Improving Federated Database Queries Using Declarative Rewrite Rules for Quantified Subqueries
Journal of Intelligent Information Systems
Web data retrieval and extraction
Data & Knowledge Engineering - Special issue: Data integration over the Web
DiscoveryLink: a system for integrated access to life sciences data sources
IBM Systems Journal - Deep computing for the life sciences
Transparent access to multiple bioinformatics information sources
IBM Systems Journal - Deep computing for the life sciences
BioFast: challenges in exploring linked life sciences sources
ACM SIGMOD Record
Integration of biological sources: current systems and challenges ahead
ACM SIGMOD Record
Data & Knowledge Engineering - Special issue: XML schema and data management
Sync your data: update propagation for heterogeneous protein databases
The VLDB Journal — The International Journal on Very Large Data Bases
Composing, optimizing, and executing plans for bioinformatics web services
The VLDB Journal — The International Journal on Very Large Data Bases
ACM Computing Surveys (CSUR)
Web-Based genomic information integration with gene ontology
APWeb'06 Proceedings of the 8th Asia-Pacific Web conference on Frontiers of WWW Research and Development
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Vast amounts of life sciences data today reside in specialized data sources, with specialized query processing capabilities. Data from one source must often be combined with data from other sources to give users the information they desire. Database middleware systems such as Garlic allow users to combine data from multiple sources in a single query. Garlic provides the user with a virtual database to which they can pose arbitrarily complex queries, though the actual data needed to answer the query may be stored in several different sources, and those sources may not even possess all the functionality needed to answer such a query themselves. The Garlic technology, as incorporated in IBM's DB2 product, forms the basis of the DiscoveryLink service offering for the life sciences industry. We describe the DiscoveryLink offering, focusing on two key contributions of Garlic, the wrapper architecture and the query optimizer, and illustrate how it can be used to integrate life sciences data from heterogeneous data sources.