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 }

cpanm Bio::Chado::Schema

perl -MCPAN -e shell
install Bio::Chado::Schema