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Convert KEGG KGML files in GPML format

Dear All,

I have a set of some what related KEGG pathways for example glycolysis. Are there any tools available that can merge these pathways say if I give KGML files of these pathways as input i can get GPML format as a output, so it can be process in PathVisio tool. Any suggestion ? Thank you in advance

pathway kegg pathvisio
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updated by cannin cannin • written by dnnxl15 • dnnxl15

A few years ago there was the following post in 'Biostars':

Merging Kegg Pathways

It may help. And also look at the right panel -

you will see some related posts.

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written by natasha.sernova natasha.sernova

1 answer

A less obvious route, but it might get you to what you want:

SBGN and SBGNML were meant as exchange formats for pathway diagrams:

Software support for SBGN maps: SBGN-ML and LibSBGN. https://www.ncbi.nlm.nih.gov/pubmed/22581176

The Pathway Commons database aggregates from many sources, including KEGG: https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Fkegg.pathway%2Fhsa00010

and puts them in common formats, like SBGN: http://www.pathwaycommons.org/pc2/get?uri=http%3A%2F%2Fidentifiers.org%2Fkegg.pathway%2Fhsa00010&format=SBGN

Pathvisio has a SBGN plugin: https://www.pathvisio.org/plugin/sbgn-plugin/

No guarantees the layout will be retained.

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written by cannin cannin

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