[Po-dev] RE: Questions about associations

[Pankaj Jaiswal]

Marty Sachs wrote:
> At 10:18 AM -0500 9/25/07, Schaeffer, Mary L. wrote:
>> I assume you mean alleles other than mutant?
> 
> Huh?  All alleles differ from each other due to mutation.  Many may not 
> be induced by a researcher in a lab setting, but natural allelic 
> variation is also due to mutation.
> 
>     -Marty
> _______________________________________________
> Po-dev mailing list
> Po-dev at plantontology.org
> http://mail.plantontology.org/mailman/listinfo/po-dev
> 

If I remember it correctly, this came up for discussion at the 2006 POC 
meeting at PAG. Chih-wei can you dig out the notes from the meeting?

To avoid this controversy of natural variations vs induced variation we 
can simply use 'variation' or 'variant' instead of mutant/allele. In any 
case, the best to start is map the variant annotations to the gene and 
use the WITH column in the association file to effectively that an 
annotation to PO term to a gene is based on the inference derived from 
(WITH) allele (in your case).

Pl take a look at the association file format section of 
http://plantontology.org/docs/otherdocs/assoc-file-format.html
there in the column-8 one can enter the allele symbol suggesting that 
the maize gene annotation to PO term is derived from allele so and so.

I will be happy to talk to you guys sometime on Friday afternoon.

Pankaj