BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies is a dataset published in Nucleic Acids Research (2025). On theSindex it has a DataRank of 0.483, placing it in the top 39.6% of the data-sharing corpus. It has been cited 14 times, with 12 citing works in its 1-hop citation network. Its calibrated FAIR score is 71/100.
Ranks in the top 40% 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.
“10.5281/zenodo.15284916”
The paper provides a DOI for the software, which is a persistent identifier scheme.
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'
“Zenodo”
The software is deposited at Zenodo, a repository listed in re3data/FAIRsharing.
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
“https://doi.org/10.5281/zenodo.15284916”
The dataset identifier appears only in the body text of the 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
“Data availability The BioPortal web server is freely available at https://bioportal.bioontology.org . All software discussed in this paper is open access, and is freely available at https://github.com/ncbo and https://doi.org/10.5281/zenodo.15284916 .”
The statement points to a repository record (Zenodo DOI) and a code repository (GitHub).
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
“BioPortal now houses 1549 biomedical ontologies (1182 of them public) that collectively include 15 293 440 terms and over 100 million cross-ontology mappings.”
The dataset's content is described in a prose sentence, not an itemised inventory. [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'
“All software discussed in this paper is open access, and is freely available at https://github.com/ncbo and https://doi.org/10.5281/zenodo.15284916 .”
The paper gives a route to the data 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
“All software discussed in this paper is open access, and is freely available at https://github.com/ncbo and https://doi.org/10.5281/zenodo.15284916 .”
The paper applies the phrase 'open access' to the software, matching the standard access- label vocabulary. [majority verdict 'yes' (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 human-subject data; 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 software will remain available; no persistence commitment or availability timing beyond the current availability is given. [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'
No file format is named for the released software; the paper names formats for the hosted ontologies but not for the study's own data. [majority verdict 'no' (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
The paper does not name a data or metadata community standard applied to the software; it mentions standards for ontologies (OWL, OBO) but not for its own data. [majority verdict 'no' (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'
“CHEBI:2509”— not found in the paper; verdict downgraded
The paper includes identifiers for external resources (e.g., CHEBI terms) that the data depend on. [downgraded to 'no' — no verifiable quote from the paper]
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 specific license token (e.g., MIT, Apache) is named for the software; 'open access' refers to the article, 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'
“https://doi.org/10.5281/zenodo.15284916”
The Zenodo DOI is a version-specific identifier, serving as a version token. [majority verdict 'yes' (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'
“https://github.com/ncbo and https://doi.org/10.5281/zenodo.15284916”
A machine-resolvable locator (GitHub URL and Zenodo DOI) is given for the software.
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)
“U24 GM143402”
An award number is explicitly attached to a named funder (National Institutes of Health). [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
“BioPortal’s stack consists of Ruby on Rails for web development, the Sinatra framework for API management, Java for handling ontology data, a triple-store based database (AllegroGraph), as well as a host of other supporting libraries.”
Specific tools and software used to build the data are named. [majority verdict 'yes' (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, data dictionary) is named 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
0.406
From this paper's citation signal
Citation Network Contribution
0.0765
From 3 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 12 citers.
National Institutes of Health
Grant: U24 GM143402
National Institutes of Health
Grant: 5U01HG009453-03
An Intelligent Concept Agent for Assisting with the Application of Metadata
National Institutes of Health
Grant: 3OT2DB000009
Department of Energy
Grant: DE-AC0205CH11231
DB NIH HHS
Grant: OT2 DB000009
NHGRI NIH HHS
Grant: U01 HG009453
National Institutes of Health
Grant: 5U24GM143402-03
BioPortal: An Expansive Knowledgebase of Biomedical Entities and Relations
National Institutes of Health
Grant: 3OT2DB000009-01S2
Enhancing the RADx Data Hub for Data FAIRness
FWCI
5.99
Citation Percentile
1.0%
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals