A standard dbix::class layer for the chado database schema.
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";
This is a standard object-relational mapping layer for use with the \s-1GMOD\s0 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 \*(L"modules\*(R", 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.
To learn how to use this DBIx::Class \s-1ORM\s0 layer, a good starting point is the DBIx::Class::Manual.
Bio::Chado::Schema::CellLine
Bio::Chado::Schema::Companalysis
Bio::Chado::Schema::Composite
Bio::Chado::Schema::Contact
Bio::Chado::Schema::Cv
Bio::Chado::Schema::Expression
Bio::Chado::Schema::General
Bio::Chado::Schema::Genetic
Bio::Chado::Schema::Library
Bio::Chado::Schema::Mage
Bio::Chado::Schema::Map
Bio::Chado::Schema::NaturalDiversity
Bio::Chado::Schema::Organism
Bio::Chado::Schema::Phenotype
Bio::Chado::Schema::Phylogeny
Bio::Chado::Schema::Project
Bio::Chado::Schema::Pub
Bio::Chado::Schema::Sequence
Bio::Chado::Schema::Stock
Basically, \s-1BCS\s0 has always followed the \s-1SVN\s0 \s-1HEAD\s0 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 \s-1BCS\s0 and Chado versions:
Chado 1.2 -- BCS 0.09000 Chado 1.11 -- BCS 0.05801 Chado 1.1 -- BCS 0.05801 older -- BCS 0.03100
Convenience method to for finding single cvterms based on the text name of the \s-1CV\s0 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.
Same as get_cvterm above, but dies with a \*(L"not found\*(R" message if the cvterm is not found. This is convenient when you don't want to be bothered with checking the return value of \*(C`get_cvterm\*(C', which for me is most of the time.
Sometimes application-specific plugins need to add relationships to the core \s-1BCS\s0 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 \s-1BCS\s0 Organism::Organism, and you would like to be able to call \*(C`$organism->myapp_specialthings\*(C' 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 }, ); );
Robert Buels, <[email protected]>
Naama Menda, <[email protected]>
Aureliano Bombarely, <[email protected]>
Jonathan \*(L"Duke\*(R" Leto, <[email protected]>