{"doi":"10.1093/nar/gkae1082","title":"InterPro: the protein sequence classification resource in 2025","abstract":"InterPro (https://www.ebi.ac.uk/interpro) is a freely accessible resource for the classification of protein sequences into families. It integrates predictive models, known as signatures, from multiple member databases to classify sequences into families and predict the presence of domains and significant sites. The InterPro database provides annotations for over 200 million sequences, ensuring extensive coverage of UniProtKB, the standard repository of protein sequences, and includes mappings to several other major resources, such as Gene Ontology (GO), Protein Data Bank in Europe (PDBe) and the AlphaFold Protein Structure Database. In this publication, we report on the status of InterPro (version 101.0), detailing new developments in the database, associated web interface and software. Notable updates include the increased integration of structures predicted by AlphaFold and the enhanced description of protein families using artificial intelligence. Over the past two years, more than 5000 new InterPro entries have been created. The InterPro website now offers access to 85 000 protein families and domains from its member databases and serves as a long-term archive for retired databases. InterPro data, software and tools are freely available.","journal":"Nucleic Acids Research","year":2024,"id":416040,"datarank":3.4333496854634618,"base_score":6.849066282633458,"endowment":6.849066282633458,"self_citation_contribution":1.0273599423950188,"citation_network_contribution":2.4059897430684427,"self_endowment_contribution":1.0273599423950188,"citer_contribution":2.4059897430684427,"corpus_percentile":93.51744410922875,"corpus_rank":839,"citation_count":942,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.944,"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":16.6667,"fair_percentile":34.85172730051972,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1198681,"name":"Antonina Andreeva","orcid":"0000-0002-0450-0091","position":1,"is_corresponding":false},{"id":1200018,"name":"Laise Cavalcanti Florentino","orcid":null,"position":2,"is_corresponding":false},{"id":104535,"name":"Sara Chuguransky","orcid":"0000-0002-0520-0736","position":3,"is_corresponding":false},{"id":59119,"name":"Tiago Grego","orcid":"0000-0002-7946-7062","position":4,"is_corresponding":false},{"id":1198682,"name":"Emma Hobbs","orcid":"0000-0002-8470-4739","position":5,"is_corresponding":false},{"id":838616,"name":"Beatriz Lázaro","orcid":"0000-0001-6837-2941","position":6,"is_corresponding":false},{"id":1200019,"name":"Ailsa Orr","orcid":null,"position":7,"is_corresponding":false},{"id":104537,"name":"Typhaine Paysan‐Lafosse","orcid":"0000-0001-5663-0894","position":8,"is_corresponding":false},{"id":1198683,"name":"Irina Ponamareva","orcid":"0009-0009-6041-5869","position":9,"is_corresponding":false},{"id":34534,"name":"Gustavo A Salazar","orcid":"0000-0001-9208-4966","position":10,"is_corresponding":false},{"id":689889,"name":"Nicola Bordin","orcid":"0000-0002-6568-9035","position":11,"is_corresponding":false},{"id":19778,"name":"Peer Bork","orcid":"0000-0002-2627-833X","position":12,"is_corresponding":false},{"id":103525,"name":"Alan Bridge","orcid":"0000-0003-2148-9135","position":13,"is_corresponding":false},{"id":838618,"name":"Lucy J. Colwell","orcid":"0000-0003-3148-0337","position":14,"is_corresponding":false},{"id":77641,"name":"Julian Gough","orcid":"0000-0002-1965-4982","position":15,"is_corresponding":false},{"id":104539,"name":"Daniel H. Haft","orcid":"0000-0001-8101-4938","position":16,"is_corresponding":false},{"id":104540,"name":"Ivica Letunić","orcid":"0000-0003-3560-4288","position":17,"is_corresponding":false},{"id":1200020,"name":"Felipe Llinares-López","orcid":null,"position":18,"is_corresponding":false},{"id":65082,"name":"Aron Marchler‐Bauer","orcid":"0000-0003-1516-0712","position":19,"is_corresponding":false},{"id":1140627,"name":"Laetitia Meng-Papaxanthos","orcid":"0000-0002-0521-621X","position":20,"is_corresponding":false},{"id":103809,"name":"Huaiyu Mi","orcid":"0000-0001-8721-202X","position":21,"is_corresponding":false},{"id":57228,"name":"Darren A. Natale","orcid":"0000-0001-5809-9523","position":22,"is_corresponding":false},{"id":58697,"name":"Christine Orengo","orcid":"0000-0002-7141-8936","position":23,"is_corresponding":false},{"id":104542,"name":"Arun Prasad Pandurangan","orcid":"0000-0001-7168-7143","position":24,"is_corresponding":false},{"id":257887,"name":"Damiano Piovesan","orcid":"0000-0001-8210-2390","position":25,"is_corresponding":false},{"id":104543,"name":"Catherine Rivoire","orcid":"0000-0002-5979-8382","position":26,"is_corresponding":false},{"id":104544,"name":"Christian J A Sigrist","orcid":"0000-0002-4348-0070","position":27,"is_corresponding":false},{"id":45590,"name":"Narmada Thanki","orcid":"0000-0003-1181-2509","position":28,"is_corresponding":false},{"id":2130,"name":"Françoise Thibaud‐Nissen","orcid":"0000-0003-4957-7807","position":29,"is_corresponding":false},{"id":4067,"name":"Paul D. Thomas","orcid":"0000-0002-9074-3507","position":30,"is_corresponding":false},{"id":3393,"name":"Silvio C. E. Tosatto","orcid":"0000-0003-4525-7793","position":31,"is_corresponding":false},{"id":57230,"name":"Cathy Wu","orcid":"0000-0001-6379-8601","position":32,"is_corresponding":false},{"id":228792,"name":"Alex Bateman","orcid":"0000-0002-6982-4660","position":33,"is_corresponding":false},{"id":104534,"name":"Matthias Blum","orcid":"0000-0001-5773-4724","position":0,"is_corresponding":true}],"reference_count":58,"raw_metadata":null,"created_at":"2026-07-19T01:56:20.964471Z","pmid":"39565202","pmcid":"PMC11701551","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":11.1111,"fair_a":50.0,"fair_i":40.0,"fair_r":33.3333,"fair_zscore":-0.7039,"fair_rationale":{"fair_score":16.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":11.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"All data are freely available from the main website (https://www.ebi.ac.uk/interpro), in bulk from the FTP site (https://ftp.ebi.ac.uk/pub/databases/interpro/), and programmatically via the REST API (https://www.ebi.ac.uk/interpro/api/).","grounded":false,"rationale":"The paper provides URLs (web addresses) for the data, not a persistent identifier scheme (DOI, Handle, ARK, or repository accession). [downgraded to 'no' — no verifiable quote from the paper]","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":"All data are freely available from the main website (https://www.ebi.ac.uk/interpro), in bulk from the FTP site (https://ftp.ebi.ac.uk/pub/databases/interpro/), and programmatically via the REST API (https://www.ebi.ac.uk/interpro/api/).","grounded":false,"rationale":"The data are hosted on the InterPro website and FTP, which are institutional hosts, not a named repository like GEO or Zenodo. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":0.0,"verdict":"no","evidence":"All data are freely available from the main website (https://www.ebi.ac.uk/interpro), in bulk from the FTP site (https://ftp.ebi.ac.uk/pub/databases/interpro/), and programmatically via the REST API (https://www.ebi.ac.uk/interpro/api/).","grounded":false,"rationale":"The statement points to website and FTP URLs, not to a repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":"Table 1. Release version and number of member database signatures integrated into InterPro version 101.0","grounded":false,"rationale":"The paper includes itemised tables (Table 1 and Table 2) that describe the dataset's content. [downgraded to 'partial' — no verifiable quote from the paper] [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":"All data are freely available from the main website (https://www.ebi.ac.uk/interpro), in bulk from the FTP site (https://ftp.ebi.ac.uk/pub/databases/interpro/), and programmatically via the REST API (https://www.ebi.ac.uk/interpro/api/).","grounded":false,"rationale":"The dataset's identifier (URL) appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper]","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":50.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All data are freely available from the main website (https://www.ebi.ac.uk/interpro), in bulk from the FTP site (https://ftp.ebi.ac.uk/pub/databases/interpro/), and programmatically via the REST API (https://www.ebi.ac.uk/interpro/api/).","grounded":false,"rationale":"The text gives a route 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":1.0,"verdict":"yes","evidence":"InterPro data, software and tools are freely available.","grounded":true,"rationale":"The paper explicitly labels the access level as 'freely available'. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are not sensitive 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No sentence states when the data become available or how long they persist. [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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format is named for the released data. [majority verdict 'no' (3/5 passes agreed)]","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Gene Ontology (GO)","grounded":true,"rationale":"The paper uses Gene Ontology (GO) terms, a community standard vocabulary. [majority verdict 'yes' (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":"IDRPred (https://doi.org/10.5281/zenodo.13735975)","grounded":false,"rationale":"The paper includes a DOI for IDRPred, a resource other than the study's own dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":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":"No reuse license is explicitly stated for the data; the 'freely available' statement is not a license.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"MobiDB-lite, a resource focused on predicting intrinsic disorder in proteins, accounted for a compute time of two hours when annotating the human proteome with InterProScan with the match lookup disabled.","grounded":true,"rationale":"The paper names specific tools like MobiDB-lite, indicating the provenance of data production. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"Table 1. Release version and number of member database signatures integrated into InterPro version 101.0","grounded":false,"rationale":"Variable definitions are provided in the article's tables, with no documentation object shipped with the data. [downgraded to 'no' — no verifiable quote from the paper]","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":0.5,"verdict":"partial","evidence":"InterPro version 101.0","grounded":false,"rationale":"The paper identifies the data snapshot with a version number (101.0). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":"The latest version of InterProScan can be downloaded from the InterPro website (https://www.ebi.ac.uk/interpro/download/interproscan/).","grounded":false,"rationale":"A machine-resolvable URL is given for the study's own code (InterProScan). [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":0.5,"verdict":"partial","evidence":"Wellcome Trust [221320/Z/20/Z]","grounded":false,"rationale":"The paper includes an award number (221320/Z/20/Z) from the Wellcome Trust. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All data are freely available from the main website (https://www.ebi.ac.uk/interpro), in bulk from the FTP site (https://ftp.ebi.ac.uk/pub/databases/interpro/), and programmatically via the REST API (https://www.ebi.ac.uk/interpro/api/).","why":"The paper provides URLs (web addresses) for the data, not a persistent identifier scheme (DOI, Handle, ARK, or repository accession). [downgraded to 'no' — no verifiable quote from the paper]","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All data are freely available from the main website (https://www.ebi.ac.uk/interpro), in bulk from the FTP site (https://ftp.ebi.ac.uk/pub/databases/interpro/), and programmatically via the REST API (https://www.ebi.ac.uk/interpro/api/).","why":"The data are hosted on the InterPro website and FTP, which are institutional hosts, not a named repository like GEO or Zenodo. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":null,"why":"No reuse license is explicitly stated for the data; the 'freely available' statement is not a license.","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All data are freely available from the main website (https://www.ebi.ac.uk/interpro), in bulk from the FTP site (https://ftp.ebi.ac.uk/pub/databases/interpro/), and programmatically via the REST API (https://www.ebi.ac.uk/interpro/api/).","why":"The text gives a route 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 genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All data are freely available from the main website (https://www.ebi.ac.uk/interpro), in bulk from the FTP site (https://ftp.ebi.ac.uk/pub/databases/interpro/), and programmatically via the REST API (https://www.ebi.ac.uk/interpro/api/).","why":"The dataset's identifier (URL) appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper]","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format is named for the released data. [majority verdict 'no' (3/5 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":"The latest version of InterProScan can be downloaded from the InterPro website (https://www.ebi.ac.uk/interpro/download/interproscan/).","why":"A machine-resolvable URL is given for the study's own code (InterProScan). [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":"partial","current":0.5,"evidence":"InterPro version 101.0","why":"The paper identifies the data snapshot with a version number (101.0). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":2.08,"priority":"useful","scored":true},{"key":"x_funding_attribution","dimension":"R","label":"Funder and award number","action":"State the funder AND the award number in the paper, and put them in the dataset's FundingReference metadata. A funder name alone cannot be linked back to the award, so the funding provenance of the data is lost the moment the paper is indexed.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Wellcome Trust [221320/Z/20/Z]","why":"The paper includes an award number (221320/Z/20/Z) from the Wellcome Trust. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":2.08,"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":"All data are freely available from the main website (https://www.ebi.ac.uk/interpro), in bulk from the FTP site (https://ftp.ebi.ac.uk/pub/databases/interpro/), and programmatically via the REST API (https://www.ebi.ac.uk/interpro/api/).","why":"The statement points to website and FTP URLs, not to a repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":"Table 1. Release version and number of member database signatures integrated into InterPro version 101.0","why":"The paper includes itemised tables (Table 1 and Table 2) that describe the dataset's content. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Table 1. Release version and number of member database signatures integrated into InterPro version 101.0","why":"Variable definitions are provided in the article's tables, with no documentation object shipped with the data. [downgraded to 'no' — no verifiable quote from the paper]","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. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not sensitive 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":"IDRPred (https://doi.org/10.5281/zenodo.13735975)","why":"The paper includes a DOI for IDRPred, a resource other than the study's own dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sentence states when the data become available or how long they persist. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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.","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) 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":"2026-07-20T10:47:11.797622Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}