Bio::Chado::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 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.

To learn how to use this DBIx::Class ORM layer, a good starting point is the DBIx::Class::Manual.

Bio::Chado::Schema - A standard DBIx::Class layer for the Chado database schema.

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

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 },
        );
    );

Robert Buels, <rmb32@cornell.edu>

Aureliano Bombarely, <ab782@cornell.edu>

Naama Menda, <nm249@cornell.edu>

Jonathan "Duke" Leto, <jonathan@leto.net>

Copyright 2009 Boyce Thompson Institute for Plant Research

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

Robert Buels <rbuels@cpan.org>

This software is copyright (c) 2011 by Robert Buels.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.