Hi Zhuang,<div><br></div><div>It looks like the Sequence Ontology is not loaded into the database. Do you remember if SO was loaded during the Chado install? See the make ontologies step of the INSTALL document:</div><div>
<a href="http://gmod.svn.sourceforge.net/viewvc/gmod/schema/trunk/chado/INSTALL.Chado?view=markup">http://gmod.svn.sourceforge.net/viewvc/gmod/schema/trunk/chado/INSTALL.Chado?view=markup</a><br><br></div><div>If it wasn't you can rerun make ontologies and specify SO. If this step was skipped entirely then you'll want to load several others too. See the install doc.</div>
<div><br></div><div>Dave C</div><div><br><div class="gmail_quote">On Mon, May 31, 2010 at 3:19 AM, zhuang chao <span dir="ltr"><<a href="mailto:freeoser@163.com">freeoser@163.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
hi , Dave :<br>
<br>
When I was loading the gff3 file into chado database using<br>
<br>
<a href="http://gmod_bulk_load_gff3.pl" target="_blank">gmod_bulk_load_gff3.pl</a>, I got the errors like this:<br>
<br>
==================================================<br>
MSG: no cvterm for protein<br>
===================================================<br>
<br>
I replaced 'protein' with 'polypeptide' in the gff<br>
<br>
file . And the sequence ontology was loaded in chado<br>
<br>
database. But I got the errors like this:<br>
<br>
===============================<br>
MSG: no cvterm for polypeptide<br>
================================<br>
<br>
Could you help me? Thank you very much !<br>
<br>
<br>
The gff file is in the attachment . It was compressed by<br>
<br>
tar . Here is a history of how I loaded previous data .<br>
<br>
=======================================================================<br>
<br>
root@debian:/home/zc/Downloads#<br>
perl /usr/local/bin/<a href="http://gmod_bulk_load_gff3.pl" target="_blank">gmod_bulk_load_gff3.pl</a> --gfffile<br>
sequences.gp.gff --organism 'abcd1' --dbname four_viruses --dbuser zc<br>
--dbpass 123456 --dbhost localhost --dbport 5432 --recreate_cache<br>
--noexon<br>
(Re)creating the uniquename cache in the database...<br>
Creating table...<br>
Populating table...<br>
Creating indexes...Done.<br>
Preparing data for inserting into the four_viruses database<br>
(This may take a while ...)<br>
<br>
------------- EXCEPTION: Bio::Root::Exception -------------<br>
MSG: no cvterm for polypeptide<br>
STACK: Error::throw<br>
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368<br>
STACK:<br>
Bio::GMOD::DB::Adapter::get_type /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm:4050<br>
STACK: /usr/local/bin/<a href="http://gmod_bulk_load_gff3.pl:755" target="_blank">gmod_bulk_load_gff3.pl:755</a><br>
-----------------------------------------------------------<br>
Issuing rollback() due to DESTROY without explicit disconnect() of<br>
DBD::Pg::db handle dbname=four_viruses;port=5432;host=localhost<br>
at /usr/share/perl5/Error.pm line 184.<br>
<br>
========================================================================<br>
<br>
<br>
<br>
<br>
On Fri, 2010-05-28 at 13:33 -0700, Dave Clements, GMOD Help Desk wrote:<br>
> Hi Zhuang,<br>
><br>
><br>
> Protein is not a first class term in the Sequence Ontology. It is a<br>
> synonym from "polypeptide".<br>
> See <a href="http://www.sequenceontology.org/miso/current_release/term/SO:0000104" target="_blank">http://www.sequenceontology.org/miso/current_release/term/SO:0000104</a>. Does the load work if you change all your "protein" to "polypeptide"? IF it still doesn't work, then the sequence ontology may not be loaded in your database.<br>
><br>
><br>
> Dave C.<br>
><br>
> On Fri, May 28, 2010 at 1:09 AM, simon rayner<br>
> <<a href="http://simon.rayner.cn" target="_blank">simon.rayner.cn</a>@<a href="http://gmail.com" target="_blank">gmail.com</a>> wrote:<br>
> Zhuang,<br>
><br>
> it could be there is an extra or missing <TAB> character in<br>
> that line for that entry in the GFF3 file. Can you post the<br>
> dump for the entry<br>
><br>
> simon<br>
><br>
><br>
> On Fri, May 28, 2010 at 3:40 AM, zhuang chao<br>
> <<a href="mailto:freeoser@163.com">freeoser@163.com</a>> wrote:<br>
> hi , all :<br>
><br>
> When I was loading the gff3 file into chado database<br>
> using<br>
> <a href="http://gmod_bulk_load_gff3.pl" target="_blank">gmod_bulk_load_gff3.pl</a>, I got the errors like this:<br>
><br>
> ==================================================<br>
> MSG: no cvterm for protein<br>
> ===================================================<br>
><br>
> I don't know why and how to handle. Could you help<br>
> me? I am looking<br>
><br>
> forward to your reply. Thank you very much !<br>
><br>
> Here is a history of how I loaded previous<br>
> data .<br>
><br>
> =======================================================================<br>
><br>
><br>
> root@debian:/home/zc/Downloads#<br>
> perl /usr/local/bin/<a href="http://gmod_bulk_load_gff3.pl" target="_blank">gmod_bulk_load_gff3.pl</a> --gfffile<br>
> sequences.gp.gff --organism 'abcd1' --dbname<br>
> four_viruses --dbuser zc<br>
> --dbpass 123456 --dbhost localhost --dbport 5432<br>
> --noexon<br>
><br>
> Preparing data for inserting into the four_viruses<br>
> database<br>
> (This may take a while ...)<br>
><br>
> ------------- EXCEPTION: Bio::Root::Exception<br>
> -------------<br>
> MSG: no cvterm for protein<br>
> STACK: Error::throw<br>
> STACK:<br>
> Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368<br>
> STACK:<br>
> Bio::GMOD::DB::Adapter::get_type /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm:4050<br>
> STACK: /usr/local/bin/<a href="http://gmod_bulk_load_gff3.pl:755" target="_blank">gmod_bulk_load_gff3.pl:755</a><br>
> -----------------------------------------------------------<br>
> Issuing rollback() due to DESTROY without explicit<br>
> disconnect() of<br>
> DBD::Pg::db handle<br>
> dbname=four_viruses;port=5432;host=localhost<br>
> at /usr/share/perl5/Error.pm line 184.<br>
> ===================================================================================<br>
><br>
><br>
><br>
><br>
><br>
><br>
> --<br>
><br>
><br>
> Simon Rayner<br>
><br>
> State Key Laboratory of Virology<br>
> Wuhan Institute of Virology<br>
> Chinese Academy of Sciences<br>
> Wuhan, Hubei 430071<br>
> P.R.China<br>
><br>
> +86 (27) 87199895 (office)<br>
> +86 15972923715 (cell)<br>
><br>
><br>
><br>
> ------------------------------------------------------------------------------<br>
><br>
><br>
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