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

TLDR

Biomedical ontologies supply essential domain knowledge for data integration, information retrieval, annotation, NLP, and decision support. BioPortal is an open web-based repository that lets users browse, search, and visualize ontologies, add community annotations and reviews, and perform integrated searches across biomedical data resources such as GEO, ClinicalTrials.gov, and ArrayExpress. BioPortal offers a one‑stop platform for programmatic ontology access and facilitates integration of diverse biomedical data resources.

Abstract

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.