<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>Please find my answers below. You are welcome to add your comments. </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 24, 2007, at 5:39 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">Shuly, Chih-Wei and group.<BR> <BR> Getting ready to send in new MaizeGDB associations files and have a few questions about format since I last did this.<BR> <BR> Looking at the cvs, it seem we are taking in associations to:<BR> genes<BR> QTL<BR> stocks or germplasm (Mutant)<BR> QUESTION: Others? <BR></SPAN></FONT></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>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?</DIV><BR><BLOCKQUOTE type="cite"><FONT face="Verdana, Helvetica, Arial"><SPAN style="font-size:12.0px"> <BR> It seems on our new, and rather swank interface, that there is a slot for ‘sequence’ and when null, it states:<BR> No peptide sequence available.<BR> For example, look up pericarp,<BR> then the Arabidopsis gene ‘CYP707A1’<BR> But, when I look at the record in question at TAIR, it seems there must be some peptide sequence. <BR> QUESTOIN: So, what is this field all about? OR rather, what must be done to populate it?<BR></SPAN></FONT></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV>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. </DIV><DIV><BR><BLOCKQUOTE type="cite"><FONT face="Verdana, Helvetica, Arial"><SPAN style="font-size:12.0px"> <BR> In the same record, there is a column indicating that it has a GO association?<BR> QUESTION: how does that get into the PO browser? <BR> <BR></SPAN></FONT></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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. </DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I just checked GOC database and didn't find any maize gene products, are you planning to provide any maize GO annotations to them?</DIV><BR><BLOCKQUOTE type="cite"><FONT face="Verdana, Helvetica, Arial"><SPAN style="font-size:12.0px"> <BR> Is there anything else I should be doing? <BR> <BR> Mary<BR class="khtml-block-placeholder"></SPAN></FONT></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>As long as your association files follow the guideline <A href="http://www.plantontology.org/docs/otherdocs/assoc-file-format.html">http://www.plantontology.org/docs/otherdocs/assoc-file-format.html</A>, you can submit the files any time. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Chih-Wei</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR><DIV><BR class="khtml-block-placeholder"></DIV><BR><BLOCKQUOTE type="cite"><FONT face="Verdana, Helvetica, Arial"><SPAN style="font-size:12.0px"> -- <BR> </SPAN></FONT><BLOCKQUOTE type="cite"><FONT face="Verdana, Helvetica, Arial"><SPAN style="font-size:12.0px"><I>Mary Schaeffer, PhD (f/k/a Mary Polacco)<BR> Geneticist/Curator MaizeGDB<BR> USDA/ARS Plant Genetics Research Unit<BR> 203 Curtis Hall<BR> Adj Assoc Professor<BR> Division of Plant Sciences<BR> University of Missouri<BR> Columbia, MO 65211<BR> Phone: 573 884 7873<BR> FAX: 573 884 7850<BR> </I></SPAN></FONT></BLOCKQUOTE><FONT face="Verdana, Helvetica, Arial"><SPAN style="font-size:12.0px"><BR> <BR> <BR> </SPAN></FONT> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>