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comparison 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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1 package Bio::EnsEMBL::Variation::Utils::Config;
2
3 use base qw(Exporter);
4
5 our @EXPORT_OK = qw(
6 @ATTRIB_TYPES
7 %ATTRIBS
8 @ATTRIB_SETS
9 @VARIATION_CLASSES
10 @OVERLAP_CONSEQUENCES
11 @FEATURE_TYPES
12 $OVERLAP_CONSEQUENCE_CLASS
13 $MAX_ATTRIB_CODE_LENGTH
14 );
15
16 our $OVERLAP_CONSEQUENCE_CLASS = 'Bio::EnsEMBL::Variation::OverlapConsequence';
17
18 our $MAX_ATTRIB_CODE_LENGTH = 20;
19
20 our @short_names = qw(1kg_hct 1kg_hct_ceu 1kg_hct_yri 1kg_hce 1kg_hce_ceu 1kg_hce_chb
21 1kg_hce_chd 1kg_hce_jpt 1kg_hce_lwk 1kg_hce_tsi 1kg_hce_yri 1kg_lc
22 1kg_lc_ceu 1kg_lc_chb_jpt 1kg_lc_yri hapmap
23 1kg 1kg_afr 1kg_amr 1kg_asn 1kg_eur 1kg_afr 1kg_amr_com 1kg_asn_com 1kg_eur_com
24 ind_venter ind_watson ind_gill ind_ak1 ind_irish ind_angrist
25 ind_gates_jr ind_gates_sr ind_kriek ind_quake ind_saqqaq ind_saqqaq_hc ind_sjk ind_yh
26 fail_all fail_nonref fail_ambig fail_gt_fq fail_incons_map fail_mult_map
27 fail_no_alleles fail_no_gt fail_no_map fail_no_seq fail_non_nt fail_mult_alleles fail_dbsnp_suspect
28 ph_hgmd_pub ph_johnson_et_al ph_nhgri ph_omim ph_variants ph_uniprot
29 ph_cosmic ph_ega precious hapmap_ceu hapmap_hcb hapmap_jpt hapmap_yri
30 Affy_500K Affy_SNP6 Cardio-Metabo_Chip HumanOmni1-Quad Illumina_1M-duo Illumina_660Q
31 );
32
33 our @dbsnp_clinical_significance_types = qw(
34 unknown
35 untested
36 non-pathogenic
37 probable-non-pathogenic
38 probable-pathogenic
39 pathogenic
40 drug-response
41 histocompatibility
42 other
43 );
44
45 our @dgva_clinical_significance_types = (
46 'Not tested',
47 'Benign',
48 'Pathogenic',
49 'Uncertain Significance',
50 'Uncertain Significance: likely benign',
51 'Uncertain Significance: likely pathogenic'
52 );
53
54 our @VARIATION_CLASSES = (
55 {
56 SO_accession => 'SO:0001483',
57 SO_term => 'SNV',
58 display_term => 'SNP',
59 somatic_display_term => 'somatic_SNV',
60 },
61 {
62 SO_accession => 'SO:1000002',
63 SO_term => 'substitution',
64 },
65 {
66 SO_accession => 'SO:0001019',
67 SO_term => 'copy_number_variation',
68 display_term => 'CNV',
69 },
70 {
71 SO_accession => 'SO:0000667',
72 SO_term => 'insertion',
73 },
74 {
75 SO_accession => 'SO:0000159',
76 SO_term => 'deletion',
77 },
78 {
79 SO_accession => 'SO:1000032',
80 SO_term => 'indel',
81 },
82 {
83 SO_accession => 'SO:0000705',
84 SO_term => 'tandem_repeat',
85 },
86 {
87 SO_accession => 'SO:0001059',
88 SO_term => 'sequence_alteration',
89 },
90 # Structural variation classes
91 {
92 SO_accession => 'SO:0001537',
93 SO_term => 'structural_variant',
94 display_term => 'SV',
95 },
96 {
97 SO_accession => 'SO:0000051',
98 SO_term => 'probe',
99 display_term => 'CNV_PROBE',
100 },
101 {
102 SO_accession => 'SO:0001742',
103 SO_term => 'copy_number_gain',
104 display_term => 'Gain',
105 },
106 {
107 SO_accession => 'SO:0001743',
108 SO_term => 'copy_number_loss',
109 display_term => 'Loss',
110 },
111 {
112 SO_accession => 'SO:1000036',
113 SO_term => 'inversion',
114 },
115 {
116 SO_accession => 'SO:0001784',
117 SO_term => 'complex_structural_alteration',
118 display_term => 'Complex',
119 },
120 {
121 SO_accession => 'SO:1000173',
122 SO_term => 'tandem_duplication',
123 display_term => 'Tandem duplication',
124 },
125 {
126 SO_accession => 'SO:0001837',
127 SO_term => 'mobile_element_insertion',
128 display_term => 'Mobile element insertion',
129 },
130 {
131 SO_accession => 'SO:0001873',
132 SO_term => 'interchromosomal_breakpoint',
133 display_term => 'Interchromosomal breakpoint',
134 },
135 {
136 SO_accession => 'SO:0001874',
137 SO_term => 'intrachromosomal_breakpoint',
138 display_term => 'Intrachromosomal breakpoint',
139 },
140 {
141 SO_accession => 'SO:0000199',
142 SO_term => 'translocation',
143 },
144 {
145 SO_accession => 'SO:1000035',
146 SO_term => 'duplication',
147 display_term => 'Duplication',
148 },
149 );
150
151 our @OVERLAP_CONSEQUENCES = (
152 {
153 SO_accession => 'SO:0001628',
154 SO_term => 'intergenic_variant',
155 display_term => 'INTERGENIC',
156 rank => '38',
157 tier => '4',
158 description => 'A sequence variant located in the intergenic region, between genes',
159 label => 'Intergenic variant',
160 is_default => 1,
161 },
162 {
163 SO_accession => 'SO:0001631',
164 SO_term => 'upstream_gene_variant',
165 display_term => 'UPSTREAM',
166 feature_SO_term => 'transcript',
167 feature_class => 'Bio::EnsEMBL::Transcript',
168 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
169 rank => '24',
170 tier => '3',
171 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::upstream',
172 description => 'A sequence variant located 5\' of a gene',
173 label => 'Upstream gene variant',
174 },
175 {
176 SO_accession => 'SO:0001632',
177 SO_term => 'downstream_gene_variant',
178 display_term => 'DOWNSTREAM',
179 feature_SO_term => 'transcript',
180 feature_class => 'Bio::EnsEMBL::Transcript',
181 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
182 rank => '25',
183 tier => '3',
184 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::downstream',
185 description => 'A sequence variant located 3\' of a gene',
186 label => 'Downstream gene variant',
187 },
188 {
189 SO_accession => 'SO:0001575',
190 SO_term => 'splice_donor_variant',
191 display_term => 'ESSENTIAL_SPLICE_SITE',
192 NCBI_term => 'splice-5',
193 feature_SO_term => 'primary_transcript',
194 feature_class => 'Bio::EnsEMBL::Transcript',
195 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
196 rank => '3',
197 tier => '3',
198 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::donor_splice_site',
199 description => 'A splice variant that changes the 2 base region at the 5\' end of an intron',
200 label => 'Splice donor variant',
201 },
202 {
203 SO_accession => 'SO:0001574',
204 SO_term => 'splice_acceptor_variant',
205 display_term => 'ESSENTIAL_SPLICE_SITE',
206 NCBI_term => 'splice-3',
207 feature_SO_term => 'primary_transcript',
208 feature_class => 'Bio::EnsEMBL::Transcript',
209 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
210 rank => '3',
211 tier => '3',
212 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::acceptor_splice_site',
213 description => 'A splice variant that changes the 2 base region at the 3\' end of an intron',
214 label => 'Splice acceptor variant',
215 },
216 {
217 SO_accession => 'SO:0001630',
218 SO_term => 'splice_region_variant',
219 display_term => 'SPLICE_SITE',
220 feature_SO_term => 'primary_transcript',
221 feature_class => 'Bio::EnsEMBL::Transcript',
222 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
223 rank => '13',
224 tier => '3',
225 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::splice_region',
226 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',
227 label => 'Splice region variant',
228 },
229 {
230 SO_accession => 'SO:0001627',
231 SO_term => 'intron_variant',
232 display_term => 'INTRONIC',
233 NCBI_term => 'intron',
234 feature_SO_term => 'primary_transcript',
235 feature_class => 'Bio::EnsEMBL::Transcript',
236 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
237 rank => '20',
238 tier => '3',
239 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_intron',
240 description => 'A transcript variant occurring within an intron',
241 label => 'Intron variant',
242 },
243 {
244 SO_accession => 'SO:0001623',
245 SO_term => '5_prime_UTR_variant',
246 display_term => '5PRIME_UTR',
247 NCBI_term => 'untranslated_5',
248 feature_SO_term => 'mRNA',
249 feature_class => 'Bio::EnsEMBL::Transcript',
250 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
251 rank => '18',
252 tier => '3',
253 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_5_prime_utr',
254 description => 'A UTR variant of the 5\' UTR',
255 label => '5 prime UTR variant',
256 },
257 {
258 SO_accession => 'SO:0001624',
259 SO_term => '3_prime_UTR_variant',
260 display_term => '3PRIME_UTR',
261 NCBI_term => 'untranslated_3',
262 feature_SO_term => 'mRNA',
263 feature_class => 'Bio::EnsEMBL::Transcript',
264 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
265 rank => '19',
266 tier => '3',
267 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_3_prime_utr',
268 description => 'A UTR variant of the 3\' UTR',
269 label => '3 prime UTR variant',
270 },
271 # {
272 # SO_accession => 'SO:0001577',
273 # SO_term => 'complex_change_in_transcript',
274 # display_term => 'COMPLEX_INDEL',
275 # feature_SO_term => 'primary_transcript',
276 # feature_class => 'Bio::EnsEMBL::Transcript',
277 # variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
278 # rank => '4',
279 # tier => '3',
280 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::complex_indel',
281 # description => 'Insertion or deletion that spans an exon/intron or coding sequence/UTR border',
282 # label => 'Complex change in transcript',
283 # },
284 {
285 SO_accession => 'SO:0001819',
286 SO_term => 'synonymous_variant',
287 display_term => 'SYNONYMOUS_CODING',
288 NCBI_term => 'cds-synon',
289 feature_SO_term => 'mRNA',
290 feature_class => 'Bio::EnsEMBL::Transcript',
291 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
292 rank => '15',
293 tier => '3',
294 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::synonymous_variant',
295 description => 'A sequence variant where there is no resulting change to the encoded amino acid',
296 label => 'Synonymous variant',
297 },
298 {
299 SO_accession => 'SO:0001583',
300 SO_term => 'missense_variant',
301 display_term => 'NON_SYNONYMOUS_CODING',
302 NCBI_term => 'missense',
303 feature_SO_term => 'mRNA',
304 feature_class => 'Bio::EnsEMBL::Transcript',
305 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
306 rank => '12',
307 tier => '3',
308 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::missense_variant',
309 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',
310 label => 'Missense variant',
311 },
312 {
313 SO_accession => 'SO:0001821',
314 SO_term => 'inframe_insertion',
315 display_term => 'NON_SYNONYMOUS_CODING',
316 feature_SO_term => 'mRNA',
317 feature_class => 'Bio::EnsEMBL::Transcript',
318 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
319 rank => '10',
320 tier => '3',
321 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_insertion',
322 description => 'An inframe non synonymous variant that inserts bases into in the coding sequence',
323 label => 'Inframe insertion',
324 },
325 {
326 SO_accession => 'SO:0001822',
327 SO_term => 'inframe_deletion',
328 display_term => 'NON_SYNONYMOUS_CODING',
329 feature_SO_term => 'mRNA',
330 feature_class => 'Bio::EnsEMBL::Transcript',
331 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
332 rank => '11',
333 tier => '3',
334 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::inframe_deletion',
335 description => 'An inframe non synonymous variant that deletes bases from the coding sequence',
336 label => 'Inframe deletion',
337 },
338 {
339 SO_accession => 'SO:0001587',
340 SO_term => 'stop_gained',
341 display_term => 'STOP_GAINED',
342 NCBI_term => 'nonsense',
343 feature_SO_term => 'mRNA',
344 feature_class => 'Bio::EnsEMBL::Transcript',
345 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
346 rank => '4',
347 tier => '3',
348 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_gained',
349 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',
350 label => 'Stop gained',
351 },
352 {
353 SO_accession => 'SO:0001578',
354 SO_term => 'stop_lost',
355 display_term => 'STOP_LOST',
356 feature_SO_term => 'mRNA',
357 feature_class => 'Bio::EnsEMBL::Transcript',
358 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
359 rank => '6',
360 tier => '3',
361 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_lost',
362 description => 'A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript',
363 label => 'Stop lost',
364 },
365 {
366 SO_accession => 'SO:0001567',
367 SO_term => 'stop_retained_variant',
368 display_term => 'SYNONYMOUS_CODING',
369 feature_SO_term => 'mRNA',
370 feature_class => 'Bio::EnsEMBL::Transcript',
371 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
372 rank => '15',
373 tier => '3',
374 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::stop_retained',
375 description => 'A sequence variant where at least one base in the terminator codon is changed, but the terminator remains',
376 label => 'Stop retained variant',
377 },
378 {
379 SO_accession => 'SO:0001582',
380 SO_term => 'initiator_codon_variant',
381 display_term => 'NON_SYNONYMOUS_CODING',
382 feature_SO_term => 'mRNA',
383 feature_class => 'Bio::EnsEMBL::Transcript',
384 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
385 rank => '7',
386 tier => '3',
387 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::affects_start_codon',
388 description => 'A codon variant that changes at least one base of the first codon of a transcript',
389 label => 'Initiator codon variant',
390 },
391 {
392 SO_accession => 'SO:0001589',
393 SO_term => 'frameshift_variant',
394 display_term => 'FRAMESHIFT_CODING',
395 NCBI_term => 'frameshift',
396 feature_SO_term => 'mRNA',
397 feature_class => 'Bio::EnsEMBL::Transcript',
398 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
399 rank => '5',
400 tier => '3',
401 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::frameshift',
402 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',
403 label => 'Frameshift variant',
404 },
405 {
406 SO_accession => 'SO:0001626',
407 SO_term => 'incomplete_terminal_codon_variant',
408 display_term => 'PARTIAL_CODON',
409 feature_SO_term => 'mRNA',
410 feature_class => 'Bio::EnsEMBL::Transcript',
411 variant_feature_class => 'Bio::EnsEMBL::Variation::VariationFeature',
412 rank => '14',
413 tier => '3',
414 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::partial_codon',
415 description => 'A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed',
416 label => 'Incomplete terminal codon variant',
417 },
418 {
419 SO_accession => 'SO:0001621',
420 SO_term => 'NMD_transcript_variant',
421 display_term => 'NMD_TRANSCRIPT',
422 feature_SO_term => 'mRNA',
423 feature_class => 'Bio::EnsEMBL::Transcript',
424 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
425 rank => '21',
426 tier => '3',
427 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_nmd_transcript',
428 description => 'A variant in a transcript that is the target of NMD',
429 label => 'NMD transcript variant',
430 },
431 {
432 SO_accession => 'SO:0001619',
433 SO_term => 'nc_transcript_variant',
434 display_term => 'WITHIN_NON_CODING_GENE',
435 feature_SO_term => 'ncRNA',
436 feature_class => 'Bio::EnsEMBL::Transcript',
437 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
438 rank => '23',
439 tier => '3',
440 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_non_coding_gene',
441 description => 'A transcript variant of a non coding RNA',
442 label => 'NC transcript variant',
443 },
444 {
445 SO_accession => 'SO:0001792',
446 SO_term => 'non_coding_exon_variant',
447 display_term => 'WITHIN_NON_CODING_GENE',
448 feature_SO_term => 'ncRNA',
449 feature_class => 'Bio::EnsEMBL::Transcript',
450 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
451 rank => '22',
452 tier => '3',
453 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::non_coding_exon_variant',
454 description => 'A sequence variant that changes non-coding exon sequence',
455 label => 'Non coding exon variant',
456 },
457 {
458 SO_accession => 'SO:0001620',
459 SO_term => 'mature_miRNA_variant',
460 display_term => 'WITHIN_MATURE_miRNA',
461 feature_SO_term => 'miRNA',
462 feature_class => 'Bio::EnsEMBL::Transcript',
463 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
464 rank => '17',
465 tier => '2',
466 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_mature_miRNA',
467 description => 'A transcript variant located with the sequence of the mature miRNA',
468 label => 'Mature miRNA variant',
469 },
470 {
471 SO_accession => 'SO:0001580',
472 SO_term => 'coding_sequence_variant',
473 display_term => 'CODING_UNKNOWN',
474 feature_SO_term => 'mRNA',
475 feature_class => 'Bio::EnsEMBL::Transcript',
476 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
477 rank => '16',
478 tier => '3',
479 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::coding_unknown',
480 description => 'A sequence variant that changes the coding sequence',
481 label => 'Coding sequence variant',
482 },
483 {
484 SO_accession => 'SO:0001566',
485 SO_term => 'regulatory_region_variant',
486 display_term => 'REGULATORY_REGION',
487 feature_SO_term => 'regulatory_region',
488 feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
489 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
490 rank => '36',
491 tier => '2',
492 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_regulatory_feature',
493 description => 'A sequence variant located within a regulatory region',
494 label => 'Regulatory region variant',
495 },
496 # {
497 # SO_accession => 'SO:X000005',
498 # SO_term => 'pre_miRNA_variant',
499 # display_term => 'WITHIN_NON_CODING_GENE',
500 # feature_SO_term => 'miRNA',
501 # feature_class => 'Bio::EnsEMBL::Transcript',
502 # rank => '13',
503 # tier => '2',
504 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_miRNA',
505 # },
506 # {
507 # SO_accession => 'SO:X000004',
508 # SO_term => 'miRNA_target_site_variant',
509 # display_term => 'REGULATORY_REGION',
510 # feature_SO_term => 'binding_site',
511 # feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature',
512 # rank => '13',
513 # tier => '2',
514 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_miRNA_target_site',
515 # description => 'In regulatory region annotated by Ensembl',
516 # label => 'Regulatory region',
517 # },
518 {
519 SO_accession => 'SO:0001782',
520 SO_term => 'TF_binding_site_variant',
521 display_term => 'REGULATORY_REGION',
522 feature_SO_term => 'TF_binding_site',
523 feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
524 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
525 rank => '30',
526 tier => '2',
527 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::within_motif_feature',
528 description => 'In regulatory region annotated by Ensembl',
529 label => 'A sequence variant located within a transcription factor binding site',
530 },
531
532 # {
533 # SO_accession => 'SO:X000002',
534 # SO_term => 'decreased_binding_affinity',
535 # display_term => 'REGULATORY_REGION',
536 # feature_SO_term => 'binding_site',
537 # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
538 # rank => '47',
539 # tier => '2',
540 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::decreased_binding_affinity',
541 # },
542 # {
543 # SO_accession => 'SO:X000001',
544 # SO_term => 'increased_binding_affinity',
545 # display_term => 'REGULATORY_REGION',
546 # feature_SO_term => 'binding_site',
547 # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
548 # rank => '48',
549 # tier => '2',
550 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::increased_binding_affinity',
551 # },
552
553
554 ## NEW FOR 68
555 #############
556
557 {
558 SO_accession => 'SO:0001893',
559 SO_term => 'transcript_ablation',
560 feature_SO_term => 'mRNA',
561 feature_class => 'Bio::EnsEMBL::Transcript',
562 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
563 rank => '1',
564 tier => '1',
565 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation',
566 description => 'A feature ablation whereby the deleted region includes a transcript feature',
567 label => 'Transcript ablation',
568 },
569 # {
570 # SO_accession => 'SO:0001886',
571 # SO_term => 'transcript_fusion',
572 # feature_SO_term => 'mRNA',
573 # feature_class => 'Bio::EnsEMBL::Transcript',
574 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
575 # rank => '2',
576 # tier => '2',
577 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::transcript_fusion',
578 # description => 'A feature fusion where the deletion brings together transcript regions',
579 # label => 'Transcript fusion',
580 # },
581 {
582 SO_accession => 'SO:0001889',
583 SO_term => 'transcript_amplification',
584 feature_SO_term => 'mRNA',
585 feature_class => 'Bio::EnsEMBL::Transcript',
586 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
587 rank => '8',
588 tier => '1',
589 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification',
590 description => 'A feature amplification of a region containing a transcript',
591 label => 'Transcript amplification',
592 },
593 # {
594 # SO_accession => 'SO:0001883',
595 # SO_term => 'transcript_translocation',
596 # feature_SO_term => 'mRNA',
597 # feature_class => 'Bio::EnsEMBL::Transcript',
598 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
599 # rank => '9',
600 #tier => '2',
601 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::transcript_translocation',
602 # description => 'A feature translocation where the region contains a transcript',
603 # label => 'Transcript translocation',
604 # },
605 {
606 SO_accession => 'SO:0001895',
607 SO_term => 'TFBS_ablation',
608 feature_SO_term => 'TF_binding_site',
609 feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
610 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
611 rank => '26',
612 tier => '2',
613 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation',
614 description => 'A feature ablation whereby the deleted region includes a transcription factor binding site',
615 label => 'TFBS ablation',
616 },
617 # {
618 # SO_accession => 'SO:0001888',
619 # SO_term => 'TFBS_fusion',
620 # feature_SO_term => 'TF_binding_site',
621 # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
622 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
623 # rank => '27',
624 #tier => '2',
625 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::motif_feature_fusion',
626 # description => 'A fusion where the deletion brings together transcription factor binding sites',
627 # label => 'TFBS fusion',
628 # },
629 {
630 SO_accession => 'SO:0001892',
631 SO_term => 'TFBS_amplification',
632 feature_SO_term => 'TF_binding_site',
633 feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
634 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
635 rank => '28',
636 tier => '2',
637 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification',
638 description => 'A feature amplification of a region containing a transcription factor binding site',
639 label => 'TFBS amplification',
640 },
641 # {
642 # SO_accession => 'SO:0001885',
643 # SO_term => 'TFBS_translocation',
644 # feature_SO_term => 'TF_binding_site',
645 # feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
646 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
647 # rank => '29',
648 #tier => '2',
649 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::motif_feature_translocation',
650 # description => 'A feature translocation where the region contains a transcription factor binding site',
651 # label => 'TFBS translocation',
652 # },
653 {
654 SO_accession => 'SO:0001894',
655 SO_term => 'regulatory_region_ablation',
656 feature_SO_term => 'TF_binding_site',
657 feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
658 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
659 rank => '31',
660 tier => '2',
661 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_ablation',
662 description => 'A feature ablation whereby the deleted region includes a regulatory region',
663 label => 'Regulatory region ablation',
664 },
665 # {
666 # SO_accession => 'SO:0001887',
667 # SO_term => 'regulatory_region_fusion',
668 # feature_SO_term => 'TF_binding_site',
669 # feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
670 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
671 # rank => '32',
672 #tier => '2',
673 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::regulatory_feature_fusion',
674 # description => 'A fusion where the deletion brings together regulatory regions',
675 # label => 'Regulatory region fusion',
676 # },
677 {
678 SO_accession => 'SO:0001891',
679 SO_term => 'regulatory_region_amplification',
680 feature_SO_term => 'TF_binding_site',
681 feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
682 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
683 rank => '33',
684 tier => '2',
685 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_amplification',
686 description => 'A feature amplification of a region containing a regulatory region',
687 label => 'Regulatory region amplification',
688 },
689 # {
690 # SO_accession => 'SO:0001884',
691 # SO_term => 'regulatory_region_translocation',
692 # feature_SO_term => 'TF_binding_site',
693 # feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
694 # variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
695 # rank => '34',
696 #tier => '2',
697 # predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::regulatory_feature_translocation',
698 # description => 'A feature translocation where the region contains a regulatory region',
699 # label => 'Regulatory region translocation',
700 # },
701 {
702 SO_accession => 'SO:0001907',
703 SO_term => 'feature_elongation',
704 feature_class => 'Bio::EnsEMBL::Feature',
705 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
706 rank => '36',
707 tier => '3',
708 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_elongation',
709 description => 'A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence',
710 label => 'Feature elongation',
711 },
712 {
713 SO_accession => 'SO:0001906',
714 SO_term => 'feature_truncation',
715 feature_class => 'Bio::EnsEMBL::Feature',
716 variant_feature_class => 'Bio::EnsEMBL::Variation::BaseVariationFeature',
717 rank => '37',
718 tier => '3',
719 predicate => 'Bio::EnsEMBL::Variation::Utils::VariationEffect::feature_truncation',
720 description => 'A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence',
721 label => 'Feature truncation',
722 },
723 );
724
725 our @FEATURE_TYPES = (
726 {
727 SO_accession => 'SO:0000234',
728 SO_term => 'mRNA',
729 ens_feature_class => 'Bio::EnsEMBL::Transcript',
730 ens_feature_subtype => 'protein_coding',
731 ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation',
732 },
733 {
734 SO_accession => 'SO:0000673',
735 SO_term => 'transcript',
736 ens_feature_class => 'Bio::EnsEMBL::Transcript',
737 ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation',
738 },
739 {
740 SO_accession => 'SO:0000185',
741 SO_term => 'primary_transcript',
742 ens_feature_class => 'Bio::EnsEMBL::Transcript',
743 ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation',
744 },
745 {
746 SO_accession => 'SO:0000655',
747 SO_term => 'ncRNA',
748 ens_feature_class => 'Bio::EnsEMBL::Transcript',
749 ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation',
750 },
751 {
752 SO_accession => 'SO:0000276',
753 SO_term => 'miRNA',
754 ens_feature_class => 'Bio::EnsEMBL::Transcript',
755 ens_variant_class => 'Bio::EnsEMBL::Variation::TranscriptVariation',
756 },
757 {
758 SO_accession => 'SO:0005836',
759 SO_term => 'regulatory_region',
760 ens_feature_class => 'Bio::EnsEMBL::Funcgen::RegulatoryFeature',
761 ens_variant_class => 'Bio::EnsEMBL::Variation::RegulatoryFeatureVariation',
762 },
763 {
764 SO_accession => 'SO:0000409',
765 SO_term => 'binding_site',
766 ens_feature_class => 'Bio::EnsEMBL::Funcgen::MotifFeature',
767 ens_variant_class => 'Bio::EnsEMBL::Variation::MotifFeatureVariation',
768 },
769 {
770 SO_accession => 'SO:0005836',
771 SO_term => 'regulatory_region',
772 ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature',
773 ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation',
774 ens_feature_subtype => 'VISTA enhancer set',
775 },
776 {
777 SO_accession => 'SO:0000409',
778 SO_term => 'binding_site',
779 ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature',
780 ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation',
781 ens_feature_subtype => 'cisRED motif',
782 },
783 {
784 SO_accession => 'SO:0005836',
785 SO_term => 'regulatory_region',
786 ens_feature_class => 'Bio::EnsEMBL::Funcgen::ExternalFeature',
787 ens_variant_class => 'Bio::EnsEMBL::Variation::ExternalFeatureVariation',
788 ens_feature_subtype => 'miRanda miRNA target',
789 },
790 {
791 SO_accession => 'SO:0000110',
792 SO_term => 'sequence_feature',
793 ens_feature_class => 'Bio::EnsEMBL::Feature',
794 ens_variant_class => 'Bio::EnsEMBL::Variation::StructuralVariationFeatureOverlap',
795 },
796 );
797
798 # 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'
799 our @ATTRIB_TYPES = (
800 {
801 code => 'SO_accession',
802 description => 'Sequence Ontology accession',
803 },
804 {
805 code => 'SO_term',
806 description => 'Sequence Ontology term',
807 },
808 {
809 code => 'display_term',
810 description => 'Ensembl display term',
811 },
812 {
813 code => 'NCBI_term',
814 description => 'NCBI term',
815 },
816 {
817 code => 'feature_SO_term',
818 description => 'Sequence Ontology term for the associated feature',
819 },
820 {
821 code => 'rank',
822 description => 'Relative severity of this variation consequence',
823 },
824 {
825 code => 'polyphen_prediction',
826 description => 'PolyPhen-2 prediction',
827 },
828 {
829 code => 'sift_prediction',
830 description => 'SIFT prediction',
831 },
832 {
833 code => 'short_name',
834 name => 'Short name',
835 description => 'A shorter name for an instance, e.g. a VariationSet',
836 },
837 {
838 code => 'dbsnp_clin_sig',
839 name => 'dbSNP clinical significance',
840 description => 'The clinical significance of a variant as reported by dbSNP',
841 },
842 {
843 code => 'dgva_clin_sig',
844 name => 'DGVa clinical significance',
845 description => 'The clinical significance of a structural variant as reported by DGVa',
846 },
847 {
848 code => 'prot_func_analysis',
849 name => 'Protein function analysis ',
850 description => 'The program used to make protein function predictions',
851 },
852
853 );
854
855 # 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
856 our %ATTRIBS = (
857 'short_name' => \@short_names,
858 'dbsnp_clin_sig' => \@dbsnp_clinical_significance_types,
859 'dgva_clin_sig' => \@dgva_clinical_significance_types,
860 'polyphen_prediction' => ['probably damaging', 'possibly damaging', 'benign', 'unknown'],
861 'sift_prediction' => [qw(tolerated deleterious)],
862 'prot_func_analysis' => [qw(sift polyphen_humvar polyphen_humdiv)],
863 );
864
865 # 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
866 our @ATTRIB_SETS = (
867 @VARIATION_CLASSES,
868 @OVERLAP_CONSEQUENCES,
869 @FEATURE_TYPES
870 );
871
872 1;