forked from OBOFoundry/OBOFoundry.github.io
-
Notifications
You must be signed in to change notification settings - Fork 0
/
ontologies.yml
8930 lines (8930 loc) · 325 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
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
review:
date: 2016
document:
label: PDF
link: https://drive.google.com/open?id=0B81h9ah4tAM_RnNTRUZnVGRyWXM
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
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
review:
date: 2010
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
browsers:
- label: DO
title: DO Browser
url: http://www.disease-ontology.org/
build:
infallible: 1
method: obo2owl
source_url: https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo
contact:
email: [email protected]
github: lschriml
label: Lynn Schriml
orcid: 0000-0001-8910-9851
depicted_by: http://www.disease-ontology.org/media/images/DO_logo.jpg
description: An ontology for describing the classification of human diseases organized
by etiology.
domain: health
homepage: http://www.disease-ontology.org
id: doid
in_foundry_order: 1
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/doid.owl
preferredPrefix: DOID
products:
- id: doid.owl
ontology_purl: http://purl.obolibrary.org/obo/doid.owl
title: Disease Ontology, OWL format. This file contains DO's is_a asserted hierarchy
plus equivalent axioms to other OBO Foundry ontologies.
- id: doid.obo
ontology_purl: http://purl.obolibrary.org/obo/doid.obo
title: Disease Ontology, OBO format. This file omits the equivalent axioms.
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/25348409
title: 'Disease Ontology 2015 update: an expanded and updated database of human
diseases for linking biomedical knowledge through disease data'
- id: https://www.ncbi.nlm.nih.gov/pubmed/34755882
title: The Human Disease Ontology 2022 update
repository: https://github.com/DiseaseOntology/HumanDiseaseOntology
review:
date: 2015
document:
label: PDF
link: https://drive.google.com/open?id=0B8vqEgF1N0NIZ082U2JETHlSTGs
tags:
- disease
taxon:
id: NCBITaxon:9606
label: Homo sapiens
title: Human Disease Ontology
tracker: https://github.com/DiseaseOntology/HumanDiseaseOntology/issues
twitter: diseaseontology
usages:
- description: Alliance of Genome Resources - MGD, RGD, SGD, FlyBase, WormBase,
ZFIN use DO
examples:
- description: Human diseases annotated to over 190,000 MOD genes, alleles, disease
models and human genes
url: https://www.alliancegenome.org/search?category=disease
- description: The landing page for Coronavirus Infectious Disease
url: https://www.alliancegenome.org/disease/DOID:0080599
user: https://www.alliancegenome.org
- description: MGI disease model annotations use DO
examples:
- description: physical disorder
url: http://www.informatics.jax.org/disease/DOID:0080015
user: http://www.informatics.jax.org/disease
- description: Immune Epitope Database
examples:
- description: Antibody and T cell epitopes associated with human diseases
url: https://www.iedb.org
user: https://www.iedb.org
- activity_status: active
browsers:
- label: AmiGO
title: Gene Ontology AmiGO 2 Browser
url: http://amigo.geneontology.org/amigo/term/GO:0008150#display-lineage-tab
contact:
email: [email protected]
github: suzialeksander
label: Suzi Aleksander
orcid: 0000-0001-6787-2901
dependencies:
- id: uberon
subset: go/extensions/uberon_import.owl
- id: cl
subset: go/extensions/cl_import.owl
- id: ncbitaxon
subset: go/extensions/ncbitaxon_import.owl
- id: ro
subset: go/extensions/ro_import.owl
- connects:
- id: nifstd
- id: go
description: Bridging axioms between nifstd and go
id: go/extensions/go-bridge-to-nifstd.owl
publications:
- id: http://www.ncbi.nlm.nih.gov/pubmed/24093723
title: 'The Gene Ontology (GO) Cellular Component Ontology: integration with
SAO (Subcellular Anatomy Ontology) and other recent developments.'
title: GO bridge to NIFSTD
type: BridgeOntology
depicted_by: http://geneontology.org/assets/go-logo-icon.mini.png
description: An ontology for describing the function of genes and gene products
domain: biological systems
homepage: http://geneontology.org/
id: go
in_foundry_order: 1
integration_server: http://build.berkeleybop.org/view/GO
label: GO
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/go.owl
preferredPrefix: GO
products:
- description: The main ontology in OWL. This is self contained and does not have
connections to other OBO ontologies
id: go.owl
ontology_purl: http://purl.obolibrary.org/obo/go.owl
page: http://geneontology.org/page/download-ontology
title: GO (OWL edition)
- description: Equivalent to go.owl, in obo format
id: go.obo
ontology_purl: http://purl.obolibrary.org/obo/go.obo
page: http://geneontology.org/page/download-ontology
title: GO (OBO Format edition)
- description: Equivalent to go.owl, in obograph json format
id: go.json
ontology_purl: http://purl.obolibrary.org/obo/go.json
page: https://github.com/geneontology/obographs/
title: GO (JSON edition)
- description: The main ontology plus axioms connecting to select external ontologies,
with subsets of those ontologies
id: go/extensions/go-plus.owl
ontology_purl: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
page: http://geneontology.org/page/download-ontology
title: GO-Plus
- description: The main ontology plus axioms connecting to select external ontologies,
excluding the external ontologies themselves
id: go/go-base.owl
ontology_purl: http://purl.obolibrary.org/obo/go/go-base.owl
page: http://geneontology.org/page/download-ontology
title: GO Base Module
- description: As go-plus.owl, in obographs json format
id: go/extensions/go-plus.json
ontology_purl: http://purl.obolibrary.org/obo/go/extensions/go-plus.json
page: https://github.com/geneontology/obographs/
title: GO-Plus
- description: Basic version of the GO, filtered such that the graph is guaranteed
to be acyclic and annotations can be propagated up the graph. The relations
included are is a, part of, regulates, negatively regulates and positively regulates.
This version excludes relationships that cross the 3 GO hierarchies.
id: go/go-basic.obo
ontology_purl: http://purl.obolibrary.org/obo/go/go-basic.obo
page: http://geneontology.org/page/download-ontology
title: GO-Basic, Filtered, for use with legacy tools
- description: As go-basic.obo, in json format
id: go/go-basic.json
ontology_purl: http://purl.obolibrary.org/obo/go/go-basic.json
page: http://geneontology.org/page/download-ontology
title: GO-Basic, Filtered, for use with legacy tools (JSON)
- description: Classes added to ncbitaxon for groupings such as prokaryotes
id: go/extensions/go-taxon-groupings.owl
ontology_purl: http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl
page: http://geneontology.org/page/download-ontology
title: GO Taxon Groupings
- description: Equivalent to go.owl, but released daily. Note the snapshot release
is not archived.
id: go/snapshot/go.owl
ontology_purl: http://purl.obolibrary.org/obo/go/snapshot/go.owl
page: http://geneontology.org/page/download-ontology
title: GO (OWL edition), daily snapshot release
- description: Equivalent to go.owl, but released daily. Note the snapshot release
is not archived.
id: go/snapshot/go.obo
ontology_purl: http://purl.obolibrary.org/obo/go/snapshot/go.obo
page: http://geneontology.org/page/download-ontology
title: GO (OBO Format edition), daily snapshot release
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/10802651
title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
Consortium'
- id: https://www.ncbi.nlm.nih.gov/pubmed/33290552
title: 'The Gene Ontology resource: enriching a GOld mine'
repository: https://github.com/geneontology/go-ontology
review:
date: 2010
tags:
- biology
taxon:
id: NCBITaxon:1
label: All life
title: Gene Ontology
tracker: https://github.com/geneontology/go-ontology/issues/
twitter: news4go
usages:
- description: The GO ontology is used by the GO consortium for functional annotation
of genes
examples:
- description: annotations to transmembrane transport
url: http://amigo.geneontology.org/amigo/term/GO:0055085
type: annotation
user: http://geneontology.org
- description: Uniprot uses GO to show the function of proteins
examples:
- description: functional annotations of human Sonic hedgehog protein
url: https://www.uniprot.org/uniprot/Q15465#function
type: annotation
user: https://www.uniprot.org
- description: Reactome annotates activities, pathways, and cellular localization
using GO
examples:
- description: protein tyrosine kinase activity of an EGFR complex
url: https://reactome.org/content/detail/R-HSA-177934
type: annotation
user: https://reactome.org
- description: The Alliance of Genome Resources uses GO for model organism gene
function annotation
examples:
- description: Functional summary of C elegans nsy-1 gene
url: https://www.alliancegenome.org/gene/WB:WBGene00003822#function---go-annotations
- description: Gene Ontology Causal Activity Models for C elegans nsy-1 gene
url: https://www.alliancegenome.org/gene/WB:WBGene00003822#pathways
type: annotation
user: https://www.alliancegenome.org
- description: Rhea uses GO to describe individual biochemical reactions
examples:
- description: Glutamine scyllo-inositol transaminase reaction and associated
GO term
url: https://www.rhea-db.org/rhea/22920
type: mapping
user: https://www.rhea-db.org
- activity_status: active
browsers:
- label: BioPortal
title: BioPortal Browser
url: http://bioportal.bioontology.org/ontologies/OBI?p=classes
build:
source_url: http://purl.obofoundry.org/obo/obi/repository/trunk/src/ontology/branches/
contact:
email: [email protected]
github: bpeters42
label: Bjoern Peters
orcid: 0000-0002-8457-6693
depicted_by: https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png
description: An integrated ontology for the description of life-science and clinical
investigations
domain: investigations
homepage: http://obi-ontology.org
id: obi
in_foundry_order: 1
integration_server: http://build.berkeleybop.org/job/build-obi/
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: http://groups.google.com/group/obi-users
ontology_purl: http://purl.obolibrary.org/obo/obi.owl
preferredPrefix: OBI
products:
- description: The full version of OBI in OWL format
id: obi.owl
ontology_purl: http://purl.obolibrary.org/obo/obi.owl
title: OBI
- description: The OBO-format version of OBI
id: obi.obo
ontology_purl: http://purl.obolibrary.org/obo/obi.obo
title: OBI in OBO
- description: A collection of important high-level terms and their relations from
OBI and other ontologies
id: obi/obi_core.owl
ontology_purl: http://purl.obolibrary.org/obo/obi/obi_core.owl
title: OBI Core
- description: Base module for OBI
id: obi/obi-base.owl
ontology_purl: http://purl.obolibrary.org/obo/obi/obi-base.owl
title: OBI Base module
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/27128319
title: The Ontology for Biomedical Investigations
repository: https://github.com/obi-ontology/obi
review:
date: 2013
document:
label: PDF
link: https://drive.google.com/open?id=0B8vqEgF1N0NIMFlSM3RvdUxGTnc
title: Ontology for Biomedical Investigations
tracker: http://purl.obolibrary.org/obo/obi/tracker
usages:
- description: The Immune Epitope Database (IEDB) is funded by NIAID that catalogs
experimental data on antibody and T cell epitopes studied in humans, non-human
primates, and other animal species in the context of infectious disease, allergy,
autoimmunity and transplantation.
examples:
- description: A specific assay curated in the IEDB using the OBI:1110180 '3H-thymidine
assay measuring epitope specific proliferation of T cells' ('3H-thymidine')
url: http://www.iedb.org/assay/1505273
user: https://www.iedb.org
- description: ENCODE is a comprehensive parts list of functional elements in the
human genome, including elements that act at the protein and RNA levels, and
regulatory elements that control cells and circumstances in which a gene is
active.
examples:
- description: A specific assay annotated in ENCODE using OBI:0000716 'ChiP-seq'
url: https://www.encodeproject.org/report/?type=Experiment&accession=ENCSR012KGU&accession=ENCSR560MXA&accession=ENCSR803FKU&accession=ENCSR216YPQ&accession=ENCSR115BCB&field=%40id&field=assay_term_name&field=assay_term_id
user: https://www.encodeproject.org/
- description: The NASA GeneLab data repository hosts space biology and space-related
datasets funded by multiple space agencies around the world.
examples:
- description: A specific assay annotated in NASA GeneLab using OBI:0001271 'RNA-seq
assay'
url: https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-464/
user: https://genelab-data.ndc.nasa.gov/genelab/projects
- description: The CFDE is providing a centralized metadata resource to allow search
across data coordination centers from multiple Common Fund programs.
examples:
- description: OBI is used in CFDE to captures types of experiments with assay
terms such as OBI:0003094 'fluorescence in-situ hybridization assay'
url: https://app.nih-cfde.org/chaise/recordset/#1/CFDE:assay_type@sort(nid)
user: https://app.nih-cfde.org/
- description: NIF is a dynamic inventory of Web-based neuroscience resources, data,
and tools accessible via any computer connected to the Internet.
examples:
- description: A specific OBI term used to autocomplete in NIF search OBI:0100026
'organism'
url: https://neuinfo.org/data/search?q=organism&l=organism#all
user: http://www.neuinfo.org
- activity_status: active
browsers:
- label: BioPortal
title: BioPortal Ontology Browser
url: https://bioportal.bioontology.org/ontologies/PATO
build:
infallible: 1
method: obo2owl
source_url: https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo
contact:
email: [email protected]
github: gkoutos
label: George Gkoutos
orcid: 0000-0002-2061-091X
description: An ontology of phenotypic qualities (properties, attributes or characteristics)
domain: phenotype
homepage: https://github.com/pato-ontology/pato/
id: pato
in_foundry_order: 1
jobs:
- id: https://travis-ci.org/pato-ontology/pato
type: travis-ci
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/pato.owl
preferredPrefix: PATO
products:
- id: pato.owl
ontology_purl: http://purl.obolibrary.org/obo/pato.owl
- id: pato.obo
ontology_purl: http://purl.obolibrary.org/obo/pato.obo
- id: pato.json
ontology_purl: http://purl.obolibrary.org/obo/pato.json
- description: Includes axioms linking to other ontologies, but no imports of those
ontologies
id: pato/pato-base.owl
ontology_purl: http://purl.obolibrary.org/obo/pato/pato-base.owl
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/28387809
title: 'The anatomy of phenotype ontologies: principles, properties and applications'
- id: https://www.ncbi.nlm.nih.gov/pubmed/15642100
title: Using ontologies to describe mouse phenotypes
repository: https://github.com/pato-ontology/pato
review:
date: 2010
title: Phenotype And Trait Ontology
tracker: https://github.com/pato-ontology/pato/issues
usages:
- description: PATO is used by the Human Phenotype Ontology (HPO) for logical definitions
of phenotypes that facilitate cross-species integration.
examples:
- description: An abnormality in a cellular process.
url: https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0011017&viewMode=All&siblings=false
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/30476213
title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
type: annotation
user: https://hpo.jax.org/app/
- activity_status: active
browsers:
- label: Planteome
title: Planteome browser
url: http://browser.planteome.org/amigo
build:
checkout: git clone https://github.com/Planteome/plant-ontology.git
infallible: 1
method: vcs
system: git
contact:
email: [email protected]
github: jaiswalp
label: Pankaj Jaiswal
orcid: 0000-0002-1005-8383
depicted_by: http://planteome.org/sites/default/files/garland_logo.PNG
description: The Plant Ontology is a structured vocabulary and database resource
that links plant anatomy, morphology and growth and development to plant genomics
data.
domain: anatomy and development
homepage: http://browser.planteome.org/amigo
id: po
in_foundry_order: 1
jobs:
- id: https://travis-ci.org/Planteome/plant-ontology
type: travis-ci
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/po.owl
page: https://github.com/Planteome/plant-ontology
preferredPrefix: PO
products:
- id: po.owl
ontology_purl: http://purl.obolibrary.org/obo/po.owl
- id: po.obo
ontology_purl: http://purl.obolibrary.org/obo/po.obo
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/23220694
title: The plant ontology as a tool for comparative plant anatomy and genomic
analyses.
- id: https://www.ncbi.nlm.nih.gov/pubmed/29186578
title: 'The Planteome database: an integrated resource for reference ontologies,
plant genomics and phenomics.'
repository: https://github.com/Planteome/plant-ontology
review:
date: 2013
document:
label: PDF
link: https://drive.google.com/open?id=0B8vqEgF1N0NIV1o0N21UOHlLSmc
taxon:
id: NCBITaxon:33090
label: Viridiplantae
title: Plant Ontology
tracker: https://github.com/Planteome/plant-ontology/issues
twitter: planteome
usages:
- description: Planteome uses PO to describe location of tissue expression for genes
in viridiplantae
examples:
- description: Genes and proteins annotate to leaf
url: http://browser.planteome.org/amigo/term/PO:0025034
user: http://planteome.org/
- description: Maize CELL genomics DB uses PO to annotate images
examples:
- description: LhG4 Promoter Drivers
url: http://maize.jcvi.org/cellgenomics/geneDB_list.php?filter=3
user: http://maize.jcvi.org/
- description: MaizeGDB uses PO for annotation of genes
examples:
- description: Introduced in gene model set 5b in assembly version RefGen_v2.
url: http://maizegdb.org/gene_center/gene/GRMZM5G863962
user: http://maizegdb.org/
- description: Gramene uses PO for the annotation of plant genes
examples:
- description: Gramene annotations to leaf from Arabidopsis
url: http://archive.gramene.org/db/ontology/search?id=PO:0025034
user: http://gramene.org/
- activity_status: active
browsers:
- label: BioPortal
title: BioPortal Browser
url: http://bioportal.bioontology.org/ontologies/PR?p=classes&conceptid=http://purl.obolibrary.org/obo/PR_000000001
- label: PRO
title: PRO Home
url: http://proconsortium.org
build:
infallible: 0
method: obo2owl
oort_args: --no-reasoner
source_url: https://proconsortium.org/download/current/pro_nonreasoned.obo
contact:
email: [email protected]
github: nataled
label: Darren Natale
orcid: 0000-0001-5809-9523
depicted_by: https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png
description: An ontological representation of protein-related entities
documentation: https://proconsortium.org/download/current/pro_readme.txt
domain: chemistry and biochemistry
homepage: http://proconsortium.org
id: pr
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/
ontology_purl: http://purl.obolibrary.org/obo/pr.owl
preferredPrefix: PR
products:
- description: PRO after reasoning has been applied, OWL format.
id: pr.owl
ontology_purl: http://purl.obolibrary.org/obo/pr.owl
title: pro_reasoned.owl
- description: PRO after reasoning has been applied, OBO format.
id: pr.obo
ontology_purl: http://purl.obolibrary.org/obo/pr.obo
title: pro_reasoned.obo
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/27899649
title: 'Protein Ontology (PRO): enhancing and scaling up the representation of
protein entities'
repository: https://github.com/PROconsortium/PRoteinOntology
review:
date: 2010
tags:
- proteins
title: PRotein Ontology (PRO)
tracker: https://github.com/PROconsortium/PRoteinOntology/issues
usages:
- description: Colorado Richly Annotated Full-Text (CRAFT) Corpus; PRO is used for
entity tagging and annotation
examples:
- description: Tagged entities (requires download)
url: https://github.com/UCDenver-ccp/CRAFT/releases/tag/v4.0.1
user: https://github.com/UCDenver-ccp/CRAFT
- description: Cell Ontology is a structured controlled vocabulary for cell types
in animals; PRO is used for cell type definitions
examples:
- description: A B cell that is CD19-positive (uses the PRO term for non-species-specific
CD19 molecule, PR:000001002)
url: http://purl.obolibrary.org/obo/CL_0001201
user: http://www.obofoundry.org/ontology/cl.html
- activity_status: active
build:
infallible: 0
method: obo2owl
source_url: https://raw.githubusercontent.com/xenopus-anatomy/xao/master/xenopus_anatomy.obo
contact:
email: [email protected]
github: seger
label: Erik Segerdell
orcid: 0000-0002-9611-1279
description: XAO represents the anatomy and development of the African frogs Xenopus
laevis and tropicalis.
domain: anatomy and development
homepage: http://www.xenbase.org/anatomy/xao.do?method=display
id: xao
in_foundry_order: 1
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/xao.owl
preferredPrefix: XAO
products:
- id: xao.owl
ontology_purl: http://purl.obolibrary.org/obo/xao.owl
- id: xao.obo
ontology_purl: http://purl.obolibrary.org/obo/xao.obo
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/18817563
title: An ontology for Xenopus anatomy and development.
- id: https://www.ncbi.nlm.nih.gov/pubmed/24139024
title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins
more accurate annotation of gene expression and queries on Xenbase.'
repository: https://github.com/xenopus-anatomy/xao
review:
date: 2010
taxon:
id: NCBITaxon:8353
label: Xenopus
title: Xenopus Anatomy Ontology
tracker: https://github.com/xenopus-anatomy/xao/issues
usages:
- description: Xenbase uses XAO to annotate gene expression.
examples:
- description: Xenopus genes expressed in the pronephric kidney.
url: http://www.xenbase.org/anatomy/showanatomy.do?method=displayAnatomySummary&anatomyId=463
user: http://www.xenbase.org
- activity_status: active
build:
infallible: 1
method: obo2owl
notes: may be ready to switch to vcs soon
source_url: https://raw.githubusercontent.com/cerivs/zebrafish-anatomical-ontology/master/src/zebrafish_anatomy.obo
contact:
email: [email protected]
github: cerivs
label: Ceri Van Slyke
orcid: 0000-0002-2244-7917
description: A structured controlled vocabulary of the anatomy and development of
the Zebrafish
domain: anatomy and development
homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
id: zfa
in_foundry_order: 1
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/zfa.owl
preferredPrefix: ZFA
products:
- id: zfa.owl
ontology_purl: http://purl.obolibrary.org/obo/zfa.owl
- id: zfa.obo
ontology_purl: http://purl.obolibrary.org/obo/zfa.obo
publications:
- id: https://www.ncbi.nlm.nih.gov/pubmed/24568621
title: 'The zebrafish anatomy and stage ontologies: representing the anatomy and
development of Danio rerio.'
repository: https://github.com/cerivs/zebrafish-anatomical-ontology
review:
date: 2010
taxon:
id: NCBITaxon:7954
label: Danio
title: Zebrafish anatomy and development ontology
tracker: https://github.com/cerivs/zebrafish-anatomical-ontology/issues
usages:
- description: ZFIN uses ZFA to annotate gene expression and phenotype
examples:
- description: zebrafish genes expressed in hindbrain and genotypes with hindbrain
phenotype
url: http://zfin.org/ZFA:0000029
user: http://zfin.org
- activity_status: active
build:
checkout: git clone https://github.com/AgriculturalSemantics/agro.git
path: .
system: git
contact:
email: [email protected]
github: marieALaporte
label: Marie-Angélique Laporte
orcid: 0000-0002-8461-9745
dependencies:
- id: envo
- id: go
- id: foodon
- id: ncbitaxon
- id: pato
- id: peco
- id: po
- id: to
- id: ro
- id: bfo
- id: iao
- id: obi
- 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
jobs:
- id: https://travis-ci.org/AgriculturalSemantics/agro
type: travis-ci
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 relavent 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: ro
- id: uberon
- id: caro
- id: pato
- id: bfo
- id: bspo
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: Defines terms and relations necessary for interoperation between epidemic
models and public health application software that interface with these models
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
- 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
repository: https://github.com/BiodiversityOntologies/bco
tags:
- biodiversity collections
title: Biological Collections Ontology
tracker: https://github.com/BiodiversityOntologies/bco/issues
- activity_status: active
build: