How to import XGMML file with Cytoscape?

[JY]

Hi all, I don't know how to import a file named "tempnetworkresult.gr" as following, it always fail.

Any advice?

Thanks in advance.

[piet molenaar]

Hi, your file is not in a tabular format, it is an xgmml file, an xml format specific for graphs, you should use File>Import>Network>File

Hope this helps,

Piet

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

[JY]

Hi Piet,

Thanks for your quick reply.

Actually, the image I attached in last letter was derived from following the steps: File>Import>Network>File. It always popup error like "The network cannot be created without selecting the source and target column". However, there only on column in  "tempnetworkresult.gr". so what should I do?

JY

On Tuesday, March 22, 2016 at 9:57:39 AM UTC-5, Piet wrote:

Hi, your file is not in a tabular format, it is an xgmml file, an xml format specific for graphs, you should use File>Import>Network>File

Hope this helps,

Piet

On Tue, Mar 22, 2016 at 3:46 PM, JY <jinyu....@gmail.com> wrote:

Hi all, I don't know how to import a file named "tempnetworkresult.gr" as following, it always fail.

Any advice?

Thanks in advance.

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[piet molenaar]

Ok, it is apparently not recognized as a xgmml file; can you send me the file? The link is not working...

Cheers,

Piet

On Tue, Mar 22, 2016 at 4:16 PM, JY <jinyu....@gmail.com> wrote:

Hi Piet,

Thanks for your quick reply.

Actually, the image I attached in last letter was derived from following the steps: File>Import>Network>File. It always popup error like "The network cannot be created without selecting the source and target column". However, there only on column in  "tempnetworkresult.gr". so what should I do?

JY

On Tuesday, March 22, 2016 at 9:57:39 AM UTC-5, Piet wrote:

Hi, your file is not in a tabular format, it is an xgmml file, an xml format specific for graphs, you should use File>Import>Network>File

Hope this helps,

Piet

On Tue, Mar 22, 2016 at 3:46 PM, JY <jinyu....@gmail.com> wrote:

Hi all, I don't know how to import a file named "tempnetworkresult.gr" as following, it always fail.

Any advice?

Thanks in advance.

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--

Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

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[piet molenaar]

Hi, renaming the file with extension xgmml will help, I sent your network in a private mail..

And yes probably Cytoscape should recognize this despite the extension. You might want to post this as a feature request.

Cheers,

Piet

[JY]

Hi Piet,

It works fine, thank you.

JY

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

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