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Software support for SBGN maps: SBGN-ML and LibSBGN.

Martijn P van Iersel1, Alice C Villéger, Tobias Czauderna

  • 1EMBL European Bioinformatics Institute, Hinxton, UK. sbgn-libsbgn@lists.sourceforge.net

Bioinformatics (Oxford, England)
|May 15, 2012
PubMed
Summary
This summary is machine-generated.

LibSBGN is a software library that simplifies working with Systems Biology Graphical Notation (SBGN) maps. It enhances the exchange and visualization of biological knowledge through the SBGN-ML format and tool integration.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • LibSBGN is a software library for managing Systems Biology Graphical Notation (SBGN) maps.
  • It supports the SBGN-ML file format for map storage and exchange.
  • The library aims to increase SBGN adoption in bioinformatics tools.

Purpose of the Study:

  • To provide a software library for reading, writing, and manipulating SBGN maps.
  • To facilitate the exchange of biological knowledge represented in SBGN maps between different software applications.
  • To support the validation of SBGN maps for compliance with specifications.

Main Methods:

  • The library is available in C++ and Java.
  • It supports the SBGN-ML file format.
  • Map validation is included to ensure compliance with SBGN specifications.

Main Results:

  • LibSBGN enables easier integration of SBGN support into developer tools.
  • It promotes the exchange of biological maps via the SBGN-ML format.
  • Map validation simplifies adherence to SBGN standards.

Conclusions:

  • LibSBGN facilitates the use and exchange of SBGN maps.
  • The library promotes precise and unambiguous visualization of biological knowledge.
  • Increased adoption of SBGN in bioinformatics tools is expected.