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Semantic Software Lab
Concordia University
Montréal, Canada

Ontology Design for Biomedical Text Mining

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TitleOntology Design for Biomedical Text Mining
Publication TypeBook Chapter
Year of Publication2007
AuthorsWitte, R., T. Kappler, and C. J. O. Baker
Refereed DesignationRefereed
EditorsBaker, C. J. O., and K. - H. Cheung
Book TitleSemantic Web: Revolutionizing Knowledge Discovery in the Life Sciences
PublisherSpringer Science+Business Media
CityNew York, NY, USA
ISBN Number978-0-387-48436-5
KeywordsNLP, ontological NLP, Ontology Design, ontology population, text mining

Text Mining in biology and biomedicine requires a large amount of domain-specific knowledge. Publicly accessible resources hold much of the information needed, yet their practical integration into natural language processing (NLP) systems is fraught with manifold hurdles, especially the problem of semantic disconnectedness throughout the various resources and components. Ontologies can provide the necessary framework for a consistent semantic integration, while additionally delivering formal reasoning capabilities to NLP.

In this chapter, we address four important aspects relating to the integration of ontology and NLP: (i) An analysis of the different integration alternatives and their respective vantages; (ii) The design requirements for an ontology supporting NLP tasks; (iii) Creation and initialization of an ontology using publicly available tools and databases; and (iv) The connection of common NLP tasks with an ontology, including technical aspects of ontology deployment in a text mining framework. A concrete application example—text mining of enzyme mutations—is provided to motivate and illustrate these points.


Copyright © 2007 Springer US. This is the authors' preprint version of the work. It is posted here for your personal use. Not for redistribution. The definitive version was published in the book Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, DOI: 10.1007/978-0-387-48438-9_14.

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