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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
_at_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 Compuge
n 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