Abstract
As new biomedical technologies are developed, the amount of publically available biomedical data continues to increase. To help manage these vast and disparate data sources, researchers have turned to the Semantic Web. Specifically, ontologies are used in data annotation, natural language processing, information retrieval, clinical decision support, and data integration tasks. The development of software applications to perform these tasks requires the integration of Web services to incorporate the wide variety of ontologies used in the health care and life sciences. The National Center for Biomedical Ontology, a National Center for Biomedical Computing created under the NIH Roadmap, developed BioPortal, which provides access to one of the largest repositories of biomedical ontologies. The NCBO Web services provide programmtic access to these ontologies and can be grouped into four categories; Ontology, Mapping, Annotation, and Data Access. The Ontology Web services provide access to ontologies, their metadata, ontology versions, downloads, navigation of the class hierarchy (parents, children, siblings) and details of each term. The Mapping Web services provide access to the millions of ontology mappings published in BioPortal. The NCBO Annotator Web service “tags” text automatically with terms from ontologies in BioPortal, and the NCBO Resource Index Web services provides access to an ontology-based index of public, online data resources. The NCBO Widgets package the Ontology Web services for use directly in Web sites. The functionality of the NCBO Web services and widgets are incorporated into semantically aware applications for ontology development and visualization, data annotation, and data integration. This overview will describe these classes of applications, discuss a few examples of each type, and which NCBO Web services are used by these applications.
Highlights
As new biomedical technologies are developed, the amount of publically available biomedical data continues to increase
The functionality of the BioPortal Web site is driven by the NCBO Web services, which include the Ontology, Mapping, Annotator, and Resource Index Web services (Figure 1)
The mapping data includes mappings from UMLS based on shared Concept Unique Identifiers, mappings specified within ontologies, user submitted mappings, and automatically generated mappings using the Lexical OWL Ontology Matcher (LOOM), which generates mappings based on lexical similarity of the preferred name and synonyms between pairs of ontologies [3]
Summary
As new biomedical technologies are developed, the amount of publically available biomedical data continues to increase. NCBO Technology overview BioPortal is an open repository of biomedical ontologies that stores ontologies developed in various formats, such as OWL, OBO format, Protégé frames, and the Rich release format, and provides access to this content via Web browsers and Web services [1,2]. The BioPortal Web interface allows users to browse the list of ontologies, search and comment on terms in ontologies, annotate text with ontology terms, and search an ontology-based index of biomedical resources.
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