GeneCup: mining PubMed and GWAS catalog for gene–keyword relationships is a dataset published in G3 Genes Genomes Genetics (2022). On theSindex it has a DataRank of 0.499, placing it in the top 38.4% of the data-sharing corpus. It has been cited 16 times, with 7 citing works in its 1-hop citation network. Its calibrated FAIR score is 50/100.
Ranks in the top 38% for downstream scientific impact
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.
“The source code of GeneCup and the link to a running instance is available at https://github.com/hakangunturkun/GeneCup .”
The only identifier for the dataset is a GitHub URL, which is a web address not in a persistent-identifier scheme. [majority verdict 'partial' (4/5 passes agreed)]
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'
“The source code of GeneCup and the link to a running instance is available at https://github.com/hakangunturkun/GeneCup .”
GitHub is a code-hosting platform, not a curated data repository listed in re3data/FAIRsharing. [majority verdict 'partial' (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
“The source code of GeneCup and the link to a running instance is available at https://github.com/hakangunturkun/GeneCup .”
The dataset identifier (GitHub URL) appears only in the body text, not in the reference list. [majority verdict 'partial' (3/5 passes agreed)]
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
“GeneCup is a free and open source web application. The source code of GeneCup and the link to a running instance is available at https://github.com/hakangunturkun/GeneCup . Supplemental material is available at G3 online.”
The statement points to GitHub (a public repository for code) and the journal's supplementary material, which is a link to archived data in a public repository. [majority verdict 'yes' (3/5 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
“As an example, we created a mini-ontology for addiction-related concepts (Supplementary Table 1).”— not found in the paper; verdict downgraded
The dataset content is described in running prose and a reference to a supplementary table, but no itemised inventory of files or variables is given. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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 source code of GeneCup and the link to a running instance is available at https://github.com/hakangunturkun/GeneCup .”
The GitHub repository is publicly accessible with no stated precondition. [majority verdict 'yes' (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
“GeneCup is free and open source software.”
The paper explicitly labels the data as 'free and open source' software, 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, and no gatekeeper is named.
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
No sentence states when the data become available or how long they will persist. [majority verdict 'no' (4/5 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'
No file format is named for the released data (source code or supplementary material).
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
No community data or metadata standard (e.g., FAIRsharing-registered checklist, ontology, or schema) is named for the study's own data.
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'
The paper does not provide a persistent identifier (DOI, accession, RRID) for any external resource; it only gives a download URL for the GWAS catalog, which is not a PID. [majority verdict 'no' (4/5 passes agreed)]
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'
“GeneCup is free and open source software.”
No specific open-source license (e.g., MIT, GPL) is named for the data.
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'
No version token or date is given for the study's own data (source code or supplementary material).
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'
“The source code of GeneCup and the link to a running instance is available at https://github.com/hakangunturkun/GeneCup .”
The study's own code is provided via a machine-resolvable GitHub URL. [majority verdict 'yes' (4/5 passes agreed)]
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)
“Funding is provided by the following NIH/NIDA grants: U01DA047638 (HC and RWW), P30DA044223 (RWW and PP), and also by NIH/NIGMS grant R01GM123489 (RWW and PP).”
Award numbers are given for the funding sources. [majority verdict 'yes' (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
The paper does not describe the provenance of the data itself (the source code); it describes the methods of the tool, not the data's production. [majority verdict 'no' (2/5 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
“As an example, we created a mini-ontology for addiction-related concepts (Supplementary Table 1).”— not found in the paper; verdict downgraded
The variable/term definitions are inside the article as a supplementary table, not in 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
0.425
From this paper's citation signal
Citation Network Contribution
0.0741
From 5 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 7 citers.
NIH/NIDA
Grant: U01DA047638 (HC and RWW), P30DA044223 (RWW and PP)
NIH/NIGMS
Grant: R01GM123489 (RWW and PP)
National Institutes of Health
Grant: 5U01DA047638-05
System genetics of menthol and nicotine addiction
National Institutes of Health
Grant: 5P30DA044223-03
Overall NIDA Core "Center of Excellence" in Transcriptomics, Systems Genetics and the Addictome
National Institutes of Health
Grant: 1R01GM123489-01A1
A Unified High Performance Web Service for Systems Genetics and Precision Medicine
FWCI
1.17
Citation Percentile
0.8%
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals