NAME
Bio::Chado::Schema - A standard DBIx::Class layer for the Chado database schema.
SYNOPSIS
use Bio::Chado::Schema;
my $chado = Bio::Chado::Schema->connect( $dsn, $user, $password );
print "number of rows in feature table: ",
$chado->resultset('Sequence::Feature')->count,
"\n";DESCRIPTION
This is a standard object-relational mapping layer for use with the GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of the very fine DBIx::Class::Schema::Loader module.
Chado is an open-source modular database schema for biological data. It is divided into several notional "modules", which are reflected in the namespace organization of this package. Note that modules in the Chado context refers to sets of tables, they are not modules in the Perl sense.
GETTING STARTED
To learn how to use this DBIx::Class ORM layer, a good starting point is the DBIx::Class::Manual.
CHADO MODULES COVERED BY THIS PACKAGE
Bio::Chado::Schema::Companalysis
Bio::Chado::Schema::Expression
Bio::Chado::Schema::NaturalDiversity
CHADO VERSIONS
Basically, BCS has always followed the SVN HEAD of Chado, since it's on a much faster release cycle than Chado itself.
Most users will not experience incompatibilities using the most recent versions of Bio::Chado::Schema with older Chado installations. However, if you encounter problems using Bio::Chado::Schema with an older Chado schema, you may want to try downgrading to an earlier version of Bio::Chado::Schema. The following rough equivalencies hold between BCS and Chado versions:
Chado 1.2 -- BCS 0.09000
Chado 1.11 -- BCS 0.05801
Chado 1.1 -- BCS 0.05801
older -- BCS 0.03100SCHEMA OBJECT METHODS
get_cvterm( "$cv_name:$cvterm_name" ) OR get_cvterm( $cv_name, $cvterm_name )
Convenience method to for finding single cvterms based on the text name of the CV and the term. The cvterm objects found with this method are cached in the schema object itself. Thus, you only use this function in the (relatively common) scenario in which you just need convenient access to a handful of different cvterms.
get_cvterm_or_die
Same as get_cvterm above, but dies with a "not found" message if the cvterm is not found. This is convenient when you don't want to be bothered with checking the return value of get_cvterm, which for me is most of the time.
CLASS METHODS
plugin_add_relationship( 'ChadoModule::SourceName', 'reltype', @args )
Sometimes application-specific plugins need to add relationships to the core BCS classes. It can't just be done normally from inside the classes of the plugins, you need to use this method.
Example: Bio::Chado::Schema::Result::MyApp::SpecialThing belongs_to the core BCS Organism::Organism, and you would like to be able to call $organism->myapp_specialthings on organisms to get their associated SpecialThings.
package Bio::Chado::Schema::MyApp::Result::SpecialThing;
# ( do table and column definitions and so forth here )
Bio::Chado::Schema->plugin_add_relationship(
'Organism::Organism', 'has_many', (
"myapp_specialthings",
"Bio::Chado::Schema::MyApp::Result::Foo",
{ "foreign.organism_id" => "self.organism_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
);AUTHOR
Robert Buels, <rmb32@cornell.edu>
CONTRIBUTORS
Naama Menda, <nm249@cornell.edu>
Aureliano Bombarely, <ab782@cornell.edu>
Jonathan "Duke" Leto, <jonathan@leto.net>