Managing biological data using bdbms

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

doi:10.1109/ICDE.2008.4497631

Managing biological data using bdbms

Mohamed Y. Eltabakh, 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 proceeding › Conference contribution › peer-review

18 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 language	English
Title of host publication	Proceedings of the 2008 IEEE 24th International Conference on Data Engineering, ICDE'08
Pages	1600-1603
Number of pages	4
DOIs	https://doi.org/10.1109/ICDE.2008.4497631
Publication status	Published - 2008
Externally published	Yes
Event	2008 IEEE 24th International Conference on Data Engineering, ICDE'08 - Cancun, Mexico Duration: 7 Apr 2008 → 12 Apr 2008

Publication series

Name	Proceedings - International Conference on Data Engineering
ISSN (Print)	1084-4627

Conference

Conference	2008 IEEE 24th International Conference on Data Engineering, ICDE'08
Country/Territory	Mexico
City	Cancun
Period	7/04/08 → 12/04/08

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10.1109/ICDE.2008.4497631

Cite this

Eltabakh, M. Y., Ouzzani, M., Aref, W. G., Elmagarmid, A. K., Laura-Silva, Y., Arshad, M. U., Salt, D., & Baxter, I. (2008). Managing biological data using bdbms. In Proceedings of the 2008 IEEE 24th International Conference on Data Engineering, ICDE'08 (pp. 1600-1603). Article 4497631 (Proceedings - International Conference on Data Engineering). https://doi.org/10.1109/ICDE.2008.4497631

@inproceedings{861e296825f143efbf5632e4b05a95cb,

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 = "Eltabakh, {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",

doi = "10.1109/ICDE.2008.4497631",

language = "English",

isbn = "9781424418374",

series = "Proceedings - International Conference on Data Engineering",

pages = "1600--1603",

booktitle = "Proceedings of the 2008 IEEE 24th International Conference on Data Engineering, ICDE'08",

note = "2008 IEEE 24th International Conference on Data Engineering, ICDE'08 ; Conference date: 07-04-2008 Through 12-04-2008",

}

Eltabakh, MY , Ouzzani, M, Aref, WG, Elmagarmid, AK, Laura-Silva, Y, Arshad, MU, Salt, D & Baxter, I 2008, Managing biological data using bdbms. in Proceedings of the 2008 IEEE 24th International Conference on Data Engineering, ICDE'08., 4497631, Proceedings - International Conference on Data Engineering, pp. 1600-1603, 2008 IEEE 24th International Conference on Data Engineering, ICDE'08, Cancun, Mexico, 7/04/08. https://doi.org/10.1109/ICDE.2008.4497631

Managing biological data using bdbms. / Eltabakh, Mohamed Y.; Ouzzani, Mourad; Aref, Walid G. et al.
Proceedings of the 2008 IEEE 24th International Conference on Data Engineering, ICDE'08. 2008. p. 1600-1603 4497631 (Proceedings - International Conference on Data Engineering).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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T1 - Managing biological data using bdbms

AU - Eltabakh, 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

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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.

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SN - 9781424418374

T3 - Proceedings - International Conference on Data Engineering

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BT - Proceedings of the 2008 IEEE 24th International Conference on Data Engineering, ICDE'08

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ER -

Managing biological data using bdbms

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