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The Open Biomedical Annotator

Abstract : 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 terms (from UMLS and NCBO BioPortal ontologies). Such annotations facilitate translational discoveries by integrating annotated data.
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Contributor : Clement Jonquet Connect in order to contact the contributor
Submitted on : Monday, June 14, 2010 - 7:59:45 PM
Last modification on : Thursday, February 25, 2021 - 9:46:04 AM
Long-term archiving on: : Tuesday, September 14, 2010 - 8:39:47 PM


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  • HAL Id : hal-00492024, version 1


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



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