Go Analysis Web Services?

Question

[Lisa]

Hi I'm creating a workflow in taverna and I need some type of GO analysis to give me statistics on the significance of my findings. I was recommended that either DAVID or GOrilla would be suitable for my purposes but I cannot find either of them as a web service. Is there any around that I am missing in my searches or should I just stick with manual submissions for now?

I know that there's a question on accessing DAVID programmatically but it's not really what I'm looking for. As you can probably all tell im kind of new to this. Thanks for your time, any help would be appreciated.

Lisa.

Answer 1

[Chris Mungall]

I believe that Taverna integrates using SOAP and WSDL files. I'm afraid I'm not aware of any enrichment tool that is available via SOAP. Within the GO we maintain a list of tools together with metadata on each:

http://www.geneontology.org/GO.tools_by_type.term_enrichment.shtml

But we don't explicitly capture details of the API (we'd be happy to include this if provided).

Within the GO we plan to make a wide variety of enrichment tools available via Galaxy. We have a beta version here:

http://galaxy.berkeleybop.org:8080/

But so far only a few enrichment tools are wrapped.

This isn't much help to you though, unless someone has written of a general purpose Galaxy-to-Taverna bridge, sorry.

[Casey Bergman]

+1 for GO+Galaxy mashup. And yes, there is a galaxy-to-taverna bridge see here: http://www.taverna.org.uk/2011/03/11/egalaxy-brings-taverna-and-galaxy-together-via-myexperiment/

[Hamish]

Taverna (http://www.taverna.org.uk/) can also use REST web services. However since few REST services have an interface description document equivalent to the WSDL provided for a SOAP service, it is more difficult to get working unless the service is relatively simple. A possible alternative would be to use the R support in current versions of Taverna to interface on the of R packages which provide GO enrichment.

[Lisa]

Cool, thanks for that. I'm going to look into this and possibly try it out. I haven't used Galaxy before but I suppose I should give it a go and see how it works. It seems like it could be good when I finish my workflow and can then integrate it into Galaxy. Although it wasn't what I expected it does offer a solution so thanks for your help. :)

Answer 2

[Palu]

Did you check this http://www.agbase.msstate.edu/cgi-bin/tools/index.cgi

[Lisa]

Hey thanks so much for your link and your help, I really do appreciate it. However after looking around it's not quite what I'm looking for as it doesn't contain any web services I could integrate into Taverna. Thanks though, it is a good site for Go Analysis and one I wouldn't have known about otherwise.

[Palu]

your welcome. i will post some other links if you need