NAME
Bio::Chado::Schema::Cv::Cvterm - A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.
ACCESSORS
cvterm_id
data_type: integer
default_value: nextval('cvterm_cvterm_id_seq'::regclass)
is_auto_increment: 1
is_nullable: 0
size: 4
cv_id
data_type: integer
default_value: undef
is_foreign_key: 1
is_nullable: 0
size: 4
The cv or ontology or namespace to which this cvterm belongs.
name
data_type: character varying
default_value: undef
is_nullable: 0
size: 1024
A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.
definition
data_type: text
default_value: undef
is_nullable: 1
size: undef
A human-readable text definition.
dbxref_id
data_type: integer
default_value: undef
is_foreign_key: 1
is_nullable: 0
size: 4
Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.
is_obsolete
data_type: integer
default_value: 0
is_nullable: 0
size: 4
Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.
is_relationshiptype
data_type: integer
default_value: 0
is_nullable: 0
size: 4
Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.
RELATIONS
acquisitionprops
Type: has_many
Related object: Bio::Chado::Schema::Mage::Acquisitionprop
acquisition_relationships
Type: has_many
Related object: Bio::Chado::Schema::Mage::AcquisitionRelationship
analysisfeatureprops
Type: has_many
Related object: Bio::Chado::Schema::Companalysis::Analysisfeatureprop
analysisprops
Type: has_many
Related object: Bio::Chado::Schema::Companalysis::Analysisprop
arraydesign_platformtype_ids
Type: has_many
Related object: Bio::Chado::Schema::Mage::Arraydesign
arraydesign_substratetype_ids
Type: has_many
Related object: Bio::Chado::Schema::Mage::Arraydesign
arraydesignprops
Type: has_many
Related object: Bio::Chado::Schema::Mage::Arraydesignprop
assayprops
Type: has_many
Related object: Bio::Chado::Schema::Mage::Assayprop
biomaterialprops
Type: has_many
Related object: Bio::Chado::Schema::Mage::Biomaterialprop
biomaterial_relationships
Type: has_many
Related object: Bio::Chado::Schema::Mage::BiomaterialRelationship
biomaterial_treatments
Type: has_many
Related object: Bio::Chado::Schema::Mage::BiomaterialTreatment
cell_line_cvterms
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLineCvterm
cell_line_cvtermprops
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLineCvtermprop
cell_lineprops
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLineprop
cell_line_relationships
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLineRelationship
contacts
Type: has_many
Related object: Bio::Chado::Schema::Contact::Contact
contact_relationships
Type: has_many
Related object: Bio::Chado::Schema::Contact::ContactRelationship
controls
Type: has_many
Related object: Bio::Chado::Schema::Mage::Control
cv
Type: belongs_to
Related object: Bio::Chado::Schema::Cv::Cv
dbxref
Type: belongs_to
Related object: Bio::Chado::Schema::General::Dbxref
cvterm_dbxrefs
Type: has_many
Related object: Bio::Chado::Schema::Cv::CvtermDbxref
cvtermpath_type_ids
Type: has_many
Related object: Bio::Chado::Schema::Cv::Cvtermpath
cvtermpath_object_ids
Type: has_many
Related object: Bio::Chado::Schema::Cv::Cvtermpath
cvtermpath_subject_ids
Type: has_many
Related object: Bio::Chado::Schema::Cv::Cvtermpath
cvtermprop_type_ids
Type: has_many
Related object: Bio::Chado::Schema::Cv::Cvtermprop
cvtermprop_cvterm_ids
Type: has_many
Related object: Bio::Chado::Schema::Cv::Cvtermprop
cvterm_relationship_type_ids
Type: has_many
Related object: Bio::Chado::Schema::Cv::CvtermRelationship
cvterm_relationship_object_ids
Type: has_many
Related object: Bio::Chado::Schema::Cv::CvtermRelationship
cvterm_relationship_subject_ids
Type: has_many
Related object: Bio::Chado::Schema::Cv::CvtermRelationship
cvtermsynonym_type_ids
Type: has_many
Related object: Bio::Chado::Schema::Cv::Cvtermsynonym
cvtermsynonym_cvterm_ids
Type: has_many
Related object: Bio::Chado::Schema::Cv::Cvtermsynonym
dbxrefprops
Type: has_many
Related object: Bio::Chado::Schema::Cv::Dbxrefprop
elements
Type: has_many
Related object: Bio::Chado::Schema::Mage::Element
element_relationships
Type: has_many
Related object: Bio::Chado::Schema::Mage::ElementRelationship
elementresult_relationships
Type: has_many
Related object: Bio::Chado::Schema::Mage::ElementresultRelationship
environment_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Genetic::EnvironmentCvterm
expression_cvterm_cvterm_ids
Type: has_many
Related object: Bio::Chado::Schema::Expression::ExpressionCvterm
expression_cvterm_cvterm_type_ids
Type: has_many
Related object: Bio::Chado::Schema::Expression::ExpressionCvterm
expression_cvtermprops
Type: has_many
Related object: Bio::Chado::Schema::Expression::ExpressionCvtermprop
expressionprops
Type: has_many
Related object: Bio::Chado::Schema::Expression::Expressionprop
features
Type: has_many
Related object: Bio::Chado::Schema::Sequence::Feature
feature_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeatureCvterm
feature_cvtermprops
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeatureCvtermprop
feature_expressionprops
Type: has_many
Related object: Bio::Chado::Schema::Expression::FeatureExpressionprop
feature_genotypes
Type: has_many
Related object: Bio::Chado::Schema::Genetic::FeatureGenotype
featuremaps
Type: has_many
Related object: Bio::Chado::Schema::Map::Featuremap
featureprops
Type: has_many
Related object: Bio::Chado::Schema::Sequence::Featureprop
feature_pubprops
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeaturePubprop
feature_relationships
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeatureRelationship
feature_relationshipprops
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeatureRelationshipprop
libraries
Type: has_many
Related object: Bio::Chado::Schema::Library::Library
library_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Library::LibraryCvterm
libraryprops
Type: has_many
Related object: Bio::Chado::Schema::Library::Libraryprop
organismprops
Type: has_many
Related object: Bio::Chado::Schema::Organism::Organismprop
phendescs
Type: has_many
Related object: Bio::Chado::Schema::Genetic::Phendesc
phenotype_assay_ids
Type: has_many
Related object: Bio::Chado::Schema::Phenotype::Phenotype
phenotype_attr_ids
Type: has_many
Related object: Bio::Chado::Schema::Phenotype::Phenotype
phenotype_observable_ids
Type: has_many
Related object: Bio::Chado::Schema::Phenotype::Phenotype
phenotype_cvalue_ids
Type: has_many
Related object: Bio::Chado::Schema::Phenotype::Phenotype
phenotype_comparison_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Genetic::PhenotypeComparisonCvterm
phenotype_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Phenotype::PhenotypeCvterm
phenstatements
Type: has_many
Related object: Bio::Chado::Schema::Genetic::Phenstatement
phylonodes
Type: has_many
Related object: Bio::Chado::Schema::Phylogeny::Phylonode
phylonodeprops
Type: has_many
Related object: Bio::Chado::Schema::Phylogeny::Phylonodeprop
phylonode_relationships
Type: has_many
Related object: Bio::Chado::Schema::Phylogeny::PhylonodeRelationship
phylotrees
Type: has_many
Related object: Bio::Chado::Schema::Phylogeny::Phylotree
protocols
Type: has_many
Related object: Bio::Chado::Schema::Mage::Protocol
protocolparam_unittype_ids
Type: has_many
Related object: Bio::Chado::Schema::Mage::Protocolparam
protocolparam_datatype_ids
Type: has_many
Related object: Bio::Chado::Schema::Mage::Protocolparam
pubs
Type: has_many
Related object: Bio::Chado::Schema::Pub::Pub
pubprops
Type: has_many
Related object: Bio::Chado::Schema::Pub::Pubprop
pub_relationships
Type: has_many
Related object: Bio::Chado::Schema::Pub::PubRelationship
quantificationprops
Type: has_many
Related object: Bio::Chado::Schema::Mage::Quantificationprop
quantification_relationships
Type: has_many
Related object: Bio::Chado::Schema::Mage::QuantificationRelationship
stocks
Type: has_many
Related object: Bio::Chado::Schema::Stock::Stock
stockcollections
Type: has_many
Related object: Bio::Chado::Schema::Stock::Stockcollection
stockcollectionprops
Type: has_many
Related object: Bio::Chado::Schema::Stock::Stockcollectionprop
stock_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Stock::StockCvterm
stockprops
Type: has_many
Related object: Bio::Chado::Schema::Stock::Stockprop
stock_relationships
Type: has_many
Related object: Bio::Chado::Schema::Stock::StockRelationship
studydesignprops
Type: has_many
Related object: Bio::Chado::Schema::Mage::Studydesignprop
studyfactors
Type: has_many
Related object: Bio::Chado::Schema::Mage::Studyfactor
studyprops
Type: has_many
Related object: Bio::Chado::Schema::Mage::Studyprop
studyprop_features
Type: has_many
Related object: Bio::Chado::Schema::Mage::StudypropFeature
synonyms
Type: has_many
Related object: Bio::Chado::Schema::Sequence::Synonym
treatments
Type: has_many
Related object: Bio::Chado::Schema::Mage::Treatment
add_synonym
Usage: $self->add_synonym($synonym , { type => 'exact' , autocreate => 1} );
Desc: adds the synonym $new_synonym to this cvterm
If the synonym $new_synonym already exists,
nothing is added.
Args: a synonym name and
options hashref as:
{
synonym_type => [e.g. exact, narrow, broad, related],
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 synonym type.
Defaults to 'synonym_type',
db_name => db.name to use for autocreated dbxrefs,
default 'null',
definitions => optional hashref of:
{ cvterm_name => definition,
}
to load into the cvterm table when autocreating cvterms
}
Ret: a Cvtermsynonym object
Example:
delete_synonym
Usage: $self->delete_synonym($synonym)
Desc: delete synonym $synonym from cvterm object
Ret: nothing
Args: $synonym
Side Effects: Will delete all cvtermsynonyms with synonym=$synonym. Case insensitive
Example:
get_secondary_dbxrefs
Usage: $self->get_secondary_dbxrefs()
Desc: find all secondary accessions associated with the cvterm
These are stored in cvterm_dbxref table as dbxref_ids
Ret: a list of accessions (e.g. GO:0000123)
Args: none
Side Effects: none
Example:
add_secondary_dbxref
Usage: $self->add_secondary_dbxref(accession, 1)
Desc: add an alternative id to cvterm. Stores in cvterm_dbxref
Ret: a CvtermDbxref object
Args: an alternative id (i.e. "GO:0001234"). A second arg will store a is_for_definition=1 (default = 0)
Side Effects: stores a new dbxref if accession is not found in dbxref table
Example:
delete_secondary_dbxref
Usage: $self->delete_secondary_dbxref($accession)
Desc: delete a cvterm_dbxref from the database
Ret: nothing
Args: full accession (db_name:dbxref_accession e.g. PO:0001234)
Side Effects:
Example: