{"doi":"10.1093/nar/gkae1091","title":"Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank","abstract":"The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.","journal":"Nucleic Acids Research","year":2024,"id":416143,"datarank":2.838495037639255,"base_score":5.6240175061873385,"endowment":5.6240175061873385,"self_citation_contribution":0.8436026259281009,"citation_network_contribution":1.994892411711154,"self_endowment_contribution":0.8436026259281009,"citer_contribution":1.994892411711154,"corpus_percentile":92.3106675949563,"corpus_rank":995,"citation_count":276,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9466,"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":8.3333,"fair_percentile":26.47508407214919,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1200264,"name":"Rusham Bhatt","orcid":null,"position":1,"is_corresponding":false},{"id":623799,"name":"Charmi Bhikadiya","orcid":"0000-0002-1587-5139","position":2,"is_corresponding":false},{"id":23495,"name":"Chunxiao Bi","orcid":null,"position":3,"is_corresponding":false},{"id":820698,"name":"Alison Biester","orcid":"0000-0003-4129-1871","position":4,"is_corresponding":false},{"id":1200265,"name":"Pratyoy Biswas","orcid":null,"position":5,"is_corresponding":false},{"id":339379,"name":"Sebastian Bittrich","orcid":"0000-0003-3576-0387","position":6,"is_corresponding":false},{"id":1200266,"name":"Santiago Blaumann","orcid":null,"position":7,"is_corresponding":false},{"id":1199116,"name":"Ronald Brown","orcid":"0000-0002-6311-5767","position":8,"is_corresponding":false},{"id":840448,"name":"Henry Chao","orcid":null,"position":9,"is_corresponding":false},{"id":1200267,"name":"Vivek Reddy Chithari","orcid":null,"position":10,"is_corresponding":false},{"id":32629,"name":"P. Craig","orcid":"0000-0002-2085-7816","position":11,"is_corresponding":false},{"id":525016,"name":"G.V. Crichlow","orcid":"0000-0003-0512-1031","position":12,"is_corresponding":false},{"id":343775,"name":"José M. Duarte","orcid":"0000-0002-9544-5621","position":13,"is_corresponding":false},{"id":23497,"name":"Shuchismita Dutta","orcid":"0000-0002-2109-5411","position":14,"is_corresponding":false},{"id":45291,"name":"Zukang Feng","orcid":"0000-0002-1788-6579","position":15,"is_corresponding":false},{"id":623802,"name":"Justin W. Flatt","orcid":"0000-0001-5406-8156","position":16,"is_corresponding":false},{"id":623803,"name":"Sutapa Ghosh","orcid":"0000-0001-8784-0894","position":17,"is_corresponding":false},{"id":23499,"name":"David S. Goodsell","orcid":"0000-0002-5932-2130","position":18,"is_corresponding":false},{"id":23498,"name":"Rachel Kramer Green","orcid":null,"position":19,"is_corresponding":false},{"id":623804,"name":"Vladimir Guranović","orcid":"0000-0001-7648-4628","position":20,"is_corresponding":false},{"id":624763,"name":"Jeremy Henry","orcid":null,"position":21,"is_corresponding":false},{"id":482714,"name":"Brian P. Hudson","orcid":"0000-0001-6121-9442","position":22,"is_corresponding":false},{"id":1200268,"name":"Mariya Joy","orcid":null,"position":23,"is_corresponding":false},{"id":387969,"name":"Jason T. Kaelber","orcid":"0000-0001-9426-1030","position":24,"is_corresponding":false},{"id":840450,"name":"Igor Khokhriakov","orcid":null,"position":25,"is_corresponding":false},{"id":1199117,"name":"Jhih‐Siang Lai","orcid":"0000-0001-5677-5890","position":26,"is_corresponding":false},{"id":469135,"name":"Catherine L. Lawson","orcid":"0000-0002-3261-7035","position":27,"is_corresponding":false},{"id":623805,"name":"Yu‐He Liang","orcid":"0000-0002-0574-2041","position":28,"is_corresponding":false},{"id":87314,"name":"Douglas Myers-Turnbull","orcid":"0000-0003-3610-4808","position":29,"is_corresponding":false},{"id":623806,"name":"Ezra Peisach","orcid":"0000-0002-7905-6327","position":30,"is_corresponding":false},{"id":623807,"name":"Irina Persikova","orcid":"0000-0001-9544-8390","position":31,"is_corresponding":false},{"id":991637,"name":"Dennis W. Piehl","orcid":"0000-0002-8315-2899","position":32,"is_corresponding":false},{"id":1200269,"name":"Aditya Pingale","orcid":null,"position":33,"is_corresponding":false},{"id":482501,"name":"Yana Rose","orcid":"0000-0003-1018-5718","position":34,"is_corresponding":false},{"id":528301,"name":"Jared M. Sagendorf","orcid":"0009-0009-1195-1753","position":35,"is_corresponding":false},{"id":91660,"name":"Andrej Săli","orcid":"0000-0003-0435-6197","position":36,"is_corresponding":false},{"id":482500,"name":"Joan Segura","orcid":"0000-0001-5593-735X","position":37,"is_corresponding":false},{"id":623808,"name":"Monica Sekharan","orcid":"0000-0002-2694-7003","position":38,"is_corresponding":false},{"id":623809,"name":"Chenghua Shao","orcid":"0000-0001-6817-7476","position":39,"is_corresponding":false},{"id":95935,"name":"James M. Smith","orcid":"0000-0002-7465-6067","position":40,"is_corresponding":false},{"id":1200270,"name":"Michael Trumbull","orcid":null,"position":41,"is_corresponding":false},{"id":623810,"name":"Brinda Vallat","orcid":"0000-0002-4076-8984","position":42,"is_corresponding":false},{"id":80508,"name":"Maria Voigt","orcid":"0000-0003-3103-7781","position":43,"is_corresponding":false},{"id":840451,"name":"Ben Webb","orcid":null,"position":44,"is_corresponding":false},{"id":624765,"name":"Shamara Whetstone","orcid":null,"position":45,"is_corresponding":false},{"id":1200271,"name":"Amy Wu-Wu","orcid":null,"position":46,"is_corresponding":false},{"id":1200272,"name":"Tongji Xing","orcid":null,"position":47,"is_corresponding":false},{"id":23502,"name":"Jasmine Young","orcid":"0000-0001-8896-6878","position":48,"is_corresponding":false},{"id":344657,"name":"Arthur O. Zalevsky","orcid":"0000-0001-6987-8119","position":49,"is_corresponding":false},{"id":23503,"name":"Christine Zardecki","orcid":"0000-0002-4149-1745","position":50,"is_corresponding":false},{"id":23506,"name":"S.K. Burley","orcid":"0000-0002-2487-9713","position":0,"is_corresponding":true}],"reference_count":62,"raw_metadata":null,"created_at":"2026-07-19T01:56:20.964471Z","pmid":"39607707","pmcid":"PMC11701563","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":0.0,"fair_a":0.0,"fair_i":0.0,"fair_r":16.6667,"fair_zscore":-1.0337,"fair_rationale":{"fair_score":8.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":0.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"The paper states that no new data were generated, so no persistent identifier for the study's data exists. [majority verdict 'no' (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":0.0,"verdict":"no","evidence":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"The paper generated no data, so no repository is named as holder of the study's data. [majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"The data availability statement says no new data were generated, which does not point to a repository record for the study's own data. [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":0.0,"verdict":"no","evidence":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"The paper does not describe a dataset of its own, so no itemized inventory of the data exists.","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":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"No dataset identifier appears because the paper generated no data. [majority verdict 'no' (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":0.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"The paper states that no new data were generated, so there is no access route to evaluate. [majority verdict 'no' (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":0.0,"verdict":"no","evidence":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"The paper explicitly states that no new data were generated, so there is no data to label an access level for. [majority verdict 'no' (4/5 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":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"The paper generated no sensitive 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":0.0,"verdict":"no","evidence":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"Since no new data were generated, no temporal commitment is made for this study's data. [majority verdict 'no' (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":0.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"No file format for the study's data is named because no data were generated. [majority verdict 'no' (4/5 passes agreed)]","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"No data community standard is named for the study's own data because no data were generated. [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":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"The study's own data is nonexistent, so there are no dependencies on other resources that require identifiers. [majority verdict 'no' (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":16.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"No new data were generated or analyzed in support of this research.","grounded":true,"rationale":"No reuse license is attached to the study's own data because no data were generated. 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[downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":"U.S. National Science Foundation [DBI-2321666, PI: to S.K.B., RCSB PDB Core Operations]; U.S. Department of Energy [DE-SC0019749, PI to S.K.B.]; National Cancer Institute, the National Institute of Allergy and Infectious Diseases, and the National Institute of General Medical Sciences of the National Institutes of Health [R01GM157729, PI to S.K.B.]","grounded":true,"rationale":"The paper lists specific grant numbers (e.g., DBI-2321666, DE-SC0019749, R01GM157729) from named funders. [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":"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 chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"No new data were generated or analyzed in support of this research.","why":"The paper states that no new data were generated, so no persistent identifier for the study's data exists. [majority verdict 'no' (4/5 passes agreed)]","gain":16.67,"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 chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"No new data were generated or analyzed in support of this research.","why":"The paper generated no data, so no repository is named as holder of the study's data. [majority verdict 'no' (4/5 passes agreed)]","gain":16.67,"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 chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"No new data were generated or analyzed in support of this research.","why":"The paper states that no new data were generated, so there is no access route to evaluate. [majority verdict 'no' (4/5 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"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":"No new data were generated or analyzed in support of this research.","why":"No reuse license is attached to the study's own data because no data were generated. [majority verdict 'no' (4/5 passes agreed)]","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 chemistry / materials formats such as CIF or MOL.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"No new data were generated or analyzed in support of this research.","why":"No file format for the study's data is named because no data were generated. [majority verdict 'no' (4/5 passes agreed)]","gain":8.33,"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":"Our release of the py-rcsbsearchapi Python library (https://github.com/rcsb/py-rcsbsearchapi)","why":"The paper provides a machine-resolvable GitHub URL for the Python library developed by the authors. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","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":"No new data were generated or analyzed in support of this research.","why":"No version token or date is given for the study's data because no data were generated.","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":"no","current":0.0,"evidence":"No new data were generated or analyzed in support of this research.","why":"The data availability statement says no new data were generated, which does not point to a repository record for the study's own data. [majority verdict 'no' (4/5 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":"no","current":0.0,"evidence":"No new data were generated or analyzed in support of this research.","why":"The paper does not describe a dataset of its own, so no itemized inventory of the data exists.","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":"No new data were generated or analyzed in support of this research.","why":"The paper explicitly states that no new data were generated, so there is no data to label an access level for. [majority verdict 'no' (4/5 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 chemistry / materials, describe the data with InChI, CIF or SMILES.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"No new data were generated or analyzed in support of this research.","why":"No data community standard is named for the study's own data because no data were generated. [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":"no","current":0.0,"evidence":"No new data were generated or analyzed in support of this research.","why":"No production methods are described for the study's own data because no data were generated. [majority verdict 'no' (4/5 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":"No new data were generated or analyzed in support of this research.","why":"No data documentation object exists because the study generated no 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":"No new data were generated or analyzed in support of this research.","why":"The paper generated no sensitive 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":"No new data were generated or analyzed in support of this research.","why":"The study's own data is nonexistent, so there are no dependencies on other resources that require identifiers. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"No new data were generated or analyzed in support of this research.","why":"Since no new data were generated, no temporal commitment is made for this study's data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","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 chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","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 chemistry / materials repository accession (e.g. from Zenodo, PubChem or the Cambridge Structural Database (CSD)) in the reference list."],"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":"2026-07-20T10:52:34.634979Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}