Editing, validating and translating of SBGN maps

被引：66

作者：

Czauderna, Tobias ^{[1
]}

Klukas, Christian ^{[1
]}

Schreiber, Falk ^{[1
,2
]}

机构：

[1] Univ Halle Wittenberg, Leibniz Inst Plant Genet & Crop Plant Res IPK Gat, Halle, Germany

[2] Univ Halle Wittenberg, Inst Comp Sci, Halle, Germany

来源：

BIOINFORMATICS | 2010年 / 26卷 / 18期

关键词：

D O I：

10.1093/bioinformatics/btq407

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

Motivation: The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate communication of biological knowledge between different research communities in the life sciences. However, to increase the use of SBGN, tools for editing, validating and translating SBGN maps are desirable. Results: We present SBGN-ED, a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from the KEGG and MetaCrop databases into SBGN and the export of SBGN maps into several file and image formats. Availability: SBGN-ED is freely available from http://vanted.ipkgatersleben.de/addons/sbgn-ed. The web site contains also tutorials and example files. Contact: schreibe@ipk-gatersleben.

引用

页码：2340 / 2341

页数：2

共 4 条

[1]

[Anonymous], 2006, BMC BIOINFORMATICS, DOI DOI 10.1186/1471-2105-7-488

[2]

MetaCrop:: a detailed database of crop plant metabolism [J].

Grafahrend-Belau, Eva ;

Weise, Stephan ;

Koschuetzki, Dirk ;

Scholz, Uwe ;

Junker, Bjoern H. ;

Schreiber, Falk .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D954-D958

[3]

KEGG for representation and analysis of molecular networks involving diseases and drugs [J].

Kanehisa, Minoru ;

Goto, Susumu ;

Furumichi, Miho ;

Tanabe, Mao ;

Hirakawa, Mika .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D355-D360

[4]

The Systems Biology Graphical Notation [J].

Le Novere, Nicolas ;

Hucka, Michael ;

Mi, Huaiyu ;

Moodie, Stuart ;

Schreiber, Falk ;

Sorokin, Anatoly ;

Demir, Emek ;

Wegner, Katja ;

Aladjem, Mirit I. ;

Wimalaratne, Sarala M. ;

Bergman, Frank T. ;

Gauges, Ralph ;

Ghazal, Peter ;

Kawaji, Hideya ;

Li, Lu ;

Matsuoka, Yukiko ;

Villeger, Alice ;

Boyd, Sarah E. ;

Calzone, Laurence ;

Courtot, Melanie ;

Dogrusoz, Ugur ;

Freeman, Tom C. ;

Funahashi, Akira ;

Ghosh, Samik ;

Jouraku, Akiya ;

Kim, Sohyoung ;

Kolpakov, Fedor ;

Luna, Augustin ;

Sahle, Sven ;

Schmidt, Esther ;

Watterson, Steven ;

Wu, Guanming ;

Goryanin, Igor ;

Kell, Douglas B. ;

Sander, Chris ;

Sauro, Herbert ;

Snoep, Jacky L. ;

Kohn, Kurt ;

Kitano, Hiroaki .

NATURE BIOTECHNOLOGY, 2009, 27 (08) :735-741

← 1 →