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: 1The 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: 1The 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: 255The name is a human-readable local name for a stock.
uniquename
data_type: 'text'
is_nullable: 0description
data_type: 'text'
is_nullable: 1The description is the genetic description provided in the stock list.
type_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 0The 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: 0RELATIONS
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