<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Mary,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>This sounds great, thank you for being supportive. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The link I mention here is the gene(or locus) page link in MaizeGDB, e.g. <A href="http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=12021">http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=12021</A>. Is this page URL a stable link? We would like to provide this link in the POC annotation detail page (<A href="http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=gp&session_id=4263b1190752135&gp=12021">http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=gp&session_id=4263b1190752135&gp=12021</A>), the current linkout to MaizeGDB is not working properly.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Chih-Wei</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On Sep 25, 2007, at 3:59 PM, Mary (Polacco) Schaeffer wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> <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" <<A href="mailto:cwt6@cornell.edu">cwt6@cornell.edu</A>> 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> > <A href="http://www.plantontology.org/amigo/go.cgi?">www.plantontology.org/amigo/go.cgi?</A> <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" <<A href="mailto:pj37@cornell.edu">pj37@cornell.edu</A>> 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> >> <A href="mailto:Po-dev@plantontology.org">Po-dev@plantontology.org</A><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> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>