Bio::Chado::Schema::Result::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.
data_type: 'integer' is_auto_increment: 1 is_nullable: 0 sequence: 'cvterm_cvterm_id_seq'
data_type: 'integer' is_foreign_key: 1 is_nullable: 0
The cv or ontology or namespace to which this cvterm belongs.
data_type: 'varchar' is_nullable: 0 size: 1024
A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.
data_type: 'text' is_nullable: 1
A human-readable text definition.
data_type: 'integer' is_foreign_key: 1 is_nullable: 0
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.
data_type: 'integer' default_value: 0 is_nullable: 0
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 Note that two terms with different primary dbxrefs may exist if one is obsolete.
data_type: 'integer' default_value: 0 is_nullable: 0
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.
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Acquisitionprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::AcquisitionRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Companalysis::Analysisfeatureprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Companalysis::Analysisprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Arraydesign
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Arraydesign
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Arraydesignprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Assayprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Biomaterialprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::BiomaterialRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::BiomaterialTreatment
Type: has_many
Related object: Bio::Chado::Schema::Result::CellLine::CellLineCvterm
Type: has_many
Related object: Bio::Chado::Schema::Result::CellLine::CellLineCvtermprop
Type: has_many
Related object: Bio::Chado::Schema::Result::CellLine::CellLineprop
Type: has_many
Related object: Bio::Chado::Schema::Result::CellLine::CellLineRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Chadoprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Contact::Contact
Type: has_many
Related object: Bio::Chado::Schema::Result::Contact::ContactRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Control
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Cvprop
Type: belongs_to
Related object: Bio::Chado::Schema::Result::Cv::Cv
Type: belongs_to
Related object: Bio::Chado::Schema::Result::General::Dbxref
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::CvtermDbxref
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Cvtermpath
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Cvtermpath
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Cvtermpath
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Cvtermprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Cvtermprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::CvtermRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::CvtermRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::CvtermRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Cvtermsynonym
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Cvtermsynonym
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Dbxrefprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Element
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::ElementRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::ElementresultRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::EnvironmentCvterm
Type: has_many
Related object: Bio::Chado::Schema::Result::Expression::ExpressionCvterm
Type: has_many
Related object: Bio::Chado::Schema::Result::Expression::ExpressionCvterm
Type: has_many
Related object: Bio::Chado::Schema::Result::Expression::ExpressionCvtermprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Expression::Expressionprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Sequence::Feature
Type: has_many
Related object: Bio::Chado::Schema::Result::Sequence::FeatureCvterm
Type: has_many
Related object: Bio::Chado::Schema::Result::Sequence::FeatureCvtermprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Expression::FeatureExpressionprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::FeatureGenotype
Type: has_many
Related object: Bio::Chado::Schema::Result::Map::Featuremap
Type: has_many
Related object: Bio::Chado::Schema::Result::Sequence::Featureprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Sequence::FeaturePubprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Sequence::FeatureRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Sequence::FeatureRelationshipprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::Genotype
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::Genotypeprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Library::Library
Type: has_many
Related object: Bio::Chado::Schema::Result::Library::LibraryCvterm
Type: has_many
Related object: Bio::Chado::Schema::Result::Library::Libraryprop
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperiment
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentprop
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStock
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStockprop
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdGeolocationprop
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdProtocol
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdProtocolprop
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdProtocolReagent
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdReagent
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdReagentprop
Type: has_many
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdReagentRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Organism::Organismprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::Phendesc
Type: has_many
Related object: Bio::Chado::Schema::Result::Phenotype::Phenotype
Type: has_many
Related object: Bio::Chado::Schema::Result::Phenotype::Phenotype
Type: has_many
Related object: Bio::Chado::Schema::Result::Phenotype::Phenotype
Type: has_many
Related object: Bio::Chado::Schema::Result::Phenotype::Phenotype
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::PhenotypeComparisonCvterm
Type: has_many
Related object: Bio::Chado::Schema::Result::Phenotype::PhenotypeCvterm
Type: has_many
Related object: Bio::Chado::Schema::Result::Phenotype::Phenotypeprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Genetic::Phenstatement
Type: has_many
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylonode
Type: has_many
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylonodeprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Phylogeny::PhylonodeRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylotree
Type: has_many
Related object: Bio::Chado::Schema::Result::Project::Projectprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Project::ProjectRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Protocol
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Protocolparam
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Protocolparam
Type: has_many
Related object: Bio::Chado::Schema::Result::Pub::Pub
Type: has_many
Related object: Bio::Chado::Schema::Result::Pub::Pubprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Pub::PubRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Quantificationprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::QuantificationRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Stock::Stock
Type: has_many
Related object: Bio::Chado::Schema::Result::Stock::Stockcollection
Type: has_many
Related object: Bio::Chado::Schema::Result::Stock::Stockcollectionprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Stock::StockCvterm
Type: has_many
Related object: Bio::Chado::Schema::Result::Stock::StockCvtermprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Stock::StockDbxrefprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Stock::Stockprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Stock::StockRelationship
Type: has_many
Related object: Bio::Chado::Schema::Result::Stock::StockRelationshipCvterm
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Studydesignprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Studyfactor
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Studyprop
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::StudypropFeature
Type: has_many
Related object: Bio::Chado::Schema::Result::Sequence::Synonym
Type: has_many
Related object: Bio::Chado::Schema::Result::Mage::Treatment
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Cvtermprop
This cvtermprops relation is a convenient synonym for the autogenerated "cvtermprop_cvterms" above, since most often you want the properties for the cvterm itself.
If you really do want the Cvtermprop rows that have this cvterm as their type, use cvtermprop_types, listed above.
Type: has_many
Related object: Bio::Chado::Schema::Result::Cv::Cvtermsynonym
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 synonym 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
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
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
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
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:
Usage: $set->create_cvtermprops({ baz => 2, foo => 'bar' });
Desc : convenience method to create cvterm 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 cvtermprop name. Default false.
cv_name => cv.name to use for the given cvtermprops.
Defaults to 'cvterm_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 cvterm
and value in the properties of the cvterm. Duplicate
values will have different ranks.
}
Ret : hashref of { propname => new cvtermprop object }
Usage: $self->root Desc: find the root cvterm Ret: Cvterm object Args: none
NOTE: This method requires that your cvtermpath table is populated.
Usage: $self->children
Desc: find the direct children of the cvterm
Ret: L<Bio::Chado::Schema::Result::Cv::CvtermRelationship> resultset of the
fetched child terms (this can be used in your program to find the
relationship type id of each child term)
Args: none
Usage: $self->direct_children Desc: find only the direct children of your term Ret: L<Bio::Chado::Schema::Result::Cv::Cvterm> Args: none Side Effects: none
NOTE: This method requires that your cvtermpath table is populated.
Usage: $self->recursive_children Desc: find all the descendants of the cvterm (children, children of children, and so on) Ret: a DBIC resultset of L<Bio::Chado::Schema::Result::Cv::Cvterm> Args: none Side Effects: none
NOTE: This method requires that your cvtermpath table is populated.
Usage: my $self->parents Desc: Find the direct parents of the cvterm Ret: L<Bio::Chado::Schema::Result::Cv::CvtermRelationship> resultset of the parent terms Args: none Side Effects: none
Usage: $self->direct_parents Desc: get only the direct parents of the cvterm (from the cvtermpath) Ret: L<Bio::Chado::Schema::Result::Cv::Cvterm> Args: none Side Effects: none
NOTE: This method requires that your cvtermpath table is populated.
Usage: $self->recursive_parents Desc: find all the ancestors of the cvterm (parents, parents of parents, and so on) Ret: L<Bio::Chado::Schema::Result::Cv::Cvterm> resultset Args: none Side Effects: none
NOTE: This method requires that your cvtermpath table is populated.
Usage: $schema->resultset('Cv::Cvterm')->create_with(
{ name => 'cvterm name',
cv => $cv || 'cv name',
db => $db || 'db name',
dbxref => $dbx || 'accession',
});
Desc: convenience method to create a cvterm, linking it to the CV and
DB that you name or provide. For any cv, db, or dbxref that
you call only by name, does a find_or_create() using that name.
Ret : a new Cvterm row
Args: hashref of:
{ name => 'cvterm name',
cv => 'cv name' or L<Bio::Chado::Schema::Result::Cv::Cvterm> row,
db => 'db name' or L<Bio::Chado::Schema::Result::General::Db> row,
dbxref => 'accession' or L<Bio::Chado::Schema::Result::General::Dbxref> row,
}
