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

  Usage: $set->create_stockprops({ baz => 2, foo => 'bar' });
  Desc : convenience method to create stock properties using stocks
          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:
                { stock_name => definition,
                }
             to load into the stock table when autocreating stocks

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

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