CySBGN: a Cytoscape Plug-in to Integrate SBGN Maps

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2013 Jan 18

PMID 23324051

Citations 8

Authors

Emanuel Goncalves

Martijn van Iersel

Julio Saez-Rodriguez

Affiliations

Soon will be listed here.

Abstract

Background: A standard graphical notation is essential to facilitate exchange of network representations of biological processes. Towards this end, the Systems Biology Graphical Notation (SBGN) has been proposed, and it is already supported by a number of tools. However, support for SBGN in Cytoscape, one of the most widely used platforms in biology to visualise and analyse networks, is limited, and in particular it is not possible to import SBGN diagrams.

Results: We have developed CySBGN, a Cytoscape plug-in that extends the use of Cytoscape visualisation and analysis features to SBGN maps. CySBGN adds support for Cytoscape users to visualize any of the three complementary SBGN languages: Process Description, Entity Relationship, and Activity Flow. The interoperability with other tools (CySBML plug-in and Systems Biology Format Converter) was also established allowing an automated generation of SBGN diagrams based on previously imported SBML models. The plug-in was tested using a suite of 53 different test cases that covers almost all possible entities, shapes, and connections. A rendering comparison with other tools that support SBGN was performed. To illustrate the interoperability with other Cytoscape functionalities, we present two analysis examples, shortest path calculation, and motif identification in a metabolic network.

Conclusions: CySBGN imports, modifies and analyzes SBGN diagrams in Cytoscape, and thus allows the application of the large palette of tools and plug-ins in this platform to networks and pathways in SBGN format.

Citing Articles

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.

Golebiewski M, Bader G, Gleeson P, Gorochowski T, Keating S, Konig M J Integr Bioinform. 2024; 21(1).

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Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.

Scholzel C, Blesius V, Ernst G, Dominik A NPJ Syst Biol Appl. 2021; 7(1):27.

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Closing the gap between formats for storing layout information in systems biology.

Hoksza D, Gawron P, Ostaszewski M, Hasenauer J, Schneider R Brief Bioinform. 2019; 21(4):1249-1260.

PMID: 31273380 PMC: 7373180. DOI: 10.1093/bib/bbz067.

SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.

Sari M, Bahceci I, Dogrusoz U, Sumer S, Aksoy B, Babur O PLoS One. 2015; 10(6):e0128985.

PMID: 26030594 PMC: 4451519. DOI: 10.1371/journal.pone.0128985.

Improving collaboration by standardization efforts in systems biology.

Drager A, Palsson B Front Bioeng Biotechnol. 2014; 2:61.

PMID: 25538939 PMC: 4259112. DOI: 10.3389/fbioe.2014.00061.

References

Smoot M, Ono K, Ruscheinski J, Wang P, Ideker T . Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2010; 27(3):431-2. PMC: 3031041. DOI: 10.1093/bioinformatics/btq675. View

Rohn H, Junker A, Hartmann A, Grafahrend-Belau E, Treutler H, Klapperstuck M . VANTED v2: a framework for systems biology applications. BMC Syst Biol. 2012; 6:139. PMC: 3610154. DOI: 10.1186/1752-0509-6-139. View

Demir E, Cary M, Paley S, Fukuda K, Lemer C, Vastrik I . The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010; 28(9):935-42. PMC: 3001121. DOI: 10.1038/nbt.1666. View

Zinovyev A, Viara E, Calzone L, Barillot E . BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics. 2007; 24(6):876-7. DOI: 10.1093/bioinformatics/btm553. View

Junker B, Klukas C, Schreiber F . VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics. 2006; 7:109. PMC: 1413562. DOI: 10.1186/1471-2105-7-109. View

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

Konig M, Drager A, Holzhutter H . CySBML: a Cytoscape plugin for SBML. Bioinformatics. 2012; 28(18):2402-3. DOI: 10.1093/bioinformatics/bts432. View

Cook D, Farley J, Tapscott S . A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems. Genome Biol. 2001; 2(4):RESEARCH0012. PMC: 31481. DOI: 10.1186/gb-2001-2-4-research0012. View

Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V . BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol. 2010; 4:92. PMC: 2909940. DOI: 10.1186/1752-0509-4-92. View

10.

Pirson I, Fortemaison N, Jacobs C, Dremier S, Dumont J, Maenhaut C . The visual display of regulatory information and networks. Trends Cell Biol. 2000; 10(10):404-8. DOI: 10.1016/s0962-8924(00)01817-1. View

11.

Kitano H, Funahashi A, Matsuoka Y, Oda K . Using process diagrams for the graphical representation of biological networks. Nat Biotechnol. 2005; 23(8):961-6. DOI: 10.1038/nbt1111. View

12.

van Iersel M, Kelder T, Pico A, Hanspers K, Coort S, Conklin B . Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics. 2008; 9:399. PMC: 2569944. DOI: 10.1186/1471-2105-9-399. View

13.

van Iersel M, Villeger A, Czauderna T, Boyd S, Bergmann F, Luna A . Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics. 2012; 28(15):2016-21. PMC: 3400951. DOI: 10.1093/bioinformatics/bts270. View

14.

Davis D, Chawla N . Exploring and exploiting disease interactions from multi-relational gene and phenotype networks. PLoS One. 2011; 6(7):e22670. PMC: 3146471. DOI: 10.1371/journal.pone.0022670. View

15.

Finney A, Hucka M . Systems biology markup language: Level 2 and beyond. Biochem Soc Trans. 2003; 31(Pt 6):1472-3. DOI: 10.1042/bst0311472. View

16.

Le Novere N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A . The Systems Biology Graphical Notation. Nat Biotechnol. 2009; 27(8):735-41. DOI: 10.1038/nbt.1558. View

17.

Czauderna T, Klukas C, Schreiber F . Editing, validating and translating of SBGN maps. Bioinformatics. 2010; 26(18):2340-1. PMC: 2935428. DOI: 10.1093/bioinformatics/btq407. View

18.

Saito R, Smoot M, Ono K, Ruscheinski J, Wang P, Lotia S . A travel guide to Cytoscape plugins. Nat Methods. 2012; 9(11):1069-76. PMC: 3649846. DOI: 10.1038/nmeth.2212. View

19.

Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader G . NetMatch: a Cytoscape plugin for searching biological networks. Bioinformatics. 2007; 23(7):910-2. DOI: 10.1093/bioinformatics/btm032. View