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An integrative approach of biomedical knowledge via ontologies for liver transcriptome analysis

GO (Gene Ontology). BIOMEKE. An integrative approach of biomedical knowledge via ontologies for liver transcriptome analysis. Gwénaëlle MARQUET, Anita BURGUN, Fouzia MOUSSOUNI, Émilie GUERIN & Olivier LOREAL

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An integrative approach of biomedical knowledge via ontologies for liver transcriptome analysis

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  1. GO (Gene Ontology) BIOMEKE An integrative approach of biomedical knowledge via ontologies for liver transcriptome analysis Gwénaëlle MARQUET, Anita BURGUN, Fouzia MOUSSOUNI, Émilie GUERIN & Olivier LOREAL INSERM U522 & LIM (Laboratoire d ’Informatique Médicale), CHU Pontchaillou, 2 rue Henri Le Guilloux, 35033 Rennes Cedex, France emilie.guerin@rennes.inserm.fr Abstract Semantic interoperability between databases and knowledge bases in medicine on one hand, and databases and knowledge bases in genomics and molecular biology on the other hand, is a means to enable further research and better patient care. The objective of the BioMedical Knowledge Extraction project (BioMeKe) is to develop a knowledge warehouse in the context of transcriptome analysis for liver diseases diagnosis. Knowledge sources include ontologies, related terminologies and annotations linked towards public databases (e.g., SwissProt). BioMeKe has been developed to have access to information by 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 data on genes expressed in liver specific DNA microarrays designed in Lab for better assistance of analysis. STORAGE mRNA from control models Protocol description of array experiment(MGED) Expression level and parameters DB GEDAW (Gene Expression Data Warehouse) mRNA from liver diseases models Exchange Format Transformation XML parsing Accession number For each spot of the array Extraction of sequence annotations BioWEB Knowledge EBI FlyBase PomBase Berkeley Drosophila Genome Project Rat Genome DataBase (RGD) Saccharomyces Genome Database (SGD) Genome Knowledge Base WormBase The Arabidopsis Information Resource (TAIR) Mouse Genome Database (MGD) The Pathogen Sequencing Unit Gramene DictyBase Compugen The Institute for Genomic Research (TIGR) MedWeb Knowledge ex Medline GOA (GO Annotations) UMLS (Unified Medical Language System) Complementary knowledge on expressed genes: BIOMEKE Bio Medical Knowledge Extractor BioMeKe : an Ontology driven Mediator Knowledge Exploration on Genes Expressed with BioMeKe Annotation cDNA ceruloplasmin Medical exploration Genomic exploration

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