{"doi":"10.1093/genetics/iyad031","title":"The Gene Ontology knowledgebase in 2023","abstract":"The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular \"pathways\" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.","journal":"Genetics","year":2023,"id":314628,"datarank":5.796683430264061,"base_score":7.917536353943631,"endowment":7.917536353943631,"self_citation_contribution":1.187630453091545,"citation_network_contribution":4.6090529771725155,"self_endowment_contribution":1.187630453091545,"citer_contribution":4.6090529771725155,"corpus_percentile":96.48797091359171,"corpus_rank":455,"citation_count":2744,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9518,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":70.8333,"fair_percentile":91.99021705900336,"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":103845,"name":"Harold Drabkin","orcid":"0000-0003-2689-5511","position":4,"is_corresponding":false},{"id":103807,"name":"Dustin Ebert","orcid":"0000-0002-6659-0416","position":5,"is_corresponding":false},{"id":103544,"name":"Marc Feuermann","orcid":"0000-0002-4187-2863","position":6,"is_corresponding":false},{"id":5919,"name":"Pascale Gaudet","orcid":"0000-0003-1813-6857","position":7,"is_corresponding":false},{"id":6466,"name":"Nomi L. Harris","orcid":"0000-0001-6315-3707","position":8,"is_corresponding":false},{"id":103846,"name":"David P. Hill","orcid":"0000-0001-7476-6306","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":1015058,"name":"Anushya Muruganugan","orcid":null,"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":711658,"name":"Jolene Ramsey","orcid":"0000-0002-3774-5896","position":19,"is_corresponding":false},{"id":103813,"name":"Deborah A. Siegele","orcid":"0000-0001-8935-0696","position":20,"is_corresponding":false},{"id":11686,"name":"Rex L. Chisholm","orcid":"0000-0002-5638-3990","position":21,"is_corresponding":false},{"id":103805,"name":"Petra Fey","orcid":"0000-0002-4532-2703","position":22,"is_corresponding":false},{"id":1013557,"name":"Maria Cristina Aspromonte","orcid":"0000-0002-4937-6952","position":23,"is_corresponding":false},{"id":1013558,"name":"María Victoria Nugnes","orcid":"0000-0001-8399-7907","position":24,"is_corresponding":false},{"id":257857,"name":"Federica Quaglia","orcid":"0000-0002-0341-4888","position":25,"is_corresponding":false},{"id":3393,"name":"Silvio C. E. Tosatto","orcid":"0000-0003-4525-7793","position":26,"is_corresponding":false},{"id":29022,"name":"Michelle Giglio","orcid":"0000-0001-7628-5565","position":27,"is_corresponding":false},{"id":70333,"name":"Suvarna Nadendla","orcid":"0000-0003-3643-281X","position":28,"is_corresponding":false},{"id":103814,"name":"Giulia Antonazzo","orcid":"0000-0003-0086-5621","position":29,"is_corresponding":false},{"id":103815,"name":"Helen Attrill","orcid":"0000-0003-3212-6364","position":30,"is_corresponding":false},{"id":103820,"name":"Gil dos Santos","orcid":"0000-0003-3507-8273","position":31,"is_corresponding":false},{"id":103818,"name":"Steven J Marygold","orcid":"0000-0003-2759-266X","position":32,"is_corresponding":false},{"id":103825,"name":"Victor Strelets","orcid":null,"position":33,"is_corresponding":false},{"id":103822,"name":"Christopher J. Tabone","orcid":"0000-0001-8746-0680","position":34,"is_corresponding":false},{"id":103826,"name":"Jim Thurmond","orcid":"0000-0002-5142-2583","position":35,"is_corresponding":false},{"id":103823,"name":"Pinglei Zhou","orcid":null,"position":36,"is_corresponding":false},{"id":1015059,"name":"Saadullah H. Ahmed","orcid":null,"position":37,"is_corresponding":false},{"id":1015060,"name":"Praoparn Asanitthong","orcid":null,"position":38,"is_corresponding":false},{"id":1013559,"name":"Diana Luna Buitrago","orcid":"0000-0003-2010-7174","position":39,"is_corresponding":false},{"id":1015061,"name":"Meltem N Erdol","orcid":null,"position":40,"is_corresponding":false},{"id":445055,"name":"Matthew Gage","orcid":"0000-0002-6668-6573","position":41,"is_corresponding":false},{"id":1015062,"name":"Mohamed Ali Kadhum","orcid":null,"position":42,"is_corresponding":false},{"id":1013560,"name":"Kan Yan Chloe Li","orcid":"0000-0001-7737-2118","position":43,"is_corresponding":false},{"id":1013561,"name":"Miao Long","orcid":"0000-0001-6683-1956","position":44,"is_corresponding":false},{"id":1015063,"name":"Aleksandra Michalak","orcid":null,"position":45,"is_corresponding":false},{"id":1015064,"name":"Angeline Pesala","orcid":null,"position":46,"is_corresponding":false},{"id":1013562,"name":"Armalya Pritazahra","orcid":"0009-0004-1737-8250","position":47,"is_corresponding":false},{"id":103831,"name":"Shirin C C Saverimuttu","orcid":"0000-0003-1191-2681","position":48,"is_corresponding":false},{"id":103834,"name":"Renzhi Su","orcid":"0000-0002-6819-5356","position":49,"is_corresponding":false},{"id":103835,"name":"Kate E. Thurlow","orcid":"0000-0001-9985-3684","position":50,"is_corresponding":false},{"id":103829,"name":"Ruth C. Lovering","orcid":"0000-0002-9791-0064","position":51,"is_corresponding":false},{"id":103828,"name":"Colin Logie","orcid":"0000-0002-8534-6582","position":52,"is_corresponding":false},{"id":598617,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851","position":53,"is_corresponding":false},{"id":11683,"name":"Judith A. Blake","orcid":"0000-0001-8522-334X","position":54,"is_corresponding":false},{"id":103843,"name":"Karen Christie","orcid":"0000-0001-5501-853X","position":55,"is_corresponding":false},{"id":227449,"name":"Lori E Corbani","orcid":"0000-0002-2366-557X","position":56,"is_corresponding":false},{"id":103844,"name":"M. Eileen Dolan","orcid":"0000-0001-7732-3295","position":57,"is_corresponding":false},{"id":103847,"name":"Li Ni","orcid":"0000-0002-9796-7693","position":60,"is_corresponding":false},{"id":103848,"name":"Dmitry Sitnikov","orcid":"0000-0003-3394-9805","position":61,"is_corresponding":false},{"id":227446,"name":"Cynthia L. Smith","orcid":"0000-0003-3691-0324","position":62,"is_corresponding":false},{"id":616185,"name":"Alayne Cuzick","orcid":"0000-0001-8941-3984","position":63,"is_corresponding":false},{"id":616196,"name":"James Seager","orcid":"0000-0001-7487-610X","position":64,"is_corresponding":false},{"id":1013563,"name":"Laurel Cooper","orcid":"0000-0002-6379-8932","position":65,"is_corresponding":false},{"id":265736,"name":"Justin Elser","orcid":"0000-0003-0921-1982","position":66,"is_corresponding":false},{"id":12774,"name":"Pankaj Jaiswal","orcid":"0000-0002-1005-8383","position":67,"is_corresponding":false},{"id":265729,"name":"Parul Gupta","orcid":"0000-0002-0190-8753","position":68,"is_corresponding":false},{"id":265728,"name":"Sushma Naithani","orcid":"0000-0001-7819-4552","position":70,"is_corresponding":false},{"id":1013564,"name":"Manuel Lera-Ramírez","orcid":"0000-0002-8666-9746","position":71,"is_corresponding":false},{"id":45148,"name":"Kim Rutherford","orcid":"0000-0001-6277-726X","position":72,"is_corresponding":false},{"id":95769,"name":"Valerie Wood","orcid":"0000-0001-6330-7526","position":73,"is_corresponding":false},{"id":122199,"name":"Jeffrey L De Pons","orcid":"0000-0001-7783-1556","position":74,"is_corresponding":false},{"id":103854,"name":"Melinda R. Dwinell","orcid":"0000-0002-9528-3618","position":75,"is_corresponding":false},{"id":103855,"name":"G. Thomas Hayman","orcid":"0000-0002-9553-7227","position":76,"is_corresponding":false},{"id":103856,"name":"Mary L. Kaldunski","orcid":"0000-0003-3645-6803","position":77,"is_corresponding":false},{"id":103857,"name":"Anne E. Kwitek","orcid":"0000-0003-1024-4116","position":78,"is_corresponding":false},{"id":103858,"name":"Stanley J. F. Laulederkind","orcid":"0000-0001-5356-4174","position":79,"is_corresponding":false},{"id":103860,"name":"Marek Tutaj","orcid":"0000-0002-1025-101X","position":80,"is_corresponding":false},{"id":103861,"name":"Mahima Vedi","orcid":"0000-0001-5361-6739","position":81,"is_corresponding":false},{"id":103862,"name":"Shur‐Jen Wang","orcid":"0000-0001-5256-8683","position":82,"is_corresponding":false},{"id":57223,"name":"Peter D’Eustachio","orcid":"0000-0002-5494-626X","position":83,"is_corresponding":false},{"id":103527,"name":"Lucila Aimo","orcid":"0000-0003-0943-6401","position":84,"is_corresponding":false},{"id":103530,"name":"Kristian B. Axelsen","orcid":"0000-0003-3889-2879","position":85,"is_corresponding":false},{"id":103525,"name":"Alan Bridge","orcid":"0000-0003-2148-9135","position":86,"is_corresponding":false},{"id":103552,"name":"Nevila Hyka‐Nouspikel","orcid":"0000-0001-7855-209X","position":87,"is_corresponding":false},{"id":796873,"name":"Anne Morgat","orcid":"0000-0002-1216-2969","position":88,"is_corresponding":false},{"id":103866,"name":"Stacia R. Engel","orcid":"0000-0001-5472-917X","position":91,"is_corresponding":false},{"id":103868,"name":"Kalpana Karra","orcid":"0000-0002-6816-2458","position":92,"is_corresponding":false},{"id":637992,"name":"Stuart R. Miyasato","orcid":"0000-0001-5250-8920","position":93,"is_corresponding":false},{"id":320078,"name":"Robert S Nash","orcid":"0000-0002-3726-7441","position":94,"is_corresponding":false},{"id":92006,"name":"Marek S. Skrzypek","orcid":"0000-0001-6749-615X","position":95,"is_corresponding":false},{"id":86953,"name":"Shuai Weng","orcid":"0000-0003-4233-0772","position":96,"is_corresponding":false},{"id":515367,"name":"Edith D. Wong","orcid":"0000-0001-9799-5523","position":97,"is_corresponding":false},{"id":1015065,"name":"Erika Bakker","orcid":null,"position":98,"is_corresponding":false},{"id":754506,"name":"Tanya Berardini","orcid":"0000-0002-3837-8864","position":99,"is_corresponding":false},{"id":103864,"name":"Suzi Aleksander","orcid":"0000-0001-6787-2901","position":0,"is_corresponding":true}],"reference_count":72,"raw_metadata":null,"created_at":"2026-07-19T01:06:02.898877Z","pmid":"36866529","pmcid":"PMC10158837","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":22.2222,"fair_a":81.25,"fair_i":60.0,"fair_r":83.3333,"fair_zscore":1.4401,"fair_rationale":{"fair_score":70.83,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":22.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Statistics and descriptions given here are based on the GO release 2022–11–03 ( http://release.geneontology.org/2022-11-03, doi:10.5281/zenodo.7407024)","grounded":false,"rationale":"The paper provides a DOI (10.5281/zenodo.7407024) for the data release, which is a persistent identifier scheme. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":"Statistics and descriptions given here are based on the GO release 2022–11–03 ( http://release.geneontology.org/2022-11-03, doi:10.5281/zenodo.7407024)","grounded":false,"rationale":"The DOI resolves to Zenodo, a recognised data repository, and the sentence predicates the data's location via that DOI. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"Data availability All GO 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 http://geneontology.org/docs/downloads/","grounded":false,"rationale":"The DAS points to a project website and GitHub, not to a repository record with an accession, so it falls in Colavizza category 2 (link to archived data but not a repository record). [downgraded to 'no' — no verifiable quote from the paper]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"answers","grounded":false,"rationale":"The dataset is described in running prose, not in an itemized inventory. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"Statistics and descriptions given here are based on the GO release 2022–11–03 ( http://release.geneontology.org/2022-11-03, doi:10.5281/zenodo.7407024)","grounded":false,"rationale":"The dataset identifier (DOI) appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":81.25,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"All GO code and resources are freely available for download and reuse.","grounded":true,"rationale":"The text states the data are freely available without any precondition, embargo, or registration requirement. [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":"All GO code and resources are freely available for download and reuse.","grounded":true,"rationale":"The paper explicitly labels the data as 'freely available', which is a synonym for open access, matching the COAR vocabulary. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are not sensitive; no gatekeeper is named or implied.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"All GO code and resources are freely available for download and reuse.","grounded":true,"rationale":"The text states current availability but gives no persistence commitment or retention period; only availability timing is addressed. [majority verdict 'partial' (3/5 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":0.5,"verdict":"partial","evidence":"OBO","grounded":false,"rationale":"Table 6 lists open, community-standard formats such as OBO, OWL-RDF/XML, JSON, and TSV for the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":1.0,"verdict":"yes","evidence":"The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products","grounded":true,"rationale":"The paper names the Gene Ontology itself, which is a community standard registered in FAIRsharing. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"answers","grounded":false,"rationale":"No identifiers for external resources (other than the paper's own dataset) are provided in the text. [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":83.33,"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","grounded":true,"rationale":"The paper explicitly names the open standard license CC BY 4.0 for the data. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"PAINT software tool","grounded":true,"rationale":"The paper names the PAINT software tool used for phylogenetic annotation, a specific tool in data production. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No documentation object (README, data dictionary, codebook) is named as travelling with the data; the paper itself provides descriptions but not a shipped file. [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"GO release 2022–11–03","grounded":true,"rationale":"The paper provides a version token 'GO release 2022–11–03' for the data snapshot. [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":1.0,"verdict":"yes","evidence":"Software (https://github.com/geneontology/) is under the BSD 3-Clause open-source license.","grounded":true,"rationale":"The paper gives a machine-resolvable URL to the code repository on GitHub. [majority verdict 'yes' (4/5 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":"U41HG002273, U24HG012212","grounded":true,"rationale":"The paper lists specific grant numbers from the National Human Genome Research Institute. [majority verdict 'yes' (4/5 passes agreed)]","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_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Statistics and descriptions given here are based on the GO release 2022–11–03 ( http://release.geneontology.org/2022-11-03, doi:10.5281/zenodo.7407024)","why":"The paper provides a DOI (10.5281/zenodo.7407024) for the data release, which is a persistent identifier scheme. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"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.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Statistics and descriptions given here are based on the GO release 2022–11–03 ( http://release.geneontology.org/2022-11-03, doi:10.5281/zenodo.7407024)","why":"The DOI resolves to Zenodo, a recognised data repository, and the sentence predicates the data's location via that DOI. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 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. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Statistics and descriptions given here are based on the GO release 2022–11–03 ( http://release.geneontology.org/2022-11-03, doi:10.5281/zenodo.7407024)","why":"The dataset identifier (DOI) appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"OBO","why":"Table 6 lists open, community-standard formats such as OBO, OWL-RDF/XML, JSON, and TSV for the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":"no","current":0.0,"evidence":"Data availability All GO 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 http://geneontology.org/docs/downloads/","why":"The DAS points to a project website and GitHub, not to a repository record with an accession, so it falls in Colavizza category 2 (link to archived data but not a repository record). [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"answers","why":"The dataset is described in running prose, not in an itemized inventory. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"essential","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":"no","current":0.0,"evidence":null,"why":"No documentation object (README, data dictionary, codebook) is named as travelling with the data; the paper itself provides descriptions but not a shipped file. [majority verdict 'no' (3/5 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":"The data are not sensitive; no gatekeeper is named or implied.","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":"answers","why":"No identifiers for external resources (other than the paper's own dataset) are provided in the text. [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":"partial","current":0.5,"evidence":"All GO code and resources are freely available for download and reuse.","why":"The text states current availability but gives no persistence commitment or retention period; only availability timing is addressed. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication.","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.","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. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable.","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."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:45:12.136160Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}