[InterMine Dev] biopax data visulization

Fengyuan Hu fh293 at cam.ac.uk
Wed Mar 14 10:55:27 GMT 2012


Hi Su,

If I understand it right, you want to create a pathway network displayer 
similar to the interaction network displayer?

Yes, you definitely can create a new one, but firstly you need some 
knowledge of CytoscapeWeb <http://cytoscapeweb.cytoscape.org/> on which 
the network displayer is built. Going though their demos and tutorial 
would be useful.

In InterMine, you need study a bit of the following source files:

webconfig-model.xml - config your network displayer as a reportdisplayer
CytoscapeNetworkDisplayer.java - the report displayer class, get a set 
of genes interacting with the report gene, in your case, the 
genes/proteins on the same pathway as the report gene/protein
cytoscapeNetworkDisplayer.jsp - the web page to display the network

since the network data structure (in xml format) is fetched via ajax 
call from cytoscapeNetworkDisplayer.jsp, you also need:

CytoscapeNetworkAjaxAction.java - the Structs action class (config in 
struts-config-model.xml) to handle the http request and call 
CytoscapeNetworkService to generate the network data. (CytoscapeWeb can 
plot a network from JSON , and it's lightweight comparing to xml. Refer 
to http://cytoscapeweb.cytoscape.org/documentation/elements. InterMine 
also has a JSON generation implementation in CytoscapeNetworkGenerator.java)

CytoscapeNetworkService.java
CytoscapeNetworkGenerator.java
CytoscapeNetworkNodeData.java
CytoscapeNetworkEdgeData.java
etc.

I've attached a diagram for the work flow (the call hierarchy of all the 
java classes) of how the network data is generated. After fetching the 
data to the web page, you can customise the outlook of the network by 
using CytoscapeWeb javascript API.

Let me know if you have further questions while you implement it.

Thanks
Fengyuan

On 14/03/12 02:49, wang su wrote:
> Hi all,
>
> I want use InterMine 0.98 create a pathway database, I had loaded my biopax level2 data into the intermine, now I want to have a figure to show the network , just like http://targetmine.nibio.go.jp:8080/targetmine/report.do?id=2013549 in targetmine, can you say something details about how could I implement this function. Thank you
>
> Best wishes!
>
> Su
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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