Bdbms. A database management system for biological data

Mohamed Y. Eltabakh, Mourad Ouzzani, Walid G. Aref

Research output: Chapter in Book/Report/Conference proceedingConference contribution

29 Citations (Scopus)

Abstract

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 with: (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.

Original languageEnglish
Title of host publicationCIDR 2007 - 3rd Biennial Conference on Innovative Data Systems Research
Pages196-206
Number of pages11
Publication statusPublished - 1 Dec 2007
Externally publishedYes
Event3rd Biennial Conference on Innovative Data Systems Research, CIDR 2007 - Asilomar, CA, United States
Duration: 7 Jan 200710 Jan 2007

Other

Other3rd Biennial Conference on Innovative Data Systems Research, CIDR 2007
CountryUnited States
CityAsilomar, CA
Period7/1/0710/1/07

Fingerprint

Storage management
Pattern matching
Metadata

ASJC Scopus subject areas

  • Information Systems

Cite this

Eltabakh, M. Y., Ouzzani, M., & Aref, W. G. (2007). Bdbms. A database management system for biological data. In CIDR 2007 - 3rd Biennial Conference on Innovative Data Systems Research (pp. 196-206)

Bdbms. A database management system for biological data. / Eltabakh, Mohamed Y.; Ouzzani, Mourad; Aref, Walid G.

CIDR 2007 - 3rd Biennial Conference on Innovative Data Systems Research. 2007. p. 196-206.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Eltabakh, MY, Ouzzani, M & Aref, WG 2007, Bdbms. A database management system for biological data. in CIDR 2007 - 3rd Biennial Conference on Innovative Data Systems Research. pp. 196-206, 3rd Biennial Conference on Innovative Data Systems Research, CIDR 2007, Asilomar, CA, United States, 7/1/07.
Eltabakh MY, Ouzzani M, Aref WG. Bdbms. A database management system for biological data. In CIDR 2007 - 3rd Biennial Conference on Innovative Data Systems Research. 2007. p. 196-206
Eltabakh, Mohamed Y. ; Ouzzani, Mourad ; Aref, Walid G. / Bdbms. A database management system for biological data. CIDR 2007 - 3rd Biennial Conference on Innovative Data Systems Research. 2007. pp. 196-206
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