-
Notifications
You must be signed in to change notification settings - Fork 9
/
PHA4GE_SARS-CoV-2_Contextual_Data_Schema.json
2693 lines (2693 loc) · 104 KB
/
PHA4GE_SARS-CoV-2_Contextual_Data_Schema.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
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
{
"$schema": "http://json-schema.org/draft/2019-09/schema#",
"required": [
"sequence_submitted_by",
"sample_collected_by",
"sequencing_instrument",
"host_scientific_name",
"isolate",
"sample_collection_date",
"host_disease",
"consensus_sequence_software_name",
"geo_loc_name_state_province_territory",
"specimen_collector_sample_id",
"consensus_sequence_software_version",
"organism",
"geo_loc_name_country"
],
"type": "object",
"properties": {
"sample_collector_contact_email": {
"examples": ["johnnyblogs@lab.ca"],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "The email address of the contact responsible for follow-up regarding the sample.",
"format": "email"
},
"depth_of_coverage_value": {
"ontology": "GENEPIO:0001474",
"type": "number",
"description": "The average number of reads representing a given nucleotide in the reconstructed sequence.",
"examples": [400.0]
},
"exposure_details": {
"ontology": "GENEPIO:0001431",
"type": "string",
"description": "Additional host exposure information.",
"examples": ["Host role - Other: Bus Driver"]
},
"breadth_of_coverage_value": {
"ontology": "GENEPIO:0001472",
"type": "number",
"description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.",
"examples": [0.95]
},
"most_recent_travel_departure_date": {
"examples": ["16/03/2020"],
"ontology": "GENEPIO:0001414",
"type": "string",
"description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.",
"format": "date"
},
"sequencing_protocol": {
"ontology": "GENEPIO:0001454",
"type": "string",
"description": "The protocol used to generate the sequence.",
"examples": [
"Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits."
]
},
"host_age_bin": {
"Enums": [
"0 - 9 [GENEPIO:0100049]",
"10 - 19 [GENEPIO:0100050]",
"20 - 29 [GENEPIO:0100051]",
"30 - 39 [GENEPIO:0100052]",
"40 - 49 [GENEPIO:0100053]",
"50 - 59 [GENEPIO:0100054]",
"60 - 69 [GENEPIO:0100055]",
"70 - 79 [GENEPIO:0100056]",
"80 - 89 [GENEPIO:0100057]",
"90 - 99 [GENEPIO:0100058]",
"100+ [GENEPIO:0100059]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001394",
"type": "string",
"description": "The age category of the host at the time of sampling.",
"examples": ["50 - 59 [GENEPIO:0100054]"]
},
"anatomical_material": {
"Enums": [
"Blood [UBERON:0000178]",
"Fluid [UBERON:0006314]",
"Fluid (Cerebrospinal (CSF)) [UBERON:0001359]",
"Fluid (Pericardial) [UBERON:0002409]",
"Fluid (Pleural) [UBERON:0001087]",
"Fluid (Vaginal) [UBERON:0036243]",
"Fluid (Amniotic) [UBERON:0000173]",
"Saliva [UBERON:0001836]",
"Tissue [UBERON:0000479]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001211",
"type": "string",
"description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.",
"examples": ["Blood [UBERON:0000178]"]
},
"sample_collection_date": {
"examples": ["19/03/2020"],
"ontology": "GENEPIO:0001174",
"type": "string",
"description": "The date on which the sample was collected. ",
"format": "date"
},
"diagnostic_pcr_ct_value_2": {
"ontology": "GENEPIO:0001512",
"type": "integer",
"description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.",
"examples": [36]
},
"number_of_vaccine_doses_received": {
"ontology": "GENEPIO:0001406",
"type": "integer",
"description": "The number of doses of the vaccine recived by the host.",
"examples": [2]
},
"lab_host": {
"Enums": [
"293/ACE2 Cell Line [GENEPIO:0100041]",
"Caco2 Cell Line [BTO:0000195]",
"Calu3 Cell Line [BTO:0002750]",
"EFK3B Cell Line [GENEPIO:0100042]",
"HEK293T Cell Line [BTO:0002181]",
"HRCE Cell Line [GENEPIO:0100043]",
"Huh7 Cell Line [BTO:0001950]",
"LLCMk2 Cell Line [CLO:0007330]",
"MDBK Cell Line [BTO:0000836]",
"NHBE Cell Line [BTO:0002924]",
"PK-15 Cell Line [BTO:0001865]",
"RK-13 Cell Line [BTO:0002909]",
"U251 Cell Line [BTO:0002035]",
"Vero Cell Line [BTO:0001444]",
"Vero E6 Cell Line [BTO:0004755]",
"Vero E6/TMPRSS2 Cell Line [GENEPIO:0100044]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001255",
"type": "string",
"description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.",
"examples": ["Vero E6 Cell Line [BTO:0004755]"]
},
"anatomical_part": {
"Enums": [
"Anus [UBERON:0001245]",
"Duodenum [UBERON:0002114]",
"Eye [UBERON:0000970]",
"Intestine [UBERON:0000160]",
"Lower respiratory tract [UBERON:0001558]",
"Bronchus [UBERON:0002185]",
"Lung [UBERON:0002048]",
"Bronchiole [UBERON:0002186]",
"Alveolar sac [UBERON:0002169]",
"Pleural sac [UBERON:0009778]",
"Pleural cavity [UBERON:0002402]",
"Trachea [UBERON:0003126]",
"Rectum [UBERON:0001052]",
"Skin [UBERON:0001003]",
"Stomach [UBERON:0000945]",
"Upper respiratory tract [UBERON:0001557]",
"Anterior Nares [UBERON:2001427]",
"Esophagus [UBERON:0001043]",
"Ethmoid sinus [UBERON:0002453]",
"Nasal Cavity [UBERON:0001707]",
"Middle Nasal Turbinate [UBERON:0005921]",
"Inferior Nasal Turbinate [UBERON:0005922]",
"Nasopharynx (NP) [UBERON:0001728]",
"Oropharynx (OP) [UBERON:0001729]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001214",
"type": "string",
"description": "An anatomical part of an organism e.g. oropharynx. ",
"examples": ["Nasopharynx (NP) [UBERON:0001728]"]
},
"host_health_outcome": {
"Enums": [
"Deceased [NCIT:C28554]",
"Deteriorating [NCIT:C25254]",
"Recovered [NCIT:C49498]",
"Stable [NCIT:C30103]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001390",
"type": "string",
"description": "Disease outcome in the host.",
"examples": ["Recovered [NCIT:C49498]"]
},
"sequencing_date": {
"examples": ["22/06/2020"],
"ontology": "GENEPIO:0001447",
"type": "string",
"description": "The date the sample was sequenced.",
"format": "date"
},
"passage_number": {
"ontology": "GENEPIO:0001261",
"type": "integer",
"description": "Number of passages.",
"examples": [3]
},
"ns_per_100_kbp": {
"ontology": "GENEPIO:0001484",
"type": "integer",
"description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.",
"examples": [300]
},
"case_id": {
"ontology": "GENEPIO:0100281",
"type": "string",
"description": "The identifier used to specify an epidemiologically detected case of disease.",
"examples": ["ABCD1234"]
},
"biosample_accession": {
"pattern": "^SAM(D|N|E([AG]?))[0-9]+",
"ontology": "GENEPIO:0001139",
"type": "string",
"description": "The identifier assigned to a BioSample in INSDC archives.",
"examples": ["SAMN14180202"]
},
"last_dose_vacicnation_date": {
"examples": ["09/04/2021"],
"ontology": "GENEPIO:0001408",
"type": "string",
"description": "The date the host received their last dose of vaccine.",
"format": "date"
},
"bioinformatics_protocol": {
"ontology": "GENEPIO:0001489",
"type": "string",
"description": "The name and version number of the bioinformatics protocol used.",
"examples": [
"https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members"
]
},
"prior_sars_cov_2_antiviral_treatment": {
"Enums": [
"Prior antiviral treatment [GENEPIO:0100037]",
"No prior antiviral treatment [GENEPIO:0100233]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001438",
"type": "string",
"description": "Whether there was prior SARS-CoV-2 treatment with an antiviral agent.",
"examples": ["Prior antiviral treatment [GENEPIO:0100037]"]
},
"gene_name_2": {
"Enums": [
"E gene (orf4) [GENEPIO:0100151]",
"M gene (orf5) [GENEPIO:0100152]",
"N gene (orf9) [GENEPIO:0100153]",
"Spike gene (orf2) [GENEPIO:0100154]",
"orf1ab (rep) [GENEPIO:0100155]",
"orf1a (pp1a) [GENEPIO:0100156]",
"nsp11 [GENEPIO:0100157]",
"nsp1 [GENEPIO:0100158]",
"nsp2 [GENEPIO:0100159]",
"nsp3 [GENEPIO:0100160]",
"nsp4 [GENEPIO:0100161]",
"nsp5 [GENEPIO:0100162]",
"nsp6 [GENEPIO:0100163]",
"nsp7 [GENEPIO:0100164]",
"nsp8 [GENEPIO:0100165]",
"nsp9 [GENEPIO:0100166]",
"nsp10 [GENEPIO:0100167]",
"RdRp gene (nsp12) [GENEPIO:0100168]",
"hel gene (nsp13) [GENEPIO:0100169]",
"exoN gene (nsp14) [GENEPIO:0100170]",
"nsp15 [GENEPIO:0100171]",
"nsp16 [GENEPIO:0100172]",
"orf3a [GENEPIO:0100173]",
"orf3b [GENEPIO:0100174]",
"orf6 (ns6) [GENEPIO:0100175]",
"orf7a [GENEPIO:0100176]",
"orf7b (ns7b) [GENEPIO:0100177]",
"orf8 (ns8) [GENEPIO:0100178]",
"orf9b [GENEPIO:0100179]",
"orf9c [GENEPIO:0100180]",
"orf10 [GENEPIO:0100181]",
"orf14 [GENEPIO:0100182]",
"SARS-COV-2 5' UTR [GENEPIO:0100183]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001510",
"type": "string",
"description": "The name of the gene used in the diagnostic RT-PCR test.",
"examples": ["RdRp gene (nsp12) [GENEPIO:0100168]"]
},
"body_product": {
"Enums": [
"Breast Milk [UBERON:0001913]",
"Feces [UBERON:0001988]",
"Mucus [UBERON:0000912]",
"Semen [UBERON:0006530]",
"Sputum [UBERON:0007311]",
"Sweat [UBERON:0001089]",
"Tear [UBERON:0001827]",
"Urine [UBERON:0001088]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001216",
"type": "string",
"description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.",
"examples": ["Feces [UBERON:0001988]"]
},
"host_age": {
"ontology": "GENEPIO:0001392",
"anyOf": [
{ "type": "integer" },
{ "pattern": "\\d+-\\d+", "type": "string" }
],
"description": "Age of host at the time of sampling.",
"examples": [79]
},
"host_ethnicity": {
"ontology": "GECKO:0000061",
"type": "string",
"description": "The self-identified ethnicity(ies) of the host.",
"examples": ["Indigenous, European"]
},
"collection_device": {
"Enums": [
"Air filter [ENVO:00003968]",
"Blood Collection Tube [OBI:0002859]",
"Bronchoscope [OBI:0002826]",
"Collection Container [OBI:0002088]",
"Collection Cup [GENEPIO:0100026]",
"Fibrobronchoscope Brush [OBI:0002825]",
"Filter [GENEPIO:0100103]",
"Fine Needle [OBI:0002827]",
"Microcapillary tube [OBI:0002858]",
"Micropipette [OBI:0001128]",
"Needle [OBI:0000436]",
"Serum Collection Tube [OBI:0002860]",
"Sputum Collection Tube [OBI:0002861]",
"Suction Catheter [OBI:0002831]",
"Swab [GENEPIO:0100027]",
"Urine Collection Tube [OBI:0002862]",
"Virus Transport Medium [OBI:0002866]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001234",
"type": "string",
"description": "The instrument or container used to collect the sample e.g. swab.",
"examples": ["Swab [GENEPIO:0100027]"]
},
"purpose_of_sequencing": {
"Enums": [
"Baseline surveillance (random sampling) [GENEPIO:0100005]",
"Targeted surveillance (non-random sampling) [GENEPIO:0100006]",
"Priority surveillance projects [GENEPIO:0100007]",
"Screening for Variants of Concern (VOC) [GENEPIO:0100008]",
"Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]",
"Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]",
"Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]",
"Re-infection surveillance [GENEPIO:0100010]",
"Vaccine escape surveillance [GENEPIO:0100011]",
"Travel-associated surveillance [GENEPIO:0100012]",
"Domestic travel surveillance [GENEPIO:0100013]",
"Interstate/ interprovincial travel surveillance [GENEPIO:0100275]",
"Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]",
"International travel surveillance [GENEPIO:0100014]",
"Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]",
"Surveillance of international border crossing by air travel [GENEPIO:0100016]",
"Surveillance of international border crossing by ground transport [GENEPIO:0100017]",
"Surveillance from international worker testing [GENEPIO:0100018]",
"Cluster/Outbreak investigation [GENEPIO:0100019]",
"Multi-jurisdictional outbreak investigation [GENEPIO:0100020]",
"Intra-jurisdictional outbreak investigation [GENEPIO:0100021]",
"Research [GENEPIO:0100022]",
"Viral passage experiment [GENEPIO:0100023]",
"Protocol testing [GENEPIO:0100024]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001445",
"type": "string",
"description": "The reason that the sample was sequenced.",
"examples": ["Baseline surveillance (random sampling) [GENEPIO:0100005]"]
},
"raw_sequence_data_processing_method": {
"ontology": "GENEPIO:0001458",
"type": "string",
"description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.",
"examples": ["Porechop 0.2.3,Porechop 0.2.3"]
},
"sequence_submitter_contact_address": {
"ontology": "GENEPIO:0001167",
"type": "string",
"description": "The mailing address of the agency submitting the sequence.",
"examples": ["123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada"]
},
"depth_of_coverage_threshold": {
"ontology": "GENEPIO:0001475",
"type": "number",
"description": "The threshold used as a cut-off for the depth of coverage.",
"examples": [100.0]
},
"specimen_processing": {
"Enums": [
"Virus Passage [GENEPIO:0100039]",
"RNA Re-Extraction (Post RT-PCR) [GENEPIO:0100040]",
"Specimens Pooled [OBI:0600016]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001253",
"type": "string",
"description": "Any processing applied to the sample during or after receiving the sample. ",
"examples": ["Virus Passage [GENEPIO:0100039]"]
},
"flow_cell_barcode": {
"ontology": "GENEPIO:0001451",
"type": "string",
"description": "The barcode of the flow cell used for sequencing.",
"examples": ["FAB06069"]
},
"r1_fastq_filename": {
"ontology": "GENEPIO:0001476",
"type": "string",
"description": "The user-specified filename of the r1 FASTQ file.",
"examples": ["ABC123_S1_L001_R1_001.fastq.gz"]
},
"destination_of_most_recent_travel_city": {
"ontology": "GENEPIO:0001411",
"type": "string",
"description": "The name of the city that was the destination of most recent travel.",
"examples": ["New York City"]
},
"r1_fastq_filepath": {
"ontology": "GENEPIO:0001478",
"type": "string",
"description": "The filepath of the r1 FASTQ file.",
"examples": [
"/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz"
]
},
"library_id": {
"ontology": "GENEPIO:0001448",
"type": "string",
"description": "The user-specified identifier for the library prepared for sequencing.",
"examples": ["XYZ_123345"]
},
"host_vaccination_status": {
"Enums": [
"Fully Vaccinated [GENEPIO:0100100]",
"Partially Vaccinated [GENEPIO:0100101]",
"Not Vaccinated [GENEPIO:0100102]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001404",
"type": "string",
"description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).",
"examples": ["Fully Vaccinated [GENEPIO:0100100]"]
},
"geo_loc_longitude": {
"ontology": "OBI:0001621",
"type": "string",
"description": "The longitude coordinates of the geographical location of sample collection.",
"examples": ["77.11 W"]
},
"genbank_ena_ddbj_accession": {
"pattern": "^([a-zA-Z]{2})\\d*.\\d{1}",
"ontology": "GENEPIO:0001145",
"type": "string",
"description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.",
"examples": ["MN908947.3"]
},
"bioproject_accession": {
"pattern": "^PRJ(N|E|D)([a-zA-Z]?)[0-9]+*",
"ontology": "GENEPIO:0001136",
"type": "string",
"description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs. ",
"examples": ["PRJNA12345"]
},
"lineage_clade_analysis_software_name": {
"ontology": "GENEPIO:0001501",
"type": "string",
"description": "The name of the software used to determine the lineage/clade.",
"examples": ["Pangolin"]
},
"location_of_exposure_geo_loc_name_country": {
"Enums": [
"Afghanistan [GAZ:00006882]",
"Albania [GAZ:00002953]",
"Algeria [GAZ:00000563]",
"American Samoa [GAZ:00003957]",
"Andorra [GAZ:00002948]",
"Angola [GAZ:00001095]",
"Anguilla [GAZ:00009159]",
"Antarctica [GAZ:00000462]",
"Antigua and Barbuda [GAZ:00006883]",
"Argentina [GAZ:00002928]",
"Armenia [GAZ:00004094]",
"Aruba [GAZ:00004025]",
"Ashmore and Cartier Islands [GAZ:00005901]",
"Australia [GAZ:00000463]",
"Austria [GAZ:00002942]",
"Azerbaijan [GAZ:00004941]",
"Bahamas [GAZ:00002733]",
"Bahrain [GAZ:00005281]",
"Baker Island [GAZ:00007117]",
"Bangladesh [GAZ:00003750]",
"Barbados [GAZ:00001251]",
"Bassas da India [GAZ:00005810]",
"Belarus [GAZ:00006886]",
"Belgium [GAZ:00002938]",
"Belize [GAZ:00002934]",
"Benin [GAZ:00000904]",
"Bermuda [GAZ:00001264]",
"Bhutan [GAZ:00003920]",
"Bolivia [GAZ:00002511]",
"Borneo [GAZ:00025355]",
"Bosnia and Herzegovina [GAZ:00006887]",
"Botswana [GAZ:00001097]",
"Bouvet Island [GAZ:00001453]",
"Brazil [GAZ:00002828]",
"British Virgin Islands [GAZ:00003961]",
"Brunei [GAZ:00003901]",
"Bulgaria [GAZ:00002950]",
"Burkina Faso [GAZ:00000905]",
"Burundi [GAZ:00001090]",
"Cambodia [GAZ:00006888]",
"Cameroon [GAZ:00001093]",
"Canada [GAZ:00002560]",
"Cape Verde [GAZ:00001227]",
"Cayman Islands [GAZ:00003986]",
"Central African Republic [GAZ:00001089]",
"Chad [GAZ:00000586]",
"Chile [GAZ:00002825]",
"China [GAZ:00002845]",
"Christmas Island [GAZ:00005915]",
"Clipperton Island [GAZ:00005838]",
"Cocos Islands [GAZ:00009721]",
"Colombia [GAZ:00002929]",
"Comoros [GAZ:00005820]",
"Cook Islands [GAZ:00053798]",
"Coral Sea Islands [GAZ:00005917]",
"Costa Rica [GAZ:00002901]",
"Cote d'Ivoire [GAZ:00000906]",
"Croatia [GAZ:00002719]",
"Cuba [GAZ:00003762]",
"Curacao [GAZ:00012582]",
"Cyprus [GAZ:00004006]",
"Czech Republic [GAZ:00002954]",
"Democratic Republic of the Congo [GAZ:00001086]",
"Denmark [GAZ:00005852]",
"Djibouti [GAZ:00000582]",
"Dominica [GAZ:00006890]",
"Dominican Republic [GAZ:00003952]",
"Ecuador [GAZ:00002912]",
"Egypt [GAZ:00003934]",
"El Salvador [GAZ:00002935]",
"Equatorial Guinea [GAZ:00001091]",
"Eritrea [GAZ:00000581]",
"Estonia [GAZ:00002959]",
"Eswatini [GAZ:00001099]",
"Ethiopia [GAZ:00000567]",
"Europa Island [GAZ:00005811]",
"Falkland Islands (Islas Malvinas) [GAZ:00001412]",
"Faroe Islands [GAZ:00059206]",
"Fiji [GAZ:00006891]",
"Finland [GAZ:00002937]",
"France [GAZ:00003940]",
"French Guiana [GAZ:00002516]",
"French Polynesia [GAZ:00002918]",
"French Southern and Antarctic Lands [GAZ:00003753]",
"Gabon [GAZ:00001092]",
"Gambia [GAZ:00000907]",
"Gaza Strip [GAZ:00009571]",
"Georgia [GAZ:00004942]",
"Germany [GAZ:00002646]",
"Ghana [GAZ:00000908]",
"Gibraltar [GAZ:00003987]",
"Glorioso Islands [GAZ:00005808]",
"Greece [GAZ:00002945]",
"Greenland [GAZ:00001507]",
"Grenada [GAZ:02000573]",
"Guadeloupe [GAZ:00067142]",
"Guam [GAZ:00003706]",
"Guatemala [GAZ:00002936]",
"Guernsey [GAZ:00001550]",
"Guinea [GAZ:00000909]",
"Guinea-Bissau [GAZ:00000910]",
"Guyana [GAZ:00002522]",
"Haiti [GAZ:00003953]",
"Heard Island and McDonald Islands [GAZ:00009718]",
"Honduras [GAZ:00002894]",
"Hong Kong [GAZ:00003203]",
"Howland Island [GAZ:00007120]",
"Hungary [GAZ:00002952]",
"Iceland [GAZ:00000843]",
"India [GAZ:00002839]",
"Indonesia [GAZ:00003727]",
"Iran [GAZ:00004474]",
"Iraq [GAZ:00004483]",
"Ireland [GAZ:00002943]",
"Isle of Man [GAZ:00052477]",
"Israel [GAZ:00002476]",
"Italy [GAZ:00002650]",
"Jamaica [GAZ:00003781]",
"Jan Mayen [GAZ:00005853]",
"Japan [GAZ:00002747]",
"Jarvis Island [GAZ:00007118]",
"Jersey [GAZ:00001551]",
"Johnston Atoll [GAZ:00007114]",
"Jordan [GAZ:00002473]",
"Juan de Nova Island [GAZ:00005809]",
"Kazakhstan [GAZ:00004999]",
"Kenya [GAZ:00001101]",
"Kerguelen Archipelago [GAZ:00005682]",
"Kingman Reef [GAZ:00007116]",
"Kiribati [GAZ:00006894]",
"Kosovo [GAZ:00011337]",
"Kuwait [GAZ:00005285]",
"Kyrgyzstan [GAZ:00006893]",
"Laos [GAZ:00006889]",
"Latvia [GAZ:00002958]",
"Lebanon [GAZ:00002478]",
"Lesotho [GAZ:00001098]",
"Liberia [GAZ:00000911]",
"Libya [GAZ:00000566]",
"Liechtenstein [GAZ:00003858]",
"Line Islands [GAZ:00007144]",
"Lithuania [GAZ:00002960]",
"Luxembourg [GAZ:00002947]",
"Macau [GAZ:00003202]",
"Madagascar [GAZ:00001108]",
"Malawi [GAZ:00001105]",
"Malaysia [GAZ:00003902]",
"Maldives [GAZ:00006924]",
"Mali [GAZ:00000584]",
"Malta [GAZ:00004017]",
"Marshall Islands [GAZ:00007161]",
"Martinique [GAZ:00067143]",
"Mauritania [GAZ:00000583]",
"Mauritius [GAZ:00003745]",
"Mayotte [GAZ:00003943]",
"Mexico [GAZ:00002852]",
"Micronesia [GAZ:00005862]",
"Midway Islands [GAZ:00007112]",
"Moldova [GAZ:00003897]",
"Monaco [GAZ:00003857]",
"Mongolia [GAZ:00008744]",
"Montenegro [GAZ:00006898]",
"Montserrat [GAZ:00003988]",
"Morocco [GAZ:00000565]",
"Mozambique [GAZ:00001100]",
"Myanmar [GAZ:00006899]",
"Namibia [GAZ:00001096]",
"Nauru [GAZ:00006900]",
"Navassa Island [GAZ:00007119]",
"Nepal [GAZ:00004399]",
"Netherlands [GAZ:00002946]",
"New Caledonia [GAZ:00005206]",
"New Zealand [GAZ:00000469]",
"Nicaragua [GAZ:00002978]",
"Niger [GAZ:00000585]",
"Nigeria [GAZ:00000912]",
"Niue [GAZ:00006902]",
"Norfolk Island [GAZ:00005908]",
"North Korea [GAZ:00002801]",
"North Macedonia [GAZ:00006895]",
"North Sea [GAZ:00002284]",
"Northern Mariana Islands [GAZ:00003958]",
"Norway [GAZ:00002699]",
"Oman [GAZ:00005283]",
"Pakistan [GAZ:00005246]",
"Palau [GAZ:00006905]",
"Panama [GAZ:00002892]",
"Papua New Guinea [GAZ:00003922]",
"Paracel Islands [GAZ:00010832]",
"Paraguay [GAZ:00002933]",
"Peru [GAZ:00002932]",
"Philippines [GAZ:00004525]",
"Pitcairn Islands [GAZ:00005867]",
"Poland [GAZ:00002939]",
"Portugal [GAZ:00004126]",
"Puerto Rico [GAZ:00006935]",
"Qatar [GAZ:00005286]",
"Republic of the Congo [GAZ:00001088]",
"Reunion [GAZ:00003945]",
"Romania [GAZ:00002951]",
"Ross Sea [GAZ:00023304]",
"Russia [GAZ:00002721]",
"Rwanda [GAZ:00001087]",
"Saint Helena [GAZ:00000849]",
"Saint Kitts and Nevis [GAZ:00006906]",
"Saint Lucia [GAZ:00006909]",
"Saint Pierre and Miquelon [GAZ:00003942]",
"Saint Martin [GAZ:00005841]",
"Saint Vincent and the Grenadines [GAZ:02000565]",
"Samoa [GAZ:00006910]",
"San Marino [GAZ:00003102]",
"Sao Tome and Principe [GAZ:00006927]",
"Saudi Arabia [GAZ:00005279]",
"Senegal [GAZ:00000913]",
"Serbia [GAZ:00002957]",
"Seychelles [GAZ:00006922]",
"Sierra Leone [GAZ:00000914]",
"Singapore [GAZ:00003923]",
"Sint Maarten [GAZ:00012579]",
"Slovakia [GAZ:00002956]",
"Slovenia [GAZ:00002955]",
"Solomon Islands [GAZ:00005275]",
"Somalia [GAZ:00001104]",
"South Africa [GAZ:00001094]",
"South Georgia and the South Sandwich Islands [GAZ:00003990]",
"South Korea [GAZ:00002802]",
"South Sudan [GAZ:00233439]",
"Spain [GAZ:00003936]",
"Spratly Islands [GAZ:00010831]",
"Sri Lanka [GAZ:00003924]",
"State of Palestine [GAZ:00002475]",
"Sudan [GAZ:00000560]",
"Suriname [GAZ:00002525]",
"Svalbard [GAZ:00005396]",
"Swaziland [GAZ:00001099]",
"Sweden [GAZ:00002729]",
"Switzerland [GAZ:00002941]",
"Syria [GAZ:00002474]",
"Taiwan [GAZ:00005341]",
"Tajikistan [GAZ:00006912]",
"Tanzania [GAZ:00001103]",
"Thailand [GAZ:00003744]",
"Timor-Leste [GAZ:00006913]",
"Togo [GAZ:00000915]",
"Tokelau [GAZ:00260188]",
"Tonga [GAZ:00006916]",
"Trinidad and Tobago [GAZ:00003767]",
"Tromelin Island [GAZ:00005812]",
"Tunisia [GAZ:00000562]",
"Turkey [GAZ:00000558]",
"Turkmenistan [GAZ:00005018]",
"Turks and Caicos Islands [GAZ:00003955]",
"Tuvalu [GAZ:00009715]",
"USA [GAZ:00002459]",
"Uganda [GAZ:00001102]",
"Ukraine [GAZ:00002724]",
"United Arab Emirates [GAZ:00005282]",
"United Kingdom [GAZ:00002637]",
"Uruguay [GAZ:00002930]",
"Uzbekistan [GAZ:00004979]",
"Vanuatu [GAZ:00006918]",
"Venezuela [GAZ:00002931]",
"Viet Nam [GAZ:00003756]",
"Virgin Islands [GAZ:00003959]",
"Wake Island [GAZ:00007111]",
"Wallis and Futuna [GAZ:00007191]",
"West Bank [GAZ:00009572]",
"Western Sahara [GAZ:00000564]",
"Yemen [GAZ:00005284]",
"Zambia [GAZ:00001107]",
"Zimbabwe [GAZ:00001106]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001410",
"type": "string",
"description": "The country where the host was likely exposed to the causative agent of the illness.",
"examples": ["South Africa [GAZ:00001094]"]
},
"sample_plan_name": {
"ontology": "GENEPIO:0100285",
"type": "string",
"description": "The name of the sample plan implemented for sample collection.",
"examples": ["CanCOGeN Sampling Strategy 1.0"]
},
"prior_sars_cov_2_antiviral_treatment_date": {
"examples": ["28/01/2021"],
"ontology": "GENEPIO:0001440",
"type": "string",
"description": "The date treatment was first administered during the prior SARS-CoV-2 infection.",
"format": "date"
},
"library_preparation_kit": {
"ontology": "GENEPIO:0001450",
"type": "string",
"description": "The name of the DNA library preparation kit used to generate the library being sequenced.",
"examples": ["Nextera XT"]
},
"fast5_filename": {
"ontology": "GENEPIO:0001480",
"type": "string",
"description": "The user-specified filename of the FAST5 file.",
"examples": ["batch1a_sequences.fast5"]
},
"diagnostic_pcr_ct_value_1": {
"ontology": "GENEPIO:0001509",
"type": "integer",
"description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.",
"examples": [21]
},
"collection_method": {
"Enums": [
"Amniocentesis [NCIT:C52009]",
"Aspiration [NCIT:C15631]",
"Suprapubic Aspiration [GENEPIO:0100028]",
"Tracheal Aspiration [GENEPIO:0100029]",
"Vacuum Aspiration [GENEPIO:0100030]",
"Biopsy [OBI:0002650]",
"Needle Biopsy [OBI:0002651]",
"Filtration [OBI:0302885]",
"Air Filtration [GENEPIO:0100031]",
"Lavage [OBI:0600044]",
"Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]",
"Gastric Lavage [GENEPIO:0100033]",
"Lumbar Puncture [NCIT:C15327]",
"Necropsy [MMO:0000344]",
"Phlebotomy [NCIT:C28221]",
"Rinsing [GENEPIO:0002116]",
"Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]",
"Scraping [GENEPIO:0100035]",
"Swabbing [GENEPIO:0002117]",
"Finger Prick [GENEPIO:0100036]",
"Washout Tear Collection [GENEPIO:0100038]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001241",
"type": "string",
"description": "The process used to collect the sample e.g. phlebotomy, necropsy.",
"examples": ["Bronchoalveolar Lavage (BAL) [GENEPIO:0100032]"]
},
"geo_loc_name_county_region": {
"ontology": "GENEPIO:0100280",
"type": "string",
"description": "The county/region of origin of the sample.",
"examples": ["Derbyshire"]
},
"consensus_genome_length": {
"ontology": "GENEPIO:0001483",
"type": "integer",
"description": "Size of the assembled genome described as the number of base pairs.",
"examples": [38677]
},
"r2_fastq_filepath": {
"ontology": "GENEPIO:0001479",
"type": "string",
"description": "The filepath of the r2 FASTQ file.",
"examples": [
"/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz"
]
},
"destination_of_most_recent_travel_state_province_territory": {
"ontology": "GENEPIO:0001412",
"type": "string",
"description": "The name of the province that was the destination of most recent travel.",
"examples": ["California"]
},
"sample_received_date": {
"examples": ["20/03/2020"],
"ontology": "GENEPIO:0001179",
"type": "string",
"description": "The date on which the sample was received.",
"format": "date"
},
"host_common_name": {
"Enums": [
"Human [NCBITaxon:9606]",
"Bat [NCBITaxon:9397]",
"Cat [NCBITaxon:9685]",
"Chicken [NCBITaxon:9031]",
"Civet [NCBITaxon:9673]",
"Cow [NCBITaxon:9913]",
"Dog [NCBITaxon:9615]",
"Lion [NCBITaxon:9689]",
"Mink [NCBITaxon:452646]",
"Pangolin [NCBITaxon:9973]",
"Pig [NCBITaxon:9825]",
"Pigeon [NCBITaxon:8930]",
"Tiger [NCBITaxon:9694]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"ontology": "GENEPIO:0001386",
"type": "string",
"description": "The commonly used name of the host.",
"examples": ["Human [NCBITaxon:9606]"]
},
"geo_loc_name_state_province_territory": {
"ontology": "GENEPIO:0001185",
"type": "string",
"description": "The state/province/territory of origin of the sample.",
"examples": ["Western Cape"]
},
"lineage_clade_analysis_software_version": {
"ontology": "GENEPIO:0001502",
"type": "string",
"description": "The version of the software used to determine the lineage/clade.",
"examples": ["2.1.10"]
},
"host_subject_id": {
"ontology": "GENEPIO:0001398",
"type": "string",
"description": "A unique identifier by which each host can be referred to e.g. #131",
"examples": ["BCxy123"]
},
"sra_accession": {
"pattern": "^(SRR|ERR|DRR)[0-9]+",
"ontology": "GENEPIO:0001142",
"type": "string",
"description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.",
"examples": ["SRR11177792"]
},
"authors": {
"ontology": "GENEPIO:0001517",
"type": "string",
"description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.",
"examples": ["Tejinder Singh, Fei Hu, Johnny Blogs"]
},
"host_role": {
"Enums": [
"Attendee [GENEPIO:0100249]",
"Student [OMRSE:00000058]",
"Patient [OMRSE:00000030]",
"Inpatient [NCIT:C25182]",
"Outpatient [NCIT:C28293]",
"Passenger [GENEPIO:0100250]",
"Resident [GENEPIO:0100251]",
"Visitor [GENEPIO:0100252]",
"Volunteer [GENEPIO:0100253]",
"Work [GENEPIO:0100254]",
"Administrator [GENEPIO:0100255]",
"First Responder [GENEPIO:0100256]",
"Firefighter [GENEPIO:0100257]",
"Paramedic [GENEPIO:0100258]",
"Police Officer [GENEPIO:0100259]",
"Housekeeper [GENEPIO:0100260]",
"Kitchen Worker [GENEPIO:0100261]",
"Laboratory Worker [GENEPIO:0100262]",
"Nurse [OMRSE:00000014]",
"Personal Care Aid [GENEPIO:0100263]",
"Pharmacist [GENEPIO:0100264]",
"Physician [OMRSE:00000013]",
"Vet [GENEPIO:0100265]",
"Social role [OMRSE:00000001]",
"Acquaintance of case [GENEPIO:0100266]",
"Relative of case [GENEPIO:0100267]",
"Child of case [GENEPIO:0100268]",
"Parent of case [GENEPIO:0100269]",
"Father of case [GENEPIO:0100270]",
"Mother of case [GENEPIO:0100271]",
"Spouse of case [GENEPIO:0100272]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",