-
Notifications
You must be signed in to change notification settings - Fork 4
/
sample_types.json
1208 lines (1201 loc) · 63.1 KB
/
sample_types.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
{
"definitions": {
"Q_BIOLOGICAL_ENTITY": {
"description": "The biological entity (e.g., human, mouse) to be studied. With this data object, information specific to the subject (e.g., age or BMI in the case of patient data) can be stored.",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_NCBI_ORGANISM": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "NCBI organism",
"description": "Specifies the organism of study according to the NCBI taxonomy (http://www.ncbi.nlm.nih.gov/taxonomy)."
},
"Q_EXTERNALDB_ID": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "External DB identifier",
"description": "This field facilitates the cross-linking to external databases outside the QBiC (e.g., confidential patient databases)."
},
"Q_PROPERTIES": {
"type": "string",
"openbis_type": "XML",
"label": "Properties",
"description": "Properties that are characteristic to this biological entity/sample. These could be experimental factors (e.g., duration of treatment) or class information (e.g., WT or KO mouse, healthy versus diseased)."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
},
"Q_NOTES": {
"type": "string",
"openbis_type": "XML",
"label": "Notes",
"description": "Notes that can be added by different users. Contains each note, user that added it with full name and timestamp of the addition."
},
"Q_GENDER": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "Gender",
"description": "Gender of the patient or other biological entity."
},
"Q_LOCI": {
"type": "string",
"openbis_type": "XML",
"label": "Genomic Loci",
"description": "XML type holding the different alleles of different genomic loci of a sample."
},
"Q_ORGANISM_DETAILED": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Detailed organism specification",
"description": "If the organism is not well-defined or a specific strain of bacteria etc."
},
"Q_SEX": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "Sex",
"description": "Sex of a patient or animal"
},
"Q_ADDITIONAL_DATA_INFO": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Additional Data Info",
"description": "some text"
},
"Q_EXPRESSION_SYSTEM": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "Expression system",
"description": "Expression systems are genetic constructs (a gene encoded by DNA) that are designed to produce a protein, or an RNA (ribonucleic acid), either inside or outside a cell. Here, the term relates to genetically engineered or infected organisms."
},
"Q_STRAIN_LAB_COLLECTION_NUMBER": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Strain lab collection number",
"description": "Identifier specifying one specimen in a strain collection of bacteria"
}
}
},
"Q_TEST_SAMPLE": {
"description": "This sample is prepared and ready for a specific analytic platform (e.g. protein extract for a proteomics MS experiment).",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_SAMPLE_TYPE": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "Sample type",
"description": "Describes the main content of the test sample."
},
"Q_PROPERTIES": {
"type": "string",
"openbis_type": "XML",
"label": "Properties",
"description": "Properties that are characteristic to this biological entity/sample. These could be experimental factors (e.g., duration of treatment) or class information (e.g., WT or KO mouse, healthy versus diseased)."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
},
"Q_EXTERNALDB_ID": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "External DB identifier",
"description": "This field facilitates the cross-linking to external databases outside the QBiC (e.g., confidential patient databases)."
},
"Q_NOTES": {
"type": "string",
"openbis_type": "XML",
"label": "Notes",
"description": "Notes that can be added by different users. Contains each note, user that added it with full name and timestamp of the addition."
},
"Q_LOCI": {
"type": "string",
"openbis_type": "XML",
"label": "Genomic Loci",
"description": "XML type holding the different alleles of different genomic loci of a sample."
},
"Q_RNA_INTEGRITY_NUMBER": {
"type": "number",
"openbis_type": "REAL",
"label": "RNA Integrity Number",
"description": "RNA integrity of a microarray experiment. The RIN algorithm assigns a 1 to 10 integrity score, where level 10 RNA is completely intact."
},
"Q_PRE_TREATMENT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Pretreatment",
"description": "Pretreatment performed on samples"
},
"Q_MOLECULAR_LABEL": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Molecular Sample Label",
"description": "An isotope label or other modification that has been added to this sample to identify it later."
}
}
},
"Q_BIOLOGICAL_SAMPLE": {
"description": "The biological sample that is extracted from the corresponding biological entity. This is the raw sample material that can be later prepared for specific analytical methods such as MS or NGS.",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_PRIMARY_TISSUE": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "Primary tissue/body fluid",
"description": "Specifies the tissue/body fluid the sample is taken from."
},
"Q_TISSUE_DETAILED": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Detailed tissue/body fluid specification",
"description": "Since the primary tissue definition could be too rough, this field specifies the sample more closely (e.g., more specific definition of the cell type)."
},
"Q_EXTERNALDB_ID": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "External DB identifier",
"description": "This field facilitates the cross-linking to external databases outside the QBiC (e.g., confidential patient databases)."
},
"Q_PROPERTIES": {
"type": "string",
"openbis_type": "XML",
"label": "Properties",
"description": "Properties that are characteristic to this biological entity/sample. These could be experimental factors (e.g., duration of treatment) or class information (e.g., WT or KO mouse, healthy versus diseased)."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
},
"Q_CREATION_TIME": {
"type": "string",
"openbis_type": "TIMESTAMP",
"label": "Time point of sample creation",
"description": "This field stores the exact time/date of sample creation (not registration!). For example, it could be used for time-series experiments."
},
"Q_CURRENT_PROCESS_STATE": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "Current process state",
"description": "If a sample is part of a modeled process (e.g., MultiscaleHCC workflow), this field describes the current state."
},
"Q_NOTES": {
"type": "string",
"openbis_type": "XML",
"label": "Notes",
"description": "Notes that can be added by different users. Contains each note, user that added it with full name and timestamp of the addition."
},
"Q_LOCI": {
"type": "string",
"openbis_type": "XML",
"label": "Genomic Loci",
"description": "XML type holding the different alleles of different genomic loci of a sample."
},
"Q_HISTOLOGY": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "Histology",
"description": "Histology of the sample, e.g. Cell or Cancer Type"
},
"Q_DIGNITY": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Tissue dignity",
"description": "Benign or malignant tissue"
},
"Q_IS_METASTASIS": {
"type": "integer",
"openbis_type": "BOOLEAN",
"label": "Metastasis",
"description": "Describes whether a sample comes form a metastasis or not"
},
"Q_TUMOR_STAGE": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Tumor Stage",
"description": "the stage of the tumor"
},
"Q_TUMOR_TYPE": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "Tumor Type",
"description": "tumor type"
},
"Q_TISSUE_LOCATION": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Tissue Location",
"description": "location of the tissue"
}
}
},
"Q_NMR_SAMPLE_RUN": {
"description": "NMR measured sample",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_POWER_ESTIMATION_RUN": {
"description": "runs of the sample size/power estimation portlet. stores input parameters, visualization (e.g. power matrix) and/or data",
"properties": {
"Q_PROPERTIES": {
"type": "string",
"openbis_type": "XML",
"label": "Properties",
"description": "Properties that are characteristic to this biological entity/sample. These could be experimental factors (e.g., duration of treatment) or class information (e.g., WT or KO mouse, healthy versus diseased)."
},
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_TECHNOLOGY_TYPE": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Technology type",
"description": "Type of technology used to measure date"
}
}
},
"Q_BMI_GENERIC_IMAGING_RUN": {
"description": "",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_EXTERNALDB_ID": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "External DB identifier",
"description": "This field facilitates the cross-linking to external databases outside the QBiC (e.g., confidential patient databases)."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
},
"Q_NOTES": {
"type": "string",
"openbis_type": "XML",
"label": "Notes",
"description": "Notes that can be added by different users. Contains each note, user that added it with full name and timestamp of the addition."
},
"Q_OMERO_IDS": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "OMERO Identifiers",
"description": "omero identifiers for linking images"
}
}
},
"Q_NGS_NANOPORE_SINGLE_SAMPLE_RUN": {
"description": "Specifies one sample run in a single sequencing run on a Nanopore sequencer.",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_EXTERNALDB_ID": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "External DB identifier",
"description": "This field facilitates the cross-linking to external databases outside the QBiC (e.g., confidential patient databases)."
}
}
},
"Q_MS_RUN": {
"description": "Specifies an individual MS measurement. For each MS run, a label is generated automatically (e.g., QPROJ_MSRUN1, QPROJ_MSRUN2, ...) and is unique within the corresponding user space.",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_PROPERTIES": {
"type": "string",
"openbis_type": "XML",
"label": "Properties",
"description": "Properties that are characteristic to this biological entity/sample. These could be experimental factors (e.g., duration of treatment) or class information (e.g., WT or KO mouse, healthy versus diseased)."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
},
"Q_EXTERNALDB_ID": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "External DB identifier",
"description": "This field facilitates the cross-linking to external databases outside the QBiC (e.g., confidential patient databases)."
},
"Q_INJECTION_VOLUME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Injection Volume",
"description": "Volume injected in an LC run"
},
"Q_SAMPLE_SOLVENT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample solvent",
"description": "Solvent used to inject sample for HPLC or similar"
}
}
},
"Q_PIPELINE_RUN": {
"description": "Pipeline run sample description",
"properties": {
"Q_WF_ID": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Workflow ID",
"description": "The identifier of a workflow"
},
"Q_PIPELINE_NAME": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "Pipeline name",
"description": "Name of the pipeline "
},
"Q_PIPELINE_VERSION": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Pipeline version",
"description": "Version of the pipeline"
},
"Q_PIPELINE_COMMAND": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Pipeline command",
"description": "The full command used to start a Nextflow pipeline"
}
}
},
"Q_WF_MS_INDIVIDUALIZED_PROTEOME_RUN": {
"description": "",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_WF_MS_LIGANDOMICS_QC_RUN": {
"description": "",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_WF_NGS_HLATYPING_RUN": {
"description": "",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_HLA_TYPING": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "HLA Typing",
"description": "The HLA Typing as multiline varchar."
},
"Q_NOTES": {
"type": "string",
"openbis_type": "XML",
"label": "Notes",
"description": "Notes that can be added by different users. Contains each note, user that added it with full name and timestamp of the addition."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"RNA": {
"description": "RNA to be measured by RNA-Seq, Microarrays or other means",
"properties": {
"SPECIES": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Species",
"description": "Species the original sample was extracted from."
},
"SAMPLE_CLASS": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample class",
"description": "This property classifies samples into groups defined by their experimental context or treatment. E.g. Control vs Disease or Wildtype."
},
"VOLUME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Volume",
"description": ""
},
"CONCENTRATION": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Concentration",
"description": ""
},
"RIN": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "RNA Integrity Number",
"description": ""
},
"AMOUNT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Amount in micrograms",
"description": "Amount of this sample type in micrograms"
},
"BIRTHDATE": {
"type": "string",
"openbis_type": "TIMESTAMP",
"label": "Birth date",
"description": "Birth date of a patient"
},
"SOURCE": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample Source",
"description": "The source this sample came from in the Project context. E.g. \"Mouse 5\""
},
"TREATMENT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Treatment",
"description": "A very short description of the treatment of this sample."
},
"TIME_POINT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Time Point",
"description": "A short description of the time point and its unit of a sample in its project context."
}
}
},
"BIOLOGICAL": {
"description": "A biological sample.",
"properties": {
"SAMPLE_CLASS": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample class",
"description": "This property classifies samples into groups defined by their experimental context or treatment. E.g. Control vs Disease or Wildtype."
},
"SPECIES": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Species",
"description": "Species the original sample was extracted from."
},
"SOURCE": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample Source",
"description": "The source this sample came from in the Project context. E.g. \"Mouse 5\""
},
"TREATMENT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Treatment",
"description": "A very short description of the treatment of this sample."
},
"TIME_POINT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Time Point",
"description": "A short description of the time point and its unit of a sample in its project context."
}
}
},
"DNA": {
"description": "Complete DNA measured by sequencing",
"properties": {
"SAMPLE_CLASS": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample class",
"description": "This property classifies samples into groups defined by their experimental context or treatment. E.g. Control vs Disease or Wildtype."
},
"SPECIES": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Species",
"description": "Species the original sample was extracted from."
},
"TREATMENT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Treatment",
"description": "A very short description of the treatment of this sample."
},
"SOURCE": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample Source",
"description": "The source this sample came from in the Project context. E.g. \"Mouse 5\""
},
"TIME_POINT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Time Point",
"description": "A short description of the time point and its unit of a sample in its project context."
}
}
},
"HCC_SAMPLE": {
"description": "Sample from hepatocellular carcinoma (HCC).",
"properties": {
"SAMPLE_CLASS": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample class",
"description": "This property classifies samples into groups defined by their experimental context or treatment. E.g. Control vs Disease or Wildtype."
},
"SPECIES": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Species",
"description": "Species the original sample was extracted from."
},
"TREATMENT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Treatment",
"description": "A very short description of the treatment of this sample."
},
"TIME_POINT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Time Point",
"description": "A short description of the time point and its unit of a sample in its project context."
},
"SOURCE": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample Source",
"description": "The source this sample came from in the Project context. E.g. \"Mouse 5\""
}
}
},
"NMR_INJECTION": {
"description": "Biological sample prepared for injection to NMR.",
"properties": {
"SAMPLE_CLASS": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample class",
"description": "This property classifies samples into groups defined by their experimental context or treatment. E.g. Control vs Disease or Wildtype."
},
"SPECIES": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Species",
"description": "Species the original sample was extracted from."
},
"TIME_POINT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Time Point",
"description": "A short description of the time point and its unit of a sample in its project context."
},
"TREATMENT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Treatment",
"description": "A very short description of the treatment of this sample."
},
"SOURCE": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample Source",
"description": "The source this sample came from in the Project context. E.g. \"Mouse 5\""
}
}
},
"Q_MHC_LIGAND_EXTRACT": {
"description": "Preparation of MHC ligands taken from a sample",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_MHC_CLASS": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "MHC class",
"description": "MHC class of a ligand sample, e.g. 1 or 2"
},
"Q_PROPERTIES": {
"type": "string",
"openbis_type": "XML",
"label": "Properties",
"description": "Properties that are characteristic to this biological entity/sample. These could be experimental factors (e.g., duration of treatment) or class information (e.g., WT or KO mouse, healthy versus diseased)."
},
"Q_ANTIBODY": {
"type": "string",
"openbis_type": "CONTROLLEDVOCABULARY",
"label": "Antibody",
"description": "Antibody or antibodies used in preparation of samples."
},
"Q_EXTERNALDB_ID": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "External DB identifier",
"description": "This field facilitates the cross-linking to external databases outside the QBiC (e.g., confidential patient databases)."
}
}
},
"Q_WF_MS_LIGANDOMICS_ID_RUN": {
"description": "",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"MS_INJECTION": {
"description": "Injection of a biological sample into a MS",
"properties": {
"SPECIES": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Species",
"description": "Species the original sample was extracted from."
},
"SAMPLE_CLASS": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample class",
"description": "This property classifies samples into groups defined by their experimental context or treatment. E.g. Control vs Disease or Wildtype."
},
"SOURCE": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample Source",
"description": "The source this sample came from in the Project context. E.g. \"Mouse 5\""
},
"TREATMENT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Treatment",
"description": "A very short description of the treatment of this sample."
},
"TIME_POINT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Time Point",
"description": "A short description of the time point and its unit of a sample in its project context."
}
}
},
"PROTEIN": {
"description": "a protein sample",
"properties": {
"SPECIES": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Species",
"description": "Species the original sample was extracted from."
},
"SAMPLE_CLASS": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample class",
"description": "This property classifies samples into groups defined by their experimental context or treatment. E.g. Control vs Disease or Wildtype."
},
"SOURCE": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Sample Source",
"description": "The source this sample came from in the Project context. E.g. \"Mouse 5\""
},
"TREATMENT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Treatment",
"description": "A very short description of the treatment of this sample."
},
"TIME_POINT": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Time Point",
"description": "A short description of the time point and its unit of a sample in its project context."
}
}
},
"Q_WF_NGS_MAPPING_RUN": {
"description": "",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_WF_MA_QUALITYCONTROL_RUN": {
"description": "Corresponds to an instance of a quality control run as produced by the Microarray QC workflow.",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_WF_MS_PEPTIDEID_RUN": {
"description": "One instance of a run of the Peptide Identification Workflow",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_WF_NGS_EPITOPE_PREDICTION_RUN": {
"description": "A workflow run for epitope prediction",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_WF_NGS_QUALITYCONTROL_RUN": {
"description": "Corresponds to an instance of a quality control run as produced by the FastQC workflow. Should be linked with NGS measurement runs.",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_WF_NGS_RNA_EXPRESSION_ANALYSIS_RUN": {
"description": "One instance of a run of the RNA Expression Analysis Workflow",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_WF_NGS_VARIANT_CALLING_RUN": {
"description": "",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_WF_NGS_VARIANT_ANNOTATION_RUN": {
"description": "",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_WF_MS_QUALITYCONTROL_RUN": {
"description": "Corresponds to an instance of a quality control run as produced by the OpenMS QC workflow. Should be linked with MS measurement runs (mzML input).",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}
}
},
"Q_ATTACHMENT_SAMPLE": {
"description": "Sample to store datasets on a project- or experiment-wide level. Used for datasets that can not be derived from specific samples or workflows or for experimental protocols uploaded in the beginning of a project.\nThe code should look like this: Q[XXXX]000 for samples for a project with code QXXXX and Q[XXXX][E] for samples for a specific experiment with code E.",
"properties": {
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
},
"Q_NOTES": {
"type": "string",
"openbis_type": "XML",
"label": "Notes",
"description": "Notes that can be added by different users. Contains each note, user that added it with full name and timestamp of the addition."
}
}
},
"Q_NGS_FLOWCELL_RUN": {
"description": "A container sample type that specifies the flowcell used (barcode) and may comprise several single sample runs (Q_NGS_SINGLE_SAMPLE_RUN).",
"properties": {
"Q_SECONDARY_NAME": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Secondary name",
"description": "While an experiment is unambiguously identified by an unique code, this secondary name might be used as a more descriptive label for the experiment or sample (e.g., \"Shotgun proteomics experiment #120\", \"Plasma sample #33\"). Also, often labs want to keep of their their in-house labels."
},
"Q_FLOWCELL_BARCODE": {
"type": "string",
"openbis_type": "VARCHAR",
"label": "Flowcell barcode",
"description": "Specifies the flowcell used for the sequencing run."
},
"Q_PROPERTIES": {
"type": "string",
"openbis_type": "XML",
"label": "Properties",
"description": "Properties that are characteristic to this biological entity/sample. These could be experimental factors (e.g., duration of treatment) or class information (e.g., WT or KO mouse, healthy versus diseased)."
},
"Q_ADDITIONAL_INFO": {
"type": "string",
"openbis_type": "MULTILINE_VARCHAR",
"label": "Additional information",
"description": "Additional notes about the experiment"
}