Software support for SBGN maps: SBGN-ML and LibSBGN

Martijn P. Van Iersel, Alice C. Villéger, Tobias Czauderna, Sarah E. Boyd, Frank T. Bergmann, Augustin Luna, Emek Demir, Anatoly Sorokin, Ugur Dogrusoz, Yukiko Matsuoka, Akira Funahashi, Mirit I. Aladjem, Huaiyu Mi, Stuart L. Moodie, Hiroaki Kitano, Nicolas Le novère, Falk Schreiber

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner.

Original languageEnglish (US)
Article numberbts270
Pages (from-to)2016-2021
Number of pages6
JournalBioinformatics
Volume28
Issue number15
DOIs
StatePublished - Aug 2012
Externally publishedYes

Fingerprint

Systems Biology
Notation
Software
Libraries
Bioinformatics
Computational Biology
C++
Application programs
Compliance
Java
Reading
Simplify
Research Personnel
Graphics
Specification
Specifications

ASJC Scopus subject areas

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

Cite this

Van Iersel, M. P., Villéger, A. C., Czauderna, T., Boyd, S. E., Bergmann, F. T., Luna, A., ... Schreiber, F. (2012). Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics, 28(15), 2016-2021. [bts270]. https://doi.org/10.1093/bioinformatics/bts270

Software support for SBGN maps : SBGN-ML and LibSBGN. / Van Iersel, Martijn P.; Villéger, Alice C.; Czauderna, Tobias; Boyd, Sarah E.; Bergmann, Frank T.; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I.; Mi, Huaiyu; Moodie, Stuart L.; Kitano, Hiroaki; Le novère, Nicolas; Schreiber, Falk.

In: Bioinformatics, Vol. 28, No. 15, bts270, 08.2012, p. 2016-2021.

Research output: Contribution to journalArticle

Van Iersel, MP, Villéger, AC, Czauderna, T, Boyd, SE, Bergmann, FT, Luna, A, Demir, E, Sorokin, A, Dogrusoz, U, Matsuoka, Y, Funahashi, A, Aladjem, MI, Mi, H, Moodie, SL, Kitano, H, Le novère, N & Schreiber, F 2012, 'Software support for SBGN maps: SBGN-ML and LibSBGN', Bioinformatics, vol. 28, no. 15, bts270, pp. 2016-2021. https://doi.org/10.1093/bioinformatics/bts270
Van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A et al. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics. 2012 Aug;28(15):2016-2021. bts270. https://doi.org/10.1093/bioinformatics/bts270
Van Iersel, Martijn P. ; Villéger, Alice C. ; Czauderna, Tobias ; Boyd, Sarah E. ; Bergmann, Frank T. ; Luna, Augustin ; Demir, Emek ; Sorokin, Anatoly ; Dogrusoz, Ugur ; Matsuoka, Yukiko ; Funahashi, Akira ; Aladjem, Mirit I. ; Mi, Huaiyu ; Moodie, Stuart L. ; Kitano, Hiroaki ; Le novère, Nicolas ; Schreiber, Falk. / Software support for SBGN maps : SBGN-ML and LibSBGN. In: Bioinformatics. 2012 ; Vol. 28, No. 15. pp. 2016-2021.
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