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

doi:10.1093/bioinformatics/bts270

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 journal › Article › peer-review

59 Scopus citations

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 language	English (US)
Article number	bts270
Pages (from-to)	2016-2021
Number of pages	6
Journal	Bioinformatics
Volume	28
Issue number	15
DOIs	https://doi.org/10.1093/bioinformatics/bts270
State	Published - Aug 2012
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

Access to Document

10.1093/bioinformatics/bts270

Cite this

Van Iersel, M. P., 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. (2012). Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics, 28(15), 2016-2021. Article bts270. https://doi.org/10.1093/bioinformatics/bts270

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

@article{6f422bd6483b495f9c325503927f6767,

title = "Software support for SBGN maps: SBGN-ML and LibSBGN",

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.",

author = "{Van Iersel}, {Martijn P.} and Vill{\'e}ger, {Alice C.} and Tobias Czauderna and Boyd, {Sarah E.} and Bergmann, {Frank T.} and Augustin Luna and Emek Demir and Anatoly Sorokin and Ugur Dogrusoz and Yukiko Matsuoka and Akira Funahashi and Aladjem, {Mirit I.} and Huaiyu Mi and Moodie, {Stuart L.} and Hiroaki Kitano and {Le nov{\`e}re}, Nicolas and Falk Schreiber",

note = "Funding Information: Funding: This work was in part supported by the Biotechnology and Biological Sciences Research Council (BBSRC); the Netherlands Consortium for Systems Biology (NCSB), which is part of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research; BioPreDyn which is a grant within the Seventh Framework Programme of the EU, the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research; and the German Ministry of Education and Research (BMBF).",

year = "2012",

month = aug,

doi = "10.1093/bioinformatics/bts270",

language = "English (US)",

volume = "28",

pages = "2016--2021",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "15",

}

TY - JOUR

T1 - Software support for SBGN maps

T2 - SBGN-ML and LibSBGN

AU - Van Iersel, Martijn P.

AU - Villéger, Alice C.

AU - Czauderna, Tobias

AU - Boyd, Sarah E.

AU - Bergmann, Frank T.

AU - Luna, Augustin

AU - Demir, Emek

AU - Sorokin, Anatoly

AU - Dogrusoz, Ugur

AU - Matsuoka, Yukiko

AU - Funahashi, Akira

AU - Aladjem, Mirit I.

AU - Mi, Huaiyu

AU - Moodie, Stuart L.

AU - Kitano, Hiroaki

AU - Le novère, Nicolas

AU - Schreiber, Falk

N1 - Funding Information: Funding: This work was in part supported by the Biotechnology and Biological Sciences Research Council (BBSRC); the Netherlands Consortium for Systems Biology (NCSB), which is part of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research; BioPreDyn which is a grant within the Seventh Framework Programme of the EU, the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research; and the German Ministry of Education and Research (BMBF).

PY - 2012/8

Y1 - 2012/8

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84865123095&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84865123095&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/bts270

DO - 10.1093/bioinformatics/bts270

M3 - Article

C2 - 22581176

AN - SCOPUS:84865123095

SN - 1367-4803

VL - 28

SP - 2016

EP - 2021

JO - Bioinformatics

JF - Bioinformatics

IS - 15

M1 - bts270

ER -

Software support for SBGN maps: SBGN-ML and LibSBGN

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this