Robert Buels > Bio-Chado-Schema > Bio::Chado::Schema::Result::Stock::Stock

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NAME ^

Bio::Chado::Schema::Result::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.

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::Result::NaturalDiversity::NdExperimentStock

dbxref

Type: belongs_to

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

type

Type: belongs_to

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

organism

Type: belongs_to

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

stockcollection_stocks

Type: has_many

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

stock_cvterms

Type: has_many

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

stock_dbxrefs

Type: has_many

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

stock_genotypes

Type: has_many

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

stockprops

Type: has_many

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

stock_pubs

Type: has_many

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

stock_relationship_subjects

Type: has_many

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

stock_relationship_objects

Type: has_many

Related object: Bio::Chado::Schema::Result::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 }

ADDITIONAL METHODS ^

stock_phenotypes_rs

   Usage: $schema->resultset("Stock::Stock")->stock_phenotypes_rs($stock_rs);
   Desc:  retrieve a resultset for stock(s) with phenotyping experiments with the following values mapped to [column name]
          stock_id [stock_id]
          phenotype.value [value]
          observable.name [observable] (the cvterm name for the phenotype.observable field)
          observable_cvterm_id [observable_id]
          observable.definition [definition]
          unit_name (from phenotype_cvterm)
          cv_name (the cv_name for the phenotype_cvterm)
          type_name (the cvterm name for the phenotype_cvterm)
          method_name (a phenotypeprop value)
          dbxref.accession [accession] of the observable cvterm
          db.name of the observable cvterm [db_name] (useful for constructing the ontology ID of the observable)
          project.description [project_description] (useful for grouping phenotype values by projects)
   Args:  a L<Bio::Chado::Schema::Result::Stock::Stock>  resultset
   Ret:   a resultset with the above columns. Access the data with e.g. $rs->get_column('stock_id')

recursive_phenotypes_rs

    Usage: $schema->resultset("Stock::Stock")->recursive_phenotypes_rs($stock_rs, \@results)
    Desc: Retrieve recursively phenotypes of stock objects and their subjects
    Args: Stock resultSet and an arrayref with the results
    Ret: listref of stock_phenotypes_rs (see function stock_phenotypes_rs for columns fetched)

stock_genotypes_rs

   Usage: $schema->resultset("Stock::Stock")->stock_genotypes_rs($stock_rs);
   Desc:  retrieve a resultset for stock(s) with genotyping experiments
          with the following values mapped to [column name]
          stock_id [stock_id]
          genotype.name [name]
          genotype.uniquname [uniquename]
          genotype.description [description]
          genotype.type.name [type_name] (the cvterm name for the genotype type)
          propvalue [propvalue] (a genotypeprop value)

   Args:  a L<Bio::Chado::Schema::Result::Stock::Stock> resultset
   Ret:   a resultset with the above columns. Access the data with e.g. $rs->get_column('stock_id')

stock_project_phenotypes

   Usage: $schema->resultset("Stock::Stock")->stock_project_phenotypes($stock_rs);
   Desc:  retrieve a list of phenotype resultsets by project name
   Args:  a L<Bio::Chado::Schema::Result::Stock::Stock> object or a stock resultset
   Ret:   hashref key = project descriptions, values = hash ref of
          {phenotypes} = phenotype resultset
          {project}   =  L<Bio::Chado::Schema::Result::Project::Project> object
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