Mercurial > repos > mahtabm > ensembl
diff variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Constants.pm @ 0:1f6dce3d34e0
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| author | mahtabm |
|---|---|
| date | Thu, 11 Apr 2013 02:01:53 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Constants.pm Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,687 @@ +package Bio::EnsEMBL::Variation::Utils::Constants; + +##################################################################### +# NB: THIS FILE HAS BEEN AUTOMATICALLY GENERATED, EDIT WITH CAUTION # +##################################################################### + +use strict; +use warnings; + +use base qw(Exporter); + +our @EXPORT_OK = qw(%OVERLAP_CONSEQUENCES %VARIATION_CLASSES $DEFAULT_OVERLAP_CONSEQUENCE SO_TERM_INDEL SO_TERM_CODING_SEQUENCE_VARIANT SO_TERM_STOP_RETAINED_VARIANT SO_TERM_COMPLEX_STRUCTURAL_ALTERATION SO_TERM_SPLICE_ACCEPTOR_VARIANT SO_TERM_TANDEM_REPEAT SO_TERM_INTERCHROMOSOMAL_BREAKPOINT SO_TERM_FEATURE_ELONGATION SO_TERM_TRANSCRIPT_ABLATION SO_TERM_TF_BINDING_SITE_VARIANT ATTRIB_TYPE_DISPLAY_TERM SO_TERM_INTRON_VARIANT SO_TERM_STOP_GAINED SO_TERM_SPLICE_DONOR_VARIANT ATTRIB_TYPE_SIFT_PREDICTION SO_TERM_FEATURE_TRUNCATION SO_TERM_INTRACHROMOSOMAL_BREAKPOINT SO_TERM_SPLICE_REGION_VARIANT SO_TERM_TFBS_ABLATION SO_TERM_REGULATORY_REGION_AMPLIFICATION SO_TERM_MISSENSE_VARIANT SO_TERM_SNV SO_TERM_STRUCTURAL_VARIANT SO_TERM_PROBE ATTRIB_TYPE_DBSNP_CLIN_SIG SO_TERM_SEQUENCE_ALTERATION SO_TERM_REGULATORY_REGION_VARIANT SO_TERM_SUBSTITUTION ATTRIB_TYPE_DGVA_CLIN_SIG SO_TERM_INCOMPLETE_TERMINAL_CODON_VARIANT SO_TERM_DUPLICATION SO_TERM_TFBS_AMPLIFICATION SO_TERM_5_PRIME_UTR_VARIANT ATTRIB_TYPE_PROT_FUNC_ANALYSIS SO_TERM_TANDEM_DUPLICATION SO_TERM_MOBILE_ELEMENT_INSERTION SO_TERM_MATURE_MIRNA_VARIANT SO_TERM_NC_TRANSCRIPT_VARIANT SO_TERM_DOWNSTREAM_GENE_VARIANT SO_TERM_INFRAME_INSERTION SO_TERM_INSERTION SO_TERM_NMD_TRANSCRIPT_VARIANT ATTRIB_TYPE_SO_TERM SO_TERM_INTERGENIC_VARIANT SO_TERM_NON_CODING_EXON_VARIANT SO_TERM_SYNONYMOUS_VARIANT ATTRIB_TYPE_SHORT_NAME SO_TERM_TRANSLOCATION SO_TERM_COPY_NUMBER_VARIATION ATTRIB_TYPE_POLYPHEN_PREDICTION SO_TERM_REGULATORY_REGION_ABLATION SO_TERM_INVERSION SO_TERM_STOP_LOST ATTRIB_TYPE_RANK SO_TERM_INITIATOR_CODON_VARIANT SO_TERM_3_PRIME_UTR_VARIANT SO_TERM_UPSTREAM_GENE_VARIANT ATTRIB_TYPE_SO_ACCESSION SO_TERM_COPY_NUMBER_LOSS ATTRIB_TYPE_NCBI_TERM SO_TERM_DELETION ATTRIB_TYPE_FEATURE_SO_TERM SO_TERM_FRAMESHIFT_VARIANT SO_TERM_COPY_NUMBER_GAIN SO_TERM_INFRAME_DELETION SO_TERM_TRANSCRIPT_AMPLIFICATION); + +our %EXPORT_TAGS = ( attrib_types => [qw(ATTRIB_TYPE_RANK ATTRIB_TYPE_NCBI_TERM ATTRIB_TYPE_SHORT_NAME ATTRIB_TYPE_FEATURE_SO_TERM ATTRIB_TYPE_DISPLAY_TERM ATTRIB_TYPE_SO_ACCESSION ATTRIB_TYPE_DBSNP_CLIN_SIG ATTRIB_TYPE_PROT_FUNC_ANALYSIS ATTRIB_TYPE_SO_TERM ATTRIB_TYPE_SIFT_PREDICTION ATTRIB_TYPE_POLYPHEN_PREDICTION ATTRIB_TYPE_DGVA_CLIN_SIG)], SO_consequence_terms => [qw(SO_TERM_NC_TRANSCRIPT_VARIANT SO_TERM_DOWNSTREAM_GENE_VARIANT SO_TERM_CODING_SEQUENCE_VARIANT SO_TERM_STOP_RETAINED_VARIANT SO_TERM_INFRAME_INSERTION SO_TERM_NMD_TRANSCRIPT_VARIANT SO_TERM_SPLICE_ACCEPTOR_VARIANT SO_TERM_INTERGENIC_VARIANT SO_TERM_FEATURE_ELONGATION SO_TERM_NON_CODING_EXON_VARIANT SO_TERM_TRANSCRIPT_ABLATION SO_TERM_SYNONYMOUS_VARIANT SO_TERM_TF_BINDING_SITE_VARIANT SO_TERM_INTRON_VARIANT SO_TERM_STOP_GAINED SO_TERM_SPLICE_DONOR_VARIANT SO_TERM_FEATURE_TRUNCATION SO_TERM_REGULATORY_REGION_ABLATION SO_TERM_TFBS_ABLATION SO_TERM_SPLICE_REGION_VARIANT SO_TERM_STOP_LOST SO_TERM_INITIATOR_CODON_VARIANT SO_TERM_3_PRIME_UTR_VARIANT SO_TERM_REGULATORY_REGION_AMPLIFICATION SO_TERM_UPSTREAM_GENE_VARIANT SO_TERM_MISSENSE_VARIANT SO_TERM_REGULATORY_REGION_VARIANT SO_TERM_INCOMPLETE_TERMINAL_CODON_VARIANT SO_TERM_FRAMESHIFT_VARIANT SO_TERM_TFBS_AMPLIFICATION SO_TERM_5_PRIME_UTR_VARIANT SO_TERM_INFRAME_DELETION SO_TERM_TRANSCRIPT_AMPLIFICATION SO_TERM_MATURE_MIRNA_VARIANT)], SO_class_terms => [qw(SO_TERM_INDEL SO_TERM_SNV SO_TERM_STRUCTURAL_VARIANT SO_TERM_COMPLEX_STRUCTURAL_ALTERATION SO_TERM_INSERTION SO_TERM_PROBE SO_TERM_COPY_NUMBER_LOSS SO_TERM_SEQUENCE_ALTERATION SO_TERM_TANDEM_REPEAT SO_TERM_INTERCHROMOSOMAL_BREAKPOINT SO_TERM_SUBSTITUTION SO_TERM_DELETION SO_TERM_COPY_NUMBER_GAIN SO_TERM_DUPLICATION SO_TERM_TRANSLOCATION SO_TERM_COPY_NUMBER_VARIATION SO_TERM_TANDEM_DUPLICATION SO_TERM_INVERSION SO_TERM_INTRACHROMOSOMAL_BREAKPOINT SO_TERM_MOBILE_ELEMENT_INSERTION)], ); + +use Bio::EnsEMBL::Variation::OverlapConsequence; + +use constant ATTRIB_TYPE_SO_ACCESSION => 'SO_accession'; +use constant ATTRIB_TYPE_SO_TERM => 'SO_term'; +use constant ATTRIB_TYPE_DISPLAY_TERM => 'display_term'; +use constant ATTRIB_TYPE_NCBI_TERM => 'NCBI_term'; +use constant ATTRIB_TYPE_FEATURE_SO_TERM => 'feature_SO_term'; +use constant ATTRIB_TYPE_RANK => 'rank'; +use constant ATTRIB_TYPE_POLYPHEN_PREDICTION => 'polyphen_prediction'; +use constant ATTRIB_TYPE_SIFT_PREDICTION => 'sift_prediction'; +use constant ATTRIB_TYPE_SHORT_NAME => 'short_name'; +use constant ATTRIB_TYPE_DBSNP_CLIN_SIG => 'dbsnp_clin_sig'; +use constant ATTRIB_TYPE_DGVA_CLIN_SIG => 'dgva_clin_sig'; +use constant ATTRIB_TYPE_PROT_FUNC_ANALYSIS => 'prot_func_analysis'; + +use constant SO_TERM_SNV => 'SNV'; +use constant SO_TERM_SUBSTITUTION => 'substitution'; +use constant SO_TERM_COPY_NUMBER_VARIATION => 'copy_number_variation'; +use constant SO_TERM_INSERTION => 'insertion'; +use constant SO_TERM_DELETION => 'deletion'; +use constant SO_TERM_INDEL => 'indel'; +use constant SO_TERM_TANDEM_REPEAT => 'tandem_repeat'; +use constant SO_TERM_SEQUENCE_ALTERATION => 'sequence_alteration'; +use constant SO_TERM_STRUCTURAL_VARIANT => 'structural_variant'; +use constant SO_TERM_PROBE => 'probe'; +use constant SO_TERM_COPY_NUMBER_GAIN => 'copy_number_gain'; +use constant SO_TERM_COPY_NUMBER_LOSS => 'copy_number_loss'; +use constant SO_TERM_INVERSION => 'inversion'; +use constant SO_TERM_COMPLEX_STRUCTURAL_ALTERATION => 'complex_structural_alteration'; +use constant SO_TERM_TANDEM_DUPLICATION => 'tandem_duplication'; +use constant SO_TERM_MOBILE_ELEMENT_INSERTION => 'mobile_element_insertion'; +use constant SO_TERM_INTERCHROMOSOMAL_BREAKPOINT => 'interchromosomal_breakpoint'; +use constant SO_TERM_INTRACHROMOSOMAL_BREAKPOINT => 'intrachromosomal_breakpoint'; +use constant SO_TERM_TRANSLOCATION => 'translocation'; +use constant SO_TERM_DUPLICATION => 'duplication'; +use constant SO_TERM_INTERGENIC_VARIANT => 'intergenic_variant'; +use constant SO_TERM_UPSTREAM_GENE_VARIANT => 'upstream_gene_variant'; +use constant SO_TERM_DOWNSTREAM_GENE_VARIANT => 'downstream_gene_variant'; +use constant SO_TERM_SPLICE_DONOR_VARIANT => 'splice_donor_variant'; +use constant SO_TERM_SPLICE_ACCEPTOR_VARIANT => 'splice_acceptor_variant'; +use constant SO_TERM_SPLICE_REGION_VARIANT => 'splice_region_variant'; +use constant SO_TERM_INTRON_VARIANT => 'intron_variant'; +use constant SO_TERM_5_PRIME_UTR_VARIANT => '5_prime_UTR_variant'; +use constant SO_TERM_3_PRIME_UTR_VARIANT => '3_prime_UTR_variant'; +use constant SO_TERM_SYNONYMOUS_VARIANT => 'synonymous_variant'; +use constant SO_TERM_MISSENSE_VARIANT => 'missense_variant'; +use constant SO_TERM_INFRAME_INSERTION => 'inframe_insertion'; +use constant SO_TERM_INFRAME_DELETION => 'inframe_deletion'; +use constant SO_TERM_STOP_GAINED => 'stop_gained'; +use constant SO_TERM_STOP_LOST => 'stop_lost'; +use constant SO_TERM_STOP_RETAINED_VARIANT => 'stop_retained_variant'; +use constant SO_TERM_INITIATOR_CODON_VARIANT => 'initiator_codon_variant'; +use constant SO_TERM_FRAMESHIFT_VARIANT => 'frameshift_variant'; +use constant SO_TERM_INCOMPLETE_TERMINAL_CODON_VARIANT => 'incomplete_terminal_codon_variant'; +use constant SO_TERM_NMD_TRANSCRIPT_VARIANT => 'NMD_transcript_variant'; +use constant SO_TERM_NC_TRANSCRIPT_VARIANT => 'nc_transcript_variant'; +use constant SO_TERM_NON_CODING_EXON_VARIANT => 'non_coding_exon_variant'; +use constant SO_TERM_MATURE_MIRNA_VARIANT => 'mature_miRNA_variant'; +use constant SO_TERM_CODING_SEQUENCE_VARIANT => 'coding_sequence_variant'; +use constant SO_TERM_REGULATORY_REGION_VARIANT => 'regulatory_region_variant'; +use constant SO_TERM_TF_BINDING_SITE_VARIANT => 'TF_binding_site_variant'; +use constant SO_TERM_TRANSCRIPT_ABLATION => 'transcript_ablation'; +use constant SO_TERM_TRANSCRIPT_AMPLIFICATION => 'transcript_amplification'; +use constant SO_TERM_TFBS_ABLATION => 'TFBS_ablation'; +use constant SO_TERM_TFBS_AMPLIFICATION => 'TFBS_amplification'; +use constant SO_TERM_REGULATORY_REGION_ABLATION => 'regulatory_region_ablation'; +use constant SO_TERM_REGULATORY_REGION_AMPLIFICATION => 'regulatory_region_amplification'; +use constant SO_TERM_FEATURE_ELONGATION => 'feature_elongation'; +use constant SO_TERM_FEATURE_TRUNCATION => 'feature_truncation'; + +our %VARIATION_CLASSES = ( +'SNV' => { + 'somatic_display_term' => 'somatic_SNV', + 'SO_accession' => 'SO:0001483', + 'display_term' => 'SNP' +} +, +'substitution' => { + 'somatic_display_term' => 'somatic_substitution', + 'SO_accession' => 'SO:1000002', + 'display_term' => 'substitution' +} +, +'copy_number_variation' => { + 'somatic_display_term' => 'somatic_CNV', + 'SO_accession' => 'SO:0001019', + 'display_term' => 'CNV' +} +, +'insertion' => { + 'somatic_display_term' => 'somatic_insertion', + 'SO_accession' => 'SO:0000667', + 'display_term' => 'insertion' +} +, +'deletion' => { + 'somatic_display_term' => 'somatic_deletion', + 'SO_accession' => 'SO:0000159', + 'display_term' => 'deletion' +} +, +'indel' => { + 'somatic_display_term' => 'somatic_indel', + 'SO_accession' => 'SO:1000032', + 'display_term' => 'indel' +} +, +'tandem_repeat' => { + 'somatic_display_term' => 'somatic_tandem_repeat', + 'SO_accession' => 'SO:0000705', + 'display_term' => 'tandem_repeat' +} +, +'sequence_alteration' => { + 'somatic_display_term' => 'somatic_sequence_alteration', + 'SO_accession' => 'SO:0001059', + 'display_term' => 'sequence_alteration' +} +, +'structural_variant' => { + 'somatic_display_term' => 'somatic_SV', + 'SO_accession' => 'SO:0001537', + 'display_term' => 'SV' +} +, +'probe' => { + 'somatic_display_term' => 'somatic_CNV_PROBE', + 'SO_accession' => 'SO:0000051', + 'display_term' => 'CNV_PROBE' +} +, +'copy_number_gain' => { + 'somatic_display_term' => 'somatic_Gain', + 'SO_accession' => 'SO:0001742', + 'display_term' => 'Gain' +} +, +'copy_number_loss' => { + 'somatic_display_term' => 'somatic_Loss', + 'SO_accession' => 'SO:0001743', + 'display_term' => 'Loss' +} +, +'inversion' => { + 'somatic_display_term' => 'somatic_inversion', + 'SO_accession' => 'SO:1000036', + 'display_term' => 'inversion' +} +, +'complex_structural_alteration' => { + 'somatic_display_term' => 'somatic_Complex', + 'SO_accession' => 'SO:0001784', + 'display_term' => 'Complex' +} +, +'tandem_duplication' => { + 'somatic_display_term' => 'somatic_Tandem duplication', + 'SO_accession' => 'SO:1000173', + 'display_term' => 'Tandem duplication' +} +, +'mobile_element_insertion' => { + 'somatic_display_term' => 'somatic_Mobile element insertion', + 'SO_accession' => 'SO:0001837', + 'display_term' => 'Mobile element insertion' +} +, +'interchromosomal_breakpoint' => { + 'somatic_display_term' => 'somatic_Interchromosomal breakpoint', + 'SO_accession' => 'SO:0001873', + 'display_term' => 'Interchromosomal breakpoint' +} +, +'intrachromosomal_breakpoint' => { + 'somatic_display_term' => 'somatic_Intrachromosomal breakpoint', + 'SO_accession' => 'SO:0001874', + 'display_term' => 'Intrachromosomal breakpoint' +} +, +'translocation' => { + 'somatic_display_term' => 'somatic_translocation', + 'SO_accession' => 'SO:0000199', + 'display_term' => 'translocation' +} +, +'duplication' => { + 'somatic_display_term' => 'somatic_Duplication', + 'SO_accession' => 'SO:1000035', + 'display_term' => 'Duplication' +} +, +); + +our $DEFAULT_OVERLAP_CONSEQUENCE = Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'tier' => '4', + 'SO_term' => 'intergenic_variant', + 'is_default' => 1, + 'label' => 'Intergenic variant', + 'description' => 'A sequence variant located in the intergenic region, between genes', + 'rank' => '38', + 'SO_accession' => 'SO:0001628', + 'display_term' => 'INTERGENIC' +} +); + + +our %OVERLAP_CONSEQUENCES = ( +'intergenic_variant' => $DEFAULT_OVERLAP_CONSEQUENCE, +'upstream_gene_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'transcript', + 'description' => 'A sequence variant located 5\' of a gene', + 'SO_accession' => 'SO:0001631', + 'SO_term' => 'upstream_gene_variant', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::upstream', + 'label' => 'Upstream gene variant', + 'rank' => '24', + 'display_term' => 'UPSTREAM', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'downstream_gene_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'transcript', + 'description' => 'A sequence variant located 3\' of a gene', + 'SO_accession' => 'SO:0001632', + 'SO_term' => 'downstream_gene_variant', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::downstream', + 'label' => 'Downstream gene variant', + 'rank' => '25', + 'display_term' => 'DOWNSTREAM', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'splice_donor_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature', + 'NCBI_term' => 'splice-5', + 'feature_SO_term' => 'primary_transcript', + 'description' => 'A splice variant that changes the 2 base region at the 5\' end of an intron', + 'SO_accession' => 'SO:0001575', + 'tier' => '3', + 'SO_term' => 'splice_donor_variant', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::donor_splice_site', + 'label' => 'Splice donor variant', + 'rank' => '3', + 'display_term' => 'ESSENTIAL_SPLICE_SITE', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'splice_acceptor_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature', + 'NCBI_term' => 'splice-3', + 'feature_SO_term' => 'primary_transcript', + 'description' => 'A splice variant that changes the 2 base region at the 3\' end of an intron', + 'SO_accession' => 'SO:0001574', + 'tier' => '3', + 'SO_term' => 'splice_acceptor_variant', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::acceptor_splice_site', + 'label' => 'Splice acceptor variant', + 'rank' => '3', + 'display_term' => 'ESSENTIAL_SPLICE_SITE', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'splice_region_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature', + 'feature_SO_term' => 'primary_transcript', + 'description' => 'A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron', + 'SO_accession' => 'SO:0001630', + 'SO_term' => 'splice_region_variant', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::splice_region', + 'label' => 'Splice region variant', + 'rank' => '13', + 'display_term' => 'SPLICE_SITE', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'intron_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'NCBI_term' => 'intron', + 'feature_SO_term' => 'primary_transcript', + 'description' => 'A transcript variant occurring within an intron', + 'SO_accession' => 'SO:0001627', + 'tier' => '3', + 'SO_term' => 'intron_variant', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_intron', + 'label' => 'Intron variant', + 'rank' => '20', + 'display_term' => 'INTRONIC', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'5_prime_UTR_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'NCBI_term' => 'untranslated_5', + 'feature_SO_term' => 'mRNA', + 'description' => 'A UTR variant of the 5\' UTR', + 'SO_accession' => 'SO:0001623', + 'tier' => '3', + 'SO_term' => '5_prime_UTR_variant', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_5_prime_utr', + 'label' => '5 prime UTR variant', + 'rank' => '18', + 'display_term' => '5PRIME_UTR', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'3_prime_UTR_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'NCBI_term' => 'untranslated_3', + 'feature_SO_term' => 'mRNA', + 'description' => 'A UTR variant of the 3\' UTR', + 'SO_accession' => 'SO:0001624', + 'tier' => '3', + 'SO_term' => '3_prime_UTR_variant', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_3_prime_utr', + 'label' => '3 prime UTR variant', + 'rank' => '19', + 'display_term' => '3PRIME_UTR', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'synonymous_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature', + 'NCBI_term' => 'cds-synon', + 'feature_SO_term' => 'mRNA', + 'description' => 'A sequence variant where there is no resulting change to the encoded amino acid', + 'SO_accession' => 'SO:0001819', + 'tier' => '3', + 'SO_term' => 'synonymous_variant', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::synonymous_variant', + 'label' => 'Synonymous variant', + 'rank' => '15', + 'display_term' => 'SYNONYMOUS_CODING', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'missense_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature', + 'NCBI_term' => 'missense', + 'feature_SO_term' => 'mRNA', + 'description' => 'A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid', + 'SO_accession' => 'SO:0001583', + 'tier' => '3', + 'SO_term' => 'missense_variant', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::missense_variant', + 'label' => 'Missense variant', + 'rank' => '12', + 'display_term' => 'NON_SYNONYMOUS_CODING', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'inframe_insertion' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'mRNA', + 'description' => 'An inframe non synonymous variant that inserts bases into in the coding sequence', + 'SO_accession' => 'SO:0001821', + 'SO_term' => 'inframe_insertion', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_insertion', + 'label' => 'Inframe insertion', + 'rank' => '10', + 'display_term' => 'NON_SYNONYMOUS_CODING', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'inframe_deletion' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'mRNA', + 'description' => 'An inframe non synonymous variant that deletes bases from the coding sequence', + 'SO_accession' => 'SO:0001822', + 'SO_term' => 'inframe_deletion', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_deletion', + 'label' => 'Inframe deletion', + 'rank' => '11', + 'display_term' => 'NON_SYNONYMOUS_CODING', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'stop_gained' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature', + 'NCBI_term' => 'nonsense', + 'feature_SO_term' => 'mRNA', + 'description' => 'A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript', + 'SO_accession' => 'SO:0001587', + 'tier' => '3', + 'SO_term' => 'stop_gained', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_gained', + 'label' => 'Stop gained', + 'rank' => '4', + 'display_term' => 'STOP_GAINED', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'stop_lost' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'mRNA', + 'description' => 'A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript', + 'SO_accession' => 'SO:0001578', + 'SO_term' => 'stop_lost', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_lost', + 'label' => 'Stop lost', + 'rank' => '6', + 'display_term' => 'STOP_LOST', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'stop_retained_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature', + 'feature_SO_term' => 'mRNA', + 'description' => 'A sequence variant where at least one base in the terminator codon is changed, but the terminator remains', + 'SO_accession' => 'SO:0001567', + 'SO_term' => 'stop_retained_variant', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_retained', + 'label' => 'Stop retained variant', + 'rank' => '15', + 'display_term' => 'SYNONYMOUS_CODING', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'initiator_codon_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'mRNA', + 'description' => 'A codon variant that changes at least one base of the first codon of a transcript', + 'SO_accession' => 'SO:0001582', + 'SO_term' => 'initiator_codon_variant', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::affects_start_codon', + 'label' => 'Initiator codon variant', + 'rank' => '7', + 'display_term' => 'NON_SYNONYMOUS_CODING', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'frameshift_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'NCBI_term' => 'frameshift', + 'feature_SO_term' => 'mRNA', + 'description' => 'A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three', + 'SO_accession' => 'SO:0001589', + 'tier' => '3', + 'SO_term' => 'frameshift_variant', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::frameshift', + 'label' => 'Frameshift variant', + 'rank' => '5', + 'display_term' => 'FRAMESHIFT_CODING', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'incomplete_terminal_codon_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::VariationFeature', + 'feature_SO_term' => 'mRNA', + 'description' => 'A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed', + 'SO_accession' => 'SO:0001626', + 'SO_term' => 'incomplete_terminal_codon_variant', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::partial_codon', + 'label' => 'Incomplete terminal codon variant', + 'rank' => '14', + 'display_term' => 'PARTIAL_CODON', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'NMD_transcript_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'mRNA', + 'description' => 'A variant in a transcript that is the target of NMD', + 'SO_accession' => 'SO:0001621', + 'SO_term' => 'NMD_transcript_variant', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_nmd_transcript', + 'label' => 'NMD transcript variant', + 'rank' => '21', + 'display_term' => 'NMD_TRANSCRIPT', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'nc_transcript_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'ncRNA', + 'description' => 'A transcript variant of a non coding RNA', + 'SO_accession' => 'SO:0001619', + 'SO_term' => 'nc_transcript_variant', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_non_coding_gene', + 'label' => 'NC transcript variant', + 'rank' => '23', + 'display_term' => 'WITHIN_NON_CODING_GENE', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'non_coding_exon_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'ncRNA', + 'description' => 'A sequence variant that changes non-coding exon sequence', + 'SO_accession' => 'SO:0001792', + 'SO_term' => 'non_coding_exon_variant', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::non_coding_exon_variant', + 'label' => 'Non coding exon variant', + 'rank' => '22', + 'display_term' => 'WITHIN_NON_CODING_GENE', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'mature_miRNA_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'miRNA', + 'description' => 'A transcript variant located with the sequence of the mature miRNA', + 'SO_accession' => 'SO:0001620', + 'SO_term' => 'mature_miRNA_variant', + 'tier' => '2', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_mature_miRNA', + 'label' => 'Mature miRNA variant', + 'rank' => '17', + 'display_term' => 'WITHIN_MATURE_miRNA', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'coding_sequence_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'mRNA', + 'description' => 'A sequence variant that changes the coding sequence', + 'SO_accession' => 'SO:0001580', + 'SO_term' => 'coding_sequence_variant', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::coding_unknown', + 'label' => 'Coding sequence variant', + 'rank' => '16', + 'display_term' => 'CODING_UNKNOWN', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'regulatory_region_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'regulatory_region', + 'description' => 'A sequence variant located within a regulatory region', + 'SO_accession' => 'SO:0001566', + 'SO_term' => 'regulatory_region_variant', + 'tier' => '2', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_regulatory_feature', + 'label' => 'Regulatory region variant', + 'rank' => '36', + 'display_term' => 'REGULATORY_REGION', + 'feature_class' => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature' +} +), +'TF_binding_site_variant' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'TF_binding_site', + 'description' => 'In regulatory region annotated by Ensembl', + 'SO_accession' => 'SO:0001782', + 'SO_term' => 'TF_binding_site_variant', + 'tier' => '2', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_motif_feature', + 'label' => 'A sequence variant located within a transcription factor binding site', + 'rank' => '30', + 'display_term' => 'REGULATORY_REGION', + 'feature_class' => 'Bio::EnsEMBL::Funcgen::MotifFeature' +} +), +'transcript_ablation' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'mRNA', + 'description' => 'A feature ablation whereby the deleted region includes a transcript feature', + 'SO_accession' => 'SO:0001893', + 'SO_term' => 'transcript_ablation', + 'tier' => '1', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation', + 'label' => 'Transcript ablation', + 'rank' => '1', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'transcript_amplification' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'mRNA', + 'description' => 'A feature amplification of a region containing a transcript', + 'SO_accession' => 'SO:0001889', + 'SO_term' => 'transcript_amplification', + 'tier' => '1', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification', + 'label' => 'Transcript amplification', + 'rank' => '8', + 'feature_class' => 'Bio::EnsEMBL::Transcript' +} +), +'TFBS_ablation' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'TF_binding_site', + 'description' => 'A feature ablation whereby the deleted region includes a transcription factor binding site', + 'SO_accession' => 'SO:0001895', + 'SO_term' => 'TFBS_ablation', + 'tier' => '2', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation', + 'label' => 'TFBS ablation', + 'rank' => '26', + 'feature_class' => 'Bio::EnsEMBL::Funcgen::MotifFeature' +} +), +'TFBS_amplification' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'TF_binding_site', + 'description' => 'A feature amplification of a region containing a transcription factor binding site', + 'SO_accession' => 'SO:0001892', + 'SO_term' => 'TFBS_amplification', + 'tier' => '2', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification', + 'label' => 'TFBS amplification', + 'rank' => '28', + 'feature_class' => 'Bio::EnsEMBL::Funcgen::MotifFeature' +} +), +'regulatory_region_ablation' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'TF_binding_site', + 'description' => 'A feature ablation whereby the deleted region includes a regulatory region', + 'SO_accession' => 'SO:0001894', + 'SO_term' => 'regulatory_region_ablation', + 'tier' => '2', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation', + 'label' => 'Regulatory region ablation', + 'rank' => '31', + 'feature_class' => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature' +} +), +'regulatory_region_amplification' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'feature_SO_term' => 'TF_binding_site', + 'description' => 'A feature amplification of a region containing a regulatory region', + 'SO_accession' => 'SO:0001891', + 'SO_term' => 'regulatory_region_amplification', + 'tier' => '2', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification', + 'label' => 'Regulatory region amplification', + 'rank' => '33', + 'feature_class' => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature' +} +), +'feature_elongation' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'description' => 'A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence', + 'SO_accession' => 'SO:0001907', + 'SO_term' => 'feature_elongation', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_elongation', + 'label' => 'Feature elongation', + 'rank' => '36', + 'feature_class' => 'Bio::EnsEMBL::Feature' +} +), +'feature_truncation' => Bio::EnsEMBL::Variation::OverlapConsequence->new_fast({ + 'variant_feature_class' => 'Bio::EnsEMBL::Variation::BaseVariationFeature', + 'description' => 'A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence', + 'SO_accession' => 'SO:0001906', + 'SO_term' => 'feature_truncation', + 'tier' => '3', + 'predicate' => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_truncation', + 'label' => 'Feature truncation', + 'rank' => '37', + 'feature_class' => 'Bio::EnsEMBL::Feature' +} +), +); + +1;