KGML missing information and visualization issues with Cytoscape

Question

[justp]

I'm having difficulties viewing KEGG pathways properly in Cytoscape. There's missing information in the XML file that prevents Cytoscape from displaying certain relationships and annotations. Is this something that is just unavoidable?

How does KEGG display pathway related information like how a certain gene leads to metabolism at the end? For example, with the pathway linked below GYS leads to metabolism, but this isn't found in the XML file. I've noticed this with a lot of other pathways. That sort of information is present in the KEGG website, but not the XML file.

http://www.genome.jp/kegg-bin/show_pathway?hsa04151

Answer 1

[Keiichiro Ono]

Unfortunately, this is the limitation of the KGML format, not Cytoscape. Some of the annotations in the background is not encoded in KGML, and there is no way to extract such information from KGML, and it is the only machine readable form of KEGG pathway data set.

[justp]

Thank you. That's what I assumed. I was hoping there was a more machine readable file that the KEGG database had in addition to the accessible xml file, but I'm guessing that doesn't exist or isn't available.