Bio::Chado::Schema::Result::Phenotype::Phenotype
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.
data_type: 'integer' is_auto_increment: 1 is_nullable: 0 sequence: 'phenotype_phenotype_id_seq'
data_type: 'text' is_nullable: 0
data_type: 'text' is_nullable: 1
data_type: 'integer' is_foreign_key: 1 is_nullable: 1
The entity: e.g. anatomy_part, biological_process.
Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.
Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.
Phenotype attribute value (state).
Evidence type.
Type: has_many
Related object: Bio::Chado::Schema::Result::Phenotype::FeaturePhenotype
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentPhenotype
Type: belongs_to
Related object: Bio::Chado::Schema::Result::Cv::Cvterm
Related object: Bio::Chado::Schema::Result::Genetic::PhenotypeComparison
Related object: Bio::Chado::Schema::Result::Phenotype::PhenotypeCvterm
Related object: Bio::Chado::Schema::Result::Phenotype::Phenotypeprop
Related object: Bio::Chado::Schema::Result::Genetic::Phenstatement
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 }
To install Bio::Chado::Schema, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Chado::Schema
CPAN shell
perl -MCPAN -e shell install Bio::Chado::Schema
For more information on module installation, please visit the detailed CPAN module installation guide.