[Gmod-schema] include a sequenceontology.obo into my chado database

[Filipe B. <fil...@gm...>]

Hi,

I am facing some major problems with my database. I want to include data.gff
on it, but this is revealing itself, quite more complicated than what i was
expecting.
When i installed chado schema, i ran the ./build ontologies and I've choose
the 3 ontologies out of 5. But now, i when i want to insert data on my
database, it does not allom me to do so.
I was told that this was happening because, the database and the computer
itself did not know how to deal with .gff files and therefore, how to
include into the database.

I've downloaded a so.obo file from
http://song.cvs.sourceforge.net/song/ontology/so.obo?view=log (the most
recent one) and i want to include it into my database.
My question is, how can i do it?
I was trying to use the commands on the install chado readme file (above)
and it is not working...is it possible anyone, to help me please?

I was expecting that these were the commands to use:

 * $  go2fmt.pl -p obo_text -w xml /path/to/obofile | \ go-apply-xslt
oboxml_to_chadoxml - > obo_text.xml *

*this command outputs this errors:*

bash:  : command not found
No such module: GO::Parsers::obo_text.xml_parser;;
Can't locate GO/Parsers/obo_text.xml_parser.pm in @INC (@INC contains:
/usr/local/Bioperl-1.6.1 /usr/local/Bioperl-1.6.1 /usr/local/Bioperl-1.6.1
/usr/lib/perl5/site_perl/5.8.8/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
/usr/lib/perl5/5.8.8/i386-linux-thread-multi /usr/lib/perl5/5.8.8 .) at
/usr/lib/perl5/site_perl/5.8.8/GO/Parser.pm line 607.
 at /usr/lib/perl5/site_perl/5.8.8/GO/Model/Root.pm line 65
        GO::Model::Root::throw('GO::Parser=HASH(0x8e01388)', 'No such
module: GO::Parsers::obo_text.xml_parser;;\x{a}Can\'t loc...') called at
/usr/lib/perl5/site_perl/5.8.8/GO/Parser.pm line 609
        GO::Parser::load_module('GO::Parser=HASH(0x8e01388)',
'GO::Parsers::obo_text.xml_parser') called at
/usr/lib/perl5/site_perl/5.8.8/GO/Parser.pm line 575
        GO::Parser::get_parser_impl('GO::Parser=HASH(0x8e01388)',
'obo_text.xml') called at /usr/lib/perl5/site_perl/5.8.8/GO/Parser.pm line
524
        GO::Parser::new('GO::Parser', 'format', 'obo_text.xml', 'handler',
'xml') called at /usr/bin/go2fmt.pl line 45

So, therefore, i have not even tried to run this second command:

* $ stag-storenode.pl \ -d
'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
\ --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml*

Does anyone knows what should I do, or at least give me some guide lines?

My regards,
Filipe