Ontology-based knowledge discovery in pharmacogenomics.

Adrien Coulet; Malika Smaïl-Tabbone; Amedeo Napoli; Marie-Dominique Devignes

inria-00585072, version 1

Ontology-based knowledge discovery in pharmacogenomics.

Adrien Coulet ^1, 2, Malika Smaïl-Tabbone ², Amedeo Napoli ², Marie-Dominique Devignes ²

Software Tools and Algorithms for Biological Systems Springer (Ed.) (2011) 357-66

1 : Stanford Center for BioMedical Informatics Research (BMIR)
http://bmir.stanford.edu
Stanford University Medical School Office Building, Room X-215 251 Campus Drive Stanford, CA 94305-5479 États-Unis
2 : ORPAILLEUR (INRIA Lorraine - LORIA)
INRIA – CNRS : UMR7503 – Université Henri Poincaré - Nancy I – Université Nancy II – Institut National Polytechnique de Lorraine (INPL) France

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inria-00585072, version 1
http://hal.archives-ouvertes.fr/inria-00585072
oai:hal.archives-ouvertes.fr:inria-00585072
Contributeur : Adrien Coulet <>
Soumis le : Lundi 11 Avril 2011, 16:29:19
Dernière modification le : Jeudi 25 Août 2011, 14:21:57

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PubMed : 21431576

DOI : 10.1007/978-1-4419-7046-6_36

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%% inria-00585072, version 1
%% http://hal.archives-ouvertes.fr/inria-00585072
@incollection{coulet:inria-00585072,
    hal_id = {inria-00585072},
    url = {http://hal.archives-ouvertes.fr/inria-00585072},
    title = {{Ontology-based knowledge discovery in pharmacogenomics.}},
    author = {Coulet, Adrien and Sma{\"\i}l-Tabbone, Malika and Napoli, Amedeo and Devignes, Marie-Dominique},
    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.}},
    language = {Anglais},
    affiliation = {Stanford Center for BioMedical Informatics Research - BMIR , ORPAILLEUR - INRIA Lorraine - LORIA},
    booktitle = {{Software Tools and Algorithms for Biological Systems}},
    publisher = {Springer},
    pages = {357-66},
    editor = {Hamid R. Arabnia and Quoc-Nam Tran },
    series = {Advances in Experimental Medicine and Biology },
    audience = {internationale },
    isbn = {978-1-4419-7046-6 },
    doi = {10.1007/978-1-4419-7046-6\_36 },
    year = {2011},
}

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