NAME

Bio::Chado::Schema::Result::Organism::Organism

DESCRIPTION

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.

ACCESSORS

organism_id

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

abbreviation

  data_type: 'varchar'
  is_nullable: 1
  size: 255

genus

  data_type: 'varchar'
  is_nullable: 0
  size: 255

species

  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.

common_name

  data_type: 'varchar'
  is_nullable: 1
  size: 255

comment

  data_type: 'text'
  is_nullable: 1

RELATIONS

biomaterials

Type: has_many

Related object: Bio::Chado::Schema::Result::Mage::Biomaterial

cell_lines

Type: has_many

Related object: Bio::Chado::Schema::Result::CellLine::CellLine

features

Type: has_many

Related object: Bio::Chado::Schema::Result::Sequence::Feature

libraries

Type: has_many

Related object: Bio::Chado::Schema::Result::Library::Library

organism_dbxrefs

Type: has_many

Related object: Bio::Chado::Schema::Result::Organism::OrganismDbxref

organismprops

Type: has_many

Related object: Bio::Chado::Schema::Result::Organism::Organismprop

phenotype_comparisons

Type: has_many

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

phylonode_organisms

Type: has_many

Related object: Bio::Chado::Schema::Result::Phylogeny::PhylonodeOrganism

stocks

Type: has_many

Related object: Bio::Chado::Schema::Result::Stock::Stock

MANY-TO-MANY RELATIONSHIPS

phylonodes

Type: many_to_many

Returns a list of phylonodes associated with this organism.

Related object: Bio::Chado::Schema::Result::Phylogeny::Phylonode

dbxrefs

Type: many_to_many

Returns a list of dbxrefs associated with the organism.

Related object: Bio::Chado::Schema::Result::General::Dbxref

ADDITIONAL METHODS

use Carp;

create_organismprops

  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 }