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Type of Talk: UTCS Collo

quium/AI

Speaker/Affiliation: Esra Erdem/Sabanci University

Date/Time: Friday, January 29, 2010, 10:45 a.m.

Location: TAY

3.128

Host: Vladimir Lifschitz

Talk Title: Querying Biomedic

al Ontologies in a Controlled Natural Language

Talk Abstract:

Recent advances in health and life sciences have led to
g

eneration of a large amount of data. To facilitate access to
its desir

ed parts, such a big mass of data has been represented
in structured

forms, like biomedical ontologies. On the other
hand, representing

biomedical ontologies in a formal language,
constructing them indepen

dently from each other and storing
them at different locations have br

ought about many challenges
for answering queries over them. One of th

e challenges for the
users is to be able represent a complex query in

a natural
language, and get its answers in an understandable form. We

address this challenge by introducing a controlled natural
langu

age --- a subset of natural language with a restricted
grammar and voc

abulary --- specifically for expressing
biomedical queries towards dru

g discovery; we call this
language BioQueryCNL. The idea is then to t

ransform a
biomedical query in BioQueryCNL into a program in answer se

t
programming (ASP) --- a formal framework to automate reasoning

about knowledge --- and compute answers to the given query over
some b

iomedical ontologies using a state-of-the-art ASP system.
We have deve

loped some algorithms to realize these ideas, and
illustrated the app

licability of our methods over some
biomedical ontologies obtained fro

m various information
repositories, such as PHARMGKB, UNIPROT, GO a

nd DRUGBANK.

Speaker Bio:

Esra Erdem rec

eived her Ph.D. in Computer Sciences at the
University of Texas at Aus

tin in 2002. She was a post-doctoral
fellow in the Cognitive Robotics

Group at the University of
Toronto (2002-2003), and a research scient

ist in the Knowledge
Based Systems Group at Vienna University of Techn

ology
(2003-2006). Since September 2006, she has been an assistant
professor at Sabanci University.