Managing Biological Data using bdbms

Mohamed Eltabakh
Mourad Ouzzani
Walid G. Aref, Purdue University
Ahmed K. Elmagarmid, Purdue University
Yasin Silva
Muhammed Arshad
David Salt
Ivan Baxter

Data Engineering, 2008. ICDE 2008. IEEE 24th International Conference on 7-12 April 2008 page(s): 1600 - 1603 Location: Cancun


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.