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.
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 Note that two terms with different primary dbxrefs may exist if one is obsolete.
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
Related object: Bio::Chado::Schema::Result::Mage::AcquisitionRelationship
Related object: Bio::Chado::Schema::Result::Companalysis::Analysisfeatureprop
Related object: Bio::Chado::Schema::Result::Companalysis::Analysisprop
Related object: Bio::Chado::Schema::Result::Mage::Arraydesign
Related object: Bio::Chado::Schema::Result::Mage::Arraydesignprop
Related object: Bio::Chado::Schema::Result::Mage::Assayprop
Related object: Bio::Chado::Schema::Result::Mage::Biomaterialprop
Related object: Bio::Chado::Schema::Result::Mage::BiomaterialRelationship
Related object: Bio::Chado::Schema::Result::Mage::BiomaterialTreatment
Related object: Bio::Chado::Schema::Result::CellLine::CellLineCvterm
Related object: Bio::Chado::Schema::Result::CellLine::CellLineCvtermprop
Related object: Bio::Chado::Schema::Result::CellLine::CellLineprop
Related object: Bio::Chado::Schema::Result::CellLine::CellLineRelationship
Related object: Bio::Chado::Schema::Result::Cv::Chadoprop
Related object: Bio::Chado::Schema::Result::Contact::Contact
Related object: Bio::Chado::Schema::Result::Contact::ContactRelationship
Related object: Bio::Chado::Schema::Result::Mage::Control
Related object: Bio::Chado::Schema::Result::Cv::Cvprop
Type: belongs_to
Related object: Bio::Chado::Schema::Result::Cv::Cv
Related object: Bio::Chado::Schema::Result::General::Dbxref
Related object: Bio::Chado::Schema::Result::Cv::CvtermDbxref
Related object: Bio::Chado::Schema::Result::Cv::Cvtermpath
Related object: Bio::Chado::Schema::Result::Cv::Cvtermprop
Related object: Bio::Chado::Schema::Result::Cv::CvtermRelationship
Related object: Bio::Chado::Schema::Result::Cv::Cvtermsynonym
Related object: Bio::Chado::Schema::Result::Cv::Dbxrefprop
Related object: Bio::Chado::Schema::Result::Mage::Element
Related object: Bio::Chado::Schema::Result::Mage::ElementRelationship
Related object: Bio::Chado::Schema::Result::Mage::ElementresultRelationship
Related object: Bio::Chado::Schema::Result::Genetic::EnvironmentCvterm
Related object: Bio::Chado::Schema::Result::Expression::ExpressionCvterm
Related object: Bio::Chado::Schema::Result::Expression::ExpressionCvtermprop
Related object: Bio::Chado::Schema::Result::Expression::Expressionprop
Related object: Bio::Chado::Schema::Result::Sequence::Feature
Related object: Bio::Chado::Schema::Result::Sequence::FeatureCvterm
Related object: Bio::Chado::Schema::Result::Sequence::FeatureCvtermprop
Related object: Bio::Chado::Schema::Result::Expression::FeatureExpressionprop
Related object: Bio::Chado::Schema::Result::Genetic::FeatureGenotype
Related object: Bio::Chado::Schema::Result::Map::Featuremap
Related object: Bio::Chado::Schema::Result::Sequence::Featureprop
Related object: Bio::Chado::Schema::Result::Sequence::FeaturePubprop
Related object: Bio::Chado::Schema::Result::Sequence::FeatureRelationship
Related object: Bio::Chado::Schema::Result::Sequence::FeatureRelationshipprop
Related object: Bio::Chado::Schema::Result::Genetic::Genotype
Related object: Bio::Chado::Schema::Result::Genetic::Genotypeprop
Related object: Bio::Chado::Schema::Result::Library::Library
Related object: Bio::Chado::Schema::Result::Library::LibraryCvterm
Related object: Bio::Chado::Schema::Result::Library::Libraryprop
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperiment
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentprop
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStock
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStockprop
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdGeolocationprop
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdProtocol
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdProtocolprop
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdProtocolReagent
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdReagent
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdReagentprop
Related object: Bio::Chado::Schema::Result::NaturalDiversity::NdReagentRelationship
Related object: Bio::Chado::Schema::Result::Organism::Organismprop
Related object: Bio::Chado::Schema::Result::Genetic::Phendesc
Related object: Bio::Chado::Schema::Result::Phenotype::Phenotype
Related object: Bio::Chado::Schema::Result::Genetic::PhenotypeComparisonCvterm
Related object: Bio::Chado::Schema::Result::Phenotype::PhenotypeCvterm
Related object: Bio::Chado::Schema::Result::Phenotype::Phenotypeprop
Related object: Bio::Chado::Schema::Result::Genetic::Phenstatement
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylonode
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylonodeprop
Related object: Bio::Chado::Schema::Result::Phylogeny::PhylonodeRelationship
Related object: Bio::Chado::Schema::Result::Phylogeny::Phylotree
Related object: Bio::Chado::Schema::Result::Project::Projectprop
Related object: Bio::Chado::Schema::Result::Project::ProjectRelationship
Related object: Bio::Chado::Schema::Result::Mage::Protocol
Related object: Bio::Chado::Schema::Result::Mage::Protocolparam
Related object: Bio::Chado::Schema::Result::Pub::Pub
Related object: Bio::Chado::Schema::Result::Pub::Pubprop
Related object: Bio::Chado::Schema::Result::Pub::PubRelationship
Related object: Bio::Chado::Schema::Result::Mage::Quantificationprop
Related object: Bio::Chado::Schema::Result::Mage::QuantificationRelationship
Related object: Bio::Chado::Schema::Result::Stock::Stock
Related object: Bio::Chado::Schema::Result::Stock::Stockcollection
Related object: Bio::Chado::Schema::Result::Stock::Stockcollectionprop
Related object: Bio::Chado::Schema::Result::Stock::StockCvterm
Related object: Bio::Chado::Schema::Result::Stock::StockCvtermprop
Related object: Bio::Chado::Schema::Result::Stock::StockDbxrefprop
Related object: Bio::Chado::Schema::Result::Stock::Stockprop
Related object: Bio::Chado::Schema::Result::Stock::StockRelationship
Related object: Bio::Chado::Schema::Result::Stock::StockRelationshipCvterm
Related object: Bio::Chado::Schema::Result::Mage::Studydesignprop
Related object: Bio::Chado::Schema::Result::Mage::Studyfactor
Related object: Bio::Chado::Schema::Result::Mage::Studyprop
Related object: Bio::Chado::Schema::Result::Mage::StudypropFeature
Related object: Bio::Chado::Schema::Result::Sequence::Synonym
Related object: Bio::Chado::Schema::Result::Mage::Treatment
This cvtermprops relation is a convenient synonym for the autogenerated "cvtermprop_cvterms" above, since most often you want the properties for the cvterm itself.
cvtermprops
If you really do want the Cvtermprop rows that have this cvterm as their type, use cvtermprop_types, listed above.
cvtermprop_types
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.
cvtermpath
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
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
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
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
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, }
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.