Software support for SBGN maps: SBGN-ML and LibSBGN

• DOI: 10.1093/bioinformatics/bts270
• Publication Date: 2012-05-12T01:02:48Z
• Authors: Martijn P. van Ie...; 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
• Keywords: Library; 0301 basic medicine; Layout Extension; Computer program; computer language; Computational biology; 03 medical and health sciences; computer program; Pathways; Biology; Visualization; biology; Systems Biology; article; Methodology; Computational Biology; methodology; systems biology; Exchange; Programming languages; Original Papers; Sbml; 004; Representation; Programming Languages; Networks; Computer language; Systems biology; Software; Diagrams

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. Availability and implementation: Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. Contact: [e-mail]