-
Notifications
You must be signed in to change notification settings - Fork 22
/
defaultSchema.json
577 lines (577 loc) · 24.3 KB
/
defaultSchema.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
{
"$comment": "version: ga4gh-beacon-variant-v2.1.0",
"$defs": {
"CaseLevelVariant": {
"description": "",
"properties": {
"alleleOrigin": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Ontology value for allele origin of variant in sample from the Variant Origin (SO:0001762). Categories are `somatic variant`, `germline variant`, `maternal variant`, `paternal variant`, `de novo variant`, `pedigree specific variant`, `population specific variant`. Corresponds to Variant Inheritance in FHIR.",
"examples": [
{
"id": "SO:0001777",
"label": "somatic variant"
},
{
"id": "SO:0001778",
"label": "germline variant"
},
{
"id": "SO:0001775",
"label": "maternal variant"
},
{
"id": "SO:0001776",
"label": "paternal variant"
},
{
"id": "SO:0001781",
"label": "de novo variant"
},
{
"id": "SO:0001779",
"label": "pedigree specific variant"
},
{
"id": "SO:0001780",
"label": "population specific variant"
}
]
},
"analysisId": {
"description": "Reference to the bioinformatics analysis ID (`analysis.id`)",
"examples": [
"pgxcs-kftvldsu"
],
"type": "string"
},
"biosampleId": {
"description": "Reference to biosample ID (`biosample.id`)",
"examples": [
"bs001104"
],
"type": "string"
},
"clinicalInterpretations": {
"items": {
"$ref": "#/$defs/PhenoClinicEffect"
},
"type": "array"
},
"id": {
"description": "Internal id of this case level *instance* of the variant. This is an optional housekeeping parameter and should not be confused with the identifier of the variant (`variantInternalId`).",
"examples": [
"id0001-var101101118"
],
"type": "string"
},
"individualId": {
"description": "Reference to individual ID (`individual.id`)",
"examples": [
"ind0001"
],
"type": "string"
},
"phenotypicEffects": {
"items": {
"$ref": "#/$defs/PhenoClinicEffect"
},
"type": "array"
},
"runId": {
"description": "Reference to the experimental run ID (`run.id`)",
"examples": [
"SRR10903401"
],
"type": "string"
},
"zygosity": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Ontology term for zygosity in which variant is present in the sample from the Zygosity Ontology (GENO:0000391) , e.g `heterozygous` (GENO:0000135)",
"examples": [
{
"id": "GENO:0000135",
"label": "heterozygous"
},
{
"id": "GENO:0000136",
"label": "homozygous"
},
{
"id": "GENO:0000604",
"label": "hemizygous X-linked"
}
]
}
},
"required": [
"biosampleId"
],
"type": "object"
},
"FrequencyInPopulations": {
"properties": {
"frequencies": {
"items": {
"$ref": "#/$defs/PopulationFrequency"
},
"minItems": 1,
"type": "array"
},
"source": {
"description": "The study",
"examples": [
"The Genome Aggregation Database (gnomAD)",
"The European Genome-phenome Archive (EGA)"
],
"type": "string"
},
"sourceReference": {
"description": "A reference to further documentation or details.",
"examples": [
"https://gnomad.broadinstitute.org/",
"https://ega-archive.org/"
],
"type": "string"
},
"version": {
"description": "version of the source data.",
"examples": [
"gnomAD v3.1.1"
],
"type": "string"
}
},
"required": [
"source",
"sourceReference",
"frequencies"
],
"type": "object"
},
"GenomicFeature": {
"description": "Genomic feature(s) related to the variant. NOTE: Although genes could also be referenced using these attributes, they have an independent section to allow direct queries.",
"properties": {
"featureClass": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Ontology term that describes the class of genomic feature affected by the variant. Values from SO (Sequence ontology) are recommended, e.g. `SO:0001623: 5 prime UTR variant`",
"examples": [
{
"id": "SO:0001623",
"label": "5 prime UTR variant"
}
]
},
"featureID": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Where applicable, ID/accession/name of genomic feature related to the `featureClass`, preferably in CURIE format. If the value is a gene id or name, it points to the gene related to the `featureClass`, e.g. `the 5 prime UTR upstream of TP53`",
"examples": [
{
"id": "HGNC:11998",
"label": "TP53"
}
]
}
},
"required": [
"featureClass"
],
"type": "object"
},
"Identifiers": {
"properties": {
"clinvarVariantId": {
"description": "ClinVar variant id. Other id values used by ClinVar can be added to `variantAlternativeIds`",
"examples": [
"clinvar:12345",
"9325"
],
"pattern": "^(clinvar:)?\\d+$",
"type": "string"
},
"genomicHGVSId": {
"description": "HGVSId descriptor.",
"examples": [
"NC_000017.11:g.43057063G>A"
],
"type": "string"
},
"proteinHGVSIds": {
"description": "List of HGVSId descriptor(s) at protein level (for protein-altering variants).",
"examples": [
[
"NP_009225.1:p.Glu1817Ter"
],
[
"LRG 199p1:p.Val25Gly (preferred)"
]
],
"items": {
"type": "string"
},
"type": "array"
},
"transcriptHGVSIds": {
"description": "List of HGVSId descriptor(s) at transcript level.",
"examples": [
[
"NC 000023.10(NM004006.2):c.357+1G"
]
],
"items": {
"type": "string"
},
"type": "array"
},
"variantAlternativeIds": {
"description": "List of cross-referencing ID(s), for the variant in other databases (e.g. dbSNP, ClinVar, ClinGen, COSMIC), as `externalReferences` with CURIE(s).",
"examples": [
[
{
"id": "dbSNP:rs587780345",
"notes": "dbSNP id",
"reference": "https://www.ncbi.nlm.nih.gov/snp/rs587780345"
},
{
"id": "ClinGen:CA152954",
"notes": "ClinGen Allele Registry id",
"reference": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA152954"
},
{
"id": "UniProtKB:P35557#VAR_003699",
"reference": "https://www.uniprot.org/uniprot/P35557#VAR_003699"
}
],
[
{
"id": "OMIM:164757.0001",
"reference": "https://www.omim.org/entry/164757#0001"
}
]
],
"items": {
"$ref": "../common/externalReference.json"
},
"type": "array"
}
},
"type": "object"
},
"LegacyVariation": {
"properties": {
"alternateBases": {
"description": "Alternate bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used as\n a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of deletions with the maximally\n trimmed, deleted sequence being indicated in `ReferenceBases`",
"examples": [
"T",
"G",
"N",
"AG",
""
],
"pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$",
"type": "string"
},
"location": {
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/Location"
},
"referenceBases": {
"description": "Reference bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used\n as a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of insertions with the maximally\n trimmed, inserted sequence being indicated in `AlternateBases`.",
"examples": [
"A",
"T",
"N",
"",
"ACG"
],
"pattern": "^([ACGTUNRYSWKMBDHV\\-\\.]*)$",
"type": "string"
},
"variantType": {
"default": "SNP",
"description": "The `variantType` declares the nature of the variation in relation to a reference. In a response, it is used to describe the variation. Examples here are e.g. structural variants such as `DUP` (increased allelic count of material from the genomic region between `start` and `end` positions without assumption about the placement of the additional sequence) or `DEL` (deletion of sequence following `start`). Either `alternateBases` or `variantType` is required in representing a `LegacyVariation`.",
"examples": [
"SNP",
"DEL",
"DUP",
"BND"
],
"type": "string"
}
},
"required": [
"variantType",
"alternateBases",
"location"
],
"type": "object"
},
"MolecularAttributes": {
"properties": {
"aminoacidChanges": {
"description": "Lisf of change(s) at aminoacid level for protein affecting variants.",
"examples": [
[
"V304*"
]
],
"items": {
"type": "string"
},
"type": "array"
},
"geneIds": {
"description": "Symbolic names or identifiers used for a gene",
"examples": [
[
"ACE2"
],
[
"BRCA1",
"ENSG00000012048"
]
],
"items": {
"type": "string"
},
"type": "array"
},
"genomicFeatures": {
"description": "List of Genomic feature(s) affected by the variant.",
"items": {
"$ref": "#/$defs/GenomicFeature"
},
"type": "array"
},
"molecularEffects": {
"description": "Ontology term that includes describes the class of molecular consequence generated by the variant. Values from SO (Sequence Ontology) are recommended, e.g. `SO:0001583: missense variant`.",
"examples": [
{
"id": "SO:0002322",
"label": "stop gained NMD escaping"
},
{
"id": "SO:0001583",
"label": "missense variant"
}
],
"items": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json"
},
"type": "array"
}
},
"type": "object"
},
"PhenoClinicEffect": {
"description": "List of annotated effects on disease or phenotypes.",
"properties": {
"annotatedWith": {
"$ref": "#/$defs/SoftwareTool"
},
"category": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Ontology term for the type of disease, condition, phenotypic measurement, etc.",
"examples": [
{
"id": "MONDO:0000001",
"label": "disease or disorder"
},
{
"id": "HP:0000118",
"label": "phenotypic abnormality"
}
]
},
"clinicalRelevance": {
"description": "Indication of the clinical relevance of the variant Recommended: A value from the five-tiered classification from the American College of Medical Genetics (ACMG) designed to describe the likelihood that a genomic sequence variant is causative of an inherited disease. (NCIT:C168798).",
"enum": [
"benign",
"likely benign",
"uncertain significance",
"likely pathogenic",
"pathogenic"
],
"example": "pathogenic",
"type": "string"
},
"conditionId": {
"description": "Internal identifier of the phenotype or clinical effect.",
"examples": [
"disease1",
"phen2234"
],
"type": "string"
},
"effect": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Ontology term for the phenotypic or clinical effect",
"examples": [
{
"id": "MONDO:0003582",
"label": "hereditary breast ovarian cancer syndrome"
},
{
"id": "HP:0000256",
"label": "macrocephaly"
}
]
},
"evidenceType": {
"$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
"description": "Ontology term for the type of evidence supporting variant-disease association Recommended: values from the Evidence & Conclusion Ontology (ECO)",
"examples": [
{
"id": "ECO:0000361",
"label": "inferential evidence"
},
{
"id": "ECO:0000006",
"label": "experimental evidence"
}
]
}
},
"required": [
"conditionId",
"effect"
],
"type": "object"
},
"PopulationFrequency": {
"properties": {
"alleleFrequency": {
"description": "Allele frequency between 0 and 1.",
"examples": [
3.186e-05
],
"type": "number"
},
"population": {
"description": "A name for the population. A population could an ethnic, geographical one or just the members of a study.",
"examples": [
"East Asian",
"ICGC Chronic Lymphocytic Leukemia-ES",
"Men",
"Children"
],
"type": "string"
}
},
"required": [
"population",
"alleleFrequency"
],
"type": "object"
},
"SoftwareTool": {
"properties": {
"toolName": {
"description": "Name of the tool.",
"examples": [
"Ensembl Variant Effect Predictor (VEP)"
],
"type": "string"
},
"toolReferences": {
"additionalProperties": true,
"description": "References to the tool",
"examples": [
{
"bio.toolsId": "https://bio.tools/vep"
},
{
"url": "https://www.ensembl.org/vep"
}
],
"minProperties": 1,
"properties": {},
"type": "object"
},
"version": {
"description": "Version used.",
"examples": [
"rel 104"
],
"type": "string"
}
},
"required": [
"toolName",
"version",
"toolReferences"
],
"type": "object"
},
"VariantLevelData": {
"properties": {
"clinicalInterpretations": {
"items": {
"$ref": "#/$defs/PhenoClinicEffect"
},
"type": "array"
},
"phenotypicEffects": {
"items": {
"$ref": "#/$defs/PhenoClinicEffect"
},
"type": "array"
}
},
"type": "object"
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": true,
"description": "Schema for a genomic variant entry.",
"properties": {
"caseLevelData": {
"description": "caseLevelData reports about the variation instances observed in individual analyses.",
"items": {
"$ref": "#/$defs/CaseLevelVariant"
},
"type": "array"
},
"frequencyInPopulations": {
"items": {
"$ref": "#/$defs/FrequencyInPopulations"
},
"type": "array"
},
"identifiers": {
"$ref": "#/$defs/Identifiers"
},
"molecularAttributes": {
"$ref": "#/$defs/MolecularAttributes"
},
"variantInternalId": {
"description": "Reference to the **internal** variant ID. This represents the primary key/identifier of that variant **inside** a given Beacon instance. Different Beacon instances may use identical id values, referring to unrelated variants. Public identifiers such as the GA4GH Variant Representation Id (VRSid) MUST be returned in the `identifiers` section. A Beacon instance can, of course, use the VRSid as their own internal id but still MUST represent this then in the `identifiers` section.",
"examples": [
"var00001",
"v110112"
],
"type": "string"
},
"variantLevelData": {
"$ref": "#/$defs/VariantLevelData"
},
"variation": {
"oneOf": [
{
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/MolecularVariation"
},
{
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/SystemicVariation"
},
{
"$ref": "#/$defs/LegacyVariation"
}
]
}
},
"required": [
"variantInternalId",
"variation"
],
"title": "Genomic Variation",
"type": "object"
}