[Po-dev] RE: Questions about associations

[Chih-Wei Tung]

Hi Mary,

This sounds great, thank you for being supportive.

The link I mention here is the gene(or locus) page link in MaizeGDB,  
e.g. http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi? 
id=12021.  Is this page URL a stable link? We would like to provide  
this link in the POC annotation detail page (http:// 
www.plantontology.org/amigo/go.cgi? 
view=details&search_constraint=gp&session_id=4263b1190752135&gp=12021),  
the current linkout to MaizeGDB is not working properly.

Chih-Wei


On Sep 25, 2007, at 3:59 PM, Mary (Polacco) Schaeffer wrote:

> 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=FBgn000 
> 32
> > 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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