Biowarehouse -> BioPAX converter

[sergepass]

Hi Guys:

Does anyone have info about the status of the Biowarehouse -> BioPAX
converter? I had only found year-old remarks that it is " Under
development by BioPAX-Boston/SRI groups". Is it available somewhere?

Thanks

[Jeremy Zucker]

Hello there,

The Biowarehouse -> BioPAX converter has not been written yet, but I
would be more than happy to help if you want to take this on.

Sincerely,

Jeremy

[sergepass]

Hello Jeremy:

Thanks, I will eventually need one, and if it doesn't exist, I will
need to write it myself, not at the moment though.
Btw, I am looking for the ways to export pathway from Biowarehouse and
present it on the Web page, then map some experimental results onto it.
The only export tool I found for that is the SBML converter from
Bio-SPICE site. I just find BioPAX more appropriate in my case because
it keeps more background information on genes, etc.. Have you ever had
any experience with the tools that may be used here, like Cytoscape,
VisAnt?

Thanks,
Sergei

[Zhenjun Hu]

Hi Sergepass:

 

In case you want to put a pathway on your web page, the new function we are developing for VisANT may be useful for you. This function is designed to enable people to publish the network/pathway on-line using HTML and Javascript only. You may experience some of the function with ORFeome web page at:

 

http://ccsb.dfci.harvard.edu/exhorfdb3/

 

Click "Single ORF Search" and then select "Entrez Gene ID" and type in "55209" as an example, and then Click "Search". In the next page, either click 1st level interaction for this gene, or click 2nd level interaction will load VisANT with corresponding information.

 

In above example, we published the interaction network on-line with no server-sider transaction. The whole interaction network is loaded when you open the above link and you can search the interaction as if there is an interaction database behind. You can do same thing for pathways.

 

For BioPAX pathways, depend on what you need. If you just want to extract binary interaction from BioPAX pathways, Cytoscape should be good enough, and you may load these interactions using Web Start (for web publish, Cytoscape is not a Java applet, scripting with complicated functions may not easier). On the other hand, if you want to visualize BioPAX without loss of information (from pathway to interaction network is a process of information reduction), we have to use advanced graph model, such as the one we named meta-graph. Unfortunately, meta-graph has not been fully implemented in VisANT yet, therefore you will not be able to construct the network with tens or hundreds pathways yet, but in general you should be able to load several pathways (you can test with BioPAX patwhay at VisANT web page, click link BioPAX).

 

If you are able to help us to test, we will be very happy to speed up corresponding functions in VisANT. In addition, you are welcome to request the function you need for your application. :D

 

Many thanks,

 

Zhenjun