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Bioinformatics, Vol 14, 486-497, Copyright © 1998 by Oxford University Press

ARTICLES

A metadata approach to query interoperation between molecular biology databases

KH Cheung, PM Nadkarni and DG Shin
Center for Medical Informatics, Yale University School of Medicine, 333 Cedar Street, TMP-3, New Haven, CT 06510, USA. kei.cheung@yale.edu

MOTIVATION: Molecular biology databases have been proliferating rapidly. Their heterogeneity and complexity pose a great challenge to efforts in database interoperation. To minimize the efforts of interoperating heterogeneous databases, it is useful to develop a system that lets a user of a particular genomic database access another related database as if the latter is structurally similar to the former. RESULTS: We extend a structurally simple model-the entity- attribute-value (EAV) model-to describe uniformly metadata relating to individual databases. Such metadata, which are necessary for performing database comparisons, include descriptions of primitive database objects (including entities, attributes, domain values and entity relationships) and specification of correspondences among the database objects. We show how to decompose SQL queries and map them from one database to another based on the EAV representation of the basic database objects. A prototype system is implemented to demonstrate query interoperation between two chromosome map databases. AVAILABILITY: Freely available (Cold Fusion source code and an Access database containing the mapping knowledge) upon request from the author. CONTACT: kei.cheung@yale.edu
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