Mercurial > repos > mahtabm > ensembl
diff variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Config.pm @ 0:1f6dce3d34e0
Uploaded
| author | mahtabm |
|---|---|
| date | Thu, 11 Apr 2013 02:01:53 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Config.pm Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,872 @@ +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;