{"doi":"10.1093/nar/gkae1088","title":"MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface","abstract":"MatrixDB, a member of the International Molecular Exchange consortium (IMEx), is a curated interaction database focused on interactions established by extracellular matrix (ECM) constituents including proteins, proteoglycans, glycosaminoglycans and ECM bioactive fragments. The architecture of MatrixDB was upgraded to ease interaction data export, allow versioning and programmatic access and ensure sustainability. The new version of the database includes more than twice the number of manually curated and experimentally-supported interactions. High-confidence predicted interactions were imported from the Integrated Interactions Database to increase the coverage of the ECM interactome. ECM and ECM-associated proteins of five species (human, murine, bovine, avian and zebrafish) were annotated with matrisome divisions and categories, which are used for computational analyses of ECM -omic datasets. Biological pathways from the Reactome Pathway Knowledgebase were also added to the biomolecule description. New transcriptomic and expanded proteomic datasets were imported in MatrixDB to generate cell- and tissue-specific ECM networks using the newly developed in-house Network Explorer integrated in the database. MatrixDB is freely available at https://matrixdb.univ-lyon1.fr.","journal":"Nucleic Acids Research","year":2024,"id":447891,"datarank":0.3032313574701575,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.011344835111860465,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.011344835111860465,"corpus_percentile":45.346948247853334,"corpus_rank":7066,"citation_count":6,"citer_count":4,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9524,"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":43.75,"fair_percentile":58.6365025985937,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":296064,"name":"Max Kotlyar","orcid":"0000-0002-1111-8667","position":1,"is_corresponding":false},{"id":257885,"name":"Sylvain D. Vallet","orcid":"0000-0001-9885-7499","position":2,"is_corresponding":false},{"id":1266017,"name":"Catherine Hayes","orcid":"0000-0002-3640-3237","position":3,"is_corresponding":false},{"id":271358,"name":"Alexandra Naba","orcid":"0000-0002-4796-5614","position":4,"is_corresponding":false},{"id":296063,"name":"Igor Jurišica","orcid":"0000-0002-2507-946X","position":5,"is_corresponding":false},{"id":45708,"name":"Frédérique Lisacek","orcid":"0000-0002-0948-4537","position":6,"is_corresponding":false},{"id":257880,"name":"Sylvie Ricard‐Blum","orcid":"0000-0001-9263-1851","position":7,"is_corresponding":false},{"id":1266016,"name":"Kasun Samarasinghe","orcid":"0000-0002-0642-6841","position":0,"is_corresponding":true}],"reference_count":33,"raw_metadata":null,"created_at":"2026-07-19T02:02:03.354708Z","pmid":"39558161","pmcid":"PMC11701626","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":60.0,"fair_r":70.8333,"fair_zscore":0.3681,"fair_rationale":{"fair_score":43.75,"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":"MatrixDB is freely available at https://matrixdb.univ-lyon1.fr","grounded":false,"rationale":"The only identifier given is a URL, not a persistent identifier scheme (e.g., DOI, Handle). [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":"MatrixDB is freely available at https://matrixdb.univ-lyon1.fr","grounded":false,"rationale":"The data are held on a web server (matrixdb.univ-lyon1.fr), not a named repository from re3data/FAIRsharing. [downgraded to 'no' — no verifiable quote from the paper] [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":"MatrixDB is freely available at https://matrixdb.univ-lyon1.fr","grounded":false,"rationale":"The statement points to a URL, not a repository record with an accession, so it is category 3 (link to archived data) but without a persistent identifier, so partial. [downgraded to 'no' — no verifiable quote from the paper] [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":0.5,"verdict":"partial","evidence":"The new experimental interaction dataset comprises ∼243 000 interactions, a two-fold increase in the number of manually curated and experimentally-supported interaction data compared to the previous version","grounded":true,"rationale":"The dataset's content and extent are described in running prose (a sentence giving the number of interactions) without an itemised inventory, section heading, or table. [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":"MatrixDB is freely available at https://matrixdb.univ-lyon1.fr","grounded":false,"rationale":"The dataset identifier (URL) appears only in the body text, not as a reference-list entry. [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":"The database is freely available through a web interface (https://matrixdb.univ-lyon1.fr), does not require any login or registration and is not password-protected.","grounded":false,"rationale":"The paper states the data are freely available with no precondition such as registration, embargo, or application. [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":"The database is freely available through a web interface ( https://matrixdb.univ-lyon1.fr ), does not require any login or registration and is not password-protected.","grounded":true,"rationale":"The paper explicitly labels the data as 'freely available', which is a natural-language equivalent of 'open access'. [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":"The data are not sensitive or human-subject; no gatekeeper is mentioned.","grounded":false,"rationale":"The data are interaction data, not human-subject data, so no gatekeeper is needed.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"MatrixDB is freely available at https://matrixdb.univ-lyon1.fr","grounded":false,"rationale":"The paper states the data are available now but gives no persistence commitment. [downgraded to 'no' — no verifiable quote from the paper] [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":"MatrixDB curated dataset and the entire interaction dataset available in MatrixDB can be downloaded from the ‘Download’ tab under the MITAB 2.7 format.","grounded":true,"rationale":"MITAB 2.7 is an open, community-standard format for molecular interaction data.","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":"Gene Ontology (GO) terms (24,25) and UniProtKB keywords (26) are displayed","grounded":false,"rationale":"The paper applies GO terms and UniProtKB keywords, which are community standards registered in FAIRsharing. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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 external data identifiers are provided in the text.","grounded":false,"rationale":"The paper only names external resources (e.g., IntAct, Bgee) without providing their accessions or DOIs.","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":70.83,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"It is distributed under the terms of the Creative Commons Attribution Licence CC BY 4.0.","grounded":true,"rationale":"CC BY 4.0 is an open standard license from the SPDX list.","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":"Interaction data available in MatrixDB are manually curated from the literature via the curation interface of the IntAct database","grounded":true,"rationale":"The paper names a specific platform (IntAct curation interface) used to produce the data. [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":"The table comprises six columns including the names and identifiers of the participants, the nature of the interaction (direct or indirect), the molecular interaction (MI) score imported from the IntAct database for experimental interactions, and the type of interaction (experimental interactions in black or predicted interactions in red).","grounded":false,"rationale":"Variable definitions are given inside the article (in prose), not as a separate 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":1.0,"verdict":"yes","evidence":"This version (release 4.0) is and the future ones will be archived in the same GitHub repository.","grounded":true,"rationale":"The paper gives a version token 'release 4.0' for the data.","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":"https://github.com/glyco-expasy/matrixdb-api and https://github.com/glyco-expasy/matrixdb-ui","grounded":false,"rationale":"The paper provides GitHub repository URLs for the study's code. [downgraded to 'partial' — no verifiable quote from the paper]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"Swiss National Science Foundation, Switzerland [SNSF_310 030_208 178 to K.S., F.L., S.R.-B.]; Institut National du Cancer, France [INCa N◦2020-123 TEN-MAX to S.R.-B.]","grounded":false,"rationale":"The paper includes specific award/grant numbers (SNSF_310 030_208 178, INCa N◦2020-123 TEN-MAX) attached to named funders. [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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"MatrixDB is freely available at https://matrixdb.univ-lyon1.fr","why":"The only identifier given is a URL, not a persistent identifier scheme (e.g., DOI, Handle). [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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"MatrixDB is freely available at https://matrixdb.univ-lyon1.fr","why":"The data are held on a web server (matrixdb.univ-lyon1.fr), not a named repository from re3data/FAIRsharing. [downgraded to 'no' — no verifiable quote from the paper] [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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The database is freely available through a web interface (https://matrixdb.univ-lyon1.fr), does not require any login or registration and is not password-protected.","why":"The paper states the data are freely available with no precondition such as registration, embargo, or application. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"MatrixDB is freely available at https://matrixdb.univ-lyon1.fr","why":"The dataset identifier (URL) appears only in the body text, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper]","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":"https://github.com/glyco-expasy/matrixdb-api and https://github.com/glyco-expasy/matrixdb-ui","why":"The paper provides GitHub repository URLs for the study's code. [downgraded to 'partial' — no verifiable quote from the paper]","gain":4.17,"priority":"important","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":"Swiss National Science Foundation, Switzerland [SNSF_310 030_208 178 to K.S., F.L., S.R.-B.]; Institut National du Cancer, France [INCa N◦2020-123 TEN-MAX to S.R.-B.]","why":"The paper includes specific award/grant numbers (SNSF_310 030_208 178, INCa N◦2020-123 TEN-MAX) attached to named funders. [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":"MatrixDB is freely available at https://matrixdb.univ-lyon1.fr","why":"The statement points to a URL, not a repository record with an accession, so it is category 3 (link to archived data) but without a persistent identifier, so partial. [downgraded to 'no' — no verifiable quote from the paper] [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":"partial","current":0.5,"evidence":"The new experimental interaction dataset comprises ∼243 000 interactions, a two-fold increase in the number of manually curated and experimentally-supported interaction data compared to the previous version","why":"The dataset's content and extent are described in running prose (a sentence giving the number of interactions) without an itemised inventory, section heading, or table. [majority verdict 'partial' (3/5 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":"Gene Ontology (GO) terms (24,25) and UniProtKB keywords (26) are displayed","why":"The paper applies GO terms and UniProtKB keywords, which are community standards registered in FAIRsharing. 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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":"The table comprises six columns including the names and identifiers of the participants, the nature of the interaction (direct or indirect), the molecular interaction (MI) score imported from the IntAct database for experimental interactions, and the type of interaction (experimental interactions in black or predicted interactions in red).","why":"Variable definitions are given inside the article (in prose), not as a separate 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. 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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 external data identifiers are provided in the text.","why":"The paper only names external resources (e.g., IntAct, Bgee) without providing their accessions or DOIs.","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":"MatrixDB is freely available at https://matrixdb.univ-lyon1.fr","why":"The paper states the data are available now but gives no persistence commitment. [downgraded to 'no' — no verifiable quote from the paper] [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.","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","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)."],"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":"2026-07-20T12:48:11.317829Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}