Gene ontology-based annotation analysis and categorization of metabolic pathways

Ali Cakmak; Mustafa Kirac; Marc R. Reynolds; Zehra M. Ozsoyoglu; Gultekin Ozsoyoglu

doi:10.1109/SSDBM.2007.35

Gene ontology-based annotation analysis and categorization of metabolic pathways

Ali Cakmak^*, Mustafa Kirac, Marc R. Reynolds, Zehra M. Ozsoyoglu, Gultekin Ozsoyoglu

^*Corresponding author for this work

Case Western Reserve University

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

6 Citations (Scopus)

Abstract

Functional characterizations of pathways provide new opportunities in defining, understanding, and comparing existing biological pathways, and in helping discover new ones in different organisms. In this paper, we present and evaluate computational techniques for categorizing pathways, based upon the Gene Ontology (GO) annotations of enzymes within metabolic pathways. Our approach is to use the notion of functionality templates, GO-functional graphs of pathways. Pathway categorization is then achieved through learning models built on different characteristics of functionality templates. We have experimentally evaluated the accuracy of automated pathway categorization with respect to different learning models and their parameters. Using KEGG metabolic pathways, the pathway categorization tool reaches to 90% and higher accuracy.

Original language	English
Title of host publication	19th International Conference on Scientific and Statistical Database Management, SSDBM 2007
DOIs	https://doi.org/10.1109/SSDBM.2007.35
Publication status	Published - 2007
Externally published	Yes
Event	19th International Conference on Scientific and Statistical Database Management, SSDBM 2007 - Banff, AB, Canada Duration: 9 Jul 2007 → 11 Jul 2007

Publication series

Name	Proceedings of the International Conference on Scientific and Statistical Database Management, SSDBM
ISSN (Print)	1099-3371

Conference

Conference	19th International Conference on Scientific and Statistical Database Management, SSDBM 2007
Country/Territory	Canada
City	Banff, AB
Period	9/07/07 → 11/07/07

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10.1109/SSDBM.2007.35

Cite this

Cakmak, A., Kirac, M., Reynolds, M. R., Ozsoyoglu, Z. M., & Ozsoyoglu, G. (2007). Gene ontology-based annotation analysis and categorization of metabolic pathways. In 19th International Conference on Scientific and Statistical Database Management, SSDBM 2007 Article 4274978 (Proceedings of the International Conference on Scientific and Statistical Database Management, SSDBM). https://doi.org/10.1109/SSDBM.2007.35

@inproceedings{2afe91d4f8e944c885738713d52706d4,

title = "Gene ontology-based annotation analysis and categorization of metabolic pathways",

abstract = "Functional characterizations of pathways provide new opportunities in defining, understanding, and comparing existing biological pathways, and in helping discover new ones in different organisms. In this paper, we present and evaluate computational techniques for categorizing pathways, based upon the Gene Ontology (GO) annotations of enzymes within metabolic pathways. Our approach is to use the notion of functionality templates, GO-functional graphs of pathways. Pathway categorization is then achieved through learning models built on different characteristics of functionality templates. We have experimentally evaluated the accuracy of automated pathway categorization with respect to different learning models and their parameters. Using KEGG metabolic pathways, the pathway categorization tool reaches to 90% and higher accuracy.",

author = "Ali Cakmak and Mustafa Kirac and Reynolds, {Marc R.} and Ozsoyoglu, {Zehra M.} and Gultekin Ozsoyoglu",

year = "2007",

doi = "10.1109/SSDBM.2007.35",

language = "English",

isbn = "0769528686",

series = "Proceedings of the International Conference on Scientific and Statistical Database Management, SSDBM",

booktitle = "19th International Conference on Scientific and Statistical Database Management, SSDBM 2007",

note = "19th International Conference on Scientific and Statistical Database Management, SSDBM 2007 ; Conference date: 09-07-2007 Through 11-07-2007",

}

Cakmak, A, Kirac, M, Reynolds, MR, Ozsoyoglu, ZM & Ozsoyoglu, G 2007, Gene ontology-based annotation analysis and categorization of metabolic pathways. in 19th International Conference on Scientific and Statistical Database Management, SSDBM 2007., 4274978, Proceedings of the International Conference on Scientific and Statistical Database Management, SSDBM, 19th International Conference on Scientific and Statistical Database Management, SSDBM 2007, Banff, AB, Canada, 9/07/07. https://doi.org/10.1109/SSDBM.2007.35

Gene ontology-based annotation analysis and categorization of metabolic pathways. / Cakmak, Ali; Kirac, Mustafa; Reynolds, Marc R. et al.
19th International Conference on Scientific and Statistical Database Management, SSDBM 2007. 2007. 4274978 (Proceedings of the International Conference on Scientific and Statistical Database Management, SSDBM).

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

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T1 - Gene ontology-based annotation analysis and categorization of metabolic pathways

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AU - Kirac, Mustafa

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AU - Ozsoyoglu, Zehra M.

AU - Ozsoyoglu, Gultekin

PY - 2007

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AB - Functional characterizations of pathways provide new opportunities in defining, understanding, and comparing existing biological pathways, and in helping discover new ones in different organisms. In this paper, we present and evaluate computational techniques for categorizing pathways, based upon the Gene Ontology (GO) annotations of enzymes within metabolic pathways. Our approach is to use the notion of functionality templates, GO-functional graphs of pathways. Pathway categorization is then achieved through learning models built on different characteristics of functionality templates. We have experimentally evaluated the accuracy of automated pathway categorization with respect to different learning models and their parameters. Using KEGG metabolic pathways, the pathway categorization tool reaches to 90% and higher accuracy.

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SN - 9780769528687

T3 - Proceedings of the International Conference on Scientific and Statistical Database Management, SSDBM

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Cakmak A, Kirac M, Reynolds MR, Ozsoyoglu ZM, Ozsoyoglu G. Gene ontology-based annotation analysis and categorization of metabolic pathways. In 19th International Conference on Scientific and Statistical Database Management, SSDBM 2007. 2007. 4274978. (Proceedings of the International Conference on Scientific and Statistical Database Management, SSDBM). doi: 10.1109/SSDBM.2007.35

Gene ontology-based annotation analysis and categorization of metabolic pathways

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