Error uploading xml file in PathVisio tool

[Aparna Chaturvedi]

Hi,

Hi, I am trying to upload a pathway I created in Cytoscape to WikiPathways, which only considers gpml or xml file formats for uploading a pathway. According to its author guide, steps are:

 1. Install PathVisio tool
 2. Import pathway in gpml or xml file formats 
 3. Upload the network using WikiPathway plugin.

I am stuck at step 2 where I tried importing my Cytoscape pathway as xml file, the PathVisio tool returned error: "Not supported file for pathway". Also, I can't generate gpml file format using Cytoscape. 

Please, guide me how I can resolve abovementioned issues to upload my pathway in WikiPathways. Also, is there any other approach or at any step where I might be doing some mistake, please let me know.

Thanks & Regards.

Aparna Chaturvedi

PhD Scholar

University of Allahabad

Uttar Pradesh, India.

[Kristina Hanspers]

Hi Aparna,

PathVisio can only read gpml files, not the xgmml format produced by Cytoscape. And as of right now, the WikiPathways app for Cytoscape does not write to gpml, although it is a planned feature.

You mentioned documentation that describes going from Cytoscape to xml to PathVisio. Can you point me to it? 

Regards,

Kristina

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[Aparna Chaturvedi]

Hi Kristina, 

Thanks for your response.

There is no statement in documentation telling from Cytoscape to xml to PathVisio in  particular. However, I noticed if PathVisio can import gpml or xml file formats, then the pathways can be uploaded to WikiPathways thereon. But after your reply I undersatnd, this can't be done as Cytoscape does not produce gpml file.

Can you please tell me I have  a pathway constructed using Cytoscape, how can I upload the same to WikiPathways?

Thanks & Reagrds.

[Kristina Hanspers]

Hi Aparna,

Unfortunately, there is no workaround right now for transferring a pathway from Cytoscape to WikiPathways. 

Regards,

Kristina

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[alex.pico]

Hi Aparna,

At this time, I would recommend sharing your Cytoscape pathway via NDEx (https://ndexbio.org). It's free and citeable. In fact, we redistribute all human WikiPathways there as well.

And just some additional information, if you are curious: the GPML format that is produced by PathVisio (for WikiPathways) includes additional information and parameters that Cytoscape simply doesn't deal with. This is why it's relatively easy to go from GPML to Cytoscape, but not the other direction.

[alex.pico]

Of course, you could also open up PathVisio and Cytoscape side-by-side and redraw the pathway. A medium sized pathway might take a 3-4 hours.

[Aparna Chaturvedi]

Thank you so much for your response Alex and Kristina, I'm considering using NDEx now as well as will see to drawing the pathway side-by-side in PathVisio. Thanks.

Regards,

Aparna