BioPAX support in CellDesigner

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

Research output: Contribution to journalArticle

12 Scopus citations

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 languageEnglish (US)
Article numberbtr586
Pages (from-to)3437-3438
Number of pages2
JournalBioinformatics
Volume27
Issue number24
DOIs
StatePublished - Dec 1 2011

ASJC Scopus subject areas

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

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    Mi, H., Muruganujan, A., Demir, E., Matsuoka, Y., Funahashi, A., Kitano, H., & Thomas, P. D. (2011). BioPAX support in CellDesigner. Bioinformatics, 27(24), 3437-3438. [btr586]. https://doi.org/10.1093/bioinformatics/btr586