title: BioMeKe: an ontology-based biomedical knowledge extraction system devoted to transcriptome analysis.
abstract: Semantic interoperability between knowledge bases in medicine, and knowledge base in genomics and molecular biology will lead to advances in fundamental research as well as to improved patient care. DNA chips strategy is used for transcriptome analysis in order to identify deregulated genes in physio-pathological conditions. The objective of the BioMedical Knowledge Extraction project (BioMeKe) is to develop a knowledge warehouse in the context of transcriptome analysis during liver diseases. Knowledge sources include ontologies, related terminologies and annotations linked towards public databases (e.g., SWISSPROT). BioMeKe has been developed to have access to information using systematic investigation upon a concept, gene, gene products, pathology, or any target keyword, and is based on the combination of several relevant resources: UMLS, GeneOntology, MeSH supplementary terms, GOA, and HUGO. Current efforts are focusing on exploiting this ontology-based Knowledge Extractor, to enrich the expression data on genes delivered by a liver specific DNA microarray for better assistance of analysis.
authors.affiliation: Laboratoire d'Informatique Médicale-Faculté de Médecine-35043 Rennes, France. gwenaelle.marquet@univ-rennes1.fr
authors.forename: Gwenaëlle
authors.initials: G
authors.lastname: Marquet
authors.forename: Anita
authors.initials: A
authors.lastname: Burgun
authors.forename: Fouzia
authors.initials: F
authors.lastname: Moussouni
authors.forename: Emilie
authors.initials: E
authors.lastname: Guérin
authors.forename: Franck
authors.initials: F
authors.lastname: Le Duff
authors.forename: Olivier
authors.initials: O
authors.lastname: Loréal
mesh_terms: D030541:Databases, Genetic; D006801:Humans; D016247:Information Storage and Retrieval; D008491:Medical Informatics Applications; D008967:Molecular Biology; D012333:RNA, Messenger / Q000235:genetics*; D017432:Unified Medical Language System
chemical_list: D012333:RNA, Messenger