NAME
Bio::Chado::Schema::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.
NAME
Bio::Chado::Schema::Organism::Organism
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::Mage::Biomaterial
cell_lines
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLine
features
Type: has_many
Related object: Bio::Chado::Schema::Sequence::Feature
libraries
Type: has_many
Related object: Bio::Chado::Schema::Library::Library
organism_dbxrefs
Type: has_many
Related object: Bio::Chado::Schema::Organism::OrganismDbxref
organismprops
Type: has_many
Related object: Bio::Chado::Schema::Organism::Organismprop
phenotype_comparisons
Type: has_many
Related object: Bio::Chado::Schema::Genetic::PhenotypeComparison
phylonode_organisms
Type: has_many
Related object: Bio::Chado::Schema::Phylogeny::PhylonodeOrganism
stocks
Type: has_many
Related object: Bio::Chado::Schema::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::Phylogeny::Phylonode
dbxrefs
Type: many_to_many
Returns a list of dbxrefs associated with the organism.
Related object: Bio::Chado::Schema::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 }
AUTHOR
Robert Buels <rbuels@cpan.org>
COPYRIGHT AND LICENSE
This software is copyright (c) 2009 by Robert Buels.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.