Ontology-Based Knowledge Discovery in Pharmacogenomics

  • Adrien Coulet
  • Malika Smaïl-Tabbone
  • Amedeo Napoli
  • Marie-Dominique Devignes
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 696)


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.


Association Rule Description Logic Formal Concept Analysis Data Mining Algorithm Knowledge Unit 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We would like to thank Dr. Pascale Benlian for her help in the interpretation of RAA results.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Adrien Coulet
    • 1
    • 2
  • Malika Smaïl-Tabbone
  • Amedeo Napoli
  • Marie-Dominique Devignes
  1. 1.Department of MedicineStanford UniversityStanfordUSA
  2. 2.LORIA (CNRS UMR7503, INRIA Nancy Grand-Est, Nancy Université)Vandoeuvre-lès-NancyFrance

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