[DL] RE: [semanticweb] Semantic Web for Bioinformatics - Tutorial-Workshop Aug 23
mpbelanger at jarg.com
Thu Aug 4 16:07:58 CEST 2005
Semantic Web for Bioinformatics - Tutorial/Workshop at Mass Biotech Council,
Cambridge, MA USA on August 23, 10 am 3 pm
Free for pre-registered MBC members, $25.00 for pre-registered non-members;
$40 at the door. Light lunch provided.
Introduction to the Semantic Web for Bioinformatics by:
Kenneth Baclawski, PhD, Associate Professor of Computer Science, College of
Computer and Information Science, Northeastern University, Boston, MA
Biologists heavily use the web, but the web is geared much more toward human
interaction than automated processing. While the web gives biologists access
to information, it does not allow them to easily integrate different data
sources or to incorporate additional analysis tools. The Semantic Web
addresses these problems by annotating web resources and by providing
reasoning and retrieval facilities from heterogeneous sources.
This tutorial introduces the basic languages of the Semantic Web from the
point of view of the life sciences, especially bioinformatics. The objective
is to cover the major web ontology languages, what they mean and how they
are used. The emphasis will be on pragmatic application issues. The goal is
for participants to have a understanding of the Semantic Web sufficient for
them to be able to make decisions about whether and how to use the Semantic
Ken Baclawski is an Associate Professor of Computer Science at Northeastern
University. He is also affiliated with the Division of Preventive Medicine
of Brigham and Womens Hospital at the Harvard Medical School. His primary
research area is formal ontologies, and he has been actively working in the
area of biomedical ontologies since 1992. He is co-founder of Jarg
Corporation and SemanTx Life Sciences, Inc. Prof. Baclawski has been active
in the development of the Semantic Web since it was first proposed, being
part of the team that developed the DAML+OIL language, later renamed the Web
Ontology Language (OWL).
Prof. Baclawski and Prof. Tianhua Niu of the Harvard Medical School have
written a book on the subject of the proposed tutorial, titled Ontologies
for Bioinformatics. This book has been accepted for publication by the MIT
Press as part of their series on Computational Molecular Biology. The book
is scheduled to ship in September, 2005.
MIT PRESS ISBN 0-262-02591-4 7 x 9, 440 pp., 70 illus.
Series: Computational Molecular Biology
"Ontologies for Bioinformatics"
Kenneth Baclawski and Tianhua Niu
Recent advances in biotechnology, spurred by the Human Genome Project, have
resulted in the accumulation of vast amounts of new data. Ontologies --
computer-readable, precise formulations of concepts (and the relationship
among them) in a given field -- are a critical framework for coping with the
exponential growth of valuable biological data generated by high-output
technologies. This book introduces the key concepts and applications of
ontologies and ontology languages in bioinformatics and will be an essential
guide for bioinformaticists, computer scientists, and life science
The three parts of Ontologies for Bioinformatics ask, and answer, three
pivotal questions: what ontologies are; how ontologies are used; and what
ontologies could be (which focuses on how ontologies could be used for
reasoning with uncertainty). The authors first introduce the notion of an
ontology, from hierarchically organized ontologies to more general network
organizations, and survey the best-known ontologies in biology and medicine.
They show how to construct and use ontologies, classifying uses into three
categories: querying, viewing, and transforming data to serve diverse
purposes. Contrasting deductive, or Boolean, logic with inductive reasoning,
they describe the goal of a synthesis that supports both styles of
reasoning. They discuss Bayesian networks as a way of expressing
uncertainty, describe data fusion, and propose that the World Wide Web can
be extended to support reasoning with uncertainty. They call this inductive
reasoning web the Bayesian web.
Kenneth Baclawski is Associate Professor of Computer Science at Northeastern
University and Cofounder of Semantx Life Sciences; Div of Jarg Corp.
Tianhua Niu is Assistant Professor of Medicine at Harvard Medical School and
Director of Bioinformatics, Division of Preventive Medicine, at Brigham and
Women's Hospital, Boston.
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