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Nucleic Acids Research Advance Access published online on May 29, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp440
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Natalya F. Noy1, Nigam H. Shah1, Patricia L. Whetzel1,*, Benjamin Dai1, Michael Dorf1, Nicholas Griffith1, Clement Jonquet1, Daniel L. Rubin1, Margaret-Anne Storey2, Christopher G. Chute3 and Mark A. Musen1

1Stanford Center for Biomedical Informatics Research, Stanford University, 2Department of Computer Science, University of Victoria, Victoria, Canada and 3Department of Biomedical Informatics, Mayo Clinic, Rochester, MN, USA

*To whom correspondence should be addressed. Tel: +650 721 2378; Fax: +650 725 7944; Email: whetzel{at}stanford.edu

Received March 6, 2009. Revised April 19, 2009. Accepted May 11, 2009.

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.


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