BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

By P. Whetzel, Natasha Noy, Nigam H. Shah, Paul R. Alexander, Csongor Nyulas, Tania Tudorache, Mark A. Musen. 2011

813 citations recorded by the source corpus.

The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

Subfields: Artificial Intelligence, Information Systems, Molecular Biology

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Citations in the corpus

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more (2020, background): “For example, the Bioportal, a repository of biomedical ontologies, contains >850 ontologies (34).”
Gateways to the FANTOM5 promoter level mammalian expression atlas (2015, methodology): “ships via a graphical and interactive user interface by using the NCBO widget [53].”
YummyData: providing high-quality open life science data (2018, methodology): “However, the next step would be to download MedDRA, and then we find that, while the ontology is browsable on BioPortal (the first result on our list), it is not possible to download the full ontology.”
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses (2012, background): “BioPortal web services (Whetzel et al. 2011) also offer PO web services as part of a larger set of methods providing access to ontological data, and generally return data in XML, although JSON format was more recently made available for most of their methods.”
Machine Learning and Decision Support in Critical Care (2016, background): “In fact, the growing number of distinct ontologies, many of which overlapping in purpose, has led researchers to create a database of ontologies [39].”
Natural Language Processing for EHR-Based Pharmacovigilance: A Structured Review (2017, methodology): “They ﬁrst used the National Center for Biomedical Ontology (NCBO) Annotator Web Service [64] to annotate disease and drug mentions in the EHR.”
Next-generation diagnostics and disease-gene discovery with the Exomiser (2015, background): “Alternatively, the HPO can be explored in a number of other websites including the Ontology Lookup Service 7,75 of the European Bioinformatics Institute (EBI) and the BioPortal of the National Center for Bio-Ontologies 76 .”
The REDCap Consortium: Building an International Community of Software Platform Partners (2019, background): “The growth of the REDCap Consortium and user base has created opportunities to collaborate with other consortia (e.g., PhenX [52,53], Medical Data Models [54], BioPortal [55], PROMIS [56]) to integrate standardized terminologies and instruments.”
Linked Open Vocabularies (LOV): A gateway to reusable semantic vocabularies on the Web (2016, background): “– Catalogues of ontologies for a specific domain such as biomedicine with the BioPortal [33], geospatial ontologies with SOCoP+OOR,39 Marine Metadata Interoperability and the SWEET [24] ontologies.”
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases (2015, methodology): “The ontologies ChEBI, CHEMINF, SIO, and UO are interfaced by the NIH Roadmap National Center for Bio-medical Ontology (NCBO) through its BioPortal [38], and comply with an evolving set of shared principles established by the Open Biomedical Ontologies (OBO) foundry [39].”
Systematic review automation technologies (2014, background): “BioPortal [73] is an ontology that maps vocabularies and includes MeSH but still lacks mappings to EMTREE or other literary database vocabularies.”
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations (2013, methodology): “Data can also be visualized by typing a query such as ‘C-reactive protein’ and using the NCBO autocomplete widget (20).”
Enabling semantic queries across federated bioinformatics databases (2019, background): “The relevance of ontologies in life sciences can be illustrated by the fact that repositories such as BioPortal (14) contain more than seven hundred biomedical ontologies, and the OBO Foundry (15) more than 170 ontologies.”
OntoLearner: A Modular Python Library for Ontology Learning with Large Language Models (2026, unknown): “In parallel, the community built ontology support infrastructure, including BioPortal (Noy et al. 2009; Whetzel et al. 2011; BioPortal 2024), Linked Open Vo-cabularies (LOV) (Vandenbussche et al. 2016), Ontology Lookup Service (OLS) (Jupp et al. 2015; Gatto 2025), the Open Biomedical Ontologies…”