incomplete import of KEGG pathway via keggscape

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Nicolai Karcher

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Mar 6, 2025, 12:13:40 PMMar 6

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Hi,

I'm cross-posting this with the issue I just opened for KEGGscape since it seems issues are generally unanswered (sorry if this bad practice, am very new to cytoscape)

Issue: For some pathways, it seems that keggscape (the cytocape plugin) is failing to import all nodes/edges.

For example, If I try to import the attached KEGG pathway xml (bvu00300 exported/downloaded from KEGG as explained in the keggscape tutorial), the imported pathway is incomplete. I'm attaching the xml file (I had to rename it to .txt since .xml file upload seems prohibited.

See below for screenshot; the bottom left part lacks a lot of edges that are evidently part of the pathway and also clearly visible in KEGG.

I am using Cytoscape version 3.10.3, keggscape version v0.9.2 on an M1 Mac.

Any input is greatly appreciated

bvu00300.xml

Kozo Nishida

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Mar 8, 2025, 6:09:13 PMMar 8

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Hi,

Thanks for your message.

I have just replied to https://github.com/idekerlab/KEGGscape/issues/31 .

Please check https://github.com/idekerlab/KEGGscape/issues/31#issuecomment-2708525165 .