[Po-dev] RE: Questions about associations

[Schaeffer, Mary L.]

Many Thanks Chih-Wei,
That was most helpful, especially the very quick reply!

Yes we do have alleles annotated to PO. Many  more than genes in fact as most of the annotation is directly to the mostly mutant alleles. Since  you list mutants as acceptable objects for association, I assume you mean alleles other than mutant? 

At this time there are no GO annotations, other than electronic for maize, but not in MaizeGDB, but other places (PlantGDB, TIGR) and none are not at the GO place.

Looking at the format page for associations, it is not clear how you wish the growth/anatomy/development sorted out. It seems that  you wish them handled separatedly,ie 3 different files, or aspects, but to use only 2 codes in the aspect column: A (anatomy) or G(growth, development).
QUESTION: is that what you mean? Or can I lump the growth and development together since they are both aspect='G'?

 mary


-----Original Message-----
From: Chih-Wei Tung [mailto:cwt6 at cornell.edu]
Sent: Mon 9/24/2007 6:49 PM
To: Schaeffer, Mary L.
Cc: Shuly Avraham; po-dev at plantontology.org
Subject: Re: Questions about associations
 
Hi Mary,

Please find my answers below. You are welcome to add your comments.

Chih-Wei


On Sep 24, 2007, at 5:39 PM, Mary (Polacco) Schaeffer wrote:

> Shuly, Chih-Wei and group.
>
> Getting ready to send in new MaizeGDB associations files and have a  
> few questions about format since I last did this.
>
> Looking at  the cvs, it seem we are taking in associations to:
>     genes
>     QTL
>     stocks or germplasm (Mutant)
> QUESTION: Others?

As described in the association file format page, one of gene,  
transcript, protein, protein structure, complex, germplasm, QTL etc  
are accepted in POC at this moment.  Regarding to "alleles", we  
haven't figured out a best way to store and display this information,  
do you have any maize alleles annotated to PO?

>
> It seems on our new, and rather swank interface, that there is a  
> slot for 'sequence' and when null, it states:
>       No peptide sequence available.
> For example, look up pericarp,
>      then the Arabidopsis gene 'CYP707A1'
> But, when I look at the record in question at TAIR, it seems there  
> must be some peptide sequence.
> QUESTOIN: So, what is this field all about? OR rather, what must be  
> done to populate it?

Right now, we are not planning to bring any sequence information to  
PO browser. This field is a default in AmiGO browser (Shuly can  
confirm this), GOC displays peptide information in this field.

>
> In the same record, there is a column indicating that it has a GO  
> association?
> QUESTION: how does that get into the PO browser?
>

What Shuly did is she retrieved TAIR's gene_associations file from  
GO's website and compared all the gene products to TAIR's gene  
association files (anatomy and temporal) to PO, and extracted all the  
genes that exist in both, associations to GO and to PO.

I just checked GOC database and didn't find any maize gene products,  
are you planning to provide any maize GO annotations to them?

>
> Is there anything else I should be doing?
>
>      Mary

As long as your association files follow the guideline http:// 
www.plantontology.org/docs/otherdocs/assoc-file-format.html, you can  
submit the files any time.

Chih-Wei





> -- 
>> Mary Schaeffer, PhD (f/k/a Mary Polacco)
>> Geneticist/Curator MaizeGDB
>> USDA/ARS Plant Genetics Research Unit
>> 203 Curtis Hall
>> Adj Assoc Professor
>> Division of Plant Sciences
>> University of Missouri
>> Columbia, MO 65211
>> Phone: 573 884 7873
>> FAX: 573 884 7850
>
>
>