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BioPortal specifications


Unique identifier OMICS_09873
Name BioPortal
Restrictions to use None
Maintained Yes


  • person_outline Patricia L. Whetzel

Publications for BioPortal

BioPortal citations


ONS: an ontology for a standardized description of interventions and observational studies in nutrition

PMCID: 5928560
PMID: 29736190
DOI: 10.1186/s12263-018-0601-y
call_split See protocol

[…] om/) was used for consistency checking. (ii) Accessible, under the Creative Commons license (CC BY 4.0), published on GitHub ( and at NCBO BioPortal ( (iii) Orthogonal to other ontologies by reusing existing terms. Besides assuring compliance with the OBO Foundry principles, we also ensure […]


An ontological approach to identifying cases of chronic kidney disease from routine primary care data: a cross sectional study

PMCID: 5894169
PMID: 29636024
DOI: 10.1186/s12882-018-0882-9

[…] idney damage (such as renal tumours or a single kidney) []. The ontology, applicable to any healthcare coding system, has been published online and can be accessed using the following link []: then identified concepts from the CKD ontology using the Read v2 hierarchy and NHS Read Code Browser Version 20.0. We identified around 1250 candidate code […]


DMTO: a realistic ontology for standard diabetes mellitus treatment

J Biomed Semantics
PMCID: 5800094
PMID: 29409535
DOI: 10.1186/s13326-018-0176-y
call_split See protocol

[…] physical examinations, and symptoms. We can assume that the patient profile is a record in a distributed EHR system.Drug adverse effects are imported from the Drug-Drug Interactions Ontology ( All types have the same identifiers as DINTO under the adverse effect upper-level class with the OAE_0000001 identifier. We can add the adverse effect sema […]


The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability

J Biomed Semantics
PMCID: 5765662
PMID: 29329592
DOI: 10.1186/s13326-017-0169-2

[…] ing these principles in an evolving non-redundant and interoperable suite []. The OBO library currently includes over 160 ontologies covering >3 million terms in biological and clinical domains. NCBO BioPortal [] has over 400 ontologies including both OBO and non-OBO ontologies. Given hundreds of ontologies developed, a critical issue is the lack of ontology interoperability, preventing the seamle […]


How much of the invader's genetic variability can slip between our fingers? A case study of secondary dispersal of Poa annua on King George Island (Antarctica)

Ecol Evol
PMCID: 5756844
PMID: 29321896
DOI: 10.1002/ece3.3675
call_split See protocol

[…] h of the burn‐in and MCMC (Markov chain Monte Carlo) of 100,000–300,000 each was performed. Finally, 500,000 burn‐ins and 500,000 iterations with 10 runs were carried out on the bioportal server ( to quantify the amount of variation of the likelihood for each K. The range of possible Ks tested was 1–10. In order to determine the optimal number of clusters (K), an ad hoc statis […]


Using semantics for representing experimental protocols

J Biomed Semantics
PMCID: 5683383
PMID: 29132408
DOI: 10.1186/s13326-017-0160-y

[…] In this stage we identified reusable terminology from other ontologies; for supporting activities throughout this stage we used BioPortal [] and Ontobee []. We also looked into minimal information standards [], guidelines and vocabularies representing research activities [–]. Issues about axioms required to represent this doma […]


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BioPortal institution(s)
Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA

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