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view variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Config.pm @ 0:1f6dce3d34e0
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| author | mahtabm |
|---|---|
| date | Thu, 11 Apr 2013 02:01:53 -0400 |
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package Bio::EnsEMBL::Variation::Utils::Config; use base qw(Exporter); our @EXPORT_OK = qw( @ATTRIB_TYPES %ATTRIBS @ATTRIB_SETS @VARIATION_CLASSES @OVERLAP_CONSEQUENCES @FEATURE_TYPES $OVERLAP_CONSEQUENCE_CLASS $MAX_ATTRIB_CODE_LENGTH ); our $OVERLAP_CONSEQUENCE_CLASS = 'Bio::EnsEMBL::Variation::OverlapConsequence'; our $MAX_ATTRIB_CODE_LENGTH = 20; our @short_names = qw(1kg_hct 1kg_hct_ceu 1kg_hct_yri 1kg_hce 1kg_hce_ceu 1kg_hce_chb 1kg_hce_chd 1kg_hce_jpt 1kg_hce_lwk 1kg_hce_tsi 1kg_hce_yri 1kg_lc 1kg_lc_ceu 1kg_lc_chb_jpt 1kg_lc_yri hapmap 1kg 1kg_afr 1kg_amr 1kg_asn 1kg_eur 1kg_afr 1kg_amr_com 1kg_asn_com 1kg_eur_com ind_venter ind_watson ind_gill ind_ak1 ind_irish ind_angrist ind_gates_jr ind_gates_sr ind_kriek ind_quake ind_saqqaq ind_saqqaq_hc ind_sjk ind_yh fail_all fail_nonref fail_ambig fail_gt_fq fail_incons_map fail_mult_map fail_no_alleles fail_no_gt fail_no_map fail_no_seq fail_non_nt fail_mult_alleles fail_dbsnp_suspect ph_hgmd_pub ph_johnson_et_al ph_nhgri ph_omim ph_variants ph_uniprot ph_cosmic ph_ega precious hapmap_ceu hapmap_hcb hapmap_jpt hapmap_yri Affy_500K Affy_SNP6 Cardio-Metabo_Chip HumanOmni1-Quad Illumina_1M-duo Illumina_660Q ); our @dbsnp_clinical_significance_types = qw( unknown untested non-pathogenic probable-non-pathogenic probable-pathogenic pathogenic drug-response histocompatibility other ); our @dgva_clinical_significance_types = ( 'Not tested', 'Benign', 'Pathogenic', 'Uncertain Significance', 'Uncertain Significance: likely benign', 'Uncertain Significance: likely pathogenic' ); our @VARIATION_CLASSES = ( { SO_accession => 'SO:0001483', SO_term => 'SNV', display_term => 'SNP', somatic_display_term => 'somatic_SNV', }, { SO_accession => 'SO:1000002', SO_term => 'substitution', }, { SO_accession => 'SO:0001019', SO_term => 'copy_number_variation', display_term => 'CNV', }, { SO_accession => 'SO:0000667', SO_term => 'insertion', }, { SO_accession => 'SO:0000159', SO_term => 'deletion', }, { SO_accession => 'SO:1000032', SO_term => 'indel', }, { SO_accession => 'SO:0000705', SO_term => 'tandem_repeat', }, { SO_accession => 'SO:0001059', SO_term => 'sequence_alteration', }, # Structural variation classes { SO_accession => 'SO:0001537', SO_term => 'structural_variant', display_term => 'SV', }, { SO_accession => 'SO:0000051', SO_term => 'probe', display_term => 'CNV_PROBE', }, { SO_accession => 'SO:0001742', SO_term => 'copy_number_gain', display_term => 'Gain', }, { SO_accession => 'SO:0001743', SO_term => 'copy_number_loss', display_term => 'Loss', }, { SO_accession => 'SO:1000036', SO_term => 'inversion', }, { SO_accession => 'SO:0001784', SO_term => 'complex_structural_alteration', display_term => 'Complex', }, { SO_accession => 'SO:1000173', SO_term => 'tandem_duplication', display_term => 'Tandem duplication', }, { SO_accession => 'SO:0001837', SO_term => 'mobile_element_insertion', display_term => 'Mobile element insertion', }, { SO_accession => 'SO:0001873', SO_term => 'interchromosomal_breakpoint', display_term => 'Interchromosomal breakpoint', }, { SO_accession => 'SO:0001874', SO_term => 'intrachromosomal_breakpoint', display_term => 'Intrachromosomal breakpoint', }, { SO_accession => 'SO:0000199', SO_term => 'translocation', }, { SO_accession => 'SO:1000035', SO_term => 'duplication', display_term => 'Duplication', }, ); our @OVERLAP_CONSEQUENCES = ( { SO_accession => 'SO:0001628', SO_term => 'intergenic_variant', display_term => 'INTERGENIC', rank => '38', tier => '4', description => 'A sequence variant located in the intergenic region, between genes', label => 'Intergenic variant', is_default => 1, }, { SO_accession => 'SO:0001631', SO_term => 'upstream_gene_variant', display_term => 'UPSTREAM', feature_SO_term => 'transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '24', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::upstream', description => 'A sequence variant located 5\' of a gene', label => 'Upstream gene variant', }, { SO_accession => 'SO:0001632', SO_term => 'downstream_gene_variant', display_term => 'DOWNSTREAM', feature_SO_term => 'transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '25', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::downstream', description => 'A sequence variant located 3\' of a gene', label => 'Downstream gene variant', }, { SO_accession => 'SO:0001575', SO_term => 'splice_donor_variant', display_term => 'ESSENTIAL_SPLICE_SITE', NCBI_term => 'splice-5', feature_SO_term => 'primary_transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '3', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::donor_splice_site', description => 'A splice variant that changes the 2 base region at the 5\' end of an intron', label => 'Splice donor variant', }, { SO_accession => 'SO:0001574', SO_term => 'splice_acceptor_variant', display_term => 'ESSENTIAL_SPLICE_SITE', NCBI_term => 'splice-3', feature_SO_term => 'primary_transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '3', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::acceptor_splice_site', description => 'A splice variant that changes the 2 base region at the 3\' end of an intron', label => 'Splice acceptor variant', }, { SO_accession => 'SO:0001630', SO_term => 'splice_region_variant', display_term => 'SPLICE_SITE', feature_SO_term => 'primary_transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '13', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::splice_region', 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', label => 'Splice region variant', }, { SO_accession => 'SO:0001627', SO_term => 'intron_variant', display_term => 'INTRONIC', NCBI_term => 'intron', feature_SO_term => 'primary_transcript', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '20', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_intron', description => 'A transcript variant occurring within an intron', label => 'Intron variant', }, { SO_accession => 'SO:0001623', SO_term => '5_prime_UTR_variant', display_term => '5PRIME_UTR', NCBI_term => 'untranslated_5', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '18', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_5_prime_utr', description => 'A UTR variant of the 5\' UTR', label => '5 prime UTR variant', }, { SO_accession => 'SO:0001624', SO_term => '3_prime_UTR_variant', display_term => '3PRIME_UTR', NCBI_term => 'untranslated_3', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '19', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_3_prime_utr', description => 'A UTR variant of the 3\' UTR', label => '3 prime UTR variant', }, # { # SO_accession => 'SO:0001577', # SO_term => 'complex_change_in_transcript', # display_term => 'COMPLEX_INDEL', # feature_SO_term => 'primary_transcript', # feature_class => 'Bio::EnsEMBL::Transcript', # variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', # rank => '4', # tier => '3', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::complex_indel', # description => 'Insertion or deletion that spans an exon/intron or coding sequence/UTR border', # label => 'Complex change in transcript', # }, { SO_accession => 'SO:0001819', SO_term => 'synonymous_variant', display_term => 'SYNONYMOUS_CODING', NCBI_term => 'cds-synon', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '15', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::synonymous_variant', description => 'A sequence variant where there is no resulting change to the encoded amino acid', label => 'Synonymous variant', }, { SO_accession => 'SO:0001583', SO_term => 'missense_variant', display_term => 'NON_SYNONYMOUS_CODING', NCBI_term => 'missense', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '12', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::missense_variant', 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', label => 'Missense variant', }, { SO_accession => 'SO:0001821', SO_term => 'inframe_insertion', display_term => 'NON_SYNONYMOUS_CODING', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '10', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_insertion', description => 'An inframe non synonymous variant that inserts bases into in the coding sequence', label => 'Inframe insertion', }, { SO_accession => 'SO:0001822', SO_term => 'inframe_deletion', display_term => 'NON_SYNONYMOUS_CODING', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '11', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_deletion', description => 'An inframe non synonymous variant that deletes bases from the coding sequence', label => 'Inframe deletion', }, { SO_accession => 'SO:0001587', SO_term => 'stop_gained', display_term => 'STOP_GAINED', NCBI_term => 'nonsense', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '4', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_gained', 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', label => 'Stop gained', }, { SO_accession => 'SO:0001578', SO_term => 'stop_lost', display_term => 'STOP_LOST', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '6', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_lost', description => 'A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript', label => 'Stop lost', }, { SO_accession => 'SO:0001567', SO_term => 'stop_retained_variant', display_term => 'SYNONYMOUS_CODING', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '15', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_retained', description => 'A sequence variant where at least one base in the terminator codon is changed, but the terminator remains', label => 'Stop retained variant', }, { SO_accession => 'SO:0001582', SO_term => 'initiator_codon_variant', display_term => 'NON_SYNONYMOUS_CODING', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '7', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::affects_start_codon', description => 'A codon variant that changes at least one base of the first codon of a transcript', label => 'Initiator codon variant', }, { SO_accession => 'SO:0001589', SO_term => 'frameshift_variant', display_term => 'FRAMESHIFT_CODING', NCBI_term => 'frameshift', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '5', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::frameshift', 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', label => 'Frameshift variant', }, { SO_accession => 'SO:0001626', SO_term => 'incomplete_terminal_codon_variant', display_term => 'PARTIAL_CODON', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature', rank => '14', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::partial_codon', description => 'A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed', label => 'Incomplete terminal codon variant', }, { SO_accession => 'SO:0001621', SO_term => 'NMD_transcript_variant', display_term => 'NMD_TRANSCRIPT', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '21', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_nmd_transcript', description => 'A variant in a transcript that is the target of NMD', label => 'NMD transcript variant', }, { SO_accession => 'SO:0001619', SO_term => 'nc_transcript_variant', display_term => 'WITHIN_NON_CODING_GENE', feature_SO_term => 'ncRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '23', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_non_coding_gene', description => 'A transcript variant of a non coding RNA', label => 'NC transcript variant', }, { SO_accession => 'SO:0001792', SO_term => 'non_coding_exon_variant', display_term => 'WITHIN_NON_CODING_GENE', feature_SO_term => 'ncRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '22', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::non_coding_exon_variant', description => 'A sequence variant that changes non-coding exon sequence', label => 'Non coding exon variant', }, { SO_accession => 'SO:0001620', SO_term => 'mature_miRNA_variant', display_term => 'WITHIN_MATURE_miRNA', feature_SO_term => 'miRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '17', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_mature_miRNA', description => 'A transcript variant located with the sequence of the mature miRNA', label => 'Mature miRNA variant', }, { SO_accession => 'SO:0001580', SO_term => 'coding_sequence_variant', display_term => 'CODING_UNKNOWN', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '16', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::coding_unknown', description => 'A sequence variant that changes the coding sequence', label => 'Coding sequence variant', }, { SO_accession => 'SO:0001566', SO_term => 'regulatory_region_variant', display_term => 'REGULATORY_REGION', feature_SO_term => 'regulatory_region', feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '36', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_regulatory_feature', description => 'A sequence variant located within a regulatory region', label => 'Regulatory region variant', }, # { # SO_accession => 'SO:X000005', # SO_term => 'pre_miRNA_variant', # display_term => 'WITHIN_NON_CODING_GENE', # feature_SO_term => 'miRNA', # feature_class => 'Bio::EnsEMBL::Transcript', # rank => '13', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_miRNA', # }, # { # SO_accession => 'SO:X000004', # SO_term => 'miRNA_target_site_variant', # display_term => 'REGULATORY_REGION', # feature_SO_term => 'binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature', # rank => '13', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_miRNA_target_site', # description => 'In regulatory region annotated by Ensembl', # label => 'Regulatory region', # }, { SO_accession => 'SO:0001782', SO_term => 'TF_binding_site_variant', display_term => 'REGULATORY_REGION', feature_SO_term => 'TF_binding_site', feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '30', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_motif_feature', description => 'In regulatory region annotated by Ensembl', label => 'A sequence variant located within a transcription factor binding site', }, # { # SO_accession => 'SO:X000002', # SO_term => 'decreased_binding_affinity', # display_term => 'REGULATORY_REGION', # feature_SO_term => 'binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', # rank => '47', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::decreased_binding_affinity', # }, # { # SO_accession => 'SO:X000001', # SO_term => 'increased_binding_affinity', # display_term => 'REGULATORY_REGION', # feature_SO_term => 'binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', # rank => '48', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::increased_binding_affinity', # }, ## NEW FOR 68 ############# { SO_accession => 'SO:0001893', SO_term => 'transcript_ablation', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '1', tier => '1', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation', description => 'A feature ablation whereby the deleted region includes a transcript feature', label => 'Transcript ablation', }, # { # SO_accession => 'SO:0001886', # SO_term => 'transcript_fusion', # feature_SO_term => 'mRNA', # feature_class => 'Bio::EnsEMBL::Transcript', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '2', # tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::transcript_fusion', # description => 'A feature fusion where the deletion brings together transcript regions', # label => 'Transcript fusion', # }, { SO_accession => 'SO:0001889', SO_term => 'transcript_amplification', feature_SO_term => 'mRNA', feature_class => 'Bio::EnsEMBL::Transcript', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '8', tier => '1', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification', description => 'A feature amplification of a region containing a transcript', label => 'Transcript amplification', }, # { # SO_accession => 'SO:0001883', # SO_term => 'transcript_translocation', # feature_SO_term => 'mRNA', # feature_class => 'Bio::EnsEMBL::Transcript', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '9', #tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::transcript_translocation', # description => 'A feature translocation where the region contains a transcript', # label => 'Transcript translocation', # }, { SO_accession => 'SO:0001895', SO_term => 'TFBS_ablation', feature_SO_term => 'TF_binding_site', feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '26', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation', description => 'A feature ablation whereby the deleted region includes a transcription factor binding site', label => 'TFBS ablation', }, # { # SO_accession => 'SO:0001888', # SO_term => 'TFBS_fusion', # feature_SO_term => 'TF_binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '27', #tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::motif_feature_fusion', # description => 'A fusion where the deletion brings together transcription factor binding sites', # label => 'TFBS fusion', # }, { SO_accession => 'SO:0001892', SO_term => 'TFBS_amplification', feature_SO_term => 'TF_binding_site', feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '28', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification', description => 'A feature amplification of a region containing a transcription factor binding site', label => 'TFBS amplification', }, # { # SO_accession => 'SO:0001885', # SO_term => 'TFBS_translocation', # feature_SO_term => 'TF_binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '29', #tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::motif_feature_translocation', # description => 'A feature translocation where the region contains a transcription factor binding site', # label => 'TFBS translocation', # }, { SO_accession => 'SO:0001894', SO_term => 'regulatory_region_ablation', feature_SO_term => 'TF_binding_site', feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '31', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation', description => 'A feature ablation whereby the deleted region includes a regulatory region', label => 'Regulatory region ablation', }, # { # SO_accession => 'SO:0001887', # SO_term => 'regulatory_region_fusion', # feature_SO_term => 'TF_binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '32', #tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::regulatory_feature_fusion', # description => 'A fusion where the deletion brings together regulatory regions', # label => 'Regulatory region fusion', # }, { SO_accession => 'SO:0001891', SO_term => 'regulatory_region_amplification', feature_SO_term => 'TF_binding_site', feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '33', tier => '2', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification', description => 'A feature amplification of a region containing a regulatory region', label => 'Regulatory region amplification', }, # { # SO_accession => 'SO:0001884', # SO_term => 'regulatory_region_translocation', # feature_SO_term => 'TF_binding_site', # feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', # rank => '34', #tier => '2', # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::regulatory_feature_translocation', # description => 'A feature translocation where the region contains a regulatory region', # label => 'Regulatory region translocation', # }, { SO_accession => 'SO:0001907', SO_term => 'feature_elongation', feature_class => 'Bio::EnsEMBL::Feature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '36', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_elongation', description => 'A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence', label => 'Feature elongation', }, { SO_accession => 'SO:0001906', SO_term => 'feature_truncation', feature_class => 'Bio::EnsEMBL::Feature', variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature', rank => '37', tier => '3', predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_truncation', description => 'A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence', label => 'Feature truncation', }, ); our @FEATURE_TYPES = ( { SO_accession => 'SO:0000234', SO_term => 'mRNA', ens_feature_class => 'Bio::EnsEMBL::Transcript', ens_feature_subtype => 'protein_coding', ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation', }, { SO_accession => 'SO:0000673', SO_term => 'transcript', ens_feature_class => 'Bio::EnsEMBL::Transcript', ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation', }, { SO_accession => 'SO:0000185', SO_term => 'primary_transcript', ens_feature_class => 'Bio::EnsEMBL::Transcript', ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation', }, { SO_accession => 'SO:0000655', SO_term => 'ncRNA', ens_feature_class => 'Bio::EnsEMBL::Transcript', ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation', }, { SO_accession => 'SO:0000276', SO_term => 'miRNA', ens_feature_class => 'Bio::EnsEMBL::Transcript', ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation', }, { SO_accession => 'SO:0005836', SO_term => 'regulatory_region', ens_feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature', ens_variant_class => 'Bio::EnsEMBL::Variation::RegulatoryFeatureVariation', }, { SO_accession => 'SO:0000409', SO_term => 'binding_site', ens_feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature', ens_variant_class => 'Bio::EnsEMBL::Variation::MotifFeatureVariation', }, { SO_accession => 'SO:0005836', SO_term => 'regulatory_region', ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature', ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation', ens_feature_subtype => 'VISTA enhancer set', }, { SO_accession => 'SO:0000409', SO_term => 'binding_site', ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature', ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation', ens_feature_subtype => 'cisRED motif', }, { SO_accession => 'SO:0005836', SO_term => 'regulatory_region', ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature', ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation', ens_feature_subtype => 'miRanda miRNA target', }, { SO_accession => 'SO:0000110', SO_term => 'sequence_feature', ens_feature_class => 'Bio::EnsEMBL::Feature', ens_variant_class => 'Bio::EnsEMBL::Variation::StructuralVariationFeatureOverlap', }, ); # attrib_types are specified as hashrefs in the @ATTRIB_TYPES array. Each hashref should have a value for the key 'code' and optionally values for the keys 'name' and 'description' our @ATTRIB_TYPES = ( { code => 'SO_accession', description => 'Sequence Ontology accession', }, { code => 'SO_term', description => 'Sequence Ontology term', }, { code => 'display_term', description => 'Ensembl display term', }, { code => 'NCBI_term', description => 'NCBI term', }, { code => 'feature_SO_term', description => 'Sequence Ontology term for the associated feature', }, { code => 'rank', description => 'Relative severity of this variation consequence', }, { code => 'polyphen_prediction', description => 'PolyPhen-2 prediction', }, { code => 'sift_prediction', description => 'SIFT prediction', }, { code => 'short_name', name => 'Short name', description => 'A shorter name for an instance, e.g. a VariationSet', }, { code => 'dbsnp_clin_sig', name => 'dbSNP clinical significance', description => 'The clinical significance of a variant as reported by dbSNP', }, { code => 'dgva_clin_sig', name => 'DGVa clinical significance', description => 'The clinical significance of a structural variant as reported by DGVa', }, { code => 'prot_func_analysis', name => 'Protein function analysis ', description => 'The program used to make protein function predictions', }, ); # attribs are specified in the %ATTRIBS hash, having the attrib_type code as hash key and a listref containing the attribs that will be loaded as value our %ATTRIBS = ( 'short_name' => \@short_names, 'dbsnp_clin_sig' => \@dbsnp_clinical_significance_types, 'dgva_clin_sig' => \@dgva_clinical_significance_types, 'polyphen_prediction' => ['probably damaging', 'possibly damaging', 'benign', 'unknown'], 'sift_prediction' => [qw(tolerated deleterious)], 'prot_func_analysis' => [qw(sift polyphen_humvar polyphen_humdiv)], ); # attrib sets are specified by putting a hashref in the @ATTRIB_SETS array having the attrib_type code as key and the attrib as value. new attrib entries will be inserted as necessary our @ATTRIB_SETS = ( @VARIATION_CLASSES, @OVERLAP_CONSEQUENCES, @FEATURE_TYPES ); 1;