{"doi":"10.1093/nar/gkaf1292","title":"The Gene Ontology knowledgebase in 2026","abstract":"The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgebase is regularly updated and improved. We describe here the major updates that have been made in the past 3 years. The ontology and annotations have been expanded and revised, particularly in several areas of biology: cellular metabolism, multi-organism interactions (e.g. host-pathogen), extracellular matrix proteins, chromatin remodeling (e.g. the \"histone code\"), and noncoding RNA functions. We have released version 2 of a comprehensive set of integrated, reviewed annotations for human genes, which we call the \"functionome.\" We have also dramatically increased the number of GO-CAM models, with over 1500 models of metabolic and signaling pathways, primarily in human, mouse, budding and fission yeast, and fruit fly. Finally, we discuss our current recommendations and future prospects of AI in the use and development of GO.","journal":"Nucleic Acids Research","year":2025,"id":508794,"datarank":0.7431017649600318,"base_score":4.564348191467836,"endowment":4.564348191467836,"self_citation_contribution":0.6846522287201755,"citation_network_contribution":0.0584495362398563,"self_endowment_contribution":0.6846522287201755,"citer_contribution":0.0584495362398563,"corpus_percentile":72.87847141641525,"corpus_rank":3507,"citation_count":95,"citer_count":95,"citers_with_citation_signal":5,"citers_with_endowment":5,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9513,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":79.1667,"fair_percentile":97.67655151329869,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":95726,"name":"James P. Balhoff","orcid":"0000-0002-8688-6599","position":1,"is_corresponding":false},{"id":103800,"name":"Seth Carbon","orcid":"0000-0001-8244-1536","position":2,"is_corresponding":false},{"id":11685,"name":"J. Michael Cherry","orcid":"0000-0001-9163-5180","position":3,"is_corresponding":false},{"id":103807,"name":"Dustin Ebert","orcid":"0000-0002-6659-0416","position":4,"is_corresponding":false},{"id":103544,"name":"Marc Feuermann","orcid":"0000-0002-4187-2863","position":5,"is_corresponding":false},{"id":5919,"name":"Pascale Gaudet","orcid":"0000-0003-1813-6857","position":6,"is_corresponding":false},{"id":6466,"name":"Nomi L. Harris","orcid":"0000-0001-6315-3707","position":7,"is_corresponding":false},{"id":103846,"name":"David P. Hill","orcid":"0000-0001-7476-6306","position":8,"is_corresponding":false},{"id":1361052,"name":"Patrick Kalita","orcid":"0000-0002-6150-307X","position":9,"is_corresponding":false},{"id":1013556,"name":"Raymond Lee","orcid":"0000-0002-8151-7479","position":10,"is_corresponding":false},{"id":103809,"name":"Huaiyu Mi","orcid":"0000-0001-8721-202X","position":11,"is_corresponding":false},{"id":6456,"name":"Sierra A. T. Moxon","orcid":"0000-0002-8719-7760","position":12,"is_corresponding":false},{"id":6476,"name":"Christopher J. Mungall","orcid":"0000-0002-6601-2165","position":13,"is_corresponding":false},{"id":4242,"name":"Anushya Muruganujan","orcid":"0000-0001-7169-5864","position":14,"is_corresponding":false},{"id":103811,"name":"Tremayne Mushayahama","orcid":"0000-0002-2874-6934","position":15,"is_corresponding":false},{"id":49667,"name":"Paul W. Sternberg","orcid":"0000-0002-7699-0173","position":16,"is_corresponding":false},{"id":4067,"name":"Paul D. Thomas","orcid":"0000-0002-9074-3507","position":17,"is_corresponding":false},{"id":35841,"name":"Kimberly Van Auken","orcid":"0000-0002-1706-4196","position":18,"is_corresponding":false},{"id":515367,"name":"Edith D. Wong","orcid":"0000-0001-9799-5523","position":19,"is_corresponding":false},{"id":95769,"name":"Valerie Wood","orcid":"0000-0001-6330-7526","position":20,"is_corresponding":false},{"id":711658,"name":"Jolene Ramsey","orcid":"0000-0002-3774-5896","position":21,"is_corresponding":false},{"id":103813,"name":"Deborah A. Siegele","orcid":"0000-0001-8935-0696","position":22,"is_corresponding":false},{"id":11686,"name":"Rex L. Chisholm","orcid":"0000-0002-5638-3990","position":23,"is_corresponding":false},{"id":1361053,"name":"Robert Dodson","orcid":"0000-0002-2757-5950","position":24,"is_corresponding":false},{"id":103805,"name":"Petra Fey","orcid":"0000-0002-4532-2703","position":25,"is_corresponding":false},{"id":1013557,"name":"Maria Cristina Aspromonte","orcid":"0000-0002-4937-6952","position":26,"is_corresponding":false},{"id":1013558,"name":"María Victoria Nugnes","orcid":"0000-0001-8399-7907","position":27,"is_corresponding":false},{"id":1361054,"name":"Ximena Aixa Castro Naser","orcid":"0000-0002-9211-1255","position":28,"is_corresponding":false},{"id":3393,"name":"Silvio C. E. 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Brown","orcid":"0000-0002-8958-7017","position":34,"is_corresponding":false},{"id":103820,"name":"Gil dos Santos","orcid":"0000-0003-3507-8273","position":35,"is_corresponding":false},{"id":103818,"name":"Steven J Marygold","orcid":"0000-0003-2759-266X","position":36,"is_corresponding":false},{"id":598802,"name":"Katja Röper","orcid":"0000-0002-3361-766X","position":37,"is_corresponding":false},{"id":1361055,"name":"Victor Strelets","orcid":"0000-0001-6556-9335","position":38,"is_corresponding":false},{"id":103822,"name":"Christopher J. Tabone","orcid":"0000-0001-8746-0680","position":39,"is_corresponding":false},{"id":103826,"name":"Jim Thurmond","orcid":"0000-0002-5142-2583","position":40,"is_corresponding":false},{"id":1361056,"name":"Pinglei Zhou","orcid":"0000-0002-3012-1044","position":41,"is_corresponding":false},{"id":103523,"name":"Rossana Zaru","orcid":"0000-0002-3358-4423","position":42,"is_corresponding":false},{"id":103829,"name":"Ruth C. 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[majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Releases of the ontology and annotations are archived at https://release.geneontology.org/ and on Zenodo (https://doi.org/10.5281/zenodo.1205166).","grounded":false,"rationale":"Zenodo is a named data repository that issues accessions and commits to retention. 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[majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Downloads are available under the CC BY 4.0 license from https://geneontology.org/docs/downloads/.","grounded":true,"rationale":"The paper explicitly labels the data as available under a CC BY 4.0 license, which is an open-access label. 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[majority verdict 'no' (2/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"go-basic OBO, JSON, and OWL-RDF/XML","grounded":true,"rationale":"The paper names OBO, JSON, and OWL-RDF/XML, all of which are open, non-proprietary formats. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The Gene Ontology (GO) knowledgebase is a comprehensive resource describing the functions of genes.","grounded":false,"rationale":"The Gene Ontology itself is a community standard for gene function annotation. 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[majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":75.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Downloads are available under the CC BY 4.0 license from https://geneontology.org/docs/downloads/.","grounded":true,"rationale":"The data are released under the open CC BY 4.0 license. 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[majority verdict 'yes' (3/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Software (https://github.com/geneontology) is under the BSD 3-Clause open-source license.","grounded":false,"rationale":"The paper gives a machine-resolvable code repository URL for the software. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"The core funding for the GOC is from the National Human Genome Research Institute (U41HG002273, U24HG012212).","grounded":true,"rationale":"The paper includes specific grant numbers for the work.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Releases of the ontology and annotations are archived at https://release.geneontology.org/ and on Zenodo (https://doi.org/10.5281/zenodo.1205166).","why":"Zenodo is a named data repository that issues accessions and commits to retention. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. 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Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Software (https://github.com/geneontology) is under the BSD 3-Clause open-source license.","why":"The paper gives a machine-resolvable code repository URL for the software. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All Gene Ontology code and resources are freely available for download and reuse. Software (https://github.com/geneontology) is under the BSD 3-Clause open-source license. Downloads are available under the CC BY 4.0 license from https://geneontology.org/docs/downloads/.","why":"The statement provides a link to the repository where data are archived, corresponding to Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In chemistry / materials, describe the data with InChI, CIF or SMILES.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The Gene Ontology (GO) knowledgebase is a comprehensive resource describing the functions of genes.","why":"The Gene Ontology itself is a community standard for gene function annotation. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"There are also several computational pipelines that produce annotations using more indirect evidence, many of which are carefully reviewed by experts to ensure accuracy, e.g. InterPro2GO [21] or rule-based approaches, such as UniRule [22].","why":"The paper names specific tools and pipelines used to generate the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Table 2. GO ontology editions","why":"Variable definitions are provided inside the article via tables, but no separate documentation object is named as accompanying the data. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sensitive data is involved.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No own dataset to qualify references to other resources. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No persistence or timing statement for this study's data. [majority verdict 'no' (2/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. 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