Re: Problems importing KEGG pathways

[Kei]

Hi.

When you tried to load the pathway with KEGGScape, which KGML file did you use?  (e.g. hsa0001.xml)

It can be a bug in the app or an unsupported pathway file.

Thanks,

Kei

2018年11月6日火曜日 5時09分16秒 UTC-8 Laurent Winckers:

Hello,

I have tried to import KEGG pathways using KGML files from the KEGG website. I used the KEGGSpace app, however, when importing I got the error: "Could not unmarshall the KGML file." 

I also tried to use CytoKegg to search for pathways. However, when clicking the 'search' button, after selecting the desired pathway, nothing happens. 

Hopefully someone can help me!

[janst...@gmail.com]

On Tuesday, 6 November 2018 14:09:16 UTC+1, Laurent Winckers wrote:
> Hello,
>
>
> I have tried to import KEGG pathways using KGML files from the KEGG website. I used the KEGGSpace app, however, when importing I got the error: "Could not unmarshall the KGML file." 
>
>
> I also tried to use CytoKegg to search for pathways. However, when clicking the 'search' button, after selecting the desired pathway, nothing happens. 
>
>
>
>
> Hopefully someone can help me!

Hi there,

I think I'm currently experiencing a similar issue when trying to import KEGG pathways using KEGGscape.

I am downloading KGML files using the KEGG API with the code: 'wget http://rest.kegg.jp/get/eco00010/kgml -O eco00010.xml'.

When I try to do 'Import > Network from file > eco00010.xml' to import the KEGG pathway into Cytoscape v3.7.0, I get the error: 'Don't know how to read file'.

Any idea what is causing this?

Many thanks in advance,
Jan

[Keiichiro Ono]

Thanks for the info.

Now we confirmed the issue.

Looks KEGGScape fails during the startup.

We’ll look into this.

Thanks,

Kei

2018年11月9日(金) 11:21 <janst...@gmail.com>:

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Keiichiro Ono
https://viz2k.com/
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[yimin...@impossiblefoods.com]

Hi,

I met the same issue, but I also want to add that if the Cytoscape 3.7 was rebooted after the installation of KEGGScape 0.8.1, there will be a "KEGGScape failed to start" error.

Thanks!