<div dir="ltr"><div><div><div><div>Hi Cathy,<br><br>I'm so sorry that our release notes have not been updated and have mislead you. <br><br>Gramene's ontology DB is built from various ontology sources including AmiGO and Ensembl gene/marker tables. Our FTP files were last created on August of 2014.<br><br>I am bit puzzled myself about the records displayed on the FTP files as looking closely at an example (AT3G18710), they differ slightly different from other resources:<br></div><br>AmiGO:<br><a href="http://amigo.geneontology.org/amigo/gene_product/TAIR:locus:2093974">http://amigo.geneontology.org/amigo/gene_product/TAIR:locus:2093974</a><br><br>UniProt:<br><a href="http://www.uniprot.org/uniprot/Q9LSA6">http://www.uniprot.org/uniprot/Q9LSA6</a><br><br>QuickGO:<br><a href="http://www.ebi.ac.uk/QuickGO/GProtein?ac=Q9LSA6">http://www.ebi.ac.uk/QuickGO/GProtein?ac=Q9LSA6</a><br><br></div>and so are our own and Ensembl Plants records (Ontology section)...<br><br><a href="http://ensembl.gramene.org/Arabidopsis_thaliana/Gene/Summary?db=core;g=AT3G18710;r=3:6434083-6435561;t=AT3G18710.1">http://ensembl.gramene.org/Arabidopsis_thaliana/Gene/Summary?db=core;g=AT3G18710;r=3:6434083-6435561;t=AT3G18710.1</a><br></div>OR<br><a href="http://plants.ensembl.org/Arabidopsis_thaliana/Gene/Summary?g=AT3G18710;r=3:6434083-6435561;t=AT3G18710.1;db=core">http://plants.ensembl.org/Arabidopsis_thaliana/Gene/Summary?g=AT3G18710;r=3:6434083-6435561;t=AT3G18710.1;db=core</a><br><br></div>Marcela<br><div><br><div><br><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 24, 2014 at 1:22 PM, <a href="mailto:feedback@gramene.org">feedback@gramene.org</a> <span dir="ltr"><<a href="mailto:feedback@gramene.org" target="_blank">feedback@gramene.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">URL : <a href="http://gramene.org/" target="_blank">http://gramene.org/</a><br>
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Subject : Site Feedback: Gramene Ontology data on ftp site<br>
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Name : Cathy Gresham<br>
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Email : <a href="mailto:gresham@igbb.msstate.edu">gresham@igbb.msstate.edu</a><br>
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Organization: Mississippi State University Institute for Genomics, Biocomputing and Biotechnology<br>
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Comments :<br>
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I was looking at the ontology go data at<br>
<a href="ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/ontology/go" target="_blank">ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/ontology/go</a><br>
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I looked at the release notes from<br>
<a href="http://gramene.org/release-notes-42" target="_blank">http://gramene.org/release-notes-42</a><br>
It says that the ontology has not been updated since release 31 May - 2010.<br>
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Does this mean the IEA annotations have not been reviewed | run since that date? The annotations have an assign date of Aug. 2014.<br>
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I looked at one record and the uniprot_id 2 entrez gene_id mapping seems to be different between the Gramene IEA record and the UniProt website. This is easily explained if the GO annotations have not been updated since May 2010.<br>
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Thanks,<br>
Cathy<br>
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<a href="http://www.warelab.org/bugs/view.php?id=5053" target="_blank">http://www.warelab.org/bugs/view.php?id=5053</a><br>
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