An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism is a dataset published in npj Systems Biology and Applications (2021). On theSindex it has a DataRank of 0.649, placing it in the top 30.7% of the data-sharing corpus. It has been cited 24 times, with 14 citing works in its 1-hop citation network. Its calibrated FAIR score is 48/100.
Ranks in the top 31% 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 genome-scale metabolic model iPau21 is available in the BioModels Database65 as an SBML Level 3 Version 1 file within a COMBINE Archive OMEX file66 including the contextualized models and metadata 67 at https://identifiers.org/biomodels.db/MODEL2106110001.”— not found in the paper; verdict downgraded
The identifier string MODEL2106110001 is a BioModels accession registered in identifiers.org, a persistent identifier scheme. [downgraded to 'partial' — no verifiable quote from the paper] [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 genome-scale metabolic model iPau21 is available in the BioModels Database as an SBML Level 3 Version 1 file within a COMBINE Archive OMEX file including the contextualized models and metadata at https://identifiers.org/biomodels.db/MODEL2106110001 .”— not found in the paper; verdict downgraded
The paper names BioModels Database, a repository listed in re3data/FAIRsharing, as the holder of the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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 genome-scale metabolic model iPau21 is available in the BioModels Database65 as an SBML Level 3 Version 1 file within a COMBINE Archive OMEX file66 including the contextualized models and metadata 67 at https://identifiers.org/biomodels.db/MODEL2106110001.”— not found in the paper; verdict downgraded
The dataset's identifier (BioModels accession) appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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
“All data for this project is available on GitHub ( https://github.com/dawsonpayne/iPau21). The genome-scale metabolic model iPau21 is available in the BioModels Database65 as an SBML Level 3 Version 1 file within a COMBINE Archive OMEX file66 including the contextualized models and metadata 67 at https://identifiers.org/biomodels.db/MODEL2106110001.”— not found in the paper; verdict downgraded
The statement points to a repository record (BioModels with accession MODEL2106110001), which is Colavizza category 3. [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 genome-scale metabolic model iPau21 is available in the BioModels Database65 as an SBML Level 3 Version 1 file within a COMBINE Archive OMEX file66 including the contextualized models and metadata 67”
The dataset's content is described in running prose (SBML file, COMBINE archive, contextualized models, metadata) but not as an itemized inventory. [majority verdict 'partial' (4/5 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'
“All data for this project is available on GitHub ( https://github.com/dawsonpayne/iPau21). The genome-scale metabolic model iPau21 is available in the BioModels Database65 as an SBML Level 3 Version 1 file within a COMBINE Archive OMEX file66 including the contextualized models and metadata 67 at https://identifiers.org/biomodels.db/MODEL2106110001.”— not found in the paper; verdict downgraded
The text gives a route (GitHub and BioModels) with no stated precondition; the data are stated to be available now. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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
“All data for this project is available on GitHub ( https://github.com/dawsonpayne/iPau21). The genome-scale metabolic model iPau21 is available in the BioModels Database65 as an SBML Level 3 Version 1 file within a COMBINE Archive OMEX file66 including the contextualized models and metadata 67 at https://identifiers.org/biomodels.db/MODEL2106110001.”— not found in the paper; verdict downgraded
The paper states the data are 'available' but does not use an explicit access-level label such as 'open access' or 'freely available'; the access action is described but not labeled. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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 not sensitive or human-subject; no gatekeeper is named or 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
“All data for this project is available on GitHub ( https://github.com/dawsonpayne/iPau21).”— not found in the paper; verdict downgraded
The paper states the data are 'available' (timing) but does not specify how long they will persist. [downgraded to 'no' — no verifiable quote from the paper]
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'
“SBML Level 3 Version 1 file”
SBML is an open, community-standard format for systems biology models. [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
“Systems Biology Ontology (SBO)52 terms can give semantic information or be used for annotation purposes.”— not found in the paper; verdict downgraded
SBO is an ontology registered in FAIRsharing, a community standard for metadata. [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'
No identifier is given for any external resource (e.g., source dataset, reference database) that the data depends on or derives from.
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 is named for the data; the article's CC-BY license does not apply to the data per scope rule.
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'
“iPau21”— not found in the paper; verdict downgraded
The model name 'iPau21' serves as a version token for the released data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]
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'
“Code used for the GENRE update and analyses have been archived in a GitHub repository ( https://github.com/dawsonpayne/iPau21).”
A machine-resolvable locator (GitHub URL) is given 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)
“R01 AI154242”
An award number is provided for a named funder (NIH).
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
“MEMOTE Version 0.9.11”
The paper names a specific version of the MEMOTE software used to assess the model. [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 a README, codebook, or schema file that travels with the data; variable definitions are not provided inside the article. [majority verdict 'no' (2/5 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
0.483
From this paper's citation signal
Citation Network Contribution
0.166
From 11 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 14 citers.
U.S. Department of Health & Human Services | National Institutes of Health
Grant: R01 AI154242
Deutsche Forschungsgemeinschaft
Grant: 390838134
National Science Foundation
Grant: REU 1950374
NIGMS NIH HHS
Grant: T32 GM145443
National Institutes of Health
Grant: 5R01AI154242-04
Multi-scale model of microbial phenotype modulation by mucins
Deutsche Forschungsgemeinschaft
Grant: unidentified
unidentified
National Science Foundation
Grant: 1950374
REU Site: Multi-Scale Systems Bioengineering and Biomedical Data Sciences
Fields of Study
MeSH Terms
Keywords
Additional file 1 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 1 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 9 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 8 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 9 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 5 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 8 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 4 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 6 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 6 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 7 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 7 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 5 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 3 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 2 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 3 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 2 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12
Additional file 4 of Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12