forked from biolink/biolink-model
-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathBiolinkModel.java
More file actions
4321 lines (4048 loc) · 154 KB
/
BiolinkModel.java
File metadata and controls
4321 lines (4048 loc) · 154 KB
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
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonPropertyDescription;
import com.fasterxml.jackson.annotation.JsonPropertyOrder;
import org.apache.commons.lang.builder.EqualsBuilder;
import org.apache.commons.lang.builder.HashCodeBuilder;
import org.apache.commons.lang.builder.ToStringBuilder;
/**
* biolink_model
* <p>
*
*
*/
@JsonInclude(JsonInclude.Include.NON_NULL)
@JsonPropertyOrder({
"AbstractEntity",
"ActivityAndBehavior",
"AnatomicalEntity",
"AnatomicalEntityToAnatomicalEntityAssociation",
"AnatomicalEntityToAnatomicalEntityOntogenicAssociation",
"AnatomicalEntityToAnatomicalEntityPartOfAssociation",
"Association",
"Attribute",
"BiologicalProcess",
"BiologicalProcessOrActivity",
"BiologicalSex",
"Carbohydrate",
"Case",
"CaseToPhenotypicFeatureAssociation",
"Cell",
"CellLine",
"CellLineToDiseaseOrPhenotypicFeatureAssociation",
"CellularComponent",
"ChemicalSubstance",
"ChemicalToChemicalAssociation",
"ChemicalToChemicalDerivationAssociation",
"ChemicalToDiseaseOrPhenotypicFeatureAssociation",
"ChemicalToGeneAssociation",
"ChemicalToPathwayAssociation",
"ClinicalEntity",
"ClinicalIntervention",
"ClinicalModifier",
"ClinicalTrial",
"CodingSequence",
"ConfidenceLevel",
"DataFile",
"DataSet",
"DataSetSummary",
"DataSetVersion",
"Device",
"Disease",
"DiseaseOrPhenotypicFeature",
"DiseaseOrPhenotypicFeatureAssociationToLocationAssociation",
"DiseaseToPhenotypicFeatureAssociation",
"DistributionLevel",
"Drug",
"DrugExposure",
"Environment",
"EnvironmentToPhenotypicFeatureAssociation",
"EnvironmentalFeature",
"EnvironmentalProcess",
"EvidenceType",
"Exon",
"ExonToTranscriptRelationship",
"FrequencyQualifierMixin",
"FrequencyQuantifier",
"FrequencyValue",
"FunctionalAssociation",
"Gene",
"GeneAsAModelOfDiseaseAssociation",
"GeneFamily",
"GeneHasVariantThatContributesToDiseaseAssociation",
"GeneOntologyClass",
"GeneOrGeneProduct",
"GeneProduct",
"GeneRegulatoryRelationship",
"GeneToDiseaseAssociation",
"GeneToExpressionSiteAssociation",
"GeneToGeneHomologyAssociation",
"GeneToGeneProductRelationship",
"GeneToGoTermAssociation",
"GeneToPhenotypicFeatureAssociation",
"Genome",
"GenomicEntity",
"GenomicSequenceLocalization",
"Genotype",
"GenotypeToGeneAssociation",
"GenotypeToGenotypePartAssociation",
"GenotypeToPhenotypicFeatureAssociation",
"GenotypeToVariantAssociation",
"GenotypicSex",
"GeographicLocation",
"GeographicLocationAtTime",
"GrossAnatomicalStructure",
"Haplotype",
"IndividualOrganism",
"LifeStage",
"MacromolecularComplex",
"MacromolecularMachine",
"MacromolecularMachineToBiologicalProcessAssociation",
"MacromolecularMachineToCellularComponentAssociation",
"MacromolecularMachineToMolecularActivityAssociation",
"MaterialSample",
"MaterialSampleDerivationAssociation",
"MaterialSampleToDiseaseOrPhenotypicFeatureAssociation",
"Metabolite",
"MicroRNA",
"MolecularActivity",
"MolecularEntity",
"NamedThing",
"NoncodingRNAProduct",
"Occurrent",
"Onset",
"OntologyClass",
"OrganismTaxon",
"PairwiseGeneToGeneInteraction",
"PathognomonicityQuantifier",
"Pathway",
"Phenomenon",
"PhenotypicFeature",
"PhenotypicSex",
"PhysicalEntity",
"PhysiologicalProcess",
"PlanetaryEntity",
"PopulationOfIndividualOrganisms",
"PopulationToPopulationAssociation",
"Procedure",
"Protein",
"ProteinIsoform",
"Provider",
"Publication",
"QuantityValue",
"RNAProduct",
"RNAProductIsoform",
"RelationshipType",
"SensitivityQuantifier",
"SequenceFeatureRelationship",
"SequenceVariant",
"SeverityValue",
"SourceFile",
"SpecificityQuantifier",
"Transcript",
"TranscriptToGeneRelationship",
"Treatment",
"VariantToDiseaseAssociation",
"VariantToPhenotypicFeatureAssociation",
"VariantToPopulationAssociation",
"Zygosity"
})
public class BiolinkModel {
/**
* AbstractEntity
* <p>
* Any thing that is not a process or a physical mass-bearing entity
*
*/
@JsonProperty("AbstractEntity")
@JsonPropertyDescription("Any thing that is not a process or a physical mass-bearing entity")
private AbstractEntity abstractEntity;
/**
* ActivityAndBehavior
* <p>
* Activity or behavior of any independent integral living, organization or mechanical actor in the world
*
*/
@JsonProperty("ActivityAndBehavior")
@JsonPropertyDescription("Activity or behavior of any independent integral living, organization or mechanical actor in the world")
private ActivityAndBehavior activityAndBehavior;
/**
* AnatomicalEntity
* <p>
* A subcellular location, cell type or gross anatomical part
*
*/
@JsonProperty("AnatomicalEntity")
@JsonPropertyDescription("A subcellular location, cell type or gross anatomical part")
private AnatomicalEntity anatomicalEntity;
/**
* AnatomicalEntityToAnatomicalEntityAssociation
* <p>
*
*
*/
@JsonProperty("AnatomicalEntityToAnatomicalEntityAssociation")
@JsonPropertyDescription("")
private AnatomicalEntityToAnatomicalEntityAssociation anatomicalEntityToAnatomicalEntityAssociation;
/**
* AnatomicalEntityToAnatomicalEntityOntogenicAssociation
* <p>
* A relationship between two anatomical entities where the relationship is ontogenic, i.e the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship
*
*/
@JsonProperty("AnatomicalEntityToAnatomicalEntityOntogenicAssociation")
@JsonPropertyDescription("A relationship between two anatomical entities where the relationship is ontogenic, i.e the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship")
private AnatomicalEntityToAnatomicalEntityOntogenicAssociation anatomicalEntityToAnatomicalEntityOntogenicAssociation;
/**
* AnatomicalEntityToAnatomicalEntityPartOfAssociation
* <p>
* A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms
*
*/
@JsonProperty("AnatomicalEntityToAnatomicalEntityPartOfAssociation")
@JsonPropertyDescription("A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms")
private AnatomicalEntityToAnatomicalEntityPartOfAssociation anatomicalEntityToAnatomicalEntityPartOfAssociation;
/**
* Association
* <p>
* A typed association between two entities, supported by evidence
*
*/
@JsonProperty("Association")
@JsonPropertyDescription("A typed association between two entities, supported by evidence")
private Association association;
/**
* Attribute
* <p>
* A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.
*
*/
@JsonProperty("Attribute")
@JsonPropertyDescription("A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.")
private Attribute attribute;
/**
* BiologicalProcess
* <p>
* One or more causally connected executions of molecular functions
*
*/
@JsonProperty("BiologicalProcess")
@JsonPropertyDescription("One or more causally connected executions of molecular functions")
private BiologicalProcess biologicalProcess;
/**
* BiologicalProcessOrActivity
* <p>
* Either an individual molecular activity, or a collection of causally connected molecular activities
*
*/
@JsonProperty("BiologicalProcessOrActivity")
@JsonPropertyDescription("Either an individual molecular activity, or a collection of causally connected molecular activities")
private BiologicalProcessOrActivity biologicalProcessOrActivity;
/**
* BiologicalSex
* <p>
*
*
*/
@JsonProperty("BiologicalSex")
@JsonPropertyDescription("")
private BiologicalSex biologicalSex;
/**
* Carbohydrate
* <p>
*
*
*/
@JsonProperty("Carbohydrate")
@JsonPropertyDescription("")
private Carbohydrate carbohydrate;
/**
* Case
* <p>
* An individual organism that has a patient role in some clinical context.
*
*/
@JsonProperty("Case")
@JsonPropertyDescription("An individual organism that has a patient role in some clinical context.")
private Case _case;
/**
* CaseToPhenotypicFeatureAssociation
* <p>
* An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype
*
*/
@JsonProperty("CaseToPhenotypicFeatureAssociation")
@JsonPropertyDescription("An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype")
private CaseToPhenotypicFeatureAssociation caseToPhenotypicFeatureAssociation;
/**
* Cell
* <p>
*
*
*/
@JsonProperty("Cell")
@JsonPropertyDescription("")
private Cell cell;
/**
* CellLine
* <p>
*
*
*/
@JsonProperty("CellLine")
@JsonPropertyDescription("")
private CellLine cellLine;
/**
* CellLineToDiseaseOrPhenotypicFeatureAssociation
* <p>
* An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype
*
*/
@JsonProperty("CellLineToDiseaseOrPhenotypicFeatureAssociation")
@JsonPropertyDescription("An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype")
private CellLineToDiseaseOrPhenotypicFeatureAssociation cellLineToDiseaseOrPhenotypicFeatureAssociation;
/**
* CellularComponent
* <p>
* A location in or around a cell
*
*/
@JsonProperty("CellularComponent")
@JsonPropertyDescription("A location in or around a cell")
private CellularComponent cellularComponent;
/**
* ChemicalSubstance
* <p>
* May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part
*
*/
@JsonProperty("ChemicalSubstance")
@JsonPropertyDescription("May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part")
private ChemicalSubstance chemicalSubstance;
/**
* ChemicalToChemicalAssociation
* <p>
* A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.
*
*/
@JsonProperty("ChemicalToChemicalAssociation")
@JsonPropertyDescription("A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.")
private ChemicalToChemicalAssociation chemicalToChemicalAssociation;
/**
* ChemicalToChemicalDerivationAssociation
* <p>
* A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction:
* IF
* R has-input C1 AND
* R has-output C2 AND
* R enabled-by P AND
* R type Reaction
* THEN
* C1 derives-into C2 <<change is catalyzed by P>>
*
*/
@JsonProperty("ChemicalToChemicalDerivationAssociation")
@JsonPropertyDescription("A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction:\n IF\n R has-input C1 AND\n R has-output C2 AND\n R enabled-by P AND\n R type Reaction\n THEN\n C1 derives-into C2 <<change is catalyzed by P>>")
private ChemicalToChemicalDerivationAssociation chemicalToChemicalDerivationAssociation;
/**
* ChemicalToDiseaseOrPhenotypicFeatureAssociation
* <p>
* An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype
*
*/
@JsonProperty("ChemicalToDiseaseOrPhenotypicFeatureAssociation")
@JsonPropertyDescription("An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype")
private ChemicalToDiseaseOrPhenotypicFeatureAssociation chemicalToDiseaseOrPhenotypicFeatureAssociation;
/**
* ChemicalToGeneAssociation
* <p>
* An interaction between a chemical entity and a gene or gene product
*
*/
@JsonProperty("ChemicalToGeneAssociation")
@JsonPropertyDescription("An interaction between a chemical entity and a gene or gene product")
private ChemicalToGeneAssociation chemicalToGeneAssociation;
/**
* ChemicalToPathwayAssociation
* <p>
* An interaction between a chemical entity and a biological process or pathway
*
*/
@JsonProperty("ChemicalToPathwayAssociation")
@JsonPropertyDescription("An interaction between a chemical entity and a biological process or pathway")
private ChemicalToPathwayAssociation chemicalToPathwayAssociation;
/**
* ClinicalEntity
* <p>
* Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities
*
*/
@JsonProperty("ClinicalEntity")
@JsonPropertyDescription("Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities")
private ClinicalEntity clinicalEntity;
/**
* ClinicalIntervention
* <p>
*
*
*/
@JsonProperty("ClinicalIntervention")
@JsonPropertyDescription("")
private ClinicalIntervention clinicalIntervention;
/**
* ClinicalModifier
* <p>
* Used to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects
*
*/
@JsonProperty("ClinicalModifier")
@JsonPropertyDescription("Used to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects")
private ClinicalModifier clinicalModifier;
/**
* ClinicalTrial
* <p>
*
*
*/
@JsonProperty("ClinicalTrial")
@JsonPropertyDescription("")
private ClinicalTrial clinicalTrial;
/**
* CodingSequence
* <p>
*
*
*/
@JsonProperty("CodingSequence")
@JsonPropertyDescription("")
private CodingSequence codingSequence;
/**
* ConfidenceLevel
* <p>
* Level of confidence in a statement
*
*/
@JsonProperty("ConfidenceLevel")
@JsonPropertyDescription("Level of confidence in a statement")
private ConfidenceLevel confidenceLevel;
/**
* DataFile
* <p>
*
*
*/
@JsonProperty("DataFile")
@JsonPropertyDescription("")
private DataFile dataFile;
/**
* DataSet
* <p>
*
*
*/
@JsonProperty("DataSet")
@JsonPropertyDescription("")
private DataSet dataSet;
/**
* DataSetSummary
* <p>
*
*
*/
@JsonProperty("DataSetSummary")
@JsonPropertyDescription("")
private DataSetSummary dataSetSummary;
/**
* DataSetVersion
* <p>
*
*
*/
@JsonProperty("DataSetVersion")
@JsonPropertyDescription("")
private DataSetVersion dataSetVersion;
/**
* Device
* <p>
* A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment
*
*/
@JsonProperty("Device")
@JsonPropertyDescription("A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment")
private Device device;
/**
* Disease
* <p>
*
*
*/
@JsonProperty("Disease")
@JsonPropertyDescription("")
private Disease disease;
/**
* DiseaseOrPhenotypicFeature
* <p>
* Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.
*
*/
@JsonProperty("DiseaseOrPhenotypicFeature")
@JsonPropertyDescription("Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.")
private DiseaseOrPhenotypicFeature diseaseOrPhenotypicFeature;
/**
* DiseaseOrPhenotypicFeatureAssociationToLocationAssociation
* <p>
* An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.
*
*/
@JsonProperty("DiseaseOrPhenotypicFeatureAssociationToLocationAssociation")
@JsonPropertyDescription("An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.")
private DiseaseOrPhenotypicFeatureAssociationToLocationAssociation diseaseOrPhenotypicFeatureAssociationToLocationAssociation;
/**
* DiseaseToPhenotypicFeatureAssociation
* <p>
* An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way
*
*/
@JsonProperty("DiseaseToPhenotypicFeatureAssociation")
@JsonPropertyDescription("An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way")
private DiseaseToPhenotypicFeatureAssociation diseaseToPhenotypicFeatureAssociation;
/**
* DistributionLevel
* <p>
*
*
*/
@JsonProperty("DistributionLevel")
@JsonPropertyDescription("")
private DistributionLevel distributionLevel;
/**
* Drug
* <p>
* A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
*
*/
@JsonProperty("Drug")
@JsonPropertyDescription("A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease")
private Drug drug;
/**
* DrugExposure
* <p>
* A drug exposure is an intake of a particular chemical substance
*
*/
@JsonProperty("DrugExposure")
@JsonPropertyDescription("A drug exposure is an intake of a particular chemical substance")
private DrugExposure drugExposure;
/**
* Environment
* <p>
* A feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes
*
*/
@JsonProperty("Environment")
@JsonPropertyDescription("A feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes")
private Environment environment;
/**
* EnvironmentToPhenotypicFeatureAssociation
* <p>
* Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype
*
*/
@JsonProperty("EnvironmentToPhenotypicFeatureAssociation")
@JsonPropertyDescription("Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype")
private EnvironmentToPhenotypicFeatureAssociation environmentToPhenotypicFeatureAssociation;
/**
* EnvironmentalFeature
* <p>
*
*
*/
@JsonProperty("EnvironmentalFeature")
@JsonPropertyDescription("")
private EnvironmentalFeature environmentalFeature;
/**
* EnvironmentalProcess
* <p>
*
*
*/
@JsonProperty("EnvironmentalProcess")
@JsonPropertyDescription("")
private EnvironmentalProcess environmentalProcess;
/**
* EvidenceType
* <p>
* Class of evidence that supports an association
*
*/
@JsonProperty("EvidenceType")
@JsonPropertyDescription("Class of evidence that supports an association")
private EvidenceType evidenceType;
/**
* Exon
* <p>
* A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing
*
*/
@JsonProperty("Exon")
@JsonPropertyDescription("A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing")
private Exon exon;
/**
* ExonToTranscriptRelationship
* <p>
* A transcript is formed from multiple exons
*
*/
@JsonProperty("ExonToTranscriptRelationship")
@JsonPropertyDescription("A transcript is formed from multiple exons")
private ExonToTranscriptRelationship exonToTranscriptRelationship;
/**
* FrequencyQualifierMixin
* <p>
* Qualifier for freqency type associations
*
*/
@JsonProperty("FrequencyQualifierMixin")
@JsonPropertyDescription("Qualifier for freqency type associations")
private FrequencyQualifierMixin frequencyQualifierMixin;
/**
* FrequencyQuantifier
* <p>
*
*
*/
@JsonProperty("FrequencyQuantifier")
@JsonPropertyDescription("")
private FrequencyQuantifier frequencyQuantifier;
/**
* FrequencyValue
* <p>
* describes the frequency of occurrence of an event or condition
*
*/
@JsonProperty("FrequencyValue")
@JsonPropertyDescription("describes the frequency of occurrence of an event or condition")
private FrequencyValue frequencyValue;
/**
* FunctionalAssociation
* <p>
* An association between a macromolecular machine (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed
*
*/
@JsonProperty("FunctionalAssociation")
@JsonPropertyDescription("An association between a macromolecular machine (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed")
private FunctionalAssociation functionalAssociation;
/**
* Gene
* <p>
*
*
*/
@JsonProperty("Gene")
@JsonPropertyDescription("")
private Gene gene;
/**
* GeneAsAModelOfDiseaseAssociation
* <p>
*
*
*/
@JsonProperty("GeneAsAModelOfDiseaseAssociation")
@JsonPropertyDescription("")
private GeneAsAModelOfDiseaseAssociation geneAsAModelOfDiseaseAssociation;
/**
* GeneFamily
* <p>
* any grouping of multiple genes or gene products related by common descent
*
*/
@JsonProperty("GeneFamily")
@JsonPropertyDescription("any grouping of multiple genes or gene products related by common descent")
private GeneFamily geneFamily;
/**
* GeneHasVariantThatContributesToDiseaseAssociation
* <p>
*
*
*/
@JsonProperty("GeneHasVariantThatContributesToDiseaseAssociation")
@JsonPropertyDescription("")
private GeneHasVariantThatContributesToDiseaseAssociation geneHasVariantThatContributesToDiseaseAssociation;
/**
* GeneOntologyClass
* <p>
* an ontology class that describes a functional aspect of a gene, gene prodoct or complex
*
*/
@JsonProperty("GeneOntologyClass")
@JsonPropertyDescription("an ontology class that describes a functional aspect of a gene, gene prodoct or complex")
private GeneOntologyClass geneOntologyClass;
/**
* GeneOrGeneProduct
* <p>
* a union of genes or gene products. Frequently an identifier for one will be used as proxy for another
*
*/
@JsonProperty("GeneOrGeneProduct")
@JsonPropertyDescription("a union of genes or gene products. Frequently an identifier for one will be used as proxy for another")
private GeneOrGeneProduct geneOrGeneProduct;
/**
* GeneProduct
* <p>
* The functional molecular product of a single gene. Gene products are either proteins or functional RNA molecules
*
*/
@JsonProperty("GeneProduct")
@JsonPropertyDescription("The functional molecular product of a single gene. Gene products are either proteins or functional RNA molecules")
private GeneProduct geneProduct;
/**
* GeneRegulatoryRelationship
* <p>
* A regulatory relationship between two genes
*
*/
@JsonProperty("GeneRegulatoryRelationship")
@JsonPropertyDescription("A regulatory relationship between two genes")
private GeneRegulatoryRelationship geneRegulatoryRelationship;
/**
* GeneToDiseaseAssociation
* <p>
*
*
*/
@JsonProperty("GeneToDiseaseAssociation")
@JsonPropertyDescription("")
private GeneToDiseaseAssociation geneToDiseaseAssociation;
/**
* GeneToExpressionSiteAssociation
* <p>
* An association between a gene and an expression site, possibly qualified by stage/timing info.
*
*/
@JsonProperty("GeneToExpressionSiteAssociation")
@JsonPropertyDescription("An association between a gene and an expression site, possibly qualified by stage/timing info.")
private GeneToExpressionSiteAssociation geneToExpressionSiteAssociation;
/**
* GeneToGeneHomologyAssociation
* <p>
* A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)
*
*/
@JsonProperty("GeneToGeneHomologyAssociation")
@JsonPropertyDescription("A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)")
private GeneToGeneHomologyAssociation geneToGeneHomologyAssociation;
/**
* GeneToGeneProductRelationship
* <p>
* A gene is transcribed and potentially translated to a gene product
*
*/
@JsonProperty("GeneToGeneProductRelationship")
@JsonPropertyDescription("A gene is transcribed and potentially translated to a gene product")
private GeneToGeneProductRelationship geneToGeneProductRelationship;
/**
* GeneToGoTermAssociation
* <p>
*
*
*/
@JsonProperty("GeneToGoTermAssociation")
@JsonPropertyDescription("")
private GeneToGoTermAssociation geneToGoTermAssociation;
/**
* GeneToPhenotypicFeatureAssociation
* <p>
*
*
*/
@JsonProperty("GeneToPhenotypicFeatureAssociation")
@JsonPropertyDescription("")
private GeneToPhenotypicFeatureAssociation geneToPhenotypicFeatureAssociation;
/**
* Genome
* <p>
* A genome is the sum of genetic material within a cell or virion.
*
*/
@JsonProperty("Genome")
@JsonPropertyDescription("A genome is the sum of genetic material within a cell or virion.")
private Genome genome;
/**
* GenomicEntity
* <p>
* an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)
*
*/
@JsonProperty("GenomicEntity")
@JsonPropertyDescription("an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)")
private GenomicEntity genomicEntity;
/**
* GenomicSequenceLocalization
* <p>
* A relationship between a sequence feature and an entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig
*
*/
@JsonProperty("GenomicSequenceLocalization")
@JsonPropertyDescription("A relationship between a sequence feature and an entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig")
private GenomicSequenceLocalization genomicSequenceLocalization;
/**
* Genotype
* <p>
* An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some extablished background
*
*/
@JsonProperty("Genotype")
@JsonPropertyDescription("An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some extablished background")
private Genotype genotype;
/**
* GenotypeToGeneAssociation
* <p>
* Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality
*
*/
@JsonProperty("GenotypeToGeneAssociation")
@JsonPropertyDescription("Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality")
private GenotypeToGeneAssociation genotypeToGeneAssociation;
/**
* GenotypeToGenotypePartAssociation
* <p>
* Any association between one genotype and a genotypic entity that is a sub-component of it
*
*/
@JsonProperty("GenotypeToGenotypePartAssociation")
@JsonPropertyDescription("Any association between one genotype and a genotypic entity that is a sub-component of it")
private GenotypeToGenotypePartAssociation genotypeToGenotypePartAssociation;
/**
* GenotypeToPhenotypicFeatureAssociation
* <p>
* Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment
*
*/
@JsonProperty("GenotypeToPhenotypicFeatureAssociation")
@JsonPropertyDescription("Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment")
private GenotypeToPhenotypicFeatureAssociation genotypeToPhenotypicFeatureAssociation;
/**
* GenotypeToVariantAssociation
* <p>
* Any association between a genotype and a sequence variant.
*
*/
@JsonProperty("GenotypeToVariantAssociation")
@JsonPropertyDescription("Any association between a genotype and a sequence variant.")
private GenotypeToVariantAssociation genotypeToVariantAssociation;
/**
* GenotypicSex
* <p>
* An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.
*
*/
@JsonProperty("GenotypicSex")
@JsonPropertyDescription("An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.")
private GenotypicSex genotypicSex;
/**
* GeographicLocation
* <p>
* a location that can be described in lat/long coordinates
*
*/
@JsonProperty("GeographicLocation")
@JsonPropertyDescription("a location that can be described in lat/long coordinates")
private GeographicLocation geographicLocation;
/**
* GeographicLocationAtTime
* <p>
* a location that can be described in lat/long coordinates, for a particular time
*
*/
@JsonProperty("GeographicLocationAtTime")
@JsonPropertyDescription("a location that can be described in lat/long coordinates, for a particular time")
private GeographicLocationAtTime geographicLocationAtTime;
/**
* GrossAnatomicalStructure
* <p>
*
*
*/
@JsonProperty("GrossAnatomicalStructure")
@JsonPropertyDescription("")
private GrossAnatomicalStructure grossAnatomicalStructure;
/**
* Haplotype
* <p>
* A set of zero or more Alleles on a single instance of a Sequence[VMC]
*
*/
@JsonProperty("Haplotype")
@JsonPropertyDescription("A set of zero or more Alleles on a single instance of a Sequence[VMC]")
private Haplotype haplotype;
/**
* IndividualOrganism
* <p>
*
*
*/
@JsonProperty("IndividualOrganism")
@JsonPropertyDescription("")
private IndividualOrganism individualOrganism;
/**
* LifeStage
* <p>
* A stage of development or growth of an organism, including post-natal adult stages
*
*/
@JsonProperty("LifeStage")
@JsonPropertyDescription("A stage of development or growth of an organism, including post-natal adult stages")
private LifeStage lifeStage;
/**
* MacromolecularComplex
* <p>
*
*
*/
@JsonProperty("MacromolecularComplex")
@JsonPropertyDescription("")
private MacromolecularComplex macromolecularComplex;
/**
* MacromolecularMachine
* <p>
* A union of gene, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.
*
*/
@JsonProperty("MacromolecularMachine")
@JsonPropertyDescription("A union of gene, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.")
private MacromolecularMachine macromolecularMachine;
/**
* MacromolecularMachineToBiologicalProcessAssociation
* <p>
* A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it
*
*/
@JsonProperty("MacromolecularMachineToBiologicalProcessAssociation")
@JsonPropertyDescription("A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it")
private MacromolecularMachineToBiologicalProcessAssociation macromolecularMachineToBiologicalProcessAssociation;
/**
* MacromolecularMachineToCellularComponentAssociation
* <p>
* A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component
*
*/
@JsonProperty("MacromolecularMachineToCellularComponentAssociation")
@JsonPropertyDescription("A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component")
private MacromolecularMachineToCellularComponentAssociation macromolecularMachineToCellularComponentAssociation;
/**
* MacromolecularMachineToMolecularActivityAssociation
* <p>
* A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution
*
*/
@JsonProperty("MacromolecularMachineToMolecularActivityAssociation")
@JsonPropertyDescription("A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution")
private MacromolecularMachineToMolecularActivityAssociation macromolecularMachineToMolecularActivityAssociation;
/**
* MaterialSample
* <p>
* A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]
*
*/
@JsonProperty("MaterialSample")
@JsonPropertyDescription("A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]")
private MaterialSample materialSample;
/**
* MaterialSampleDerivationAssociation
* <p>
* An association between a material sample and the material entity it is derived from
*
*/
@JsonProperty("MaterialSampleDerivationAssociation")
@JsonPropertyDescription("An association between a material sample and the material entity it is derived from")
private MaterialSampleDerivationAssociation materialSampleDerivationAssociation;
/**
* MaterialSampleToDiseaseOrPhenotypicFeatureAssociation
* <p>
* An association between a material sample and a disease or phenotype
*
*/
@JsonProperty("MaterialSampleToDiseaseOrPhenotypicFeatureAssociation")
@JsonPropertyDescription("An association between a material sample and a disease or phenotype")
private MaterialSampleToDiseaseOrPhenotypicFeatureAssociation materialSampleToDiseaseOrPhenotypicFeatureAssociation;
/**
* Metabolite
* <p>
* Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.
*
*/
@JsonProperty("Metabolite")
@JsonPropertyDescription("Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.")
private Metabolite metabolite;
/**
* MicroRNA
* <p>
*
*
*/
@JsonProperty("MicroRNA")
@JsonPropertyDescription("")
private MicroRNA microRNA;
/**
* MolecularActivity
* <p>
* An execution of a molecular function carried out by a gene product or macromolecular complex.
*
*/
@JsonProperty("MolecularActivity")
@JsonPropertyDescription("An execution of a molecular function carried out by a gene product or macromolecular complex.")
private MolecularActivity molecularActivity;
/**
* MolecularEntity
* <p>