From: Lu, Zhiyong (NIH/NLM/NCBI) [E]
Sent: Monday, March 10, 2008 9:12 AM
To: NLM/NCBI List ncbi-seminar
Subject: NCBI seminar 10am Thursday March 13

Time: 10am Thursday March 13
Location: 8th Floor Conference Room
Speaker: Adam Lee (Host: Zhiyong Lu)

Title: A Framework for Discovering Associations from the Annotated  
Biological Web

Abstract:

During the last decade, biomedical researchers gained access to the  
entire
human genome, reliable high-throughput biotechnologies, and affordable
computational resources and network access. In combination, these new
tools created a new model for biomedical research that no longer uses
computational tools merely to monitor research, but instead exploits  
these
tools to acquire knowledge and make discoveries.

We have developed a tool to discover meaningful patterns across  
resources
and ontologies. These patterns, corresponding to associations of  
pairs of
CV (controlled vocabulary) terms, may yield actionable nuggets of
previously unknown knowledge. Moreover, the bridge of associations  
across
CV terms will reflect the practice of how scientists annotate data.

We execute a protocol to follow hyperlinks, extract annotations, and
generate background LSLink (Life Sciences Link) datasets of term-links.
We then mine the term-links to find potentially meaningful associations.
We use two classes of metrics to identify significant associations of
pairs of CV terms. The first class is based on the LOD (logarithm of the
odds) ratio and is a measure of the extent to which a specific
association of CV terms deviates from one resulting from chance alone
(a random association). The second class of metric is based on the
hypergeometric distribution; it gives a quantification of the level of
one's surprise at finding over-representation for a particular pair of
CV terms in a user dataset, in comparison to the background dataset.

This is the ongoing research with Louiqa Raschid and Padmini Srinivasan.

About the speaker:

Woei-jyh (Adam) Lee received his BS degree from the National Taiwan  
University in 1993 and his MS degree from the New York University in  
1998. He worked on distributed objects and fault tolerance at the  
AT&T Labs - Research in 1997. He investigated network software and  
management at the Bell Laboratories Research from 1998 till 2000. He  
visited the Integrated Media Systems Center at the University of  
Southern California specializing in continuous media streaming and  
multimedia networking from 2002 to 2003.  He also contributed in  
protein domain parsing and boundary prediction at the National Cancer  
Institute in 2004. He is currently pursuing a PhD degree in the  
Center for Bioinformatics and Computational Biology and the  
Department of Computer Science in the University of Maryland at  
College Park. His research interests include bioinformatics and  
computational biology, data management and information integration,  
systems simulation and performance evaluation. He is a member of the  
ACM, the IEEE, the ISCB and the ISENG.