all right Dave!<br><br>thank you!<br><br><div class="gmail_quote">2009/7/2 Dave Clements, GMOD Help Desk <span dir="ltr"><<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Fernando,<br>
<br>
You also need to load the Chado feature properties ontology, which my<br>
memory tell me can also be loaded with make ontologies.<br>
<div><div></div><div class="h5"><br>
On Wed, Jul 1, 2009 at 11:06 AM, fernando bueno<<a href="mailto:stradlinbueno@gmail.com">stradlinbueno@gmail.com</a>> wrote:<br>
> an using the sequence ontology appears this error<br>
><br>
><br>
> Preparing data for inserting into the chado database<br>
> (This may take a while ...)<br>
><br>
> ------------- EXCEPTION: Bio::Root::Exception -------------<br>
> MSG: I couldn't find the 'Note' cvterm in the database;<br>
> Did you load the feature property controlled vocabulary?<br>
> STACK: Error::throw<br>
> STACK: Bio::Root::Root::throw<br>
> /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:357<br>
> STACK: Bio::GMOD::DB::Adapter::handle_note<br>
> /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm:3512<br>
> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:908<br>
> -----------------------------------------------------------<br>
> Issuing rollback() due to DESTROY without explicit disconnect() of<br>
> DBD::Pg::db handle dbname=chado;port=5432;host=localhost at<br>
> /usr/local/share/perl/5.10.0/Error.pm line 184.<br>
><br>
><br>
> 2009/7/1 fernando bueno <<a href="mailto:stradlinbueno@gmail.com">stradlinbueno@gmail.com</a>><br>
>><br>
>> hello Dave!<br>
>><br>
>><br>
>> the steps related in chado install were executed.<br>
>> this erro appears when I execute the commans listed in this How to<br>
>><br>
>> <a href="http://gmod.org/wiki/Load_GFF_Into_Chado" target="_blank">http://gmod.org/wiki/Load_GFF_Into_Chado</a><br>
>><br>
>><br>
>> forgive my poor english!<br>
>><br>
>><br>
>> thank you!<br>
>><br>
>><br>
>> Fernando<br>
>><br>
>><br>
>> 2009/6/30 Dave Clements, GMOD Help Desk <<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>><br>
>>><br>
>>> Hi Fernando,<br>
>>><br>
>>> Chromosome is a defined term in the sequence ontology. I believe this<br>
>>> error means that either the "make ontologies" step was not run, or<br>
>>> their was a problem with it. Was this step run? Were the<br>
>>> relationship and sequence ontologies loaded?<br>
>>><br>
>>> See<br>
>>><br>
>>> <a href="http://gmod.cvs.sourceforge.net/*checkout*/gmod/schema/chado/INSTALL.Chado" target="_blank">http://gmod.cvs.sourceforge.net/*checkout*/gmod/schema/chado/INSTALL.Chado</a><br>
>>> for more on the make ontologies step.<br>
>>><br>
>>> Cheers,<br>
>>><br>
>>> Dave C.<br>
>>><br>
>>> On Mon, Jun 29, 2009 at 10:33 AM, fernando bueno<<a href="mailto:stradlinbueno@gmail.com">stradlinbueno@gmail.com</a>><br>
>>> wrote:<br>
>>> > Hi!<br>
>>> ><br>
>>> > I'm from Brazil. I'm with a problem to insert data in my CHADO schema.<br>
>>> > When the command :<br>
>>> > gmod_bulk_load_gff3.pl --organism yeast saccharomyces_cerevisiae.gff<br>
>>> > is executed, this error appears:<br>
>>> ><br>
>>> > ------------- EXCEPTION: Bio::Root::Exception -------------<br>
>>> > MSG: no cvterm for chromosome<br>
>>> > STACK: Error::throw<br>
>>> > STACK: Bio::Root::Root::throw<br>
>>> > /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:357<br>
>>> > STACK: Bio::GMOD::DB::Adapter::get_type<br>
>>> > /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm:4224<br>
>>> > STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:783<br>
>>> > -----------------------------------------------------------<br>
>>> > Issuing rollback() due to DESTROY without explicit disconnect() of<br>
>>> > DBD::Pg::db handle dbname=chado;port=5432;host=localhost at<br>
>>> > /usr/local/share/perl/5.10.0/Error.pm line 184.<br>
>>> ><br>
>>> ><br>
>>> > could your help me?<br>
>>> ><br>
>>> ><br>
>>> > thanks!!!<br>
>>> ><br>
>>> ><br>
>>> > Fernando<br>
>>> ><br>
>>> ><br>
>>> ><br>
>>> > ------------------------------------------------------------------------------<br>
>>> ><br>
>>> > _______________________________________________<br>
>>> > Gmod-schema mailing list<br>
>>> > <a href="mailto:Gmod-schema@lists.sourceforge.net">Gmod-schema@lists.sourceforge.net</a><br>
>>> > <a href="https://lists.sourceforge.net/lists/listinfo/gmod-schema" target="_blank">https://lists.sourceforge.net/lists/listinfo/gmod-schema</a><br>
>>> ><br>
>>> ><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>> Was this helpful? Let us know at <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
>>><br>
>>> Learn more about GMOD at:<br>
>>> ISMB/ECCB: <a href="http://www.iscb.org/ismbeccb2009/" target="_blank">http://www.iscb.org/ismbeccb2009/</a><br>
>>> (BioMart, Chado, Galaxy, InterMine)<br>
>><br>
><br>
><br>
<br>
<br>
<br>
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