=Paper=
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|pdfUrl=https://ceur-ws.org/Vol-1014/talk3.pdf
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<pdf width="1500px">https://ceur-ws.org/Vol-1014/talk3.pdf</pdf>
<pre>
    Drugs, Genetics and Phenotypes: An Admission of
       Formal Semantics in Biomedical Research

                                   Michel Dumontier

                        Department of Biology Carleton University
                         michel dumontier@carleton.ca



Abstract
With its focus on investigating the nature and basis for the sustained existence of living
systems, modern biology has always been a fertile, if not challenging, domain for formal
knowledge representation and automated reasoning. Over the past 15 years, hundreds
of projects have developed or leveraged ontologies for entity recognition and relation
extraction, semantic annotation, data integration, query answering, consistency check-
ing, association mining and other forms of knowledge discovery. In this talk, I will
discuss our efforts to build a rich foundational network of ontology-annotated linked
data, discover significant biological associations across these data using a set of par-
tially overlapping ontologies, and identify new avenues for drug discovery by applying
measures of semantic similarity over phenotypic descriptions. As the portfolio of Se-
mantic Web technologies continue to mature in terms of functionality, scalability and
an understanding of how to maximize their value, increasing numbers of biomedical re-
searchers will be strategically poised to pursue increasingly sophisticated KR projects
aimed at improving our overall understanding of the capability and behaviour of bio-
logical systems.


Short CV. Dr. Michel Dumontier, PhD is an Associate Professor of Bioinformatics
in the Department of Biology, the Institute of Biochemistry and School of Computer
Science at Carleton University in Ottawa, Canada. His research focuses on the devel-
opment of computational methods to increase our understanding of how living systems
respond to chemical agents. At the core of the research program is the development
and use of Semantic Web technologies to formally represent and reason about data and
services so as (1) to facilitate the publishing, sharing and discovery of scientific knowl-
edge produced by individuals and small collectives, (2) to enable the formulation and
evaluation scientific hypotheses using our collective tools and knowledge and (3) to
create and make available computational methods to investigate the structure, function
and behaviour of living systems. Dr. Dumontier serves as a co-chair for the World Wide
Web Consortium Semantic Web in Health Care and Life Sciences Interest Group (W3C
HCLSIG) and is the Scientific Director for Bio2RDF, a widely used open-source project
to create and provide linked data for life sciences.

</pre>