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kgml parsing by python

Hello everyone! A question has engaged my head for long time! do KGML and SVG the same? How can I convert KGML to SVG by python! is there any library in python for it?

kgml xml svg python
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updated by Joe Joe • written by EFN • EFN

1 answer

I'm not super familiar with it personally, but judging by this, I'd say not:

KGML (KEGG Markup Language) XML representation of KEGG pathway maps

The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format. KGML enables automatic drawing of KEGG pathways and provides facilities for computational analysis and modeling of gene/protein networks and chemical networks. The KGML files for metabolic pathway maps contain two types of graph object patterns, how boxes (enzymes) are linked by "relations" and how circles (chemical compounds) are linked by "reactions". The KGML files for non-metabolic pathway maps contain only the aspect of how boxes (proteins) are linked by "relations". The prefix for the pathway map identifiers indicates the following: ko - reference pathway map linked to KO entries (K numbers) rn - reference pathway map linked to REACTION entries (R numbers) ec - reference pathway map linked to ENZYME entries (EC numbers) org (three- or four-letter organism code) - organism-specific pathway map linked to GENES entries (gene IDs) (Note) The "map" prefix represents the internal format of KGML+ (KGML+SVG), which is used for generating ko/rn/ec files for metabolic pathways and ko files for non-metabolic pathways.

It sound to my like KGML is an XML style for describing how to draw Kegg pathways etc (a 'map'). and internally uses SVGs for rendering them.

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written by Joe Joe

Thanks for response!

if it has SVG inside itself, so we would able to extract and display them,wouldn't we?

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written by EFN • EFN

I would think so. They might be rendered on the fly though, so it might be difficult.

My only suggestion is just to find an example KGML file and inspect it. There are XML parsing libraries (a quick google should find some) so you might be able to read it in to some sort of existing structure.

I would doubt anything preexists to do this job, but I’ll give way to people more familiar with Kegg.

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written by Joe Joe

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