Robert Buels > Bio-Chado-Schema-0.20000 > Bio::Chado::Schema::Result::Phenotype::Phenotype

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NAME ^

Bio::Chado::Schema::Result::Phenotype::Phenotype

DESCRIPTION ^

A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.

ACCESSORS ^

phenotype_id

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

uniquename

  data_type: 'text'
  is_nullable: 0

name

  data_type: 'text'
  is_nullable: 1

observable_id

  data_type: 'integer'
  is_foreign_key: 1
  is_nullable: 1

The entity: e.g. anatomy_part, biological_process.

attr_id

  data_type: 'integer'
  is_foreign_key: 1
  is_nullable: 1

Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.

value

  data_type: 'text'
  is_nullable: 1

Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.

cvalue_id

  data_type: 'integer'
  is_foreign_key: 1
  is_nullable: 1

Phenotype attribute value (state).

assay_id

  data_type: 'integer'
  is_foreign_key: 1
  is_nullable: 1

Evidence type.

RELATIONS ^

feature_phenotypes

Type: has_many

Related object: Bio::Chado::Schema::Result::Phenotype::FeaturePhenotype

nd_experiment_phenotypes

Type: has_many

Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentPhenotype

assay

Type: belongs_to

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

attr

Type: belongs_to

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

observable

Type: belongs_to

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

cvalue

Type: belongs_to

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

phenotype_comparison_phenotype1s

Type: has_many

Related object: Bio::Chado::Schema::Result::Genetic::PhenotypeComparison

phenotype_comparison_phenotype2s

Type: has_many

Related object: Bio::Chado::Schema::Result::Genetic::PhenotypeComparison

phenotype_cvterms

Type: has_many

Related object: Bio::Chado::Schema::Result::Phenotype::PhenotypeCvterm

phenotypeprops

Type: has_many

Related object: Bio::Chado::Schema::Result::Phenotype::Phenotypeprop

phenstatements

Type: has_many

Related object: Bio::Chado::Schema::Result::Genetic::Phenstatement

create_phenotypeprops

  Usage: $set->create_phenotypeprops({ baz => 2, foo => 'bar' });
  Desc : convenience method to create phenotype 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 phenotypeprop name.  Default false.

            cv_name => cv.name to use for the given phenotypeprops.
                       Defaults to 'phenotype_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 phenotype
                and value in the properties of the phenotype.  Duplicate
                values will have different ranks.
          }
  Ret  : hashref of { propname => new phenotypeprop object }
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