The Open Biomedical Annotator

Clement Jonquet (1) , Nigam Shah (1) , Mark A. Musen (1)

1 BMIR - Stanford Center for BioMedical Informatics Research

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 (www.bioontology.org). The biomedical community can use the annotator service to tag datasets automatically with ontology terms (from UMLS and NCBO BioPortal ontologies). Such annotations facilitate translational discoveries by integrating annotated data.

Mots clés: semantic annotation; biomedical ontologies; annotator

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Web

Clement Jonquet, Nigam Shah, Mark A. Musen. The Open Biomedical Annotator. AMIA Summit on Translational Bioinformatics, Mar 2009, San Francisco, CA, United States. pp.56-60. ⟨hal-00492024⟩