GENOMIC DATA EXCHANGE
Abstract
Genomic data exchange is currently becoming more and more important. Along with the rise in demand for sharing genomic information, many techniques, tools, and languages have been proposed to facilitate this task in the last 5 years. Extensible Markup Language (XML) is a universal language that has been proposed for this purpose. Relying in an XML framework, some markup languages, such as BIOLML DTD, MAMAL, and GEML, have been proposed the bioinformatics area. Moreover, ontology languages, such as XOL, OML, and ONTOLINGUA have been proposed by AI research to facilitate the sharing and reusing of knowledge.
One goal of this thesis is to review and to compare XML-based as well as ontology-based approaches to facilitate the exchange of genomic information. Moreover, case studies are conducted to evaluate the suitability of particular tools that have been proposed for this purpose. In particular, XML DTD, XML-DBMS, and GEML tools are reviewed and evaluated in a case study using a M.D. Anderson Microarray database (part of ACCG database) as a test bed. Moreover, the mapping problems between relational, frame-based, and XML-based knowledge representation schemes will be analyzed as part of the case study.
Date: Friday, May 3, 2002
Time: 1:00 PM
Place: 550-PGH
Faculty, students, and the general public are invited.
Thesis Advisor: Dr. Eick