Un service Web pour l’annotation sémantique de données biomédicales avec des ontologies
msra(2009)
摘要
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 lise 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.
ClinicaITrial.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.
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关键词
annotation,controlled vocabularies,medical informatics applications,information storage and retrieval,semantics,unified medical language system,terminology,semantic annotation not in mesh,knowledge from mesh + ontology
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