[Gmod-help] Loading new organisms into Chado

[Dave Clements, GMOD Help Desk]

Hi Barry,
I'm cross-posting my response to Don Gilbert, creator of GMODTools, and the
Chado list where others can see it.
On Fri, Apr 24, 2009 at 7:50 AM, Barry Dancis <bdancis at digiconasp.com>wrote:

> Hi --
>
>  I am trying to learn the Bulk files processing methods(
> http://gmod.org/wiki/GMODTools_TestCase) but when I ran the upload on the
> converted file into my exisitng Chado db
>
>  perl $lbin/gmod_bulk_load_gff3.pl -gfffile gff3/EU852811.gbk.gff -organism
> fromdata -dbname Chado -debug >& gmod-load.log
>
>  I got the following errors from in my log file:
>
> Preparing data for inserting into the Chado database
> (This may take a while ...)
> Organism Bio::Annotation::SimpleValue=HASH(0xa37a7d8) from data
> DBD::Pg::st fetchrow_array failed: no statement executing at
> /usr/local/share/pe
> rl/5.10.0/Bio/GMOD/DB/Adapter.pm line 1112, <GEN0> line 7.
> Bio::Annotation::SimpleValue=HASH(0xa37a7d8) organism not found in the
> database
> at /usr/local/bin/gmod_bulk_load_gff3.pl line 711, <GEN0> line 7.
> Issuing rollback() for database handle being DESTROY'd without explicit
> disconne
> ct() at /usr/local/bin/gmod_bulk_load_gff3.pl line 711.


>
>  The top of the original genbank file is
> LOCUS       EU852811               70578 bp    DNA     circular PLN
> 05-MAR-2009
> DEFINITION  Saccharomyces pastorianus Weihenstephan 34/70 mitochondrion,
>            complete genome.
> ACCESSION   EU852811
>
> and the organism is not one of the 12 that got loaded in the organism table
> during the installation of the Chado db.
>
> Is there a separate source for allowable organisms or should the bulk
> loader be able to load organisms not in the organism table?

You can define any organism by inserting it into the organism table (
http://gmod.org/wiki/Chado_Organism_Module#Table:_organism).  What I don't
know is how GMODTools maps the DEFINITION line to the organism table.  That
is, I don't know what part of "Saccharomyces pastorianus Weihenstephan 34/70
mitochondrion, complete genome." GMODTools looks for in the organism table.
Don, any advice on this?


>
> Looking at the GBrowse Configuration HOWTO document(

http://gmod.org/wiki/GBrowse_Configuration_HOWTO) it describes the use of
> bp_bulk_load_gff.pl for creating databases from scratch, but when I run
>
bp_full_load_gff.pl creates a database specifically tuned to power GBrowse.
 This is an entirely different beast than Chado.  For loading Chado, stick
with GMODTools.
Dave C.


>  perl $lbin/bp_bulk_load_gff3.pl -gfffile gff3/EU852811.gbk.gff -organism
> fromdata -dbname Chado -user postgres -passwd postgres -debug >&
> gmod-load.log
>
> I get
>
> Can't open perl script "/usr/local/bin/bp_bulk_load_gff3.pl": No such file
> or directory
>
> and I can't find the file in either the GMODTools tree or the GMOD
> installation kit.
>
> What is the diff betw gmod_bulk_load_gff3.pl and bp_bulk_load_gff3.pl? Do
>  they have diff purposes?
>
> Thanks,
>
> Barry
>
> ps I also posted this on
> http://osdir.com/ml/science.biology.gmod.devel/2008-02/msg00000.html but I
> got no reply so I am posting it again here.
>
>
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