NAME

Bio::Chado::Schema::Stock::Stock

DESCRIPTION

Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.

NAME

Bio::Chado::Schema::Stock::Stock

ACCESSORS

stock_id

data_type: 'integer'
is_auto_increment: 1
is_nullable: 0
sequence: 'stock_stock_id_seq'

dbxref_id

data_type: 'integer'
is_foreign_key: 1
is_nullable: 1

The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.

organism_id

data_type: 'integer'
is_foreign_key: 1
is_nullable: 1

The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined.

name

data_type: 'varchar'
is_nullable: 1
size: 255

The name is a human-readable local name for a stock.

uniquename

data_type: 'text'
is_nullable: 0

description

data_type: 'text'
is_nullable: 1

The description is the genetic description provided in the stock list.

type_id

data_type: 'integer'
is_foreign_key: 1
is_nullable: 0

The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.

is_obsolete

data_type: 'boolean'
default_value: false
is_nullable: 0

RELATIONS

nd_experiment_stocks

Type: has_many

Related object: Bio::Chado::Schema::NaturalDiversity::NdExperimentStock

dbxref

Type: belongs_to

Related object: Bio::Chado::Schema::General::Dbxref

type

Type: belongs_to

Related object: Bio::Chado::Schema::Cv::Cvterm

organism

Type: belongs_to

Related object: Bio::Chado::Schema::Organism::Organism

stockcollection_stocks

Type: has_many

Related object: Bio::Chado::Schema::Stock::StockcollectionStock

stock_cvterms

Type: has_many

Related object: Bio::Chado::Schema::Stock::StockCvterm

stock_dbxrefs

Type: has_many

Related object: Bio::Chado::Schema::Stock::StockDbxref

stock_genotypes

Type: has_many

Related object: Bio::Chado::Schema::Stock::StockGenotype

stockprops

Type: has_many

Related object: Bio::Chado::Schema::Stock::Stockprop

stock_pubs

Type: has_many

Related object: Bio::Chado::Schema::Stock::StockPub

stock_relationship_subjects

Type: has_many

Related object: Bio::Chado::Schema::Stock::StockRelationship

stock_relationship_objects

Type: has_many

Related object: Bio::Chado::Schema::Stock::StockRelationship

create_stockprops

Usage: $set->create_stockprops({ baz => 2, foo => 'bar' });
Desc : convenience method to create stock properties using cvterms
        from the ontology with the given name
Args : hashref of { propname => value, ...},
       options hashref as:
        {
          autocreate => 0,
             (optional) boolean, if passed, automatically create cv,
             cvterm, and dbxref rows if one cannot be found for the
             given stockprop name.  Default false.

          cv_name => cv.name to use for the given stockprops.
                     Defaults to 'stock_property',

          db_name => db.name to use for autocreated dbxrefs,
                     default 'null',

          dbxref_accession_prefix => optional, default
                                     'autocreated:',
          definitions => optional hashref of:
              { cvterm_name => definition,
              }
           to load into the cvterm table when autocreating cvterms

           rank => force numeric rank. Be careful not to pass ranks that already exist
                   for the property type. The function will die in such case.

           allow_duplicate_values => default false.
              If true, allow duplicate instances of the same stock
              and value in the properties of the stock.  Duplicate
              values will have different ranks.
        }
Ret  : hashref of { propname => new stockprop object }

AUTHOR

Robert Buels <rbuels@cpan.org>

COPYRIGHT AND LICENSE

This software is copyright (c) 2009 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.

cpanm Bio::Chado::Schema

perl -MCPAN -e shell
install Bio::Chado::Schema