KEGG converter

[tho...@douglasconnect.com]

Dear WikiPathways community:

We would like to compare the WikiPathways with KEGG using PathVisio. However, the converter for the KEGG files is unfortunately not available right now (probably due to the shutdown of the Maastricht servers as a result of a hacking). Is there a way to access the tools (perhaps as an standalone software) or are the converted pathways available somewhere.

Thanks a lot.

Thomas

[Alex Pico]

I suspect we haven’t been able to run that script this KEGG licensed their content and started charging for access. Our tool does not get around that barrier. Do you own your own copy of KEGG content? Perhaps the tool could be adapted to run from that...

 - Alex

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[thomas.exner]

Dear Alex and all:

Thanls for you reply. And yes. This is the idea to adapt it to locally provided KEGG pathway files. However, I am not sure what to take as starting point. Where should I take the code from and is there anyone who could point me to where the changes have to be made?

Thanks.

Thomas

Von meinem Samsung Galaxy Smartphone gesendet.

-------- Ursprüngliche Nachricht --------

Von: Alex Pico <alex...@gladstone.ucsf.edu>

Datum: 07.03.20 00:34 (GMT+01:00)

An: wikipathways-discuss <wikipathwa...@googlegroups.com>

Betreff: Re: [wp-discuss] KEGG converter

[Martina Summer-Kutmon]

Dear Thomas,

The code is very old and hasn't been updated in a long time. I feel like there will not be a fast and straight-forward solution.

Can I ask what you want to do with the pathways? Do you want to perform pathway statistics or create certain data visualizations?

Best, Tina

To view this discussion on the web visit https://groups.google.com/d/msgid/wikipathways-discuss/5e65ea7b.1c69fb81.cac19.f323%40mx.google.com.

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Martina Summer-Kutmon, PhD
email: mku...@gmail.com

[Thomas Exner]

Dear Tina:
Thanks for your reply. We would be mainly interested in pathway statistics but data/pathway visualizations would be also of interest at a later stage. Do you have another idea how we could do this comparing WikiPathways and KEGG?
Thanks.
Thomas


Martina Summer-Kutmon schrieb:

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___________________________________________________________________________________

Dr. Thomas E. Exner
Chief Scientific Officer
Edelweiss Connect GmbH.

www: www.edelweissconnect.com
e-mail: thomas...@edelweissconnect.com
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[Martina Summer-Kutmon]

For pathway statistics, I can provide a converter that creates gene lists in GPML for KEGG pathways. Then they can simply be combined in the analysis. 

This will not work for data visualization, but for that you could probably use a Cytoscape apps for KEGG pathways. I have no experience for that but I know there are KEGG apps for Cytoscape (e.g.  http://apps.cytoscape.org/apps/cytokegg) which allow data visualization. 

Would that help? 

Best, Tina

[Thomas Exner]

Dear Tina:
It would be great if you could share the converter for generating the gene lists. And we will also start to play with Cytoscape.
Thanks again.
Thomas


Martina Summer-Kutmon schrieb:

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[Martina Summer-Kutmon]

Hi Thomas,

You can find the simple KEGG2GPML parser here: https://github.com/mkutmon/KEGG2GPML/releases/tag/1.0.0. It's a simple Java script so hopefully it will be easy to run. You have to select the species and output directory. Please let me know if you run into any problems or have any questions.

Best, Tina