{"doi":"10.1093/nar/gkac1071","title":"GENCODE: reference annotation for the human and mouse genomes in 2023","abstract":"GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.","journal":"Nucleic Acids Research","year":2022,"id":231648,"datarank":5.060220746924039,"base_score":6.498282149476434,"endowment":6.498282149476434,"self_citation_contribution":0.9747423224214652,"citation_network_contribution":4.085478424502574,"self_endowment_contribution":0.9747423224214652,"citer_contribution":4.085478424502574,"corpus_percentile":95.80722518759187,"corpus_rank":543,"citation_count":663,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9492,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":54.1667,"fair_percentile":68.66401712014674,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":59135,"name":"Sílvia Carbonell Sala","orcid":"0000-0001-7956-6215","position":1,"is_corresponding":false},{"id":16842,"name":"Mark Diekhans","orcid":"0000-0002-0430-0989","position":2,"is_corresponding":false},{"id":292,"name":"Irwin Jungreis","orcid":"0000-0002-3197-5367","position":3,"is_corresponding":false},{"id":24601,"name":"Jane E Loveland","orcid":"0000-0002-7669-2934","position":4,"is_corresponding":false},{"id":105367,"name":"Jonathan M. Mudge","orcid":"0000-0003-4789-7495","position":5,"is_corresponding":false},{"id":43162,"name":"Cristina Sisu","orcid":"0000-0001-9371-0797","position":6,"is_corresponding":false},{"id":43288,"name":"James C. Wright","orcid":"0000-0001-6950-4328","position":7,"is_corresponding":false},{"id":839080,"name":"Carme Arnan","orcid":"0000-0002-7431-2088","position":8,"is_corresponding":false},{"id":18893,"name":"If Barnes","orcid":"0000-0001-9303-4610","position":9,"is_corresponding":false},{"id":250690,"name":"Abhimanyu Banerjee","orcid":"0000-0003-3047-6803","position":10,"is_corresponding":false},{"id":42924,"name":"Ruth Bennett","orcid":"0000-0002-9009-4607","position":11,"is_corresponding":false},{"id":42926,"name":"Andrew Berry","orcid":"0000-0001-5096-7701","position":12,"is_corresponding":false},{"id":18895,"name":"Alexandra Bignell","orcid":"0000-0002-5926-7020","position":13,"is_corresponding":false},{"id":4960,"name":"Carles B. Adsera","orcid":"0000-0001-9212-856X","position":14,"is_corresponding":false},{"id":59138,"name":"Ferriol Calvet","orcid":"0000-0003-1841-9881","position":15,"is_corresponding":false},{"id":642665,"name":"Daniel Cerdán-Vélez","orcid":"0000-0003-4499-6201","position":16,"is_corresponding":false},{"id":35062,"name":" Fiona Cunningham","orcid":"0000-0002-7445-2419","position":17,"is_corresponding":false},{"id":105333,"name":"Claire Davidson","orcid":"0000-0002-4910-8202","position":18,"is_corresponding":false},{"id":42963,"name":"Sarah Donaldson","orcid":"0000-0002-2576-3173","position":19,"is_corresponding":false},{"id":21390,"name":"Cagatay Dursun","orcid":"0000-0002-0897-7671","position":20,"is_corresponding":false},{"id":105336,"name":"Reham Fatima","orcid":"0000-0002-9914-4893","position":21,"is_corresponding":false},{"id":839081,"name":"Stefano Giorgetti","orcid":"0000-0001-5424-9723","position":22,"is_corresponding":false},{"id":30915,"name":"Carlos García Girón","orcid":"0000-0002-0935-7271","position":23,"is_corresponding":false},{"id":37971,"name":"Jose Manuel Gonzalez","orcid":"0000-0001-5569-0705","position":24,"is_corresponding":false},{"id":43255,"name":"Matthew P. Hardy","orcid":"0000-0001-6420-1715","position":25,"is_corresponding":false},{"id":56289,"name":"Peter W. Harrison","orcid":"0000-0002-4007-2899","position":26,"is_corresponding":false},{"id":30880,"name":"Thibaut Hourlier","orcid":"0000-0003-4894-7773","position":27,"is_corresponding":false},{"id":839082,"name":"Zoe Hollis","orcid":"0000-0002-4435-4666","position":28,"is_corresponding":false},{"id":18874,"name":"Toby Hunt","orcid":"0000-0001-8377-0841","position":29,"is_corresponding":false},{"id":39697,"name":"Benjamin T. James","orcid":"0000-0002-6228-055X","position":30,"is_corresponding":false},{"id":19719,"name":"Yunzhe Jiang","orcid":"0000-0001-8768-0050","position":31,"is_corresponding":false},{"id":11760,"name":"Todd A. Johnson","orcid":"0000-0003-4607-2782","position":32,"is_corresponding":false},{"id":18871,"name":"Mike Kay","orcid":"0000-0002-3282-0834","position":33,"is_corresponding":false},{"id":11723,"name":"Julien Lagarde","orcid":"0000-0002-0290-7445","position":34,"is_corresponding":false},{"id":24505,"name":"Fergal J. Martin","orcid":"0000-0002-1672-050X","position":35,"is_corresponding":false},{"id":59136,"name":"Laura Martínez Gómez","orcid":"0000-0001-9843-1332","position":36,"is_corresponding":false},{"id":77897,"name":"Surag Nair","orcid":"0000-0002-6216-2457","position":37,"is_corresponding":false},{"id":21455,"name":"Pengyu Ni","orcid":"0000-0001-9878-5480","position":38,"is_corresponding":false},{"id":59137,"name":"Fernando Campo del Pozo","orcid":"0000-0001-7688-6045","position":39,"is_corresponding":false},{"id":840515,"name":"Vivek Ramalingam","orcid":null,"position":40,"is_corresponding":false},{"id":29376,"name":"Magali Ruffier","orcid":"0000-0002-8386-1580","position":41,"is_corresponding":false},{"id":59128,"name":"Bianca M. Schmitt","orcid":"0000-0003-4341-2972","position":42,"is_corresponding":false},{"id":4922,"name":"Jacob Matthew Schreiber","orcid":"0000-0003-4230-6625","position":43,"is_corresponding":false},{"id":105355,"name":"Emily Steed","orcid":"0000-0003-4742-2860","position":44,"is_corresponding":false},{"id":18873,"name":"Marie-Marthe Suner","orcid":"0000-0002-0380-7171","position":45,"is_corresponding":false},{"id":399408,"name":"Dulika Sumathipala","orcid":"0000-0002-3206-5509","position":46,"is_corresponding":false},{"id":839083,"name":"Irina Sycheva","orcid":"0000-0003-3784-0508","position":47,"is_corresponding":false},{"id":43283,"name":"Barbara Uszczyńska-Ratajczak","orcid":"0000-0003-0150-3841","position":48,"is_corresponding":false},{"id":839084,"name":"Elizabeth Wass","orcid":"0000-0002-8605-9921","position":49,"is_corresponding":false},{"id":59139,"name":"Yucheng T. Yang","orcid":"0000-0002-6873-5279","position":50,"is_corresponding":false},{"id":59133,"name":"Andrew Yates","orcid":"0000-0002-8886-4772","position":51,"is_corresponding":false},{"id":840516,"name":"Zahoor Zafrulla","orcid":null,"position":52,"is_corresponding":false},{"id":17805,"name":"Jyoti Sharma Choudhary","orcid":"0000-0003-0881-5477","position":53,"is_corresponding":false},{"id":108504,"name":"Mark Gerstein","orcid":"0000-0002-9746-3719","position":54,"is_corresponding":false},{"id":103609,"name":"Roderic Guigó","orcid":"0000-0002-5738-4477","position":55,"is_corresponding":false},{"id":2131,"name":"Tim Hubbard","orcid":"0000-0002-1767-9318","position":56,"is_corresponding":false},{"id":103614,"name":"Manolis Kellis","orcid":"0000-0001-7113-9630","position":57,"is_corresponding":false},{"id":360,"name":"Anshul Kundaje","orcid":"0000-0003-3084-2287","position":58,"is_corresponding":false},{"id":108063,"name":"Benedict Paten","orcid":"0000-0001-8863-3539","position":59,"is_corresponding":false},{"id":285032,"name":"Michael L. Tress","orcid":"0000-0001-9046-6370","position":60,"is_corresponding":false},{"id":105371,"name":"Paul Flicek","orcid":"0000-0002-3897-7955","position":61,"is_corresponding":false},{"id":105364,"name":"Adam Frankish","orcid":"0000-0002-4333-628X","position":0,"is_corresponding":true}],"reference_count":43,"raw_metadata":null,"created_at":"2026-07-19T00:20:51.245255Z","pmid":"36420896","pmcid":"PMC9825462","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":50.0,"fair_a":81.25,"fair_i":20.0,"fair_r":33.3333,"fair_zscore":0.7804,"fair_rationale":{"fair_score":54.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.","grounded":true,"rationale":"The paper provides a web address (URL) for the data, not a persistent identifier scheme. [majority verdict 'partial' (4/5 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":"Each release is versioned and made available immediately upon release from Ensembl and https//www.gencodegenes.org","grounded":true,"rationale":"The holders named are Ensembl (a genome browser) and the GENCODE website (a project site), not a dedicated data repository. [majority verdict 'partial' (2/5 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":"No new data were generated or analysed in support of this research.","grounded":true,"rationale":"The data-availability statement declares no new data were generated, so it does not point to a repository record. [majority verdict 'no' (4/5 passes agreed)]","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":1.0,"verdict":"yes","evidence":"Table 1. Total numbers of genes and transcripts in the GENCODE 41 (human) and GENCODE M30 (mouse) releases by gene functional biotype.","grounded":true,"rationale":"The paper includes a table (Table 1) that itemises the counts of genes and transcripts, serving as an itemised inventory of the dataset. [majority verdict 'yes' (4/5 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":0.5,"verdict":"partial","evidence":"The current human release is GENCODE 41 (July 2022) and the current mouse release is GENCODE M30 (July 2022).","grounded":true,"rationale":"The dataset version string appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (4/5 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":"We make all our annotation freely available to support genome interpretation and biomedical research.","grounded":true,"rationale":"The paper states the data are freely available with no precondition.","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":"We make all our annotation freely available to support genome interpretation and biomedical research.","grounded":true,"rationale":"The paper explicitly states the data are 'freely available', which is a direct access-level label.","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 paper describes no sensitive or human-subject data, so no gatekeeper is named.","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":"Each release is versioned and made available immediately upon release from Ensembl and https//www.gencodegenes.org","grounded":true,"rationale":"The paper states the data are available immediately upon release but does not specify a retention period. [majority verdict 'partial' (4/5 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":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Ensembl FTP site (ftp://ftp.ensembl.org/pub/), which includes genesets in GFF3, Genbank and GTF formats","grounded":false,"rationale":"The paper names GFF3, GTF, and Genbank formats, which are open, community-standard formats. [downgraded to 'partial' — no verifiable quote from the paper]","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No community data or metadata standard (e.g., MIAME, Dublin Core) is named for the data. [majority verdict 'no' (4/5 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":null,"grounded":false,"rationale":"No identifier (accession, DOI, RRID, etc.) for an external resource is provided in the text.","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":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name any licence for the data itself; only the article's licence is mentioned.","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":0.5,"verdict":"partial","evidence":"we have implemented the use of the tmerge pipeline (https://github.com/julienlag/tmerge) within TAGENE","grounded":false,"rationale":"The paper names specific tools and pipelines (e.g., tmerge, TAGENE) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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, codebook) is named as travelling with the data. [majority verdict 'no' (2/5 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":"The current human release is GENCODE 41 (July 2022) and the current mouse release is GENCODE M30 (July 2022).","grounded":true,"rationale":"The paper provides version tokens (GENCODE 41, M30) for the data snapshots.","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":"we have implemented the use of the tmerge pipeline (https://github.com/julienlag/tmerge) within TAGENE","grounded":false,"rationale":"The paper gives a GitHub URL for the tool, which is a machine-resolvable locator for the study's code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":"National Human Genome Research Institute of the National Institutes of Health [U41HG007234, R01HG004037]; Wellcome Trust [WT222155 /Z/20/Z]","grounded":true,"rationale":"The paper includes specific grant numbers (U41HG007234, R01HG004037, WT222155/Z/20/Z) for the funding.","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":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name any licence for the data itself; only the article's licence is mentioned.","gain":16.67,"priority":"essential","scored":true},{"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. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.","why":"The paper provides a web address (URL) for the data, not a persistent identifier scheme. [majority verdict 'partial' (4/5 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. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Each release is versioned and made available immediately upon release from Ensembl and https//www.gencodegenes.org","why":"The holders named are Ensembl (a genome browser) and the GENCODE website (a project site), not a dedicated data repository. [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. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The current human release is GENCODE 41 (July 2022) and the current mouse release is GENCODE M30 (July 2022).","why":"The dataset version string appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"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. Prefer open proteomics formats such as mzML or mzIdentML.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Ensembl FTP site (ftp://ftp.ensembl.org/pub/), which includes genesets in GFF3, Genbank and GTF formats","why":"The paper names GFF3, GTF, and Genbank formats, which are open, community-standard formats. [downgraded to 'partial' — no verifiable quote from the paper]","gain":4.17,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"we have implemented the use of the tmerge pipeline (https://github.com/julienlag/tmerge) within TAGENE","why":"The paper gives a GitHub URL for the tool, which is a machine-resolvable locator for the study's code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 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":"No new data were generated or analysed in support of this research.","why":"The data-availability statement declares no new data were generated, so it does not point to a repository record. [majority verdict 'no' (4/5 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 proteomics, describe the data with mzML or MIAPE.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No community data or metadata standard (e.g., MIAME, Dublin Core) is named for the data. [majority verdict 'no' (4/5 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":"we have implemented the use of the tmerge pipeline (https://github.com/julienlag/tmerge) within TAGENE","why":"The paper names specific tools and pipelines (e.g., tmerge, TAGENE) used to produce the data. [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_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, codebook) is named as travelling with the data. [majority verdict 'no' (2/5 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 paper describes no sensitive or human-subject data, so no gatekeeper is named.","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 identifier (accession, DOI, RRID, etc.) for an external resource is provided in the text.","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":"Each release is versioned and made available immediately upon release from Ensembl and https//www.gencodegenes.org","why":"The paper states the data are available immediately upon release but does not specify a retention period. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","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. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","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. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","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. Prefer open proteomics formats such as mzML or mzIdentML."],"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":"2026-07-20T10:47:52.397601Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}