W170–W173 Nucleic Acids Research, 2009, Vol. 37, Web Server issue doi:10.1093/nar/gkp440 Published online 29 May 2009 BioPortal: ontologies and integrated data resources at the click of a mouse Natalya F. Noy1, Nigam H. Shah 1 , 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 Received March 6, 2009; Revised April 19, 2009; Accepted May 11, 2009 ABSTRACT Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language pro- cessing 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 Prote´ g e´ 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. INTRODUCTION As the number of biomedical ontologies increases, so does the number of repositories that index and organize ontologies. Some repositories crawl the Web to collect ontologies (e.g. Swoogle, http://swoogle.umbc.edu;, Watson, http://watson.kmi.open.ac.uk/Overview.html; and OntoSelect, http://olp.dfki.de/ontoselect?wicket: bookmarkablePage=wicket-0:de.dfki.ontoselect.Home), some request users to submit their ontologies themselves (e.g. the DAML ontology library. http://www.daml.org/ ontologies; and SchemaWeb, http://www.schemaweb. info) and others are limited to storage of ontologies based on ontology representation language [Ontology Lookup Service, http://www.ebi.ac.uk/ontology-lookup/ (1,2)]. BioPortal is an open repository of biomedical ontol- ogies that stores ontologies developed in various formats, that provides for automatic updates by user submissions of new versions, and that provides access via Web brow- sers and through Web services. BioPortal users can browse and search the ontologies, submit new versions of the ontologies in the repository, comment on any ontology (or portion of an ontology) in the repository, add a review of the ontology, describe their experience in using the ontology or make suggestions to ontology developers. The focus on enabling members of the community to con- tribute actively to BioPortal content and to increase the value of that content to other users distinguishes BioPortal from other ontology repositories. Most researchers in biomedicine, however, are inter- ested in biomedical data and not the ontologies per se. Indeed, ontologies provide the means for users to interpret and integrate the data. One of the key features of BioPortal is the Open Biomedical Repository (OBR). To create OBR, we have indexed biomedical data sets avail- able online (e.g. entries in GEO, ClinicalTrials.gov) with ontologies in BioPortal. The index links the underlying data sets to the terms in the ontologies in BioPortal. While the content of BioPortal focuses on the biomedical domain, the BioPortal technology is domain-independent. *To whom correspondence should be addressed. Tel: +001 650 721 2378; Fax: +001 650 725 7944; Email: whetzel@stanford.edu 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.