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

Natalya F. Noy (1) , Nigam H. Shah (1) , Patricia L. Whetzel (1) , Benjamin Dai (1) , Michael Dorf (1) , Nicholas B. Griffith (1) , Clement Jonquet (1) , Daniel L. Rubin (1) , Margaret-Anne Storey (2) , Christopher G. Chute (3) , Mark A. Musen (1)

1 BMIR - Stanford Center for BioMedical Informatics Research
2 CHISEL - Computer Human Interaction & Software Engineering Lab
3 MC - Mayo Clinic

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.

Mots clés: biomedical ontologies; BioPortal; semantic web

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Web

Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Benjamin Dai, Michael Dorf, et al.. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research, 2009, 37, pp.170-173. ⟨10.1093/nar/gkp440⟩. ⟨hal-00492020v1⟩