Glycoprotein-Notebook: A Pan-Cancer Glycoproteomic Database and Toolkit for Analysis of Protein Glycosylation Changes Associated With Cancer Phenotypes is a dataset published in Molecular & Cellular Proteomics (2025). On theSindex it has a DataRank of 0.169, placing it in the top 67.1% of the data-sharing corpus. It has been cited 2 times, with 2 citing works in its 1-hop citation network. Its calibrated FAIR score is 54/100.
Ranks in the top 67% 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.
“All processed data tables and precomputed results are stored at Zenodo ( https://zenodo.org/records/14019975 ).”
The paper gives a web URL (https://zenodo.org/records/14019975) for the data, not a PID-scheme string (DOI, Handle, ARK, or repository accession). [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'
“All processed data tables and precomputed results are stored at Zenodo ( https://zenodo.org/records/14019975 ).”
Zenodo is a named repository that is listed in re3data and issues DOIs, fulfilling the 'yes' criterion.
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
“All processed data tables and precomputed results are stored at Zenodo ( https://zenodo.org/records/14019975 ).”
The dataset identifier appears only in the body text (Data Availability section), not as a reference-list entry. [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
“All processed data tables and precomputed results are stored at Zenodo ( https://zenodo.org/records/14019975 ).”
The data availability statement points to a repository record (Zenodo) with a persistent link, falling under 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
“We identified 432,750 N-linked IGPs (sequence + glycan), 408,728 glycoforms, 26,277 glycosites, and 11,641 glycoproteins from the 10 cancer types, all under a glycopeptide-spectrum match FDR threshold of 0.01.”
The dataset's content and size are described in running prose without an itemised inventory (section, table, or list) in the paper body. [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 processed data tables and precomputed results are stored at Zenodo ( https://zenodo.org/records/14019975 ).”
The paper states the data are stored at a public repository with no stated precondition (embargo, registration, or application). [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
“All processed data tables and precomputed results are stored at Zenodo ( https://zenodo.org/records/14019975 ).”
The paper describes where data can be downloaded but does not label the access level with an explicit term such as 'open access' or 'freely available'. [majority verdict 'partial' (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 from human subjects (CPTAC) but deposited in open repositories with no gatekeeper or access procedure 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
The paper states neither how long the data will remain available nor any persistence commitment. [majority verdict 'no' (3/5 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 token (open or proprietary) is named for the released data in the main text or supplementary materials.
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, ontology) is named as applied to the data. The paper uses KEGG and GO for analysis but not as a standard for the data itself.
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'
“Zeng W.-F., et al. Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3. Nat. Methods. 2021;18:1515–1523. doi: 10.1038/s41592-021-01306-0.”— not found in the paper; verdict downgraded
The paper cites external resources (e.g., pGlyco3) with DOIs in the reference list, providing identifiers for resources the data depend on. [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 data. The CC BY license 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 dataset. The Zenodo record URL implies a specific version, but the paper does not explicitly state it. [majority verdict 'no' (4/5 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'
“Users can utilize access and run the Jupyter notebooks available in the Glycoprotein-Notebook GitHub repository ( https://github.com/huizhanglab-jhu/glycoproteinnotebook ).”— not found in the paper; verdict downgraded
The paper provides a machine-resolvable URL to a code repository (GitHub), fulfilling the 'yes' criterion. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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)
“This work was supported by the National Cancer Institute Clinical Proteomic Tumor Analysis Consortium, National Institutes of Health grant U24CA271079.”
The paper includes a specific grant number (U24CA271079) attached to a named funder.
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
“GPQuest 3.0 (Zhang Lab) (32, 33, 34).”— not found in the paper; verdict downgraded
The paper names specific software (GPQuest 3.0) and instruments used to produce the data, providing a proper-noun production record. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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
“Statistics on identified glycopeptides and corresponding glycoproteins are summarized in Supplementary Table S1.”— not found in the paper; verdict downgraded
Variable definitions are provided inside the article (supplementary table), not as 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
0.165
From this paper's citation signal
Citation Network Contribution
4.68 × 10⁻³
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 2 citers.
NIH NCI
Grant: U24CA271079
National Institutes of Health
Fields of Study
MeSH Terms
Keywords