{"doi":"10.1101/gr.280790.125","title":"The PanOryza pangene catalog of Asian cultivated rice","abstract":"The rice genome underpins fundamental research and breeding, but the Nipponbare ( japonica ) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was developed, comprising high-quality assemblies of 16 rice cultivars to represent the japonica , indica , aus , and aromatic varietal groups. The RPRP has been consistently annotated and supported by extensive experimental data, and here, we report the computational assignment, characterization, and dissemination of stably identified pangenes, collectively called the PanOryza data set. We identify 25,178 core pangenes shared across all cultivars, alongside cultivar-specific and family-enriched genes. Core genes exhibit higher gene expression and proteomic evidence, higher confidence protein domains, and AlphaFold structures, whereas cultivar-specific genes are enriched for domains under selective breeding pressure, such as for disease resistance. We identify more than 5000 genes absent in the IRGSP rice reference genome and present in at least two other Oryza cultivars. We demonstrate the utility of this resource through various examples of pangenes and their protein domains. This resource, integrated into public databases, enables researchers to explore genetic and functional diversity via a population-aware “reference guide” across rice genomes, advancing both basic and applied research.","journal":"Genome Research","year":2025,"id":559666,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":22.178386323199504,"corpus_rank":9377,"citation_count":1,"citer_count":1,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.947,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":54.1667,"fair_percentile":68.66401712014674,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1461492,"name":"Eshan Sharma","orcid":"0000-0003-2897-2314","position":1,"is_corresponding":false},{"id":1013827,"name":"Shradha Saraf","orcid":"0000-0002-6433-8356","position":2,"is_corresponding":false},{"id":265740,"name":"Guy Naamati","orcid":"0000-0002-0523-4071","position":3,"is_corresponding":false},{"id":265729,"name":"Parul Gupta","orcid":"0000-0002-0190-8753","position":4,"is_corresponding":false},{"id":265736,"name":"Justin Elser","orcid":"0000-0003-0921-1982","position":5,"is_corresponding":false},{"id":1021588,"name":"Dmytro Chebotarov","orcid":"0000-0003-1351-9453","position":6,"is_corresponding":false},{"id":265734,"name":"Kapeel Chougule","orcid":"0000-0002-1967-4246","position":7,"is_corresponding":false},{"id":615094,"name":"Zhenyuan Lu","orcid":"0000-0003-1758-2636","position":8,"is_corresponding":false},{"id":1286974,"name":"Xuehong Wei","orcid":"0000-0002-4585-3264","position":9,"is_corresponding":false},{"id":265730,"name":"Andrew Olson","orcid":"0000-0003-4946-9021","position":10,"is_corresponding":false},{"id":1198764,"name":"Ian Tsang","orcid":"0009-0006-1999-3251","position":11,"is_corresponding":false},{"id":615760,"name":"Disha Lodha","orcid":"0000-0002-1592-9395","position":12,"is_corresponding":false},{"id":1021586,"name":"Yong Zhou","orcid":"0000-0002-1662-9589","position":13,"is_corresponding":false},{"id":1021587,"name":"Zhichao Yu","orcid":"0000-0003-2155-4830","position":14,"is_corresponding":false},{"id":498752,"name":"Wen Zhao","orcid":"0000-0001-6649-3926","position":15,"is_corresponding":false},{"id":219595,"name":"Jianwei Zhang","orcid":"0000-0001-8030-5346","position":16,"is_corresponding":false},{"id":232927,"name":"Sandeep Amberkar","orcid":"0000-0001-5544-6059","position":17,"is_corresponding":false},{"id":1461493,"name":"Kawinnat Sue-Ob","orcid":"0000-0002-9456-0716","position":18,"is_corresponding":false},{"id":557232,"name":"Zhi Sun","orcid":"0000-0003-3324-6851","position":19,"is_corresponding":false},{"id":57226,"name":"María Martin","orcid":"0000-0001-5454-2815","position":20,"is_corresponding":false},{"id":1021603,"name":"Kenneth McNally","orcid":"0000-0002-9613-5537","position":21,"is_corresponding":false},{"id":265747,"name":"Doreen Ware","orcid":"0000-0002-8125-3821","position":22,"is_corresponding":false},{"id":6362,"name":"Eric W. Deutsch","orcid":"0000-0001-8732-0928","position":23,"is_corresponding":false},{"id":1021600,"name":"Dario Copetti","orcid":"0000-0002-2680-2568","position":24,"is_corresponding":false},{"id":258656,"name":"Rod A. Wing","orcid":"0000-0001-6633-6226","position":25,"is_corresponding":false},{"id":12774,"name":"Pankaj Jaiswal","orcid":"0000-0002-1005-8383","position":26,"is_corresponding":false},{"id":616188,"name":"Sarah Dyer","orcid":"0000-0001-5690-9633","position":27,"is_corresponding":false},{"id":74630,"name":"Andrew R. Jones","orcid":"0000-0001-6118-9327","position":28,"is_corresponding":false},{"id":265739,"name":"Bruno Contreras‐Moreira","orcid":"0000-0002-5462-907X","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:55:39.010633Z","pmid":"41386984","pmcid":"PMC12758395","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":55.5556,"fair_a":25.0,"fair_i":60.0,"fair_r":41.6667,"fair_zscore":0.7804,"fair_rationale":{"fair_score":54.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":55.56,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"A permanent DOI has also been created for the pangene matrix and identifiers (https://zenodo.org/records/14772953)","grounded":false,"rationale":"The paper asserts a DOI for the dataset, and the given URL resolves to a Zenodo record, which is a persistent identifier. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 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":"Zenodo","grounded":true,"rationale":"The paper names Zenodo, a repository listed in re3data/FAIRsharing, as the holder of the data. [majority verdict 'yes' (3/5 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":0.5,"verdict":"partial","evidence":"Data access The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).","grounded":false,"rationale":"The statement points to a repository record with a link (Colavizza category 3). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":0.5,"verdict":"partial","evidence":"We identify 25,178 core pangenes shared across all cultivars, alongside cultivar-specific and family-enriched genes.","grounded":true,"rationale":"The dataset's content is described in running prose rather than an itemised inventory. [majority verdict 'partial' (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":"Data access The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).","grounded":false,"rationale":"The dataset identifier appears only in the body text, not in a reference list entry. [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":25.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).","grounded":false,"rationale":"The data are deposited in a public repository with no stated precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":0.0,"verdict":"no","evidence":"The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).","grounded":false,"rationale":"The paper describes the deposit action but does not apply an explicit access-level label such as 'open access'. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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 or human-subject, and 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No statement about how long data will persist or when they become available beyond the current deposit. [majority verdict 'no' (2/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"We first collected whole-genome sequences, gene and protein sequences (all FASTA format), and gene model coordinates (GFF format) for the RPRP rice population.","grounded":true,"rationale":"FASTA and GFF are open, community-standard formats named for the data. [majority verdict 'yes' (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":null,"grounded":false,"rationale":"No community-standard vocabulary or checklist is explicitly named for the dataset itself. [majority verdict 'no' (2/5 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":"AlphaFold models for O. sativa (reference id: UP000059680) were retrieved from the AlphaFold protein structure database","grounded":true,"rationale":"The paper includes an identifier (UniProt proteome ID) for a resource used in the analysis, not the own dataset. [majority verdict 'yes' (4/5 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":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license is stated for the data; the article's CC-BY license does not apply to the data.","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 ran the GET_PANGENES pipeline (version 11012024) (Contreras-Moreira et al. 2023), which performs WGA using minimap2 (version 2.17) (Li 2018), followed by BEDTools intersect (Quinlan and Hall 2010) to determine overlaps in each pairwise alignment.","grounded":false,"rationale":"Specific tools with version numbers are named for data production. [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":0.5,"verdict":"partial","evidence":"Supplemental Table S1 contains the matrix of pangenes, with their stable identifier (column 1) and then 16 further columns, one per input genome, containing transcript identifiers (if any) from each genome that have been mapped to that pangene.","grounded":true,"rationale":"The variable definitions are provided inside the article (Supplemental Table S1), not as a separate file shipped with the data.","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is provided for the dataset snapshot. [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":1.0,"verdict":"yes","evidence":"Code is available at GitHub (GET_PANGENES: https://github.com/Ensembl/plant-scripts/blob/master/pangenes/ ; Nipponbare merged genes: https://github.com/Ensembl/plant-scripts/tree/master/scripts ).","grounded":true,"rationale":"Machine-resolvable code forge URLs are provided. [majority verdict 'yes' (3/5 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":"Financial support was provided by the Biotechnology and Biological Sciences Research Council (BB/T015691/1 and BB/T015608/1)","grounded":true,"rationale":"The paper includes award numbers 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":"No license is stated for the data; the article's CC-BY license does not apply to the data.","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":"A permanent DOI has also been created for the pangene matrix and identifiers (https://zenodo.org/records/14772953)","why":"The paper asserts a DOI for the dataset, and the given URL resolves to a Zenodo record, which is a persistent identifier. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).","why":"The data are deposited in a public repository with no stated precondition. [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_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":"no","current":0.0,"evidence":"Data access The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).","why":"The dataset identifier appears only in the body text, not in a reference list entry. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":8.33,"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 dataset snapshot. [majority verdict 'no' (3/5 passes agreed)]","gain":4.17,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data access The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).","why":"The statement points to a repository record with a link (Colavizza category 3). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","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":"partial","current":0.5,"evidence":"We identify 25,178 core pangenes shared across all cultivars, alongside cultivar-specific and family-enriched genes.","why":"The dataset's content is described in running prose rather than an itemised inventory. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"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'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The input data for running GET_PANGENES pipeline and the output files generated by the pipeline have been deposited at Zenodo (https://zenodo.org/records/14772953).","why":"The paper describes the deposit action but does not apply an explicit access-level label such as 'open access'. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"important","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-standard vocabulary or checklist is explicitly named for the dataset itself. [majority verdict 'no' (2/5 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 ran the GET_PANGENES pipeline (version 11012024) (Contreras-Moreira et al. 2023), which performs WGA using minimap2 (version 2.17) (Li 2018), followed by BEDTools intersect (Quinlan and Hall 2010) to determine overlaps in each pairwise alignment.","why":"Specific tools with version numbers are named for data production. [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":"partial","current":0.5,"evidence":"Supplemental Table S1 contains the matrix of pangenes, with their stable identifier (column 1) and then 16 further columns, one per input genome, containing transcript identifiers (if any) from each genome that have been mapped to that pangene.","why":"The variable definitions are provided inside the article (Supplemental Table S1), not as a separate file shipped with the data.","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 or human-subject, and no gatekeeper is named.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No statement about how long data will persist or when they become available beyond the current deposit. [majority verdict 'no' (2/5 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.","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. 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.","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":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:39:48.763492Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}