"Could not parse XGMML file"

[Mike Smanski]

Hi all,

 

I am new to cytoscape and am just trying to load a network file downloaded from UCSF's SFLD site. The network I want to view is pretty large, but even when I really constrain the number of edges (blast cutoff < 10e-300), such that there are <10,000 nodes and <50,000 edges, I get the error message noted in the subject line. The available memory dictated in the 'cytoscape.vmoptions" file is 3600 Mb, which should be large enough for a network this size according to the cytoscape wiki. Any suggestions?

 

Thanks,

Mike

[Tim Hull]

Do you have a link to the specific network you're trying to export?

Tim

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[Matthew Bauerle]

I too am having this problem.  I have downloaded the Radical SAM superfamily network to an E value of 10^-20.  Attempts to open it have given me the same "Could not parse XGMML file" message. The network is very large so I assume that the size is causing a problem. The following is the link from the SFLD website: http://sfld.rbvi.ucsf.edu/django/superfamily/29/

Thank you in advance for your help.

On Wednesday, March 19, 2014 3:07:37 PM UTC-4, Tim Hull wrote:

Do you have a link to the specific network you're trying to export?

Tim

On Wed, Mar 19, 2014 at 11:37 AM, Mike Smanski <sma...@mit.edu> wrote:

Hi all,

 

I am new to cytoscape and am just trying to load a network file downloaded from UCSF's SFLD site. The network I want to view is pretty large, but even when I really constrain the number of edges (blast cutoff < 10e-300), such that there are <10,000 nodes and <50,000 edges, I get the error message noted in the subject line. The available memory dictated in the 'cytoscape.vmoptions" file is 3600 Mb, which should be large enough for a network this size according to the cytoscape wiki. Any suggestions?

 

Thanks,

Mike

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[Scooter Morris]

Hi all,
    I'm looking into this... stay tuned...

-- scooter

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[Scooter Morris]

Mike,
    What superfamily are you downloading?

-- scooter

[Scooter Morris]

On 04/10/2014 08:50 AM, Matthew Bauerle wrote:

I too am having this problem.  I have downloaded the Radical SAM superfamily network to an E value of 10^-20.  Attempts to open it have given me the same "Could not parse XGMML file" message. The network is very large so I assume that the size is causing a problem. The following is the link from the SFLD website: http://sfld.rbvi.ucsf.edu/django/superfamily/29/

Hi Matthew,
    That network may stress most Cytoscape installations -- it's a 2.4GB XGMML file with 48,000 nodes and over 9 million edges.  My suggestion would be to use a much more stringent cutoff...

-- scooter

Thank you in advance for your help.
On Wednesday, March 19, 2014 3:07:37 PM UTC-4, Tim Hull wrote:

Do you have a link to the specific network you're trying to export?

Tim

On Wed, Mar 19, 2014 at 11:37 AM, Mike Smanski <sma...@mit.edu> wrote:

Hi all,

 

I am new to cytoscape and am just trying to load a network file downloaded from UCSF's SFLD site. The network I want to view is pretty large, but even when I really constrain the number of edges (blast cutoff < 10e-300), such that there are <10,000 nodes and <50,000 edges, I get the error message noted in the subject line. The available memory dictated in the 'cytoscape.vmoptions" file is 3600 Mb, which should be large enough for a network this size according to the cytoscape wiki. Any suggestions?

 

Thanks,

Mike

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[Satomi]

Hello!

I used to write xgmml files to create cytoscape networks, but since I got a new version of cytoscape (v3) , the same files don't seem to work....?!  As a simple test, I have exported the existing network I made before into both xml and xgmml files, but only xml file is imported correctly when I load it to cytoscape (attached).  I recently created a new xgmml file which I really want to put in cytoscape but I also get 'Could not parse XGMML file' message. 

What would be the problems in this xgmml file (expressionetc.xgmml ), or using it?

Thank you very much in advance.

[Tim Hull]

First of all, did you export these networks using the "File-Export-Network" or "File-Export-Network and View" option? Note that using "Network and View" is necessary if you want to preserve the view (as the "updated ETC050614.xml" does, but the "updated ETC050614.xgmml" does not).

Finally, with respect to the "expressionetc.xgmml" that will not load - can you share the session file from which this was exported, or another session file that produces a similarly invalid XGMML file when exported?

Tim

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[Satomi]

Thank you very much for your quick help!!

I attach the session file.....thank you again!!

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[Scooter Morris]

Hi Satomi,
    I've been able to successfully export this as File->Export->Network and View "/tmp/DR-ETC90.xgmml" and then been able re-import it after doing a "New->Session".

-- scooter

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[Scooter Morris]

So, the problem with expressionetc.xgmml is that for node ATP5I there are real values that are exported as 'value=""':

<node id="9" label="ATP5I">
  <att type="real" name="ID" value="9"/>
  <att type="string" name="name" value="ATP5I"/>
  <att type="real" name="3m-1" value=""/>
  <att type="real" name="3m-2" value="9"/>
  <att type="string" name="3m-3" value="ATP5I"/>
  <att type="real" name="AL15-1" value="-920.6"/>
  <att type="real" name="AL15-2" value="490.3"/>
  <att type="real" name="AL15-3" value=""/>
  <att type="real" name="DR15-1" value="9"/>
  <att type="string" name="DR15-2" value="ATP5I"/>
  <att type="real" name="DR15-3" value="-920.6"/>
  <att type="real" name="AL24-1" value="490.3"/>
  <att type="real" name="AL24-2" value=""/>
  <att type="real" name="AL24-3" value="9"/>
  <att type="string" name="DR24-1" value="ATP5I"/>
  <att type="real" name="DR24-2" value="-920.6"/>
  <att type="real" name="DR24-3" value="490.3"/>
  <att type="real" name="AL30-1" value=""/>
  <att type="real" name="AL30-2" value="9"/>
  <att type="string" name="AL30-3" value="ATP5I"/>
  <att type="real" name="DR30-1" value="-920.6"/>
  <att type="real" name="DR30-2" value="490.3"/>
  <att type="real" name="DR30-3" value=""/>
  <graphics type="ELLIPSE" x="490.3" y="-920.6" fill="#ff0000"/>
</node>

Note the instances where you have 'value=""'.  The right thing to do would be:

<node id="9" label="ATP5I">
  <att type="real" name="ID" value="9"/>
  <att type="string" name="name" value="ATP5I"/>
  <att type="real" name="3m-2" value="9"/>
  <att type="string" name="3m-3" value="ATP5I"/>
  <att type="real" name="AL15-1" value="-920.6"/>
  <att type="real" name="AL15-2" value="490.3"/>
  <att type="real" name="DR15-1" value="9"/>
  <att type="string" name="DR15-2" value="ATP5I"/>
  <att type="real" name="DR15-3" value="-920.6"/>
  <att type="real" name="AL24-1" value="490.3"/>
  <att type="real" name="AL24-3" value="9"/>
  <att type="string" name="DR24-1" value="ATP5I"/>
  <att type="real" name="DR24-2" value="-920.6"/>
  <att type="real" name="DR24-3" value="490.3"/>
  <att type="real" name="AL30-2" value="9"/>
  <att type="string" name="AL30-3" value="ATP5I"/>
  <att type="real" name="DR30-1" value="-920.6"/>
  <att type="real" name="DR30-2" value="490.3"/>
  <graphics type="ELLIPSE" x="490.3" y="-920.6" fill="#ff0000"/>
</node>
 
Note that we've dropped all entries where the value isn't set.

-- scooter

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[Satomi]

Thank you so much!!!!! Now working! 

Satomi