package Bio::Chado::Schema::Result::Cv::Cvterm; BEGIN { $Bio::Chado::Schema::Result::Cv::Cvterm::AUTHORITY = 'cpan:RBUELS'; } { $Bio::Chado::Schema::Result::Cv::Cvterm::VERSION = '0.20000'; } # Created by DBIx::Class::Schema::Loader # DO NOT MODIFY THE FIRST PART OF THIS FILE use strict; use warnings; use base 'DBIx::Class::Core'; =head1 NAME Bio::Chado::Schema::Result::Cv::Cvterm =head1 DESCRIPTION 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. =cut __PACKAGE__->table("cvterm"); =head1 ACCESSORS =head2 cvterm_id data_type: 'integer' is_auto_increment: 1 is_nullable: 0 sequence: 'cvterm_cvterm_id_seq' =head2 cv_id data_type: 'integer' is_foreign_key: 1 is_nullable: 0 The cv or ontology or namespace to which this cvterm belongs. =head2 name 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. =head2 definition data_type: 'text' is_nullable: 1 A human-readable text definition. =head2 dbxref_id 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. =head2 is_obsolete 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 Note that two terms with different primary dbxrefs may exist if one is obsolete. =head2 is_relationshiptype 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. =cut __PACKAGE__->add_columns( "cvterm_id", { data_type => "integer", is_auto_increment => 1, is_nullable => 0, sequence => "cvterm_cvterm_id_seq", }, "cv_id", { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, "name", { data_type => "varchar", is_nullable => 0, size => 1024 }, "definition", { data_type => "text", is_nullable => 1 }, "dbxref_id", { data_type => "integer", is_foreign_key => 1, is_nullable => 0 }, "is_obsolete", { data_type => "integer", default_value => 0, is_nullable => 0 }, "is_relationshiptype", { data_type => "integer", default_value => 0, is_nullable => 0 }, ); __PACKAGE__->set_primary_key("cvterm_id"); __PACKAGE__->add_unique_constraint("cvterm_c2", ["dbxref_id"]); __PACKAGE__->add_unique_constraint("cvterm_c1", ["name", "cv_id", "is_obsolete"]); =head1 RELATIONS =head2 acquisitionprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "acquisitionprops", "Bio::Chado::Schema::Result::Mage::Acquisitionprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 acquisition_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "acquisition_relationships", "Bio::Chado::Schema::Result::Mage::AcquisitionRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 analysisfeatureprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "analysisfeatureprops", "Bio::Chado::Schema::Result::Companalysis::Analysisfeatureprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 analysisprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "analysisprops", "Bio::Chado::Schema::Result::Companalysis::Analysisprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 arraydesign_platformtypes Type: has_many Related object: L =cut __PACKAGE__->has_many( "arraydesign_platformtypes", "Bio::Chado::Schema::Result::Mage::Arraydesign", { "foreign.platformtype_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 arraydesign_substratetypes Type: has_many Related object: L =cut __PACKAGE__->has_many( "arraydesign_substratetypes", "Bio::Chado::Schema::Result::Mage::Arraydesign", { "foreign.substratetype_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 arraydesignprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "arraydesignprops", "Bio::Chado::Schema::Result::Mage::Arraydesignprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 assayprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "assayprops", "Bio::Chado::Schema::Result::Mage::Assayprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 biomaterialprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "biomaterialprops", "Bio::Chado::Schema::Result::Mage::Biomaterialprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 biomaterial_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "biomaterial_relationships", "Bio::Chado::Schema::Result::Mage::BiomaterialRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 biomaterial_treatments Type: has_many Related object: L =cut __PACKAGE__->has_many( "biomaterial_treatments", "Bio::Chado::Schema::Result::Mage::BiomaterialTreatment", { "foreign.unittype_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cell_line_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "cell_line_cvterms", "Bio::Chado::Schema::Result::CellLine::CellLineCvterm", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cell_line_cvtermprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "cell_line_cvtermprops", "Bio::Chado::Schema::Result::CellLine::CellLineCvtermprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cell_lineprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "cell_lineprops", "Bio::Chado::Schema::Result::CellLine::CellLineprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cell_line_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "cell_line_relationships", "Bio::Chado::Schema::Result::CellLine::CellLineRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 chadoprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "chadoprops", "Bio::Chado::Schema::Result::Cv::Chadoprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 contacts Type: has_many Related object: L =cut __PACKAGE__->has_many( "contacts", "Bio::Chado::Schema::Result::Contact::Contact", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 contact_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "contact_relationships", "Bio::Chado::Schema::Result::Contact::ContactRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 controls Type: has_many Related object: L =cut __PACKAGE__->has_many( "controls", "Bio::Chado::Schema::Result::Mage::Control", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvprops", "Bio::Chado::Schema::Result::Cv::Cvprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cv Type: belongs_to Related object: L =cut __PACKAGE__->belongs_to( "cv", "Bio::Chado::Schema::Result::Cv::Cv", { cv_id => "cv_id" }, { cascade_copy => 0, cascade_delete => 0, is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE", }, ); =head2 dbxref Type: belongs_to Related object: L =cut __PACKAGE__->belongs_to( "dbxref", "Bio::Chado::Schema::Result::General::Dbxref", { dbxref_id => "dbxref_id" }, { cascade_copy => 0, cascade_delete => 0, is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE", }, ); =head2 cvterm_dbxrefs Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvterm_dbxrefs", "Bio::Chado::Schema::Result::Cv::CvtermDbxref", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvtermpath_types Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvtermpath_types", "Bio::Chado::Schema::Result::Cv::Cvtermpath", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvtermpath_objects Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvtermpath_objects", "Bio::Chado::Schema::Result::Cv::Cvtermpath", { "foreign.object_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvtermpath_subjects Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvtermpath_subjects", "Bio::Chado::Schema::Result::Cv::Cvtermpath", { "foreign.subject_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvtermprop_types Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvtermprop_types", "Bio::Chado::Schema::Result::Cv::Cvtermprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvtermprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvtermprops", "Bio::Chado::Schema::Result::Cv::Cvtermprop", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvterm_relationship_types Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvterm_relationship_types", "Bio::Chado::Schema::Result::Cv::CvtermRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvterm_relationship_objects Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvterm_relationship_objects", "Bio::Chado::Schema::Result::Cv::CvtermRelationship", { "foreign.object_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvterm_relationship_subjects Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvterm_relationship_subjects", "Bio::Chado::Schema::Result::Cv::CvtermRelationship", { "foreign.subject_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvtermsynonym_types Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvtermsynonym_types", "Bio::Chado::Schema::Result::Cv::Cvtermsynonym", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvtermsynonyms Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvtermsynonyms", "Bio::Chado::Schema::Result::Cv::Cvtermsynonym", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 dbxrefprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "dbxrefprops", "Bio::Chado::Schema::Result::Cv::Dbxrefprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 elements Type: has_many Related object: L =cut __PACKAGE__->has_many( "elements", "Bio::Chado::Schema::Result::Mage::Element", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 element_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "element_relationships", "Bio::Chado::Schema::Result::Mage::ElementRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 elementresult_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "elementresult_relationships", "Bio::Chado::Schema::Result::Mage::ElementresultRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 environment_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "environment_cvterms", "Bio::Chado::Schema::Result::Genetic::EnvironmentCvterm", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 expression_cvterm_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "expression_cvterm_cvterms", "Bio::Chado::Schema::Result::Expression::ExpressionCvterm", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 expression_cvterm_cvterm_types Type: has_many Related object: L =cut __PACKAGE__->has_many( "expression_cvterm_cvterm_types", "Bio::Chado::Schema::Result::Expression::ExpressionCvterm", { "foreign.cvterm_type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 expression_cvtermprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "expression_cvtermprops", "Bio::Chado::Schema::Result::Expression::ExpressionCvtermprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 expressionprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "expressionprops", "Bio::Chado::Schema::Result::Expression::Expressionprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 features Type: has_many Related object: L =cut __PACKAGE__->has_many( "features", "Bio::Chado::Schema::Result::Sequence::Feature", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_cvterms", "Bio::Chado::Schema::Result::Sequence::FeatureCvterm", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_cvtermprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_cvtermprops", "Bio::Chado::Schema::Result::Sequence::FeatureCvtermprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_expressionprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_expressionprops", "Bio::Chado::Schema::Result::Expression::FeatureExpressionprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_genotypes Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_genotypes", "Bio::Chado::Schema::Result::Genetic::FeatureGenotype", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 featuremaps Type: has_many Related object: L =cut __PACKAGE__->has_many( "featuremaps", "Bio::Chado::Schema::Result::Map::Featuremap", { "foreign.unittype_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 featureprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "featureprops", "Bio::Chado::Schema::Result::Sequence::Featureprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_pubprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_pubprops", "Bio::Chado::Schema::Result::Sequence::FeaturePubprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_relationships", "Bio::Chado::Schema::Result::Sequence::FeatureRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 feature_relationshipprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "feature_relationshipprops", "Bio::Chado::Schema::Result::Sequence::FeatureRelationshipprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 genotypes Type: has_many Related object: L =cut __PACKAGE__->has_many( "genotypes", "Bio::Chado::Schema::Result::Genetic::Genotype", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 genotypeprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "genotypeprops", "Bio::Chado::Schema::Result::Genetic::Genotypeprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 libraries Type: has_many Related object: L =cut __PACKAGE__->has_many( "libraries", "Bio::Chado::Schema::Result::Library::Library", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 library_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "library_cvterms", "Bio::Chado::Schema::Result::Library::LibraryCvterm", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 libraryprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "libraryprops", "Bio::Chado::Schema::Result::Library::Libraryprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_experiments Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_experiments", "Bio::Chado::Schema::Result::NaturalDiversity::NdExperiment", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_experimentprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_experimentprops", "Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_experiment_stocks Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_experiment_stocks", "Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStock", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_experiment_stockprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_experiment_stockprops", "Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStockprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_geolocationprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_geolocationprops", "Bio::Chado::Schema::Result::NaturalDiversity::NdGeolocationprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_protocols Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_protocols", "Bio::Chado::Schema::Result::NaturalDiversity::NdProtocol", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_protocolprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_protocolprops", "Bio::Chado::Schema::Result::NaturalDiversity::NdProtocolprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_protocol_reagents Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_protocol_reagents", "Bio::Chado::Schema::Result::NaturalDiversity::NdProtocolReagent", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_reagents Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_reagents", "Bio::Chado::Schema::Result::NaturalDiversity::NdReagent", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_reagentprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_reagentprops", "Bio::Chado::Schema::Result::NaturalDiversity::NdReagentprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 nd_reagent_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "nd_reagent_relationships", "Bio::Chado::Schema::Result::NaturalDiversity::NdReagentRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 organismprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "organismprops", "Bio::Chado::Schema::Result::Organism::Organismprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phendescs Type: has_many Related object: L =cut __PACKAGE__->has_many( "phendescs", "Bio::Chado::Schema::Result::Genetic::Phendesc", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenotype_assays Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenotype_assays", "Bio::Chado::Schema::Result::Phenotype::Phenotype", { "foreign.assay_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenotype_attrs Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenotype_attrs", "Bio::Chado::Schema::Result::Phenotype::Phenotype", { "foreign.attr_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenotype_observables Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenotype_observables", "Bio::Chado::Schema::Result::Phenotype::Phenotype", { "foreign.observable_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenotype_cvalues Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenotype_cvalues", "Bio::Chado::Schema::Result::Phenotype::Phenotype", { "foreign.cvalue_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenotype_comparison_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenotype_comparison_cvterms", "Bio::Chado::Schema::Result::Genetic::PhenotypeComparisonCvterm", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenotype_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenotype_cvterms", "Bio::Chado::Schema::Result::Phenotype::PhenotypeCvterm", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenotypeprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenotypeprops", "Bio::Chado::Schema::Result::Phenotype::Phenotypeprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phenstatements Type: has_many Related object: L =cut __PACKAGE__->has_many( "phenstatements", "Bio::Chado::Schema::Result::Genetic::Phenstatement", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phylonodes Type: has_many Related object: L =cut __PACKAGE__->has_many( "phylonodes", "Bio::Chado::Schema::Result::Phylogeny::Phylonode", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phylonodeprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "phylonodeprops", "Bio::Chado::Schema::Result::Phylogeny::Phylonodeprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phylonode_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "phylonode_relationships", "Bio::Chado::Schema::Result::Phylogeny::PhylonodeRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 phylotrees Type: has_many Related object: L =cut __PACKAGE__->has_many( "phylotrees", "Bio::Chado::Schema::Result::Phylogeny::Phylotree", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 projectprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "projectprops", "Bio::Chado::Schema::Result::Project::Projectprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 project_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "project_relationships", "Bio::Chado::Schema::Result::Project::ProjectRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 protocols Type: has_many Related object: L =cut __PACKAGE__->has_many( "protocols", "Bio::Chado::Schema::Result::Mage::Protocol", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 protocolparam_unittypes Type: has_many Related object: L =cut __PACKAGE__->has_many( "protocolparam_unittypes", "Bio::Chado::Schema::Result::Mage::Protocolparam", { "foreign.unittype_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 protocolparam_datatypes Type: has_many Related object: L =cut __PACKAGE__->has_many( "protocolparam_datatypes", "Bio::Chado::Schema::Result::Mage::Protocolparam", { "foreign.datatype_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 pubs Type: has_many Related object: L =cut __PACKAGE__->has_many( "pubs", "Bio::Chado::Schema::Result::Pub::Pub", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 pubprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "pubprops", "Bio::Chado::Schema::Result::Pub::Pubprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 pub_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "pub_relationships", "Bio::Chado::Schema::Result::Pub::PubRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 quantificationprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "quantificationprops", "Bio::Chado::Schema::Result::Mage::Quantificationprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 quantification_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "quantification_relationships", "Bio::Chado::Schema::Result::Mage::QuantificationRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stocks Type: has_many Related object: L =cut __PACKAGE__->has_many( "stocks", "Bio::Chado::Schema::Result::Stock::Stock", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stockcollections Type: has_many Related object: L =cut __PACKAGE__->has_many( "stockcollections", "Bio::Chado::Schema::Result::Stock::Stockcollection", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stockcollectionprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "stockcollectionprops", "Bio::Chado::Schema::Result::Stock::Stockcollectionprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stock_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "stock_cvterms", "Bio::Chado::Schema::Result::Stock::StockCvterm", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stock_cvtermprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "stock_cvtermprops", "Bio::Chado::Schema::Result::Stock::StockCvtermprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stock_dbxrefprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "stock_dbxrefprops", "Bio::Chado::Schema::Result::Stock::StockDbxrefprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stockprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "stockprops", "Bio::Chado::Schema::Result::Stock::Stockprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stock_relationships Type: has_many Related object: L =cut __PACKAGE__->has_many( "stock_relationships", "Bio::Chado::Schema::Result::Stock::StockRelationship", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 stock_relationship_cvterms Type: has_many Related object: L =cut __PACKAGE__->has_many( "stock_relationship_cvterms", "Bio::Chado::Schema::Result::Stock::StockRelationshipCvterm", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 studydesignprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "studydesignprops", "Bio::Chado::Schema::Result::Mage::Studydesignprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 studyfactors Type: has_many Related object: L =cut __PACKAGE__->has_many( "studyfactors", "Bio::Chado::Schema::Result::Mage::Studyfactor", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 studyprops Type: has_many Related object: L =cut __PACKAGE__->has_many( "studyprops", "Bio::Chado::Schema::Result::Mage::Studyprop", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 studyprop_features Type: has_many Related object: L =cut __PACKAGE__->has_many( "studyprop_features", "Bio::Chado::Schema::Result::Mage::StudypropFeature", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 synonyms Type: has_many Related object: L =cut __PACKAGE__->has_many( "synonyms", "Bio::Chado::Schema::Result::Sequence::Synonym", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 treatments Type: has_many Related object: L =cut __PACKAGE__->has_many( "treatments", "Bio::Chado::Schema::Result::Mage::Treatment", { "foreign.type_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); # Created by DBIx::Class::Schema::Loader v0.07010 @ 2011-11-07 13:19:16 # DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:cPH9EGtsJO7PK5U3UZ9LvA use Carp; =head1 ADDITIONAL RELATIONS =head2 cvtermprops Type: has_many Related object: L This C relation is a convenient synonym for the autogenerated L 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 B, use C, listed above. =cut __PACKAGE__->has_many( "cvtermprops", "Bio::Chado::Schema::Result::Cv::Cvtermprop", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head2 cvtermsynonyms Type: has_many Related object: L =cut __PACKAGE__->has_many( "cvtermsynonyms", "Bio::Chado::Schema::Result::Cv::Cvtermsynonym", { "foreign.cvterm_id" => "self.cvterm_id" }, { cascade_copy => 0, cascade_delete => 0 }, ); =head1 ADDITIONAL METHODS =head2 add_synonym Usage: $self->add_synonym($synonym , { type => 'exact' , autocreate => 1} ); Desc: adds the synonym $new_synonym to this cvterm If the synonym $new_synonym already exists, nothing is added. Args: a synonym name and options hashref as: { synonym_type => [e.g. exact, narrow, broad, related], autocreate => 0, (optional) boolean, if passed, automatically create cv, cvterm, and dbxref rows if one cannot be found for the given synonym name. Default false. cv_name => cv.name to use for the given synonym type. Defaults to 'synonym_type', db_name => db.name to use for autocreated dbxrefs, default 'null', definitions => optional hashref of: { cvterm_name => definition, } to load into the cvterm table when autocreating cvterms } Ret: a Cvtermsynonym object =cut sub add_synonym { my ($self, $synonym, $opts) = @_; my $schema = $self->result_source->schema; $opts ||= {}; $opts->{cv_name} = 'synonym_type' unless defined $opts->{cv_name}; $opts->{db_name} = 'null' unless defined $opts->{db_name}; $opts->{dbxref_accession_prefix} = 'autocreated:' unless defined $opts->{dbxref_accession_prefix}; my $data; $data->{synonym} = $synonym; if (defined $opts->{synonym_type} ) { my $synonym_type= $opts->{synonym_type} ; my $synonym_db; #< set as needed below my $synonym_cv = do { my $cvrs = $schema->resultset('Cv::Cv'); my $find_or_create = $opts->{autocreate} ? 'find_or_create' : 'find'; $cvrs->$find_or_create({ name => $opts->{cv_name}}, { key => 'cv_c1' }) or croak "cv '$opts->{cv_name}' not found and autocreate option not passed, cannot continue"; }; # find/create cvterm and dbxref for the synonym, my $existing_cvterm = $synonym_cv->find_related('cvterms', { name => $synonym_type, is_obsolete => 0, }, { key => 'cvterm_c1' }, ); # if there is no existing cvterm for this synonym type, and we # have the autocreate flag set true, then create a cvterm, # dbxref, and db for it if necessary unless( $existing_cvterm ) { $opts->{autocreate} or croak "cvterm not found for cvterm synonym type '$synonym_type', and autocreate option not passed, cannot continue"; # look up the db object if we don't already have it, now # that we know we need it $synonym_db ||= $self->result_source->schema ->resultset('General::Db') ->find_or_create( { name => $opts->{db_name} }, { key => 'db_c1' } ); # find or create the dbxref for this cvterm we are about # to create my $dbx_acc = $synonym_type; my $dbxref = $synonym_db->find_or_create_related('dbxrefs',{ accession => $dbx_acc }) || $synonym_db->create_related('dbxrefs',{ accession => $dbx_acc, version => 1, }); # look up any definition we might have been given for this # propname, so we can insert it if given my $def = $opts->{definition}; my $synonym_type_cvterm= $synonym_cv->create_related('cvterms', { name => $synonym_type, is_obsolete => 0, dbxref_id => $dbxref->dbxref_id, $def ? (definition => $def) : (), } ); $data->{type_id} = $synonym_type_cvterm->cvterm_id(); } else { $data->{type_id} = $existing_cvterm->cvterm_id(); } } my ($cvtermsynonym)= $self->search_related('cvtermsynonyms', { type_id => $data->{type_id} })-> search({ 'lower(synonym)' => {like => lc($synonym) } } ); #search({ 'lower(synonym)' => { like => 'blah'}}) #my $rs = $c->model("DB::Dbentry")->$search({ #'lower('.$key.')' => $q }, #search({ \'lower(synonym)' => { like => 'blah'}}) $cvtermsynonym= $self->create_related('cvtermsynonyms' , $data) unless defined $cvtermsynonym; return $cvtermsynonym; } =head2 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 =cut sub delete_synonym { my $self=shift; my $synonym=shift; my $schema = $self->result_source->schema; $self->result_source ->schema ->resultset("Cv::Cvtermsynonym") ->search( { cvterm_id => $self->get_column('cvterm_id'), synonym => { 'like' , lc($synonym) } }) ->delete(); } =head2 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 =cut sub get_secondary_dbxrefs { my $self=shift; my $schema = $self->result_source->schema; my @list; my @s = $self->search_related('cvterm_dbxrefs' , { is_for_definition => 0} ); foreach (@s) { my $accession = $_->dbxref->accession; my $db_name = $_->dbxref->db->name; push @list, $db_name . ":" . $accession; } return @list; } =head2 add_secondary_dbxref Usage: $self->add_secondary_dbxref(accession, 1) Desc: add an alternative id to cvterm. Stores in cvterm_dbxref Ret: a CvtermDbxref object Args: an alternative id (i.e. "GO:0001234"). A second arg will store a is_for_definition=1 (default = 0) Side Effects: stores a new dbxref if accession is not found in dbxref table =cut sub add_secondary_dbxref { my ($self, $accession, $def)=@_; $def = 0 if !$def; my $schema = $self->result_source->schema; my ($db_name, $acc) = split (/:/, $accession); if (!$db_name || !$acc) { croak "Accession must be of the form :. You passed '$accession'" ; } my $db = $schema->resultset("General::Db")->find_or_create( { name => $db_name }, { key => 'db_c1' } ); my $dbxref = $db->search_related('dbxrefs', { accession => $acc })->first || $db->create_related('dbxrefs', { accession => $acc }); my $cvterm_dbxref = $schema->resultset("Cv::CvtermDbxref")->search( { dbxref_id => $dbxref->get_column('dbxref_id'), cvterm_id => $self->get_column('cvterm_id') } )->first(); if ($cvterm_dbxref) { $cvterm_dbxref->update( { is_for_definition => $def } ) if $def; }else { $cvterm_dbxref = $schema->resultset("Cv::CvtermDbxref")->create( { dbxref_id => $dbxref->get_column('dbxref_id'), cvterm_id => $self->get_column('cvterm_id'), is_for_definition => $def, } ); } return $cvterm_dbxref; } =head2 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: =cut sub delete_secondary_dbxref { my $self=shift; my $accession=shift; my $schema = $self->result_source->schema; my ($db_name, $acc) = split (/:/, $accession); if (!$db_name || !$accession) { croak "Did not pass a legal accession! ($accession)" ; } my ($cvterm_dbxref) = $schema->resultset("General::Db")->search( { name => $db_name } )-> search_related('dbxrefs' , { accession => $acc } )-> search_related('cvterm_dbxrefs', { cvterm_id => $self->get_column('cvterm_id') } ); if ($cvterm_dbxref) { $cvterm_dbxref->delete() ; } } =head2 create_cvtermprops Usage: $set->create_cvtermprops({ baz => 2, foo => 'bar' }); Desc : convenience method to create cvterm properties using cvterms from the ontology with the given name Args : hashref of { propname => value, ...}, options hashref as: { autocreate => 0, (optional) boolean, if passed, automatically create cv, cvterm, and dbxref rows if one cannot be found for the given cvtermprop name. Default false. cv_name => cv.name to use for the given cvtermprops. Defaults to 'cvterm_property', db_name => db.name to use for autocreated dbxrefs, default 'null', dbxref_accession_prefix => optional, default 'autocreated:', definitions => optional hashref of: { cvterm_name => definition, } to load into the cvterm table when autocreating cvterms rank => force numeric rank. Be careful not to pass ranks that already exist for the property type. The function will die in such case. allow_duplicate_values => default false. If true, allow duplicate instances of the same cvterm and value in the properties of the cvterm. Duplicate values will have different ranks. } Ret : hashref of { propname => new cvtermprop object } =cut sub create_cvtermprops { my ($self, $props, $opts) = @_; # process opts $opts->{cv_name} = 'cvterm_property' unless defined $opts->{cv_name}; return Bio::Chado::Schema::Util->create_properties ( properties => $props, options => $opts, row => $self, prop_relation_name => 'cvtermprops', ); } =head2 root Usage: $self->root Desc: find the root cvterm Ret: Cvterm object Args: none NOTE: This method requires that your C table is populated. =cut sub root { my $self = shift; my $root = $self->search_related('cvtermpath_subjects', {} , { order_by => { -desc => 'pathdistance'}, rows => 1, } ) ->single ->find_related('object' , {}); return $root; } =head2 children Usage: $self->children Desc: find the direct children of the cvterm Ret: L 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 =cut sub children { shift->search_related('cvterm_relationship_objects'); } =head2 direct_children Usage: $self->direct_children Desc: find only the direct children of your term Ret: L Args: none Side Effects: none NOTE: This method requires that your C table is populated. =cut sub direct_children { my $self = shift; return $self->search_related ( 'cvtermpath_subjects', { pathdistance => { '<' => 0 }, } )->search_related('object'); } #the same using cvtermpath # return $self->search_related('cvtermpath_objects' , undef , { #pathdistance => 1 , } #); =head2 recursive_children 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 Args: none Side Effects: none NOTE: This method requires that your C table is populated. =cut sub recursive_children { my $self = shift; return $self->search_related( 'cvtermpath_objects', { pathdistance => { '>' => 0 }, } )->search_related('subject'); } =head2 parents Usage: my $self->parents Desc: Find the direct parents of the cvterm Ret: L resultset of the parent terms Args: none Side Effects: none =cut sub parents { shift->search_related('cvterm_relationship_subjects'); } =head2 direct_parents Usage: $self->direct_parents Desc: get only the direct parents of the cvterm (from the cvtermpath) Ret: L Args: none Side Effects: none NOTE: This method requires that your C table is populated. =cut sub direct_parents { my $self = shift; return $self->search_related( 'cvtermpath_objects', { pathdistance => { '<' => 0 } , } )->search_related( 'subject'); } =head2 recursive_parents Usage: $self->recursive_parents Desc: find all the ancestors of the cvterm (parents, parents of parents, and so on) Ret: L resultset Args: none Side Effects: none NOTE: This method requires that your C table is populated. =cut sub recursive_parents { my $self = shift; return $self->search_related( 'cvtermpath_subjects', { pathdistance => { '>' => 0 } , } )->search_related( 'object'); } ############ CVTERM CUSTOM RESULTSET PACKAGE ############################# __PACKAGE__->resultset_class('Bio::Chado::Schema::Result::Cv::Cvterm::ResultSet'); package Bio::Chado::Schema::Result::Cv::Cvterm::ResultSet; BEGIN { $Bio::Chado::Schema::Result::Cv::Cvterm::ResultSet::AUTHORITY = 'cpan:RBUELS'; } { $Bio::Chado::Schema::Result::Cv::Cvterm::ResultSet::VERSION = '0.20000'; } use base qw/ DBIx::Class::ResultSet /; use Carp; =head2 create_with Usage: $schema->resultset('Cv::Cvterm')->create_with( { name => 'cvterm name', cv => $cv || 'cv name', db => $db || 'db name', dbxref => $dbx || 'accession', }); Desc: convenience method to create a cvterm, linking it to the CV and DB that you name or provide. For any cv, db, or dbxref that you call only by name, does a find_or_create() using that name. Ret : a new Cvterm row Args: hashref of: { name => 'cvterm name', cv => 'cv name' or L row, db => 'db name' or L row, dbxref => 'accession' or L row, } =cut sub create_with { my ($self, $opts) = @_; $opts or croak 'must provide a hashref of values to create_with'; $opts->{name} or croak 'must provide a name for the new cvterm'; # cv and db default to 'null' $opts->{cv} = 'null' unless defined $opts->{cv}; $opts->{db} = 'null' unless defined $opts->{db}; # dbxref defaults to autocreated: $opts->{dbxref} = 'autocreated:'.$opts->{name} unless defined $opts->{dbxref}; # if cv, dbxref, or db are row objects, make sure that they are # actually stored in the db, since we need to make foreign key # relationships to them $_->insert_or_update for grep ref, @{$opts}{qw| cv dbxref db |}; my $schema = $self->result_source->schema; # use, find, or create the given cv my $cv = ref $opts->{cv} ? $opts->{cv} : $schema->resultset('Cv::Cv') ->find_or_create({ name => $opts->{cv} }); # return our cvterm if it exists already if( my $cvterm = $cv->find_related( 'cvterms', { name => $opts->{name}, is_obsolete => '0', }) ) { return $cvterm; } # now figure out which dbxref to use (creating the dbxref and db if necessary) my $dbx = _find_dbxref( $schema, $opts->{dbxref}, $opts->{db} ); # and finally make a cvterm to go with the cv and dbxref we found return $cv->create_related( 'cvterms', { name => $opts->{name}, dbxref_id => $dbx->dbxref_id, } ); } sub _find_dbxref { my ( $schema, $dbx, $db ) = @_; # if we have a dbxref object to begin with, use it return $dbx if ref $dbx; ### otherwise, need to find the db unless( ref $db ) { # convert db name string into object if necessary $db = $schema->resultset('General::Db') ->find_or_create({ name => $db }); } #now find or create the dbxref from the db return $db->find_or_create_related('dbxrefs', { accession => $dbx }, ); } 1;