Managing Biological Data using bdbms


We demonstrate bdbms, an extensible database engine for biological databases, bdbms started on the observation that database technology has not kept pace with the specific requirements of biological databases and that several needed key functionalities are not supported at the engine level. While bdbms aims at supporting several of these functionalities, this demo focuses on: (1) Annotation and provenance management including storage, indexing, querying, and propagation, (2) Local dependency tracking of dependencies and derivations among data items, and (3) Update authorization to support data curation. We demonstrate how bdbms enables biologists to manipulate their databases, annotations, and derivation information in a unified database system using the Purdue ionomics information management system (PiiMS) as a case study.


authorisation, biology computing, database indexing, query processing, scientific information systems

Date of this Version



Data Engineering, 2008. ICDE 2008. IEEE 24th International Conference, 7-12 April 2008, pgs:1600 - 1603; Cancun