BioPortal 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. It allows users to browse, search, and visualize ontologies. The Web interface 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 provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies and supports integration of data from various biomedical resources. BioPortal contains ontologies covering a wide range of subjects such as anatomy, phenotype, experimental conditions, imaging, chemistry, and health. It includes 72 ontologies (300,000 total classes) as of March 2008, and has almost doubled to 134 ontologies (680,000 total classes) in the last year. Metadata for each ontology includes keyword terms, text descriptions, version information, release date, ontology author contact information, and links to documentation. Ontology content and metadata can be updated automatically or by user submission. Prior ontology versions can be accessed through both the Web services and Web interface and are available for download. Users can add notes to all ontology classes in BioPortal, discussing the rationale for modeling decisions, pointing out problems with definitions, and requesting changes from ontology authors. Notes are RSS-enabled to provide timely updates when new notes are added. The content of the notes can be exported and used in context with ontology editing software to incorporate changes to the ontology. BioPortal also supports peer reviews of ontologies. Users can submit descriptions of their ontology-based projects to BioPortal and link these descriptions to BioPortal ontologies. They can provide comments on the ontology along several different dimensions, such as degree of formality, documentation and support, usability, domain coverage, and quality of content. BioPortal represents mappings between terms in different ontologies. Users can browse the mappings, create new point-to-point mappings, upload mappings created with other tools, and download the mappings. They can add notes on existing mappings and carry out discussions about the mappings. Each mapping has its own set of metadata that describes who created the mapping and when, which algorithm was used to produce the mapping, application context in which the mapping might be valid, the specific mapping relationship, and other properties. BioPortal also includes the Open Biomedical Repository (OBR), which automatically indexes the metadata for important biomedical data sets available online and links the underlying data sets to the terms in the ontologies in BioPortal and UMLS.BioPortal 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. It allows users to browse, search, and visualize ontologies. The Web interface 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 provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies and supports integration of data from various biomedical resources. BioPortal contains ontologies covering a wide range of subjects such as anatomy, phenotype, experimental conditions, imaging, chemistry, and health. It includes 72 ontologies (300,000 total classes) as of March 2008, and has almost doubled to 134 ontologies (680,000 total classes) in the last year. Metadata for each ontology includes keyword terms, text descriptions, version information, release date, ontology author contact information, and links to documentation. Ontology content and metadata can be updated automatically or by user submission. Prior ontology versions can be accessed through both the Web services and Web interface and are available for download. Users can add notes to all ontology classes in BioPortal, discussing the rationale for modeling decisions, pointing out problems with definitions, and requesting changes from ontology authors. Notes are RSS-enabled to provide timely updates when new notes are added. The content of the notes can be exported and used in context with ontology editing software to incorporate changes to the ontology. BioPortal also supports peer reviews of ontologies. Users can submit descriptions of their ontology-based projects to BioPortal and link these descriptions to BioPortal ontologies. They can provide comments on the ontology along several different dimensions, such as degree of formality, documentation and support, usability, domain coverage, and quality of content. BioPortal represents mappings between terms in different ontologies. Users can browse the mappings, create new point-to-point mappings, upload mappings created with other tools, and download the mappings. They can add notes on existing mappings and carry out discussions about the mappings. Each mapping has its own set of metadata that describes who created the mapping and when, which algorithm was used to produce the mapping, application context in which the mapping might be valid, the specific mapping relationship, and other properties. BioPortal also includes the Open Biomedical Repository (OBR), which automatically indexes the metadata for important biomedical data sets available online and links the underlying data sets to the terms in the ontologies in BioPortal and UMLS.