title: Seamless integration of biological applications within a database framework.
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.
authors.affiliation: Data Logic, A Division of Gene Logic Inc., Berkeley, CA 94704, USA. thodoros@genelogic.com
authors.forename: T
authors.initials: T
authors.lastname: Topaloglou
authors.forename: A
authors.initials: A
authors.lastname: Kosky
authors.forename: V
authors.initials: V
authors.lastname: Markowitz
mesh_terms: D019295:Computational Biology; D016208:Databases, Factual; D012106:Research; D012984:Software