<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 12 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.Section1
{page:Section1;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=EN-US link=blue vlink=purple>
<div class=Section1>
<p class=MsoNormal>I’m getting exceptions while attempting to load RefSeq
into CHADO with gmod_bulk_load_gff3.pl. I was able to load S. cerevisiae OK, so
I assume I have a mostly good installation. But the human ref seq files are
failing with errors, depending on chromosome, such as<o:p></o:p></p>
<p class=MsoNormal>MSG: no cvterm for processed_transcript<o:p></o:p></p>
<p class=MsoNormal>or<o:p></o:p></p>
<p class=MsoNormal>MSG: no cvterm for Region<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I found that there is a “region” but not a “Region”,
so this means pgsql is case sensitive?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I followed the instructions for loading ontologies in the
INSTALL.Chado file and selected all optional ontologies. Then I followed the
Load RefSeq into Chado wiki up to the point where is says to run gmod_load_gff3.pl,
could not be found, so I’m using gmod_bulk_load_gff3.pl.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Can you give me some advice?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-size:9.0pt'>Michael Yourshaw<br>
<br>
<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:9.0pt'>UCLA Geffen School of Medicine<br>
Department of Human Genetics, Nelson Lab<br>
695 Charles E Young Drive S<br>
Gonda 5554<br>
Los Angeles CA 90095-8348 USA<br>
<span style='color:#1F497D'><a href="mailto:myourshaw@ucla.edu"><span
style='color:blue'>myourshaw@ucla.edu</span></a><br>
</span></span><span style='font-size:9.0pt'>970.691.8299<br>
<br>
</span><span style='font-size:9.0pt'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:7.0pt;color:#1F497D'>This message is
intended only for the use of the addressee and may contain information that is
PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you
are not the intended recipient, you are hereby notified that any dissemination
of this communication is strictly prohibited. If you have received this
communication in error, please erase all copies of the message and its
attachments and notify us immediately. Thank you.</span><o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
</div>
</body>
</html>