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API for AmiGO in R?

Ben Hitz hitz at genome.Stanford.EDU
Tue Feb 27 16:46:19 PST 2007


>
Chi-Wai -

There is no direct R interface.  I have not worked much with R, but I  
am pretty sure there are open-source solutions to run R code on a  
mysql database.

There is a perl api to the mysql database.
Various database files (including mysql dumps) are available from:  
http://www.geneontology.org/GO.downloads.shtml

Documentation  can be found here:
http://www.godatabase.org/dev/

The perl modules and other files are available by anonymous CVS from

http://sourceforge.net/projects/geneontology
or

 >cvs -d:ext:anonymous at geneontology.cvs.sourceforge.net:/cvsroot/ 
geneontology go-dev

Hope this helps.

Ben

> Begin forwarded message:
>
>> From: noreply at genome.stanford.edu
>> Date: February 22, 2007 4:01:37 PM PST
>> To: Chi-WaiL at alleninstitute.org
>> Subject: GO Help query (from website)
>>
>> contactName: Chi-Wai Lau
>> contactEmail: Chi-WaiL at alleninstitute.org
>> contactText: Researchers at Allen Institute for Brain Science are  
>> extensive users of AmiGO. We often acquire data from AmiGO and  
>> perform indepth analysis in R. However, we have to export our data  
>> from the web browser and then import it back to R. Is there  
>> actually a simple API available for us to access the AmiGO data  
>> directly in R?
>>
>> Thank you.
>
>
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--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu




--
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