Enzyme-constrained metabolic model of Treponema pallidum identified glycerol-3-phosphate dehydrogenase as an alternate electron sink is a dataset published in mSystems (2025). On theSindex it has a DataRank of 0.208, placing it in the top 64.8% of the data-sharing corpus. It has been cited 3 times. Its calibrated FAIR score is 50/100.
Ranks in the top 65% 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.
“The codes and resources supporting this study are available on GitHub at https://github.com/ssbio/Treponema_pallidum_Nichols”
The paper gives a GitHub URL, which is a web address not in a persistent identifier scheme (DOI, Handle, etc.). [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 codes and resources supporting this study are available on GitHub at https://github.com/ssbio/Treponema_pallidum_Nichols”
GitHub is a named host but not a curated data repository (e.g., not 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 codes and resources supporting this study are available on GitHub at https://github.com/ssbio/Treponema_pallidum_Nichols”
The dataset identifier (GitHub URL) appears only in the body text, not in the reference list. [majority verdict 'partial' (4/5 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 codes and resources supporting this study are available on GitHub at https://github.com/ssbio/Treponema_pallidum_Nichols”
The statement points to a GitHub repository URL, which is a public repository but without a persistent identifier or accession, so it is not a repository record with a DOI. [majority verdict 'partial' (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
“Overall, iTP251 includes 600 reactions, 605 metabolites, and 251 genes”
The paper provides a summary of the model's contents in running prose, not an itemised list 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 codes and resources supporting this study are available on GitHub at https://github.com/ssbio/Treponema_pallidum_Nichols”
The paper gives a direct URL to a public GitHub repository with no stated precondition. [majority verdict 'yes' (4/5 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 codes and resources supporting this study are available on GitHub at https://github.com/ssbio/Treponema_pallidum_Nichols”
The paper describes where the data can be obtained (GitHub URL) but does not apply an explicit access-level label from the standard vocabulary. [majority verdict 'partial' (4/5 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 a metabolic model, not sensitive human-subject data, 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
The paper does not state how long the data will be retained or when they become available. [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'
The paper does not name any file format for the released 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
“complete Systems Biology Ontology annotation (100%) enhances transparency and compatibility with systems biology resources.”— not found in the paper; verdict downgraded
The paper states that the model uses Systems Biology Ontology (SBO) annotation, which is a community-standard metadata vocabulary. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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'
“genome data from NCBI RefSeq (KBase Genome ID: NC_021490 )”
The paper provides a RefSeq accession (NC_021490) for the genome used as a resource, which is an identifier for an external resource. [majority verdict 'yes' (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'
The paper does not state a license for the data; the CC-BY license applies to the article only.
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'
The paper does not provide a version token or date for the released 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 codes and resources supporting this study are available on GitHub at https://github.com/ssbio/Treponema_pallidum_Nichols”
The paper gives a machine-resolvable code repository URL for the study's own code. [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)
“National Institutes of Health (NIH) R35 MIRA grant (5R35GM143009) and National Science Foundation (NSF) CAREER grant (1943310)”
The paper provides specific grant numbers attached to named funders. [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
“All computational analyses were performed using Python, specifically with the COBRApy 0.29.0 package for constraint-based modeling.”
The paper names specific software and tools (COBRApy 0.29.0, DLKcat, MEMOTE) 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 paper does not name any documentation object (README, codebook) that accompanies the data.
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
0.208
From this paper's citation signal
Citation Network Contribution
0
Citation network not refreshed for this result
This paper's DataRank is currently driven only by its base citation score. Citation network data was not refreshed for this result.
Learn more about DataRank methodology →National Institutes of Health
Grant: 5R35GM143009
National Science Foundation
Grant: 1943310
CAREER: Dissecting a Metabolically Versatile Non-Model Bacterium's Lignin-Derived Compound Catabolism
NIGMS NIH HHS
Grant: R35 GM143009
National Institutes of Health
Grant: 5R35GM143009-02
A Predictive Modeling Framework to Dissect the Dynamic Immunometabolic Responses to Pathogenic infection and the Kinetic Reprogramming of Metabolism in Cancer Cell System
University of Nebraska-Lincoln
FWCI
2.21
Citation Percentile
0.9%
Citation Trend
Fields of Study
MeSH Terms
Keywords