Software support for SBGN maps: SBGN-ML and LibSBGN

Iersel, Martijn P. van; Villéger, A. C.; Czauderna, T.; Boyd, S. E.; Bergmann, F. T.; Luna, A.; Demir, E.; Sorokin, A.; Dogrusoz, U.; Matsuoka, Y.; Funahashi, A.; Aladjem, M. I.; Mi, H.; Moodie, S. L.; Kitano, H.; Le novère, N.; Schreiber, F.

doi:10.1093/bioinformatics/bts270

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Author

Iersel, Martijn P. van

Villéger, A. C.

Czauderna, T.

Boyd, S. E.

Bergmann, F. T.

Luna, A.

Demir, E.

Sorokin, A.

Dogrusoz, U.

Matsuoka, Y.

Funahashi, A.

Aladjem, M. I.

Mi, H.

Moodie, S. L.

Kitano, H.

Le novère, N.

Schreiber, F.

Date

2012

Source Title

Bioinformatics

Print ISSN

1367-4803

Publisher

Oxford University Press

Volume

Issue

Pages

2016 - 2021

Language

English

Type

Article

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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. © The Author(s) 2012. Published by Oxford University Press.