name: CFDE REVEAL Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: digcfdekg - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: impc - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: bridge2ai - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: sparc product_url: https://cfdeknowledge.org/r/cfde_reveal secondary_source: - 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relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways - category: Product compression: gzip description: PubChem substance information in SDF format format: sdf id: pubchem.substances.sdf name: PubChem Substances SDF original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways publications: - authors: - William S York - Raja Mazumder - Rene Ranzinger - Nathan Edwards - Robel Kahsay - Kiyoko F Aoki-Kinoshita - Matthew P Campbell - Richard D Cummings - Ten Feizi - Maria Martin - Darren A Natale - Nicolle H Packer - Robert J Woods - Gaurav Agarwal - Sena Arpinar - Sanath Bhat - Judith Blake - Leyla Jael Garcia Castro - Brian Fochtman - Jeffrey Gildersleeve - Radoslav Goldman - Xavier Holmes - Vinamra Jain - Sujeet Kulkarni - Rupali Mahadik - Akul Mehta - Reza Mousavi - Sandeep Nakarakommula - Rahi Navelkar - Nagarajan Pattabiraman - Michael J Pierce - Karen Ross - Preethi Vasudev - Jeet Vora - Tatiana Williamson - Wenjin Zhang doi: 10.1093/glycob/cwz080 id: doi:10.1093/glycob/cwz080 journal: Glycobiology preferred: true title: 'GlyGen: Computational and Informatics Resources for Glycoscience' year: '2020' repository: https://github.com/glygener/glygen-backend-api - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://glytoucan.org/ label: GlyTouCan / GlySpace Project (Soka University, Japan) creation_date: '2026-06-03T00:00:00Z' description: GlyTouCan is the international glycan structure repository, assigning globally unique and persistent accession numbers to registered glycan structures. It accepts structures ranging in resolution from monosaccharide composition to fully defined structures, providing a freely available, uncurated registry that serves as a common reference for glycan identifiers across glycoscience resources. domains: - chemistry and biochemistry - proteomics - biological systems homepage_url: https://glytoucan.org/ id: glytoucan last_modified_date: '2026-06-05T00:00:00Z' 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: GlyTouCan products: - category: GraphicalInterface description: Web interface for searching, browsing, and registering glycan structures and looking up GlyTouCan accession numbers. format: http id: glytoucan.portal name: GlyTouCan Web Portal original_source: - relation_type: prov:hadPrimarySource source: glytoucan product_url: https://glytoucan.org/ - category: ProgrammingInterface description: Public REST API (documented via Swagger UI) for programmatic access to GlyTouCan glycan structures and accession numbers. format: http id: glytoucan.api is_public: true name: GlyTouCan API original_source: - relation_type: prov:hadPrimarySource source: glytoucan product_url: https://api.glytoucan.org/ - category: ProgrammingInterface description: SPARQL endpoint providing RDF access to the GlyTouCan glycan structure repository and its semantic annotations. format: http id: glytoucan.sparql is_public: true name: GlyTouCan SPARQL Endpoint original_source: - relation_type: prov:hadPrimarySource source: glytoucan product_url: https://ts.glytoucan.org/sparql - category: Product description: GlycoNAVI glycan structure table with GlyTouCan identifiers and WURCS strings, available through browser views and JSON, CSV, and TSV downloads. format: mixed id: glyconavi.glycans name: GlycoNAVI Glycans original_source: - relation_type: prov:hadPrimarySource source: glyconavi product_url: https://glyconavi.org/Glycans secondary_source: - relation_type: prov:wasInformedBy source: glytoucan publications: - authors: - Kiyoko Aoki-Kinoshita - Sanjay Agravat - Nobuyuki P. Aoki - Sena Arpinar - Richard D. Cummings - Akihiro Fujita - Noriaki Fujita - Gerald M. Hart - Stuart M. Haslam - Toshisuke Kawasaki - Masaaki Matsubara - Kelley W. Moreman - Shujiro Okuda - Michael Pierce - René Ranzinger - Toshihide Shikanai - Daisuke Shinmachi - Elena Solovieva - Yoshinori Suzuki - Shinichiro Tsuchiya - Issaku Yamada - William S. York - Joseph Zaia - Hisashi Narimatsu doi: 10.1093/nar/gkv1041 id: https://doi.org/10.1093/nar/gkv1041 journal: Nucleic Acids Research title: GlyTouCan 1.0 - The international glycan structure repository year: '2016' synonyms: - GlyTouCan - 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 evaluation_page: resource/gnbr/gnbr_eval.html homepage_url: https://github.com/jakelever/GNBR id: gnbr infores_id: gnbr last_modified_date: '2026-06-22T00:00:00Z' 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: GNBR products: - category: GraphProduct description: Text-mined biomedical knowledge graph of gene–disease–drug relationships (semantic themes) format: http id: gnbr.graph name: GNBR graph original_source: - relation_type: prov:hadPrimarySource source: gnbr - relation_type: prov:hadPrimarySource source: pubtator - relation_type: prov:hadPrimarySource source: pubmed product_url: https://zenodo.org/records/3459420 - category: GraphProduct description: Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases edge_count: 500958 format: mixed id: pharmkg.graph name: PharmKG graph node_count: 7603 original_source: - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: gnbr - relation_type: prov:hadPrimarySource source: humannet - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pharmkg - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: ttd product_url: https://zenodo.org/record/4077338 - category: GraphProduct compression: targz description: DRKG graph files, including a TSV of triples, embeddings, ID mappings, and a glossary of relation types. format: mixed id: drkg.graph name: DRKG graph original_source: - relation_type: prov:hadPrimarySource source: drkg - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: gnbr - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: string product_file_size: 216650245 product_url: https://dgl-data.s3-us-west-2.amazonaws.com/dataset/DRKG/drkg.tar.gz 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: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.usgs.gov/ label: U.S. Geological Survey (USGS) creation_date: '2026-06-18T00:00:00Z' description: The Geographic Names Information System (GNIS) is the U.S. federal and national standard for geographic nomenclature, serving as the official repository of names and attributes for physical and cultural geographic features across the United States, its territories, and Antarctica. It is developed and maintained by the U.S. Geological Survey's National Geospatial Program in support of the U.S. Board on Geographic Names. For each feature it records the official name, feature class, state and county, geographic coordinates, elevation, historical and variant names, and related metadata. GNIS is the upstream source for the KnowWhereGraph geospatial knowledge graph. domains: - general - information technology - environment homepage_url: https://www.usgs.gov/tools/geographic-names-information-system-gnis id: gnis last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: https://www.usa.gov/government-works label: U.S. Government Work (public domain) name: Geographic Names Information System products: - category: GraphicalInterface description: Domestic Names search application for querying GNIS geographic features by name, feature class, state, and county. format: http id: gnis.search name: GNIS Domestic Names Search original_source: - relation_type: prov:hadPrimarySource source: gnis product_url: https://edits.nationalmap.gov/apps/gaz-domestic/public/search/names - category: Product description: GNIS data download portal providing bulk geographic names files for the United States, individual states, and topical extracts. format: http id: gnis.download name: GNIS Data Download original_source: - relation_type: prov:hadPrimarySource source: gnis product_url: https://www.usgs.gov/us-board-on-geographic-names/download-gnis-data - category: GraphicalInterface description: GNIS-LD, the Linked Data (RDF/GeoSPARQL) version of GNIS published by the STKO Lab at UC Santa Barbara, with a public SPARQL endpoint and downloadable triples. format: http id: gnis.linkeddata name: GNIS-LD (Linked Data) original_source: - relation_type: prov:hadPrimarySource source: gnis product_url: https://gnis-ld.org/ - 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 original_source: - relation_type: prov:hadPrimarySource source: knowwheregraph - relation_type: prov:wasDerivedFrom source: wikidata - relation_type: prov:hadPrimarySource source: bluesky - relation_type: prov:hadPrimarySource source: cdc-places - relation_type: prov:hadPrimarySource source: cdc-svi - relation_type: prov:hadPrimarySource source: cropland-data-layer - relation_type: prov:hadPrimarySource source: epa-aqs - relation_type: prov:hadPrimarySource source: gadm - relation_type: prov:hadPrimarySource source: gnis - relation_type: prov:hadPrimarySource source: hifld - relation_type: prov:hadPrimarySource source: mtbs - relation_type: prov:hadPrimarySource source: nhpn - relation_type: prov:hadPrimarySource source: nifc - relation_type: prov:hadPrimarySource source: noaa-hms - relation_type: prov:hadPrimarySource source: noaa-ncei - relation_type: prov:hadPrimarySource source: openfema - relation_type: prov:hadPrimarySource source: reliefweb - relation_type: prov:hadPrimarySource source: ssurgo - relation_type: prov:hadPrimarySource source: us-census - relation_type: prov:hadPrimarySource source: usdm - relation_type: prov:hadPrimarySource source: usgs-comcat product_url: https://knowwheregraph.org/ - 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: '2026-04-15T00:00:00Z' 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: 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 original_source: - relation_type: prov:hadPrimarySource source: gno product_file_size: 215188241 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 original_source: - relation_type: prov:hadPrimarySource source: gno product_file_size: 168981263 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 original_source: - relation_type: prov:hadPrimarySource source: gno product_file_size: 359497890 product_url: http://purl.obolibrary.org/obo/gno.json publications: - authors: - Zhang, Wenjin - Edwards, Nathan J. doi: 10.5281/zenodo.6678278 id: https://doi.org/10.5281/zenodo.6678278 journal: Zenodo title: GNOme - Glycan Naming and Subsumption Ontology year: '2021' repository: https://github.com/glygen-glycan-data/GNOme - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://ccms.ucsd.edu/ label: UC San Diego Center for Computational Mass Spectrometry creation_date: '2026-06-02T00:00:00Z' description: Global Natural Products Social Molecular Networking (GNPS) is a web-based mass spectrometry ecosystem and open-access knowledge base for organizing, sharing, analyzing, and annotating raw, processed, or identified tandem mass spectrometry data. domains: - chemistry and biochemistry - biomedical - microbiology homepage_url: https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp id: gnps last_modified_date: '2026-06-27T00:00:00Z' layout: resource_detail name: Global Natural Products Social Molecular Networking products: - category: GraphicalInterface description: GNPS web interface for molecular networking, library search, MASST search, public dataset browsing, spectral library curation, and related mass spectrometry analysis workflows. format: http id: gnps.portal name: GNPS Web Portal original_source: - relation_type: prov:hadPrimarySource source: gnps product_url: https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp - category: DocumentationProduct description: GNPS documentation covering the platform, analysis tools, data preparation, molecular networking, spectral library search, dataset sharing, and community features. format: http id: gnps.docs name: GNPS Documentation original_source: - relation_type: prov:hadPrimarySource source: gnps product_url: https://gnpsdocs.readthedocs.io/ - _replace_warnings: true category: Product description: GNPS public MS/MS reference spectral library browser and curation interface. format: http id: gnps.spectral_libraries name: GNPS Reference Spectral Libraries original_source: - relation_type: prov:hadPrimarySource source: gnps product_url: https://external.gnps2.org/gnpslibrary warnings: [] - category: GraphProduct description: RDF knowledge graph materialized by the MetaBoKG workflow from public metabolomics repository outputs, GNPS molecular-networking jobs, annotation evidence, sample metadata, and environmental and taxonomic context. The repository documents generated per-job Turtle files under mapping/kg and loading into Virtuoso named graphs. format: mixed id: metabokg.graph latest_version: arXiv v1 demonstration name: MetaboKG RDF Graph original_source: - relation_type: prov:hadPrimarySource source: metabokg - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubmedcentral - relation_type: prov:hadPrimarySource source: gnps - relation_type: prov:hadPrimarySource source: massive - relation_type: prov:hadPrimarySource source: redu product_url: https://github.com/HolobiomicsLab/MetaBoKG secondary_source: - relation_type: prov:used source: ms - relation_type: prov:used source: chebi - relation_type: prov:used source: ncbitaxon - relation_type: prov:used source: envo - relation_type: prov:used source: ncit - relation_type: prov:used source: uberon - relation_type: prov:used source: chmo - relation_type: prov:used source: sio - relation_type: prov:used source: prov-o - relation_type: prov:used source: dcat - relation_type: prov:used source: afo warnings: - No static public graph release or hosted endpoint was available in the GitHub repository when curated on 2026-06-02; the repository documents local Turtle materialization and Virtuoso loading. - category: MappingProduct description: RML mappings and configuration templates used to transform GNPS, molecular networking, feature-based molecular networking, and ReDU data into RDF. format: http id: metabokg.rml_mappings license: id: https://www.apache.org/licenses/LICENSE-2.0 label: Apache License 2.0 name: MetaBoKG RML Mappings original_source: - relation_type: prov:hadPrimarySource source: metabokg product_url: https://github.com/HolobiomicsLab/MetaBoKG/tree/main/mapping/rml secondary_source: - relation_type: prov:wasInformedBy source: gnps - relation_type: prov:wasInformedBy source: massive - relation_type: prov:wasInformedBy source: redu - category: GraphicalInterface description: Pan-ReDU dashboard and file-selection interface for exploring daily updated public metabolomics metadata and selecting public data for GNPS reanalysis. format: http id: redu.dashboard name: Pan-ReDU Dashboard original_source: - relation_type: prov:hadPrimarySource source: redu product_url: https://redu.gnps2.org/selection/ secondary_source: - relation_type: prov:wasInformedBy source: gnps - relation_type: prov:wasInformedBy source: massive - category: GraphProduct description: RDF knowledge graph of the Experimental Natural Products Knowledge Graph, integrating experimental LC-MS/MS spectra and GNPS-based annotations, ISDB-LOTUS structural annotations, taxonomic and bioactivity metadata, cross-linked to Wikidata and served from the public GraphDB/SPARQL endpoint. format: ttl id: kg-enp.graph license: id: https://creativecommons.org/publicdomain/zero/1.0/legalcode label: CC0-1.0 name: ENPKG RDF Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: kg-enp - relation_type: prov:hadPrimarySource source: gnps - relation_type: prov:hadPrimarySource source: lotus - relation_type: prov:hadPrimarySource source: wikidata product_url: https://enpkg.commons-lab.org/graphdb secondary_source: - relation_type: prov:wasInfluencedBy source: open-tree-of-life - relation_type: prov:wasInfluencedBy source: chembl warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 406 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 406 error when accessing file' publications: - authors: - Mingxun Wang - Jeremy J Carver - Vanessa V Phelan - Laura M Sanchez - Neha Garg - Yao Peng - Don Duy Nguyen doi: 10.1038/nbt.3597 id: doi:10.1038/nbt.3597 journal: Nature Biotechnology preferred: true title: Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking year: '2016' repository: https://github.com/CCMS-UCSD/GNPSDocumentation synonyms: - GNPS - Global Natural Products Social Molecular Networking - 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 - category: Organization contact_details: - contact_type: url value: https://geneontology.org/ id: gene-ontology-consortium label: Gene Ontology Consortium creation_date: '2025-03-16T00:00:00Z' description: An ontology for describing the function of genes and gene products domains: - biomedical - biological systems homepage_url: http://geneontology.org/ id: go infores_id: go last_modified_date: '2026-06-22T00:00:00Z' 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: 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) original_source: - relation_type: prov:hadPrimarySource source: go product_file_size: 129706298 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) original_source: - relation_type: prov:hadPrimarySource source: go product_file_size: 36555702 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) original_source: - relation_type: prov:hadPrimarySource source: go product_url: http://purl.obolibrary.org/obo/go.json warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: 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 original_source: - relation_type: prov:hadPrimarySource source: go product_file_size: 236488701 product_url: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl - category: OntologyProduct description: As go-plus.owl, in obographs json format format: json id: go.extensions.go-plus.json name: GO-Plus original_source: - relation_type: prov:hadPrimarySource source: go product_url: http://purl.obolibrary.org/obo/go/extensions/go-plus.json warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - 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 original_source: - relation_type: prov:hadPrimarySource source: go product_file_size: 160974965 product_url: http://purl.obolibrary.org/obo/go/go-base.owl - 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 original_source: - relation_type: prov:hadPrimarySource source: go product_file_size: 32126692 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) original_source: - relation_type: prov:hadPrimarySource source: go product_url: http://purl.obolibrary.org/obo/go/go-basic.json warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: OntologyProduct description: Classes added to ncbitaxon for taxon subsets such as prokaryotes format: owl id: go.extensions.go-taxon-subsets.owl name: GO Taxon Subsets original_source: - relation_type: prov:hadPrimarySource source: go product_file_size: 5795 product_url: http://purl.obolibrary.org/obo/go/extensions/go-taxon-subsets.owl - 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 original_source: - relation_type: prov:hadPrimarySource source: go product_file_size: 129908636 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 original_source: - relation_type: prov:hadPrimarySource source: go product_file_size: 36684860 product_url: http://purl.obolibrary.org/obo/go/snapshot/go.obo - category: GraphicalInterface description: Official GO browser for ontology terms, gene products, and annotations. format: http id: go.amigo is_public: true name: AmiGO 2 original_source: - relation_type: prov:hadPrimarySource source: go product_url: https://amigo.geneontology.org/amigo - category: ProgrammingInterface description: Official Gene Ontology API for term, annotation, and related programmatic access. format: http id: go.api is_public: true name: Gene Ontology API original_source: - relation_type: prov:hadPrimarySource source: go product_url: https://api.geneontology.org/ - category: GraphicalInterface description: Browser for searching and viewing Gene Ontology terms and GOA annotations format: http id: goa.quickgo name: QuickGO Browser original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa 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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa product_url: https://ftp.ebi.ac.uk/pub/databases/GO/goa/ secondary_source: - relation_type: prov:wasInformedBy source: uniprot - relation_type: prov:wasInformedBy source: rnacentral - relation_type: prov:wasInformedBy source: complexportal - category: Product description: GO annotations for all UniProtKB entries format: txt id: goa.uniprot latest_version: '232' name: UniProt GOA Annotations original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: uniprot product_url: https://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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: uniprot product_url: https://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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: uniprot product_url: https://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/ - 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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: uniprot product_url: https://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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: pdbe product_url: https://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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa product_url: https://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ - category: GraphProduct compression: gzip description: Pathway-like GO-CAM causal activity models distributed as RDF Turtle. format: ttl id: go.gocams.ttl name: GO-CAM TTL Archive original_source: - 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relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: progenomes - relation_type: prov:hadPrimarySource source: proteomehd - relation_type: prov:hadPrimarySource source: pubmedcentral - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: swissmodel - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wormbase product_file_size: 281505096430 product_url: https://stringdb-downloads.org/download/network_schema.v12.0.sql.gz - description: The MechRepoNet knowledge graph in its original format format: mixed id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - 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relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://multiomics.transltr.io/mbkp - 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: - relation_type: prov:hadPrimarySource source: bioportal - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: genemania - relation_type: prov:hadPrimarySource source: go - 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relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Graph database dump and additional relationship files for the Clinical Knowledge Graph. format: neo4j id: ckg.graph latest_version: '1' license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: CKG Graph Database Dump original_source: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: ckg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: Product description: Gene Ontology Causal Activity Model (GO-CAM) annotations manually curated by Gene Ontology biocurators linking genes, proteins, and biological processes. Distributed as the canonical noctua-models repository, where each model is stored as a Turtle (TTL) file. format: ttl id: cam-kp.go-cams name: Gene Ontology CAMs original_source: - relation_type: prov:hadPrimarySource source: cam-kp - relation_type: prov:hadPrimarySource source: go product_url: https://github.com/geneontology/noctua-models - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j format: http id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb product_url: https://arax.ncats.io/ - category: GraphProduct description: RNA-KG as a Neo4j Dump format: neo4j id: rna-kg.kg.neo4j name: RNA-KG Neo4j Dump original_source: - 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category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: circbase - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rna-kg - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: vo - relation_type: prov:hadPrimarySource source: wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: circbase - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rna-kg - 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relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: orkg - relation_type: prov:hadPrimarySource source: wikidata - relation_type: prov:hadPrimarySource source: geonames - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: omit - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: stato - relation_type: prov:hadPrimarySource source: obi product_file_size: 642902930 product_url: https://orkg.org/files/rdf-dumps/rdf-export-orkg.nt - category: OntologyProduct description: OWL release of Monochrom Ontology format: owl id: chr.model.owl name: Monochrom Ontology OWL release original_source: - relation_type: prov:hadPrimarySource source: chr - relation_type: prov:hadPrimarySource source: geno - relation_type: prov:hadPrimarySource source: gff - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: iao - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: skos product_file_size: 102365 product_url: https://raw.githubusercontent.com/monarch-initiative/monochrom/refs/heads/master/chr.owl - category: Product description: Gene ontology annotations from the Gene Ontology Consortium format: http id: genecards.gene.ontology name: GeneCards Gene Ontology Annotations original_source: - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: go product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 error when accessing file - category: Product compression: 7z description: Compressed CSV file containing ProteomeHD v1.1, with 10,323 proteins measured across 294 SILAC ratios format: csv id: proteomehd.data name: ProteomeHD Data original_source: - relation_type: prov:hadPrimarySource source: proteomehd product_file_size: 9427082 product_url: https://raw.githubusercontent.com/Rappsilber-Laboratory/ProteomeHD/master/Data/ProteomeHD_v1_1.7z - category: MappingProduct description: Mappings between InterPro entries and Gene Ontology (GO) terms format: tsv id: interpro.interpro2go name: InterPro to GO Mappings original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: interpro product_file_size: 3088718 product_url: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro2go - 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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: ncbigene product_file_size: 1322439983 product_url: https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz - category: GraphProduct description: GO term hierarchy edges format: csv id: prokn.go.goterm.is_a.goterm.edges name: ProKN GO Term Hierarchy Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 11917762 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.GOTerm.IS_A.GOTerm.edges.csv - category: GraphProduct description: GO protein acts upstream of GO term edges format: csv id: prokn.go.protein.acts_upstream_of.goterm.edges name: ProKN GO Acts Upstream Of Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 158931 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.ACTS_UPSTREAM_OF.GOTerm.edges.csv - category: GraphProduct description: GO protein acts upstream of negative effect edges format: csv id: prokn.go.protein.acts_upstream_of_negative_effect.goterm.edges name: ProKN GO Acts Upstream Negative Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 10441 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.ACTS_UPSTREAM_OF_NEGATIVE_EFFECT.GOTerm.edges.csv - category: GraphProduct description: GO protein acts upstream of or within edges format: csv id: prokn.go.protein.acts_upstream_of_or_within.goterm.edges name: ProKN GO Acts Upstream Or Within Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 714349 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.ACTS_UPSTREAM_OF_OR_WITHIN.GOTerm.edges.csv - category: GraphProduct description: GO protein acts upstream of or within negative effect edges format: csv id: prokn.go.protein.acts_upstream_of_or_within_negative_effect.goterm.edges name: ProKN GO Acts Upstream Or Within Negative Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 4257 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.ACTS_UPSTREAM_OF_OR_WITHIN_NEGATIVE_EFFECT.GOTerm.edges.csv - category: GraphProduct description: GO protein acts upstream of or within positive effect edges format: csv id: prokn.go.protein.acts_upstream_of_or_within_positive_effect.goterm.edges name: ProKN GO Acts Upstream Or Within Positive Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 13894 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.ACTS_UPSTREAM_OF_OR_WITHIN_POSITIVE_EFFECT.GOTerm.edges.csv - category: GraphProduct description: GO protein acts upstream of positive effect edges format: csv id: prokn.go.protein.acts_upstream_of_positive_effect.goterm.edges name: ProKN GO Acts Upstream Positive Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 32541 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.ACTS_UPSTREAM_OF_POSITIVE_EFFECT.GOTerm.edges.csv - category: GraphProduct description: GO protein colocalizes with GO term edges format: csv id: prokn.go.protein.colocalizes_with.goterm.edges name: ProKN GO Colocalizes Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 261555 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.COLOCALIZES_WITH.GOTerm.edges.csv - category: GraphProduct description: GO protein contributes to GO term edges format: csv id: prokn.go.protein.contributes_to.goterm.edges name: ProKN GO Contributes To Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 310541 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.CONTRIBUTES_TO.GOTerm.edges.csv - category: GraphProduct description: GO protein enables GO term edges format: csv id: prokn.go.protein.enables.goterm.edges name: ProKN GO Enables Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 53141599 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.ENABLES.GOTerm.edges.csv - category: GraphProduct description: GO protein involved in GO term edges format: csv id: prokn.go.protein.involved_in.goterm.edges name: ProKN GO Involved In Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 43447452 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.INVOLVED_IN.GOTerm.edges.csv - category: GraphProduct description: GO protein active in GO term edges format: csv id: prokn.go.protein.is_active_in.goterm.edges name: ProKN GO Active In Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 1630623 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.IS_ACTIVE_IN.GOTerm.edges.csv - category: GraphProduct description: GO protein located in GO term edges format: csv id: prokn.go.protein.located_in.goterm.edges name: ProKN GO Located In Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 50784436 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.LOCATED_IN.GOTerm.edges.csv - category: GraphProduct description: GO protein not acts upstream of or within edges format: csv id: prokn.go.protein.not_acts_upstream_of_or_within.goterm.edges name: ProKN GO Not Acts Upstream Or Within Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 1796 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.NOT_ACTS_UPSTREAM_OF_OR_WITHIN.GOTerm.edges.csv - category: GraphProduct description: GO protein not acts upstream of or within negative effect edges format: csv id: prokn.go.protein.not_acts_upstream_of_or_within_negative_effect.goterm.edges name: ProKN GO Not Acts Upstream Negative Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 455 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.NOT_ACTS_UPSTREAM_OF_OR_WITHIN_NEGATIVE_EFFECT.GOTerm.edges.csv - category: GraphProduct description: GO protein not colocalizes with GO term edges format: csv id: prokn.go.protein.not_colocalizes_with.goterm.edges name: ProKN GO Not Colocalizes Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 3336 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.NOT_COLOCALIZES_WITH.GOTerm.edges.csv - category: GraphProduct description: GO protein not contributes to GO term edges format: csv id: prokn.go.protein.not_contributes_to.goterm.edges name: ProKN GO Not Contributes Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 3198 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.NOT_CONTRIBUTES_TO.GOTerm.edges.csv - category: GraphProduct description: GO protein not enables GO term edges format: csv id: prokn.go.protein.not_enables.goterm.edges name: ProKN GO Not Enables Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 129748 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.NOT_ENABLES.GOTerm.edges.csv - category: GraphProduct description: GO protein not involved in GO term edges format: csv id: prokn.go.protein.not_involved_in.goterm.edges name: ProKN GO Not Involved In Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 143198 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.NOT_INVOLVED_IN.GOTerm.edges.csv - category: GraphProduct description: GO protein not active in GO term edges format: csv id: prokn.go.protein.not_is_active_in.goterm.edges name: ProKN GO Not Active In Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 893 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.NOT_IS_ACTIVE_IN.GOTerm.edges.csv - category: GraphProduct description: GO protein not located in GO term edges format: csv id: prokn.go.protein.not_located_in.goterm.edges name: ProKN GO Not Located In Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 52743 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.NOT_LOCATED_IN.GOTerm.edges.csv - category: GraphProduct description: GO protein not part of GO term edges format: csv id: prokn.go.protein.not_part_of.goterm.edges name: ProKN GO Not Part Of Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 4731 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.NOT_PART_OF.GOTerm.edges.csv - category: GraphProduct description: GO protein part of GO term edges format: csv id: prokn.go.protein.part_of.goterm.edges name: ProKN GO Part Of Edges original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: prokn product_file_size: 3629548 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/GO.Protein.PART_OF.GOTerm.edges.csv - 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: - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: unibiomap product_url: https://aideepmed.com/UniBioMap/database/unibiomap/go_desc.json warnings: - File was not able to be retrieved when checked on 2026-03-30_ No Content-Length header found - category: MappingProduct compression: gzip description: Mapping of OMA identifiers to Gene Ontology terms format: tsv id: oma.mapping.go name: OMA to GO Mapping original_source: - relation_type: prov:hadPrimarySource source: oma - relation_type: prov:hadPrimarySource source: go product_url: https://omabrowser.org/All/oma-go.txt.gz warnings: [] - category: Product compression: gzip description: Gene association file for Reactome GO annotations format: txt id: reactome.go-associations.txt name: Reactome Gene Association File original_source: - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go product_file_size: 835232 product_url: https://download.reactome.org/96/gene_association.reactome.gz - category: Product description: Mapping from Reactome pathways to Gene Ontology terms format: txt id: reactome.pathways.go-terms.txt name: Reactome Pathways to GO Terms original_source: - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go product_file_size: 60582 product_url: https://download.reactome.org/96/Pathways2GoTerms_human.txt - category: GraphProduct description: Neo4j graph database integrating Enrichr gene set libraries with genes, terms, pathways, diseases, drugs, cell types, and other functional annotations dump_format: neo4j format: neo4j id: enrichr-kg.graph name: Enrichr-KG Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: enrichr-kg - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases product_file_size: 522141103 product_url: https://s3.amazonaws.com/maayan-kg/enrichr-kg/dumps/enrichr-kg-042123.dump - category: Product description: Edge-table CSV snapshot from the Enrichr-KG downloads page using source.relation.target edge triples format: csv id: enrichr-kg.edges-csv name: Enrichr-KG Edge CSV Snapshot original_source: - relation_type: prov:hadPrimarySource source: enrichr-kg - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: go product_file_size: 35177347 product_url: https://s3.amazonaws.com/maayan-kg/enrichr-kg/current/GO_Biological_Process_2021.GO_BP.Gene.edges.csv - 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. format: kgx id: genophenoenvo-kg.data name: GenoPhenoEnvo KG Data original_source: - relation_type: prov:hadPrimarySource source: genophenoenvo-kg - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: peco - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: interpro product_url: https://datacommons.cyverse.org/browse/iplant/home/shared/genophenoenvo - category: GraphicalInterface description: Browser for complete Hetionet v1.0 graph database in Neo4j format: http id: hetionet.neo4j name: Hetionet v1.0 Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 format: neo4j id: hetionet.data.neo4j name: Hetionet v1.0 Neo4j original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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) original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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) original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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: hetionet.hetnetpy name: hetnetpy original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral product_url: https://het.io/search - 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 original_source: - relation_type: prov:hadPrimarySource source: lncrnalyzr - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: doid product_url: https://github.com/MaayanLab/lncRNAlyzr - category: GraphicalInterface description: Graphical interface for MedKG format: http id: medkb.site name: MedKG Site original_source: - 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category: GraphProduct description: Neo4j knowledge graph serialization of Harmonizome processed datasets, including genes, attributes, resources, datasets, and gene-attribute associations. dump_format: neo4j format: neo4j id: harmonizome.kg-neo4j latest_version: '3.0' name: Harmonizome Knowledge Graph Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://harmonizome-kg.maayanlab.cloud/ secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - 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relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://sugi.bio/biobtree/api/ - 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 original_source: - relation_type: prov:hadPrimarySource source: go product_url: http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: aminode - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: bitterdb - relation_type: prov:hadPrimarySource source: cdd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: craft - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: ena - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: fabric - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: gard - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: geneorganizer - relation_type: prov:hadPrimarySource source: genomernai - relation_type: prov:hadPrimarySource source: glyconnect - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: gtrnadb - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: homologene - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hprd - relation_type: prov:hadPrimarySource source: humancyc - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: iid - relation_type: prov:hadPrimarySource source: imgt - relation_type: prov:hadPrimarySource source: innatedb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: lncbase - relation_type: prov:hadPrimarySource source: lncbook - relation_type: prov:hadPrimarySource source: lncipedia - relation_type: prov:hadPrimarySource source: lncrnadisease - relation_type: prov:hadPrimarySource source: malacards - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: medlineplus - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: mint - relation_type: prov:hadPrimarySource source: mirbase - relation_type: prov:hadPrimarySource source: mirgenedb - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: modomics - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: nextprot - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathwaycommons - relation_type: prov:hadPrimarySource source: paxdb - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pdbe - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pirsf - relation_type: prov:hadPrimarySource source: prosite - relation_type: prov:hadPrimarySource source: proteomicsdb - relation_type: prov:hadPrimarySource source: proteopedia - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubtator - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rfam - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: scop - relation_type: prov:hadPrimarySource source: sfld - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: silva - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: snodb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: snopy - relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ - category: GraphProduct compatibility: - standard: biolink version: 4.2.1 compression: gzip description: Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - 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: - relation_type: prov:hadPrimarySource source: eco-kg - relation_type: prov:hadPrimarySource source: eol-traitbank - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: maizegdb - relation_type: prov:hadPrimarySource source: planteome - relation_type: prov:hadPrimarySource source: rapdb product_url: https://github.com/Knowledge-Graph-Hub/eco-kg - category: GraphProduct description: GenomicKB 1.0 Neo4j Database Dump (Requires license) dump_format: neo4j format: http id: genomickb.graph name: GenomicKB Graph Dump original_source: - relation_type: prov:hadPrimarySource source: genomickb - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: dbvar - relation_type: prov:hadPrimarySource source: endb - relation_type: prov:hadPrimarySource source: enhanceratlas - relation_type: prov:hadPrimarySource source: ccre - relation_type: prov:hadPrimarySource source: fire - relation_type: prov:hadPrimarySource source: motifmap product_url: https://available-inventions.umich.edu/product/genomickb-a-knowledgebase-for-the-human-genome - category: GraphProduct description: GP_KG.txt edge_count: 1246726 format: txt id: gp-kg.graph name: GP-KG node_count: 61146 original_source: - relation_type: prov:hadPrimarySource source: gp-kg - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: mgi - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: goa - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: umls - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: faers - relation_type: prov:wasDerivedFrom source: phenomebrowser - relation_type: prov:wasDerivedFrom source: treatkb product_file_size: 48397035 product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt - 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: - relation_type: prov:hadPrimarySource source: kg-covid-19 - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cord-19 - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: uniprot product_url: https://kghub.io/kg-covid-19/ warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 404 error when accessing file' - 'Download offline as of 2026-07-01: the KG-Hub reorganization has taken this file offline. The kghub.io and kg-hub.berkeleybop.io hosts return HTTP 404 for all kg-covid-19 artifacts (current and dated) and the kg-hub-public-data S3 objects return HTTP 403. No replacement public download URL is available.' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' - category: GraphProduct description: KGX Distribution of KG-IDG format: kgx id: kg-idg.graph name: KGX Distribution of KG-IDG original_source: - relation_type: prov:hadPrimarySource source: kg-idg - relation_type: prov:hadPrimarySource source: atc - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ogms - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tcrd product_url: https://kg-hub.berkeleybop.io/kg-idg/current/kg-idg.tar.gz warnings: - 'File was not able to be retrieved when checked on 2026-07-10: HTTP 404 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-01: HTTP 404 error. The kg-hub.berkeleybop.io host is being reorganized and KG-IDG downloads are pending relocation to a new home; no live download is currently available.' - 'File was not able to be retrieved when checked on 2026-07-15: HTTP 404 error when accessing file' - category: GraphProduct description: Merged KG with ontology-grounded KG and literature-based graph as TSV file format: tsv id: np-kg.graph.tsv name: NP-KG TSV original_source: - relation_type: prov:hadPrimarySource source: np-kg - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: dideo - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: indra - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: oae - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pheknowlator - relation_type: prov:hadPrimarySource source: pmc - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semrep - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon product_file_size: 1074149258 product_url: https://zenodo.org/records/12536780/files/NP-KG_v3.0.0.tsv?download=1 - category: GraphProduct description: Merged KG with ontology-grounded KG and literature-based graph as NetworkX multidigraph object dump_format: gpickle format: mixed id: np-kg.graph.networkx name: NP-KG gpickle original_source: - relation_type: prov:hadPrimarySource source: np-kg - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: dideo - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: indra - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: oae - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pheknowlator - relation_type: prov:hadPrimarySource source: pmc - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semrep - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon product_file_size: 936065236 product_url: https://zenodo.org/records/12536780/files/NP-KG_v3.0.0.gpickle?download=1 - category: GraphProduct description: The full PrimeKG dataset containing disease relationships. format: csv id: primekg.graph name: PrimeKG Full Dataset original_source: - relation_type: prov:hadPrimarySource source: primekg - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: umls product_url: https://dataverse.harvard.edu/api/access/datafile/6180620 warnings: - File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 error when accessing file - File was not able to be retrieved when checked on 2026-02-04_ Timeout connecting to URL - category: GraphProduct description: KGX distribution of the SRI-Reference KG format: kgx id: sri-reference-kg.graph name: SRI-Reference KG (KGX distribution) original_source: - relation_type: prov:hadPrimarySource source: sri-reference-kg - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: wormbase - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: zfin - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bspo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ddanat - relation_type: prov:hadPrimarySource source: ddpheno - 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category: GraphProduct description: Integrated rare-disease knowledge graph produced by the RD-Clust workflow, connecting rare diseases to genes, phenotypes, Gene Ontology terms, drugs/ligands, and pathway interactions. Distributed as the processed disease ontograph within the RD-Clust repository. format: http id: ncatsgardkg.graph name: NCATS GARD Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: ncatsgardkg - relation_type: prov:hadPrimarySource source: gard product_url: https://github.com/ncats/RD-Clust/tree/main/data/processed secondary_source: - relation_type: prov:wasInfluencedBy source: hp - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: mondo - relation_type: prov:wasInfluencedBy source: orphanet - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: pharos - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: chebi - relation_type: prov:wasInfluencedBy source: pubchem - relation_type: prov:wasInfluencedBy source: pathwaycommons - category: GraphProduct description: The SPOKE-OKN knowledge graph, an OKN-hosted RDF publication of the SPOKE biomedical and environmental health knowledge graph, served through FRINK query services. format: ttl id: spoke-okn.graph name: SPOKE-OKN Graph original_source: - relation_type: prov:hadPrimarySource source: spoke-okn - relation_type: prov:wasDerivedFrom source: spoke product_url: https://spoke.ucsf.edu secondary_source: - relation_type: prov:wasInfluencedBy source: bgee - relation_type: prov:wasInfluencedBy source: bindingdb - relation_type: prov:wasInfluencedBy source: bv-brc - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: civic - relation_type: prov:wasInfluencedBy source: cl - relation_type: prov:wasInfluencedBy source: clinicaltrialsgov - relation_type: prov:wasInfluencedBy source: diseases - relation_type: prov:wasInfluencedBy source: doid - relation_type: prov:wasInfluencedBy source: drugbank - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: foodb - relation_type: prov:wasInfluencedBy source: gdsc - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: gwascatalog - relation_type: prov:wasInfluencedBy source: hpa - relation_type: prov:wasInfluencedBy source: interpro - relation_type: prov:wasInfluencedBy source: kegg - relation_type: prov:wasInfluencedBy source: lincs-l1000 - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: metacyc - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: ncbitaxon - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pathophenodb - relation_type: prov:wasInfluencedBy source: pfam - relation_type: prov:wasInfluencedBy source: pid - relation_type: prov:wasInfluencedBy source: protcid - relation_type: prov:wasInfluencedBy source: pubmed - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: sider - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikipathways publications: - authors: - Ashburner M - Ball CA - Blake JA - Botstein D - Butler H - Cherry JM - Davis AP - Dolinski K - Dwight SS - Eppig JT - Harris MA - Hill DP - Issel-Tarver L - Kasarskis A - Lewis S - Matese JC - Richardson JE - Ringwald M - Rubin GM - Sherlock G doi: 10.1038/75556 id: https://www.ncbi.nlm.nih.gov/pubmed/10802651 journal: Nat Genet title: 'Gene ontology: tool for the unification of biology. The Gene Ontology Consortium' year: '2000' - authors: - Gene Ontology Consortium doi: 10.1093/nar/gkaa1113 id: https://www.ncbi.nlm.nih.gov/pubmed/33290552 journal: Nucleic Acids Res title: 'The Gene Ontology resource: enriching a GOld mine' year: '2021' repository: https://github.com/geneontology/go-ontology synonyms: - GO 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: '2026-06-27T00:00:00Z' 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: 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource 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: - relation_type: prov:hadPrimarySource source: go-cam product_url: https://github.com/geneontology/noctua-models - category: DataModelProduct description: LinkML YAML schema for representing Gene Ontology Causal Activity Models (GO-CAMs) format: yaml id: go-cam.linkml-schema name: GO-CAM LinkML Schema original_source: - relation_type: prov:hadPrimarySource source: go-cam product_file_size: 7830 product_url: https://raw.githubusercontent.com/geneontology/gocam-py/main/src/gocam/schema/gocam.yaml - category: ProgrammingInterface connection_url: http://api.geneontology.org/ description: Programmatic access to GO-CAM models through the Gene Ontology API format: http id: go-cam.api is_public: true name: GO-CAM API original_source: - relation_type: prov:hadPrimarySource source: go-cam product_url: http://api.geneontology.org/ - category: ProcessProduct description: Server-side component for storing, validating, and reasoning over GO-CAM models id: go-cam.minerva name: Minerva original_source: - relation_type: prov:hadPrimarySource source: go-cam product_url: https://github.com/geneontology/minerva - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for GO-CAM distributed via the NCATS Translator release site (release 2026_03_06; build go_cam_2026-01-23_b6972b4a_2025sep1_4.3.6; source version 2026-01-23; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 4539 format: kgx-jsonl id: translator.go_cam.graph latest_version: '2026_03_06' license: id: https://opensource.org/license/mit/ label: MIT name: Translator GO-CAM KGX Graph node_count: 3181 original_source: - relation_type: prov:hadPrimarySource source: go-cam - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/go_cam/latest/ versions: - '2026_03_06' - go_cam_2026-01-23_b6972b4a_2025sep1_4.3.6 - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: go-cam - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathbank - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: text-mining-kp - relation_type: prov:hadPrimarySource source: translator - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://kgx-storage.rtx.ai/releases/translator_kg/latest/ versions: - '2026_03_27' - 423af7989cac 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 journal: Nature Genetics 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: 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/ id: goa infores_id: goa last_modified_date: '2026-06-18T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: goa product_url: https://www.ebi.ac.uk/GOA/ - category: GraphicalInterface description: Browser for searching and viewing Gene Ontology terms and GOA annotations format: http id: goa.quickgo name: QuickGO Browser original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa 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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa product_url: https://ftp.ebi.ac.uk/pub/databases/GO/goa/ secondary_source: - relation_type: prov:wasInformedBy source: uniprot - relation_type: prov:wasInformedBy source: rnacentral - relation_type: prov:wasInformedBy source: complexportal - category: Product description: GO annotations for all UniProtKB entries format: txt id: goa.uniprot latest_version: '232' name: UniProt GOA Annotations original_source: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: uniprot product_url: https://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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: uniprot product_url: https://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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: uniprot product_url: https://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/ - 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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: uniprot product_url: https://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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: pdbe product_url: https://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: - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: goa product_url: https://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ - category: DocumentationProduct description: Documentation including FAQ, About pages, and contact information format: http id: goa.documentation name: GOA Documentation original_source: - relation_type: prov:hadPrimarySource source: goa product_url: https://www.ebi.ac.uk/GOA/about - category: GraphProduct description: HumanGOA Automat format: kgx-jsonl id: automat.humangoa infores_id: automat-human-goa name: humangoa_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: goa product_url: https://stars.renci.org/var/plater/bl-4.2.1/HumanGOA_Automat/06f107a4e9e8e547/ - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: KGX JSONL graph package for GOA distributed via the NCATS Translator release site (release 2026_03_06; build goa_2026-01-23_5fdd3125_2025sep1_4.3.6; source version 2026-01-23; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 1132872 format: kgx-jsonl id: translator.goa.graph latest_version: '2026_03_06' license: id: https://opensource.org/license/mit/ label: MIT name: Translator GOA KGX Graph node_count: 91993 original_source: - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: translator product_url: https://kgx-storage.rtx.ai/releases/goa/latest/ versions: - '2026_03_06' - goa_2026-01-23_5fdd3125_2025sep1_4.3.6 - category: Product compression: 7z description: Compressed CSV file containing ProteomeHD v1.1, with 10,323 proteins measured across 294 SILAC ratios format: csv id: proteomehd.data name: ProteomeHD Data original_source: - relation_type: prov:hadPrimarySource source: proteomehd product_file_size: 9427082 product_url: https://raw.githubusercontent.com/Rappsilber-Laboratory/ProteomeHD/master/Data/ProteomeHD_v1_1.7z - category: GraphProduct compatibility: - standard: biolink version: 4.3.6 description: Aggregated KGX JSONL graph package combining 29 Translator release sources (release 2026_03_27; build 423af7989cac; Biolink 4.3.6; Node Normalizer 2025sep1). edge_count: 29243943 format: kgx-jsonl id: translator.translator_kg.graph latest_version: '2026_03_27' license: id: https://opensource.org/license/mit/ label: MIT name: Translator Aggregate KGX Graph node_count: 1696790 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cohd - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: ctkp - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: drug-approvals-kp - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: gene2phenotype - relation_type: prov:hadPrimarySource source: geneticskp - relation_type: prov:hadPrimarySource source: go-cam - relation_type: prov:hadPrimarySource source: goa - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathbank - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: text-mining-kp - relation_type: prov:hadPrimarySource source: translator - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ubergraph product_url: https://kgx-storage.rtx.ai/releases/translator_kg/latest/ versions: - '2026_03_27' - 423af7989cac - category: GraphProduct description: GP_KG.txt edge_count: 1246726 format: txt id: gp-kg.graph name: GP-KG node_count: 61146 original_source: - relation_type: prov:hadPrimarySource source: gp-kg - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: mgi - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: goa - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: umls - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: faers - relation_type: prov:wasDerivedFrom source: phenomebrowser - relation_type: prov:wasDerivedFrom source: treatkb product_file_size: 48397035 product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt - category: GraphProduct description: KGX distribution of the SRI-Reference KG format: kgx id: sri-reference-kg.graph name: SRI-Reference KG (KGX distribution) original_source: - relation_type: prov:hadPrimarySource source: sri-reference-kg - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - 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relation_type: prov:hadPrimarySource source: bspo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: ddanat - relation_type: prov:hadPrimarySource source: ddpheno - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: dpo - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: emapa - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: foodon - relation_type: prov:hadPrimarySource source: fypo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: mpath - relation_type: prov:hadPrimarySource source: nbo - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: oba - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: upheno - relation_type: prov:hadPrimarySource source: wbbt - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: wbphenotype - relation_type: prov:hadPrimarySource source: xao - relation_type: prov:hadPrimarySource source: xpo - relation_type: prov:hadPrimarySource source: zfa - relation_type: prov:hadPrimarySource source: zfs - relation_type: prov:hadPrimarySource source: zp - relation_type: prov:hadPrimarySource source: icd10cm - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: decipher - relation_type: prov:hadPrimarySource source: mmrrc - relation_type: prov:hadPrimarySource source: cureid - relation_type: prov:hadPrimarySource source: phenopacket-store product_file_size: 230046094 product_url: https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.tar.gz - 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: '2026-06-27T00:00:00Z' 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: - relation_type: prov:hadPrimarySource source: goldterms product_file_size: 4602231 product_url: https://raw.githubusercontent.com/cmungall/gold-ontology/main/gold.owl - category: GraphicalInterface format: owl id: goldterms.bioportal name: GOLDTERMS on BioPortal original_source: - relation_type: prov:hadPrimarySource source: goldterms product_url: https://bioportal.bioontology.org/ontologies/GOLDTERMS - category: DataModelProduct format: yaml id: goldterms.definitions.yaml name: GOLD definitions in YAML format original_source: - relation_type: prov:hadPrimarySource source: goldterms product_file_size: 27808 product_url: https://raw.githubusercontent.com/cmungall/gold-ontology/main/gold_definitions.yaml - category: Product description: Trait data table listing all 140+ harmonized traits available in metaTraits, mapped to standardized ontologies. format: http id: metatraits.traits name: metaTraits Trait List original_source: - relation_type: prov:hadPrimarySource source: bacdive - relation_type: prov:hadPrimarySource source: bv-brc - relation_type: prov:hadPrimarySource source: goldterms - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:hadPrimarySource source: progenomes product_url: https://metatraits.embl.de/traits - category: Product description: Family-level harmonized trait annotations aggregated for NCBI taxonomy in compressed TSV format. format: tsv id: metatraits.ncbi.family-summary name: metaTraits NCBI Family Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: ncbi - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 913932 product_url: https://www.bork.embl.de/~robbani/metatraits/ncbi_family_summary_no_predictions.tsv.gz - category: Product description: Genus-level harmonized trait annotations aggregated for NCBI taxonomy in compressed TSV format. format: tsv id: metatraits.ncbi.genus-summary name: metaTraits NCBI Genus Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: ncbi - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 2431808 product_url: https://www.bork.embl.de/~robbani/metatraits/ncbi_genus_summary_no_predictions.tsv.gz - category: Product description: Species-level harmonized trait annotations aggregated for NCBI taxonomy in compressed TSV format. format: tsv id: metatraits.ncbi.species-summary name: metaTraits NCBI Species Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: ncbi - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 6523019 product_url: https://www.bork.embl.de/~robbani/metatraits/ncbi_species_summary_no_predictions.tsv.gz - category: Product description: Family-level harmonized trait annotations aggregated for GTDB taxonomy in compressed TSV format. format: tsv id: metatraits.gtdb.family-summary name: metaTraits GTDB Family Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: gtdb - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 1513013 product_url: https://www.bork.embl.de/~robbani/metatraits/gtdb_family_summary_no_predictions.tsv.gz - category: Product description: Genus-level harmonized trait annotations aggregated for GTDB taxonomy in compressed TSV format. format: tsv id: metatraits.gtdb.genus-summary name: metaTraits GTDB Genus Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: gtdb - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 4965442 product_url: https://www.bork.embl.de/~robbani/metatraits/gtdb_genus_summary_no_predictions.tsv.gz - category: Product description: Species-level harmonized trait annotations aggregated for GTDB taxonomy in compressed TSV format. format: tsv id: metatraits.gtdb.species-summary name: metaTraits GTDB Species Summary original_source: - relation_type: prov:hadPrimarySource source: metatraits - relation_type: prov:wasDerivedFrom source: gtdb - relation_type: prov:wasDerivedFrom source: bacdive - relation_type: prov:wasDerivedFrom source: bv-brc - relation_type: prov:wasDerivedFrom source: goldterms - relation_type: prov:wasDerivedFrom source: progenomes product_file_size: 12570522 product_url: https://www.bork.embl.de/~robbani/metatraits/gtdb_species_summary_no_predictions.tsv.gz repository: https://github.com/cmungall/gold-ontology tags: - biopragmatics - core - activity_status: active category: DataSource collection: - ber contacts: - category: Organization contact_details: - contact_type: url value: https://www.nib.si/eng label: National Institute of Biology (NIB), Slovenia creation_date: '2026-06-18T00:00:00Z' description: GoMapMan is a manually curated, open database that integrates, consolidates, and visualizes plant gene functional annotations organized within the MapMan ontology, a hierarchical scheme of functional "bins" tailored to plant biology. It maps genes to MapMan bins across several crop and model plant species, including Arabidopsis, potato, and tomato, and harmonizes annotations drawn from multiple sources into a single consolidated, expert-reviewed resource. The portal provides interactive browsing and visualization of the ontology and gene-to-bin mappings, and its curated mappings are widely reused to annotate genes in plant systems-biology and transcriptomics analyses. It is an upstream source for the Stress Knowledge Map (SKM). domains: - genomics - pathways - agriculture - systems biology homepage_url: https://gomapman.nib.si/ id: gomapman last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: '' label: Not specified name: GoMapMan products: - category: GraphicalInterface description: Web portal for browsing, searching, and visualizing the MapMan ontology and manually curated plant gene functional annotations across supported crop and model plant species. format: http id: gomapman.portal name: GoMapMan Web Portal original_source: - relation_type: prov:hadPrimarySource source: gomapman product_url: https://gomapman.nib.si/ - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 548527 product_url: https://skm.nib.si/downloads/pss/public/sbml - category: GraphProduct description: PSS model (v1.0.0, October 2023) in DOT Language format compatible with Graphviz. The live/current DOT export endpoint was retired upstream; this points to the latest published versioned DOT export. format: dot id: skm.pss.live.dot name: PSS Download (DOT, v1.0.0) original_source: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 405988 product_url: https://skm.nib.si/downloads/pss-version/v1.0.0/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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 2732107 product_url: https://skm.nib.si/downloads/ckn/v2-2023.06/edges - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 885747 product_url: https://skm.nib.si/downloads/ckn/v2-2023.06/nodes - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 318666 product_url: https://skm.nib.si/downloads/ckn/v1-2018.06/edges - 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: - relation_type: prov:hadPrimarySource source: skm - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: metacyc - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: araport - relation_type: prov:hadPrimarySource source: gomapman product_file_size: 702407 product_url: https://skm.nib.si/downloads/ckn/v1-2018.06/nodes publications: - authors: - Ramsak Z - Baebler S - Rotter A - Korbar M - Mozetic I - Usadel B - Gruden K doi: 10.1093/nar/gkt1056 id: https://www.ncbi.nlm.nih.gov/pubmed/24194592 journal: Nucleic Acids Res preferred: true title: 'GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology' year: '2014' - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.google.com/maps label: Google LLC creation_date: '2026-07-03T00:00:00Z' description: Google Reviews are user-contributed ratings and free-text reviews of places and organizations, surfaced through Google Maps and Google Business Profiles. Each review includes a review identifier, a star rating, review text, and author information associated with a named place or service. domains: - general - public health homepage_url: https://www.google.com/maps id: google-reviews last_modified_date: '2026-07-03T00:00:00Z' layout: resource_detail name: Google Reviews products: - category: GraphicalInterface description: User-contributed ratings and reviews of places and organizations, accessed through Google Maps. format: http id: google-reviews.site is_public: true name: Google Maps Reviews original_source: - relation_type: prov:hadPrimarySource source: google-reviews product_url: https://www.google.com/maps - category: GraphProduct description: DREAM-KG homelessness and social-services knowledge graph for the Philadelphia region, integrating social service directory records and provider reviews. Served via the DREAM-KG SPARQL and Triple Pattern Fragments endpoints. format: ttl id: dreamkg.graph is_public: true name: DREAM-KG Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: dreamkg - relation_type: prov:hadPrimarySource source: auntbertha - relation_type: prov:hadPrimarySource source: google-reviews product_url: https://dreamkg.com/ secondary_source: - relation_type: prov:wasInfluencedBy source: opendataphilly - 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: - biomedical 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: '2026-06-27T00:00:00Z' layout: resource_detail name: GP-KG products: - category: GraphProduct description: GP_KG.txt edge_count: 1246726 format: txt id: gp-kg.graph name: GP-KG node_count: 61146 original_source: - relation_type: prov:hadPrimarySource source: gp-kg - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: mgi - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: goa - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: umls - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: faers - relation_type: prov:wasDerivedFrom source: phenomebrowser - relation_type: prov:wasDerivedFrom source: treatkb product_file_size: 48397035 product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt - category: ProcessProduct description: A computational framework for drug repurposing, used with GP-KG id: gp-kg.process.kg-predict name: KG-Predict original_source: - relation_type: prov:hadPrimarySource source: gp-kg product_url: http://nlp.case.edu/public/data/GPKG-Predict/code/ publications: - authors: - Gao Z - Ding P - Xu R doi: 10.1016/j.jbi.2022.104133 id: doi:10.1016/j.jbi.2022.104133 journal: Journal of Biomedical Informatics 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 - 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 original_source: - relation_type: prov:hadPrimarySource source: greengenes 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 original_source: - relation_type: prov:hadPrimarySource source: greengenes product_url: http://ftp.microbio.me/greengenes_release/current/ - 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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. 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Requires UMLS API key to access. dump_format: neo4j format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - 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relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: epigraphdb - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: vectology - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: prsatlas - relation_type: prov:hadPrimarySource source: eqtlgen - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: cpic - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: mrbase product_url: https://docs.epigraphdb.org/graph-database/ - 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: - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: gtex product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 error when accessing file - category: GraphProduct description: Neo4j knowledge graph integrating transcription factor target libraries, coexpression networks, and benchmark datasets used by the ChEA3 resource dump_format: neo4j format: neo4j id: chea-kg.graph name: ChEA-KG Database original_source: - relation_type: prov:hadPrimarySource source: chea-kg - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: remap - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: geo - relation_type: prov:hadPrimarySource source: tcga secondary_source: - relation_type: prov:wasInfluencedBy source: chea - category: Product description: Download catalog for ChEA3 transcription factor target libraries, benchmark datasets, and additional supporting libraries format: http id: chea-kg.libraries name: ChEA-KG Library Downloads original_source: - relation_type: prov:hadPrimarySource source: chea-kg - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: remap - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: geo - relation_type: prov:hadPrimarySource source: tcga product_url: https://maayanlab.cloud/chea3/index.html#content4-13 secondary_source: - relation_type: prov:wasInfluencedBy source: chea - category: Product description: Download catalog for ChEA3 transcription factor target libraries and benchmark datasets format: http id: chea.libraries name: ChEA Library Downloads original_source: - relation_type: prov:hadPrimarySource source: chea - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: remap - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: geo - relation_type: prov:hadPrimarySource source: tcga product_url: https://maayanlab.cloud/chea3/index.html#content4-13 - category: GraphProduct description: GTEx expression anatomy nodes (GTEXEXP) used in ProKN format: csv id: prokn.gtexexp.anatomy.nodes name: ProKN GTEx Anatomy Nodes original_source: - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: prokn product_file_size: 6993 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_GTEXEXP.Anatomy.nodes.csv - category: GraphProduct description: GTEx gene expressed in anatomy edges format: csv id: prokn.gtexexp.gene.expressed_in.anatomy.edges name: ProKN GTEx Gene Expression Edges original_source: - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: prokn product_file_size: 341113044 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_GTEXEXP.Gene.EXPRESSED_IN.Anatomy.edges.csv - category: GraphProduct description: GTEx expression to anatomy edges (GTExEXP node type) format: csv id: prokn.gtexexp.gtexexp.expressed_in.anatomy.edges name: ProKN GTExEXP Anatomy Expression Edges original_source: - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: prokn product_file_size: 406384547 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_GTEXEXP.GTExEXP.EXPRESSED_IN.Anatomy.edges.csv - category: GraphProduct description: GTEx expression to gene edges (GTExEXP node type) format: csv id: prokn.gtexexp.gtexexp.expressed_in.gene.edges name: ProKN GTExEXP Gene Expression Edges original_source: - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: prokn product_file_size: 386708211 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_GTEXEXP.GTExEXP.EXPRESSED_IN.Gene.edges.csv - category: GraphProduct description: GTEx expression to expression bins edges format: csv id: prokn.gtexexp.gtexexp.has_expression.expbins.edges name: ProKN GTExEXP Expression Bin Edges original_source: - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: prokn product_file_size: 413542626 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_GTEXEXP.GTExEXP.HAS_EXPRESSION.EXPBINS.edges.csv - 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 original_source: - relation_type: prov:hadPrimarySource source: cfde-gse - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: motrpac - category: Product description: Standardized gene set collections from Common Fund programs in GMT format format: txt id: cfde-gse.genesets name: CFDE Gene Set Collections original_source: - relation_type: prov:hadPrimarySource source: cfde-gse - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: motrpac product_url: https://gse.cfde.cloud/downloads/ - category: GraphProduct description: Neo4j graph database integrating Enrichr gene set libraries with genes, terms, pathways, diseases, drugs, cell types, and other functional annotations dump_format: neo4j format: neo4j id: enrichr-kg.graph name: Enrichr-KG Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: enrichr-kg - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases product_file_size: 522141103 product_url: https://s3.amazonaws.com/maayan-kg/enrichr-kg/dumps/enrichr-kg-042123.dump - 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 original_source: - relation_type: prov:hadPrimarySource source: lncrnalyzr - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: doid product_url: https://github.com/MaayanLab/lncRNAlyzr - 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: - relation_type: prov:hadPrimarySource source: petagraph - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: lincs product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: tcrd product_url: https://unmtid-dbs.net/download/TCRD/ secondary_source: - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: gtex - relation_type: prov:wasInfluencedBy source: omim warnings: - File was not able to be retrieved when checked on 2026-03-30_ Timeout connecting to URL - category: ProgrammingInterface description: RESTful API providing programmatic access to TCRD data through Pharos for computational workflows and custom applications format: http id: tcrd.api is_public: true name: Pharos API original_source: - relation_type: prov:hadPrimarySource source: tcrd product_url: https://pharos.nih.gov/api secondary_source: - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: gtex - relation_type: prov:wasInfluencedBy source: omim - category: DocumentationProduct description: Comprehensive documentation describing TCRD data sources, schema structure, and usage guidelines format: http id: tcrd.documentation name: TCRD Documentation original_source: - relation_type: prov:hadPrimarySource source: tcrd product_url: https://unmtid-dbs.net/download/TCRD/ secondary_source: - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: gtex - relation_type: prov:wasInfluencedBy source: omim warnings: - File was not able to be retrieved when checked on 2026-03-30_ Timeout connecting to URL - category: GraphProduct description: GP-KG tab-delimited knowledge graph containing 1,246,726 associations between 61,146 entities from multiple genotypic and phenotypic databases format: tsv id: kg-predict.gpkg name: GP-KG Knowledge Graph Data original_source: - relation_type: prov:hadPrimarySource source: kg-predict product_file_size: 48397035 product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt secondary_source: - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: faers - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: mgi - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: string - relation_type: prov:wasDerivedFrom source: umls - category: Product description: Harmonizome 3.0 processed dataset downloads, including dataset-specific association files and knowledge graph serialization downloads. format: mixed id: harmonizome.downloads name: Harmonizome Downloads original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://maayanlab.cloud/Harmonizome/download secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - 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relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ - category: GraphProduct description: Core TF–target regulon knowledge graph (multi-species) with confidence levels (A–E) id: dorothea.graph name: DoRothEA Regulon Graph original_source: - 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relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: dbvar - relation_type: prov:hadPrimarySource source: endb - relation_type: prov:hadPrimarySource source: enhanceratlas - relation_type: prov:hadPrimarySource source: ccre - relation_type: prov:hadPrimarySource source: fire - relation_type: prov:hadPrimarySource source: motifmap product_url: https://available-inventions.umich.edu/product/genomickb-a-knowledgebase-for-the-human-genome - category: GraphProduct description: GP_KG.txt edge_count: 1246726 format: txt id: gp-kg.graph name: GP-KG node_count: 61146 original_source: - relation_type: prov:hadPrimarySource source: gp-kg - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: mgi - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: goa - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: umls - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: faers - relation_type: prov:wasDerivedFrom source: phenomebrowser - relation_type: prov:wasDerivedFrom source: treatkb product_file_size: 48397035 product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt - category: GraphProduct description: Statistically inferred genomic evidence graph connecting genes, gene sets, inferred disease mechanisms, and human phenotypes. Gene sets are derived from eleven NIH Common Fund programs (GlyGen, GTEx, IDG, IMPC/KOMP2, LINCS, MoTrPAC, Bridge2AI, HuBMAP, Metabolomics Workbench, SenNet, and SPARC) and phenotype-gene set relationships are computed with PIGEAN (Priors Inferred from GEne ANnotations). format: http id: digcfdekg.graph name: CFDE REVEAL Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: digcfdekg - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: impc - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: bridge2ai - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: sparc product_url: https://cfdeknowledge.org/r/cfde_reveal secondary_source: - relation_type: prov:wasInfluencedBy source: hubmap - category: GraphProduct description: Live TRAPI/BioThings metadata endpoint for the Multiomics BigGIM-DrugResponse KP, exposing the multiomics knowledge graph served by the Multiomics Provider (built from GTEx, TCGA, and drug-response data, with additional clinical-trials, drug-approval and knowledge-resource inputs). format: json id: multiomics-kp.graph name: Multiomics KP Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: multiomics-kp - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: tcga - relation_type: prov:hadPrimarySource source: gdsc - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: dailymed - relation_type: prov:hadPrimarySource source: faers product_url: https://biothings.transltr.io/biggim_drugresponse_kp/metadata secondary_source: - relation_type: prov:wasInfluencedBy source: aact - relation_type: prov:wasInfluencedBy source: biogrid - relation_type: prov:wasInfluencedBy source: huri - relation_type: prov:wasInfluencedBy source: cellmarker - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: ttd - relation_type: prov:wasInfluencedBy source: pubmed publications: - authors: - François Aguet - GTEx Consortium doi: 10.1126/science.aaz1776 id: doi:10.1126/science.aaz1776 journal: Science title: The GTEx Consortium atlas of genetic regulatory effects across human tissues year: '2020' - authors: - Kristin G. Ardlie - GTEx Consortium doi: 10.1126/science.1262110 id: doi:10.1126/science.1262110 journal: Science 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 - biomedical - drug discovery homepage_url: https://www.guidetopharmacology.org id: gtopdb infores_id: gtopdb last_modified_date: '2026-06-17T00:00:00Z' 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 format: http id: gtopdb.web name: Guide to Pharmacology Web Interface original_source: - relation_type: prov:hadPrimarySource source: gtopdb product_url: https://www.guidetopharmacology.org - category: ProgrammingInterface description: RESTful web services enabling computational access to most of the GtoPdb data in JSON format format: json id: gtopdb.api.rest name: Guide to Pharmacology REST API original_source: - relation_type: prov:hadPrimarySource source: gtopdb 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 original_source: - relation_type: prov:hadPrimarySource source: gtopdb product_url: https://www.guidetopharmacology.org/DATA/targets_and_families.csv warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: 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 original_source: - relation_type: prov:hadPrimarySource source: gtopdb product_url: https://www.guidetopharmacology.org/DATA/ligands.csv warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: 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 original_source: - relation_type: prov:hadPrimarySource source: gtopdb product_url: https://www.guidetopharmacology.org/DATA/interactions.csv warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: Product description: Detailed interactions list for approved drugs and their targets format: csv id: gtopdb.approved_drugs.csv name: GtoPdb Approved Drugs Dataset original_source: - relation_type: prov:hadPrimarySource source: gtopdb product_url: https://www.guidetopharmacology.org/DATA/approved_drug_detailed_interactions.csv warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - 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 original_source: - relation_type: prov:hadPrimarySource source: gtopdb product_url: https://www.guidetopharmacology.org/DATA/all_ligands.sdf warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: 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 original_source: - relation_type: prov:hadPrimarySource source: gtopdb product_url: https://www.guidetopharmacology.org/DATA/rdf/2025.1/gtp-rdf.n3 warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: Product description: Complete PostgreSQL database dump of the current Guide to Pharmacology database format: postgres id: gtopdb.database name: GtoPdb Full Database original_source: - relation_type: prov:hadPrimarySource source: gtopdb product_url: https://www.guidetopharmacology.org/DATA/public_iuphardb_v2025.1.zip warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: GraphicalInterface description: An extension of the Guide to PHARMACOLOGY database providing immunological access-point to GtoPdb data format: http id: gtopdb.immunopharmacology name: Guide to IMMUNOPHARMACOLOGY original_source: - relation_type: prov:hadPrimarySource source: gtopdb product_url: https://www.guidetopharmacology.org/immuno/index.jsp - category: GraphicalInterface description: A specialized portal providing optimized access for the malaria research community format: http id: gtopdb.malaria name: Guide to MALARIA PHARMACOLOGY original_source: - relation_type: prov:hadPrimarySource source: gtopdb 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: - 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relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - 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relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ publications: - authors: - Patricia P. Chan - Todd M. Lowe doi: 10.1093/nar/gkv1309 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 doi: 10.1093/nar/gkn787 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://biothings.ncats.io/gtrx label: NCATS Translator creation_date: '2025-11-05T00:00:00Z' description: Genome-to-Treatment (GTRx) is a NCATS Translator knowledge provider exposed through a BioThings API. It contains recommended acute treatments and interventions for seriously ill newborns, infants, and children with newly diagnosed genetic diseases, including therapeutics, dietary changes, surgery, medical devices, and other interventions. domains: - genomics - pharmacology - precision medicine - biomedical homepage_url: https://biothings.ncats.io/gtrx id: gtrx infores_id: gtrx last_modified_date: '2026-06-02T00:00:00Z' layout: resource_detail name: Genome-to-Treatment products: - category: ProgrammingInterface connection_url: https://biothings.ncats.io/gtrx/query description: BioThings API for querying Genome-to-Treatment association records through `/query`, `/metadata`, and related BioThings endpoints format: json id: gtrx.api infores_id: biothings-gtrx is_public: true latest_version: '2022-02-01' name: gTRx API original_source: - relation_type: prov:hadPrimarySource source: gtrx product_url: https://biothings.ncats.io/gtrx secondary_source: - relation_type: prov:wasDerivedFrom source: biothings - category: Product description: BioThings GTRx association collection built from Genome-to-Treatment source records; the 20220802 build reports 695 association records format: mixed id: gtrx.data latest_version: '20220802' name: gTRx Data original_source: - relation_type: prov:hadPrimarySource source: gtrx product_url: https://biothings.ncats.io/gtrx/metadata secondary_source: - relation_type: prov:wasInformedBy source: ncbigene - relation_type: prov:wasInformedBy source: mondo - relation_type: prov:wasInformedBy source: pubchem warnings: - The historical source website reported in the BioThings metadata, https://gtrx.rbsapp.net/about.html, returned HTTP 404 during curation on 2026-06-02. publications: - authors: - Mallory J. Owen - Sebastien Lefebvre - Christian Hansen - Chris M. Kunard - David P. Dimmock - Laurie D. Smith - Gunter Scharer - Rebecca Mardach doi: 10.1038/s41467-022-31446-6 id: doi:10.1038/s41467-022-31446-6 journal: Nature Communications preferred: true title: An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases year: '2022' repository: https://github.com/biothings/GTRx synonyms: - gTRx - 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: '2026-06-18T00:00:00Z' layout: resource_detail name: GutMGene products: - category: GraphicalInterface description: GutMGene data and interface format: http id: gutmgene.site name: GutMGene site original_source: - relation_type: prov:hadPrimarySource source: gutmgene product_url: http://bio-computing.hrbmu.edu.cn/gutmgene - category: ProcessProduct description: Code for generating MGMLink id: mgmlink.code name: MGMLink code original_source: - relation_type: prov:hadPrimarySource source: gutmgene - relation_type: prov:hadPrimarySource source: mgmlink - relation_type: prov:hadPrimarySource source: pheknowlator product_url: https://github.com/bsantan/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 journal: Nucleic Acids Research title: '''gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites''' year: '2022' - 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 journal: Nucleic Acids Research 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. 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relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://spoke.ucsf.edu/data-tools - 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. format: python id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: nihreporter - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: cellmarker - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: indra product_url: https://github.com/gyorilab/indra_cogex - 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: - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: clinicalkg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Graph database dump and additional relationship files for the Clinical Knowledge Graph. format: neo4j id: ckg.graph latest_version: '1' license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: CKG Graph Database Dump original_source: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: ckg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). format: http id: disgenet.data name: DisGeNET Data original_source: - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: mgd - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: psygenet - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: phewascat - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: finngen - relation_type: prov:hadPrimarySource source: clinicaltrialsgov product_url: https://www.disgenet.com/ - 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: - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: gwascatalog product_url: https://www.genecards.org/ warnings: - File was not able to be retrieved when checked on 2026-03-30_ HTTP 403 error when accessing file - category: GraphProduct description: Neo4j graph database integrating Enrichr gene set libraries with genes, terms, pathways, diseases, drugs, cell types, and other functional annotations dump_format: neo4j format: neo4j id: enrichr-kg.graph name: Enrichr-KG Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: enrichr-kg - relation_type: prov:hadPrimarySource source: enrichr - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: achilles - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: archs4 - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: kg-jensenlab-diseases product_file_size: 522141103 product_url: https://s3.amazonaws.com/maayan-kg/enrichr-kg/dumps/enrichr-kg-042123.dump - category: GraphicalInterface description: Graphical interface for MedKG format: http id: medkb.site name: MedKG Site original_source: - relation_type: prov:hadPrimarySource source: medkg - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: chebi - 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relation_type: prov:wasInformedBy source: omim - relation_type: prov:wasInformedBy source: pubchem - relation_type: prov:wasInformedBy source: uniprot - category: Product description: TSV export of MarkerDB genetic biomarkers with associated conditions. format: tsv id: markerdb.sequence_variants.tsv name: MarkerDB Genetic Biomarkers TSV original_source: - relation_type: prov:hadPrimarySource source: markerdb product_url: https://markerdb.ca/pages/download_all_sequence_variants?format=tsv secondary_source: - relation_type: prov:wasInformedBy source: dbsnp - relation_type: prov:wasInformedBy source: gwascatalog - relation_type: prov:wasInformedBy source: omim warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: Product compression: zip description: PheWAS association results for SNPs from GWAS Catalog analyzed against EMR-derived phenotypes format: csv id: phewascat.associations name: PheWAS Association Data original_source: - 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relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct description: Neo4j knowledge graph serialization of Harmonizome processed datasets, including genes, attributes, resources, datasets, and gene-attribute associations. dump_format: neo4j format: neo4j id: harmonizome.kg-neo4j latest_version: '3.0' name: Harmonizome Knowledge Graph Neo4j Database original_source: - 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relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - 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A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - 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relation_type: prov:hadPrimarySource source: cmap - relation_type: prov:hadPrimarySource source: kinomescan - relation_type: prov:hadPrimarySource source: dsstoxdb - relation_type: prov:hadPrimarySource source: gelinea - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv - category: GraphProduct description: The SPOKE-OKN knowledge graph, an OKN-hosted RDF publication of the SPOKE biomedical and environmental health knowledge graph, served through FRINK query services. format: ttl id: spoke-okn.graph name: SPOKE-OKN Graph original_source: - relation_type: prov:hadPrimarySource source: spoke-okn - relation_type: prov:wasDerivedFrom source: spoke product_url: https://spoke.ucsf.edu secondary_source: - relation_type: prov:wasInfluencedBy source: bgee - relation_type: prov:wasInfluencedBy source: bindingdb - relation_type: prov:wasInfluencedBy source: bv-brc - relation_type: prov:wasInfluencedBy source: chembl - relation_type: prov:wasInfluencedBy source: civic - relation_type: prov:wasInfluencedBy source: cl - relation_type: prov:wasInfluencedBy source: clinicaltrialsgov - relation_type: prov:wasInfluencedBy source: diseases - relation_type: prov:wasInfluencedBy source: doid - relation_type: prov:wasInfluencedBy source: drugbank - relation_type: prov:wasInfluencedBy source: drugcentral - relation_type: prov:wasInfluencedBy source: foodb - relation_type: prov:wasInfluencedBy source: gdsc - relation_type: prov:wasInfluencedBy source: go - relation_type: prov:wasInfluencedBy source: gwascatalog - relation_type: prov:wasInfluencedBy source: hpa - relation_type: prov:wasInfluencedBy source: interpro - relation_type: prov:wasInfluencedBy source: kegg - relation_type: prov:wasInfluencedBy source: lincs-l1000 - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: metacyc - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: ncbitaxon - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pathophenodb - relation_type: prov:wasInfluencedBy source: pfam - relation_type: prov:wasInfluencedBy source: pid - relation_type: prov:wasInfluencedBy source: protcid - relation_type: prov:wasInfluencedBy source: pubmed - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: sider - relation_type: prov:wasInfluencedBy source: string - relation_type: prov:wasInfluencedBy source: uberon - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikipathways publications: - authors: - Sollis E - Mosaku A - Abid A - Buniello A - Cerezo M - Gil L - Groza T - Güneş O - Hall P - Hayhurst J - Ibrahim A - Ji Y - John S - Lewis E - MacArthur JAL - McMahon A - Osumi-Sutherland D - Panoutsopoulou K - Pendlington Z - Ramachandran S - Stefancsik R - Stewart J - Whetzel P - Wilson R - Hindorff L - Cunningham F - Lambert SA - Inouye M - Parkinson H - Harris LW doi: 10.1093/nar/gkac1010 id: https://www.ncbi.nlm.nih.gov/pubmed/36350656 journal: Nucleic Acids Res preferred: true title: 'The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource' year: '2023' - activity_status: active category: KnowledgeGraph creation_date: '2026-04-06T00:00:00Z' description: HALD (Human Aging and Longevity Database) is a human aging and longevity knowledge graph generated from text-mined PubMed literature and organized around entities, relations, and biomarkers relevant to aging and longevity research. domains: - biomedical - literature - precision medicine homepage_url: https://bis.zju.edu.cn/hald id: hald last_modified_date: '2026-05-28T00:00:00Z' 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 Aging and Longevity Database products: - category: Product description: Version 6 JSON file containing literature metadata for the HALD corpus. format: json id: hald.literature-info.json latest_version: v6 name: HALD Literature Info original_source: - relation_type: prov:hadPrimarySource source: hald - relation_type: prov:hadPrimarySource source: pubmed product_file_size: 854292307 product_url: https://ndownloader.figshare.com/files/43612512 - category: Product description: Version 6 JSON file containing entity-level metadata extracted for HALD. format: json id: hald.entity-info.json latest_version: v6 name: HALD Entity Info original_source: - relation_type: prov:hadPrimarySource source: hald - relation_type: prov:hadPrimarySource source: pubmed product_file_size: 296732271 product_url: https://ndownloader.figshare.com/files/43612509 - category: GraphProduct description: Version 6 JSON file containing relation triples extracted for HALD. format: json id: hald.relation-info.json latest_version: v6 name: HALD Relation Info original_source: - relation_type: prov:hadPrimarySource source: hald - relation_type: prov:hadPrimarySource source: pubmed product_file_size: 98203237 product_url: https://ndownloader.figshare.com/files/43612506 - category: Product description: Version 6 JSON file containing aging biomarker records from HALD. format: json id: hald.aging-biomarkers.json latest_version: v6 name: HALD Aging Biomarkers original_source: - relation_type: prov:hadPrimarySource source: hald - relation_type: prov:hadPrimarySource source: pubmed product_file_size: 1199321 product_url: https://ndownloader.figshare.com/files/43612503 - category: Product description: Version 6 JSON file containing longevity biomarker records from HALD. format: json id: hald.longevity-biomarkers.json latest_version: v6 name: HALD Longevity Biomarkers original_source: - relation_type: prov:hadPrimarySource source: hald - relation_type: prov:hadPrimarySource source: pubmed product_file_size: 339386 product_url: https://ndownloader.figshare.com/files/43612497 - category: Product description: Version 6 CSV file containing entity rows for loading HALD into Neo4j. format: csv id: hald.entities.csv latest_version: v6 name: HALD Neo4j Entities original_source: - relation_type: prov:hadPrimarySource source: hald - relation_type: prov:hadPrimarySource source: pubmed product_file_size: 239792 product_url: https://ndownloader.figshare.com/files/43612494 - category: Product description: Version 6 CSV file containing relationship rows for loading HALD into Neo4j. format: csv id: hald.roles.csv latest_version: v6 name: HALD Neo4j Roles original_source: - relation_type: prov:hadPrimarySource source: hald - relation_type: prov:hadPrimarySource source: pubmed product_file_size: 5077672 product_url: https://ndownloader.figshare.com/files/43612500 - category: GraphicalInterface description: Interactive web interface for searching, browsing, and exploring HALD. format: http id: hald.browser name: HALD Web Interface original_source: - relation_type: prov:hadPrimarySource source: hald - relation_type: prov:hadPrimarySource source: pubmed product_url: https://bis.zju.edu.cn/hald publications: - authors: - Zexu Wu - Cong Feng - Yanshi Hu - Yincong Zhou - Sida Li - Shilong Zhang - Yueming Hu - Yuhao Chen - Haoyu Chao - Qingyang Ni - Ming Chen doi: 10.1038/s41597-023-02781-0 id: https://doi.org/10.1038/s41597-023-02781-0 journal: Scientific Data preferred: true title: HALD, a human aging and longevity knowledge graph for precision gerontology and geroscience analyses year: '2023' repository: https://github.com/zexuwu/hald taxon: - NCBITaxon:9606 - 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 - organisms homepage_url: https://ebispot.github.io/hancestro/ id: hancestro last_modified_date: '2026-06-05T00:00:00Z' 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 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 original_source: - relation_type: prov:hadPrimarySource source: 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 2026-07-10: HTTP 404 error when accessing file' - 'File was not able to be retrieved when checked on 2026-07-15: 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: - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: cob - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: ecto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: fbbt - relation_type: prov:hadPrimarySource source: fbdv - relation_type: prov:hadPrimarySource source: fma - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hancestro - 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relation_type: prov:hadPrimarySource source: omit - relation_type: prov:hadPrimarySource source: omo - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: po - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: semapv - relation_type: prov:hadPrimarySource source: skos - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: to - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wbls - relation_type: prov:hadPrimarySource source: zfa product_file_size: 64058275 product_url: https://www.ebi.ac.uk/efo/efo.obo publications: - authors: - Morales J - Welter D - Bowler EH - Cerezo M - Harris LW - McMahon AC - Hall P - Junkins HA - Milano A - Hastings E - Malangone C - Buniello A - Burdett T - Flicek P - Parkinson H - Cunningham F - Hindorff LA - MacArthur JAL doi: 10.1186/s13059-018-1396-2 id: https://www.ncbi.nlm.nih.gov/pubmed/29448949 journal: Genome Biol title: A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog year: '2018' 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: '2026-04-15T00:00:00Z' 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: Hymenoptera Anatomy Ontology products: - category: OntologyProduct description: Hymenoptera Anatomy Ontology in OWL format format: owl id: hao.owl name: hao.owl original_source: - relation_type: prov:hadPrimarySource source: hao 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 original_source: - relation_type: prov:hadPrimarySource source: hao 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 original_source: - relation_type: prov:hadPrimarySource source: hao product_file_size: 33370 product_url: http://purl.obolibrary.org/obo/hao/depictions.owl publications: - authors: - Yoder MJ - Mikó I - Seltmann KC - Bertone MA - Deans AR doi: 10.1371/journal.pone.0015991 id: https://www.ncbi.nlm.nih.gov/pubmed/21209921 journal: PLoS One title: A gross anatomy ontology for hymenoptera year: '2010' repository: https://github.com/hymao/hao taxon: - NCBITaxon:7399 - activity_status: active category: Aggregator 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: '2026-06-02T00:00:00Z' description: Harmonizome is an aggregator of processed gene and protein datasets from diverse online biomedical resources. 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relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways publications: - authors: - Ido Diamant - Daniel J B Clarke - John Erol Evangelista - Nathania Lingam - Avi Ma'ayan doi: 10.1093/nar/gkae1080 id: doi:10.1093/nar/gkae1080 journal: Nucleic Acids Research preferred: true title: 'Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources' year: '2025' - authors: - Rouillard AD - Gundersen GW - Fernandez NF - Wang Z - Monteiro CD - McDermott MG - Ma'ayan A doi: 10.1093/database/baw100 id: doi:10.1093/database/baw100 journal: Database preferred: false 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/HarmonizomePythonScripts taxon: - NCBITaxon:9606 - 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 - biological systems evaluation_page: resource/hetionet/hetionet_eval.html homepage_url: https://het.io/ id: hetionet infores_id: hetionet last_modified_date: '2026-06-22T00:00:00Z' 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: 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 original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 format: neo4j id: hetionet.data.neo4j name: Hetionet v1.0 Neo4j original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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) original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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) original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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: hetionet.hetnetpy name: hetnetpy original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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 original_source: - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: drugcentral 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: - relation_type: prov:hadPrimarySource source: alzkb - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dsstox - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hrpimp - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmacotherapydb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://alzkb.ai:7473/login secondary_source: - relation_type: prov:wasInfluencedBy source: hetionet - category: GraphProduct description: Memgraph data release for AlzKB. format: mixed id: alzkb.data name: AlzKB Data Release (Version 2.0.0) original_source: - relation_type: prov:hadPrimarySource source: alzkb - relation_type: prov:hadPrimarySource source: aop-db - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dsstox - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hrpimp - relation_type: prov:hadPrimarySource source: lincs-l1000 - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pharmacotherapydb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://github.com/EpistasisLab/AlzKB/releases/tag/v2.0.0 secondary_source: - relation_type: prov:wasInfluencedBy source: hetionet - description: The MechRepoNet knowledge graph in its original format format: mixed id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: complexportal - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: mechreponet - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: unii product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication - category: GraphProduct description: Hetio Automat format: kgx-jsonl id: automat.hetio name: hetio_automat original_source: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: hetionet product_url: https://stars.renci.org/var/plater/bl-4.2.1/Hetio_Automat/85a5f53e63150e1e/ - category: GraphProduct compression: targz description: DRKG graph files, including a TSV of triples, embeddings, ID mappings, and a glossary of relation types. format: mixed id: drkg.graph name: DRKG graph original_source: - relation_type: prov:hadPrimarySource source: drkg - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: gnbr - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: string product_file_size: 216650245 product_url: https://dgl-data.s3-us-west-2.amazonaws.com/dataset/DRKG/drkg.tar.gz - category: GraphProduct description: Data files for SynLethKG, the knowledge graph used by KG4SL and described as constructed from SynLethDB (v1.0/v2.0) and Hetionet. format: mixed id: kg4sl.synlethkg name: SynLethKG Data Files original_source: - relation_type: prov:hadPrimarySource source: kg4sl - relation_type: prov:hadPrimarySource source: synlethdb product_url: https://github.com/JieZheng-ShanghaiTech/KG4SL/tree/main/data secondary_source: - relation_type: prov:wasInfluencedBy source: hetionet - category: GraphProduct compression: gzip description: PharMeBINet V2 JSON release published on February 6, 2024. format: json id: pharmebinet.json latest_version: v2 name: PharMeBINet JSON Release original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 1942958027 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_24_02_06.json.gz/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct compression: zip description: PharMeBINet V2 TSV release published on February 6, 2024. format: tsv id: pharmebinet.tsv latest_version: v2 name: PharMeBINet TSV Release original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 1922614551 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_tsv_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct compression: zip description: PharMeBINet V2 GraphML release published on February 6, 2024. format: mixed id: pharmebinet.graphml latest_version: v2 name: PharMeBINet GraphML Release original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 2027519087 product_url: https://zenodo.org/api/records/17814889/files/PharMeBiNet_graphml_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - 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relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct compression: zip description: PharMeBINet V2 Neo4j database release published on February 6, 2024. format: neo4j id: pharmebinet.neo4j latest_version: v2 name: PharMeBINet Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 3847978577 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct compression: zip description: PharMeBINet V2 Neo4j dump release published on February 6, 2024. dump_format: neo4j format: neo4j id: pharmebinet.neo4j.dump latest_version: v2 name: PharMeBINet Neo4j Dump original_source: - relation_type: prov:hadPrimarySource source: pharmebinet product_file_size: 3598325722 product_url: https://zenodo.org/api/records/17814889/files/pharmebinet_dump_24_02_06.zip/content secondary_source: - relation_type: prov:wasDerivedFrom source: adrecs - relation_type: prov:wasDerivedFrom source: aelous - relation_type: prov:wasDerivedFrom source: atc - relation_type: prov:wasDerivedFrom source: bindingdb - relation_type: prov:wasDerivedFrom source: biogrid - relation_type: prov:wasDerivedFrom source: cl - relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways 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: 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: '2022' 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: '2026-06-18T00:00:00Z' 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: 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: - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 4253807 product_url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.obo - 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: - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 6489789 product_url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.owl.gz - 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: - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 4855839 product_url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.json.gz - 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: - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 1816550 product_url: https://w3id.org/biopragmatics/resources/hgnc/hgnc.sssom.tsv - 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: - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 185057 product_url: https://w3id.org/biopragmatics/resources/hgnc.genegroup/hgnc.genegroup.obo - 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: - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 231939 product_url: https://w3id.org/biopragmatics/resources/hgnc.genegroup/hgnc.genegroup.owl - 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: - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: obo-db-ingest product_file_size: 207059 product_url: https://w3id.org/biopragmatics/resources/hgnc.genegroup/hgnc.genegroup.json - 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: - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: scibite product_file_size: 8114434 product_url: https://raw.githubusercontent.com/elsevier-health/scibite-ontology/main/hgnc_2026-04-01.owl.zip repository: https://github.com/elsevier-health/scibite-ontology - category: MappingProduct description: MONDO SSSOM. Mappings from MONDO identifiers to other namespaces. format: sssom id: mondo.sssom name: MONDO SSSOM original_source: - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo product_file_size: 1437457 product_url: https://raw.githubusercontent.com/monarch-initiative/mondo/refs/heads/master/src/ontology/mappings/mondo.sssom.tsv - 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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.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: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: clinicalkg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: automat - relation_type: prov:hadPrimarySource source: hgnc product_url: https://stars.renci.org/var/plater/bl-4.2.1/HGNC_Automat/dee31cfce74e5944/ - 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: - relation_type: prov:hadPrimarySource source: bioportal - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: genemania - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pheknowlator - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vo 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 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: - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: hgnc product_file_size: 974440 product_url: https://www.omim.org/static/omim/data/mim2gene.txt - category: ProgrammingInterface description: Plover-hosted TRAPI web API for querying the Multiomics Microbiome knowledge graph format: http id: microbiomekg.api is_public: true name: MicrobiomeKG Plover TRAPI API original_source: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: eupathdb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: microbiomekg - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://multiomics.transltr.io/mbkp - category: GraphicalInterface description: Web portal for searching and browsing ncRNA sequences, structures, and annotations format: http id: rnacentral.portal name: RNAcentral Portal original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: crd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: ena - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: evlncrnas - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: greengenes - relation_type: prov:hadPrimarySource source: gtrnadb - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: lncbase - relation_type: prov:hadPrimarySource source: lncbook - relation_type: prov:hadPrimarySource source: lncipedia - relation_type: prov:hadPrimarySource source: lncrnadb - relation_type: prov:hadPrimarySource source: malacards - relation_type: prov:hadPrimarySource source: mgnify - relation_type: prov:hadPrimarySource source: mirbase - relation_type: prov:hadPrimarySource source: mirgenedb - relation_type: prov:hadPrimarySource source: modomics - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: pdbe - relation_type: prov:hadPrimarySource source: pirbase - relation_type: prov:hadPrimarySource source: plncdb - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: rdp - relation_type: prov:hadPrimarySource source: rediportal - relation_type: prov:hadPrimarySource source: rfam - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: ribocentre - relation_type: prov:hadPrimarySource source: ribovision - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: silva - relation_type: prov:hadPrimarySource source: snodb - relation_type: prov:hadPrimarySource source: snopy - 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NCBITaxon:9606 - activity_status: active category: DataSource contacts: - category: Organization contact_details: - contact_type: url value: https://www.dhs.gov/ label: U.S. Department of Homeland Security creation_date: '2026-06-18T00:00:00Z' description: Homeland Infrastructure Foundation-Level Data (HIFLD) is a U.S. Department of Homeland Security program that provides national geospatial datasets describing the location and attributes of critical infrastructure across the United States. 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relation_type: prov:wasDerivedFrom source: chebi - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: dbsnp - relation_type: prov:wasDerivedFrom source: ddinter - relation_type: prov:wasDerivedFrom source: doid - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: drugcentral - relation_type: prov:wasDerivedFrom source: efo - relation_type: prov:wasDerivedFrom source: fideo - relation_type: prov:wasDerivedFrom source: foodon - relation_type: prov:wasDerivedFrom source: gencc - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hetionet - relation_type: prov:wasDerivedFrom source: hgnc - relation_type: prov:wasDerivedFrom source: hippie - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: iid - relation_type: prov:wasDerivedFrom source: iptmnet - relation_type: prov:wasDerivedFrom source: markerdb - relation_type: prov:wasDerivedFrom source: med-rt - relation_type: prov:wasDerivedFrom source: mirbase - relation_type: prov:wasDerivedFrom source: mondo - relation_type: prov:wasDerivedFrom source: ncbigene - relation_type: prov:wasDerivedFrom source: ndfrt - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pharmgkb - relation_type: prov:wasDerivedFrom source: ptmd - relation_type: prov:wasDerivedFrom source: pubchem - relation_type: prov:wasDerivedFrom source: qptm - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: refseq - relation_type: prov:wasDerivedFrom source: rnadisease - relation_type: prov:wasDerivedFrom source: rnainter - relation_type: prov:wasDerivedFrom source: sider - relation_type: prov:wasDerivedFrom source: smpdb - relation_type: prov:wasDerivedFrom source: ttd - relation_type: prov:wasDerivedFrom source: uberon - relation_type: prov:wasDerivedFrom source: uniprot - relation_type: prov:wasDerivedFrom source: wikipathways publications: - authors: - Gregorio Alanis-Lobato - Miguel A. Andrade-Navarro - Martin H. Schaefer doi: 10.1093/nar/gkw985 id: doi:10.1093/nar/gkw985 journal: Nucleic Acids Research preferred: true title: 'HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks' year: '2017' synonyms: - HIPPIE - Human Integrated Protein-Protein Interaction rEference 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: - biomedical - chemistry and biochemistry homepage_url: https://www.hmdb.ca/ id: hmdb infores_id: hmdb last_modified_date: '2026-07-01T00:00:00Z' layout: resource_detail license: id: https://www.hmdb.ca/downloads label: HMDB Data Use (non-commercial without permission) name: Human Metabolome Database products: - 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relation_type: prov:hadPrimarySource source: pathwhiz product_url: https://pathbank.org/pathwhiz/pathways secondary_source: - relation_type: prov:wasInformedBy source: drugbank - relation_type: prov:wasInformedBy source: hmdb - relation_type: prov:wasInformedBy source: pathbank - category: Product description: Harmonizome 3.0 processed dataset downloads, including dataset-specific association files and knowledge graph serialization downloads. format: mixed id: harmonizome.downloads name: Harmonizome Downloads original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://maayanlab.cloud/Harmonizome/download secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphProduct description: Neo4j knowledge graph serialization of Harmonizome processed datasets, including genes, attributes, resources, datasets, and gene-attribute associations. dump_format: neo4j format: neo4j id: harmonizome.kg-neo4j latest_version: '3.0' name: Harmonizome Knowledge Graph Neo4j Database original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://harmonizome-kg.maayanlab.cloud/ secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom source: compartments - relation_type: prov:wasDerivedFrom source: corum - relation_type: prov:wasDerivedFrom source: cosmic - relation_type: prov:wasDerivedFrom source: ctd - relation_type: prov:wasDerivedFrom source: depmap - relation_type: prov:wasDerivedFrom source: diseases - relation_type: prov:wasDerivedFrom source: disgenet - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: encode - relation_type: prov:wasDerivedFrom source: gdsc - relation_type: prov:wasDerivedFrom source: geo - relation_type: prov:wasDerivedFrom source: glygen - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: gwascatalog - relation_type: prov:wasDerivedFrom source: hmdb - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: hpa - relation_type: prov:wasDerivedFrom source: hubmap - relation_type: prov:wasDerivedFrom source: impc - relation_type: prov:wasDerivedFrom source: interpro - relation_type: prov:wasDerivedFrom source: kegg - relation_type: prov:wasDerivedFrom source: lincs-l1000 - relation_type: prov:wasDerivedFrom source: mirtarbase - relation_type: prov:wasDerivedFrom source: motrpac - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: msigdb - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: panther - relation_type: prov:wasDerivedFrom source: pathwaycommons - relation_type: prov:wasDerivedFrom source: pfocr - relation_type: prov:wasDerivedFrom source: phosphositeplus - relation_type: prov:wasDerivedFrom source: pid - relation_type: prov:wasDerivedFrom source: reactome - relation_type: prov:wasDerivedFrom source: tcga - relation_type: prov:wasDerivedFrom source: tissues - relation_type: prov:wasDerivedFrom source: wikipathways - category: GraphicalInterface description: Web interface that allows searching, browsing, and exploring food compounds and their properties. format: http id: foodb.web name: FooDB Web Interface original_source: - relation_type: prov:hadPrimarySource source: foodb product_url: https://foodb.ca/ secondary_source: - relation_type: prov:wasInformedBy source: hmdb - relation_type: prov:wasInformedBy source: pubchem - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: kegg - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: pubmed - relation_type: prov:wasInformedBy source: itis - relation_type: prov:wasInformedBy source: wikipedia - relation_type: prov:wasInformedBy source: wikispecies - category: Product compression: targz description: Complete FooDB database in CSV format format: csv id: foodb.data.csv name: FooDB CSV Data original_source: - relation_type: prov:hadPrimarySource source: foodb product_file_size: 998314299 product_url: https://foodb.ca/public/system/downloads/foodb_2020_4_7_csv.tar.gz secondary_source: - relation_type: prov:wasInformedBy source: hmdb - relation_type: prov:wasInformedBy source: pubchem - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: kegg - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: pubmed - relation_type: prov:wasInformedBy source: itis - relation_type: prov:wasInformedBy source: wikipedia - relation_type: prov:wasInformedBy source: wikispecies - category: Product compression: targz description: Complete FooDB database in XML format format: xml id: foodb.data.xml name: FooDB XML Data original_source: - relation_type: prov:hadPrimarySource source: foodb product_file_size: 6731854848 product_url: https://foodb.ca/public/system/downloads/foodb_2020_4_7_xml.tar.gz secondary_source: - relation_type: prov:wasInformedBy source: hmdb - relation_type: prov:wasInformedBy source: pubchem - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: kegg - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: pubmed - relation_type: prov:wasInformedBy source: itis - relation_type: prov:wasInformedBy source: wikipedia - relation_type: prov:wasInformedBy source: wikispecies - category: Product compression: zip description: Complete FooDB database in JSON format format: json id: foodb.data.json name: FooDB JSON Data original_source: - relation_type: prov:hadPrimarySource source: foodb product_file_size: 90852659 product_url: https://foodb.ca/public/system/downloads/foodb_2020_04_07_json.zip secondary_source: - relation_type: prov:wasInformedBy source: hmdb - relation_type: prov:wasInformedBy source: pubchem - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: kegg - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: pubmed - relation_type: prov:wasInformedBy source: itis - relation_type: prov:wasInformedBy source: wikipedia - relation_type: prov:wasInformedBy source: wikispecies - category: Product compression: targz description: Complete FooDB database as MySQL dump format: mysql id: foodb.data.mysql name: FooDB MySQL Dump original_source: - relation_type: prov:hadPrimarySource source: foodb product_file_size: 180900659 product_url: https://foodb.ca/public/system/downloads/foodb_2020_4_7_mysql.tar.gz secondary_source: - relation_type: prov:wasInformedBy source: hmdb - relation_type: prov:wasInformedBy source: pubchem - relation_type: prov:wasInformedBy source: chebi - relation_type: prov:wasInformedBy source: kegg - relation_type: prov:wasInformedBy source: ncbitaxon - relation_type: prov:wasInformedBy source: pubmed - relation_type: prov:wasInformedBy source: itis - relation_type: prov:wasInformedBy source: wikipedia - relation_type: prov:wasInformedBy source: wikispecies - category: ProgrammingInterface description: REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases. format: http id: biobtree.api is_public: true name: BioBTree REST API original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot product_url: https://sugi.bio/biobtree/api/ - category: GraphicalInterface description: Web-based interface for searching and browsing comprehensive gene-centric information integrating data from over 200 sources format: http id: genecards.web.interface name: GeneCards Web Interface original_source: - relation_type: prov:hadPrimarySource source: 5srrnadb - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: aminode - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biocyc - relation_type: prov:hadPrimarySource source: biogps - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: bitterdb - relation_type: prov:hadPrimarySource source: cdd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: civic - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: compartments - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: craft - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: dbsuper - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: dgv - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: ena - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: epd - relation_type: prov:hadPrimarySource source: fabric - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: flybase - relation_type: prov:hadPrimarySource source: gard - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: genecards - relation_type: prov:hadPrimarySource source: geneorganizer - relation_type: prov:hadPrimarySource source: genomernai - relation_type: prov:hadPrimarySource source: glyconnect - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: gtrnadb - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: homologene - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hprd - relation_type: prov:hadPrimarySource source: humancyc - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: icd11 - relation_type: prov:hadPrimarySource source: iid - relation_type: prov:hadPrimarySource source: imgt - relation_type: prov:hadPrimarySource source: innatedb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: lncbase - relation_type: prov:hadPrimarySource source: lncbook - relation_type: prov:hadPrimarySource source: lncipedia - relation_type: prov:hadPrimarySource source: lncrnadisease - relation_type: prov:hadPrimarySource source: malacards - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: medlineplus - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mgi - relation_type: prov:hadPrimarySource source: mint - relation_type: prov:hadPrimarySource source: mirbase - relation_type: prov:hadPrimarySource source: mirgenedb - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: modomics - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncit - relation_type: prov:hadPrimarySource source: nextprot - relation_type: prov:hadPrimarySource source: noncode - relation_type: prov:hadPrimarySource source: omim - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: pathwaycommons - relation_type: prov:hadPrimarySource source: paxdb - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pdbe - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pid - relation_type: prov:hadPrimarySource source: pirsf - relation_type: prov:hadPrimarySource source: prosite - relation_type: prov:hadPrimarySource source: proteomicsdb - relation_type: prov:hadPrimarySource source: proteopedia - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: pubtator - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rfam - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: scop - relation_type: prov:hadPrimarySource source: sfld - relation_type: prov:hadPrimarySource source: sgd - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: silva - relation_type: prov:hadPrimarySource source: simap - relation_type: prov:hadPrimarySource source: smart - relation_type: prov:hadPrimarySource source: snodb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: snopy - relation_type: prov:hadPrimarySource source: srpdb - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tair - relation_type: prov:hadPrimarySource source: tarbase - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: treefam - relation_type: prov:hadPrimarySource source: ttd - relation_type: prov:hadPrimarySource source: ucnebase - relation_type: prov:hadPrimarySource source: ucsc - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vista - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: wikipedia - relation_type: prov:hadPrimarySource source: wormbase product_url: https://www.genecards.org/ - category: GraphProduct compatibility: - standard: biolink version: 4.2.1 compression: gzip description: Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo. edge_count: 132075627 format: kgx id: biobtree.graph.human-subgraph license: id: https://creativecommons.org/licenses/by-nc-sa/4.0/ label: CC-BY-NC-SA-4.0 name: BioBTree Knowledge Graph - Human Subgraph (KGX) node_categories: - biolink:BiologicalProcess - biolink:Cell - biolink:CellLine - biolink:CellularComponent - biolink:CodingSequence - biolink:Disease - biolink:DiseaseOrPhenotypicFeature - biolink:Drug - biolink:Exon - biolink:Gene - biolink:GrossAnatomicalStructure - biolink:MacromolecularComplex - biolink:MolecularActivity - biolink:NoncodingRNAProduct - biolink:NucleicAcidSequenceMotif - biolink:OrganismTaxon - biolink:Pathway - biolink:PhenotypicFeature - biolink:Protein - biolink:ProteinDomain - biolink:ProteinFamily - biolink:Publication - biolink:RegulatoryRegion - biolink:SequenceVariant - biolink:SmallMolecule - biolink:Transcript node_count: 40160474 original_source: - relation_type: prov:hadPrimarySource source: biobtree - relation_type: prov:hadPrimarySource source: alphafold - relation_type: prov:hadPrimarySource source: alphamissense - relation_type: prov:hadPrimarySource source: bao - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: brenda - relation_type: prov:hadPrimarySource source: cellphonedb - relation_type: prov:hadPrimarySource source: cellxgene - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: collectri - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: eco - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: encode - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: expressionatlas - relation_type: prov:hadPrimarySource source: fantom5 - relation_type: prov:hadPrimarySource source: gencc - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: lipidmaps - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: mirdb - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: pdb - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: rhea - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: surechembl - relation_type: prov:hadPrimarySource source: swisslipid - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot predicates: - biolink:actively_involved_in - biolink:affects - biolink:associated_with - biolink:close_match - biolink:derives_from - biolink:directly_physically_interacts_with - biolink:enables - biolink:expressed_in - biolink:gene_associated_with_condition - biolink:gene_product_of - biolink:has_adverse_event - biolink:has_gene_product - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:in_clinical_trials_for - biolink:in_taxon - biolink:interacts_with - biolink:is_sequence_variant_of - biolink:located_in - biolink:member_of - biolink:mentions - biolink:orthologous_to - biolink:paralogous_to - biolink:participates_in - biolink:physically_interacts_with - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:transcribed_from - biolink:translates_to - biolink:treats_or_applied_or_studied_to_treat product_url: https://zenodo.org/records/20816742 - 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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: bigg - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: ctrp - relation_type: prov:hadPrimarySource source: cmap - relation_type: prov:hadPrimarySource source: kinomescan - relation_type: prov:hadPrimarySource source: dsstoxdb - relation_type: prov:hadPrimarySource source: gelinea - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 3676906360 product_url: https://molepro.s3.amazonaws.com/nodes.tsv - 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: - relation_type: prov:hadPrimarySource source: molecular-data-kp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: pharos - relation_type: prov:hadPrimarySource source: tcrd - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: rxnorm - relation_type: prov:hadPrimarySource source: pharmgkb - relation_type: prov:hadPrimarySource source: bigg - relation_type: prov:hadPrimarySource source: depmap - relation_type: prov:hadPrimarySource source: ctrp - relation_type: prov:hadPrimarySource source: cmap - relation_type: prov:hadPrimarySource source: kinomescan - relation_type: prov:hadPrimarySource source: dsstoxdb - relation_type: prov:hadPrimarySource source: gelinea - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: drugrephub - relation_type: prov:hadPrimarySource source: chembank - relation_type: prov:hadPrimarySource source: inxight-drugs - relation_type: prov:hadPrimarySource source: probe-miner product_file_size: 20140191116 product_url: https://molepro.s3.amazonaws.com/edges.tsv - category: Product compression: gzip description: PubChem substance information in ASN.1 format format: xml id: pubchem.substances.asn name: PubChem Substances ASN original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/ASN/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways - category: Product compression: gzip description: PubChem substance information in SDF format format: sdf id: pubchem.substances.sdf name: PubChem Substances SDF original_source: - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: glygen - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: lipidmaps product_url: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/ secondary_source: - relation_type: prov:wasInfluencedBy source: clinvar - relation_type: prov:wasInfluencedBy source: dbsnp - relation_type: prov:wasInfluencedBy source: dgidb - relation_type: prov:wasInfluencedBy source: mesh - relation_type: prov:wasInfluencedBy source: ncbigene - relation_type: prov:wasInfluencedBy source: omim - relation_type: prov:wasInfluencedBy source: pharmgkb - relation_type: prov:wasInfluencedBy source: reactome - relation_type: prov:wasInfluencedBy source: unichem - relation_type: prov:wasInfluencedBy source: uniprot - relation_type: prov:wasInfluencedBy source: wikidata - relation_type: prov:wasInfluencedBy source: wikipathways publications: - authors: - Wishart DS - Guo A - Oler E - Wang F - Anjum A - Peters H - Dizon R - Sayeeda Z - Tian S - Lee BL - Berjanskii M - Mah R - Yamamoto M - Jovel J - Torres-Calzada C - Hiebert-Giesbrecht M - Lui VW - Varshavi D - Varshavi D - Allen D - Arndt D - Khetarpal N - Sivakumaran A - Harford K - Sanford S - Yee K - Cao X - Budinski Z - Liigand J - Zhang L - Zheng J - Mandal R - Karu N - Dambrova M - Schiöth HB - Greiner R - Gautam V doi: 10.1093/nar/gkab1062 id: https://pubmed.ncbi.nlm.nih.gov/34986597 journal: Nucleic Acids Res preferred: true title: 'HMDB 5.0: the Human Metabolome Database for 2022' year: '2022' taxon: - NCBITaxon:9606 - activity_status: active category: DataSource creation_date: '2026-06-18T00:00:00Z' description: HOCOMOCO (HOmo sapiens COmprehensive MOdel COllection) is a curated database of transcription factor (TF) binding models, primarily position weight matrices (PWMs), for human and mouse. The models are derived from large-scale ChIP-Seq and HT-SELEX experiments and are manually curated, benchmarked, and annotated with quality ratings and recommended score thresholds. HOCOMOCO covers over a thousand human and mouse TFs, including secondary motif subtypes, and is a widely used upstream source for downstream regulatory resources such as DoRothEA. domains: - genomics - systems biology - proteomics homepage_url: https://hocomoco.autosome.org id: hocomoco last_modified_date: '2026-06-18T00:00:00Z' layout: resource_detail license: id: http://www.wtfpl.net/ label: WTFPL name: HOCOMOCO products: - category: Product description: HOCOMOCO v11 core collection human mononucleotide PWMs (flat text) format: txt id: hocomoco.core-pwms name: HOCOMOCO v11 Core Human Mononucleotide PWMs original_source: - relation_type: prov:hadPrimarySource source: hocomoco product_url: https://hocomoco11.autosome.org/final_bundle/hocomoco11/core/HUMAN/mono/HOCOMOCOv11_core_pwms_HUMAN_mono.txt warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: Product description: HOCOMOCO v11 full collection human mononucleotide PWMs (flat text), including secondary motif subtypes format: txt id: hocomoco.full-pwms name: HOCOMOCO v11 Full Human Mononucleotide PWMs original_source: - relation_type: prov:hadPrimarySource source: hocomoco product_url: https://hocomoco11.autosome.org/final_bundle/hocomoco11/full/HUMAN/mono/HOCOMOCOv11_full_pwms_HUMAN_mono.txt warnings: - 'File was not able to be retrieved when checked on 2026-07-10: No Content-Length header found' - 'File was not able to be retrieved when checked on 2026-07-15: No Content-Length header found' - category: Product description: HOCOMOCO download portal with PWM/PCM models for human and mouse in multiple formats (JASPAR, MEME, TRANSFAC, HOMER) plus annotations and thresholds format: http id: hocomoco.downloads name: HOCOMOCO Downloads original_source: - relation_type: prov:hadPrimarySource source: hocomoco product_url: https://hocomoco14.autosome.org/downloads_v11 - category: GraphProduct description: Core TF–target regulon knowledge graph (multi-species) with confidence levels (A–E) id: dorothea.graph name: DoRothEA Regulon Graph original_source: - relation_type: prov:hadPrimarySource source: dorothea - relation_type: prov:hadPrimarySource source: remap - relation_type: prov:hadPrimarySource source: jaspar - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hocomoco - relation_type: prov:hadPrimarySource source: oreganno - relation_type: prov:hadPrimarySource source: trrust - relation_type: prov:hadPrimarySource source: tfacts - relation_type: prov:hadPrimarySource source: tred product_url: https://github.com/saezlab/dorothea/releases/tag/v1.0.0 publications: - authors: - Ivan V. Kulakovskiy - Ilya E. Vorontsov - Ivan S. Yevshin - Ruslan N. Sharipov - Alla D. Fedorova - Eugene I. Rumynskiy - Yulia A. Medvedeva - Arturo Magana-Mora - Vladimir B. Bajic - Dmitry A. Papatsenko - Fedor A. Kolpakov - Vsevolod J. Makeev doi: 10.1093/nar/gkx1106 id: https://www.ncbi.nlm.nih.gov/pubmed/29140464 journal: Nucleic Acids Res preferred: true title: 'HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis' year: '2018' - 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: '2026-04-15T00:00:00Z' 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: Homology Ontology products: - category: OntologyProduct description: Homology Ontology in OWL format format: owl id: hom.owl name: hom.owl original_source: - relation_type: prov:hadPrimarySource source: hom product_file_size: 9398 product_url: http://purl.obolibrary.org/obo/hom.owl publications: - authors: - Julien Roux - Marc Robinson-Rechavi doi: 10.1016/j.tig.2009.12.012 id: https://doi.org/10.1016/j.tig.2009.12.012 journal: Trends in Genetics title: An ontology to clarify homology-related concepts year: '2010' 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 - category: Organization contact_details: - contact_type: url value: https://monarchinitiative.org/ id: monarchinitiative label: Monarch Initiative 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 - phenotype homepage_url: http://www.human-phenotype-ontology.org/ id: hp infores_id: hpo last_modified_date: '2026-06-22T00:00:00Z' 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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) original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp 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 original_source: - relation_type: prov:hadPrimarySource source: hp product_file_size: 20533481 product_url: http://purl.obolibrary.org/obo/hp/genes_to_phenotype.txt - category: GraphProduct description: HPO gene-to-phenotype association edges format: csv id: prokn.hgnchpo.gene.associated_with.diseaseorphenotype.edges name: ProKN HPO Gene-to-Phenotype Association Edges original_source: - relation_type: prov:hadPrimarySource source: hp.genes_to_phenotype.txt - relation_type: prov:hadPrimarySource source: prokn product_file_size: 155778514 product_url: https://research.bioinformatics.udel.edu/prokn_dp/downloads/current/DDKG_HGNCHPO.Gene.ASSOCIATED_WITH.DiseaseOrPhenotype.edges.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 format: neo4j id: ubkg.neo4j name: UBKG Neo4j Docker Distribution original_source: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - 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: - relation_type: prov:hadPrimarySource source: 4dn - relation_type: prov:hadPrimarySource source: biomarker - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: connectivitymap - relation_type: prov:hadPrimarySource source: dct - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: edam - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: erccrbp - relation_type: prov:hadPrimarySource source: erccreg - relation_type: prov:hadPrimarySource source: faldo - relation_type: prov:hadPrimarySource source: gencode - relation_type: prov:hadPrimarySource source: glycocoo - relation_type: prov:hadPrimarySource source: glycordf - relation_type: prov:hadPrimarySource source: gtex - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hra - relation_type: prov:hadPrimarySource source: hsapdv - relation_type: prov:hadPrimarySource source: hubmap - relation_type: prov:hadPrimarySource source: icd10 - relation_type: prov:hadPrimarySource source: kidsfirst - relation_type: prov:hadPrimarySource source: lincs - relation_type: prov:hadPrimarySource source: loinc - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: motrpac - relation_type: prov:hadPrimarySource source: mp - relation_type: prov:hadPrimarySource source: msigdb - relation_type: prov:hadPrimarySource source: mw - relation_type: prov:hadPrimarySource source: npo - relation_type: prov:hadPrimarySource source: obi - relation_type: prov:hadPrimarySource source: obib - relation_type: prov:hadPrimarySource source: opentargets - relation_type: prov:hadPrimarySource source: ordo - relation_type: prov:hadPrimarySource source: pato - relation_type: prov:hadPrimarySource source: pgo - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: sbo - relation_type: prov:hadPrimarySource source: sckan - relation_type: prov:hadPrimarySource source: sennet - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stellar - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ubkg - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo - relation_type: prov:hadPrimarySource source: wikipathways product_url: https://ubkg-downloads.xconsortia.org/ - category: GraphProduct description: KGX Distribution of KG-Monarch edge_count: 15211571 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: 1462594 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: 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:affects - biolink:applied_to_treat - biolink:associated_with_increased_likelihood_of - biolink:capable_of - biolink:caused_by - biolink:causes - biolink:coexists_with - biolink:colocalizes_with - biolink:contributes_to - biolink:correlated_with - biolink:derives_from - biolink:develops_from - biolink:directly_physically_interacts_with - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:expresses - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_adverse_event - biolink:has_disease - biolink:has_gene - biolink:has_input - biolink:has_mode_of_inheritance - biolink:has_output - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:in_taxon - biolink:interacts_with - biolink:is_active_in - biolink:is_input_of - biolink:is_output_of - biolink:is_sequence_variant_of - biolink:located_in - biolink:location_of - biolink:model_of - biolink:occurs_in - biolink:orthologous_to - biolink:overlaps - biolink:part_of - biolink:participates_in - biolink:preceded_by - biolink:precedes - biolink:produced_by - biolink:produces - biolink:regulates - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:temporally_related_to - biolink:treats - 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 - category: GraphProduct description: KGX JSON-Lines Distribution of KG-Monarch edge_count: 15211571 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: 1462594 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: 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:affects - biolink:applied_to_treat - biolink:associated_with_increased_likelihood_of - biolink:capable_of - biolink:caused_by - biolink:causes - biolink:coexists_with - biolink:colocalizes_with - biolink:contributes_to - biolink:correlated_with - biolink:derives_from - biolink:develops_from - biolink:directly_physically_interacts_with - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:expresses - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_adverse_event - biolink:has_disease - biolink:has_gene - biolink:has_input - biolink:has_mode_of_inheritance - biolink:has_output - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:in_taxon - biolink:interacts_with - biolink:is_active_in - biolink:is_input_of - biolink:is_output_of - biolink:is_sequence_variant_of - biolink:located_in - biolink:location_of - biolink:model_of - biolink:occurs_in - biolink:orthologous_to - biolink:overlaps - biolink:part_of - biolink:participates_in - biolink:preceded_by - biolink:precedes - biolink:produced_by - biolink:produces - biolink:regulates - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:temporally_related_to - biolink:treats - 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 - category: GraphProduct description: RDF Distribution of KG-Monarch edge_count: 15211571 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: 1462594 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: 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:affects - biolink:applied_to_treat - biolink:associated_with_increased_likelihood_of - biolink:capable_of - biolink:caused_by - biolink:causes - biolink:coexists_with - biolink:colocalizes_with - biolink:contributes_to - biolink:correlated_with - biolink:derives_from - biolink:develops_from - biolink:directly_physically_interacts_with - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:expresses - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_adverse_event - biolink:has_disease - biolink:has_gene - biolink:has_input - biolink:has_mode_of_inheritance - biolink:has_output - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:in_taxon - biolink:interacts_with - biolink:is_active_in - biolink:is_input_of - biolink:is_output_of - biolink:is_sequence_variant_of - biolink:located_in - biolink:location_of - biolink:model_of - biolink:occurs_in - biolink:orthologous_to - biolink:overlaps - biolink:part_of - biolink:participates_in - biolink:preceded_by - biolink:precedes - biolink:produced_by - biolink:produces - biolink:regulates - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:temporally_related_to - biolink:treats - 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 - category: GraphProduct description: Neo4j Dump of KG-Monarch dump_format: neo4j edge_count: 15211571 format: neo4j 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: 1462594 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: 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:affects - biolink:applied_to_treat - biolink:associated_with_increased_likelihood_of - biolink:capable_of - biolink:caused_by - biolink:causes - biolink:coexists_with - biolink:colocalizes_with - biolink:contributes_to - biolink:correlated_with - biolink:derives_from - biolink:develops_from - biolink:directly_physically_interacts_with - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:expresses - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_adverse_event - biolink:has_disease - biolink:has_gene - biolink:has_input - biolink:has_mode_of_inheritance - biolink:has_output - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:in_taxon - biolink:interacts_with - biolink:is_active_in - biolink:is_input_of - biolink:is_output_of - biolink:is_sequence_variant_of - biolink:located_in - biolink:location_of - biolink:model_of - biolink:occurs_in - biolink:orthologous_to - biolink:overlaps - biolink:part_of - biolink:participates_in - biolink:preceded_by - biolink:precedes - biolink:produced_by - biolink:produces - biolink:regulates - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:temporally_related_to - biolink:treats - 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 warnings: [] - category: GraphProduct description: DuckDB database of KG-Monarch edge_count: 15211571 format: mixed 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: 1462594 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: 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:affects - biolink:applied_to_treat - biolink:associated_with_increased_likelihood_of - biolink:capable_of - biolink:caused_by - biolink:causes - biolink:coexists_with - biolink:colocalizes_with - biolink:contributes_to - biolink:correlated_with - biolink:derives_from - biolink:develops_from - biolink:directly_physically_interacts_with - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:expresses - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_adverse_event - biolink:has_disease - biolink:has_gene - biolink:has_input - biolink:has_mode_of_inheritance - biolink:has_output - biolink:has_part - biolink:has_participant - biolink:has_phenotype - biolink:has_sequence_variant - biolink:homologous_to - biolink:in_taxon - biolink:interacts_with - biolink:is_active_in - biolink:is_input_of - biolink:is_output_of - biolink:is_sequence_variant_of - biolink:located_in - biolink:location_of - biolink:model_of - biolink:occurs_in - biolink:orthologous_to - biolink:overlaps - biolink:part_of - biolink:participates_in - biolink:preceded_by - biolink:precedes - biolink:produced_by - biolink:produces - biolink:regulates - biolink:related_to - biolink:same_as - biolink:subclass_of - biolink:temporally_related_to - biolink:treats - biolink:treats_or_applied_or_studied_to_treat product_file_size: 6827814912 product_url: https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.duckdb - category: GraphProduct compression: targz description: KGX JSON-Lines Distribution of KG-Monarch (Edges) edge_count: 15211571 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: 1462594 original_source: - relation_type: prov:hadPrimarySource source: alliance - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: dictybase - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: kg-monarch - relation_type: prov:hadPrimarySource source: maxo - relation_type: prov:hadPrimarySource source: panther - relation_type: prov:hadPrimarySource source: phenio - relation_type: prov:hadPrimarySource source: pombase - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: xenbase - relation_type: prov:hadPrimarySource source: 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:affects - biolink:applied_to_treat - biolink:associated_with_increased_likelihood_of - biolink:capable_of - biolink:caused_by - biolink:causes - biolink:coexists_with - biolink:colocalizes_with - biolink:contributes_to - biolink:correlated_with - biolink:derives_from - biolink:develops_from - biolink:directly_physically_interacts_with - biolink:disease_has_location - biolink:disrupts - biolink:enables - biolink:expressed_in - biolink:expresses - biolink:gene_associated_with_condition - biolink:genetically_associated_with - biolink:has_adverse_event - biolink:has_disease - biolink:has_gene - biolink:has_input - biolink:has_mode_of_inheritance - biolink:has_output - biolink:has_part - biolink:has_participant - biolink:has_phenotype - 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category: GraphProduct description: Full unfiltered UniBioMap predicted graph edges file. format: csv id: unibiomap.pred.full name: UniBioMap Predicted Graph (Full) original_source: - relation_type: prov:hadPrimarySource source: unibiomap - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bindingdb - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: tcdb - relation_type: prov:hadPrimarySource source: biogrid - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: unichem - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: batman - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: compath - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: inchikey - relation_type: prov:hadPrimarySource source: 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. format: python id: indra.cogex.code name: INDRA CoGEx Build Code original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: wikipathways - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: nihreporter - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: pubmed - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: cellmarker - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: bgee - relation_type: prov:hadPrimarySource source: ccle - relation_type: prov:hadPrimarySource source: clinicaltrialsgov - relation_type: prov:hadPrimarySource source: indra product_url: https://github.com/gyorilab/indra_cogex - description: The MechRepoNet knowledge graph in its original format format: mixed id: mechreponet.kg name: MechRepoNet Knowledge Graph original_source: - relation_type: prov:hadPrimarySource source: biolink - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: complexportal - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hetionet - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: interpro - relation_type: prov:hadPrimarySource source: mechreponet - relation_type: prov:hadPrimarySource source: mirtarbase - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: unii product_url: https://github.com/SuLab/MechRepoNet/releases/tag/publication - 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: - relation_type: prov:hadPrimarySource source: bioportal - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: ctd - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: genemania - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: medgen - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pheknowlator - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: ro - relation_type: prov:hadPrimarySource source: so - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: vo 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 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: - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: clinicalkg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: uo product_url: https://data.mendeley.com/datasets/mrcf7f4tc2/1 - category: GraphProduct description: Graph database dump and additional relationship files for the Clinical Knowledge Graph. format: neo4j id: ckg.graph latest_version: '1' license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 name: CKG Graph Database Dump original_source: - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: cancer-genome-interpreter - relation_type: prov:hadPrimarySource source: ckg - relation_type: prov:hadPrimarySource source: corum - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: diseases - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: foodb - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: hgnc - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: hpa - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: mi - relation_type: prov:hadPrimarySource source: mod - relation_type: prov:hadPrimarySource source: ms - relation_type: prov:hadPrimarySource source: mutationds - relation_type: prov:hadPrimarySource source: oncokb - relation_type: prov:hadPrimarySource source: pfam - relation_type: prov:hadPrimarySource source: phosphositeplus - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: refseq - relation_type: prov:hadPrimarySource source: sider - relation_type: prov:hadPrimarySource source: signor - relation_type: prov:hadPrimarySource source: smpdb - relation_type: prov:hadPrimarySource source: snomedct - relation_type: prov:hadPrimarySource source: stitch - relation_type: prov:hadPrimarySource source: string - relation_type: prov:hadPrimarySource source: tissues - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - 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: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb 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 - category: ProgrammingInterface description: Neo4j distribution of the RTX-KG2 as a graph database dump_format: neo4j format: http id: rtx-kg2.neo4j is_neo4j: true is_public: false name: RTX-KG2 Neo4j original_source: - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: drugbank - relation_type: prov:hadPrimarySource source: kegg - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: drugcentral - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: ncbitaxon - relation_type: prov:hadPrimarySource source: dgidb - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: gtopdb - relation_type: prov:hadPrimarySource source: rtx-kg2 - relation_type: prov:hadPrimarySource source: semmeddb - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: intact - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: smpdb product_url: https://arax.ncats.io/ - 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: - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: icees-kg product_url: https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/1.5.0/ - 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: - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: translator product_url: https://robokop.renci.org/api-docs/docs/automat/icees-kg-trapi - 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: - relation_type: prov:hadPrimarySource source: mesh - relation_type: prov:hadPrimarySource source: pubchem - relation_type: prov:hadPrimarySource source: chembl - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: umls - relation_type: prov:hadPrimarySource source: hmdb - relation_type: prov:hadPrimarySource source: icees-kg - relation_type: prov:hadPrimarySource source: translator product_url: https://robokop.renci.org/api-docs/docs/automat/metadata-metadata-get-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: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: circbase - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rna-kg - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: vo - relation_type: prov:hadPrimarySource source: wikipathways product_file_size: 3976840239 product_url: https://rna-kg.biodata.di.unimi.it/rnakgv20.dump - category: GraphProduct description: RNA-KG Nodes in CSV format format: csv id: rna-kg.kg.nodes name: RNA-KG Nodes original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: circbase - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rna-kg - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: vo - relation_type: prov:hadPrimarySource source: wikipathways product_file_size: 4424633304 product_url: https://rna-kg.biodata.di.unimi.it/nodes.csv - category: GraphProduct description: RNA-KG Edges in CSV format format: csv id: rna-kg.kg.edges name: RNA-KG Edges original_source: - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: circbase - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: cosmic - relation_type: prov:hadPrimarySource source: dbsnp - relation_type: prov:hadPrimarySource source: ensembl - relation_type: prov:hadPrimarySource source: go - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: mondo - relation_type: prov:hadPrimarySource source: ncbigene - relation_type: prov:hadPrimarySource source: pr - relation_type: prov:hadPrimarySource source: pw - relation_type: prov:hadPrimarySource source: reactome - relation_type: prov:hadPrimarySource source: rna-kg - relation_type: prov:hadPrimarySource source: rnacentral - relation_type: prov:hadPrimarySource source: uberon - relation_type: prov:hadPrimarySource source: vo - relation_type: prov:hadPrimarySource source: wikipathways product_file_size: 18370248815 product_url: https://rna-kg.biodata.di.unimi.it/edges.csv - category: GraphProduct description: DisGeNET data, including gene to disease associations and variant to disease associations (requires registration and subscription). format: http id: disgenet.data name: DisGeNET Data original_source: - relation_type: prov:hadPrimarySource source: clingen - relation_type: prov:hadPrimarySource source: clinvar - relation_type: prov:hadPrimarySource source: mgd - relation_type: prov:hadPrimarySource source: rgd - relation_type: prov:hadPrimarySource source: orphanet - relation_type: prov:hadPrimarySource source: psygenet - relation_type: prov:hadPrimarySource source: uniprot - relation_type: prov:hadPrimarySource source: disgenet - relation_type: prov:hadPrimarySource source: hp - relation_type: prov:hadPrimarySource source: gwascatalog - relation_type: prov:hadPrimarySource source: phewascat - relation_type: prov:hadPrimarySource source: ukbiobank - relation_type: prov:hadPrimarySource source: finngen - relation_type: prov:hadPrimarySource source: clinicaltrialsgov product_url: https://www.disgenet.com/ - category: OntologyProduct description: The latest release of EFO in OWL format format: owl id: efo.owl name: EFO OWL original_source: - relation_type: prov:hadPrimarySource source: bfo - relation_type: prov:hadPrimarySource source: bto - relation_type: prov:hadPrimarySource source: chebi - relation_type: prov:hadPrimarySource source: cl - relation_type: prov:hadPrimarySource source: clo - relation_type: prov:hadPrimarySource source: cob - relation_type: prov:hadPrimarySource source: dc - relation_type: prov:hadPrimarySource source: doid - relation_type: prov:hadPrimarySource source: ecto - relation_type: prov:hadPrimarySource source: efo - relation_type: prov:hadPrimarySource source: fbbt - 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relation_type: prov:hadPrimarySource source: kg-predict product_file_size: 48397035 product_url: http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt secondary_source: - relation_type: prov:wasDerivedFrom source: drugbank - relation_type: prov:wasDerivedFrom source: faers - relation_type: prov:wasDerivedFrom source: go - relation_type: prov:wasDerivedFrom source: gtex - relation_type: prov:wasDerivedFrom source: hp - relation_type: prov:wasDerivedFrom source: mgi - relation_type: prov:wasDerivedFrom source: mp - relation_type: prov:wasDerivedFrom source: omim - relation_type: prov:wasDerivedFrom source: string - relation_type: prov:wasDerivedFrom source: umls - category: Product description: Downloadable gene set files in GMT, XML, and other formats for human collections including hallmarks, curated pathways, ontologies, and computational signatures; free registration is required for downloads format: mixed id: msigdb.downloads.human name: MSigDB Human Gene Sets Downloads original_source: - relation_type: prov:hadPrimarySource source: msigdb product_url: https://www.gsea-msigdb.org/gsea/downloads.jsp#msigdb secondary_source: - relation_type: prov:used source: go - relation_type: prov:used source: hp - relation_type: prov:used source: kegg - relation_type: prov:used source: mirbase - relation_type: prov:used source: pid - relation_type: prov:used source: reactome - relation_type: prov:used source: wikipathways warnings: - Downloads redirect unauthenticated users to the GSEA/MSigDB login page; registration is free but required for direct file access. - category: Product description: Downloadable gene set files for mouse collections including mouse-ortholog hallmarks, curated pathways, ontologies, and cell type signatures; free registration is required for downloads format: mixed id: msigdb.downloads.mouse name: MSigDB Mouse Gene Sets Downloads original_source: - relation_type: prov:hadPrimarySource source: msigdb product_url: https://www.gsea-msigdb.org/gsea/downloads.jsp#msigdb secondary_source: - relation_type: prov:used source: go - relation_type: prov:used source: hp - relation_type: prov:used source: kegg - relation_type: prov:used source: mirbase - relation_type: prov:used source: pid - relation_type: prov:used source: reactome - relation_type: prov:used source: wikipathways warnings: - Downloads redirect unauthenticated users to the GSEA/MSigDB login page; registration is free but required for direct file access. - category: ProgrammingInterface description: TRAPI 1.4 API for predicted drug treatments, drug-disease associations, similar entities, model metadata, and explanation endpoints format: http id: openpredict.api name: OpenPredict API original_source: - relation_type: prov:hadPrimarySource source: openpredict product_url: https://openpredict.semanticscience.org/docs secondary_source: - relation_type: prov:used source: biolink - relation_type: prov:used source: drugbank - relation_type: prov:used source: go - relation_type: prov:used source: hp - relation_type: prov:used source: kegg - relation_type: prov:used source: mesh - relation_type: prov:used source: omim - category: Product description: Pre-computed prediction outputs exposed through API operations for predicted drugs, predicted diseases, similar entities, and evidence paths format: mixed id: openpredict.predictions name: OpenPredict Prediction Data original_source: - relation_type: prov:hadPrimarySource source: openpredict product_url: https://openpredict.semanticscience.org/docs secondary_source: - relation_type: prov:used source: drugbank - relation_type: prov:used source: go - relation_type: prov:used source: hp - relation_type: prov:used source: kegg - relation_type: prov:used source: mesh - relation_type: prov:used source: omim warnings: - Prediction results are exposed through POST/GET API operations rather than as a stable public bulk data file. - category: Product description: Orphanet scientific knowledge files for rare disease alignments, classifications, genes, phenotypes, functional consequences, epidemiology, and natural history format: xml id: orphanet.scientific_knowledge_files name: Orphanet Scientific Knowledge Files original_source: - relation_type: prov:hadPrimarySource source: orphanet product_url: https://sciences.orphadata.com/orphanet-scientific-knowledge-files/ secondary_source: - relation_type: prov:wasInformedBy source: hp - relation_type: prov:wasInformedBy source: mesh - relation_type: prov:wasInformedBy source: mondo - relation_type: prov:wasInformedBy source: omim - category: Product description: Harmonizome 3.0 processed dataset downloads, including dataset-specific association files and knowledge graph serialization downloads. format: mixed id: harmonizome.downloads name: Harmonizome Downloads original_source: - relation_type: prov:hadPrimarySource source: harmonizome product_url: https://maayanlab.cloud/Harmonizome/download secondary_source: - relation_type: prov:wasDerivedFrom source: achilles - relation_type: prov:wasDerivedFrom source: biogps - relation_type: prov:wasDerivedFrom source: ccle - relation_type: prov:wasDerivedFrom source: cellmarker - relation_type: prov:wasDerivedFrom source: chea - relation_type: prov:wasDerivedFrom source: clinvar - relation_type: prov:wasDerivedFrom source: cmap - relation_type: prov:wasDerivedFrom