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Semantic Software Lab
Concordia University
Montréal, Canada

Enhanced semantic access to the protein engineering literature using ontologies populated by text mining

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TitleEnhanced semantic access to the protein engineering literature using ontologies populated by text mining
Publication TypeJournal Article
Year of Publication2007
AuthorsWitte, R., T. Kappler, and C. J. O. Baker
Refereed DesignationRefereed
JournalInt.\ J.\ Bioinformatics Research and Applications (IJBRA)
Keywordsautomated reasoning in bioinformatics, description logics, ontological NLP, protein mutations, querying OWL-DL ontologies, Semantic Web, text mining

The biomedical literature is growing at an ever-increasing rate, which pronounces the need to support scientists with advanced, automated means of accessing knowledge. We investigate a novel approach employing description logics (DL)-based queries made to formal ontologies that have been created using the results of text mining full-text research papers. In this paradigm, an OWL-DL ontology becomes populated with instances detected through natural language processing (NLP). The generated ontology can be queried by biologists using DL reasoners or integrated into bioinformatics workflows for further automated analyses. We demonstrate the feasibility of this approach with a system targeting the protein mutation literature.


PMID: 18048198


Copyright © 2007 Inderscience Enterprises Ltd. This is the authors' postprint version of the work. It is posted here by permission of Inderscience Publishers for your personal use. Not for redistribution. The definitive version was published in the International Journal of Bioinformatics Research and Applications (IJBRA), DOI: 10.1504/IJBRA.2007.015009

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