import stke pathway xml file into cytoscape

Question

[pengchy]

Hi,

I have downloaded the STKE pathway data from here and want to visualize them using cytoscape version 3.2.0. According to the documentation from STKE (http://stke.sciencemag.org/sites/default/files/adv_page_assets/Connections-Map-XML-Schema-Version-7.0.pdf), the network was represented using "Systems Biology Markup Language (SBML)-compatible XML format.". However, when I import the network xml file through "File->import->network" and select the file type "SBML file (*.xml)", there is an error window like this:

Can anyone help me out?

Thanks!

Pengcheng Yang

[Jean-Karim Heriche]

I can reproduce this. Either the SBML file is malformed or there's a bug in the Cytoscape SBML parser. What I also find often with so called XML standards, is that there are different interpretations of them that end up being incompatible. That could also be the case here. If you want to report a bug you can provide the log found in CytoscapeConfiguration/3/framework-cytoscape.log

Answer 1

[pengchy]

This problem has been solved and tracked here: https://code.cytoscape.org/redmine/issues/3375

In brief, changing xmlns="" to xmlns="http://www.sbml.org/sbml/level2" for the pathway files. The annotation data of nodes and edges can be parsed into tabular format and loaded into Cytoscape.