BioPAX support in CellDesigner

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

Research output: Contribution to journalArticle

11 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 languageEnglish
Article numberbtr586
Pages (from-to)3437-3438
Number of pages2
JournalBioinformatics
Volume27
Issue number24
DOIs
Publication statusPublished - 2011 Dec

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Pathway
Software
Databases
Biological Phenomena
Information Storage and Retrieval
Genomics
Software packages
Language
Diagram
Software Package
Data analysis

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

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

BioPAX support in CellDesigner. / Mi, Huaiyu; Muruganujan, Anushya; Demir, Emek; Matsuoka, Yukiko; Funahashi, Akira; Kitano, Hiroaki; Thomas, Paul D.

In: Bioinformatics, Vol. 27, No. 24, btr586, 12.2011, p. 3437-3438.

Research output: Contribution to journalArticle

Mi, H, Muruganujan, A, Demir, E, Matsuoka, Y, Funahashi, A, Kitano, H & Thomas, PD 2011, 'BioPAX support in CellDesigner', Bioinformatics, vol. 27, no. 24, btr586, pp. 3437-3438. https://doi.org/10.1093/bioinformatics/btr586
Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H et al. BioPAX support in CellDesigner. Bioinformatics. 2011 Dec;27(24):3437-3438. btr586. https://doi.org/10.1093/bioinformatics/btr586
Mi, Huaiyu ; Muruganujan, Anushya ; Demir, Emek ; Matsuoka, Yukiko ; Funahashi, Akira ; Kitano, Hiroaki ; Thomas, Paul D. / BioPAX support in CellDesigner. In: Bioinformatics. 2011 ; Vol. 27, No. 24. pp. 3437-3438.
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