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Colloquia Archive

A Database Management System for Biological Data

November 19, 2007

This colloquium is co-sponsored by CIS-IEEE.

Host: Jake Chen

Abstract

Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, and annotations from various sources. Current database technology lacks the functionality required by biological databases. This talk introduces bdbms, an extensible prototype database management system for biological data, which has

  • Storage, indexing, manipulation, and querying of annotation and provenance as first class objects
  • Local dependency tracking
  • Update authorization to support data curation via content-based authorization, and
  • New access methods and operators that support pattern matching on various kinds of compressed biological data types.

The talk covers the design of bdbms, extensions to SQL and other techniques that support its functionality, and some open issues in building bdbms.

Biography

Walid G. Aref is Professor of Computer Science at Purdue University, West Lafayette. He received his Ph.D. in Computer Science from the University of Maryland at College Park in 1993. His research interests are in extending the functionality of database systems to support spatial, spatio-temporal, multimedia, biological, and sensor databases. He is also interested in indexing, data mining, and geographic information systems (GIS). Professor Aref's research has been supported by the National Science Foundation, the National Institute of Health, Purdue Research Foundation, CERIAS, Panasonic, and Microsoft Corp. In 2001, he received the CAREER Award from the National Science Foundation and in 2004, he received a Purdue University Faculty Scholar award. Professor Aref is a member of Purdue's Discovery Park Bindley Bioscience and Cyber Centers. He is on the editorial board of the VLDB Journal, a senior member of the IEEE, and a member of the ACM.