UniProt: the Universal Protein Knowledgebase in 2025 is a dataset published in Nucleic Acids Research (2024). On theSindex it has a DataRank of 4.6, placing it in the top 4.7% of the data-sharing corpus. It has been cited 2,086 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 54/100.
Ranks in the top 5% 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 aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/ ) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information.”
The paper gives a web address (https://www.uniprot.org/) for the data, which is not a persistent-identifier scheme and carries no 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'
“The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/ ) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information.”
The paper names the UniProt database as the holder of the data, which is a recognised data repository in re3data. [majority verdict 'yes' (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
“UniProt releases are published every 8 weeks. We provide customizable views and downloads in a range of formats via the website, and file sets at the FTP site ( www.uniprot.org/downloads ), and supply users with a number of different options for computational access to the data ( www.uniprot.org/help/programmatic_access ).”
The dataset's identifier (the FTP URL) appears only in the body text, not as a reference-list entry.
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
“UniProt releases are published every 8 weeks. We provide customizable views and downloads in a range of formats via the website, and file sets at the FTP site ( www.uniprot.org/downloads ), and supply users with a number of different options for computational access to the data ( www.uniprot.org/help/programmatic_access ).”
The data availability statement points to the UniProt repository and provides a persistent link (FTP site and website), qualifying as a repository record with a persistent link. [majority verdict 'yes' (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
“UniProt release 2024_04 contains approximately 246 million sequence records in UniProtKB.”
The dataset's extent is stated in running prose, but there is no itemised inventory (section, table, or list) of files or variables. [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 aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/ ) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information.”
The paper states the data are freely accessible with no precondition, and the data availability statement provides a direct download route.
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 aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/ ) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information.”
The paper explicitly states that the data are freely accessible and provides an access route with no stated precondition.
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 because access is open.
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
“UniProt releases are published every 8 weeks.”
The paper states the timing of releases (availability) but does not commit to a retention period or permanent archival.
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 mentions 'a range of formats' but does not name any specific file format token.
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
“We curated the publication in UniProtKB/Swiss-Prot and provided functional information in the form of human readable text summaries and structured vocabularies, such as the Gene Ontology (GO) (14), Rhea or ChEBI (15).”— not found in the paper; verdict downgraded
The paper states that the data are annotated using community standards (GO, Rhea, ChEBI). [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'
“EnzChemRED, a rich enzyme chemistry relation extraction dataset [Data set]. 2024; Zenodo https://zenodo.org/records/11067998 .”
The paper includes a DOI for an external dataset (EnzChemRED) in the Data Citations section. [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'
No license is named for the data; the CC BY license applies to the article only, not 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'
“UniProt release 2024_04 contains approximately 246 million sequence records in UniProtKB.”
The paper specifies a version token ('2024_04') for 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'
No locator for the study's own code is provided; only third-party tools and APIs are 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)
“Funding National Human Genome Research Institute (NHGRI) [HG002273]; Office of the Director, NIH OD [U24HG007822]; National Institute of Allergy and Infectious Diseases (NIAID); National Institute on Aging (NIA); National Institute of General Medical Sciences (NIGMS) [R35GM141873]; National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK); National Eye Institute (NEI); National Cancer Institute (NCI); National Heart, Lung, and Blood Institute (NHLBI); Biotechnology and Biological Sciences Research Council (BBSRC) [BB/T015608/1]; National Science Foundation’s Directorate for Biological Sciences [BB/X002179/1]; Open Targets; Horizon 2020 - Research and Innovation Framework Programme [825575]; State Secretariat for Education, Research and Innovation (SERI); European Molecular Biology Laboratory (EMBL) Australia.”
The paper lists multiple grant numbers associated with named funders.
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 rule-based computational annotation UniRule system (20) uses these groupings to transfer experimentally verified annotations onto unstudied proteins, adding properties, such as protein name, functional annotation, catalytic activity, pathway, GO terms and subcellular location.”— not found in the paper; verdict downgraded
The paper names specific tools and methods (UniRule, InterPro, ProtNLM, BUSCO) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 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
No documentation object (README, codebook, data dictionary) is mentioned as accompanying 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
1.1
From this paper's citation signal
Citation Network Contribution
3.5
From 100 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 100 citers.
National Human Genome Research Institute
Grant: HG002273
Office of the Director
Grant: U24HG007822
National Institute of General Medical Sciences
Grant: R35GM141873
Biotechnology and Biological Sciences Research Council
Grant: BB/T015608/1
BBSRC-NSF/BIO PanOryza: Globally coordinated genomes, proteomes and pathways for rice
National Science Foundation’s Directorate for Biological Sciences
Grant: BB/X002179/1
2021BBSRC-NSF/BIO UniPlex - Genome-Wide Protein Complex Prediction and Validation
Horizon 2020 - Research and Innovation Framework Programme
Grant: 825575
European Joint Programme on Rare Diseases
NHGRI NIH HHS
Grant: R01 HG002273
NHGRI NIH HHS
Grant: U24 HG012212
NIH HHS
Grant: U24 OD038424
NHGRI NIH HHS
Grant: U41 HG002273
NHGRI NIH HHS
Grant: U41 HG007822
NHGRI NIH HHS
Grant: P41 HG002273
National Institutes of Health
Grant: 5R35GM141873-04
Protein Knowledge Networks and Semantic Computing for Disease Discovery
National Institutes of Health
Grant: 5U24HG007822-12
UniProt: A Protein Sequence and Function Resource for Biomedical Science
National Institutes of Health
Grant: 5P41HG002273-08
Gene Ontology Consortium
European Molecular Biology Laboratory (EMBL) Australia
NIDDK NIH HHS
National Cancer Institute
State Secretariat for Education, Research and Innovation
National Heart, Lung, and Blood Institute
NCI NIH HHS
National Institute on Aging
NEI NIH HHS
NHLBI NIH HHS
NIA NIH HHS
National Eye Institute
National Institute of Allergy and Infectious Diseases
National Institute of Diabetes and Digestive and Kidney Diseases
FWCI
337.76
Citation Percentile
1.0%
Influential Citations
93
Citation Trend
Fields of Study
MeSH Terms
Keywords
uniprot-mcp: A Model Context Protocol server for the UniProt protein knowledgebase
uniprot-mcp: A Model Context Protocol server for the UniProt protein knowledgebase
Published protein sequence sets for the evaluation of bioinformatics tools
Published protein sequence sets for the evaluation of bioinformatics tools
uniprot-mcp: A Model Context Protocol server for the UniProt protein knowledgebase
uniprot-mcp: A Model Context Protocol server for the UniProt protein knowledgebase
uniprot-mcp: A Model Context Protocol server for the UniProt protein knowledgebase
uniprot-mcp: A Model Context Protocol server for the UniProt protein knowledgebase
uniprot-mcp: A Model Context Protocol server for the UniProt protein knowledgebase
Evaluation of relations extraction in Biopatternsg without small molecules
Evaluation of relations extraction in Biopatternsg with small molecules
Evaluation of pairs-like relations generation in Biopatternsg without small molecules
Evaluation of pairs-like relations generation in Biopatternsg with small molecules
Evaluation of relations extraction in biopatternsg (level 3)
An instance of report.txt for CREB-phosphorylation
Evaluation of pairs-like relations generation in biopatternsg (level 2)
Evaluation of names recognition in biopatternsg (level 1)
Pathways Commons sif file of the reactome’s pathway named creb phosphorylation (prolog format)
Restricted GRN to explore subnetworks for COVID-19 and CXCR4
Work-flow for the semantic modeling and analyzing of a GRN