forked from OBOFoundry/OBOFoundry.github.io
-
Notifications
You must be signed in to change notification settings - Fork 0
/
ontologies.yml
9496 lines (9496 loc) · 354 KB
/
ontologies.yml
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
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
title: Chemical Methods Ontology
tracker: https://github.com/rsc-ontologies/rsc-cmo/issues
- activity_status: active
contact:
email: [email protected]
github: yongqunh
label: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically
represent and standardize various aspects of coronavirus infectious diseases,
including their etiology, transmission, epidemiology, pathogenesis, diagnosis,
prevention, and treatment.
domain: health
homepage: https://github.com/cido-ontology/cido
id: cido
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/cido.owl
preferredPrefix: CIDO
products:
- id: cido.owl
ontology_purl: http://purl.obolibrary.org/obo/cido.owl
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/36271389
title: 'A comprehensive update on CIDO: the community-based coronavirus infectious
disease ontology'
repository: https://github.com/cido-ontology/cido
title: Coronavirus Infectious Disease Ontology
tracker: https://github.com/cido-ontology/cido/issues
- activity_status: active
contact:
email: [email protected]
github: fbastian
label: Frédéric Bastian
orcid: 0000-0002-9415-5104
description: An ontology to capture confidence information about annotations.
domain: information
homepage: https://github.com/BgeeDB/confidence-information-ontology
id: cio
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/cio.owl
preferredPrefix: CIO
products:
- id: cio.owl
ontology_purl: http://purl.obolibrary.org/obo/cio.owl
- id: cio.obo
ontology_purl: http://purl.obolibrary.org/obo/cio.obo
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/25957950
title: 'The Confidence Information Ontology: a step towards a standard for asserting
confidence in annotations'
repository: https://github.com/BgeeDB/confidence-information-ontology
title: Confidence Information Ontology
tracker: https://github.com/BgeeDB/confidence-information-ontology
- activity_status: active
canonical: cl.owl
contact:
email: [email protected]
github: addiehl
label: Alexander Diehl
orcid: 0000-0001-9990-8331
dependencies:
- id: chebi
- id: go
- id: ncbitaxon
- id: pato
- id: pr
- id: ro
- id: uberon
depicted_by: /images/CL-logo.jpg
description: The Cell Ontology is a structured controlled vocabulary for cell types
in animals.
domain: anatomy and development
homepage: https://obophenotype.github.io/cell-ontology/
id: cl
label: Cell Ontology
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/g/cl_edit
ontology_purl: http://purl.obolibrary.org/obo/cl.owl
preferredPrefix: CL
products:
- description: Complete ontology, plus inter-ontology axioms, and imports modules
format: owl-rdf/xml
id: cl.owl
is_canonical: true
ontology_purl: http://purl.obolibrary.org/obo/cl.owl
title: Main CL OWL edition
uses:
- uberon
- chebi
- go
- pr
- pato
- ncbitaxon
- ro
- derived_from: cl.owl
description: Complete ontology, plus inter-ontology axioms, and imports modules
merged in
format: obo
id: cl.obo
ontology_purl: http://purl.obolibrary.org/obo/cl.obo
title: CL obo format edition
- description: Basic version, no inter-ontology axioms
format: obo
id: cl/cl-basic.obo
ontology_purl: http://purl.obolibrary.org/obo/cl/cl-basic.obo
title: Basic CL
- description: complete CL but with no imports or external axioms
id: cl/cl-base.owl
ontology_purl: http://purl.obolibrary.org/obo/cl/cl-base.owl
title: CL base module
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/27377652
title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
interoperability.'
repository: https://github.com/obophenotype/cell-ontology
tags:
- cells
taxon:
id: NCBITaxon:33208
label: Metazoa
title: Cell Ontology
tracker: https://github.com/obophenotype/cell-ontology/issues
twitter: CellOntology
usages:
- description: The BICCN created a high-resolution atlas of cell types in the primary
motor based on single cell transcriptomics. These cell types are represented
in the brain data standards ontology which anchors to cell types in the cell
ontology.
examples:
- description: cell type card of a cell type linked to a PCL cell type (L2/3 IT
primary motor cortex glutamatergic neuron) which is a subclass of cell types
in CL (CL:4023041)
url: https://knowledge.brain-map.org/celltypes/CCN202002013/CS202002013_193
- description: PCL cell type used in cell type cards linked directly to CL cell
types
url: https://www.ebi.ac.uk/ols/ontologies/pcl/terms?iri=http://purl.obolibrary.org/obo/PCL_0011193
publications:
- id: https://doi.org/10.1101/2021.10.10.463703
title: 'Brain Data Standards Ontology: A data-driven ontology of transcriptomically
defined cell types in the primary motor cortex'
type: annotation
user: https://biccn.org/
- description: HuBMAP develops tools to create an open, global atlas of the human
body at the cellular level. The Cell Ontology is used in annotating cell types
in the tools developed.
examples:
- description: ASCT+B reporter showing CL being used to annotate cell types in
the heart
url: https://hubmapconsortium.github.io/ccf-asct-reporter/vis?selectedOrgans=heart-v1.1&playground=false
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/31597973
title: 'The human body at cellular resolution: the NIH Human Biomolecular Atlas
Program.'
type: annotation
user: https://hubmapconsortium.org/
- description: The Human Cell Atlas (HCA) is an international group of researchers
using a combination of these new technologies to create cellular reference maps.
The HCA use CL to annotate cells in their reference maps.
examples:
- description: HCA collection studies that are related B cell (CL:0000236) that
is filtered through CL annotation
url: https://singlecell.broadinstitute.org/single_cell?type=study&page=1&facets=cell_type%3ACL_0000236&scpbr=human-cell-atlas-main-collection
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/29206104
title: The Human Cell Atlas
type: annotation
user: https://www.humancellatlas.org/
- description: The EBI single cell expression atlas is an extension to EBI expression
atlas that displays gene expression in single cells. Cell types in the single
cell expression atlas linked with terms from the Cell Ontology.
examples:
- description: RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice
cells in RIKEN FANTOM5 project annotated using cell types from CL
url: https://www.ebi.ac.uk/gxa/experiments/E-MTAB-3578/Results
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/31665515
title: 'Expression Atlas update: from tissues to single cells'
type: annotation
user: https://www.ebi.ac.uk/gxa/home
- description: The National Human Genome Research Institute (NHGRI) launched a public
research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September
2003, to carry out a project to identify all functional elements in the human
genome sequence. The ENCODE DCC uses Uberon to annotate samples
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/25776021
title: Ontology application and use at the ENCODE DCC
seeAlso: https://doi.org/10.25504/FAIRsharing.v0hbjs
type: annotation
user: https://www.encodeproject.org/
- description: FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome
analyses with cell-type and tissue-level specificity.
examples:
- description: FANTOM5 samples annotated to neuron
url: http://fantom.gsc.riken.jp/5/sstar/CL:0000540
type: annotation
user: http://fantom5-collaboration.gsc.riken.jp/
- activity_status: active
build:
checkout: git clone https://github.com/luis-gonzalez-m/Collembola.git
path: .
system: git
contact:
email: [email protected]
github: luis-gonzalez-m
label: Luis González-Montaña
orcid: 0000-0002-9136-9932
dependencies:
- id: ro
description: 'CLAO is an ontology of anatomical terms employed in morphological
descriptions for the Class Collembola (Arthropoda: Hexapoda).'
domain: anatomy and development
homepage: https://github.com/luis-gonzalez-m/Collembola
id: clao
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/clao.owl
preferredPrefix: CLAO
products:
- id: clao.owl
ontology_purl: http://purl.obolibrary.org/obo/clao.owl
- id: clao.obo
ontology_purl: http://purl.obolibrary.org/obo/clao.obo
pull_request_added: 1337
repository: https://github.com/luis-gonzalez-m/Collembola
title: Collembola Anatomy Ontology
tracker: https://github.com/luis-gonzalez-m/Collembola/issues
- activity_status: active
contact:
email: [email protected]
github: zhengj2007
label: Jie Zheng
orcid: 0000-0002-2999-0103
dependencies:
- id: cl
- id: doid
- id: ncbitaxon
- id: uberon
description: An ontology to standardize and integrate cell line information and
to support computer-assisted reasoning.
domain: anatomy and development
homepage: https://github.com/CLO-Ontology/CLO
id: clo
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/clo.owl
preferredPrefix: CLO
products:
- id: clo.owl
ontology_purl: http://purl.obolibrary.org/obo/clo.owl
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/25852852
title: 'CLO: The Cell Line Ontology'
repository: https://github.com/CLO-Ontology/CLO
title: Cell Line Ontology
tracker: https://github.com/CLO-Ontology/CLO/issues
- activity_status: active
build:
checkout: git clone https://github.com/EBISPOT/clyh_ontology.git
path: .
system: git
contact:
email: [email protected]
github: L-Leclere
label: Lucas Leclere
orcid: 0000-0002-7440-0467
dependencies:
- id: iao