Thodoros Topaloglou, Anthony Kosky and Victor Markowitz
Abstract
There are more than two hundred biological data repositories available
for public access, and a vast number of applications to process
and interpret biological data. A major challenge for bioinformaticians
is to extract and process data from multiple data sources using
a variety of query interfaces and analytical tools. In this paper,
we describe tools that respond to this challenge by providing
support for cross-database queries and for integrating analytical
tools in a query processing environment. In particular, we describe
two alternative methods for integrating biological data processing
within traditional database queries: (a) "light-weight"
application integration based on Application Specific Data
Types (ASDTs) and (b) "heavy-duty" integration of analytical
tools based on mediators and wrappers. These methods are supported
by the Object-Protocol Model (OPM) suite of tools for managing
biological databases.