Export of filetypes into Pathvisio fails

[Lechu K.]

Hi all,

I would like to open with Pathvisio pathway files downloaded from KEGG website (as .xml files, though web browser).

I am getting this error while doing it: screenshot. Are these file not compatible, or is there a way around?

In fact, I have a similar problem trying to export other types of files (.owl).

Thank in advance for any help.

Cheers

Lech

[Alexander Pico]

KEGG no longer allows bulk conversion without a license, so the last time we produced KGML->GPML files was back in 2011 or thereabouts. We might be able to dig these up, if interested. If you just want 1 or 2 pathways converted, let us know and we might be able to do those manually. Frankly, the conversions aren’t great, since they KGMLs are poorly annotated. Personally, I would just redraw the pathway if it’s not already in WikiPathways...

BioPAX can be imported via this plugin: https://www.pathvisio.org/plugin/biopax3-plugin/

Browse the other plugins to see other functions: https://www.pathvisio.org/plugins/plugins-repo/ 

Cheers,

 - Alex

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