Building federated bioinformatics databases using Web services

Abstract

Bioinformatics laboratories around the world continue to generate massive amounts of genomic and functional genomic data. Access to these data resources via Federated Databases through the Web is an important emerging technology. Federated databases allow several databases to be integrated while not discarding existing databases or losing local control over the administration of the databases. In order to achieve this desirable goal, technology needed to emerge to handle the heterogeneity and local autonomy of distributed database systems. Web service technology, including semantic Web service technology, provides a new opportunity to make federated databases a practical reality. This thesis presents architecture and an implementation to build federated databases using Web services. In particular, it demonstrates how Web service technology can provide the flexibility to create a dynamic federation of databases with sufficient abstraction to maintain the autonomy of the component systems and robustness to handle the heterogeneous nature of the disparate databases. A case study is conducted that involves federating six existing bioinformatics databases, CryptoDB, GiardiaDB, PlasmoDB, ToxoDB, TrichDB and TryTrypDB, to create the EuPathDB (formerly ApiDB) federated database.