Integration into COMBINE archive

Provided files for COMBINE Archive

The idea of this project is to generate reusable and shareable standardised information and provide it to the community. Thus, we decided to provide as many useful file formats as possible.

First of all, we provided a SBGN-ML file. Since some tools in the community may not be maintained very well and the latest version of SBGN-ML was published quite recently, we decided to publish the SBGN-ML in version 0.2 [1]. Second, we exported graphic formats, i.e. Inkscape Scalable Vector Graphics (SVG) and Portable Network Graphics (PNG). Third, we uploaded the .nwt file to allow importing and editing using the Newt Editor. The graphical formats and the .nwt was provided as both the original, SBGN-conform version as well as the beautified version.

Besides, we also decided to provide the adjusted versions for all other tools used to facilitate and encourage re-use with a tool of choice. Our alternatively provided versions are marked with the prefix "sub_" for substitute. Accordingly, the files we primarily worked with are marked with the prefix "main_".

File	Format	Description
main_BachmannPD_beautified.nwt	NWT	Newt Editor file encoding the beautified figure generated using Newt Editor
main_BachmannPD_beautified.png	PNG	beautified figure of PD map generated using Newt Editor
main_BachmannPD_beautified.svg	SVG	beautified figure of PD map generated using Newt Editor
main_BachmannPD_newt.png	PNG	raw figure of PD map generated using Newt Editor
main_BachmannPD_newt.sbgn	SBGN-ML 0.2	SBGN-ML encoding PD map generated using Newt Editor with manual changes
main_BachmannPD_newt.svg	SVG	raw figure of PD map generated using Newt Editor
sub_BachmannPD_SBGNViz.png	PNG	figure of PD map exported from SBGNViz
sub_BachmannPD_SBGNViz.sbgn	SBGN-ML 0.2	SGBN-ML validated with and exported from and exported from SBGNViz
sub_BachmannPD_krayon.png	PNG	figure of PD map exported from Krayon for SBGN
sub_BachmannPD_krayon.sbgn	SBGN-ML 0.2	SGBN-ML validated with and exported from SBGNViz
sub_BachmannPD_krayon.svg	SVG	figure of PD map exported from Krayon for SBGN
sub_BachmannPD_vanted.graphml	GraphML	GraphML encoding figure PD map exported from VANTED with SBGN-ED
sub_BachmannPD_vanted.png	PNG	figure of PD map exported from VANTED with SBGN-ED
sub_BachmannPD_vanted.sbgn	SBGN-ML 0.2	SGBN-ML validated with and exported from VANTED with SBGN-ED
sub_BachmannPD_vanted.svg	SVG	figure of PD map exported from VANTED with SBGN-ED
sub_Bachmann_original.jpg	JPEG	Figure 2 from original publication

Table 1: Content of the sbgn directory of the COMBINE archive listing all files with their format and description

References

[1] Bergmann, F. T. et al. Systems biology graphical notation markup language (SBGNML) version 0.3. Journal of Integrative Bioinformatics 17, 20200016 (2020). https://doi.org/10.1515/jib-2020-0016