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BioWarehouse: A bioinformatics database warehouse toolkit

Author(s): Lee TJ, Pouliot Y, Wagner V, Gupta P, Stringer-Calvert DW, et al.

Abstract

This paper describes an evolving open source toolkit for constructing DB warehouses that combines different collections of bioinformatics DBs within a single physical DB management system (DBMS) to facilitate queries that span multiple DBs. We emphasize that BioWarehouse is a flexible toolkit that supports multiple alternative warehouses: our goal is to enable different investigators to create different warehouse instances that combine collections of DBs relevant to their interests. The warehouse also facilitates integration of locally produced data with other public bioinformatics DBs in pursuit of goals such as capture of experimental data, sharing experimental data with collaborators, Internet publishing of data to the scientific community, and data mining and global integrative studies across multiple DBs. The data sources supported by BioWarehouse are particularly well suited to integration of pathway information, although pathways are only one of many datatypes supported by BioWarehouse.

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