The Open Biomedical Annotator
- 1 March 2009
- journal article
- Vol. 2009, 56-60
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 (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.[1]Keywords
This publication has 9 references indexed in Scilit:
- Ontology-driven indexing of public datasets for translational bioinformaticsBMC Bioinformatics, 2009
- Essie: A Concept-based Search Engine for Structured Biomedical TextJournal of the American Medical Informatics Association, 2007
- A Comparative Evaluation of Full-text, Concept-based, and Context-sensitive SearchJournal of the American Medical Informatics Association, 2007
- Bio-ontologies: current trends and future directionsBriefings in Bioinformatics, 2006
- Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics.2006
- Ontology-based annotation and query of tissue microarray data.2006
- Towards the development of a conceptual distance metric for the UMLSJournal of Biomedical Informatics, 2004
- IndexFinder: a method of extracting key concepts from clinical texts for indexing.2003
- Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program.2001