{"doi":"10.1093/nar/gkab1006","title":"The IntAct database: efficient access to fine-grained molecular interaction data","abstract":"The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way.","journal":"Nucleic Acids Research","year":2021,"id":145498,"datarank":4.308339554062352,"base_score":5.971261839790462,"endowment":5.971261839790462,"self_citation_contribution":0.8956892759685695,"citation_network_contribution":3.4126502780937824,"self_endowment_contribution":0.8956892759685695,"citer_contribution":3.4126502780937824,"corpus_percentile":94.85572832056936,"corpus_rank":666,"citation_count":391,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9492,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":77.0833,"fair_percentile":97.3096912259248,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":103840,"name":"Anjali Shrivastava","orcid":"0000-0002-7471-2663","position":1,"is_corresponding":false},{"id":614236,"name":"Eliot Ragueneau","orcid":"0000-0002-7876-6503","position":2,"is_corresponding":false},{"id":95742,"name":"Birgit H M Meldal","orcid":"0000-0003-4062-6158","position":3,"is_corresponding":false},{"id":617740,"name":"Colin Combe","orcid":"0000-0003-2526-2587","position":4,"is_corresponding":false},{"id":13237,"name":"Elisabet Barrera","orcid":"0000-0002-7245-9692","position":5,"is_corresponding":false},{"id":12455,"name":"Livia Perfetto","orcid":"0000-0003-4392-8725","position":6,"is_corresponding":false},{"id":619406,"name":"Karyn How","orcid":null,"position":7,"is_corresponding":false},{"id":297053,"name":"Prashansa Ratan","orcid":null,"position":8,"is_corresponding":false},{"id":297054,"name":"Gautam Shirodkar","orcid":null,"position":9,"is_corresponding":false},{"id":617741,"name":"Odilia Lu","orcid":"0000-0003-0928-0144","position":10,"is_corresponding":false},{"id":617742,"name":"Bálint Mészáros","orcid":"0000-0003-0919-4449","position":11,"is_corresponding":false},{"id":103522,"name":"Xavier Watkins","orcid":"0000-0001-9327-5887","position":12,"is_corresponding":false},{"id":103509,"name":"Sangya Pundir","orcid":"0000-0003-4526-6833","position":13,"is_corresponding":false},{"id":296065,"name":"Luana Licata","orcid":"0000-0001-5084-9000","position":14,"is_corresponding":false},{"id":296062,"name":"Marta Iannuccelli","orcid":"0000-0002-2374-3531","position":15,"is_corresponding":false},{"id":40483,"name":"Matteo Pellegrini","orcid":"0000-0001-9355-9564","position":16,"is_corresponding":false},{"id":57226,"name":"María Martin","orcid":"0000-0001-5454-2815","position":17,"is_corresponding":false},{"id":228801,"name":"Simona Panni","orcid":"0000-0002-7500-4028","position":18,"is_corresponding":false},{"id":103837,"name":"Margaret Duesbury","orcid":"0000-0002-4904-1247","position":19,"is_corresponding":false},{"id":257885,"name":"Sylvain D. Vallet","orcid":"0000-0001-9885-7499","position":20,"is_corresponding":false},{"id":351338,"name":"Juri Rappsilber","orcid":"0000-0001-5999-1310","position":21,"is_corresponding":false},{"id":257880,"name":"Sylvie Ricard‐Blum","orcid":"0000-0001-9263-1851","position":22,"is_corresponding":false},{"id":12283,"name":"Gianni Cesareni","orcid":"0000-0002-9528-6018","position":23,"is_corresponding":false},{"id":30375,"name":"Łukasz Salwiński","orcid":"0000-0003-4522-1969","position":24,"is_corresponding":false},{"id":5925,"name":"Sandra Orchard","orcid":"0000-0002-8878-3972","position":25,"is_corresponding":false},{"id":103839,"name":"Pablo Porras","orcid":"0000-0002-8429-8793","position":26,"is_corresponding":false},{"id":560412,"name":"Kalpana Panneerselvam","orcid":"0000-0003-2534-198X","position":27,"is_corresponding":false},{"id":5922,"name":"Henning Hermjakob","orcid":"0000-0001-8479-0262","position":28,"is_corresponding":false},{"id":89049,"name":"Noemí del‐Toro","orcid":"0000-0001-5272-7613","position":0,"is_corresponding":true}],"reference_count":30,"raw_metadata":null,"created_at":"2026-07-18T23:42:12.871665Z","pmid":"34761267","pmcid":"PMC8728211","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":50.0,"fair_a":75.0,"fair_i":60.0,"fair_r":62.5,"fair_zscore":1.6875,"fair_rationale":{"fair_score":77.08,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"all data is freely available through the web interface, API, and from https://www.ebi.ac.uk/intact/download under the CC BY 4.0 licence.","grounded":true,"rationale":"The strongest identifier is a URL (https://www.ebi.ac.uk/intact/download), which is not a persistent identifier scheme.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions","grounded":false,"rationale":"The IntAct database is named as the repository holding the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":1.0,"verdict":"yes","evidence":"IntAct is open source, open data. The source code is available from https://github.com/intact-portal , all data is freely available through the web interface, API, and from https://www.ebi.ac.uk/intact/download under the CC BY 4.0 licence.","grounded":true,"rationale":"The statement points to the IntAct repository's download page, a persistent link to the data repository. [majority verdict 'yes' (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":0.0,"verdict":"no","evidence":"Data Content Since the last IntAct NAR publication, data content has grown from 408 000 (Jamuary 2014) to 1 114 500 (June 2021)) interaction evidences, and the number of referenced publications has risen from 12 500 to 22 500.","grounded":false,"rationale":"The dataset is described in running prose, without an itemised inventory or table. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"all data is freely available through the web interface, API, and from https://www.ebi.ac.uk/intact/download under the CC BY 4.0 licence.","grounded":true,"rationale":"The dataset identifier (URL) appears only in the body text, not in the reference list.","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":75.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"all data is freely available through the web interface, API, and from https://www.ebi.ac.uk/intact/download under the CC BY 4.0 licence.","grounded":true,"rationale":"The data are stated to be freely available with no preconditions.","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":"all data is freely available through the web interface, API, and from https://www.ebi.ac.uk/intact/download under the CC BY 4.0 licence.","grounded":true,"rationale":"The paper labels the data as 'freely available', which is an explicit access-level label.","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"The IntAct database provides a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions.","grounded":false,"rationale":"The data are not sensitive human-subject data, and no gatekeeper is mentioned.","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 retention period or persistence is made. [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":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"the feature-rich PSI-MI XML format","grounded":true,"rationale":"PSI-MI XML is an open, community-standard format. [majority verdict 'yes' (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":0.5,"verdict":"partial","evidence":"Curation practices and controlled vocabularies/ontologies are continuously updated, driven by the development of new methods like BioID (term in PSI-MI Ontology","grounded":false,"rationale":"The PSI-MI Ontology is a community standard vocabulary used for the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No identifiers for external resources that the data depend on are provided. [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":62.5,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"under the CC BY 4.0 licence.","grounded":true,"rationale":"CC BY 4.0 is an open standard licence.","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":0.0,"verdict":"no","evidence":"members of the International Molecular Exchange Consortium (IMEx) have collaboratively curated molecular interaction data from the scientific literature and from direct data depositions","grounded":false,"rationale":"The production is described in generic terms without naming specific instruments or software. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No documentation object (README, codebook) is named as accompanying 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":0.5,"verdict":"partial","evidence":"as of August 2021","grounded":true,"rationale":"A date is provided to pin the snapshot, but no version token.","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":"The source code is available from https://github.com/intact-portal","grounded":true,"rationale":"A code-forge URL is provided for the study's own code.","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":"Open Targets [OTAR-044, OTAR02-048, OTAR02-066]; Wellcome Trust [Biomedical Resources grants INVAR #3367 and 218294, and Centre grant 203149]","grounded":true,"rationale":"Award numbers are given for multiple funders.","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"all data is freely available through the web interface, API, and from https://www.ebi.ac.uk/intact/download under the CC BY 4.0 licence.","why":"The strongest identifier is a URL (https://www.ebi.ac.uk/intact/download), which is not a persistent identifier scheme.","gain":8.33,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions","why":"The IntAct database is named as the repository holding the data. [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":"partial","current":0.5,"evidence":"all data is freely available through the web interface, API, and from https://www.ebi.ac.uk/intact/download under the CC BY 4.0 licence.","why":"The dataset identifier (URL) appears only in the body text, not in the reference list.","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":"as of August 2021","why":"A date is provided to pin the snapshot, but no version token.","gain":2.08,"priority":"useful","scored":true},{"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":"Data Content Since the last IntAct NAR publication, data content has grown from 408 000 (Jamuary 2014) to 1 114 500 (June 2021)) interaction evidences, and the number of referenced publications has risen from 12 500 to 22 500.","why":"The dataset is described in running prose, without an itemised inventory or table. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In proteomics, describe the data with mzML or MIAPE.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Curation practices and controlled vocabularies/ontologies are continuously updated, driven by the development of new methods like BioID (term in PSI-MI Ontology","why":"The PSI-MI Ontology is a community standard vocabulary used for the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_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":"members of the International Molecular Exchange Consortium (IMEx) have collaboratively curated molecular interaction data from the scientific literature and from direct data depositions","why":"The production is described in generic terms without naming specific instruments or software. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No documentation object (README, codebook) is named as accompanying 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":"The IntAct database provides a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions.","why":"The data are not sensitive human-subject data, and no gatekeeper is mentioned.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifiers for external resources that the data depend on are provided. [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":null,"why":"No statement about retention period or persistence is made. [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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","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.","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."],"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":"2026-07-20T10:49:33.967407Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}