forked from OBOFoundry/OBOFoundry.github.io
-
Notifications
You must be signed in to change notification settings - Fork 0
/
ontologies.jsonld
13343 lines (13343 loc) · 577 KB
/
ontologies.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
{
"@context": "http://obofoundry.github.io/registry/context.jsonld",
"ontologies": [
{
"activity_status": "active",
"contact": {
"email": "[email protected]",
"github": "akodamullil",
"label": "Alpha Tom Kodamullil",
"orcid": "0000-0001-9896-3531"
},
"dependencies": [
{
"id": "bfo"
}
],
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"domain": "health",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"id": "ado",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/ado.owl",
"preferredPrefix": "ADO",
"products": [
{
"id": "ado.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/ado.owl"
}
],
"repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"title": "Alzheimer's Disease Ontology",
"tracker": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues"
},
{
"activity_status": "active",
"contact": {
"email": "[email protected]",
"github": "Melek-C",
"label": "Melek Chaouch",
"orcid": "0000-0001-5868-4204"
},
"description": "AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in a standardised and structured format. The AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using a language or ethnicity identifier or synonyms.",
"domain": "organisms",
"homepage": "https://github.com/h3abionet/afpo",
"id": "afpo",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/afpo.owl",
"preferredPrefix": "AfPO",
"products": [
{
"description": "The main ontology in OWL. Contains all MP terms and links to other OBO ontologies",
"id": "afpo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/afpo.owl",
"title": "AfPO (OWL edition)"
},
{
"description": "A direct translation of the AfPO (OWL edition) into OBO format",
"id": "afpo.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/afpo.obo",
"page": "https://github.com/h3abionet/afpo",
"title": "AfPO (OBO edition)"
},
{
"description": "A direct translation of the AfPO (OWL edition) into OBOGraph JSON format",
"id": "afpo.json",
"ontology_purl": "http://purl.obolibrary.org/obo/afpo.json",
"page": "https://github.com/h3abionet/afpo",
"title": "AfPO (obographs JSON edition)"
}
],
"repository": "https://github.com/h3abionet/afpo",
"tags": [
"ancestry"
],
"title": "African Population Ontology",
"tracker": "https://github.com/h3abionet/afpo/issues"
},
{
"activity_status": "active",
"contact": {
"email": "[email protected]",
"github": "marieALaporte",
"label": "Marie-Angélique Laporte",
"orcid": "0000-0002-8461-9745"
},
"dependencies": [
{
"id": "bfo"
},
{
"id": "envo"
},
{
"id": "foodon"
},
{
"id": "go"
},
{
"id": "iao"
},
{
"id": "ncbitaxon"
},
{
"id": "obi"
},
{
"id": "pato"
},
{
"id": "peco"
},
{
"id": "po"
},
{
"id": "ro"
},
{
"id": "to"
},
{
"id": "uo"
},
{
"id": "xco"
}
],
"description": "Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments",
"domain": "agriculture",
"homepage": "https://github.com/AgriculturalSemantics/agro",
"id": "agro",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/agro.owl",
"preferredPrefix": "AGRO",
"products": [
{
"description": "Contains all AgrO terms and links to other relevant ontologies.",
"id": "agro.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/agro.owl",
"title": "AgrO"
}
],
"publications": [
{
"id": "http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf",
"title": "Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics."
}
],
"repository": "https://github.com/AgriculturalSemantics/agro",
"tags": [
"agronomy"
],
"title": "Agronomy Ontology",
"tracker": "https://github.com/AgriculturalSemantics/agro/issues/",
"usages": [
{
"description": "AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO.",
"user": "https://agrofims.org/about"
},
{
"description": "AgrO is being used by GARDIAN to facilitate data search within publications and datasets for use in quantitative analyses.",
"user": "https://gardian.bigdata.cgiar.org/"
}
]
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/insect-morphology/aism",
"path": ".",
"system": "git"
},
"contact": {
"email": "[email protected]",
"github": "JCGiron",
"label": "Jennifer C. Girón",
"orcid": "0000-0002-0851-6883"
},
"dependencies": [
{
"id": "bfo"
},
{
"id": "bspo"
},
{
"id": "caro"
},
{
"id": "pato"
},
{
"id": "ro"
},
{
"id": "uberon"
}
],
"description": "The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology.",
"domain": "anatomy and development",
"homepage": "https://github.com/insect-morphology/aism",
"id": "aism",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/aism.owl",
"preferredPrefix": "AISM",
"products": [
{
"id": "aism.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/aism.owl"
},
{
"id": "aism.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/aism.obo"
},
{
"id": "aism.json",
"ontology_purl": "http://purl.obolibrary.org/obo/aism.json"
}
],
"repository": "https://github.com/insect-morphology/aism",
"title": "Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)",
"tracker": "https://github.com/insect-morphology/aism/issues"
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/EBISPOT/amphx_ontology.git",
"path": ".",
"system": "git"
},
"contact": {
"email": "[email protected]",
"github": "hescriva",
"label": "Hector Escriva",
"orcid": "0000-0001-7577-5028"
},
"dependencies": [
{
"id": "uberon"
}
],
"description": "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).",
"domain": "anatomy and development",
"homepage": "https://github.com/EBISPOT/amphx_ontology",
"id": "amphx",
"layout": "ontology_detail",
"license": {
"label": "CC BY 3.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "http://creativecommons.org/licenses/by/3.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/amphx.owl",
"preferredPrefix": "AMPHX",
"products": [
{
"id": "amphx.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/amphx.owl"
},
{
"id": "amphx.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/amphx.obo"
}
],
"repository": "https://github.com/EBISPOT/amphx_ontology",
"title": "The Amphioxus Development and Anatomy Ontology",
"tracker": "https://github.com/EBISPOT/amphx_ontology/issues"
},
{
"activity_status": "active",
"build": {
"method": "obo2owl",
"source_url": "https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo"
},
"contact": {
"email": "[email protected]",
"github": "srengel",
"label": "Stacia R Engel",
"orcid": "0000-0001-5472-917X"
},
"description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi",
"domain": "phenotype",
"homepage": "http://www.yeastgenome.org/",
"id": "apo",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/apo.owl",
"preferredPrefix": "APO",
"products": [
{
"id": "apo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/apo.owl"
},
{
"id": "apo.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/apo.obo"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/20157474",
"title": "New mutant phenotype data curation system in the Saccharomyces Genome Database"
}
],
"repository": "https://github.com/obophenotype/ascomycete-phenotype-ontology",
"taxon": {
"id": "NCBITaxon:4890",
"label": "Ascomycota"
},
"title": "Ascomycete phenotype ontology",
"tracker": "https://github.com/obophenotype/ascomycete-phenotype-ontology/issues"
},
{
"activity_status": "active",
"contact": {
"email": "[email protected]",
"github": "hoganwr",
"label": "William Hogan",
"orcid": "0000-0002-9881-1017"
},
"description": "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.",
"domain": "health",
"homepage": "https://github.com/ApolloDev/apollo-sv",
"id": "apollo_sv",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/apollo_sv.owl",
"preferredPrefix": "APOLLO_SV",
"products": [
{
"id": "apollo_sv.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/apollo_sv.owl"
}
],
"publications": [
{
"id": "https://doi.org/10.1186/s13326-016-0092-y",
"title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation"
}
],
"repository": "https://github.com/ApolloDev/apollo-sv",
"title": "Apollo Structured Vocabulary",
"tracker": "https://github.com/ApolloDev/apollo-sv/issues",
"usages": [
{
"description": "Apollo-SV terms are used in the new MIDAS portal (https://midasnetwork.us/catalog/) for making data discoverable.",
"examples": [
{
"description": "A 'hospital stay dataset' reference in the midasnetwork.us resource",
"url": "https://midasnetwork.us/ontology/class-oboapollo_sv_00000600.html"
}
],
"seeAlso": "https://midasnetwork.us/catalog/",
"type": "annotation",
"user": "https://midasnetwork.us/"
}
]
},
{
"activity_status": "active",
"contact": {
"email": "[email protected]",
"github": "agmcarthur",
"label": "Andrew G. McArthur",
"orcid": "0000-0002-1142-3063"
},
"description": "Antibiotic resistance genes and mutations",
"domain": "microbiology",
"homepage": "https://github.com/arpcard/aro",
"id": "aro",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"mailing_list": "https://mailman.mcmaster.ca/mailman/listinfo/card-l",
"ontology_purl": "http://purl.obolibrary.org/obo/aro.owl",
"preferredPrefix": "ARO",
"products": [
{
"id": "aro.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/aro.owl"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/31665441",
"title": "CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database."
}
],
"repository": "https://github.com/arpcard/aro",
"title": "Antibiotic Resistance Ontology",
"tracker": "https://github.com/arpcard/aro/issues"
},
{
"activity_status": "active",
"contact": {
"email": "[email protected]",
"github": "ramonawalls",
"label": "Ramona Walls",
"orcid": "0000-0001-8815-0078"
},
"description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.",
"domain": "organisms",
"homepage": "https://github.com/BiodiversityOntologies/bco",
"id": "bco",
"in_foundry": false,
"layout": "ontology_detail",
"license": {
"label": "CC0 1.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png",
"url": "https://creativecommons.org/publicdomain/zero/1.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/bco.owl",
"preferredPrefix": "BCO",
"products": [
{
"id": "bco.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/bco.owl"
}
],
"publications": [
{
"id": "https://doi.org/10.1371/journal.pone.0089606",
"title": "Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies"
}
],
"repository": "https://github.com/BiodiversityOntologies/bco",
"tags": [
"biodiversity collections"
],
"title": "Biological Collections Ontology",
"tracker": "https://github.com/BiodiversityOntologies/bco/issues"
},
{
"activity_status": "active",
"browsers": [
{
"label": "BioPortal",
"title": "BioPortal Browser",
"url": "http://bioportal.bioontology.org/ontologies/BFO?p=classes"
}
],
"contact": {
"email": "[email protected]",
"github": "phismith",
"label": "Barry Smith",
"orcid": "0000-0003-1384-116X"
},
"depicted_by": "https://avatars2.githubusercontent.com/u/12972134?v=3&s=200",
"description": "The upper level ontology upon which OBO Foundry ontologies are built.",
"domain": "upper",
"homepage": "http://ifomis.org/bfo/",
"id": "bfo",
"in_foundry_order": 1,
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "http://creativecommons.org/licenses/by/4.0/"
},
"mailing_list": "https://groups.google.com/forum/#!forum/bfo-discuss",
"ontology_purl": "http://purl.obolibrary.org/obo/bfo.owl",
"preferredPrefix": "BFO",
"products": [
{
"id": "bfo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/bfo.owl"
},
{
"id": "bfo.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/bfo.obo"
}
],
"repository": "https://github.com/BFO-ontology/BFO",
"title": "Basic Formal Ontology",
"tracker": "https://github.com/BFO-ontology/BFO/issues",
"usages": [
{
"description": "BFO is imported by multiple OBO ontologies to standardize upper level structure",
"type": "owl_import",
"user": "http://obofoundry.org"
}
]
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/obophenotype/biological-spatial-ontology.git",
"infallible": 1,
"method": "vcs",
"path": "src/ontology",
"system": "git"
},
"contact": {
"email": "[email protected]",
"github": "cmungall",
"label": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
"description": "An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces",
"domain": "anatomy and development",
"homepage": "https://github.com/obophenotype/biological-spatial-ontology",
"id": "bspo",
"layout": "ontology_detail",
"license": {
"label": "CC BY 3.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "http://creativecommons.org/licenses/by/3.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/bspo.owl",
"preferredPrefix": "BSPO",
"products": [
{
"id": "bspo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/bspo.owl"
},
{
"id": "bspo.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/bspo.obo"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/25140222",
"title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology."
}
],
"repository": "https://github.com/obophenotype/biological-spatial-ontology",
"title": "Biological Spatial Ontology",
"tracker": "https://github.com/obophenotype/biological-spatial-ontology/issues"
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/BRENDA-Enzymes/BTO.git",
"path": ".",
"system": "git"
},
"contact": {
"email": "[email protected]",
"github": "chdudek",
"label": "Christian-Alexander Dudek",
"orcid": "0000-0001-9117-7909"
},
"description": "A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.",
"domain": "anatomy and development",
"homepage": "http://www.brenda-enzymes.org",
"id": "bto",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/bto.owl",
"page": "https://en.wikipedia.org/wiki/BRENDA_tissue_ontology",
"preferredPrefix": "BTO",
"products": [
{
"id": "bto.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/bto.owl"
},
{
"id": "bto.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/bto.obo"
},
{
"id": "bto.json",
"ontology_purl": "http://purl.obolibrary.org/obo/bto.json"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21030441",
"title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources"
}
],
"repository": "https://github.com/BRENDA-Enzymes/BTO",
"title": "BRENDA tissue / enzyme source",
"tracker": "https://github.com/BRENDA-Enzymes/BTO/issues"
},
{
"activity_status": "active",
"build": {
"method": "obo2owl",
"notes": "moving to owl soon",
"source_url": "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/caro.obo"
},
"contact": {
"email": "[email protected]",
"github": "mellybelly",
"label": "Melissa Haendel",
"orcid": "0000-0001-9114-8737"
},
"description": "An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species",
"domain": "anatomy and development",
"homepage": "https://github.com/obophenotype/caro/",
"id": "caro",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/caro.owl",
"preferredPrefix": "CARO",
"products": [
{
"id": "caro.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/caro.owl"
}
],
"repository": "https://github.com/obophenotype/caro",
"title": "Common Anatomy Reference Ontology",
"tracker": "https://github.com/obophenotype/caro/issues"
},
{
"activity_status": "active",
"build": {
"method": "owl2obo",
"source_url": "http://purl.obolibrary.org/obo/cdao.owl"
},
"contact": {
"email": "[email protected]",
"github": "balhoff",
"label": "Jim Balhoff",
"orcid": "0000-0002-8688-6599"
},
"description": "a formalization of concepts and relations relevant to evolutionary comparative analysis",
"domain": "organisms",
"homepage": "https://github.com/evoinfo/cdao",
"id": "cdao",
"layout": "ontology_detail",
"license": {
"label": "CC0 1.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png",
"url": "https://creativecommons.org/publicdomain/zero/1.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/cdao.owl",
"preferredPrefix": "CDAO",
"products": [
{
"id": "cdao.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/cdao.owl"
}
],
"publications": [
{
"id": "https://doi.org/10.4137/EBO.S2320",
"title": "Initial Implementation of a Comparative Data Analysis Ontology"
}
],
"repository": "https://github.com/evoinfo/cdao",
"title": "Comparative Data Analysis Ontology",
"tracker": "https://github.com/evoinfo/cdao/issues"
},
{
"activity_status": "active",
"build": {
"checkout": "git clone https://github.com/CompositionalDietaryNutritionOntology/cdno.git",
"path": ".",
"system": "git"
},
"contact": {
"email": "[email protected]",
"github": "LilyAndres",
"label": "Liliana Andres Hernandez",
"orcid": "0000-0002-7696-731X"
},
"dependencies": [
{
"id": "bfo"
},
{
"id": "chebi"
},
{
"id": "envo"
},
{
"id": "pato"
},
{
"id": "ro"
}
],
"description": "CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet.",
"domain": "diet, metabolomics, and nutrition",
"homepage": "https://cdno.info/",
"id": "cdno",
"layout": "ontology_detail",
"license": {
"label": "CC BY 3.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/3.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/cdno.owl",
"preferredPrefix": "CDNO",
"products": [
{
"id": "cdno.owl",
"name": "Compositional Dietary Nutrition Ontology main release in OWL format",
"ontology_purl": "http://purl.obolibrary.org/obo/cdno.owl"
},
{
"id": "cdno.obo",
"name": "Compositional Dietary Nutrition Ontology additional release in OBO format",
"ontology_purl": "http://purl.obolibrary.org/obo/cdno.obo"
}
],
"publications": [
{
"id": "https://doi.org/10.3389/fnut.2022.928837",
"title": "Establishing a Common Nutritional Vocabulary - From Food Production to Diet"
}
],
"repository": "https://github.com/CompositionalDietaryNutritionOntology/cdno",
"title": "Compositional Dietary Nutrition Ontology",
"tracker": "https://github.com/CompositionalDietaryNutritionOntology/cdno/issues"
},
{
"activity_status": "active",
"browsers": [
{
"label": "CHEBI",
"title": "EBI CHEBI Browser",
"url": "http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:24431#graphView"
}
],
"build": {
"infallible": 1,
"method": "obo2owl",
"source_url": "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo"
},
"contact": {
"email": "[email protected]",
"github": "amalik01",
"label": "Adnan Malik",
"orcid": "0000-0001-8123-5351"
},
"depicted_by": "https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png",
"description": "A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.",
"domain": "chemistry and biochemistry",
"homepage": "http://www.ebi.ac.uk/chebi",
"id": "chebi",
"in_foundry_order": 1,
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/chebi.owl",
"page": "http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual",
"preferredPrefix": "CHEBI",
"products": [
{
"id": "chebi.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi.owl"
},
{
"id": "chebi.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi.obo"
},
{
"id": "chebi.owl.gz",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi.owl.gz",
"title": "chebi, compressed owl"
},
{
"id": "chebi/chebi_lite.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi/chebi_lite.obo",
"title": "chebi_lite, no syns or xrefs"
},
{
"id": "chebi/chebi_core.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/chebi/chebi_core.obo",
"title": "chebi_core, no xrefs"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/26467479",
"title": "ChEBI in 2016: Improved services and an expanding collection of metabolites."
}
],
"repository": "https://github.com/ebi-chebi/ChEBI",
"title": "Chemical Entities of Biological Interest",
"tracker": "https://github.com/ebi-chebi/ChEBI/issues",
"twitter": "chebit",
"usages": [
{
"description": "Rhea uses CHEBI to annotate reaction participants",
"examples": [
{
"description": "Query for all usages of CHEBI:29748 (chorismate)",
"url": "https://www.rhea-db.org/searchresults?q=CHEBI:29748"
}
],
"user": "https://www.rhea-db.org/"
},
{
"description": "ZFIN uses CHEBI to annotate experiments",
"examples": [
{
"description": "A curated zebrafish experiment involving exposure to (5Z,8Z,14Z)-11,12-dihydroxyicosatrienoic acid (CHEBI:63969)",
"url": "http://zfin.org/action/expression/experiment?id=ZDB-EXP-190627-10"
}
],
"user": "http://zfin.org"
}
]
},
{
"activity_status": "active",
"build": {
"method": "owl2obo",
"source_url": "https://raw.githubusercontent.com/semanticchemistry/semanticchemistry/master/ontology/cheminf.owl"
},
"contact": {
"email": "[email protected]",
"github": "egonw",
"label": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"description": "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.",
"domain": "chemistry and biochemistry",
"homepage": "https://github.com/semanticchemistry/semanticchemistry",
"id": "cheminf",
"layout": "ontology_detail",
"license": {
"label": "CC0 1.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png",
"url": "http://creativecommons.org/publicdomain/zero/1.0/"
},
"mailing_list": "https://groups.google.com/forum/#!forum/cheminf-ontology",
"ontology_purl": "http://purl.obolibrary.org/obo/cheminf.owl",
"preferredPrefix": "CHEMINF",
"products": [
{
"id": "cheminf.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/cheminf.owl"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/21991315",
"title": "The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web"
}
],
"repository": "https://github.com/semanticchemistry/semanticchemistry",
"title": "Chemical Information Ontology",
"tracker": "https://github.com/semanticchemistry/semanticchemistry/issues",
"usages": [
{
"description": "ChEMBL uses CHEMINF in the RDF download",
"examples": [
{
"description": "The RDF is provided as SPARQL endpoint by Maastricht University.",
"url": "https://chemblmirror.rdf.bigcat-bioinformatics.org/"
}
],
"user": "https://www.ebi.ac.uk/chembl/"
},
{
"description": "PubChem uses CHEMINF in their RDF representation",
"examples": [
{
"description": "Physicochemical properties are represented as classes that are typed with CHEMINF classes",
"url": "https://pubchem.ncbi.nlm.nih.gov/rest/rdf/descriptor/CID161282_Canonical_SMILES"
}
],
"user": "https://pubchem.ncbi.nlm.nih.gov/"
}
]
},
{
"activity_status": "active",
"contact": {
"email": "[email protected]",
"github": "nicolevasilevsky",
"label": "Nicole Vasilevsky",
"orcid": "0000-0001-5208-3432"
},
"dependencies": [
{
"id": "chebi"
},
{
"id": "go"
},
{
"id": "hp"
},
{
"id": "mp"
},
{
"id": "ncbitaxon"
},
{
"id": "pr"
},
{
"id": "uberon"
}
],
"description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.",
"domain": "chemistry and biochemistry",
"homepage": "https://github.com/obophenotype/chiro",
"id": "chiro",
"layout": "ontology_detail",
"license": {
"label": "CC0 1.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png",
"url": "http://creativecommons.org/publicdomain/zero/1.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/chiro.owl",
"preferredPrefix": "CHIRO",
"products": [
{
"id": "chiro.owl",
"name": "CHEBI Integrated Role Ontology main release in OWL format",
"ontology_purl": "http://purl.obolibrary.org/obo/chiro.owl"
},
{
"id": "chiro.obo",
"name": "CHEBI Integrated Role Ontology additional release in OBO format",
"ontology_purl": "http://purl.obolibrary.org/obo/chiro.obo"
}
],
"publications": [
{
"id": "https://doi.org/10.26434/chemrxiv.12591221",
"title": "Extension of Roles in the ChEBI Ontology"
}
],
"repository": "https://github.com/obophenotype/chiro",
"title": "CHEBI Integrated Role Ontology",
"tracker": "https://github.com/obophenotype/chiro/issues"
},
{
"activity_status": "active",
"contact": {
"email": "[email protected]",
"github": "batchelorc",
"label": "Colin Batchelor",
"orcid": "0000-0001-5985-7429"
},
"description": "CHMO, the chemical methods ontology, describes methods used to",
"domain": "health",
"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
"id": "chmo",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "http://creativecommons.org/licenses/by/4.0/"
},
"mailing_list": "[email protected]",
"ontology_purl": "http://purl.obolibrary.org/obo/chmo.owl",
"preferredPrefix": "CHMO",
"products": [
{
"id": "chmo.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/chmo.owl"
}
],
"repository": "https://github.com/rsc-ontologies/rsc-cmo",