-
Notifications
You must be signed in to change notification settings - Fork 4
/
gfvo_bioportal.xml
2093 lines (1717 loc) · 146 KB
/
gfvo_bioportal.xml
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
<?xml version="1.0"?>
<!DOCTYPE rdf:RDF [
<!ENTITY dc "http://purl.org/dc/terms/" >
<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
<!ENTITY obo "http://purl.obolibrary.org/obo/" >
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
<!ENTITY sio "http://semanticscience.org/resource/" >
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
<!ENTITY faldo "http://biohackathon.org/resource/faldo#" >
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
]>
<rdf:RDF xmlns="https://github.com/BioInterchange/Ontologies/gfvo#"
xml:base="https://github.com/BioInterchange/Ontologies/gfvo"
xmlns:dc="http://purl.org/dc/terms/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:sio="http://semanticscience.org/resource/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:faldo="http://biohackathon.org/resource/faldo#">
<owl:Ontology rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#">
<owl:versionInfo>1.0.6</owl:versionInfo>
<dc:rights>CC0 [https://creativecommons.org/publicdomain/zero/1.0/].</dc:rights>
<dc:contributor xml:lang="en">Begum Durgahee</dc:contributor>
<rdfs:comment xml:lang="en">Best Practices
1.) The class hierarchy, object- and datatype-property hierarchies are modeled to match SIO's hierarchies.
2.) Every class and property has a label (rdfs:label) as well as a description (rdfs:comment). The description may contain an example of how a class/property is being applied.
3.) Classes that are directly related to either GFF3, GTF, GVF or VCF specification have a link-out to the specification's document as provenance indicator (via rdfs:isDefinedBy).
4.) Link-outs to Wikipedia are provided for classes wherever possible.
5.) Ontology terms are encoded in the URIs using camel case, i.e. letters following a white space in an ontology term are capitalized followed by the removal of the white space.
</rdfs:comment>
<dc:contributor xml:lang="en">Chris Mungall</dc:contributor>
<dc:contributor xml:lang="en">CODAMONO</dc:contributor>
<dc:contributor xml:lang="en">Erick Antezana</dc:contributor>
<dc:contributor xml:lang="en">Francesco Strozzi</dc:contributor>
<dc:title xml:lang="en">Genomic Feature and Variation Ontology (GFVO)</dc:title>
<dc:creator xml:lang="en">Joachim Baran</dc:creator>
<dc:contributor xml:lang="en">Joachim Baran</dc:contributor>
<dc:contributor xml:lang="en">Karen Eilbeck</dc:contributor>
<dc:contributor xml:lang="en">Michel Dumontier</dc:contributor>
<dc:contributor xml:lang="en">Raoul Bonnal</dc:contributor>
<dc:contributor xml:lang="en">Robert Hoehndorf</dc:contributor>
<dc:contributor xml:lang="en">Stephen Kan (GitHub: Helisquinde)</dc:contributor>
<dc:contributor xml:lang="en">Takatomo Fujisawa</dc:contributor>
<dc:description xml:lang="en">The Genomic Feature and Variation Ontology (GFVO) is modeled to represent genomic data using the Resource Description Format (RDF). It is captures the contents of data files that adhere to the Generic Feature Format Version 3 (GFF3, http://www.sequenceontology.org/resources/gff3.html), the General Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html), the Genome Variation Format Version 1 (GVF, http://www.sequenceontology.org/resources/gvf.html), and the Variant Call Format (VCF, http://vcftools.sourceforge.net/specs.html). The creation of the ontology was inspired by previous work of Robert Hoehndorf on RDF2OWL (http://code.google.com/p/rdf2owl).</dc:description>
<dc:contributor xml:lang="en">Toshiaki Katayama</dc:contributor>
<rdfs:seeAlso>https://github.com/BioInterchange/Ontologies</rdfs:seeAlso>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- https://github.com/BioInterchange/Ontologies/gfvo#describes -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#describes">
<rdfs:label>describes</rdfs:label>
<rdfs:comment xml:lang="en">Links to an entity for which supportive information is being provided.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasAnnotation -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasAnnotation">
<rdfs:label>has annotation</rdfs:label>
<rdfs:comment xml:lang="en">Links to additional annotations about an entity.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute">
<rdfs:label>has attribute</rdfs:label>
<rdfs:comment xml:lang="en">Links out to aggregate information for an entity.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasEvidence -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasEvidence">
<rdfs:label>has evidence</rdfs:label>
<rdfs:comment xml:lang="en">References an entity or resource that provides supporting/refuting evidence.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#references"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasFirstPart -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasFirstPart">
<rdfs:label>has first part</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the first entity of an ordered part relationship.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasOrderedPart"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasIdentifier -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasIdentifier">
<rdfs:label>has identifier</rdfs:label>
<rdfs:comment xml:lang="en">Links out to an identifier.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasInput -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasInput">
<rdfs:label>has input</rdfs:label>
<rdfs:comment xml:lang="en">Links out to an entity that is the input of a "Process" subclass.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasLastPart -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasLastPart">
<rdfs:label>has last part</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the last entity of an ordered part relationship.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasOrderedPart"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasMember -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasMember">
<rdfs:label>has member</rdfs:label>
<rdfs:comment xml:lang="en">Denotes membership for "Collection", "Catalog" and "File" instances.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasOrderedPart -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasOrderedPart">
<rdfs:label>has ordered part</rdfs:label>
<rdfs:comment xml:lang="en">Denotes a compositional relationship to other entities, where the ordering of the composition of entities carries meaning.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasPart"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasOutput -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasOutput">
<rdfs:label>has output</rdfs:label>
<rdfs:comment xml:lang="en">Links out to an entity that is the output of a "Process" subclass.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasPart -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasPart">
<rdfs:label>has part</rdfs:label>
<rdfs:comment xml:lang="en">Denotes a compositional relationship to other entities.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasParticipant -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasParticipant">
<rdfs:label>has participant</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the participation of other entities in processes.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasQuality -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasQuality">
<rdfs:label>has quality</rdfs:label>
<rdfs:comment xml:lang="en">Links out to an entity that provides qualitative information.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasSource -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasSource">
<rdfs:label>has source</rdfs:label>
<rdfs:comment xml:lang="en">Denotes information origin.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isAbout -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isAbout">
<rdfs:label>is about</rdfs:label>
<rdfs:comment xml:lang="en">References an entity about which information is provided for.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#describes"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isAffectedBy -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isAffectedBy">
<rdfs:label>is affected by</rdfs:label>
<rdfs:comment xml:lang="en">Denotes that an entity is affected by another entity.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isParticipantIn"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isAfter -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isAfter">
<rdfs:label>is after</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the trailing occurrence or succession of the subject in regards to the object.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isAttributeOf -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isAttributeOf">
<rdfs:label>is attribute of</rdfs:label>
<rdfs:comment xml:lang="en">Denotes that an entity is an attribute of the entity that this property links out to.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isBefore -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isBefore">
<rdfs:label>is before</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the leading occurrence or precedence of the subject in regards to the object.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isCreatedBy -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isCreatedBy">
<rdfs:label>is created by</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the process or method that created an entity.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isDescribedBy -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isDescribedBy">
<rdfs:label>is described by</rdfs:label>
<rdfs:comment xml:lang="en">Provides a description of the subject via reference to an object that provides further information on the subject.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isLocatedOn -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isLocatedOn">
<rdfs:label>is located on</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the location of genomic feature on a landmark.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isPartOf -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isPartOf">
<rdfs:label>is part of</rdfs:label>
<rdfs:comment xml:lang="en">Denotes that an entity is an intrinsic component of an encapsulating entity.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isLocatedOn"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isParticipantIn -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isParticipantIn">
<rdfs:label>is participant in</rdfs:label>
<rdfs:comment xml:lang="en">Denotes participation with another entity.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isRefutedBy -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isRefutedBy">
<rdfs:label>is refuted by</rdfs:label>
<rdfs:comment xml:lang="en">References an entity or resource that provides refuting evidence.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasEvidence"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isSourceOf -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isSourceOf">
<rdfs:label>is source of</rdfs:label>
<rdfs:comment xml:lang="en">Denotes that an entity is the source of the entity that this property links out to.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isAttributeOf"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo">
<rdfs:label>is spatiotemporally related to</rdfs:label>
<rdfs:comment xml:lang="en">Denotes spatio-temporal relations to other entities.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isSupportedBy -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isSupportedBy">
<rdfs:label>is supported by</rdfs:label>
<rdfs:comment xml:lang="en">References an entity or resource that provides supporting evidence.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasEvidence"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isTemporarilyPartOf -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isTemporarilyPartOf">
<rdfs:label>is temporarily part of</rdfs:label>
<rdfs:comment xml:lang="en">Denotes a temporarily constraint "isPartOf" relationship. The temporal restriction expresses that the relationship is not universally true.
This property can be used to express "Derives_from" relations in GFF3.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isPartOf"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#references -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#references">
<rdfs:label>references</rdfs:label>
<rdfs:comment xml:lang="en">References another entity or resource.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#refersTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#refersTo -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#refersTo">
<rdfs:label>refers to</rdfs:label>
<rdfs:comment xml:lang="en">References an entity, where additional information is provided to augment the reference.</rdfs:comment>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasValue -->
<owl:DatatypeProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasValue">
<rdfs:label>has value</rdfs:label>
<rdfs:comment xml:lang="en">Representation of any literal that is associated with a GFVO class instance. Domain restrictions might apply. For example, "Codon Sequence" entities restrict "has value" to be a non-empty string consisting of A, C, G, or T letters, and whose length is a multiple of 3.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:DatatypeProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Alias -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Alias">
<rdfs:label>Alias</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Name"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Pseudonym</rdfs:seeAlso>
<rdfs:comment xml:lang="en">An alias is an alternative name for an entity. The use of an alias is mostly secondary, whereas instances of the "Name" class should be used to denote primary names.
Encodes for the "Alias" attribute in GFF3 and GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#AlleleCount -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#AlleleCount">
<rdfs:label>Allele Count</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Quantity"/>
<rdfs:comment xml:lang="en">Count of a specific allele in genotypes.
Encodes for "AC" additional information in VCF files.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#AlleleFrequency -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#AlleleFrequency">
<rdfs:label>Allele Frequency</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Quantity"/>
<rdfs:subClassOf>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;double"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:maxInclusive rdf:datatype="&xsd;double">1.0</xsd:maxInclusive>
</rdf:Description>
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;double">0.0</xsd:minInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;float"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;float">0.0</xsd:minInclusive>
</rdf:Description>
<rdf:Description>
<xsd:maxInclusive rdf:datatype="&xsd;float">1.0</xsd:maxInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Allele_frequency</rdfs:seeAlso>
<rdfs:comment xml:lang="en">Proportion of a particular gene allele in a gene pool or genotype.
Encodes for "AF" additional information in VCF files.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#AminoAcid -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#AminoAcid">
<rdfs:label>Amino Acid</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#ChemicalEntity"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;string"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:pattern>[A-Z]</xsd:pattern>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment xml:lang="en">"Amino Acid" encodes for the "Variant_aa" and "Reference_aa" attributes in GVF files. Linking an "Amino Acid" instance to a "Reference Sequence" or "Sequence Variant" instance denotes the genomic context of the amino acid.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Amino_acid</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#AncestralSequence -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#AncestralSequence">
<rdfs:label>Ancestral Sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#ReferenceSequence"/>
<rdfs:comment xml:lang="en">Denotes an ancestral allele of a feature.
May be used to denote the "ancestral allele" ("AA" additional information) of VCF formatted files.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Ancestral_reconstruction</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ArrayComparativeGenomicHybridization -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ArrayComparativeGenomicHybridization">
<rdfs:label>Array Comparative Genomic Hybridization</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#GenomicAscertainingMethod"/>
<rdfs:comment xml:lang="en">Feature provenance is based on array-comparative genomic hybridization.
Used by the "data-source" structured pragma in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Attribute -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Attribute">
<rdfs:label>Attribute</rdfs:label>
<rdfs:comment xml:lang="en">An attribute denotes characteristics of an entity. At this stage, "Quality" is the only direct subclass of "Attribute", whose subclasses denote qualitative properties such as sex ("Female", "Male", "Hermaphrodite"), zygosity ("Hemizygous", "Heterozygous", "Homozygous"), etc.
The object property "has quality" (or subproperties thereof) should be utilized to express qualities of entities. The "hasAttribute" object property should be used to denote relationships to "Object" or "Process" instances, unless there is a better object property suitable to represent the relationship between entities.</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#AverageCoverage -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#AverageCoverage">
<rdfs:label>Average Coverage</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Coverage"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Shotgun_sequencing#Coverage</rdfs:seeAlso>
<rdfs:comment xml:lang="en">Average coverage depth for a genomic locus (a region or single base pair), i.e. the average number of reads representing a given nucleotide in the reconstructed sequence.
Captures the "technology-platform" structured pragma in GVF files ("Average_coverage" tag).</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#BaseQuality -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#BaseQuality">
<rdfs:label>Base Quality</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Score"/>
<rdfs:comment xml:lang="en">Root mean square base quality.
Accounts for "BQ" additional information in VCF files.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#BiologicalEntity -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#BiologicalEntity">
<rdfs:label>Biological Entity</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#MaterialEntity"/>
<rdfs:comment xml:lang="en">A biological entity an entity that contains genomic material or utilizes genomic material during its existance. Genomic material itself is represented as subclasses of "Chemical Entity".</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#BiopolymerSequencing -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#BiopolymerSequencing">
<rdfs:label>Biopolymer Sequencing</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#GenomicAscertainingMethod"/>
<rdfs:comment xml:lang="en">Information about features and variants is based on biopolymer sequencing.
This class is not directly instantiated, but its subclasses "DNA Sequencing" and "RNA Sequencing" are used to describe the "data-source" structured pragma in GVF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Sequencing</rdfs:seeAlso>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Breakpoint -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Breakpoint">
<rdfs:label>Breakpoint</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Locus"/>
<rdfs:comment xml:lang="en">A breakpoint describes the source or destination of a zero-length sequence alteration. These alterations are typically insertions, deletions or translocations according to the GVF specification (see "Breakpoint_detail" in http://sequenceontology.org/resources/gvf.html). Breakpoint coordinates should be provided using classes of the Feature Annotation Location Description Ontology.
The class encodes for the "Breakpoint_detail" and "Breakpoint_range" attributes in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Catalog -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Catalog">
<rdfs:label>Catalog</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Collection"/>
<rdfs:comment xml:lang="en">A catalog is a specialization of a "Collection", where all of its contents are of the same type. The requirement of same type cannot be enforced formally via this ontology; data providers need to verify this condition manually or programmatically, or alternatively, use the more generic "Collection" class instead.</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Cell -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Cell">
<rdfs:label>Cell</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#BiologicalEntity"/>
<rdfs:comment xml:lang="en">A cell is a biological unit that in itself forms a living organism or is part of a larger organism that is composed of many other cells. The subclasses "Germline Cell" and "Somatic Cell" can be used to denote the biological material that was used in an experiment.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Cell_(biology)</rdfs:seeAlso>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ChemicalEntity -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ChemicalEntity">
<rdfs:label>Chemical Entity</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#MaterialEntity"/>
<rdfs:comment xml:lang="en">A chemical entity is an entity related to biochemistry. This class is typically not instantiated, but instead, its subclasses "Amino Acid", "Chromosome", "Peptide Sequence", etc., are used to represent specific chemical entities.</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Chromosome -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Chromosome">
<rdfs:label>Chromosome</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#ChemicalEntity"/>
<rdfs:comment xml:lang="en">A chromosome can be used as an abstract representation of a (not necessarily named) chromosome to represent ploidy within a data set. The "Chromosome" instance is then used for for denoting the locus of phased genotypes.
For placing genomic features ("Feature" class instances) on a chromosome, contig, scaffold, etc., please see the "Landmark" class. It is encouraged that Sequence Ontology terms are used to annotate a Landmark with a biological type (s.a. "chromosome", "contig", etc.).
Encodes for "sequencing-scope" pragma in GVF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Chromosome</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#CircularHelix -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#CircularHelix">
<rdfs:label>Circular Helix</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#HelixStructure"/>
<owl:disjointWith rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#WatsonCrickHelix"/>
<rdfs:comment xml:lang="en">A circular helix structure.
Can be used to indicate a true "Is_circular" attribute in GFF3 and GVF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Circular_DNA</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#CodingFrameOffset -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#CodingFrameOffset">
<rdfs:label>Coding Frame Offset</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Quality"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;integer"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;integer">0</xsd:minInclusive>
</rdf:Description>
<rdf:Description>
<xsd:maxInclusive rdf:datatype="&xsd;integer">2</xsd:maxInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Reading_frame</rdfs:seeAlso>
<rdfs:comment xml:lang="en">Coding frame offset of a genomic feature that is a coding sequence or other genomic feature that contributes to transcription and translation. A feature's coding frame offset can be either 0, 1, or 2.
It is referred to as "frame" in GTF, but called "phase" in GFF3 and GVF. "phase" is defined in GVF, but unused.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#CodonSequence -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#CodonSequence">
<rdfs:label>Codon Sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#DNASequence"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;string"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:pattern>([ACGT]{3})+</xsd:pattern>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Codon</rdfs:seeAlso>
<rdfs:comment xml:lang="en">A codon sequence is a nucleotide sequence underlying a potential amino acid sequence. Codon sequences are three bases of length or multiples thereof.
Encodes for "Variant_codon" and "Reference_codon" attributes in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Collection -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Collection">
<rdfs:label>Collection</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">A collection is a container for genomic data. A collection may contain information about genomic data including -- but not limited to -- contents of GFF3, GTF, GVF and VCF files. The latter are better represented by "File" class instances, whereas the result of unions or intersections between different "File" class instances should be captured within this format-independent "Collection" class. When importing data whose provenance is not file based, instances of "Collection" should be utilized (e.g., database exports).</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Comment -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Comment">
<rdfs:label>Comment</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">A comment is a remark about a piece of information, an observation or statement. In the context of GFF3, GVF, etc., genomic feature and variation descriptions, "isAfter" and "isBefore" relationships should be used to indicate where a comment is situated between pragma or feature statements of GFF3, GTF, GVF or VCF files.
For specific descriptions or textual annotations of genomic features, the use of the "Note" class is encouraged.</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ConditionalGenotypeQuality -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ConditionalGenotypeQuality">
<rdfs:label>Conditional Genotype Quality</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#PhredScore"/>
<rdfs:comment xml:lang="en">Conditional genotype quality expressed in form of a "Phred Score". It denotes the score of the genotype being wrong under the assumption/condition that the genomic site is a sequence variant.
Encodes for "GQ" additional information in VCF files.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Contig -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Contig">
<rdfs:label>Contig</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Collection"/>
<rdfs:comment xml:lang="en">A contig is a contiguous DNA sequence that has been assembled from shorter overlapping DNA segments. "Contig" is a specialization of a "Collection" and should be used to aggregate features, but not for indicating that a "Landmark" is representing a contig. It is encouraged that the latter is annotated by a term of the Sequence Ontology.
Encodes for "sequencing-scope" in GVF and the "contig" information field in VCF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Contig</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Coverage -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Coverage">
<rdfs:label>Coverage</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Quantity"/>
<rdfs:subClassOf>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;double"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;double">0.0</xsd:minInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;float"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;float">0.0</xsd:minInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;integer"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;integer">0</xsd:minInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:comment xml:lang="en">Number of nucleic acid sequence reads for a particular genomic locus (a region or single base pair).
Accounts for "DP" additional information in VCF files.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#DNAMicroarray -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#DNAMicroarray">
<rdfs:label>DNA Microarray</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#GenomicAscertainingMethod"/>
<rdfs:comment xml:lang="en">Feature information is based on DNA microarray probes.
Used by the "data-source" structured pragma in GVF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/DNA_microarray_experiment</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#DNASequence -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#DNASequence">
<rdfs:label>DNA Sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Sequence"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;string"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:pattern>([ACGT])+</xsd:pattern>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<owl:disjointWith rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#PeptideSequence"/>
<rdfs:comment xml:lang="en">A DNA sequence is a sequence of nucleic acids.
It can be used to describe "FASTA" annotations in both GFF3 and GVF files as well as short sequences in VCF files.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Dna_sequence</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#DNASequencing -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#DNASequencing">
<rdfs:label>DNA Sequencing</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#BiopolymerSequencing"/>
<owl:disjointWith rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#RNASequencing"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/DNA_sequencing</rdfs:seeAlso>
<rdfs:comment xml:lang="en">Information about features and variants is based on DNA sequencing.
Used by the "data-source" structured pragma in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Exome -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Exome">
<rdfs:label>Exome</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#BiologicalEntity"/>
<rdfs:comment xml:lang="en">Representation of an exome. Features that constitute the exome may be linked via one or more "Collection", "Catalog", "Contig", "Scaffold" or "File" instances.
"Exome" can be used for describing data contents of the "sequencing-scope" pragma in GVF files.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Exome</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ExperimentalMethod -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ExperimentalMethod">
<rdfs:label>Experimental Method</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Process"/>
<rdfs:comment xml:lang="en">An experimental method is a procedure that yields an experimental outcome (result). Experimental methods can be in vivo, in vitro or in silico procedures that are well described and can be referenced.
Encodes for "source" column contents of GFF3, GTF, and GVF file formats as well as the "CHROM" column in VCF. Can be used to describe the "capture-method" pragma in GVF; it can describe "VALIDATED" additional information in VCF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ExternalReference -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ExternalReference">
<rdfs:label>External Reference</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">A cross-reference to associate an entity to a representation in another database.
Encodes for the "Dbxref" attribute in GFF3 and GVF. Can be used to describe the contents of the "source" column in GTF files. Captures the "genome-build" pragma, "source-method", "attribute-method", "phenotype-description", and "phased-genotypes" structured pragmas in GVF. Accounts for the "assembly" and "pedigreeDB" information fields, and "DB", "H2", "H3", "1000G" additional information in VCF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Feature -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Feature">
<rdfs:label>Feature</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">The feature class captures information about genomic sequence features and variations. A genomic feature can be a large object, such as a chromosome or contig, down to single base-pair reference or variant alleles.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Female -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Female">
<rdfs:label>Female</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Sex"/>
<rdfs:comment xml:lang="en">Denoting sex of a female individual, who is defined as an individual producing ova.
This quality can be used to encode for the "sex" pragma in GVF files.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Female</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#File -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#File">
<rdfs:label>File</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Collection"/>
<rdfs:comment xml:lang="en">A file represents the contents of a GFF3, GTF, GVF or VCF file. It can capture genomic meta-data that is specific to any of these file formats. The result of unions, intersections or other operations between "File" class instances should be capture with the generic "Collection" class, which is format independent.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ForwardReferenceSequenceFrameshift -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ForwardReferenceSequenceFrameshift">
<rdfs:label>Forward Reference Sequence Frameshift</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#SequenceAlignmentOperation"/>
<rdfs:comment xml:lang="en">Denotes a frameshift forward in the reference sequence.
Encodes for the "Target" attribute in GFF3, encodes for "Target" attribute and "sequence-alignment" pragma in GVF, and, encodes "CIGAR" additional information in VCF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#FragmentReadPlatform -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#FragmentReadPlatform">
<rdfs:label>Fragment Read Platform</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#SequencingTechnologyPlatform"/>
<owl:disjointWith rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#PairedEndReadPlatform"/>
<rdfs:comment xml:lang="en">Details about the fragment-read (single-end read) sequencing technology used to gather the data in a set.
Encodes for the "technology-platform-read-type" pragma in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#FunctionalSpecification -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#FunctionalSpecification">
<rdfs:label>Functional Specification</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">A functional specification of bioinformatics data, i.e. the specification of genomic material that potentially has biological function. This class should not be directly instantiated, but instead, its subclass "Genotype" should be used.</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#GameticPhase -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#GameticPhase">
<rdfs:label>Gametic Phase</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Quality"/>
<rdfs:comment xml:lang="en">Denotes the presence of information that required capturing the gametic phase. For diploid organisms, this quality indicates that information is available about which chromosome of a chromosome pair contributed data.
"Gametic Phase" encodes for the "Phase" attribute in GVF. It encodes for "GT" and "PS" additional information in VCF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Gametic_phase</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Genome -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Genome">
<rdfs:label>Genome</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#BiologicalEntity"/>
<rdfs:comment xml:lang="en">Representation of a genome. Genomic features that constitute the genome may be linked via one or more "Collection", "Catalog", "Contig", "Scaffold" or "File" instances.
"Genome" can be used for describing data contents of the "genome-build" and "sequencing-scope" pragmas in GVF files.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Genome</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#GenomeAnalysis -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#GenomeAnalysis">
<rdfs:label>Genome Analysis</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#ExperimentalMethod"/>
<rdfs:comment xml:lang="en">A genome analysis denotes the type of procedure that was carried out to derive information from a genome assembly.
"Genome Analysis" can be instantiated for cases where an application of "FILTER" in VCF cannot be linked to "Genotyping" or "Variant Calling", which are subclasses of "Genome Analysis". If possible, further annotation should be provided to indicate the actually utilized filter type.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Genomics#Genome_analysis</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#GenomicAscertainingMethod -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#GenomicAscertainingMethod">
<rdfs:label>Genomic Ascertaining Method</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#ExperimentalMethod"/>
<rdfs:comment xml:lang="en">Provides information about the source of data.
Subclasses of the class can be used to encode for the "data-source" structured pragma in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Genotype -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Genotype">
<rdfs:label>Genotype</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#FunctionalSpecification"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Genotype</rdfs:seeAlso>
<rdfs:comment xml:lang="en">The genotype is the genetic information captured in a particular genome. It can also refer to one or more populations, if statistical distributions are provided that assign genetic codes to groups of individuals.
A genotype is denoted by a string of slash-separated list of alleles ("has value" property). The length of the list is dependent on the ploidy of the studied species as well as sequencing technique used.
Example: "A/G" denotes a genotype with alleles "A" and "G".
Encodes for the "Genotype" attribute in GVF and "GT" additional information in VCF.</rdfs:comment>