{"doi":"10.1016/j.xgen.2024.100527","title":"A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats","abstract":"The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.","journal":"Cell Genomics","year":2024,"id":421310,"datarank":0.6873532536808731,"base_score":3.4339872044851463,"endowment":3.4339872044851463,"self_citation_contribution":0.515098080672772,"citation_network_contribution":0.17225517300810117,"self_endowment_contribution":0.515098080672772,"citer_contribution":0.17225517300810117,"corpus_percentile":70.9213274541657,"corpus_rank":3760,"citation_count":30,"citer_count":14,"citers_with_citation_signal":8,"citers_with_endowment":8,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9263,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1163223,"name":"Yanchao Pan","orcid":"0000-0002-4288-3046","position":1,"is_corresponding":false},{"id":649906,"name":"Pasi Rastas","orcid":"0000-0003-2768-1339","position":2,"is_corresponding":false},{"id":317100,"name":"Daniel Munro","orcid":"0000-0002-0724-218X","position":3,"is_corresponding":false},{"id":122206,"name":"Monika Tutaj","orcid":"0000-0002-0378-4002","position":4,"is_corresponding":false},{"id":109860,"name":"Huda Akil","orcid":"0000-0003-0623-1056","position":5,"is_corresponding":false},{"id":68655,"name":"Christopher Benner","orcid":"0000-0002-4618-0719","position":6,"is_corresponding":false},{"id":1163224,"name":"Denghui Chen","orcid":"0000-0002-6541-3418","position":7,"is_corresponding":false},{"id":813003,"name":"Apurva S. Chitre","orcid":"0000-0003-1709-9214","position":8,"is_corresponding":false},{"id":2108,"name":"William Chow","orcid":"0000-0002-9056-201X","position":9,"is_corresponding":false},{"id":469971,"name":"Vincenza Colonna","orcid":"0000-0002-3966-0474","position":10,"is_corresponding":false},{"id":241309,"name":"Clifton L. Dalgard","orcid":"0000-0003-2025-8239","position":11,"is_corresponding":false},{"id":122200,"name":"Wendy M Demos","orcid":"0000-0002-8037-076X","position":12,"is_corresponding":false},{"id":525485,"name":"Peter A. Doris","orcid":"0000-0002-0565-7939","position":13,"is_corresponding":false},{"id":109462,"name":"Erik Garrison","orcid":"0000-0003-3821-631X","position":14,"is_corresponding":false},{"id":286498,"name":"Aron M. Geurts","orcid":"0000-0002-4347-2505","position":15,"is_corresponding":false},{"id":1214103,"name":"Hakan M. Gunturkun","orcid":null,"position":16,"is_corresponding":false},{"id":15634,"name":"Victor Guryev","orcid":"0000-0002-5810-6022","position":17,"is_corresponding":false},{"id":30880,"name":"Thibaut Hourlier","orcid":"0000-0003-4894-7773","position":18,"is_corresponding":false},{"id":108064,"name":"Kerstin Howe","orcid":"0000-0003-2237-513X","position":19,"is_corresponding":false},{"id":1163225,"name":"Jun Huang","orcid":"0000-0002-3005-4822","position":20,"is_corresponding":false},{"id":281278,"name":"Ted Kalbfleisch","orcid":"0000-0002-2370-8189","position":21,"is_corresponding":false},{"id":1163226,"name":"Panjun Kim","orcid":"0000-0001-8767-4080","position":22,"is_corresponding":false},{"id":731755,"name":"Ling Li","orcid":"0000-0002-3280-9475","position":23,"is_corresponding":false},{"id":829133,"name":"Spencer Mahaffey","orcid":"0000-0001-7035-9930","position":24,"is_corresponding":false},{"id":24505,"name":"Fergal J. Martin","orcid":"0000-0002-1672-050X","position":25,"is_corresponding":false},{"id":29313,"name":"Pejman Mohammadi","orcid":"0000-0003-4457-8552","position":26,"is_corresponding":false},{"id":345464,"name":"Ayse Bilge Ozel","orcid":"0000-0002-1112-4258","position":27,"is_corresponding":false},{"id":829431,"name":"Oksana Polesskaya","orcid":"0000-0003-3024-114X","position":28,"is_corresponding":false},{"id":703759,"name":"Michal Pravenec","orcid":"0000-0001-9197-5871","position":29,"is_corresponding":false},{"id":24530,"name":"Pjotr Prins","orcid":"0000-0002-8021-9162","position":30,"is_corresponding":false},{"id":3004,"name":"Jonathan Sebat","orcid":"0000-0002-9087-526X","position":31,"is_corresponding":false},{"id":70227,"name":"Jennifer R. Smith","orcid":null,"position":32,"is_corresponding":false},{"id":551740,"name":"Leah C. Solberg Woods","orcid":"0000-0002-7943-798X","position":33,"is_corresponding":false},{"id":405077,"name":"Boris Tabakoff","orcid":"0000-0001-5132-5030","position":34,"is_corresponding":false},{"id":92288,"name":"Alan Tracey","orcid":"0000-0002-4805-9058","position":35,"is_corresponding":false},{"id":550050,"name":"Marcela Uliano‐Silva","orcid":"0000-0001-6723-4715","position":36,"is_corresponding":false},{"id":24559,"name":"Flavia Villani","orcid":"0000-0003-3633-0610","position":37,"is_corresponding":false},{"id":285291,"name":"Hongyang Wang","orcid":"0000-0002-2971-503X","position":38,"is_corresponding":false},{"id":1163227,"name":"Burt M. Sharp","orcid":"0000-0002-3765-8848","position":39,"is_corresponding":false},{"id":583612,"name":"Francesca Telese","orcid":"0000-0003-3877-0628","position":40,"is_corresponding":false},{"id":285292,"name":"Zhihua Jiang","orcid":"0000-0003-1986-088X","position":41,"is_corresponding":false},{"id":395615,"name":"Laura Saba","orcid":"0000-0001-9649-1294","position":42,"is_corresponding":false},{"id":97163,"name":"Xusheng Wang","orcid":"0000-0002-1759-9588","position":43,"is_corresponding":false},{"id":2099,"name":"Terence D. Murphy","orcid":"0000-0001-9311-9745","position":44,"is_corresponding":false},{"id":230002,"name":"Abraham A. Palmer","orcid":"0000-0003-3634-0747","position":45,"is_corresponding":false},{"id":103857,"name":"Anne E. Kwitek","orcid":"0000-0003-1024-4116","position":46,"is_corresponding":false},{"id":103854,"name":"Melinda R. Dwinell","orcid":"0000-0002-9528-3618","position":47,"is_corresponding":false},{"id":348393,"name":"Robert W. Williams","orcid":"0000-0001-8924-4447","position":48,"is_corresponding":false},{"id":235834,"name":"Jun Z. Li","orcid":"0000-0001-6727-0812","position":49,"is_corresponding":false},{"id":356630,"name":"Hao Chen","orcid":"0000-0002-2680-6921","position":50,"is_corresponding":false},{"id":1163222,"name":"Tristan V. de Jong","orcid":"0000-0003-0385-0089","position":0,"is_corresponding":true}],"reference_count":113,"raw_metadata":null,"created_at":"2026-07-19T01:57:36.298171Z","pmid":"38537634","pmcid":"PMC11019364","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":94.4444,"fair_a":62.5,"fair_i":40.0,"fair_r":25.0,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":94.44,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"https://doi.org/10.5281/zenodo.10398344","grounded":true,"rationale":"The paper gives a DOI (10.5281/zenodo.10398344) for the joint variant calling dataset, which is a persistent identifier in a recognised scheme. [majority verdict 'yes' (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":1.0,"verdict":"yes","evidence":"NIH SRA","grounded":true,"rationale":"The paper names NIH SRA as the repository for the WGS data, and Zenodo for other resources; both are established data repositories. [majority verdict 'yes' (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":1.0,"verdict":"yes","evidence":"WGS data generated for this work have been uploaded to NIH SRA (see Table S8 for SRA IDs). Other resources are available from Zenodo (See key resources table).","grounded":true,"rationale":"The data-availability statement points to two public repositories (NIH SRA with accession numbers, Zenodo with DOIs) — a Colavizza category 3 statement. [majority verdict 'yes' (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":"Deposited data","grounded":true,"rationale":"The paper includes a 'Key resources table' that itemises the deposited datasets (e.g., 'Join calling of 163 WGS rat samples (VCF)') — an itemised inventory of the data. [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":"Join calling of 163 WGS rat samples (VCF) This paper https://doi.org/10.5281/zenodo.10398344","grounded":true,"rationale":"The dataset's identifier (DOI) appears in the paper's key resources table (body text) but 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":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"WGS data generated for this work have been uploaded to NIH SRA (see Table S8 for SRA IDs). Other resources are available from Zenodo (See key resources table).","grounded":true,"rationale":"The text gives a route to the data (NIH SRA, Zenodo) with no stated precondition; the data are publicly available now. [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":0.5,"verdict":"partial","evidence":"WGS data generated for this work have been uploaded to NIH SRA (see Table S8 for SRA IDs). Other resources are available from Zenodo (See key resources table).","grounded":true,"rationale":"The paper describes the access action (uploaded to repositories) but does not apply an explicit access-level label such as 'open access' or 'publicly available' to the data themselves. [majority verdict 'partial' (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":"answers","grounded":false,"rationale":"The data are from rats, not human subjects, so no gatekeeper is needed.","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":0.0,"verdict":"no","evidence":"answers","grounded":false,"rationale":"No sentence in the paper addresses how long the data will be retained. [majority verdict 'no' (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":40.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"answers","grounded":false,"rationale":"The deposited data are in VCF format, an open community standard. [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":0.0,"verdict":"no","evidence":"answers","grounded":false,"rationale":"No data or metadata community standard (checklist, schema, ontology) is explicitly named as applied to 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":1.0,"verdict":"yes","evidence":"GCA_015244455.1","grounded":true,"rationale":"The paper gives a GenBank accession (GCA_015244455.1) for the alternative pseudo-haplotype of the mRatBN7.2 assembly, which is a resource other than the study's own dataset. [majority verdict 'yes' (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":25.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"answers","grounded":false,"rationale":"No licence is stated for the data; the CC BY licence applies only to the article.","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":"answers","grounded":false,"rationale":"The paper names specific instruments and software, e.g., PacBio CLR, Deepvariant. [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":"answers","grounded":false,"rationale":"Sample metadata are provided in Table S8, which is inside the article, not shipped with the data. 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[majority verdict 'no' (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":"answers","grounded":false,"rationale":"A GitHub repository URL and a Zenodo DOI are given for the code. [downgraded to 'partial' — no verifiable quote from the paper]","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":"R01HL064541","grounded":true,"rationale":"The acknowledgments list specific grant numbers, including NIH NHLBI R01HL064541. [majority verdict 'yes' (3/5 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":"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":"answers","why":"No licence is stated for the data; the CC BY licence applies only to the article.","gain":16.67,"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. 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Prefer open proteomics formats such as mzML or mzIdentML.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"answers","why":"The deposited data are in VCF format, an open community standard. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","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":"answers","why":"A GitHub repository URL and a Zenodo DOI are given for the code. [downgraded to 'partial' — no verifiable quote from the paper]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No version token or date is provided for the study's own dataset; the Zenodo DOIs are versioned by the platform but the paper does not state a version string. [majority verdict 'no' (3/5 passes agreed)]","gain":4.17,"priority":"useful","scored":true},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. 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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":"answers","why":"No data or metadata community standard (checklist, schema, ontology) is explicitly named as applied to 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":"answers","why":"The paper names specific instruments and software, e.g., PacBio CLR, Deepvariant. [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":"answers","why":"Sample metadata are provided in Table S8, which is inside the article, not shipped with the data. [downgraded to 'no' — no verifiable quote from the paper] [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":"answers","why":"The data are from rats, not human subjects, so no gatekeeper is needed.","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":"answers","why":"No sentence in the paper addresses how long the data will be retained. [majority verdict 'no' (3/5 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.","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.","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).","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset."],"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":"2026-07-20T11:37:16.075605Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}