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Ontology-Based MEDLINE Document Classification

Camous, Fabrice and Blott, Stephen and Smeaton, Alan F. (2007) Ontology-Based MEDLINE Document Classification. In: BIRD 2007 - 1st International Conference on Bioinformatics Research and Development, 12-14 March 2007, Berlin, Germany. ISBN 978-3-540-71232-9

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An increasing and overwhelming amount of biomedical information is available in the research literature mainly in the form of free-text. Biologists need tools that automate their information search and deal with the high volume and ambiguity of free-text. Ontologies can help automatic information processing by providing standard concepts and information about the relationships between concepts. The Medical Subject Headings (MeSH) ontology is already available and used by MEDLINE indexers to annotate the conceptual content of biomedical articles. This paper presents a domain-independent method that uses the MeSH ontology inter-concept relationships to extend the existing MeSH-based representation of MEDLINE documents. The extension method is evaluated within a document triage task organized by the Genomics track of the 2005 Text REtrieval Conference (TREC). Our method for extending the representation of documents leads to an improvement of 17% over a non-extended baseline in terms of normalized utility, the metric defined for the task. The SVMlight software is used to classify documents.

Item Type:Conference or Workshop Item (Paper)
Event Type:Conference
Additional Information:The original publication is available at
Subjects:Computer Science > Information retrieval
DCU Faculties and Centres:Research Initiatives and Centres > Centre for Digital Video Processing (CDVP)
Research Initiatives and Centres > Adaptive Information Cluster (AIC)
DCU Faculties and Schools > Faculty of Engineering and Computing > School of Computing
Published in:Hochreiter, Sepp and Wagner, Roland, (eds.) Bioinformatics Research and Development. Lecture Notes in Computer Science Volume 4414. Springer Berlin / Heidelberg. ISBN 978-3-540-71232-9
Publisher:Springer Berlin / Heidelberg
Official URL:
Use License:This item is licensed under a Creative Commons Attribution-NonCommercial-Share Alike 3.0 License. View License
Funders:Enterprise Ireland, EI SC-2003-0047-Y, European Commission FP6-027026
ID Code:258
Deposited On:07 Mar 2008 by DORAS Administrator. Last Modified 05 May 2010 12:48

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