[Gmod-help] Re: [Gmod-schema] a question of loading data into chado (an attachment)
Scott Cain
scott at scottcain.net
Tue Jun 1 16:33:47 EDT 2010
Hi Dave,
I already answered Zhuang on another thread (he seems to have
several); he had "polypeptide " with a trailing space.
Scott
On Tue, Jun 1, 2010 at 4:12 PM, Dave Clements, GMOD Help Desk
<help at gmod.org> wrote:
> Hi Zhuang,
> 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:
> http://gmod.svn.sourceforge.net/viewvc/gmod/schema/trunk/chado/INSTALL.Chado?view=markup
>
> 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.
> Dave C
> On Mon, May 31, 2010 at 3:19 AM, zhuang chao <freeoser at 163.com> wrote:
>>
>> hi , Dave :
>>
>> When I was loading the gff3 file into chado database using
>>
>> gmod_bulk_load_gff3.pl, I got the errors like this:
>>
>> ==================================================
>> MSG: no cvterm for protein
>> ===================================================
>>
>> I replaced 'protein' with 'polypeptide' in the gff
>>
>> file . And the sequence ontology was loaded in chado
>>
>> database. But I got the errors like this:
>>
>> ===============================
>> MSG: no cvterm for polypeptide
>> ================================
>>
>> Could you help me? Thank you very much !
>>
>>
>> The gff file is in the attachment . It was compressed by
>>
>> tar . Here is a history of how I loaded previous data .
>>
>> =======================================================================
>>
>> root at debian:/home/zc/Downloads#
>> perl /usr/local/bin/gmod_bulk_load_gff3.pl --gfffile
>> sequences.gp.gff --organism 'abcd1' --dbname four_viruses --dbuser zc
>> --dbpass 123456 --dbhost localhost --dbport 5432 --recreate_cache
>> --noexon
>> (Re)creating the uniquename cache in the database...
>> Creating table...
>> Populating table...
>> Creating indexes...Done.
>> Preparing data for inserting into the four_viruses database
>> (This may take a while ...)
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: no cvterm for polypeptide
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368
>> STACK:
>> Bio::GMOD::DB::Adapter::get_type
>> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm:4050
>> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:755
>> -----------------------------------------------------------
>> Issuing rollback() due to DESTROY without explicit disconnect() of
>> DBD::Pg::db handle dbname=four_viruses;port=5432;host=localhost
>> at /usr/share/perl5/Error.pm line 184.
>>
>> ========================================================================
>>
>>
>>
>>
>> On Fri, 2010-05-28 at 13:33 -0700, Dave Clements, GMOD Help Desk wrote:
>> > Hi Zhuang,
>> >
>> >
>> > Protein is not a first class term in the Sequence Ontology. It is a
>> > synonym from "polypeptide".
>> > See
>> > http://www.sequenceontology.org/miso/current_release/term/SO:0000104. 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.
>> >
>> >
>> > Dave C.
>> >
>> > On Fri, May 28, 2010 at 1:09 AM, simon rayner
>> > <simon.rayner.cn at gmail.com> wrote:
>> > Zhuang,
>> >
>> > it could be there is an extra or missing <TAB> character in
>> > that line for that entry in the GFF3 file. Can you post the
>> > dump for the entry
>> >
>> > simon
>> >
>> >
>> > On Fri, May 28, 2010 at 3:40 AM, zhuang chao
>> > <freeoser at 163.com> wrote:
>> > hi , all :
>> >
>> > When I was loading the gff3 file into chado database
>> > using
>> > gmod_bulk_load_gff3.pl, I got the errors like this:
>> >
>> > ==================================================
>> > MSG: no cvterm for protein
>> > ===================================================
>> >
>> > I don't know why and how to handle. Could you help
>> > me? I am looking
>> >
>> > forward to your reply. Thank you very much !
>> >
>> > Here is a history of how I loaded previous
>> > data .
>> >
>> >
>> > =======================================================================
>> >
>> >
>> > root at debian:/home/zc/Downloads#
>> > perl /usr/local/bin/gmod_bulk_load_gff3.pl --gfffile
>> > sequences.gp.gff --organism 'abcd1' --dbname
>> > four_viruses --dbuser zc
>> > --dbpass 123456 --dbhost localhost --dbport 5432
>> > --noexon
>> >
>> > Preparing data for inserting into the four_viruses
>> > database
>> > (This may take a while ...)
>> >
>> > ------------- EXCEPTION: Bio::Root::Exception
>> > -------------
>> > MSG: no cvterm for protein
>> > STACK: Error::throw
>> > STACK:
>> > Bio::Root::Root::throw
>> > /usr/share/perl5/Bio/Root/Root.pm:368
>> > STACK:
>> > Bio::GMOD::DB::Adapter::get_type
>> > /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm:4050
>> > STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:755
>> >
>> > -----------------------------------------------------------
>> > Issuing rollback() due to DESTROY without explicit
>> > disconnect() of
>> > DBD::Pg::db handle
>> > dbname=four_viruses;port=5432;host=localhost
>> > at /usr/share/perl5/Error.pm line 184.
>> >
>> > ===================================================================================
>> >
>> >
>> >
>> >
>> >
>> >
>> > --
>> >
>> >
>> > Simon Rayner
>> >
>> > State Key Laboratory of Virology
>> > Wuhan Institute of Virology
>> > Chinese Academy of Sciences
>> > Wuhan, Hubei 430071
>> > P.R.China
>> >
>> > +86 (27) 87199895 (office)
>> > +86 15972923715 (cell)
>> >
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> >
>> >
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > Gmod-schema at lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>> >
>> >
>> > --
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>
>
>
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--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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