Proteomic analysis of the Treponema pallidum subsp. pallidum SS14 strain: coverage and comparison with the Nichols strain proteome is a dataset published in Frontiers in Microbiology (2024). On theSindex it has a DataRank of 0.129, placing it in the top 70.9% of the data-sharing corpus. It has been cited 1 time, with 1 citing works in its 1-hop citation network. Its calibrated FAIR score is 58/100.
Ranks in the top 71% 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 data presented in the study are deposited in the MassIVE repository, accession number MSV000095818 (ProteomeXchange identifier PXD055753).”
A ProteomeXchange identifier (PXD055753) is a persistent identifier scheme. [majority verdict 'yes' (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'
“MassIVE repository”
MassIVE is a curated data repository listed in re3data.
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 data presented in the study are deposited in the MassIVE repository, accession number MSV000095818 (ProteomeXchange identifier PXD055753).”
The dataset identifier appears in the body text (Data availability statement), not in the reference list.
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 datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.”
The statement points to a repository record (MassIVE) with accession, fitting Colavizza category 3.
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
“In the present study, 7,163 unique T. pallidum peptides were identified which allowed for the detection of 607 of 987 proteins within treponemes from the SS14 strain, representing 61.5% of the total proteome”
The dataset's content is described in running prose only, without an itemised inventory.
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 data presented in the study are deposited in the MassIVE repository, accession number MSV000095818 (ProteomeXchange identifier PXD055753).”
The text gives a route to the data (MassIVE repository with accession) with no stated precondition.
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 data presented in the study are deposited in the MassIVE repository, accession number MSV000095818 (ProteomeXchange identifier PXD055753).”
The paper does not explicitly label the access level of the data (e.g. 'open access'), but describes the access action of depositing in a public repository, from which the level must be inferred. [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 not sensitive or human-subject, so 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 addresses when the data become available or how long they persist.
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.
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. MIAPE, MIAME) is named for the data. [majority verdict 'no' (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'
“NCBI reference sequence NC_021490”
The paper gives an identifier (NCBI reference sequence) for the reference genome used, which is a resource other than the study's own dataset.
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 licence is named for the data; the CC BY licence on the article 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 given 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'
No code availability is mentioned.
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)
“R37AI051334, U19AI144133 and U01AI182035”
Grant numbers from NIAID are given.
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
“Orbitrap Fusion Tribrid mass spectrometer”
The paper names the specific instrument used to produce the data.
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
No documentation object (README, codebook) is said to accompany the data. [majority verdict 'no' (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
0.104
From this paper's citation signal
Citation Network Contribution
0.0252
From 1 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 1 citer.
NIAID NIH HHS
Grant: U19 AI144133
NIAID NIH HHS
Grant: R37 AI051334
NIAID NIH HHS
Grant: U01 AI182035
National Institutes of Health
Grant: 5R37AI051334-21
Extracellular Matrix Adhesins of Treponema pallidum
National Institutes of Health
Grant: 1U01AI182035-01
Development of a Chimeric Syphilis Vaccine Candidate to Combat Local, Disseminated and Congenital Syphilis Infection
National Institutes of Health
Grant: 3U19AI144133-05S1
University of Washington (UW) Sexually Transmitted Infections (STI) Cooperative Research Center (CRC) - Syphilis Vaccine to Protect against Local and Disseminated T. pallidum Infection
FWCI
0.48
Citation Percentile
0.7%
Citation Trend
Fields of Study
Keywords