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 Hagit Shatkay

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Talk Title:
Life by the Book: Pragmatically Using Text in Large Scale -Omics

Date/Time:
April 9, 2008, 6:00pm

Affiliation:
School of Computing, Queen’s University

URL:
Hagit Shatkay

Abstract:
The genomic era, which dawned upon us with the sequencing of the human genome, is characterized by tremendous amounts of biomedical data, accompanied by a significant increase in the number of related scientific publications.

Much biomedical knowledge is hidden within the abundant literature. The ability to rapidly and effectively survey the literature can support numerous applications, including multiple stages in the design and the interpretation of large-scale experiments.

A variety of methods are being applied to the biomedical literature in an attempt to meet these goals, mostly through careful mining of text for gene/protein names and interactions, using natural language processing methods. However, the idea
of general “biomedical text mining” remains elusive.

Rather than view biomedical text mining as one monolithic (and not very well
defined) task, we attend to specific biological goals that may benefit from the use of text. The talk will focus on several concrete biological applications/problems involving text, and discuss some non-traditional, coarse-grain methods, that we use to effectively address them.

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Introductory Speaker:

Leon French

Talk Title:
Automated recognition of brain region mentions in biomedical literature

Affiliation:
Pavlidis Lab, UBC Centre for High-througput Biology