BioPAX support in CellDesigner

Huaiyu Mi; Anushya Muruganujan; Emek Demir; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Paul D. Thomas

doi:10.1093/bioinformatics/btr586

BioPAX support in CellDesigner

Huaiyu Mi, Anushya Muruganujan, Emek Demir, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano, Paul D. Thomas

Department of Biosciences and Informatics

Research output: Contribution to journal › Article › peer-review

15 Citations (Scopus)

Abstract

Motivation: BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format.

Original language	English
Article number	btr586
Pages (from-to)	3437-3438
Number of pages	2
Journal	Bioinformatics
Volume	27
Issue number	24
DOIs	https://doi.org/10.1093/bioinformatics/btr586
Publication status	Published - 2011 Dec

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btr586

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AU - Mi, Huaiyu

AU - Muruganujan, Anushya

AU - Demir, Emek

AU - Matsuoka, Yukiko

AU - Funahashi, Akira

AU - Kitano, Hiroaki

AU - Thomas, Paul D.

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BioPAX support in CellDesigner

Abstract

ASJC Scopus subject areas

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