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Seamless integration of biological applications within a database framework.

Authors
  • Topaloglou, T
  • Kosky, A
  • Markowitz, V
Type
Published Article
Journal
International Conference on Intelligent Systems for Molecular Biology
Publication Date
1999
Pages
272–281
Identifiers
PMID: 10786310
Source
Medline
License
Unknown

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.

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