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<TITLE>Re: [Po-dev] RE: Questions about associations</TITLE>
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<FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>Hi Chih-Wei,<BR>
<BR>
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. <BR>
<BR>
As FYI, most loci with associations inferred from phenotype (IMP) have one or two alleles <B>that have associations to one or more anatomy terms</B>. 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. <BR>
<BR>
Re links to MaizeGDB – there is a stable link: provided 2-3 years ago – not sure where the link you have below came from?<BR>
<BR>
</SPAN></FONT><FONT SIZE="1"><FONT FACE="Monaco, Courier New"><SPAN STYLE='font-size:9.0px'>> We have a hyperlink prefix that works for any ID in MaizeGDB, regardless<BR>
> of<BR>
> object type:<BR>
><BR>
> <FONT COLOR="#0000FF"><U><a href="http://www.maizegdb.org/cgi-bin/id_search.cgi?id">http://www.maizegdb.org/cgi-bin/id_search.cgi?id</a></U></FONT>=<BR>
><BR>
<BR>
<FONT COLOR="#0000FF"><U><a href="http://www.maizegdb.org/cgi-bin/id_search.cgi?id">http://www.maizegdb.org/cgi-bin/id_search.cgi?id</a></U></FONT>=12327<BR>
<BR>
><BR>
</SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'><BR>
Let me know if this works for you,<BR>
<BR>
mary<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
On 9/25/07 1:47 PM, "Chih-Wei Tung" <cwt6@cornell.edu> wrote:<BR>
<BR>
<FONT COLOR="#0000FF">> Hi Mary,<BR>
> <BR>
> I am wondering if it is a practical way to display many alleles in <BR>
> POC database? I just looked at this maize gene, adh1, it has 575 <BR>
> variations/alleles (<a href="http://www.maizegdb.org/cgi-bin/">http://www.maizegdb.org/cgi-bin/</a> <BR>
> displaylocusrecord.cgi?id=12021, <a href="http://www.maizegdb.org/cgi-bin/">http://www.maizegdb.org/cgi-bin/</a> <BR>
> locusvarreport.cgi?id=12021).<BR>
> <BR>
> If most of maize genes have such huge amount of alleles, I think <BR>
> providing a external link to MaizeGDB should be sufficient. I <BR>
> searched POC database, "MaizeGDB:12021" link in this page http:// <BR>
> www.plantontology.org/amigo/go.cgi? <BR>
> view=details&search_constraint=gp&session_id=9624b1190744163&gp=12021 <BR>
> didn't direct me to the proper page in MaizeGDB. Does MaizeGDB have <BR>
> stable URL ID to link back to POC?<BR>
> <BR>
> Here is one example that GOC link back to Flybase, and users can find <BR>
> all the alleles in Flybase page (<a href="http://amigo.geneontology.org/cgi-">http://amigo.geneontology.org/cgi-</a> <BR>
> bin/amigo/go.cgi? <BR>
> search_constraint=gp&view=details&session_id=762b1190743889&gp=FBgn00032 <BR>
> 05, click "FB:FBgn0003205", it points to http:// <BR>
> flybase.bio.indiana.edu/reports/FBgn0003205.html)<BR>
> <BR>
> <BR>
> Chih-Wei<BR>
> <BR>
> <BR>
> <BR>
> On Sep 25, 2007, at 1:30 PM, Mary (Polacco) Schaeffer wrote:<BR>
> <BR>
</FONT><FONT COLOR="#008000">>> On 9/25/07 10:53 AM, "Pankaj Jaiswal" <pj37@cornell.edu> wrote:<BR>
>> <BR>
</FONT><FONT COLOR="#808080">>>> Pl take a look at the association file format section of<BR>
>>> <a href="http://plantontology.org/docs/otherdocs/assoc-file-format.html">http://plantontology.org/docs/otherdocs/assoc-file-format.html</a><BR>
>>> there in the column-8 one can enter the allele symbol suggesting that<BR>
>>> the maize gene annotation to PO term is derived from allele so and <BR>
>>> so.<BR>
>>> <BR>
>>> I will be happy to talk to you guys sometime on Friday afternoon.<BR>
</FONT><FONT COLOR="#008000">>> <BR>
>> This Fri is out for me - but next one would be ok if it seems we <BR>
>> need to<BR>
>> talk.<BR>
>> <BR>
>> With well-studied genes there will be many alleles annotated to a <BR>
>> PO term.<BR>
>> Is the PO database is OK taking in multiple rows that differ only <BR>
>> in the<BR>
>> 'column 8' listing of alleles?<BR>
>> m<BR>
>> <BR>
>> <BR>
>> _______________________________________________<BR>
>> Po-dev mailing list<BR>
>> Po-dev@plantontology.org<BR>
>> <a href="http://mail.plantontology.org/mailman/listinfo/po-dev">http://mail.plantontology.org/mailman/listinfo/po-dev</a><BR>
</FONT><FONT COLOR="#0000FF">> <BR>
</FONT></SPAN></FONT>
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