Bio::Chado::Schema::Result::Organism::Organism
The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.
data_type: 'integer' is_auto_increment: 1 is_nullable: 0 sequence: 'organism_organism_id_seq'
data_type: 'varchar' is_nullable: 1 size: 255
data_type: 'varchar' is_nullable: 0 size: 255
A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.
data_type: 'text' is_nullable: 1
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Biomaterial
Related object: Bio::Chado::Schema::Result::CellLine::CellLine
Related object: Bio::Chado::Schema::Result::Sequence::Feature
Related object: Bio::Chado::Schema::Result::Library::Library
Related object: Bio::Chado::Schema::Result::Organism::OrganismDbxref
Related object: Bio::Chado::Schema::Result::Organism::Organismprop
Related object: Bio::Chado::Schema::Result::Genetic::PhenotypeComparison
Related object: Bio::Chado::Schema::Result::Phylogeny::PhylonodeOrganism
Related object: Bio::Chado::Schema::Result::Stock::Stock
Type: many_to_many
Returns a list of phylonodes associated with this organism.
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylonode
Returns a list of dbxrefs associated with the organism.
Related object: Bio::Chado::Schema::Result::General::Dbxref
use Carp;
Usage: $set->create_organismprops({ baz => 2, foo => 'bar' }); Desc : convenience method to create organism 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 featureprop name. Default false. cv_name => cv.name to use for the given organismprops. Defaults to 'organism_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 allow_duplicate_values => default false. If true, allow duplicate instances of the same cvterm and value in the properties of the feature. Duplicate values will have different ranks. } Ret : hashref of { propname => new organismprop 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.