Can any softwares or tools convert .KGML files(XML edited) to SVG ones?

hugh_hang · 04-11-2013, 01:02 AM

In the KEGG website, I've downloaded a KGML file which contains all informations of a pathway. But I want to get the vector graphic of the pathway such as SVG file.

maubp · 04-11-2013, 01:54 AM

Something like that is likely coming to Biopython, probably in the next release:
https://github.com/biopython/biopython/pull/173

Leighton's blog posts about this work:
http://armchairbiology.blogspot.co.u...ch-part-i.html
http://armchairbiology.blogspot.co.u...h-part-ii.html
http://armchairbiology.blogspot.co.u...-part-iii.html

This using Python to parse the KGML XML files, which can then be rendered using the manual layout positions KEGG provide. The examples produce PDF, but underneath this uses the ReportLab library for the graphics which supports vector output including PDF and SVG (and also bitmap output like PNG) so using this for SVG output should in principle be possible.

You can also overlay this information on top of the template PNG images KEGG provide to make annotated variations, for example to emphasise a particular pathway.

hugh_hang · 04-11-2013, 11:20 PM

Quote:

Originally Posted by maubp

Something like that is likely coming to Biopython, probably in the next release:
https://github.com/biopython/biopython/pull/173

Leighton's blog posts about this work:
http://armchairbiology.blogspot.co.u...ch-part-i.html
http://armchairbiology.blogspot.co.u...h-part-ii.html
http://armchairbiology.blogspot.co.u...-part-iii.html

This using Python to parse the KGML XML files, which can then be rendered using the manual layout positions KEGG provide. The examples produce PDF, but underneath this uses the ReportLab library for the graphics which supports vector output including PDF and SVG (and also bitmap output like PNG) so using this for SVG output should in principle be possible.

You can also overlay this information on top of the template PNG images KEGG provide to make annotated variations, for example to emphasise a particular pathway.

Thank you! I‘ll pay attention to it.

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04-11-2013, 01:02 AM	#1
hugh_hang Member Location: Hangzhou, China Join Date: Jan 2013 Posts: 28	Can any softwares or tools convert .KGML files(XML edited) to SVG ones? In the KEGG website, I've downloaded a KGML file which contains all informations of a pathway. But I want to get the vector graphic of the pathway such as SVG file.

04-11-2013, 01:54 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Something like that is likely coming to Biopython, probably in the next release: https://github.com/biopython/biopython/pull/173 Leighton's blog posts about this work: http://armchairbiology.blogspot.co.u...ch-part-i.html http://armchairbiology.blogspot.co.u...h-part-ii.html http://armchairbiology.blogspot.co.u...-part-iii.html This using Python to parse the KGML XML files, which can then be rendered using the manual layout positions KEGG provide. The examples produce PDF, but underneath this uses the ReportLab library for the graphics which supports vector output including PDF and SVG (and also bitmap output like PNG) so using this for SVG output should in principle be possible. You can also overlay this information on top of the template PNG images KEGG provide to make annotated variations, for example to emphasise a particular pathway.