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Ontology-based knowledge discovery in pharmacogenomics.

Adrien Coulet 1, 2 Malika Smaïl-Tabbone 2 Amedeo Napoli 2 Marie-Dominique Devignes 2 
2 ORPAILLEUR - Knowledge representation, reasonning
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
Abstract : One current challenge in biomedicine is to analyze large amounts of complex biological data for extracting domain knowledge. This work holds on the use of knowledge-based techniques such as knowledge discovery (KD) and knowledge representation (KR) in pharmacogenomics, where knowledge units represent genotype-phenotype relationships in the context of a given treatment. An objective is to design knowledge base (KB, here also mentioned as an ontology) and then to use it in the KD process itself. A method is proposed for dealing with two main tasks: (1) building a KB from heterogeneous data related to genotype, phenotype, and treatment, and (2) applying KD techniques on knowledge assertions for extracting genotype-phenotype relationships. An application was carried out on a clinical trial concerned with the variability of drug response to montelukast treatment. Genotype-genotype and genotype-phenotype associations were retrieved together with new associations, allowing the extension of the initial KB. This experiment shows the potential of KR and KD processes, especially for designing KB, checking KB consistency, and reasoning for problem solving.
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Submitted on : Monday, April 11, 2011 - 4:29:19 PM
Last modification on : Friday, November 18, 2022 - 9:24:13 AM




Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes. Ontology-based knowledge discovery in pharmacogenomics.. Hamid R. Arabnia and Quoc-Nam Tran. Software Tools and Algorithms for Biological Systems, 696, Springer, pp.357-66, 2011, Advances in Experimental Medicine and Biology, 978-1-4419-7046-6. ⟨10.1007/978-1-4419-7046-6_36⟩. ⟨inria-00585072⟩



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