BioPortal

Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format OWL RDF Rich Release Format (RRF) Prot¨«¨«g¨«¨« frames and LexGrid XML. Functionality includes the ability to browse search and visualize ontologies as well as to comment on and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. BioPortal Features:* Browse search and visualize ontologies.* Support for ontologies in multiple formats (OBO format OWL RDF RRF Prot¨«¨«g¨«¨« frames and LexGrid XML).* Add Notes: discuss the ontology structure and content propose new terms or changes to terms upload images as examples for terms. Notification of new Notes is RSS-enabled Notes can be browsed via BioPortal and are accessible via Web services.* Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology.* Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services.* NCBO Annotator: The Annotator is a tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g. is_a relations).* NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically using the NCBO Annotator and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics University of Michigan) to produce a set of annotations and expand them using ontology is_a relations.* Web services: Documentation on all Web services and example code is available at: BioPortal Web services.

Resource Type: 
Parent organization: 
National Center for Biomedical Ontology Stanford University; California; USA
PMID: 
19483092 21672956 18999306