2006/12/22 by Mohamed Y. Eltabakh, Eltabakh, Mohamed Y., Mourad Ouzzani +3
Computer Science · Decision Sciences · #Advanced Data Storage Technologies #Advanced Database Systems and Queries #Databases (cs.DB) #FOS: Computer and information sciences #Scientific Computing and Data Management #cs.DB
paper · pdf · doi:10.48550/arxiv.cs/0612127
This article is published under a Creative Commons License Agreement (http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute, display, and perform the work, make derivative works and make commercial use of the work, but, you must attribute the work to the author and CIDR 2007. 3rd Biennial Conference on Innovative Data Systems Research (CIDR) January 710, 2007, Asilomar, California, USA
arxiv created 2006/12/22 · openalex publication_date 2006/12/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current database technology lacks several functionalities that are needed by biological databases. In this paper, we introduce bdbms, an extensible prototype database management system for supporting biological data. bdbms extends the functionalities of current DBMSs to include: (1) Annotation and provenance management including storage, indexing, manipulation, and querying of annotation and provenance as first class objects in bdbms, (2) Local dependency tracking to track the dependencies and derivations among data items, (3) Update authorization to support data curation via content-based authorization, in contrast to identity-based authorization, and (4) New access methods and their supporting operators that support pattern matching on various types of compressed biological data types. This paper presents the design of bdbms along with the techniques proposed to support these functionalities including an extension to SQL. We also outline some open issues in building bdbms.