SBGN_Tools
To get an overview of available tools and their features, we consulted the SBGN website.
Figure 1: Screenshot SGBN Editors listed on SGBN website 21/06/2021
Since we decided to work with the SBGN Process Description (PD) language, all editors listed at the time of accessing the website, where suitable for PD. Two of the listed editors didn't support SGBN-ML directly, thus, weren't suitable for our project. Due to the short period of time we couldn't test all tools identified as possibly useful.
Eventually, we used the web-based Newt Editor (v3.0.3) to create the SBGN network de novo [1, 2]. We chose this tool because of five reasons. First, multiple tutorial videos are online on YouTube making it easy to get a quick idea of how the tool works. Besides, there is a rich tutorial section on the webpage. Second, it is easily available on the web and does not require any installation. Third, it provides export of a variety of file formats, i.e. different SBGN-ML versions, different graphic formats, SBML, and formats to import into other tools. Fourth, it offers an integrated validation tool with suggestions for fixing. Fifth, it was maintained and updated at least until last year.
To validate the generated map, we used the Newt Editor itself, as well as VANTED (v2.8) with the corresponding SGBN-ED plugin (v1.6) [3, 4, 5], Krayon for SBGN (v1.0.1) [6] and SBGNViz (v2.0) [2].
- recently released web-based editor
- offers integrated validation tool including guided fixing for SBGN PDs
- allows loading of SBML, Simple Interaction Format (SIF) & CellDesigner files
- export of SBGN-ML 0.2 and 0.3 as well as SBML, Simple Interaction Format (SIF) & CellDesigner files
- latest release 01/04/2020
- Java-based desktop application
- add-on for VANTED
- import of SBGN-ML 0.2, SBML and various other formats
- export of SBGN-ML 0.2, SIF, various graphic file formats, and other different graph describing formats
- latest release 15/09/2016
- either available as desktop application (only windows) or as plugin for IntelliJ IDEA
- import of SBGN-ML
- export of SBGN-ML and various graphical formats
- latest release 13/09/2018
- web-based visualizer
- import of SGBN-ML or SIF
- export as PNG or JPG
- latest release 08/04/2021
All tools can be found in the tool box.
[1] Balci, H., Siper, M.C., Saleh, N. et al. Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. Bioinformatics 37, 1475–1477 (2021). https://doi.org/10.1093/bioinformatics/btaa850
[2] Sari, M., Bahceci, I., Dogrusoz, U. et al. SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps. PLoS ONE 10, e0128985 (2015). https://doi.org/10.1371/journal.pone.0128985
[3] Rohn, H., Junker, A., Hartmann, A. et al. VANTED v2: a framework for systems biology applications. BMC Syst Biol 6, 139 (2012). https://doi.org/10.1186/1752-0509-6-139
[4] Junker, B.H., Klukas, C. & Schreiber, F. VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7, 109 (2006). https://doi.org/10.1186/1471-2105-7-109
[5] Czauderna, T., Klukas, C. & Schreiber, F. Editing, validating and translating of SBGN maps. Bioinformatics 26, 2340–2341 (2010). https://doi.org/10.1093/bioinformatics/btq407
[6] Wiese, R. Krayon for SBGN. https://github.com/wiese42/krayon4sbgn