is an Aggregator.
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics, maintained by the United States National Library of Medicine (NLM) at the National Institutes of Health (NIH). MEDLINE is NLM's premier bibliographic database containing more than 31 million references to journal articles indexed with Medical Subject Headings (MeSH). PubMed comprises more than 39 million citations for biomedical literature from MEDLINE, life science journals, and online books, with citations including links to full-text content from PubMed Central and publisher web sites. The database is updated daily and covers publications from the 1950s to the present.
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| pubmed.portal | PubMed Web Portal | pubmed.ncbi.nlm.nih.gov | Graphical Interface | http | Web interface for searching and brows... |
| pubmed.eutils | PubMed E-utilities API | NBK25501 | Programming Interface | http | Entrez Programming Utilities (E-utili... |
| pubmed.baseline | PubMed Annual Baseline Files | baseline | Product | xml | Annual baseline set of PubMed citatio... |
| pubmed.updates | PubMed Daily Update Files | updatefiles | Product | xml | Daily update files containing new, re... |
| pubmed.help | PubMed Help Documentation | help | Documentation | http | Comprehensive PubMed help documentati... |
| pubmed.advanced.search | PubMed Advanced Search | advanced | Graphical Interface | http | Advanced search builder with field-sp... |
| pubmed.clinical.queries | PubMed Clinical Queries | clinical | Graphical Interface | http | Specialized clinical queries interfac... |
| pubmed.dtd | PubMed DTD Documentation | index.html | Documentation | http | PubMed DTD documentation with annotat... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| ncbigene.gene2pubmed | Gene to PubMed Mapping | gene2pubmed.gz (255.0 MB) | Mapping | tsv | had primary source | Gene to PubMed mapping data providing... |
| spoke.graph | SPOKE Graph | data-tools | Graph | http | had primary source | The SPOKE knowledge graph containing ... |
| indra.cogex.code | INDRA CoGEx Build Code | indra_cogex | Process | python | had primary source | INDRA CoGEx is a graph database integ... |
| genecards.literature ⚠ | GeneCards Literature References | www.genecards.org | Product | http | had primary source | Literature references from PubMed aut... |
| omnicorp.cooccurrence | OmniCorp Co-occurrence Data | OmniCorp | Product | mixed | had primary source | Co-occurrence database generated from... |
| omnicorp.api ⚠ | OmniCorp API | OmniCorp | Programming Interface | http | had primary source | API behavior documented for adding co... |
| atom.kg ⚠ | ATOM Knowledge Graph | BIBM47256.2019.8983062 | Graph | mixed | was derived from | Anti-tumor biomaterial knowledge grap... |
| amyco.annotations | AmyCo Curated Annotations | ❔ | Product | ❔ | had primary source | Manually curated disease-gene associa... |
| medgen.pubmed-links | MedGen PubMed Links | medgen_pubmed_lnk.txt.gz (81.6 MB) | Product | txt | had primary source | Links between MedGen concepts and Pub... |
| atom.pipeline ⚠ | ATOM Construction Pipeline | BIBM47256.2019.8983062 | Process | mixed | was derived from | Natural language processing pipeline ... |
| forum.webapp | FORUM Web Application | forum-webapp.semantic-metabolomics.fr | Graphical Interface | http | had primary source | FORUM web application interface for s... |
| forum.api | FORUM API | openapi-documentation | Programming Interface | http | had primary source | FORUM REST API for programmatic acces... |
| forum.void | FORUM VoID Metadata | void (94.2 KB) | Documentation | ttl | had primary source | FORUM VoID (Vocabulary of Interlinked... |
| gnbr.graph | GNBR graph | 3459420 | Graph | http | had primary source | Text-mined biomedical knowledge graph... |
| hald.literature-info.json | HALD Literature Info | 43612512 (814.7 MB) | Product | json | had primary source | Version 6 JSON file containing litera... |
| hald.entity-info.json | HALD Entity Info | 43612509 (283.0 MB) | Product | json | had primary source | Version 6 JSON file containing entity... |
| hald.relation-info.json | HALD Relation Info | 43612506 (93.7 MB) | Graph | json | had primary source | Version 6 JSON file containing relati... |
| hald.aging-biomarkers.json | HALD Aging Biomarkers | 43612503 (1.1 MB) | Product | json | had primary source | Version 6 JSON file containing aging ... |
| hald.longevity-biomarkers.json | HALD Longevity Biomarkers | 43612497 (331.4 KB) | Product | json | had primary source | Version 6 JSON file containing longev... |
| hald.entities.csv | HALD Neo4j Entities | 43612494 (234.2 KB) | Product | csv | had primary source | Version 6 CSV file containing entity ... |
| hald.roles.csv | HALD Neo4j Roles | 43612500 (4.8 MB) | Product | csv | had primary source | Version 6 CSV file containing relatio... |
| hald.browser | HALD Web Interface | hald | Graphical Interface | http | had primary source | Interactive web interface for searchi... |
| ikraph.site | BioKDE | biokde.insilicom.com | Graphical Interface | http | had primary source | Biomedical Knowledge Discovery Engine... |
| ikraph.code | iKraph Code | iKraph | Process | mixed | had primary source | Code for named entity recognition, re... |
| ikraph.graph | iKraph graph metadata | data.tar.gz?download=1 (58.3 MB) | Graph | json | had primary source | Graph metadata for iKraph, including ... |
| ikraph.graphdata | iKraph graph data | iKraph_full.tar.gz?download=1 (1.3 GB) | Graph | mixed | had primary source | Complete graph data for iKraph with a... |
| medkg.site | MedKG Site | medkg | Graphical Interface | http | had primary source | Graphical interface for MedKG |
| reprotox-kg.portal | ReproTox-KG Explorer | reprotox-kg | Graphical Interface | http | had primary source | Public web interface for querying and... |
| reprotox-kg.data | ReproTox-KG Downloads | downloads | Product | http | had primary source | Downloads page listing the ReproTox-K... |
| suppkg.docs | SuppKG Documentation | SuppKG | Documentation | http | had primary source | Translator wiki page describing SuppK... |
| suppkg.source-data | SuppKG Source Data Repository | SuppKG | Process | http | had primary source | Source data directory used for SuppKG... |
| tbkg.data | TBKG Knowledge Graph Data | full#supplementary-material | Graph | mixed | was derived from | Weighted heterogeneous knowledge grap... |
| tbkg.osimertinib_case_study | TBKG Osimertinib ADR Case Study Data | full#supplementary-material | Product | mixed | was derived from | Clinical validation dataset with calc... |
| ttd.targets-raw ⚠ | TTD Targets Information | P1-01-TTD_target_download.txt | Product | txt | had primary source | Raw format target information includi... |
| ttd.drug-disease ⚠ | Drug-Disease Mapping | P1-05-Drug_disease.txt | Product | txt | had primary source | Drug to disease mapping with ICD iden... |
| ttd.target-disease ⚠ | Target-Disease Mapping | P1-06-Target_disease.txt | Product | txt | had primary source | Target to disease mapping with ICD id... |
| ttd.target-drug ⚠ | Target-Drug Mapping | P1-07-Drug-TargetMapping.xlsx | Product | csv | had primary source | Target to drug mapping with mode of a... |
| ttd.biomarker-disease ⚠ | Biomarker-Disease Mapping | P1-08-Biomarker_disease.txt | Product | txt | had primary source | Biomarker to disease mapping with ICD... |
| ttd.target-compound ⚠ | Target-Compound Activity Data | P1-09-Target_compound_activity.txt | Product | txt | had primary source | Target to compound mapping with exper... |
| glkb.site | GLKB Site | glkb.org | Graphical Interface | http | was influenced by | Graphical interface for GLKB |
| entrez.eutils | Entrez E-utilities | NBK25501 | Programming Interface | json | was informed by | E-utilities API for programmatic acce... |
| gendr.data | GenDR Data Download | dataset.zip (8.0 KB) | Product | csv | was informed by | Downloadable dataset of dietary restr... |
| gendr.expression-signatures | GenDR Dietary Restriction Expression Signatures | TableS2.xls (48.0 KB) | Product | http | was informed by | Excel spreadsheet of dietary-restrict... |
| litvar.web_interface | LitVar Web Interface | litvar2 | Graphical Interface | http | was derived from | Web interface for searching and retri... |
| litvar.api | LitVar API | litvar2-api | Programming Interface | http | was derived from | RESTful API providing programmatic ac... |
| metabokg.graph ⚠ | MetaboKG RDF Graph | MetaBoKG | Graph | mixed | had primary source | RDF knowledge graph materialized by t... |
| dbptm.downloads | dbPTM Download Datasets | download.php | Product | tsv | was derived from | dbPTM downloads for experimental and ... |
| dbsno.downloads ⚠ | dbSNO Download Dataset | download.php | Product | tsv | was derived from | Tab-delimited dbSNO 3.0 S-nitrosylati... |
| phosphoelm.dataset | Phospho.ELM Dataset | dataset.html | Product | mixed | was derived from | Phospho.ELM version 9.0 dataset reque... |
| rlims-p.portal | RLIMS-P Web Portal | rlimsp2 | Graphical Interface | http | used | RLIMS-P web portal for searching phos... |
| rlims-p.text-mining-service | RLIMS-P Text-Mining Service | rlimsp2 | Process | http | used | Rule-based text-mining service for ex... |
| acukg.csv | AcuKG CSV tables | AcuKG | Graph | csv | had primary source | Source CSV tables for AcuKG, includin... |
| acukg.rdf | AcuKG RDF Turtle files | AcuKG_RDF | Graph | ttl | had primary source | RDF Turtle representation of AcuKG re... |
| acukg.json | AcuKG JSON files | AcuKG_json | Graph | json | had primary source | JSON representation of AcuKG relation... |
| foodb.web | FooDB Web Interface | foodb.ca | Graphical Interface | http | was informed by | Web interface that allows searching, ... |
| foodb.data.csv | FooDB CSV Data | foodb_2020_4_7_csv.tar.gz (952.1 MB) | Product | csv | was informed by | Complete FooDB database in CSV format |
| foodb.data.xml | FooDB XML Data | foodb_2020_4_7_xml.tar.gz (6.3 GB) | Product | xml | was informed by | Complete FooDB database in XML format |
| foodb.data.json | FooDB JSON Data | foodb_2020_04_07_json.zip (86.6 MB) | Product | json | was informed by | Complete FooDB database in JSON format |
| foodb.data.mysql | FooDB MySQL Dump | foodb_2020_4_7_mysql.tar.gz (172.5 MB) | Product | mysql | was informed by | Complete FooDB database as MySQL dump |
| ickg.graph-data | ICKG graph data | data | Graph | csv | had primary source | Immune cell type-specific node and re... |
| myaura.graph | myAURA epilepsy knowledge graph | myaura | Graph | mixed | had primary source | Multilayer epilepsy knowledge graph g... |
| genecards.web.interface | GeneCards Web Interface | www.genecards.org | Graphical Interface | http | had primary source | Web-based interface for searching and... |
| forum.graph.dump | FORUM Knowledge Graph SPARQL Endpoint | sparql | Graph | http | had primary source | Public SPARQL endpoint (OpenLink Virt... |
| np-kg.graph.tsv | NP-KG TSV | NP-KG_v3.0.0.tsv?download=1 (1.0 GB) | Graph | tsv | had primary source | Merged KG with ontology-grounded KG a... |
| np-kg.graph.networkx | NP-KG gpickle | NP-KG_v3.0.0.gpickle?download=1 (892.7 MB) | Graph | mixed | had primary source | Merged KG with ontology-grounded KG a... |
| nlm-ckn.graph | nlm-ckn-graph | nlm-ckn.org | Graph | http | had primary source | The NLM-CKN knowledge graph of cellul... |
| spoke-okn.graph | SPOKE-OKN Graph | spoke.ucsf.edu | Graph | ttl | was influenced by | The SPOKE-OKN knowledge graph, an OKN... |
| multiomics-kp.graph | Multiomics KP Knowledge Graph | metadata | Graph | json | was influenced by | Live TRAPI/BioThings metadata endpoin... |
| pubmed-knowledge-graph.website | PubMed Knowledge Graph Homepage | pubmedkg.github.io | Graphical Interface | http | had primary source | Project homepage for the PubMed Knowl... |
| micromap.api | MicroMap API | docs | Programming Interface | http | was derived from | REST API and MCP server over the prod... |
| europepmc.portal | Europe PMC Website | europepmc.org | Graphical Interface | http | had primary source | Europe PMC website for searching and ... |
| europepmc.rest-api | Europe PMC Articles RESTful API | rest | Programming Interface | http | had primary source | REST API for searching Europe PMC and... |
| togows.rest-api ⚠ | TogoWS REST API | help | Programming Interface | http | had primary source | REST API for retrieving entries, or i... |
| klocd.portal | KLOCD Web Interface | www.organchip.cn | Graphical Interface | http | had primary source | KLOCD web interface for searching its... |
| nihreporter.publications | NIH-Funded Publications Database | publications | Product | csv | had primary source | Database of publications linked to NI... |
| nihreporter.linktables | NIH-Funded Publications Link Tables | linktables | Product | csv | had primary source | Database of publication link tables f... |
| stitch.portal | STITCH Web Portal | stitch-db.org | Product | http | had primary source | Web interface for searching and visua... |
| stitch.downloads | STITCH Data Downloads | download.pl | Product | tsv | had primary source | Downloadable data files containing ch... |
| stitch.api | STITCH API | access.pl?footer_active_subpage=apis | Programming Interface | http | had primary source | API for programmatic access to STITCH... |
| cacao.portal | CACAO Platform | cacao.wiki | Graphical Interface | http | had primary source | CACAO annotation competition platform... |
| cacao.go-annotations | CACAO GO Annotations | annotations?assignedBy=CACAO | Product | http | had primary source | GO annotations contributed by CACAO c... |
| cacao.gowiki | CACAO GO Wiki Page | Category:CACAO | Graphical Interface | http | had primary source | Archived GONUTS wiki category for the... |
| cacao.api | GONUTS MediaWiki API | api.php | Programming Interface | http | had primary source | MediaWiki API endpoint for accessing ... |
| medgen.csv | CSV Data Files | csv | Product | csv | had primary source | CSV format data files directory with ... |
| service-kp.trapi | Service Provider TRAPI | Service%20Provider | Programming Interface | http | had primary source | TRAPI endpoint for the Service Provid... |
| genereviews.titles | GeneReviews Titles | GRtitle_shortname_NBKid.txt (21.0 KB) | Product | tsv | had primary source | Tab-delimited list of GeneReviews cha... |
| ecrin-mdr.portal | ECRIN MDR Portal | newmdr.ecrin.org | Graphical Interface | http | had primary source | Web portal for searching clinical stu... |
| ecrin-mdr.api | ECRIN MDR API | index.html | Programming Interface | http | had primary source | REST API behind the MDR portal (MDR_F... |
| babel.compendia | Babel Compendia | compendia | Product | json | had primary source | Babel compendia, one file per Biolink... |
| rdf-portal.sparql.ncbi | RDF Portal NCBI SPARQL Endpoint | sparql | Programming Interface | http | was derived from | SPARQL endpoint for NCBI- and NLM-der... |
| reprotox-kg.graph.core | ReproTox-KG Core Graph | reprotox_serialization.valid.json (1.6 MB) | Graph | json | had primary source | Core ReproTox-KG graph linking birth ... |
| reprotox-kg.graph.drugshot-hpo | ReproTox-KG DrugShot HPO-Drug Graph | Drugshot_HPO_to_Drug.valid.json (8.5 MB) | Graph | json | had primary source | Birth defect phenotype to drug associ... |
| reprotox-kg.graph.geneshot-hpo | ReproTox-KG GeneShot HPO-Gene Graph | Geneshot_HPO_to_Gene.valid.json (6.9 MB) | Graph | json | had primary source | Birth defect phenotype to gene associ... |
| drugshot.drugrif | DrugRIF Drug-Publication Associations | DrugRIF.tsv.gz (8.6 MB) | Product | tsv | had primary source | About 2 million drug to PubMed articl... |
| drugshot.autorif | AutoRIF Drug-Publication Associations | AutoRIF.tsv.gz (31.8 MB) | Product | tsv | had primary source | About 8 million drug to PubMed articl... |
| drugshot.autorif-cooccurrence | AutoRIF Drug Co-mention Matrix | autorif_cooccur.h5 (154.6 MB) | Product | hdf5 | had primary source | Drug-drug co-mention matrix computed ... |
| drugshot.drugrif-cooccurrence | DrugRIF Drug Co-mention Matrix | drugrif_cooccur.h5 (146.6 MB) | Product | hdf5 | had primary source | Drug-drug co-mention matrix computed ... |
| geneshot.generif | GeneRIF Gene-Publication Associations | generif.tsv (13.9 MB) | Product | tsv | had primary source | Human gene to PubMed article associat... |
| geneshot.autorif | AutoRIF Gene-Publication Associations | autorif.tsv (597.8 MB) | Product | tsv | had primary source | Automatically generated human gene to... |
| htridb.downloads ⚠ | HTRIdb Downloads | pagdown.jsp | Product | http | was derived from | HTRIdb download page offering all tra... |
| redfly.search | REDfly Search | options?sequence=1&assayed=1&cellCulture=1&range=10000 | Graphical Interface | http | was derived from | REDfly search interface for querying ... |
| yeastract.scerevisiae | Yeastract (S. cerevisiae) | scerevisiae | Graphical Interface | http | was derived from | Yeastract web interface for Saccharom... |
| yeastract.pathoyeastract | PathoYeastract | pathoyeastract | Graphical Interface | http | was derived from | PathoYeastract web interface with cur... |
| yeastract.ncyeastract | N.C.Yeastract | ncyeastract | Graphical Interface | http | was derived from | N.C.Yeastract web interface with cura... |
| linked-discoveries.site | Linked Discoveries Web Interface | linkeddiscoveries.ncbi.nlm.nih.gov | Graphical Interface | http | was derived from | Interactive web interface for explori... |
Created: October 31, 2025 | Last modified: September 16, 2026