Résumé
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. This paper presents the Open Biomedical Annotator (OBA), an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag datasets automatically with ontology and terminology terms (from UMLS and NCBO). We have used the annotator service internally to index several online datasets (e.g., ArrayExpress, PubMed, ClinicalTrial.gov). The index is directly queriable in the NCBO BioPortal ontology repository (www.bioontology.org). Such semantic annotations facilitate translational discoveries by integrating annotated data.