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It provides an intuitive answer to the question 'where is a gene expressed?' and supports research in cancer and agriculture, as well as evolutionary biology.", "license": { "terms_of_use_url": "https://www.bgee.org/about/", "terms_of_use_description": "You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.", "license_name": "CC0", "license_url": "https://creativecommons.org/publicdomain/zero/1.0/" }, "url": [ null ], "version": "15.2" }, { "@type": "Dataset", "identifier": "bindingdb", "name": "BindingDb", "description": "The Binding Database (\"BindingDb\") is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. As of July 31, 2021, BindingDB contains thousands of dataset Entries, each with a DOI, containing millions of binding assay results for thousands of protein targets assayed against over a million distinct small molecule ligands.", "license": { "terms_of_use_description": "All data and download files in bindingDB are freely available under a 'Creative Commons BY 3.0' license." }, "url": [ "BindingDb bulk downloads - https://www.bindingdb.org/rwd/bind/downloads/" ], "version": "202606" }, { "@type": "Dataset", "identifier": "chembl", "name": "ChEMBL Reference Ingest Guide", "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.", "license": { "license_name": "Creative Commons Attribution-ShareAlike 3.0 Unported license", "license_url": "https://creativecommons.org/licenses/by-sa/3.0/" }, "url": [ "https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/" ], "version": "36" }, { "@type": "Dataset", "identifier": "cohd", "name": "Columbia Open Health Data", "description": "The COHD provides access to counts and patient prevalence (i.e., prevalence from electronic health records) of conditions, procedures, drug exposures, and patient demographics, and the co-occurrence frequencies between them. Count and frequency data were derived from the Columbia University Irving Medical Center's OHDSI database including inpatient and outpatient data. Counts are the number of patients with the concept, e.g., diagnosed with a condition, exposed to a drug, or who had a procedure. Frequencies are the number of patients with the concept divided by the total number of patients in the dataset. Clinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the OMOP Common Data Model. To protect patient privacy, all concepts and pairs of concepts where the count \u2264 10 were excluded, and counts were randomized by the Poisson distribution.", "license": { "terms_of_use_url": null, "terms_of_use_description": null, "license name": null, "license url": null }, "url": "https://stars.renci.org/var/data_services/cohd_2/cohd_nodes.jsonl", "version": "2024-11-25" }, { "@type": "Dataset", "identifier": "ctkp", "name": "Multiomics Clinical Trials Knowledge Provider (CTKP) Reference Ingest Guide", "description": "The Clinical Trials KP provides information on Clinical Trials, ultimately derived from researcher submissions to clinicaltrials.gov, via the Aggregate Analysis of Clinical Trials (AACT) database. Information on select trials includes the NCT Identifier of the trial, interventions used, diseases/conditions relevant to the trial, adverse events, etc. ", "license": { "terms_of_use_description": "Freely available" }, "url": [ "Direct download links for the latest version are given in the manifest file: https://github.com/multiomicsKP/clinical_trials_kp/blob/main/manifest.json" ], "version": "3.1.38" }, { "@type": "Dataset", "identifier": "dakp", "name": "Multiomics Drug Approvals Knowledge Provider (DAKP) Reference Ingest Guide", "description": "The Drug Approvals KP provides information on FDA-approved drugs and their approved indications, derived from DailyMed and FAERS data. Information includes drug-disease treatment relationships with FDA approval status, approval numbers, and supporting evidence from adverse event reports.", "license": { "terms_of_use_description": "Freely available" }, "url": [ "Direct download links for the latest version are given in the manifest file: https://github.com/multiomicsKP/drug_approvals_kp/blob/main/manifest.json" ], "version": "0.5.6" }, { "@type": "Dataset", "identifier": "diseases", "name": "Jensen Lab DISEASES Database Reference Ingest Guide", "description": "The DISEASES database is a web resource that integrates knowledge on gene-disease associations. It generates de novo associations through automated text mining, and aggregates associations from external sources of manually curated knowledge and GWAS-based study results. The associations are assigned a confidence score to facilitate comparisons across data types and sources.", "license": { "license_name": "CC BY 4.0" }, "url": [ "https://diseases.jensenlab.org/Downloads" ], "version": "2026_06_12" }, { "@type": "Dataset", "identifier": "drug_rep_hub", "name": "Drug-Repurposing Hub Reference Ingest Guide", "description": "The Drug Repurposing Hub is a curated and annotated collection of FDA-approved drugs, clinical trial drugs, and selected pre-clinical tool compounds. Because the compounds are annotated and well characterized, the collection is a novel tool to explore known biological targets and pathways, and a powerful way to discover new biological insights, better understand disease mechanisms, and discover new activities of existing molecules. ", "license": { "license_name": "The Repurposing Hub compound metadata (including compound names, structures, targets, mechanisms, and indications) are made available under the permissive CC-BY 4.0 license. Restrictions: The Drug Repurposing Hub data is provided for non-commercial use only.", "license_url": "https://repo-hub.broadinstitute.org/repurposing#about" }, "url": [ "https://repo-hub.broadinstitute.org/repurposing#download-data" ], "version": "2025-08-19" }, { "@type": "Dataset", "identifier": "drugcentral", "name": "DrugCentral Reference Ingest Guide", "description": "DrugCentral is an open-access online drug information repository. It covers over 4950 drugs, incorporating structural, physicochemical, and pharmacological details to support drug discovery, development, and repositioning.", "license": { "terms_of_use_url": "https://drugcentral.org/privacy", "terms_of_use_description": "DrugCentral's webpage says DrugCentral is available under the Creative Commons license. In the 2023 papers, DrugCentral is described as available 'free of charge, without registration' (https://pmc.ncbi.nlm.nih.gov/articles/PMC10692006/#notes3) thru its website, public instance, a full database dump, and a Docker container (https://pmc.ncbi.nlm.nih.gov/articles/PMC9825566/#SEC6).", "license name": "CC BY-SA" }, "url": [ "Download and database access info: https://drugcentral.org/download" ], "version": "2023_11_01" }, { "@type": "Dataset", "identifier": "gene2phenotype", "name": "EBI Gene2Phenotype Reference Ingest Guide", "description": "EBI's Gene2Phenotype dataset contains high-quality gene-disease associations curated by UK disease domain experts and consultant clinical geneticists. It integrates data on genes, their variants, and related disorders. It is constructed by experts reviewing published literature, and it is primarily an inclusion list to allow targeted filtering of genome-wide data for diagnostic purposes. Each entry associates a gene with a disease, including a confidence level, allelic requirement and molecular mechanism.", "license": { "terms_of_use_description": "Unsure, but likely uses EMBL-EBI terms of use (linked in website footer). Currently don't see a formal standard license. Various resource webpages (About -> The G2P Project, Downloads, Publications) say that all data is 'freely available' and to please cite the date accessed/data version and Thorman et al 2019", "terms_of_use_url": "https://www.ebi.ac.uk/about/terms-of-use/#general" }, "url": [ "Latest data is provided at https://www.ebi.ac.uk/gene2phenotype/download (downloads created on-the-fly)", "Archived static releases provided on the FTP site at https://ftp.ebi.ac.uk/pub/databases/gene2phenotype/G2P_data_downloads/" ], "version": "2026_06_21" }, { "@type": "Dataset", "identifier": "geneticskp", "name": "GeneticsKP Reference Ingest Guide", "description": "GeneticsKP provides gene-disease associations derived from GWAS data using MAGMA analysis. It integrates genetic evidence from genome-wide association studies to identify genes associated with various diseases and traits.", "license": { "terms_of_use_description": "Freely available" }, "url": [ "Data is provided as a checked-in tar.gz file in the translator-ingests repository" ], "version": "2026-06-21" }, { "@type": "Dataset", "identifier": "go_cam", "name": "Gene Ontology Causal Activity Models (GO-CAM) Reference Ingest Guide", "description": "GO-CAM (Gene Ontology Causal Activity Models) is a framework that extends standard GO annotations by connecting molecular functions, biological processes, and cellular components into causally linked pathways. GO-CAMs provide explicit causal connections between gene products and their activities within specific biological contexts, enabling more detailed representation of biological mechanisms than traditional GO annotations.", "license": { "license_name": "CC BY 4.0 - Creative Commons Attribution 4.0 International License" }, "url": [ "GO-CAMs are downloaded model by model, via kghub-downloader that takes an index file that shows all possible gocams by identifier, and then iterates one by one through the identifiers, downloading each gocam.", "Index: https://s3.amazonaws.com/provider-to-model.json", "URL pattern: https://live-go-cam.geneontology.io/product/yaml/go-cam/[id].json" ], "version": "2026-05-19" }, { "@type": "Dataset", "identifier": "goa", "name": "GO Annotations (GOA) Reference Ingest Guide", "description": "GO Annotations connect genes to a Gene Ontology term that describes a molecular function it enables, a biological process in which it participates, or a cellular component in which it is located. Most are produced through rigorous manual curation of the literature, although some are based on automated pipelines that assign GO terms based on things like orthology or sequence similarity.", "license": { "terms_of_use_url": "https://geneontology.org/docs/go-citation-policy/", "license_name": "CC BY 4.0", "license_url": "https://creativecommons.org/licenses/by/4.0/legalcode#s3a1" }, "url": [ "All downloads: https://geneontology.org/docs/download-go-annotations/", "Commonly studied organisms: https://current.geneontology.org/products/pages/downloads.html" ], "version": "2026-05-19" }, { "@type": "Dataset", "identifier": "gtopdb", "name": "The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) Reference Ingest Guide", "description": "The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; https://www.guidetopharmacology.org) is an open-access, expert-curated, online database that provides succinct overviews and key references for pharmacological targets and their recommended experimental ligands. It includes over 3039 protein targets and 12,163 ligand molecules, including approved drugs, small molecules, peptides and antibodies. GtoPdb) was established and developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). It originated from the IUPHAR-DB, a former resource focused on receptors and channels that was first compiled in 2003 and from the BPS\u2018 Guide to Receptors and Channels\u2019, a compendium of a wider range of targets than those originally covered in IUPHAR-DB", "license": { "license_name": "Creative Commons Attribution 4.0 International", "license_url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "url": [ "gtoPdb Downloads: https://www.guidetopharmacology.org/download.jsp (this page includes file sizes and simple data dictionaries for each download)" ], "version": "2026.2" }, { "@type": "Dataset", "identifier": "icees", "name": "ICEES (Integrated Clinical and Environmental Exposures Service)", "description": "ICEES KG is the KG version of the Integrated Clinical and Environmental Exposures Service (ICEES), which provides regulatory-compliant open access to clinical data (e.g., electronic health records, survey data, clinical research data) that have been integrated at the patient level with environmental exposures data (e.g., airborne pollutants, landfills, concentrated animal feeding operations, socio-economic indicators).", "license": { "terms_of_use_url": "https://github.com/NCATSTranslator/Translator-All/wiki/Exposures-Provider-ICEES-and-ICEES-KG-Terms-and-Conditions-of-Use", "terms_of_use_description": "UNC Health is permitted to provide under 45 C.F.R. \u00c2\u00a7 164.502(d)(2)" }, "url": [ "https://stars.renci.org/var/plater/bl-4.2.1/icees-kg/8-20-2024/ - Automat ICEES Plater loaded KGX jsonl files, plus meta_knowledge_graph.json" ], "version": "2024-08-20" }, { "@type": "Dataset", "identifier": "intact", "name": "IntAct Reference Ingest Guide", "description": "IntAct is a curated, open data resource of molecular interactions hosted by EMBL-EBI. It stores experimentally determined molecular interactions, primarily protein\u2013protein interactions, derived from literature curation and direct user submissions. IntAct uses detailed controlled vocabularies (e.g., PSI-MI) to describe experimental details such as interaction type, detection method, and participant roles, enabling consistent representation and downstream reuse of fine-grained interaction evidence.", "license": "", "url": [ { "IntAct main site": "https://www.ebi.ac.uk/intact/" }, { "IntAct Download / FTP or bulk access": "https://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip" } ], "version": "2026_01_14" }, { "@type": "Dataset", "identifier": "ncbi_gene", "name": "NCBI Gene Reference Ingest Guide", "description": "\"The NCBI Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.\"", "license": { "terms_of_use_url": "https://www.ncbi.nlm.nih.gov/home/about/policies/", "license_name": "NCBI Public Domain", "license_url": "https://www.ncbi.nlm.nih.gov/home/about/policies/" }, "url": [ "NCBI FTP Site: https://ftp.ncbi.nih.gov/gene/DATA/" ], "version": "2026_06_18" }, { "@type": "Dataset", "identifier": "panther", "name": "Panther Gene Orthology and Annotation RIG", "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis. The core of PANTHER is a comprehensive, annotated library of gene family phylogenetic trees. All nodes in the tree have persistent identifiers that are maintained between versions of PANTHER, providing a stable substrate for annotations of protein properties like subfamily and function.", "license": { "terms_of_use_url": "http://www.pantherdb.org/tou.jsp" }, "url": [ "http://data.pantherdb.org/ftp/" ], "version": "19.0" }, { "@type": "Dataset", "identifier": "sider", "name": "SIDER Reference Ingest Guide", "description": "SIDER contains information on marketed drugs and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The current version of the database contains data on 1,430 drugs and 5,868 adverse drug reactions.", "license": "Creative Commons Attribution-Noncommercial-Share Alike 4.0 License", "url": [ "http://sideeffects.embl.de/download/" ], "version": "4.1" }, { "@type": "Dataset", "identifier": "signor", "name": "SIGnaling Network Open Resource (Signor) Reference Ingest Guide", "description": "SIGNOR 3.0, https://signor.uniroma2.it, is a public repository that captures causal information and represents it according to an 'activity-flow' model. SIGNOR provides freely-accessible static maps of causal interactions that can be tailored, pruned and refined to build dynamic and predictive models. Each signaling relationship is annotated with an effect (up/down-regulation) and with the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing the regulation of the target entity. Since its latest release, SIGNOR has undergone a significant upgrade including: (i) a new website that offers an improved user experience and novel advanced search and graph tools; (ii) a significant content growth adding up to a total of approx. 33,000 manually-annotated causal relationships between more than 8900 biological entities; (iii) an increase in the number of manually annotated pathways, currently including pathways deregulated by SARS-CoV-2 infection or involved in neurodevelopment synaptic transmission and metabolism, among others; (iv) additional features such as new model to represent metabolic reactions and a new confidence score assigned to each interaction.", "license": { "license_name": "Creative Commons Attribution 4.0 International", "license_url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "url": [ "Signor 3.0 Downloads: https://signor.uniroma2.it/downloads.php (this page includes file sizes and simple data dictionaries for each download)" ], "version": "2026_March" }, { "@type": "Dataset", "identifier": "ubergraph", "name": "Ubergraph Ontological Hierarchy Reference Ingest Guide", "description": "Ubergraph is a unified OWL ontology integrating multiple biomedical ontologies including GO, UBERON, CL, CHEBI, HP, and others. It provides both redundant (with full inference closure for subclass relations) and non-redundant graph representations. This ingest uses the redundant version which contains complete transitive, reflexive subclass relations for ontological hierarchy reasoning.", "license": { "license_name": "CC0 1.0 Universal (CC0 1.0) Public Domain Dedication", "license_url": "https://raw.githubusercontent.com/INCATools/ubergraph/master/LICENSE.txt" }, "url": [ "Ubergraph Downloads: https://ubergraph.apps.renci.org/downloads/current/", "redundant-graph-table.tgz contains complete inference closure", "nonredundant-graph-table.tgz contains direct assertions only" ], "version": "2026-05-31" } ] }