MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface is a dataset published in Nucleic Acids Research (2024). On theSindex it has a DataRank of 0.303, placing it in the top 54.7% of the data-sharing corpus. It has been cited 6 times, with 4 citing works in its 1-hop citation network. Its calibrated FAIR score is 44/100.
Ranks in the top 55% for downstream scientific impact
Linked data & code
DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?
FAIR checklist signals are shown for context only and do not affect DataRank scoring.
Full FAIR picture · advisory
The headline score is computed from the scored criteria — the fact-shaped checks (a repository, an accession, a licence) that two independent models agree on. The advisory criteria below are real FAIR guidance but rest on judgment calls that models read differently, so they inform without moving the number.
“MatrixDB is freely available at https://matrixdb.univ-lyon1.fr”— not found in the paper; verdict downgraded
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]
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'
“MatrixDB is freely available at https://matrixdb.univ-lyon1.fr”— not found in the paper; verdict downgraded
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)]
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
“MatrixDB is freely available at https://matrixdb.univ-lyon1.fr”— not found in the paper; verdict downgraded
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]
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'
Advisory · not in the published score
“MatrixDB is freely available at https://matrixdb.univ-lyon1.fr”— not found in the paper; verdict downgraded
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)]
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
“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”
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)]
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'
“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.”— not found in the paper; verdict downgraded
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)]
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'
Advisory · not in the published score
“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.”
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)]
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
“The data are not sensitive or human-subject; no gatekeeper is mentioned.”— not found in the paper; verdict downgraded
The data are interaction data, not human-subject data, so no gatekeeper is needed.
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
“MatrixDB is freely available at https://matrixdb.univ-lyon1.fr”— not found in the paper; verdict downgraded
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)]
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'
“MatrixDB curated dataset and the entire interaction dataset available in MatrixDB can be downloaded from the ‘Download’ tab under the MITAB 2.7 format.”
MITAB 2.7 is an open, community-standard format for molecular interaction data.
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
Advisory · not in the published score
“Gene Ontology (GO) terms (24,25) and UniProtKB keywords (26) are displayed”— not found in the paper; verdict downgraded
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)]
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'
“No external data identifiers are provided in the text.”— not found in the paper; verdict downgraded
The paper only names external resources (e.g., IntAct, Bgee) without providing their accessions or DOIs.
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'
“It is distributed under the terms of the Creative Commons Attribution Licence CC BY 4.0.”
CC BY 4.0 is an open standard license from the SPDX list.
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'
“This version (release 4.0) is and the future ones will be archived in the same GitHub repository.”
The paper gives a version token 'release 4.0' for the data.
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'
“https://github.com/glyco-expasy/matrixdb-api and https://github.com/glyco-expasy/matrixdb-ui”— not found in the paper; verdict downgraded
The paper provides GitHub repository URLs for the study's code. [downgraded to 'partial' — no verifiable quote from the paper]
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)
“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.]”— not found in the paper; verdict downgraded
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)]
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
Advisory · not in the published score
“Interaction data available in MatrixDB are manually curated from the literature via the curation interface of the IntAct database”
The paper names a specific platform (IntAct curation interface) used to produce the data. [majority verdict 'yes' (3/5 passes agreed)]
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
“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).”— not found in the paper; verdict downgraded
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]
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
Calibrated FAIR score — a parallel quality metric, independent of the DataRank citation score. See the full evaluation →
Base Score Contribution
0.292
From this paper's citation signal
Citation Network Contribution
0.0113
From 2 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 4 citers.
Swiss National Science Foundation
Grant: SNSF_310 030_208 178
Institut National du Cancer
Grant: INCa N° 2020-123
Office of Strategic Coordination
Grant: U01HG012680
National Cancer Institute
Grant: R21CA261642
NHGRI NIH HHS
NIH HHS
National Institutes of Health
National Human Genome Research Institute
NIH HHS
NHGRI NIH HHS
NIH HHS
NIH HHS
FWCI
0.99
Citation Percentile
0.7%
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals