KEGG pathway conversion

[Marina Costa]

Good afternoon,

Has anyone ever tried to convert a file taken from KEGG to the pathwayVisio programme? I'm having problems converting the file. I used the GPT chat to make the code, but I always have problems when I try to open it in PathwayVisio.

Thank you.

[Kristina Hanspers]

Hi Marina,

We have developed KEGG converters in the past, but we don't have working code at the moment. You mentioned you have gpml from some custom code; if you want to share the gpml we can maybe figure out what the issue is.

Regards,

Kristina

WikiPathways admin

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[Kozo Nishida]

Hi Marina, Kristina,

I am also very interested in that, but I have not done it because it was not clear whether it would violate KEGG's license. If there is no need to worry about that, I would like to support you.

Let me know if it is okay to create the conversion automation (without such concerns).

Kozo

[Marina Costa]

Hi Kristina, 

Attached is the gplm file converted from a xml file, but it doesn't work at Pathvisio.

Thank you very much.

Best regards,

Marina

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[Kristina Hanspers]

Hi Kozo and Marina,

In regards to the KEGG license terms (https://www.kegg.jp/kegg/legal.html / https://www.pathway.jp/en/academic.html), I believe it is ok for individual academic users to use the downloaded KGML (I think this could include conversion to another format for use in a specific application). I interpreted Marina's original question to fall in this category. In terms of converting a large number of pathways automatically for inclusion into (for example) WikiPathways, I believe this is not allowed without a license. The scripts we have pre-date the change in KEGGs change in FTP access policy.

Marina: The gpml you sent is basically empty, it contains only a partial pathway information and no nodes or edges. Normally, I would recommend transcribing individual pathways from KEGG manually using PathVisio, and I can recommend some strategies for making this as efficient as possible. But looking at the pathway you referenced in the gpml, https://www.kegg.jp/kegg-bin/show_pathway?sot01110, I would not recommend this. If you need to visualize data on the entire pathway I would recommend using Cytoscape and one of the apps that enable import from KEGG (https://apps.cytoscape.org/search?q=KEGG), or break it up into the most relevant smaller chunks for manual curation.

Regards,

Kristina

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[Marina Costa]

Hi Kristina and Kozo,

Sorry for the late reply.

I'm a PhD student with a project grant. As part of the project, I need the metabolic pathway in question in gpml format so that I can use it in the MetaboScape software from Bruker UPLC-QTOF-MS.

I just found the pathway I need at KEGG, but maybe I will have to do the pathway manually. Is there some way to do it easier?

Thank you very much for your help.

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[Kristina Hanspers]

Hi Marina,

I'm not familiar with the MetaboScape software, but I'm assuming you're using it for data visualization? Unless you can develop your own KGML-GPML converter, I would really consider using a different tool for the analysis, where you can import that particular KEGG pathway (and others) directly from KEGG: 

KEGG Mapper tool from KEGG: https://www.genome.jp/kegg/mapper/, https://www.genome.jp/kegg/webapp/color_gui.html

Pathview R package: https://bioconductor.org/packages/release/bioc/html/pathview.html

Kristina

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