[Gmod-help] Re: [Gmod-schema] a question of loading data into chado (no attachment)

[zhuang chao]

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)
>         
>         
>         
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