I can't import KEGG files to Cystoscape. HELP

[Juliana T]

Hi, everyone. 

I'm having some trouble with importing KEGG files to cytoscape. I don't know what is happening and why. 

When I click to import a network from a file, it appears those windows attached here and simply does not open anything more. 

In most of the cases, the file keeps loading and a red hyphen appears, like in the number 3. Today, appeared "could not unmarshall KGML file" (number 2).

Please, help me. I need the KEGG pathways to do my analysis! 

Hope someone can help. 

Juliana

[piet molenaar]

Hi Juliana,

Can you send me the KEGG file you're trying to import?

Cheers,

Piet

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
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the Netherlands

tel (+31) 20-5666592
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[Juliana T]

Hey, Piet.

Here it is! 

Hope you can explain me whats going on :/

Anyways, I tried to upload these files in a different software, in a MAC OS X, and they didn't uploaded as well.

Should I download the files there, in the other desktop? Because I used the files I have already downloaded before. 

Juliana.

[Juliana T]

I've just realized that I can import only the KEGG files from the reference pathways. What it means I cannot select the species.

The point is that I don't know if, in that way, the file is useful to make the analysis. We need the gene names and in that "reference mode" the genes appears as a code. 

Juliana. 

[piet molenaar]

I imported the files using with the keggscape app installed. However when I ticked the Import additional details from Kegg box I got the same error as you got. 

Furthermore the networks only contain one or two edges, but that's all that is present in the actual xml files....

Find attached the .cys file.

I'm not sure what you mean by importing Kegg files only from reference pathways?

Cheers,

Piet

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[Juliana T]

Hey Piet!

So... Can I import the KEGG pathway only by not ticking 'import details from Kegg pathways' box?

The "reference pathways" are the ones that only appears codes, instead of genes properlly. This happens especifically when you don't select an species. The name of these reference pathways files begins with 'ko1234'.xml. I think I sent you one. Link of the reference pathway of "Proteasome" : http://www.genome.jp/kegg-bin/show_pathway?org_name=ko&mapno=03050&mapscale=&show_description=hide

We can download the KGML file of reference pathways. Currently I can only import these kind of files. I can't import the rno4141.xml or rno3008.xml, for example. 

Thank you again!!

Juliana.

[piet molenaar]

Yes, that should be possible. 

What kind of organism do you use? I can download xml files from homo sapiens for example...

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[Juliana T]

Hey, Piet.

How it was from holidays? Hoping you're doing just fine. 

I did it. I finally imported the KEGG files correctly!! I think the problem was just by ticking the 'import details from Kegg pathways' box.

Thank you again.

I use 'rattus norvegicus'. 

Juliana. 

[piet molenaar]

Nice! Good to hear, and if you run in any trouble don't hesitate to ask.

Cheers,

Piet

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[AKASH DAS]

if i am not too late to join the conversation...haha

Hello  Juliana, 

You pointed towards the exact problem that I am currently facing. 

As I work on RICE, I have tried to import both Reference pathways and rice (Osa) specific KGML files into cytoscape , but unfortunately i am not able to import any of them even after unchecking 'import details from Kegg pathways'.

Can you or Piet guide me on this....

How can i import this -   https://www.genome.jp/kegg-bin/show_pathway?osa00940   

Thanks 

Akash D

On Wednesday, January 11, 2017 at 8:07:22 PM UTC+5:30 Piet wrote:

Nice! Good to hear, and if you run in any trouble don't hesitate to ask.

Cheers,

Piet

On Wed, Jan 11, 2017 at 3:32 PM, Juliana T <toledo....@uol.com.br> wrote:

Hey, Piet.

How it was from holidays? Hoping you're doing just fine. 

I did it. I finally imported the KEGG files correctly!! I think the problem was just by ticking the 'import details from Kegg pathways' box.

Thank you again.

I use 'rattus norvegicus'. 

Juliana. 

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[Scooter Morris]

Hi Akash,

   Can you give us a bit more information about what errors you're getting?

-- scooter

[Scooter Morris]

By the way, I was able to import that pathway by *not* clicking on that box, although it imported as a network, not a pathway.

-- scooter

[Scooter Morris]

I was able to get a bit further by using the CytoKEGG app rather than importing the KGML directly.  You may give that a try.

-- scooter