get children or parents of a speciﬁc concept, and get details of a concept. Users can request ontology content based on the ontology identiﬁer, in which case BioPortal provides a response based on the latest available version of the ontology, or they can use a speciﬁc version identi- ﬁer. In the search service, users can specify whether to search the whole repository or a speciﬁc set of ontologies, whether to use exact or approximate matching, and whether to search only in concept names and synonyms or in property values as well. A detailed list of Web ser- vices is available at http://bioontology.org/wiki/index .php/BioPortal_REST_services. Additional Web services include a hierarchy service to provide all paths to the root and all paths to the leaf node terms. These services can be used to develop applications using ontologies with- out the need to create a local store of the ontology. A few examples of projects accessing ontology content from BioPortal include ISAcreator (http://isatab.sourceforge .net/isacreator.html), which enables users to structure experimental metadata, BioLit (5), which provides metadata describing the content of full text articles from PubMed Central as ontology terms, and the Microsoft Word Add-in for Ontology Recognition (http://ucsdbiolit.codeplex.com/), which enables authors to include semantic content in documents at the time of writing. We are also developing Web services to retrieve the content of the annotated resources. A few example services include get all resources, get all annotations for a given concept (BioPortal or UMLS), and get all annota- tions for a given resource identiﬁer from GEO, Reactome, or OMIM for example. Ontology-indexed content can be accessed and then displayed on a site of interest. For example, ontology-indexed annotations from GEO using the Rat Strain ontology and anatomy ontology can be generated and then the data displayed on a third party Web site such as the Rat Genome Database by retrieving the data via the Web services. DISCUSSION BioPortal is a repository for ontologies developed in various formats that allows multiple mechanisms for con- tent updates and that provides access via Web services. Nucleic Acids Research, 2009, Vol. 37, Web Server issue W173 The incorporation of a variety of Web 2.0 features allows the system to behave not only as a comprehensive ontology repository, but also as a general infrastructure to support community-based access, peer-review, mapping and annotation of ontology content. BioPortal not only provides investigators, clinicians and developers ‘one-stop shopping’ to programmatically access biomedical ontolo- gies, but also integrates data from various biomedical resources. The BioPortal technology is open-source and is domain-independent. Thus, other communities can reuse the software to maintain their own ontology repositories. Currently, the Marine Metadata Interoperability Project (http://marinemetadata.org/aboutmmi) and National Cancer Institute (http://bioportal.nci.nih.gov/ ncbo/faces/index.xhtml) are using BioPortal as their ontology repository. FUNDING National Center for Biomedical Ontology, under road- map-initiative from the National Institutes of Health [grant U54 HG004028]. Funding for open access charge: National Institutes of Health [grant U54 HG004028]. Conﬂict of interest statement. None declared. REFERENCES 1. Cote,R.G., Jones,P., Martens,L., Apweiler,R. and Hermjakob,H. (2008) The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res., 36, W372–W376. 2. Cote,R.G., Jones,P., Apweiler,R. and Hermjakob,H. (2006) The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics, 7, 97. 3. Shah,N.H., Jonquet,C., Chiang,A.P., Butte,A.J., Chen,R. and Musen,M.A. (2009) Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics, 10(Suppl. 2), S1. 4. Smith,B., Ashburner,M., Rosse,C., Bard,J., Bug,W., Ceusters,W., Goldberg,L.J., Eilbeck,K., Ireland,A., Mungall,C.J. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251–1255. 5. Fink,J.L., Kushch,S., Williams,P.R. and Bourne,P.E. (2008) BioLit: integrating biological literature with databases. Nucleic Acids Res., 36, W385–W389.