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Bio-Chado-Schema-0.20000
River stage one • 3 direct dependents • 3 total dependents
/ Bio::Chado::Schema::Result::Stock::Stock

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