{ "@id": "https://stars.renci.org/var/translator/releases/translator_kg/2025_11_13", "@type": "sc:Dataset", "name": "translator_kg", "description": "A merged knowledge graph built for the NCATS Biomedical Data Translator project using Translator-Ingests, Biolink Model, and Node Normalizer.", "license": "MIT", "url": "https://stars.renci.org/var/translator/releases/translator_kg/2025_11_13", "version": "2025_11_13", "dateCreated": "2025_11_13", "biolinkVersion": "4.3.4", "babelVersion": "2025sep1", "distribution": [ { "@id": "translator_kg.tar.xz", "@type": "cr:FileObject", "contentUrl": "translator_kg.tar.xz", "encodingFormat": "application/x-xz", "description": "Compressed tar archive containing the KGX files: nodes.jsonl and edges.jsonl" } ], "isBasedOn": [ { "id": "alliance", "name": "Alliance of Genome Resources (AGR) Reference Ingest Guide", "description": "The Alliance of Genome Resources (AGR) is a consortium of model organism databases and the Gene Ontology Consortium that provides a unified view of gene function, biological processes, phenotypes, and disease associations across multiple model organisms. The AGR aggregates and harmonizes data from member databases including MGI (mouse), RGD (rat), SGD (yeast), WormBase (C. elegans), FlyBase (D. melanogaster), ZFIN (zebrafish), and Xenbase (X. laevis and X. tropicalis).", "license": { "terms_of_use_url": "https://www.alliancegenome.org/privacy-warranty-licensing", "license_name": "CC0 1.0 Universal", "license_url": "https://creativecommons.org/publicdomain/zero/1.0/" }, "url": [ "All downloads: https://www.alliancegenome.org/downloads", "FMS (File Management System): https://fms.alliancegenome.org/download/" ], "version": "8.2.0" }, { "id": "ctd", "name": "CTD Resource Ingest Guide", "description": "CTD is a robust, publicly available database that aims to advance understanding about how environmental exposures affect human health. It provides knowledge, manually curated from the literature, about chemicals and their relationship to other biological entities: chemical to gene/protein interactions plus chemical to disease and gene to disease relationships. These data are integrated with functional and pathway data to aid in the development of hypotheses about the mechanisms underlying environmentally influenced diseases. It also generates novel inferences by further analyzing the knowledge they curate/create - based on statistically significant connections with intermediate concept (e.g. Chemical X associated with Disease Y based on shared associations with a common set of genes).", "license": { "terms_of_use_url": "https://ctdbase.org/about/legal.jsp", "terms_of_use_description": "Bespoke terms describing specific conditions for use of CTD data. No formal license." }, "url": [ "CTD Bulk Downloads - http://ctdbase.org/downloads/ (this page includes file sizes and simple data dictionaries for each download)", "CTD Catalog - https://ctdbase.org/reports/ (a simple list of files, reports the number of rows in each file)" ], "version": "October_2025" }, { "id": "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": "2025_11_09" }, { "id": "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": "2025_11_13" }, { "id": "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": "v1" }, { "id": "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": "2025-10-10" }, { "id": "hpoa", "name": "Human Phenotype Ontology Annotations", "description": "The [Human Phenotype Ontology (HPO)](https://hpo.jax.org/) provides a standard vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. HPO currently contains over 18,000 terms and over 156,000 annotations to hereditary diseases. The HPO project and others have developed software for phenotype-driven differential diagnostics, genomic diagnostics, and translational research.\nThe Human Phenotype Ontology group curates and assembles over 115,000 HPO-related annotations (\"HPOA\") to hereditary diseases using the HPO ontology. Here we create Biolink associations between diseases and phenotypic features, together with their evidence, and age of onset and frequency (if known). Disease annotations here are also cross-referenced to the MONarch Disease Ontology (MONDO) (https://mondo.monarchinitiative.org/).\nThere are four HPOA ingests ('disease-to-phenotype' (includes capture of disease modes of inheritance, 'gene-to-phenotype' and 'gene-to-disease') that parse out records from the HPO Phenotype Annotation File (http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa).", "license": { "terms_of_use_url": "https://hpo.jax.org/license", "terms_of_use_description": "Bespoke terms describing specific conditions for use of HPOA data. No formal license." }, "url": [ "https://hpo.jax.org/data/annotations" ], "version": "2025-10-22" }, { "id": "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" }, { "id": "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" } ], "schema": { "nodes": [ { "category": [ "biolink:SmallMolecule" ], "count": 10133, "id_prefixes": { "CHEBI": 6250, "PUBCHEM.COMPOUND": 2175, "UNII": 1708 }, "attributes": { "name": 10133, "equivalent_identifiers": 10133, "information_content": 6249 } }, { "category": [ "biolink:Drug", "biolink:SmallMolecule" ], "count": 1693, "id_prefixes": { "CHEBI": 1626, "UNII": 53, "PUBCHEM.COMPOUND": 14 }, "attributes": { "name": 1693, "equivalent_identifiers": 1693, "information_content": 1617 } }, { "category": [ "biolink:MolecularMixture" ], "count": 851, "id_prefixes": { "PUBCHEM.COMPOUND": 390, "UNII": 231, "CHEBI": 230 }, "attributes": { "name": 851, "equivalent_identifiers": 851, "information_content": 230 } }, { "category": [ "biolink:Drug" 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