[Po-dev] RE: Questions about associations

[Mary (Polacco) Schaeffer]

Hi Chih-Wei,

If it works best for you, I can restrict to one (column 8, for a gene assoc
file) and where possible,  list an allele that is maintained by Marty at the
Stock Center. 

As FYI, most loci with associations  inferred from phenotype (IMP)  have one
or two alleles that have associations to one or more anatomy terms.  A few
do have hundreds of alleles.  Currently, there are a total of some 16,292
alleles associated to PO body_parts by evidence code IMP; these in turn
represent some 4268 genes and QTL.

Re links to MaizeGDB ­ there is a stable link: provided 2-3 years ago ­ not
sure where the link you have below came from?

> We have a hyperlink prefix that works for any ID in MaizeGDB, regardless
> of
> object type:
>
> http://www.maizegdb.org/cgi-bin/id_search.cgi?id=
>

http://www.maizegdb.org/cgi-bin/id_search.cgi?id=12327

>

Let me know if this works for you,

     mary






On 9/25/07 1:47 PM, "Chih-Wei Tung" <cwt6 at cornell.edu> wrote:

> Hi Mary,
> 
> I am wondering if it is a practical way to display many alleles in
> POC database? I just looked at this maize gene, adh1, it has 575
> variations/alleles (http://www.maizegdb.org/cgi-bin/
> displaylocusrecord.cgi?id=12021, http://www.maizegdb.org/cgi-bin/
> locusvarreport.cgi?id=12021).
> 
> If most of maize genes have such huge amount of alleles, I think
> providing a external link to MaizeGDB should be sufficient.  I
> searched POC database,  "MaizeGDB:12021" link in this page http://
> www.plantontology.org/amigo/go.cgi?
> view=details&search_constraint=gp&session_id=9624b1190744163&gp=12021
> didn't direct me to the proper page in MaizeGDB.  Does MaizeGDB have
> stable URL ID to link back to POC?
> 
> Here is one example that GOC link back to Flybase, and users can find
> all the alleles in Flybase page (http://amigo.geneontology.org/cgi-
> bin/amigo/go.cgi?
> search_constraint=gp&view=details&session_id=762b1190743889&gp=FBgn00032
> 05, click "FB:FBgn0003205", it points to http://
> flybase.bio.indiana.edu/reports/FBgn0003205.html)
> 
> 
> Chih-Wei
> 
> 
> 
> On Sep 25, 2007, at 1:30 PM, Mary (Polacco) Schaeffer wrote:
> 
>> On 9/25/07 10:53 AM, "Pankaj Jaiswal" <pj37 at cornell.edu> wrote:
>> 
>>> 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.
>> 
>> This Fri is out for me - but next one would be ok if it seems we
>> need to
>> talk.
>> 
>> With well-studied genes there will be many alleles annotated to a
>> PO term.
>> Is the PO database is OK taking in multiple rows that differ only
>> in the
>> 'column 8' listing of alleles?
>>   m
>> 
>> 
>> _______________________________________________
>> Po-dev mailing list
>> Po-dev at plantontology.org
>> http://mail.plantontology.org/mailman/listinfo/po-dev
> 

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