forked from SynBioDex/sbol-visual-ontology
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsbol-vo.txt
2374 lines (2231 loc) · 132 KB
/
sbol-vo.txt
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"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xml:base="http://sbols.org/visual/v3"
xmlns="http://sbols.org/visual/v3#">
<owl:Ontology rdf:about="http://sbols.org/visual/v3">
<owl:imports rdf:resource="https://raw.githubusercontent.com/SynBioDex/sbol-owl3/main/sbolowl3.rdf"/>
</owl:Ontology>
<owl:ObjectProperty rdf:about="#isGlyphOf">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">isGlyphOf</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasGlyph">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hasGlyph</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasHead">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hasHead</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasTail">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hasTail</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasIncoming">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hasIncoming</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasOutgoing">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hasOutgoing</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#isAlternativeOf">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">isAlternativeOf</rdfs:label>
</owl:ObjectProperty>
<owl:AnnotationProperty rdf:about="#defaultGlyph">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">defaultGlyph</rdfs:label>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="#glyphDirectory">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glyphDirectory</rdfs:label>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="#recommended">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">recommended</rdfs:label>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="#prototypicalExample">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">prototypicalExample</rdfs:label>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="#notes">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">notes</rdfs:label>
</owl:AnnotationProperty>
<owl:Class rdf:about="#Glyph">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyph</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#InteractionGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">InteractionGlyph</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#InteractionNodeGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">InteractionNodeGlyph</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#MolecularSpeciesGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MolecularSpeciesGlyph</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#SequenceFeatureGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SequenceFeatureGlyph</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#SignatureGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001978"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The signature glyph is a box sitting atop the backbone with an X and line inside it, suggesting a signature on a form:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SignatureGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">signature-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/signature</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Barcode</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#CompositeGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
The glyph for Composite is dashed "expanding lines" connecting any "base" glyph representing the more abstract composite (e.g., Omitted Detail, or Terminator, or Promoter) to a backbone diagramming the contents of the composite. Note the bounding box is indicating the location of the base glyph, and would scale with that glyph.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CompositeGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">composite-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/composite</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An "expression cassette" containing a ribosome entry site, coding sequence, and terminator.
In this case, the recommended "base" glyph would be Engineered Region.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An "abbreviated" representation of composite, simply indicating that more structure is available, can be made by using short lines and placing only an Omitted Detail glyph in the secondary backbone. For example, here is an example of an abbreviated composite promoter:
and a composite with an Engineered Region of otherwise unspecified content:
</notes>
</owl:Class>
<owl:Class rdf:about="#NoGlyphAssignedGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
When a part has no assigned glyph it is RECOMMENDED that a user provide their own glyph. The user is also encouraged to submit the new glyph for possible adoption into the SBOLv standard.
An alternative is brackets, suggesting information that needs to be filled in:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NoGlyphAssignedGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">no-glyph-assigned-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/no-glyph-assigned</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">No Glyph Assigned is intended to be used for any Component that is not covered by other SBOL Visual glyphs.
For example, at present there is no glyph recommended for representing a transposon.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">No Glyph Assigned is intended for constructs with a defined specific role that happens to not yet be covered by available approved glyphs (other than the root "Sequence Feature"). It is more likely to appear in machine-generated diagrams than in human-generated diagrams, since humans are likely to invent and use their own glyph for the purpose.</notes>
</owl:Class>
<owl:Class rdf:about="#AptamerGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000031"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The aptamer glyph is a cartoon diagram of a prototypical nucleic acid secondary structure for an aptamer:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AptamerGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aptamer-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/aptamer</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">theophylline aptamer</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#ChromosomalLocusGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000830"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
The glyph to indicate integration into a chromosome is an S-shaped curve of the backbone, suggesting something that might be part of a larger looping structure:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChromosomalLocusGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">chromosomal-locus-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/chromosomal-locus</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">_B. subtilis_ amyE locus</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Complementary "left" and "right" versions of this glyph SHOULD be used together, flanking the region whose genomic context is being described.
The Omitted Detail glyph SHOULD generally be contatenated to indicate that there is information about the chromosome not being represented.
Examples of RECOMMENDED usage:
- A functional unit consisting of promoter, ribosome entry site, CDS, and terminator, all integrated together into the chromosome:
- Two functional units, one integrated into the amyE locus, another integrated into the ganA locus:
</notes>
</owl:Class>
<owl:Class rdf:about="#OriginofTransferGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000724"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The origin of transfer glyph is circular like origin of replication, but also includes an outbound arrow:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OriginofTransferGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">origin-of-transfer-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/origin-of-transfer</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">oriT</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*This section left deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#PolypeptideRegionGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000839"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A polypeptide region inside a coding sequence is indicated by insertion of triangular boundaries inside of the CDS, parallel to the 3' side of the CDS. This will produce chevron segments on the 3' side and a CDS shape on the 5' side:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PolypeptideRegionGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">polypeptide-region-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/polypeptide-region</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">degradation tag on a protein coding sequence
nuclear localization tag on a protein coding sequence
coding sequence for the membrane-crossing region of a protein
This glyph is intended to be used in composition or superposition with the glyph for the coding sequence of which the polypeptide regions are fragments: Example of a coding sequence with three designated domains, an N-tag (blue), C-tag (yellow), and internal region (red):
</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Polypeptide region can also be used to represent regions that involve cleavage, such as a 2A self-cleaving polypeptide region (SO:0002224, a child term of SO:0000839). It is RECOMMENDED that cleavage-inducing polypeptide regions be visually distinguished from intact, e.g., through the use of dashed lines.
</notes>
</owl:Class>
<owl:Class rdf:about="#StabilityElementGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001979"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001955"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001546"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stability Element is a "stem-top" glyph for describing small sites. In this system:
- the top glyph indicates the type of site (e.g., Stability Element)
- the stem glyph indicates whether the site affects DNA, RNA, or protein (respectively: straight, wavy, or looped)</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">StabilityElementGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">stem-top-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/stability-element</glyphDirectory>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PEST tag, 3’ Hairpin</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNA Stability Element glyph was previously also associated with SO:0001957, but that SO term has been declared obsolete in Sequence Ontology.
This glyph is not backwards compatible with SBOL Visual 1.
Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stability Element, since the length of a Stability Element is typically multiple bases / amino acids.</notes>
</owl:Class>
<owl:Class rdf:about="#DnaStabilityElementGlyph">
<rdfs:subClassOf rdf:resource="#StabilityElementGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The top for a Stability Element is a pentagon suggesting the shape of a shield, on top of a stem connecting to the backbone at the point where the stability element is located (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DnaStabilityElementGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dna-stability-element-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/stability-element</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#RnaStabilityElementGlyph">
<rdfs:subClassOf rdf:resource="#StabilityElementGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001979"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The top for a Stability Element is a pentagon suggesting the shape of a shield, on top of a stem connecting to the backbone at the point where the stability element is located (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RnaStabilityElementGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">rna-stability-element-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/stability-element</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#ProteinStabilityElementGlyph">
<rdfs:subClassOf rdf:resource="#StabilityElementGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001955"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001546"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The top for a Stability Element is a pentagon suggesting the shape of a shield, on top of a stem connecting to the backbone at the point where the stability element is located (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ProteinStabilityElementGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protein-stability-element-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/stability-element</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#OmittedDetailGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Omitted Detail glyph is a break in the backbone with an ellipsis to indicate that material would normally be in that location:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OmittedDetailGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">omitted-detail-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/omitted-detail</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A diagram in which a sequence feature is not drawn.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This glyph actually places a "break" in the nucleic acid backbone.</notes>
</owl:Class>
<owl:Class rdf:about="#EngineeredRegionGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000804"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
Engineered Region is represented by a plain rectangle suggesting a blank slate to be written upon:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EngineeredRegionGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">engineered-region-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/engineered-region</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An "expression cassette" containing a ribosome entry site, coding sequence, and terminator.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#CleavageSiteGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001688"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001687"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001977"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001956"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage Site is a "stem-top" glyph for describing small sites. In this system:
- the top glyph indicates the type of site (e.g., Cleavage Site)
- the stem glyph indicates whether the site affects DNA, RNA, or protein (respectively: straight, wavy, or looped)</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CleavageSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">stem-top-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cleavage-site</glyphDirectory>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNAse E site, BamHI</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0000061 (which was previously associated with Restriction Enzyme Recognition Site in SBOL Visual 1) is no longer associated with the DNA Cleavage glyph in SBOL Visual 2 or 3, as SO:0000061 refers to the binding site and not the location of cleavage.
The Ribonuclease Site, Protease Site, and Restriction Enzyme Recognition Site glyphs from SBOL Visual 1.0 are now replaced by the Cleavage Site glyph with the appropriate stem.
Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DNA backbone (as done previously in SBOL Visual 1.0 via the Restriction Enzyme Recognition Site glyph) can persist in a SBOL Visual 2 or 3 diagram and still be considered compliant with SBOL Visual 2 or 3, where it is now classified as a Biopolymer Location (which is a superclass of cleavage sites). Thus, the Biopolymer Location glyph from SBOL Visual 2 or 3 is backwards compatible with the Restriction Enzyme Recognition Site glyph from SBOL Visual 1.
The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restriction Site glyphs remain unchanged, and are more specific children/derivatives of the DNA-Stem Cleavage-Top glyph.
A 2A self-cleaving polypeptide region (SO:0002224) SHOULD NOT be represented by a protease site, as its cleavage mechanism is different. Instead, 2A sequences should be represented using the Polypeptide Region glyph (see example in its specification).</notes>
</owl:Class>
<owl:Class rdf:about="#DnaCleavageSiteGlyph">
<rdfs:subClassOf rdf:resource="#CleavageSiteGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001688"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001687"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Cleavage Site top is an "X" suggesting slicing on top of a stem connecting to the backbone at the point where cleavage will occur (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DnaCleavageSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nuclease-site-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cleavage-site</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#RnaCleavageSiteGlyph">
<rdfs:subClassOf rdf:resource="#CleavageSiteGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001977"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Cleavage Site top is an "X" suggesting slicing on top of a stem connecting to the backbone at the point where cleavage will occur (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RnaCleavageSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ribonuclease-site-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cleavage-site</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#ProteinCleavageSiteGlyph">
<rdfs:subClassOf rdf:resource="#CleavageSiteGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001956"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Cleavage Site top is an "X" suggesting slicing on top of a stem connecting to the backbone at the point where cleavage will occur (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ProteinCleavageSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protease-site-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cleavage-site</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#OperatorBindingSiteGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000057"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000409"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The operator glyph is an open "cup" suggesting a binding location:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OperatorBindingSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">operator-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/operator</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gal4 binding site in an activatable promoter.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This glyph puts a "dent" in the backbone line.</notes>
</owl:Class>
<owl:Class rdf:about="#OriginofReplicationGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000296"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The origin of replication glyph is a circle suggesting the "bulge" opened in a piece of circular DNA when replication is beginning:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OriginofReplicationGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">origin-of-replication-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/origin-of-replication</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">human herpesvirus-6 OOR</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The label on an origin of replication glyph is RECOMMENDED as the location to label either specifically the identity of the origin of replication or the name of the entire plasmid backbone more generally.</notes>
</owl:Class>
<owl:Class rdf:about="#TerminatorGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000141"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The terminator is a T sitting atop the backbone:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TerminatorGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">terminator-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/terminator</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">T1 terminator</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#CDSGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000316"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The coding sequence glyph is a "box" with one side bent out arrow-like to show direction:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDSGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cds-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cds</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">α-Hemoglobin coding sequence</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#CDSGlyphAlternative">
<rdfs:subClassOf rdf:resource="#CDSGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isAlternativeOf"/>
<owl:someValuesFrom rdf:resource="#CDSGlyph"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alternately, CDS may be represented as a block arrow:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDSGlyphAlternative</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cds-arrow-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cds</glyphDirectory>
</owl:Class>
<owl:Class rdf:about="#AssemblyScarGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001953"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The assembly scar glyph is an "equal sign" image, the pattern produced by the union of a 5' sticky end and 3' sticky end glyph. The scar will cover the backbone, creating a visual break suggesting the potential disruption associated with a scar:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AssemblyScarGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">assembly-scar-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/assembly-scar</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ligated sticky ends following BioBrick assembly.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#AssemblyScarGlyphAlternative">
<rdfs:subClassOf rdf:resource="#AssemblyScarGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isAlternativeOf"/>
<owl:someValuesFrom rdf:resource="#AssemblyScarGlyph"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">With a double-stranded backbone:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AssemblyScarGlyphAlternative</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">assembly-scar-specification-doublestrand.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/assembly-scar</glyphDirectory>
</owl:Class>
<owl:Class rdf:about="#SpecificRecombinationSiteGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000299"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The specific recombination site glyph is a triangle, centered on the backbone, as has appeared in a number of recombinase circuit papers:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SpecificRecombinationSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">specific-recombination-site-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/specific-recombination-site</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">flippase recognition target (FRT) site</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*This section left deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#PrimerBindingSiteGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0005850"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The primer binding site glyph is a line with a bent end suggesting a partially complementary strand of nucleic acid attaching to the backbone:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PrimerBindingSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">primer-binding-site-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/primer-binding-site</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">seq-F</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#Non-CodingRNAGeneGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001263"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000834"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The non-coding RNA glyph is a rectangular box whose top is a single-stranded RNA "wiggle":</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Non-CodingRNAGeneGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ncrna-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/non-coding-rna</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">gRNA sequence for targeting a dCas9 repressor</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*This section left deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#BiopolymerLocationGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000699"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001236"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001237"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
Biopolymer Location is a "stem-top" glyph for describing small sites. In this system:
- the top glyph indicates the type of site (e.g., Biopolymer Location)
- the stem glyph indicates whether the site affects DNA, RNA, or protein (respectively: straight, wavy, or looped)</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BiopolymerLocationGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">stem-top-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/location</glyphDirectory>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CRISPR-targeted insertion site, protease site, mutation site</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biopolymer Location is a general glyph for all zero- and one-length sequence features, including insertion and deletion sites and X-ase cut sites.
Note also that Biopolymer Location does not cover stability elements, since their length is typically multiple bases / amino acids.
Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DNA backbone (as done previously in SBOL Visual 1 via the Restriction Enzyme Recognition Site glyph) can persist in a SBOL Visual 2 or 3 diagram and still be considered compliant with SBOL Visual 2 or 3, where it is now classified as a Biopolymer Location (which is a superclass of cleavage sites). Thus, the Biopolymer Location glyph from SBOL Visual 2 or 3 is backwards compatible with the Restriction Enzyme Recognition Site glyph from SBOL Visual 1.</notes>
</owl:Class>
<owl:Class rdf:about="#DnaBiopolymerLocationGlyph">
<rdfs:subClassOf rdf:resource="#BiopolymerLocationGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000699"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001236"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DnaBiopolymerLocationGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">location-dna-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/location</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>