Managing biological data using bdbms

Mohamed Y. Eltabkh, Mourad Ouzzani, Walid G. Aref, Ahmed K. Elmagarmid, Yasin Laura-Silva, Muhammad U. Arshad, David Salt, Ivan Baxter

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

14 Citations (Scopus)

Abstract

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.

Original languageEnglish
Title of host publication2008 IEEE 24th International Conference on Data Engineering, Vols 1-3
Place of PublicationNew York
PublisherIEEE Press
Pages1600-1603
Number of pages4
ISBN (Print)978-1-4244-1836-7, 1424418364
Publication statusPublished - 2008
Event24th IEEE International Conference on Data Engineering - Cancun
Duration: 7 Apr 200812 Apr 2008

Conference

Conference24th IEEE International Conference on Data Engineering
CityCancun
Period7/04/0812/04/08

Cite this

Eltabkh, M. Y., Ouzzani, M., Aref, W. G., Elmagarmid, A. K., Laura-Silva, Y., Arshad, M. U., ... Baxter, I. (2008). Managing biological data using bdbms. In 2008 IEEE 24th International Conference on Data Engineering, Vols 1-3 (pp. 1600-1603). New York: IEEE Press.

Managing biological data using bdbms. / Eltabkh, Mohamed Y.; Ouzzani, Mourad; Aref, Walid G.; Elmagarmid, Ahmed K.; Laura-Silva, Yasin; Arshad, Muhammad U.; Salt, David; Baxter, Ivan.

2008 IEEE 24th International Conference on Data Engineering, Vols 1-3. New York : IEEE Press, 2008. p. 1600-1603.

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

Eltabkh, MY, Ouzzani, M, Aref, WG, Elmagarmid, AK, Laura-Silva, Y, Arshad, MU, Salt, D & Baxter, I 2008, Managing biological data using bdbms. in 2008 IEEE 24th International Conference on Data Engineering, Vols 1-3. IEEE Press, New York, pp. 1600-1603, 24th IEEE International Conference on Data Engineering, Cancun, 7/04/08.
Eltabkh MY, Ouzzani M, Aref WG, Elmagarmid AK, Laura-Silva Y, Arshad MU et al. Managing biological data using bdbms. In 2008 IEEE 24th International Conference on Data Engineering, Vols 1-3. New York: IEEE Press. 2008. p. 1600-1603
Eltabkh, Mohamed Y. ; Ouzzani, Mourad ; Aref, Walid G. ; Elmagarmid, Ahmed K. ; Laura-Silva, Yasin ; Arshad, Muhammad U. ; Salt, David ; Baxter, Ivan. / Managing biological data using bdbms. 2008 IEEE 24th International Conference on Data Engineering, Vols 1-3. New York : IEEE Press, 2008. pp. 1600-1603
@inproceedings{0b6535aec65b470fa73304cb750318d7,
title = "Managing biological data using bdbms",
abstract = "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.",
author = "Eltabkh, {Mohamed Y.} and Mourad Ouzzani and Aref, {Walid G.} and Elmagarmid, {Ahmed K.} and Yasin Laura-Silva and Arshad, {Muhammad U.} and David Salt and Ivan Baxter",
year = "2008",
language = "English",
isbn = "978-1-4244-1836-7",
pages = "1600--1603",
booktitle = "2008 IEEE 24th International Conference on Data Engineering, Vols 1-3",
publisher = "IEEE Press",

}

TY - GEN

T1 - Managing biological data using bdbms

AU - Eltabkh, Mohamed Y.

AU - Ouzzani, Mourad

AU - Aref, Walid G.

AU - Elmagarmid, Ahmed K.

AU - Laura-Silva, Yasin

AU - Arshad, Muhammad U.

AU - Salt, David

AU - Baxter, Ivan

PY - 2008

Y1 - 2008

N2 - 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.

AB - 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.

M3 - Conference contribution

SN - 978-1-4244-1836-7

SN - 1424418364

SP - 1600

EP - 1603

BT - 2008 IEEE 24th International Conference on Data Engineering, Vols 1-3

PB - IEEE Press

CY - New York

ER -