-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathontology.jsonld
2076 lines (2076 loc) · 92.2 KB
/
ontology.jsonld
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
[ {
"@id" : "_:genid1",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "https://purl.org/emi#ChemicalStructure"
}, {
"@id" : "https://purl.org/emi#ChemicalTaxonAnnotation"
} ]
} ]
}, {
"@id" : "_:genid12",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "https://purl.org/emi#ChemicalStructure"
}, {
"@id" : "https://purl.org/emi#ChemicalTaxonAnnotation"
} ]
} ]
}, {
"@id" : "_:genid15",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "http://www.w3.org/ns/sosa/Sample"
}, {
"@id" : "https://purl.org/emi#InChIKey"
} ]
} ]
}, {
"@id" : "_:genid18",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "https://purl.org/emi#Chemical"
}, {
"@id" : "https://purl.org/emi#SpectrumAnnotation"
} ]
} ]
}, {
"@id" : "_:genid21",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "https://purl.org/emi#Spec2VecDoc"
}, {
"@id" : "https://purl.org/emi#StructuralAnnotation"
} ]
} ]
}, {
"@id" : "_:genid24",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "https://purl.org/emi#MS2Spectrum"
}, {
"@id" : "https://purl.org/emi#StructuralAnnotation"
} ]
} ]
}, {
"@id" : "_:genid27",
"@type" : [ "http://www.w3.org/2002/07/owl#Restriction" ],
"http://www.w3.org/2002/07/owl#allValuesFrom" : [ {
"@id" : "http://www.w3.org/ns/prov#Entity"
} ],
"http://www.w3.org/2002/07/owl#onProperty" : [ {
"@id" : "http://www.w3.org/ns/prov#used"
} ]
}, {
"@id" : "_:genid28",
"@type" : [ "http://www.w3.org/2002/07/owl#Restriction" ],
"http://www.w3.org/2002/07/owl#allValuesFrom" : [ {
"@id" : "http://www.w3.org/ns/prov#Agent"
} ],
"http://www.w3.org/2002/07/owl#onProperty" : [ {
"@id" : "http://www.w3.org/ns/prov#wasAssociatedWith"
} ]
}, {
"@id" : "_:genid29",
"@type" : [ "http://www.w3.org/2002/07/owl#Restriction" ],
"http://www.w3.org/2002/07/owl#onDataRange" : [ {
"@id" : "http://www.w3.org/2001/XMLSchema#string"
} ],
"http://www.w3.org/2002/07/owl#onProperty" : [ {
"@id" : "https://purl.org/emi#inChIKey"
} ],
"http://www.w3.org/2002/07/owl#qualifiedCardinality" : [ {
"@type" : "http://www.w3.org/2001/XMLSchema#nonNegativeInteger",
"@value" : "1"
} ]
}, {
"@id" : "_:genid30",
"@type" : [ "http://www.w3.org/2002/07/owl#Restriction" ],
"http://www.w3.org/2002/07/owl#onProperty" : [ {
"@id" : "https://purl.org/emi#isInChIKey2DOf"
} ],
"http://www.w3.org/2002/07/owl#someValuesFrom" : [ {
"@id" : "https://purl.org/emi#InChIKey"
} ]
}, {
"@id" : "_:genid31",
"@type" : [ "http://www.w3.org/2002/07/owl#Restriction" ],
"http://www.w3.org/2002/07/owl#onDataRange" : [ {
"@id" : "http://www.w3.org/2001/XMLSchema#string"
} ],
"http://www.w3.org/2002/07/owl#onProperty" : [ {
"@id" : "https://purl.org/emi#inChIKey2D"
} ],
"http://www.w3.org/2002/07/owl#qualifiedCardinality" : [ {
"@type" : "http://www.w3.org/2001/XMLSchema#nonNegativeInteger",
"@value" : "1"
} ]
}, {
"@id" : "_:genid32",
"@type" : [ "http://www.w3.org/2002/07/owl#Restriction" ],
"http://www.w3.org/2002/07/owl#allValuesFrom" : [ {
"@id" : "https://purl.org/emi#InformationSource"
} ],
"http://www.w3.org/2002/07/owl#onProperty" : [ {
"@id" : "http://www.w3.org/ns/prov#wasDerivedFrom"
} ]
}, {
"@id" : "_:genid33",
"@type" : [ "http://www.w3.org/2002/07/owl#Restriction" ],
"http://www.w3.org/2002/07/owl#allValuesFrom" : [ {
"@id" : "https://purl.org/emi#Analysis"
} ],
"http://www.w3.org/2002/07/owl#onProperty" : [ {
"@id" : "http://www.w3.org/ns/prov#wasGeneratedBy"
} ]
}, {
"@id" : "_:genid34",
"@type" : [ "http://www.w3.org/2002/07/owl#Restriction" ],
"http://www.w3.org/2002/07/owl#onProperty" : [ {
"@id" : "https://purl.org/emi#hasChemicalStructure"
} ],
"http://www.w3.org/2002/07/owl#someValuesFrom" : [ {
"@id" : "https://purl.org/emi#InChIKey2D"
} ]
}, {
"@id" : "_:genid35",
"@type" : [ "http://www.w3.org/2002/07/owl#Restriction" ],
"http://www.w3.org/2002/07/owl#onProperty" : [ {
"@id" : "http://www.w3.org/2004/02/skos/core#broader"
} ],
"http://www.w3.org/2002/07/owl#someValuesFrom" : [ {
"@id" : "https://purl.org/npc#Superclass"
} ]
}, {
"@id" : "_:genid36",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "https://purl.org/npc#Pathway"
}, {
"@id" : "https://purl.org/npc#Superclass"
} ]
} ]
}, {
"@id" : "_:genid39",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "https://purl.org/npc#Class"
}, {
"@id" : "https://purl.org/npc#Superclass"
} ]
} ]
}, {
"@id" : "_:genid4",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "https://purl.org/emi#Chemical"
}, {
"@id" : "https://purl.org/emi#SpectrumAnnotation"
} ]
} ]
}, {
"@id" : "_:genid42",
"@type" : [ "http://www.w3.org/2002/07/owl#Restriction" ],
"http://www.w3.org/2002/07/owl#onProperty" : [ {
"@id" : "http://www.w3.org/2004/02/skos/core#broader"
} ],
"http://www.w3.org/2002/07/owl#someValuesFrom" : [ {
"@id" : "https://purl.org/npc#Pathway"
} ]
}, {
"@id" : "_:genid43",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "https://purl.org/npc#Class"
}, {
"@id" : "https://purl.org/npc#Pathway"
} ]
} ]
}, {
"@id" : "_:genid9",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2002/07/owl#unionOf" : [ {
"@list" : [ {
"@id" : "https://purl.org/emi#ChemicalStructure"
}, {
"@id" : "https://purl.org/emi#ChemicalTaxonAnnotation"
} ]
} ]
}, {
"@id" : "http://orcid.org/0000-0001-9292-9463",
"http://www.w3.org/ns/org#memberOf" : [ {
"@id" : "https://www.sib.swiss"
} ],
"http://xmlns.com/foaf/0.1/name" : [ {
"@language" : "en",
"@value" : "Marco Pagni"
} ]
}, {
"@id" : "http://orcid.org/0000-0002-3648-7362",
"http://www.w3.org/ns/org#memberOf" : [ {
"@id" : "https://www.unige.ch"
} ],
"http://xmlns.com/foaf/0.1/name" : [ {
"@language" : "en",
"@value" : "Arnaud Gaudry"
} ]
}, {
"@id" : "http://orcid.org/0000-0002-9619-1707",
"http://www.w3.org/ns/org#memberOf" : [ {
"@id" : "https://www.sib.swiss"
} ],
"http://xmlns.com/foaf/0.1/name" : [ {
"@language" : "en",
"@value" : "Florence Mehl"
} ]
}, {
"@id" : "http://orcid.org/0000-0003-3389-2191",
"http://www.w3.org/ns/org#memberOf" : [ {
"@id" : "https://www.unifr.ch"
} ],
"http://xmlns.com/foaf/0.1/name" : [ {
"@language" : "en",
"@value" : "Pierre-Marie Allard"
} ]
}, {
"@id" : "http://org.semanticweb.owlapi/error#Error1",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ]
}, {
"@id" : "http://purl.org/dc/terms/abstract",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/dc/terms/contributor",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/dc/terms/creator",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/dc/terms/description",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/dc/terms/issue",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/dc/terms/issued",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/dc/terms/license",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/dc/terms/modified",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/dc/terms/publisher",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/dc/terms/replaces",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ],
"http://purl.org/dc/terms/description" : [ {
"@language" : "en",
"@value" : "This property is intended to be used with non-literal values. This property is an inverse property of Is Replaced By."
} ],
"http://purl.org/dc/terms/issued" : [ {
"@type" : "http://www.w3.org/2001/XMLSchema#date",
"@value" : "2000-07-11"
} ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@language" : "en",
"@value" : "A related resource that is supplanted, displaced, or superseded by the described resource."
} ],
"http://www.w3.org/2000/01/rdf-schema#isDefinedBy" : [ {
"@id" : "http://purl.org/dc/terms/"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@language" : "en",
"@value" : "Replaces"
} ]
}, {
"@id" : "http://purl.org/dc/terms/title",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/ontology/bibo/status",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/vocab/vann/example",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/vocab/vann/preferredNamespacePrefix",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://purl.org/vocab/vann/preferredNamespaceUri",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://schema.org/codeRepository",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://www.w3.org/2001/XMLSchema#date",
"@type" : [ "http://www.w3.org/2000/01/rdf-schema#Datatype" ]
}, {
"@id" : "http://www.w3.org/2004/02/skos/core#altLabel",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@language" : "en",
"@value" : "The range of skos:altLabel is the class of RDF plain literals."
}, {
"@language" : "en",
"@value" : "skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties."
} ],
"http://www.w3.org/2000/01/rdf-schema#isDefinedBy" : [ {
"@id" : "http://www.w3.org/2004/02/skos/core"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@language" : "en",
"@value" : "alternative label"
} ],
"http://www.w3.org/2000/01/rdf-schema#subPropertyOf" : [ {
"@id" : "http://www.w3.org/2000/01/rdf-schema#label"
} ],
"http://www.w3.org/2004/02/skos/core#definition" : [ {
"@language" : "en",
"@value" : "An alternative lexical label for a resource."
} ],
"http://www.w3.org/2004/02/skos/core#example" : [ {
"@language" : "en",
"@value" : "Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel)."
} ]
}, {
"@id" : "http://www.w3.org/2004/02/skos/core#definition",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://www.w3.org/2004/02/skos/core#example",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://www.w3.org/2004/02/skos/core#prefLabel",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@language" : "en",
"@value" : "A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag."
}, {
"@language" : "en",
"@value" : "The range of skos:prefLabel is the class of RDF plain literals."
}, {
"@language" : "en",
"@value" : "skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise\n disjoint properties."
} ],
"http://www.w3.org/2000/01/rdf-schema#isDefinedBy" : [ {
"@id" : "http://www.w3.org/2004/02/skos/core"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@language" : "en",
"@value" : "preferred label"
} ],
"http://www.w3.org/2000/01/rdf-schema#subPropertyOf" : [ {
"@id" : "http://www.w3.org/2000/01/rdf-schema#label"
} ],
"http://www.w3.org/2004/02/skos/core#definition" : [ {
"@language" : "en",
"@value" : "The preferred lexical label for a resource, in a given language."
} ]
}, {
"@id" : "http://www.w3.org/ns/org#memberOf",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://www.w3.org/ns/sosa/hasFeatureOfInterest",
"http://purl.org/vocab/vann/example" : [ {
"@value" : "@prefix : <https://purl.org/emi/abox#> .\n@prefix emi: <https://purl.org/emi#> .\n@prefix sosa: <http://www.w3.org/ns/sosa/> .\n:VGF138_A02_neg.mzXML rdf:type emi:LCMSAnalysisNeg, emi:LCMSAnalysis, sosa:Observation ;\n sosa:hasFeatureOfInterest :VGF138_A02.\n:VGF138_A02 rdf:type emi:ExtractSample, sosa:Sample."
} ]
}, {
"@id" : "http://www.w3.org/ns/sosa/hasSample",
"http://purl.org/vocab/vann/example" : [ {
"@value" : "@prefix : <https://purl.org/emi/abox#> .\n@prefix emi: <https://purl.org/emi#> .\n@prefix sosa: <http://www.w3.org/ns/sosa/> .\n:V111819GP-01 rdf:type emi:RawMaterial, sosa:Sample . ;\n sosa:hasSample :VGF138_A02.\n:VGF138_A02 rdf:type emi:ExtractSample, sosa:Sample."
} ]
}, {
"@id" : "http://www.w3.org/ns/sosa/isFeatureOfInterest",
"http://purl.org/vocab/vann/example" : [ {
"@value" : "@prefix : <https://purl.org/emi/abox#> .\n@prefix emi: <https://purl.org/emi#> .\n@prefix sosa: <http://www.w3.org/ns/sosa/> .\n:VGF138_A02 rdf:type emi:ExtractSample, sosa:Sample. ;\n sosa:isFeatureOfInterest :VGF138_A02_neg.mzXML.\n:VGF138_A02_neg.mzXML rdf:type emi:LCMSAnalysisNeg, emi:LCMSAnalysis, sosa:Observation."
} ]
}, {
"@id" : "http://www.w3.org/ns/sosa/isResultOf",
"http://purl.org/vocab/vann/example" : [ {
"@value" : "@prefix : <https://purl.org/emi/abox#> .\n@prefix emi: <https://purl.org/emi#> .\n@prefix sosa: <http://www.w3.org/ns/sosa/> .\n:VGF153_A02_lcms_feature_list_neg rdf:type emi:LCMSFeatureSet ;\n sosa:isResultOf :VGF153_A02_neg.mzXML .\n:VGF153_A02_neg.mzXML rdf:type emi:LCMSAnalysisNeg, emi:LCMSAnalysis, sosa:Observation ."
}, {
"@value" : "@prefix : <https://purl.org/emi/abox#> .\n@prefix emi: <https://purl.org/emi#> .\n@prefix sosa: <http://www.w3.org/ns/sosa/> .\n:VGF153_A02_neg.mzXML rdf:type emi:LCMSAnalysisNeg, emi:LCMSAnalysis, sosa:Observation ;\n sosa:hasResult :VGF153_A02_lcms_feature_list_neg .\n:VGF153_A02_lcms_feature_list_neg rdf:type emi:LCMSFeatureSet."
} ]
}, {
"@id" : "http://www.w3.org/ns/sosa/isSampleOf",
"http://purl.org/vocab/vann/example" : [ {
"@value" : "@prefix : <https://purl.org/emi/abox#> .\n@prefix emi: <https://purl.org/emi#> .\n@prefix sosa: <http://www.w3.org/ns/sosa/> .\n:VGF138_A02 rdf:type emi:ExtractSample, sosa:Sample. ;\n sosa:isSampleOf :V111819GP-01.\n:V111819GP-01 rdf:type emi:RawMaterial, sosa:Sample."
} ]
}, {
"@id" : "http://www.wikidata.org/entity/Q16521",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "An organism taxon in Wikidata."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Wikidata taxon"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#Taxon"
} ]
}, {
"@id" : "http://xmlns.com/foaf/0.1/Organization",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ]
}, {
"@id" : "http://xmlns.com/foaf/0.1/depiction",
"@type" : [ "http://www.w3.org/2002/07/owl#ObjectProperty" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "http://www.simolecule.com/cdkdepict/depict/bow/svg?smi=CCCCCCCCCCCC%5BC%40%40H%5D(O)%5BC%40H%5D1CCC(C2CCC(CC(O)CCCCC%5BC%40%40H%5D(O)CC3%3DC%5BC%40H%5D(C)OC3%3DO)O2)O1&zoom=2.0&annotate=cip"
} ]
}, {
"@id" : "http://xmlns.com/foaf/0.1/homepage",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "http://xmlns.com/foaf/0.1/logo",
"@type" : [ "http://www.w3.org/2002/07/owl#AnnotationProperty" ]
}, {
"@id" : "https://orcid.org/0000-0002-1269-2038",
"http://www.w3.org/ns/org#memberOf" : [ {
"@id" : "https://www.unifr.ch"
} ],
"http://xmlns.com/foaf/0.1/name" : [ {
"@language" : "en",
"@value" : "Luca Cappelletti"
} ]
}, {
"@id" : "https://orcid.org/0000-0002-3175-5372",
"http://www.w3.org/ns/org#memberOf" : [ {
"@id" : "https://www.sib.swiss"
} ],
"http://xmlns.com/foaf/0.1/name" : [ {
"@language" : "en",
"@value" : "Tarcisio Mendes de Farias"
} ]
}, {
"@id" : "https://orcid.org/0000-0003-3213-4495",
"http://www.w3.org/ns/org#memberOf" : [ {
"@id" : "https://www.sib.swiss"
} ],
"http://xmlns.com/foaf/0.1/name" : [ {
"@language" : "en",
"@value" : "Ana Claudia Sima"
} ]
}, {
"@id" : "https://purl.org/emi",
"@type" : [ "http://www.w3.org/2002/07/owl#Ontology" ],
"http://purl.org/dc/terms/abstract" : [ {
"@value" : "The Earth Metabolome Initiative ontology is mainly designed as data schema to structure and describe natural product taxonomy, spectrum annotation provenance, sample and observation data, mass spectrometry data and analysis, and chemical structure representations. The EMI ontology replaces the [ENPKG vocabulary](https://enpkg.commons-lab.org/doc/index.html)."
} ],
"http://purl.org/dc/terms/contributor" : [ {
"@id" : "http://orcid.org/0000-0001-9292-9463"
}, {
"@id" : "http://orcid.org/0000-0002-3648-7362"
}, {
"@id" : "http://orcid.org/0000-0002-9619-1707"
}, {
"@id" : "http://orcid.org/0000-0003-3389-2191"
}, {
"@id" : "https://orcid.org/0000-0002-1269-2038"
}, {
"@id" : "https://orcid.org/0000-0002-3175-5372"
}, {
"@id" : "https://orcid.org/0000-0003-3213-4495"
} ],
"http://purl.org/dc/terms/created" : [ {
"@type" : "http://www.w3.org/2001/XMLSchema#date",
"@value" : "2023-11-02"
} ],
"http://purl.org/dc/terms/creator" : [ {
"@id" : "https://orcid.org/0000-0002-3175-5372"
} ],
"http://purl.org/dc/terms/description" : [ {
"@language" : "en",
"@value" : "The Earth Metabolome Initiative (EMI) ontology is designed to capture and structure the metabolic content of all currently known species on our planet."
} ],
"http://purl.org/dc/terms/issue" : [ {
"@type" : "http://www.w3.org/2001/XMLSchema#date",
"@value" : "2024-04-03"
} ],
"http://purl.org/dc/terms/license" : [ {
"@id" : "https://creativecommons.org/publicdomain/zero/1.0/"
} ],
"http://purl.org/dc/terms/modified" : [ {
"@type" : "http://www.w3.org/2001/XMLSchema#date",
"@value" : "2024-04-25"
} ],
"http://purl.org/dc/terms/publisher" : [ {
"@id" : "https://www.earthmetabolome.org"
} ],
"http://purl.org/dc/terms/replaces" : [ {
"@id" : "https://enpkg.commons-lab.org/kg/ontology_version/0.1.0"
} ],
"http://purl.org/dc/terms/title" : [ {
"@language" : "en",
"@value" : "The Earth Metabolome Initiative (EMI) ontology"
} ],
"http://purl.org/ontology/bibo/status" : [ {
"@id" : "http://purl.org/ontology/bibo/status/draft"
} ],
"http://purl.org/vocab/vann/preferredNamespacePrefix" : [ {
"@value" : "emi"
} ],
"http://purl.org/vocab/vann/preferredNamespaceUri" : [ {
"@id" : "https://purl.org/emi#"
} ],
"http://schema.org/codeRepository" : [ {
"@type" : "http://www.w3.org/2001/XMLSchema#anyURI",
"@value" : "https://github.com/digital-botanical-gardens-initiative/earth_metabolome_ontology"
} ],
"http://www.w3.org/2000/01/rdf-schema#seeAlso" : [ {
"@id" : "https://bioschemas.org"
}, {
"@id" : "https://schema.org"
}, {
"@id" : "https://enpkg.commons-lab.org/doc/index.html"
} ],
"http://www.w3.org/2002/07/owl#imports" : [ {
"@id" : "http://www.w3.org/2004/02/skos/core"
}, {
"@id" : "http://www.w3.org/ns/prov-o-20130430"
}, {
"@id" : "http://www.w3.org/ns/sosa/"
}, {
"@id" : "https://purl.org/npc"
} ],
"http://www.w3.org/2002/07/owl#versionIRI" : [ {
"@id" : "https://purl.org/emi/version/0.1"
} ],
"http://www.w3.org/2002/07/owl#versionInfo" : [ {
"@value" : "0.1"
} ],
"http://xmlns.com/foaf/0.1/logo" : [ {
"@id" : "https://kg.earthmetabolome.org/static/img/logo.svg"
} ],
"https://w3id.org/widoco/vocab#introduction" : [ {
"@value" : "The Earth Metabolome Initiative (EMI) ontology replaces the Experimental Natural Products Knowledge Graph [(ENPKG) vocabulary]( https://enpkg.commons-lab.org/doc/index.html). The EMI ontology is used to structure spectrum annotation provenance by reusing the [PROV-O ontology](https://www.w3.org/TR/prov-o/) (a W3C recommendation) and sample and observation data by applying the [SOSA ontology](https://www.w3.org/TR/vocab-ssn/). EMI reuses the SOSA ontology as a data schema for struturing the Sample and Observation data. SOSA (Sensor, Observation, Sample, and Actuator) is a subset of SSN (Semantic Sensor Network Ontology) that is a W3C recommendation. Although, the SSN was developed with ontology engineers in mind as the primary audience. They addressed changes in scope and audience that currently also includes scientific observations that may make heavy use of sampling strategies, and, therefore, the Sampling, Sampler, and Sample classes, as well as their corresponding properties, have been added to SOSA and SSN. Chemical taxonomy is also highly structure in EMI by relying on a taxonomy derived from NPClassifier (i.e., EMI imports [Natural Product Classifier vocabulary](https://purl.org/npc)). This taxonomy was defined for EMI with the [SKOS vocabulary](https://www.w3.org/TR/skos-reference). Indeed, it is an SKOS-based vocabulary for the structural classification of natural products. The skos:broder term is used to represent the hierarchy among Classes, Superclasses and Pathways. npc:Class, npc:Superclass and npc:Pathway are subclasses of skos:Concept. rdfs:label is assigned for each term of the taxonomy that are instances of one of the subclasses of skos:Concept.\n\nSOSA reuse. We consider a Mass Spectrometer as a sosa:Platform. The MS detector that belongs to a Mass Spectrometer is a Sensor. If we do not want to capture the equipment (Mass Spectrometer for provenance) of the generated analysis such as by Liquid chromatography–mass spectrometry (LCMS), we can ignore/ommit it. The observation is interpreted as a prov:Activity/sosa:Observation/emi:Analysis (the Analysis as defined in the Earth Metabolome Intiative model). This observation (a.k.a. LCMS Analysis) uses (prov:use/sosa:hasFeatureOfInterest) some sample. This sample comes from some emi:System (e.g., species or another sample like a Raw Material, a broader specimen). All EMI model classes related to samples are subclasses of sosa:Sample, notably emi:Aliquot, emi:Blank, emi:ExtractSample, emi:RawMaterial and emi:QCSample.\n\nWe can classify each Specimen by using some Specimen taxonomy, for example, [specimenType](https://isamplesorg.github.io/models/generated/vocabularies/specimenType.html) that relies on SKOS. Moreover, we can also classify a sample with an external material taxonomy (e.g., [materialType](https://isamplesorg.github.io/models/generated/vocabularies/materialType.html#organicmaterial)). The raw material (emi:RawMaterial) is also a sosa:sample. In case it is needed to describe the \"Mass Spectrometer\" as a sampler too, we can apply the sosa:Sampler class to define it. The sampling process resuts on subsamples (e.g., emi:Aliquot). The extracted sample can be classified with an external taxonomy (e.g., an Specimen taxonomy) with the term emi:isClassifiedWith.\n\nOther metabolomics data are structured with specific EMI classes such as emi:ChemicalStrucutre for represeting molecules, emi:MS2Spectrum for the mass spectrometry (MS2 spectra), emi:LCMSFeatureSet that represents features obtained from the processing of a given LCMS analysis, please refer to classes and properties descriptions. "
} ]
}, {
"@id" : "https://purl.org/emi#Aliquot",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A sample taken from an extract sample for chemical analysis or other treatment."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Aliquot"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "http://www.w3.org/ns/sosa/Sample"
} ]
}, {
"@id" : "https://purl.org/emi#Analysis",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "Any analysis performed over a sample."
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "http://www.w3.org/ns/sosa/Observation"
}, {
"@id" : "_:genid27"
}, {
"@id" : "_:genid28"
} ]
}, {
"@id" : "https://purl.org/emi#BioAssayResults",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "An object to store bioactivity results."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Bioassay result"
} ]
}, {
"@id" : "https://purl.org/emi#BioassayAnalysis",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A bioassay is an analytical method to determine the concentration or potency of a substance by its effect on living animals or plants (in vivo), or on living cells or tissues(in vitro)."
} ],
"http://www.w3.org/2000/01/rdf-schema#isDefinedBy" : [ {
"@value" : "https://en.wikipedia.org/wiki/Bioassay"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Bioassay analysis"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#Analysis"
} ]
}, {
"@id" : "https://purl.org/emi#Blank",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A blank sample"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Blank sample"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "http://www.w3.org/ns/sosa/Sample"
} ]
}, {
"@id" : "https://purl.org/emi#CSpair",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A pair of 2 GNPSConsensusSpectra."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "GNPS consensus spectra pair"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#SpectralPair"
} ]
}, {
"@id" : "https://purl.org/emi#Chemical",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A chemical. Recommendation: the instances of this class are ideally Wikidata chemical entries. If it is not a Wikidata entry we recommend to be as much as possible consistent in the whole dataset. Metadata can also be provided in order to describe the provenance of the instance (a chemical), for example, by stating the property prov-o:wasDerivedFrom (PROV-Ontology)."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Chemical"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#ChemicalEntity"
} ]
}, {
"@id" : "https://purl.org/emi#ChemicalEntity",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A chemical entity (chemical structure or class)."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Chemical entity"
} ]
}, {
"@id" : "https://purl.org/emi#ChemicalStructure",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A representation of one or more chemical structures. This representation can be defined as molecular information encodings, compact encoding representations, chemical formulas and graphical representations."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Chemical structure representation"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#ChemicalEntity"
} ]
}, {
"@id" : "https://purl.org/emi#ChemicalTaxon",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "As a taxonomy for chemicals such as natural products, we recommend to use the taxonomy derived from NPClassifier (i.e. https://purl.org/npc)."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Chemical taxon"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#ChemicalEntity"
} ]
}, {
"@id" : "https://purl.org/emi#ChemicalTaxonAnnotation",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://purl.org/vocab/vann/example" : [ {
"@value" : "@prefix : <https://purl.org/emi/abox#> .\n@prefix emi: <https://purl.org/emi#> .\n:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:ChemicalTaxonAnnotation ."
} ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "This class is used to annotate a spectrum feature with a chemical taxon. Prefer the Chemical structure annotation class, if the annotation is mainly to assign a chemical representation structure as defined in the emi:ChemicalStructure."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Chemical taxon annotation"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#SpectrumAnnotation"
} ],
"http://www.w3.org/2002/07/owl#disjointWith" : [ {
"@id" : "https://purl.org/emi#StructuralAnnotation"
} ]
}, {
"@id" : "https://purl.org/emi#ComputationalAnalysis",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#Analysis"
} ]
}, {
"@id" : "https://purl.org/emi#ExtractSample",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A natural extract obtained from the processing of a RawMaterial"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Extract sample"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "http://www.w3.org/ns/sosa/Sample"
} ]
}, {
"@id" : "https://purl.org/emi#FBMNComponent",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "Feature-based molecular network component."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "FBMN component"
} ]
}, {
"@id" : "https://purl.org/emi#GNPSAnnotation",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A spectrum structural annotation by GNPS"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "GNPS structural annotation"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#StructuralAnnotation"
} ],
"http://www.w3.org/2002/07/owl#deprecated" : [ {
"@value" : "delete it, it is better to model the source separately becuase otherwise it would require to add a new class each time a new source of annotation appears. the only advantage of keeping the model like this is to reduce the number of triples."
} ]
}, {
"@id" : "https://purl.org/emi#GNPSConsensusSpectrum",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "An MS2 spectrum corresponding to the GNPS consensus spectrum of 1 or more LCMSFeature. Recommendation: instances of this class are ideally built as follows: \"https://metabolomics-usi.ucsd.edu/dashinterface/?usi1={id}\", e.g.: \"https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=mzspec:MassIVE:TASK-773effaad17c4124b9ea9004eaa3f526-spectra/specs_ms.mgf:scan:1028\""
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "GNPS consensus MS2 spectrum"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#MS2Spectrum"
} ]
}, {
"@id" : "https://purl.org/emi#ISDBAnnotation",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A spectrum structural annotation by comparison with an in-silico spectral DB, coupled to chemical and taxonomical reweighting"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "ISDB structural annotation"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#StructuralAnnotation"
} ],
"http://www.w3.org/2002/07/owl#deprecated" : [ {
"@value" : "delete it, it is better to model the source separately becuase otherwise it would require to add a new class each time a new source of annotation appears. the only advantage of keeping the model like this is to reduce the number of triples."
} ]
}, {
"@id" : "https://purl.org/emi#InChIKey",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A chemical structure represented by its InChIKey."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "InChIKey"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#ChemicalStructure"
}, {
"@id" : "_:genid29"
} ]
}, {
"@id" : "https://purl.org/emi#InChIKey2D",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A collection of chemical structures that share the first 14 characters of their InChIKeys, often returned by mass spectrometry based annotation tools."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "2D InChIKey"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#ChemicalStructure"
}, {
"@id" : "_:genid30"
}, {
"@id" : "_:genid31"
} ]
}, {
"@id" : "https://purl.org/emi#InformationSource",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "The source of information. For example, the source of a given annotation that might be a bioinformatics database or machine learning classification model."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Information source"
} ],
"http://www.w3.org/2004/02/skos/core#note" : [ {
"@value" : "This can be replaced by or related with the provenance ontology (W3C recommendation).\nhttps://www.w3.org/TR/prov-o/"
} ]
}, {
"@id" : "https://purl.org/emi#LCMSAnalysis",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A liquid chromatography–mass spectrometry (LCMS) analysis in a given ionization mode (pos or neg)"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "LCMS analysis"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#Analysis"
} ]
}, {
"@id" : "https://purl.org/emi#LCMSAnalysisNeg",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "An LCMS analysis in negative ionization mode (pos or neg)"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Negative LCMS analysis"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#LCMSAnalysis"
} ],
"https://purl.org/emi#hasIonization" : [ {
"@value" : "negative"
} ]
}, {
"@id" : "https://purl.org/emi#LCMSAnalysisPos",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "An LCMS analysis in positive ionization mode (positive or negative)."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Positive LCMS analysis"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#LCMSAnalysis"
} ],
"https://purl.org/emi#hasIonization" : [ {
"@value" : "positive"
} ]
}, {
"@id" : "https://purl.org/emi#LCMSFeature",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://purl.org/vocab/vann/example" : [ {
"@value" : "@prefix emi: <https://purl.org/emi#> .\n@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .\nusi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature ."
} ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "An LCMS feature from a processed LCMS analysis. Recommendation: instances of this class are ideally built as follows: \"https://metabolomics-usi.ucsd.edu/dashinterface/?usi1={id}\" (e.g., https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=mzspec:MSV000090090:DBGI_01_04_001_features_ms2_pos.mgf:scan:1)"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "LCMS individual MS2 spectrum"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#MS2Spectrum"
} ]
}, {
"@id" : "https://purl.org/emi#LCMSFeatureSet",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://purl.org/vocab/vann/example" : [ {
"@value" : "@prefix : <https://purl.org/emi/abox#> .\n@prefix emi: <https://purl.org/emi#> .\n:VGF153_A02_lcms_feature_list_neg rdf:type emi:LCMSFeatureSet ."
} ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A set of Liquid chromatography–mass spectrometry (LCMS) features obtained from the processing of a given LCMS analysis"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "LCMS feature set"
} ]
}, {
"@id" : "https://purl.org/emi#LFpair",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A pair of LCMSFeature"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "LCMS feature pair"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#SpectralPair"
} ]
}, {
"@id" : "https://purl.org/emi#LabObject",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "An object that correspond to a physical laboratory object"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Laboratory object"
} ],
"http://www.w3.org/2002/07/owl#deprecated" : [ {
"@value" : "To remove, it was replaced with Sample from Sosa, because the Lab Objcts in the EMI model so far are only kind of samples. Hence, there is no need of generalizing to any lab object or making it specific to a \"lab\"."
} ]
}, {
"@id" : "https://purl.org/emi#MS2Spectrum",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://purl.org/vocab/vann/example" : [ {
"@value" : "@prefix : <https://purl.org/emi/abox#> .\n@prefix emi: <https://purl.org/emi#> .\n@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .\nusi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:MS2Spectrum ."
} ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A fragmentation mass spectrometry (or MS2) spectrum"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "MS2 spectrum"
} ]
}, {
"@id" : "https://purl.org/emi#Organism",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A living being, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. Example: animal, human being. An organim is associated to a taxon such as \"Homo Sapiens\", NCBI taxonomy identifier: 9606."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Organism"
} ],
"http://www.w3.org/2000/01/rdf-schema#seeAlso" : [ {
"@id" : "http://purl.org/net/orth#Organism"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#System"
} ],
"http://www.w3.org/2004/02/skos/core#altLabel" : [ {
"@value" : "Living being"
} ]
}, {
"@id" : "https://purl.org/emi#QCSample",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A quality control (QC) sample"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Quality control sample"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "http://www.w3.org/ns/sosa/Sample"
} ]
}, {
"@id" : "https://purl.org/emi#RawMaterial",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A raw laboratory biological material, i.e. before extraction"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Raw material"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "http://www.w3.org/ns/sosa/Sample"
} ]
}, {
"@id" : "https://purl.org/emi#SIRIUSAnnotation",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A spectrum structural annotation by SIRIUS"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "SIRIUS structural annotation"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#StructuralAnnotation"
} ],
"http://www.w3.org/2002/07/owl#deprecated" : [ {
"@value" : "delete it, it is better to model the source separately becuase otherwise it would require to add a new class each time a new source of annotation appears. the only advantage of keeping the model like this is to reduce the number of triples."
} ]
}, {
"@id" : "https://purl.org/emi#SiriusCanopusAnnotation",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A spectrum chemical class annotation by SIRIUS-CANOPUS"
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "CANOPUS chemical class annotation"
} ],
"http://www.w3.org/2000/01/rdf-schema#subClassOf" : [ {
"@id" : "https://purl.org/emi#ChemicalTaxonAnnotation"
} ],
"http://www.w3.org/2002/07/owl#deprecated" : [ {
"@value" : "to delete?"
} ]
}, {
"@id" : "https://purl.org/emi#Spec2VecDoc",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "Document about improved mass spectral similarity scoring through learning of structural relationships. Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data. Analysis and benchmarking of mass spectra similarity measures using GNPS data set."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "Spec2vec document"
} ]
}, {
"@id" : "https://purl.org/emi#SpectralPair",
"@type" : [ "http://www.w3.org/2002/07/owl#Class" ],
"http://www.w3.org/2000/01/rdf-schema#comment" : [ {
"@value" : "A pair of two tandem mass spectrometry (MS2 spectra)."
} ],
"http://www.w3.org/2000/01/rdf-schema#label" : [ {
"@value" : "MS2Spectra pair"
} ]
}, {
"@id" : "https://purl.org/emi#SpectrumAnnotation",