-
Notifications
You must be signed in to change notification settings - Fork 4
/
apollo_sv-base.json
15076 lines (15076 loc) · 683 KB
/
apollo_sv-base.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
{
"graphs" : [ {
"id" : "http://purl.obolibrary.org/obo/apollo_sv/apollo_sv-base.json",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Amanda Hicks"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "John Levander"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Josh Hanna"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Matt Diller"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Mike Wagner"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "Shawn T. Brown"
}, {
"pred" : "http://purl.org/dc/elements/1.1/contributor",
"val" : "William R. Hogan"
}, {
"pred" : "http://purl.org/dc/elements/1.1/creator",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.org/dc/elements/1.1/title",
"val" : "Apollo Structured Vocabulary (Apollo-SV)"
}, {
"pred" : "http://purl.org/dc/elements/1.1/type",
"val" : "http://purl.obolibrary.org/obo/IAO_8000001"
}, {
"pred" : "http://purl.org/dc/terms/description",
"val" : "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation."
}, {
"pred" : "http://purl.org/dc/terms/license",
"val" : "https://creativecommons.org/licenses/by/4.0/"
}, {
"pred" : "http://www.referent-tracking.com/RTS_00000001",
"val" : "C87985BA-6A8A-483A-A6B6-63975101F672"
}, {
"pred" : "http://www.referent-tracking.com/RTS_00000002",
"val" : "082D5D78-D916-457E-B4FD-365F86F45B30"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
"val" : "When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI)."
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2023-01-10"
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2024-04-19"
} ],
"version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-04-19/apollo_sv-base.json"
},
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113",
"lbl" : "atmosphere of the Earth",
"type" : "INDIVIDUAL"
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000107",
"lbl" : "atmosphere",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force"
},
"comments" : [ "atmosphere of Earth, Earth's moon, Saturn, Titan, etc.", "outer, gaseous layers of exoplanets are called extraterrestrial atmosphere." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force"
}, {
"pred" : "http://purl.org/dc/elements/1.1/creator",
"val" : "William R. Hogan"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000000",
"lbl" : "purely intentional entity",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an \"act\") that is laden with determinate, uniformily structured content."
},
"comments" : [ "MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an \"act\") that is laden with determinate, uniformily structured content."
}, {
"pred" : "http://purl.org/dc/elements/1.1/source",
"val" : "Ingarden, R. (1964) Der Streit um die Existenz der Welt I. Existentalontologie. Max Niemeyer, Tübingen."
}, {
"pred" : "http://purl.org/dc/elements/1.1/source",
"val" : "Ingarden, R. (1965a) Das literarische Kunstwerk. 3. Auflage. Max Niemeyer, Tübingen."
}, {
"pred" : "http://purl.org/dc/elements/1.1/source",
"val" : "Ingarden, R. (1965b) Der Streit um die Existenz der Welt II/1. Formalontologie 1. Teil. Max Niemeyer, Tübingen."
}, {
"pred" : "http://purl.org/dc/elements/1.1/source",
"val" : "Johansson I. (2009) Proof of the existence of universals – and Roman Ingarden's Ontology. Metaphysica. International Journal for Ontology & Metaphysics. 10, 65-87"
}, {
"pred" : "http://purl.org/dc/elements/1.1/source",
"val" : "Thomasson AL. \"Ingarden and the Ontology of Cultural Objects.\" In: Chrudziminski A (ed.): Existence, Culture, and Person. The Ontology of Roman Ingarden. Frankfurt: ontos, 2005, 115-136."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000001",
"lbl" : "epidemic model",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A disease transmission model whose concretization is realized as a simulation of infectious disease epidemic or infectious disease pandemic."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "William Hogan and Michael Wagner"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "An algorithm the concretizations of which models the transmission of transmissible disease."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000002",
"lbl" : "basic reproduction number",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The average number of transmissions of an infectious agent from an infectious organism to a susceptible organism within a completely susceptible population."
},
"comments" : [ "MB: Here we run into the well know DL problem that we cannot specify that the infectious agent that is transmitted is of the same type that the infectious agent the population is susceptible to." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "William R. Hogan"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The number of organisms that each infected organism infects in a completely susceptible population during its infectious period."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "basicReproductionNumbers"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000003",
"lbl" : "population immunity survey",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A population survey that assesses the level of immunity against a particular pathogen in a specified population."
},
"comments" : [ "Comment from Mike (to do!):\nI checked because an infection and immunity census would involve two different census methods. One would be some kind of disease surveillance that counts infections. The other is some kind of immunity census process based on seroprevalence studies or vaccination registries." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A population survey that assesses the level of immunity against a particular pathogen in a specified population."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000004",
"lbl" : "basis of",
"type" : "PROPERTY",
"meta" : {
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000005",
"lbl" : "simulating of process of type X",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "a planned process that (1) has at least one process part that has as participants representations of participants (in place of those participants) of processes of type X, and where all such process parts substitute for parts of processes of type X, and (2) is carried out for the purpose of planning for processes of type X, learning more about processes of type X, or teaching about processes of type X."
},
"comments" : [ "For example, in a simulated volcano eruption, representations of lava, lava tubes, vents, etc. take the place of actual lava, lava tubes, vents, etc.\n\nEven in the case of a simulated disaster scenario where actual ambulances, fire trucks, and people participate, representations of catastrophic events and injuries, etc. take the place of real ones." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A process that replaces the essential participants of another type of process with representations of those participants."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "simulating of process of type X"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000006",
"lbl" : "simulation requester identifier",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An identifier that refers to the legal person that commissions a simulation process."
},
"comments" : [ "Class was originally created to correspond with a complex type from Apollo XSD v3.1.0." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "An identifier that refers to the person or organization who is requesting one or more executions of the simulator software."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000007",
"lbl" : "simulation software application",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A software application that provides a model of a real phenomenon based on a set of mathematical formulas."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://en.wikipedia.org/wiki/Simulation_software"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A software application that provides a model of a real phenomenon based on a set of mathematical formulas."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "simulator"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008",
"lbl" : "software development",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A planned process that has specified output a software product and that involves the creation of source code."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "William R. Hogan"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://en.wikipedia.org/wiki/Software_development"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A planned process resulting in a software product involving the creation of source code."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000009",
"lbl" : "simulator developer identifier",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An identifier that refers to the legal person that creates and maintains a simulator."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "An identifier that refers to the person or organization who is responsible for the simulator. It is intended to uniquely identify a person or organization. That said, we do not plan to control the namespace for simulator developer at this point in development. We will add our ideas about alternatives at a future date."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000010",
"lbl" : "simulator identifier",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An identifier that refers to all version of a specific simulator."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "An identifier that refers to all versions of a specific simulator, such as “FRED”. We intend that it uniquely identify a simulator when combined with simulator developer. For example, the combination www.psc.edu/FRED would differentiate the FRED simulator created by a Pittsburgh organization from another “FRED” simulator maintained elsewhere. The implementation of namespace control for simulator name (i.e., making sure that they don’t use “FRED” twice) is the responsibility of simulator developer."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000011",
"lbl" : "control strategy reactive start time information",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A control strategy start time information item that is based on a condition that triggers the control strategy."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A control strategy start time information item that is based on a condition that triggers the control strategy."
} ],
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000012",
"lbl" : "simulation time step value",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A numeral that is part of a simulation time step action specification."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A number of time step units in a time step of a simulation. \n\nFor example, if the time step is 6 hours, then this value is 6.\n"
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "numberOfUnitsOfTimeInOneSimulatorStep"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000013",
"lbl" : "simulator version identifier",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An identifier that, as part of a complete simulator identifier, refers to one specific version of a simulator software."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "An identifier that refers to a unique version of a simulator. Simulator version distinguishes, for example, version “2.0” from “2.0.b”"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000014",
"lbl" : "simulation time step unit",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A time unit that is part of a simulation time step action specification."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A unit of time for each time step of a simulation, such as “hours” or “days”."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "unitOfTimeForSimulatorTimeStep"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000015",
"lbl" : "simulation run length",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The action specification that specifies the number of time steps a simulation is going to run."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The number of time steps in a simulator run.\n\nFor example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.\n"
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "runLength"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000016",
"lbl" : "infectious period duration",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A duration of the parts of an infection during which the host bears an infectious disposition in a population of hosts."
},
"comments" : [ "MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A period when an individual of a particular species, who is infected with a particular pathogen, is able to infect susceptible organisms of a particular species.\n\nNote that the susceptible and infectious organisms can be of different species."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "infectiousPeriodDuration"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000017",
"lbl" : "latent period duration",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts."
},
"comments" : [ "MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs", "The duration of the period between when an organism becomes infected and when it becomes infectious." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species. \n\nNote that the susceptible and infected organisms can be of different species.\n\n"
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "latentPeriodDuration"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000018",
"lbl" : "count of simulated susceptible population",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000019",
"lbl" : "count of simulated exposed population",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000020",
"lbl" : "count of simulated contagious population",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000021",
"lbl" : "count of simulated resistant population",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000022",
"lbl" : "count of simulated population",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The count of (simulated organisms) in a simulated population."
},
"comments" : [ "MW: I know this causes problems with our set-theoretic definition. Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step. \n\nAny ideas? I’ve considered and rejected allowing individual organisms to be fractional. Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’\n" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The number of simulated organisms in a simulated population. The number does not have to be an integer. "
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000023",
"lbl" : "vaccination dose schedule",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. "
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000024",
"lbl" : "vaccination compliance",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination."
},
"comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy” and “control measure efficacy delay.” We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level. We have not represented those control measures yet.\n" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000025",
"lbl" : "vaccination efficacy",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The infectious disease treatment efficacy of a vaccine."
},
"comments" : [ "Notes: \n1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer", "need to generate class restriction. Something like:\n\n'is realized by' some (processual_entity and (has_participant some ('Anatomical structure' and ('is physical basis of' some 'protective resistance'))\n\nwe'd also like to say that the protective resistance disposition began to exist during the process. \n\ncan't recall whether we should use process or processual_entity for future BFO compatibility." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The degree to which a particular vaccination reduces the probability that a vaccinated individual will have a particular vaccination preventable outcome."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "vaccinationEfficacies"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000026",
"lbl" : "facility survey",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A planned process involving counting numbers of facilities in a specific region."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A planned process involving counting numbers of facilities in a specific region."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000027",
"lbl" : "school facility census",
"type" : "CLASS",
"meta" : {
"comments" : [ "Motivating use case is Synthia synthetic population data." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000028",
"lbl" : "obsolete is based on",
"type" : "PROPERTY",
"meta" : {
"comments" : [ "p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption. " ],
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000029",
"lbl" : "infectious disease control strategy execution",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease. "
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease. "
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000030",
"lbl" : "hospital patient population",
"type" : "CLASS",
"meta" : {
"comments" : [ "Key motivating use case was Synthia synthetic population data." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000031",
"lbl" : "simulated population",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A simulated population is a set of simulated organisms. The set can be null (e.g., the set of 200 year-old H. sapiens). A simulated population can include more than one species, in which case it may be convenient to define each species as a simulated population and form the overall simulated population by set union. Similarly, it may be convenient to define sociodemographic or geographic strata within a simulated population as simulated populations and obtain the overall simulated population by set union. See examples in “Programmer’s Guide, page x)"
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "simulatorReferencablePopulation"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032",
"lbl" : "count",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A measurement datum that is the output of counting."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A measurement datum that is the output of counting."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "count"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033",
"lbl" : "counting",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The planned process of finding the number of elements in a finite set of objects."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
"val" : "http://en.wikipedia.org/wiki/Counting"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The planned process of finding the number of elements in a finite set of objects."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000034",
"lbl" : "simulation of organism",
"type" : "CLASS",
"meta" : {
"comments" : [ "a simulation that is about an organism" ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000035",
"lbl" : "organism population universal",
"type" : "INDIVIDUAL"
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000036",
"lbl" : "normal distribution",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A continuous parametric probability distribution that is uniform; centered around the mean, parameter μ; and whose spread of standard deviations, parameter σ, adheres to the empirical rule."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A continuous probability distribution in which the parameter μ is the mean or expectation of the distribution and the parameter σ is its standard deviation"
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "NormalDistribution"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000037",
"lbl" : "commissions",
"type" : "PROPERTY",
"meta" : {
"definition" : {
"val" : "a commissions b, iff a does not participate in the creation or execution of b and participates in a legal agreement that c participates on the creation or execution of b and c getting something in exchange for that participation."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A relation between two entities where the first entity formally requests a third party to create or execute the second entity."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "commissions"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000038",
"lbl" : "simulation of exposed organism",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A simulation of an infectious agent host that is not contagious and is part of a simulated population."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A simulated organism in a simulated population that has acquired a particular simulated disease but is not yet able to transmit the disease to another simulated organism."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000039",
"lbl" : "simulated population location identifier",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An identifier that refers to a geographical location to be used as location of a population in a simulation."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000040",
"lbl" : "simulation of infectious organism",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A simulation of an infectious organism host that is contagious."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A simulated organism in a simulated population that has acquired a particular simulated disease and is able to transmit the disease to another simulated organism."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000041",
"lbl" : "simulation of recovered organism",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A simulated organism in a simulated population that is not susceptible. "
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’ However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’ The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.\n"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000042",
"lbl" : "simulation of disease",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A representation of a disposition realized in a represented disease course that at least part of the simulated population is represented as participating in."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The disease being simulated."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "disease"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000043",
"lbl" : "reproduction number",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. "
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The number of susceptible organisms that each infected organism infects. ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "ReproductionNumber"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000044",
"lbl" : "nursery school student population",
"type" : "CLASS",
"meta" : {
"comments" : [ "Key motivating use case was Synthia synthetic population data." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000045",
"lbl" : "obsolete asymptomatic infection fraction",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The fraction given to express the probability that an organism will become infected, but stay asymptomatic."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The fraction of infectious individuals who do not develop symptoms during the course of their infections."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "asymptomatic infection fraction"
} ],
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000046",
"lbl" : "vaccine supply schedule",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An action specification giving the number of doses of vaccine to be made available over a specific time period."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The counts of vaccine doses that become available in a specific population location during (at the start of would be unambiguous) each simulator time step."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000047",
"lbl" : "vaccination administration capacity",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An action specification giving the number of vaccinations possible in a population during a specific time interval."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The counts of individuals that could be vaccinated in a population location per time step unit in the absence of any vaccine supply constraints. It represents the capacity of medical system to vaccinate individuals."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000048",
"lbl" : "antiviral treatment efficacy",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The infectious disease treatment efficacy of an antiviral drug."
},
"comments" : [ "MB: For DL reasons the easiest way to formalize the definition was to assume only organism that are either host or not immune undergo antiviral treatment. Is that adequate? I assume this'll create problems…" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The degree to which a particular antiviral drug reduces the probability that a treated individual will have a particular preventable outcome.\n\nPreventable outcomes include but are not limited to infection, infectiousness, symptoms, and hospitalization."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "AntiviralTreatmentEfficacy"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000049",
"lbl" : "antiviral efficacy delay",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. "
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. "
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000050",
"lbl" : "antiviral compliance",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible."
},
"comments" : [ "MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class \"eligibility rule\" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.", "MW: Since the estimates that modelers use are from real populations, I have two questions:\n1. Should we distinguish between real and simulated population?\n2. If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population?\n\nMB: This issue will need to be taken care of in the axiomatization of simulated population" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The fraction of individuals in a simulated population that will accept antiviral treatment if offered. "
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "antiviral cm compliance"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000051",
"lbl" : "antiviral supply schedule",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An action specification giving the number of doses of an antiviral to be made available during a specific time interval. "
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "Counts of antiviral doses that become available in a specific location per time step unit."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000052",
"lbl" : "antiviral administration schedule",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An action specification that tells the total number of antiviral doses available to be administered to a population during a specific time interval."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "Counts of antiviral doses that can be administered in a specific location per time step unit."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000053",
"lbl" : "simulation of organism awaiting control measure",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A simulated organism that is assumed “eligible, willing and able” to participate with a particular control measure."
},
"comments" : [ "MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to \"will\". Both classes have been made disjoint in the OWL file, though.", "This class will need more ontological reasoning, since the \"willing\" part of the definition is not representable in BFO to date." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A simulated organism in a simulated population that is “eligible, willing and able” to participate with a particular simulated control measure."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000054",
"lbl" : "complete simulator identifier",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An identifier that refers to a specific simulator."
},
"comments" : [ "MB: I am not 100% happy with the elucidation. Can't we just say that this is the full identifier identifying the simulator with both its name and its version number?" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "The combination of simulator developer, simulator name, and simulator version, for example “www.psc.edu/FRED/2.0” The combination is intended to uniquely identify the simulation algorithm that produced output X, given input Y to support scientific audit, error analysis, and reproducibility of results."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000055",
"lbl" : "epidemic simulating",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A simulating of a disease epidemic or pandemic."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "the process of simulating a disease epidemic or pandemic. This term is not currently used in Apollo-WS."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "epidemic simulation"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000056",
"lbl" : "hospital patient population census",
"type" : "CLASS",
"meta" : {
"comments" : [ "Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast)." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
"val" : "Mathias Brochhausen"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000057",
"lbl" : "instantiates",
"type" : "PROPERTY",
"meta" : {
"definition" : {
"val" : "A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. "
},
"comments" : [ "Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222." ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000058",
"lbl" : "simulation of organism not awaiting control measure",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A simulated organism that is assumed “ineligible, unwilling or unable” to participate with a particular control measure."
},
"comments" : [ "MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to \"will\". Both classes have been made disjoint in the OWL file, though.", "This class will need more ontological reasoning, since the \"unwilling\" part of the definition is not representable in BFO to date." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A simulated organism in a simulated population that is “ineligible, unwilling or unable” to participate with a particular simulated control measure."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000059",
"lbl" : "simulation of organism awaiting effect of control measure",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A simulated organism that participates in a particular control measure that has not yet been effective."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "This concept represents a simulated organism that has received a control measure such as vaccination in which a period of time must elapse before the benefit of the control measure accrues. A simulated organism is ‘awaiting efficacy’ if ‘efficacy delay’ (e.g. the concept ‘antiviral efficacy delay’ for the particular simulated control measure is greater than the elapsed time between application of the control measure and the current simulated time."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000060",
"lbl" : "simulation of antiviral control measure",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "The simulation of an antiviral control measure. "
},
"comments" : [ "MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.\n" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "antiviral control measure"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000061",
"lbl" : "simulation of vaccination control measure",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A simulation of a vaccination control measure."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A type of control measure that uses vaccination to create immunity in simulated organisms to specific pathogens."
}, {
"pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040",
"val" : "simulation of vaccination control measure"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000062",
"lbl" : "primary school student population",
"type" : "CLASS",
"meta" : {
"comments" : [ "Key motivating use case was Synthia synthetic population data." ]
}
}, {