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Kitakaze Hironori


XML pathway format comparison between Genomic Object Net and Systems Biology Markup Language Level 2

大島商船高等専門学校紀要 Volume 38 Page 9-20
published_at 2005-12
OS10038000002.pdf
[fulltext] 6.9 MB
Title
GONとSBMLにおけるXMLパスウェイ形式の対応
XML pathway format comparison between Genomic Object Net and Systems Biology Markup Language Level 2
Creators Kitakaze Hironori
Creators Matsuno Hiroshi
Creators Miyano Satoru
Source Identifiers
Creator Keywords
Genomic Object Net SBML Level2 Conversion XML pathway
In this paper, two formats of XML description in Genomic Object Net (GON) and System Biology Markup Language Level 2 (SBML Level 2) are compared. First, we discuss about the difference in representations of biological pathways with these two methods. Second, we compare these two formats step-by-step from small models to large models in the following order: (1) initial stage, (2) arrange one continuous place, (3) control variables, (4) arrange one continuous transition, (5) add arc from place to transition, and (6) several connections between elements. Based on these comparisons, we considered about problems which will be arise in performing conversion between these two formats, and discuss the method to improve these problems.
Languages jpn
Resource Type departmental bulletin paper
Publishers 大島商船高等専門学校
Date Issued 2005-12
File Version Version of Record
Access Rights open access
Relations
[ISSN]0387-9232
[NCID]AN00031668