Improving Federated Database Queries Using Declarative Rewrite Rules for Quantified Subqueries
Journal of Intelligent Information Systems
Towards transparent access to multiple biological databanks
APBC '03 Proceedings of the First Asia-Pacific bioinformatics conference on Bioinformatics 2003 - Volume 19
A Functional Data Model Approach to Querying RDF/RDFS Data
BNCOD '08 Proceedings of the 25th British national conference on Databases: Sharing Data, Information and Knowledge
Distributed processing of large biomedical 3d images
VECPAR'04 Proceedings of the 6th international conference on High Performance Computing for Computational Science
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Developments in our ability to integrate and analyse the data held in existing heterogeneous data resources can lead to an increase in our understanding of biological function at all levels. However, supporting ad-hoc queries across multiple data resources and correlating the data retrieved from these is still difficult. To address this, we are building a mediator based on the functional data model database, P/FDM, which integrates access to heterogeneous, distributed biological databases, while making use of existing search engines and indexes, without infringing on the autonomy of the underlying databases. Central to our design philosophy is the use of schemas. We have adopted a federated architecture with a five-level schema, arising from the use of the ANSI-SPARC three-level schema to describe both the existing autonomous data resources and the mediator itself. We describe the use of mapping functions and list comprehensions in query splitting, producing execution plans, code generation and result fusion. We give an example of cross-database querying involving data held locally in P/FDM systems and external data in the Sequence Retrieval System (SRS).