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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
[email protected]
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)
mRNA from liver
diseases models
DB
Expression level and
parameters
Exchange Format Transformation
(Gene Expression Data
Warehouse)
XML parsing
For each spot of
the array
Accession number
GEDAW
Extraction of sequence
annotations
BioWEB Knowledge
EBI
MedWeb Knowledge
FlyBase
GOA (GO Annotations)
PomBase
Berkeley Drosophila Genome Project
Complementary knowledge on
expressed genes:
BIOMEKE
Bio Medical Knowledge Extractor
UMLS
ex Medline
(Unified Medical
Language System)
Rat Genome DataBase (RGD)
GO (Gene Ontology)
Saccharomyces Genome Database (SGD)
Genome Knowledge Base
WormBase
BioMeKe : an Ontology driven Mediator
The Arabidopsis Information Resource (TAIR)
Mouse Genome Database (MGD)
The Pathogen Sequencing Unit
Knowledge Exploration on Genes Expressed with BioMeKe
Gramene
DictyBase
Compugen
Annotation
cDNA ceruloplasmin
Medical exploration
Genomic exploration
BIOMEKE
The Institute for Genomic Research (TIGR)