A statistical analysis of relation degree of compound pair on online biological pathway databases

Myungha Jang; Arang Rhie; Jiyoung Whang; Sanduk Yang; Hyun S. Park

doi:10.1145/1516241.1516355

A statistical analysis of relation degree of compound pair on online biological pathway databases

Myungha Jang, Arang Rhie, Jiyoung Whang, Sanduk Yang, Hyun S. Park

Department of Computer Science & Engineering

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

Abstract

The basic graph layout technique, one of the visualization te chniques, deals with the problem of positioning the vertices i n a way to maximize understandability and usability in a grap h. This technique is becoming a vital part for further develop ment in the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genome scale flow of metabolism requires understanding of the charac teristics of metabolites and reactions, which suggest valuable information to bioinformatics software developers for better visualization of automatic graph layout. In this paper, we define the term relation degree of a compound pair to provide a reasonable way to visualize metabolic pathway atlas, based on the parsing result of the publicly available XML files. It is a preliminary step for future research in the area of automatic 1 ayout techniques in large-scale biological pathway domain.

Original language	English
Title of host publication	Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09
Pages	644-649
Number of pages	6
DOIs	https://doi.org/10.1145/1516241.1516355
State	Published - 2009
Event	3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09 - Suwon, Korea, Republic of Duration: 15 Jan 2009 → 16 Jan 2009

Publication series

Name	Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09

Conference

Conference	3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09
Country/Territory	Korea, Republic of
City	Suwon
Period	15/01/09 → 16/01/09

Bibliographical note

Funding Information:
The work reported herein forms part of an investigation into 'Design for safety of structures subject to dimce-type loads' financed bya grant h m EPSRC. The authors are also gratefbl for Dr B. R. Ellis, BRE, and Dr A. J. Bell, UMIST, for their constructive comments ont he paper.

Keywords

Drawing algorithm
Edge crossing
Metabolic pathway
Parsing
Relation degree
XML

Access to Document

10.1145/1516241.1516355

Cite this

Jang, M., Rhie, A., Whang, J., Yang, S., & Park, H. S. (2009). A statistical analysis of relation degree of compound pair on online biological pathway databases. In Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09 (pp. 644-649). (Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09). https://doi.org/10.1145/1516241.1516355

Jang, Myungha ; Rhie, Arang ; Whang, Jiyoung et al. / A statistical analysis of relation degree of compound pair on online biological pathway databases. Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09. 2009. pp. 644-649 (Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09).

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abstract = "The basic graph layout technique, one of the visualization te chniques, deals with the problem of positioning the vertices i n a way to maximize understandability and usability in a grap h. This technique is becoming a vital part for further develop ment in the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genome scale flow of metabolism requires understanding of the charac teristics of metabolites and reactions, which suggest valuable information to bioinformatics software developers for better visualization of automatic graph layout. In this paper, we define the term relation degree of a compound pair to provide a reasonable way to visualize metabolic pathway atlas, based on the parsing result of the publicly available XML files. It is a preliminary step for future research in the area of automatic 1 ayout techniques in large-scale biological pathway domain.",

keywords = "Drawing algorithm, Edge crossing, Metabolic pathway, Parsing, Relation degree, XML",

author = "Myungha Jang and Arang Rhie and Jiyoung Whang and Sanduk Yang and Park, {Hyun S.}",

note = "Funding Information: The work reported herein forms part of an investigation into 'Design for safety of structures subject to dimce-type loads' financed bya grant h m EPSRC. The authors are also gratefbl for Dr B. R. Ellis, BRE, and Dr A. J. Bell, UMIST, for their constructive comments ont he paper.; 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09 ; Conference date: 15-01-2009 Through 16-01-2009",

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language = "English",

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Jang, M, Rhie, A, Whang, J, Yang, S & Park, HS 2009, A statistical analysis of relation degree of compound pair on online biological pathway databases. in Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09. Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09, pp. 644-649, 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09, Suwon, Korea, Republic of, 15/01/09. https://doi.org/10.1145/1516241.1516355

A statistical analysis of relation degree of compound pair on online biological pathway databases. / Jang, Myungha; Rhie, Arang; Whang, Jiyoung et al.
Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09. 2009. p. 644-649 (Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09).

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

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Jang M, Rhie A, Whang J, Yang S, Park HS. A statistical analysis of relation degree of compound pair on online biological pathway databases. In Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09. 2009. p. 644-649. (Proceedings of the 3rd International Conference on Ubiquitous Information Management and Communication, ICUIMC'09). doi: 10.1145/1516241.1516355

A statistical analysis of relation degree of compound pair on online biological pathway databases

Abstract

Publication series

Conference

Bibliographical note

Keywords

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Cite this