PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units

Pierre Monnin 1 Clement Jonquet 2, 3 Joël Legrand 1 Amedeo Napoli 1 Adrien Coulet 1
1 ORPAILLEUR - Knowledge representation, reasonning
Inria Nancy - Grand Est, LORIA - NLPKD - Department of Natural Language Processing & Knowledge Discovery
2 SMILE - Système Multi-agent, Interaction, Langage, Evolution
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : We present in this article a lightweight ontology named PGxO and a set of rules for its instantiation, which we developed as a frame for reconciling and tracing pharmacogenomics (PGx) knowledge. PGx studies how genomic variations impact variations in drug response phenotypes. Knowledge in PGx is typically composed of units that have the form of ternary relationships gene variant–drug–adverse event, stating that an adverse event may occur for patients having the gene variant when being exposed to the drug. These knowledge units (i) are available in reference databases, such as PharmGKB, are reported in the scientific biomedical literature and (ii) may be discovered by mining clinical data such as Electronic Health Records (EHRs). Therefore, knowledge in PGx is heterogeneously described (i.e., with various quality, granularity, vocabulary, etc.). It is consequently worth to extract, then compare, assertions from distinct resources. Using PGxO, one can represent multiple provenances for pharmacogenomic knowledge units, and reconcile duplicates when they come from distinct sources.
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Contributor : Adrien Coulet <>
Submitted on : Wednesday, January 23, 2019 - 6:56:52 PM
Last modification on : Thursday, February 7, 2019 - 5:23:40 PM


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Pierre Monnin, Clement Jonquet, Joël Legrand, Amedeo Napoli, Adrien Coulet. PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units. Methods, tools & platforms for Personalized Medicine in the Big Data Era, Oct 2017, Palermo, Italy. ⟨10.7287/peerj.preprints.3140v1⟩. ⟨hal-01593184v2⟩



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