PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes is a dataset published in Database (2023). On theSindex it has a DataRank of 0.386, placing it in the top 47.1% of the data-sharing corpus. It has been cited 10 times, with 2 citing works in its 1-hop citation network. Its calibrated FAIR score is 38/100.
Ranks in the top 47% 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.
“Database URL: https://github.com/djparente/PYK-DB”
The identifier is a URL, not a persistent identifier scheme. [majority verdict 'partial' (3/5 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 PYK-SubstitutinonOME database is available at https://github.com/djparente/PYK-DB.”— not found in the paper; verdict downgraded
The data are hosted on GitHub, a general file-hosting service, not a curated data repository. [downgraded to 'no' — no verifiable quote from the paper]
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
“Database URL: https://github.com/djparente/PYK-DB”
The dataset identifier 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
“The PYK-SubstitutinonOME database is available at https://github.com/djparente/PYK-DB.”— not found in the paper; verdict downgraded
The data availability statement points to a link on a public repository (GitHub) without a DOI or accession, but the link is a persistent URL. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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 PYK-SubstitutionOME database comprises two main units. Unit 1 comprises an Excel workbook... Unit 2 contains three PYK sequence alignments in FASTA format.”— not found in the paper; verdict downgraded
The database content is described in running prose, not in an itemised inventory such as a table or section heading. [downgraded to 'no' — no verifiable quote from the paper]
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 PYK-SubstitutinonOME database is available at https://github.com/djparente/PYK-DB.”— not found in the paper; verdict downgraded
The data are stated to be available at a public URL with no precondition. [downgraded to 'partial' — no verifiable quote from the paper]
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 PYK-SubstitutinonOME database is available at https://github.com/djparente/PYK-DB.”— not found in the paper; verdict downgraded
The data availability statement gives a URL but does not label the access level with a standard term like 'open access'. [downgraded to 'no' — no verifiable quote from the paper]
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 PYK-SubstitutinonOME database is available at https://github.com/djparente/PYK-DB.”— not found in the paper; verdict downgraded
The data are non-sensitive and openly available with no gatekeeper mentioned.
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 statement about when the data become available or how long they persist is present.
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'
“Unit 2 contains three PYK sequence alignments in FASTA format.”
At least one open, community-standard format (FASTA) is named for the data. [majority verdict 'yes' (4/5 passes agreed)]
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 data or metadata community standard (e.g., MIAME, MIxS, an ontology) is named as being applied to the 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'
“PDB4IMA”— not found in the paper; verdict downgraded
The paper contains identifiers for external resources, such as PDB IDs for structures used in the study. [downgraded to 'no' — no verifiable quote from the paper] [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'
No license or reuse terms are stated for the dataset itself; the article-level CC BY license does not apply to 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'
Neither a version token nor a date is provided to identify a specific snapshot of 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'
“The Python code used to create this worksheet from sequence alignments (Unit 2) is presented in Supplemental Information 2.”
The code is located in the article's supplementary material, not in a versioned repository or with a DOI.
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)
“GM115340”
Specific grant numbers are provided for the funding sources. [majority verdict 'yes' (3/5 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 third major section... summarizes the comprehensive biochemical data of more than 1000 PYK variants that we have collected over the past decades.”— not found in the paper; verdict downgraded
The methods describe the collection and processing generically, without naming specific instruments, kits, or software. [downgraded to 'no' — no verifiable quote from the paper] [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
“The second worksheet in this workbook, 'Legends and Definitions', contains brief descriptions of the data, definitions and expanded color legends for each of the four major sections.”
A documentation object (the 'Legends and Definitions' worksheet) is named as part of the deposited data. [majority verdict 'yes' (3/5 passes agreed)]
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
0.360
From this paper's citation signal
Citation Network Contribution
0.0260
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 2 citers.
NIGMS NIH HHS
Grant: R24 GM111072
NIA NIH HHS
Grant: P30 AG035982
National Institutes of Health
Grant: DK78076 GM115340 GM118589 P20 RR17708 P30 AG035982 R24GM111072
the U.S. Department of Energy, Basic Energy Sciences, Office of Science
Grant: DE-AC02-06CH11357
W.M. Keck Foundation
KUMC School of Medicine
National Center for Research Resources
Natural Sciences and Engineering Research Council of Canada
MeSH Terms