BioPortal: ontologies and integrated data resources at the click of a mouse

By P. Whetzel, Natasha Noy, Nigam H. Shah, Paul R. Alexander, M. Dorf, Ray W. Fergerson, Margaret-Anne D. Storey, Barry Smith, Christopher G. Chute, Mark A. Musen. Nucleic Acids Res., 2009

1,011 citations recorded by the source corpus.

Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. Thus, BioPortal not only provides investigators, clinicians, and developers ‘one-stop shopping’ to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.

Subfields: Molecular Biology

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Citations in the corpus

Controlled vocabularies and semantics in systems biology (2011, methodology): “KiSAO is an open ontology, accessible in OWL2 format via the project homepage (http://biomodels.net/kisao/) or through the NCBO BioPortal (ontology 1410, http://purl. bioontology.org/ontology/KiSAO).”
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature (2018, background): “At the time of writing BioPortal [112], an open repository of biomedical ontologies, has 551 ontologies.”
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications (2011, neutral): “BioPortal ﬁlls these gaps (2).”
WikiPathways: building research communities on biological pathways (2011, methodology): “Therefore, we recently implemented an ontology annotation feature that allows each pathway to be annotated with terms from several ontologies covering different topics [these currently include the Pathway, Human disease and Cell type ontologies from the BioPortal collection (5)].”
Leveraging Logical Rules for Efficacious Representation of Large Orthology Datasets (2017, background): “The interest in ontologies in biomedicine can be illustrated by the fact that repositories such as BioPortal [12] contain at the time of writing more than six hundred biomedical ontologies, terminologies and controlled vocabularies.”
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…”
Unveiling differential adverse event profiles in vaccines via LLM text embeddings and ontology semantic analysis (2025, unknown): “…mapping to HPO and OAE terms using the tool BioPortal Anno-tator ( h t t p s : / / b i o p o r t a l . b i o o n t o l o g y . o r g / a n n o t a t o r ) [17] and an in-house tool OntoRetriever (available at h t t p s : / / g i t h u b . c o m / C e t o m a t o / O n t o R e t r i e v e r).”