forked from OBOFoundry/OBOFoundry.github.io
-
Notifications
You must be signed in to change notification settings - Fork 0
/
ontologies.yml
2409 lines (2409 loc) · 117 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:
- contact: {email: David Blackburn, label: david.c.blackburn@gmail.com}
homepage: http://github.com/seger/aao
id: aao
is_obsolete: true
layout: ontology_detail
replaced_by: uberon
taxon: {id: 'NCBITaxon:8292', label: Amphibia}
title: Amphibian gross anatomy
- contact: {email: Animal Diversity Web technical staff, label: adw_geeks@umich.edu}
homepage: http://www.animaldiversity.org
id: adw
is_obsolete: true
layout: ontology_detail
title: Animal natural history and life history
- build: {checkout: 'git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git',
method: vcs, path: src/ontology, system: git}
contact: {email: J.Bard@ed.ac.uk, label: Jonathan Bard}
description: AEO is an ontology of anatomical structures that expands CARO, the
Common Anatomy Reference Ontology
domain: anatomy
homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
id: aeo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/aeo.owl
products:
- {id: aeo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/aeo.owl'}
title: Anatomical Entity Ontology
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/aero.owl'}
contact: {email: mcourtot@gmail.com, label: Melanie Courtot}
description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at
supporting clinicians at the time of data entry, increasing quality and accuracy
of reported adverse events
domain: health
homepage: http://purl.obolibrary.org/obo/aero
id: aero
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/aero.owl
products:
- {id: aero.owl, ontology_purl: 'http://purl.obolibrary.org/obo/aero.owl'}
title: Adverse Event Reporting Ontology
- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/ascomycete_phenotype.obo'}
contact: {email: maria@genome.stanford.edu, label: Maria Costanza}
description: A structured controlled vocabulary for the phenotypes of Ascomycete
fungi
domain: phenotype
homepage: http://www.yeastgenome.org/
id: apo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/apo.owl
products:
- {id: apo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/apo.owl'}
taxon: {id: 'NCBITaxon:4890', label: Ascomycota}
title: Ascomycete phenotype ontology
- contact: {email: David Blackburn, label: david.c.blackburn@gmail.com}
homepage: http://www.amphibanat.org
id: ato
is_obsolete: true
layout: ontology_detail
taxon: {id: 'NCBITaxon:8292', label: Amphibia}
title: Amphibian taxonomy
- contact: {email: jiezheng@upenn.edu, label: Jie Zheng}
description: An application ontology built for beta cell genomics studies.
homepage: https://github.com/obi-bcgo/bcgo
id: bcgo
in_foundry: false
layout: ontology_detail
license: {label: CC-BY, 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/bcgo.owl
products:
- {id: bcgo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bcgo.owl'}
title: Beta Cell Genomics Ontology
tracker: https://github.com/obi-bcgo/bcgo/issues
- contact: {email: rwalls2008@gmail.com, label: Ramona Walls}
description: An ontology to support the interoperability of biodiversity data, including
data on museum collections, environmental/metagenomic samples, and ecological
surveys.
homepage: https://github.com/tucotuco/bco
id: bco
in_foundry: false
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/bco.owl
products:
- {id: bco.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bco.owl'}
title: Biological Collections Ontology
tracker: https://github.com/tucotuco/bco/issues
- browsers:
- {label: BioPortal, title: BioPortal Browser, url: 'http://bioportal.bioontology.org/ontologies/BFO?p=classes'}
contact: {email: phismith@buffalo.edu, label: Barry Smith}
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
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
mailing_list: https://groups.google.com/forum/#!forum/bfo-discuss
ontology_purl: http://purl.obolibrary.org/obo/bfo.owl
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'}
title: Basic Formal Ontology
tracker: https://github.com/BFO-ontology/BFO/issues
- build: {method: obo2owl, source_url: 'http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo'}
contact: {email: henrich@embl.de, label: Thorsten Heinrich}
domain: anatomy
homepage: http://4dx.embl.de/4DXpress
id: bila
is_obsolete: true
layout: ontology_detail
products:
- {id: bila.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bila.owl'}
replaced_by: uberon
taxon: {id: 'NCBITaxon:33213', label: Bilateria}
title: Bilateria anatomy
- contact: {email: Vivian Lee, label: vlee@ebi.ac.uk}
homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html
id: bootstrep
is_obsolete: true
layout: ontology_detail
replaced_by: molecular_function
title: Gene Regulation Ontology
- build: {checkout: 'git clone https://github.com/obophenotype/biological-spatial-ontology.git',
infallible: 1, method: vcs, path: src/ontology, system: git}
contact: {email: cjmungall@lbl.gov, label: Chris Mungall}
description: An ontology for respresenting spatial concepts, anatomical axes, gradients,
regions, planes, sides, and surfaces
domain: anatomy
homepage: https://github.com/obophenotype/biological-spatial-ontology
id: bspo
layout: ontology_detail
license: {label: CC-BY, 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
products:
- {id: bspo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bspo.owl'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/25140222', title: 'Nose to tail, roots
to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial
Ontology.'}
title: Biological Spatial Ontology
tracker: https://github.com/obophenotype/biological-spatial-ontology/issues
- build: {method: obo2owl, source_url: 'http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO'}
contact: {email: a.chang@tu-bs.de, label: Antje Chang}
description: A structured controlled vocabulary for the source of an enzyme comprising
tissues, cell lines, cell types and cell cultures.
domain: anatomy
homepage: http://www.brenda-enzymes.info
id: bto
layout: ontology_detail
license: {alert: Restricted, label: BRENDA license, url: 'http://www.brenda-enzymes.org/copy.php'}
ontology_purl: http://purl.obolibrary.org/obo/bto.owl
page: https://en.wikipedia.org/wiki/BRENDA_tissue_ontology
products:
- {id: bto.owl, ontology_purl: 'http://purl.obolibrary.org/obo/bto.owl'}
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'}
title: BRENDA tissue / enzyme source
- 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: haendel@ohsu.edu, label: Melissa Haendel}
description: An upper level ontology to facilitate interoperability between existing
anatomy ontologies for different species
domain: anatomy
homepage: https://github.com/obophenotype/caro/
id: caro
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/caro.owl
products:
- {id: caro.owl, ontology_purl: 'http://purl.obolibrary.org/obo/caro.owl'}
title: Common Anatomy Reference Ontology
tracker: https://github.com/obophenotype/caro/issues
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/cdao.owl'}
contact: {email: balhoff@nescent.org, label: Jim Balhoff}
description: a formalization of concepts and relations relevant to evolutionary
comparative analysis
homepage: http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page
id: cdao
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/cdao.owl
products:
- {id: cdao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/cdao.owl'}
title: Comparative Data Analysis Ontology
- build: {checkout: 'git clone https://github.com/obophenotype/cephalopod-ontology.git',
method: vcs, path: src/ontology, system: git}
contact: {email: cjmungall@lbl.gov, label: Chris Mungall}
description: An anatomical and developmental ontology for cephalopods
domain: anatomy
homepage: https://github.com/obophenotype/cephalopod-ontology
id: ceph
layout: ontology_detail
license: {label: CC-BY, 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/ceph.owl
products:
- {id: ceph.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ceph.owl'}
taxon: {id: 'NCBITaxon:6605', label: Cephalopod}
title: Cephalopod Ontology
tracker: https://github.com/obophenotype/cephalopod-ontology/issues
- alternatePrefix: ChEBI
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: archive, path: archive/main, source_url: 'http://build.berkeleybop.org/job/build-chebi/lastSuccessfulBuild/artifact/*zip*/archive.zip'}
contact: {email: hastings@ebi.ac.uk, label: Janna Hastings}
description: A structured classification of chemical compounds of biological relevance.
domain: biochemistry
homepage: http://www.ebi.ac.uk/chebi
id: chebi
in_foundry_order: 1
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/chebi.owl
page: http://www.ebi.ac.uk/chebi/init.do?toolBarForward=userManual
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'}
title: Chemical entities of biological interest
tracker: https://sourceforge.net/p/chebi/curator-requests/
twitter: chebit
- build: {method: owl2obo, source_url: 'http://semanticchemistry.googlecode.com/svn/trunk/ontology/cheminf.owl'}
contact: {email: hastings@ebi.ac.uk, label: Janna Hastings}
description: Includes terms for the descriptors commonly used in cheminformatics
software applications and the algorithms which generate them.
domain: biochemistry
homepage: http://code.google.com/p/semanticchemistry/
id: cheminf
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/cheminf.owl
products:
- {id: cheminf.owl, ontology_purl: 'http://purl.obolibrary.org/obo/cheminf.owl'}
title: Chemical Information Ontology
- contact: {email: batchelorc@rsc.org, label: Colin Batchelor}
description: CHMO, the chemical methods ontology, describes methods used to
domain: health
homepage: http://code.google.com/p/rsc-cmo/
id: chmo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/chmo.owl
products:
- {id: chmo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/chmo.owl'}
title: Chemical Methods Ontology
tracker: http://code.google.com/p/rsc-cmo/issues/list
- build: {checkout: 'git clone https://github.com/obophenotype/cell-ontology.git',
email_cc: cl_edit@googlegroups.com, infallible: 1, method: vcs, system: git}
canonical: cl.owl
dependencies:
- {id: uberon}
- {id: go}
- {id: ro}
- {id: chebi}
- {id: pato}
description: The Cell Ontology is a structured controlled vocabulary for cell types
in animals.
domain: cells
id: cl
integration_server: http://build.berkeleybop.org/job/build-cl/
label: Cell Ontology
layout: ontology_detail
license: {label: CC-BY, logo: 'http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png',
url: 'http://creativecommons.org/licenses/by/3.0/'}
mailing_list: https://lists.sourceforge.net/lists/listinfo/obo-cell-type
ontology_purl: http://purl.obolibrary.org/obo/cl.owl
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]
- {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}
taxon: {id: 'NCBITaxon:33208', label: Metazoa}
termgenie: http://cl.termgenie.org
title: Cell Ontology
tracker: https://github.com/obophenotype/cell-ontology/issues
- build: {checkout: 'svn --ignore-externals co http://clo-ontology.googlecode.com/svn/trunk/src/ontology',
method: vcs, post_processing_command: owltools --use-catalog clo.owl --merge-imports-closure
--ni -o -f obo --no-check clo.obo, system: svn}
contact: {email: Sirarat.Sarntivijai@fda.hhs.gov, label: Sirarat Sarntivijai}
dependencies:
- {id: uberon}
- {id: cl}
- {id: doid}
- {id: ncbitaxon}
description: An ontology to standardize and integrate cell line information and
to support computer-assisted reasoning.
homepage: http://www.clo-ontology.org
id: clo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/clo.owl
products:
- {id: clo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/clo.owl'}
title: Cell Line Ontology
- contact: {email: Michael Grove, label: grovmi@ohsu.edu}
homepage: https://code.google.com/p/craniomaxillofacial-ontology/
id: cmf
layout: ontology_detail
title: CranioMaxilloFacial ontology
- browsers:
- {label: RGD, title: RGD Ontology Browser, url: 'http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000'}
build: {method: obo2owl, source_url: 'ftp://rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo'}
contact: {email: shimoyama@mcw.edu, label: Mary Shimoyama}
description: Morphological and physiological measurement records generated from
clinical and model organism research and health programs.
domain: clinical
homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
id: cmo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/cmo.owl
page: ftp://rgd.mcw.edu/pub/ontology/clinical_measurement/
products:
- {id: cmo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/cmo.owl'}
- {id: cmo.obo, ontology_purl: 'http://purl.obolibrary.org/obo/cmo.obo'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22654893', title: Three ontologies to
define phenotype measurement data.}
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24103152', title: 'The clinical measurement,
measurement method and experimental condition ontologies: expansion, improvements
and new applications.'}
title: Clinical measurement ontology
- build: {checkout: 'git clone https://github.com/obophenotype/ctenophore-ontology.git',
method: vcs, path: src/ontology, system: git}
contact: {email: cjmungall@lbl.gov, label: Chris Mungall}
dependencies:
- {id: uberon}
- {id: ro}
description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
domain: anatomy
homepage: https://github.com/obophenotype/ctenophore-ontology
id: cteno
layout: ontology_detail
license: {label: CC-BY, 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/cteno.owl
products:
- {id: cteno.owl, ontology_purl: 'http://purl.obolibrary.org/obo/cteno.owl'}
taxon: {id: 'NCBITaxon:10197', label: Ctenophore}
title: Ctenophore Ontology
tracker: https://github.com/obophenotype/ctenophore-ontology/issues
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/cvdo.owl'}
contact: {email: adrien.barton@gmail.com, label: Adrien Barton}
description: An ontology to describe entities related to cardiovascular diseases
domain: health
homepage: https://code.google.com/p/cvdo/
id: cvdo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/cvdo.owl
products:
- {id: cvdo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/cvdo.owl'}
title: Cardiovascular Disease Ontology
tracker: https://code.google.com/p/cvdo/issues/list
- contact: {email: Lindsay Cowell, label: Lindsay.Cowell@utsouthwestern.edu}
homepage: http://www.dukeontologygroup.org/Projects.html
id: dc_cl
is_obsolete: true
layout: ontology_detail
replaced_by: cl
taxon: {id: all, label: null}
title: Dendritic cell
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_anatomy.obo'}
contact: {email: r-chisholm@northwestern.edu, label: Rex Chisholm}
description: A structured controlled vocabulary of the anatomy of the slime-mould
<i>Dictyostelium discoideum</i>.
domain: anatomy
homepage: http://dictybase.org/
id: ddanat
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/ddanat.owl
products:
- {id: ddanat.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ddanat.owl'}
taxon: {id: 'NCBITaxon:44689', label: Dictyostelium discoideum}
title: Dictyostelium discoideum anatomy
tracker: http://sourceforge.net/tracker/?group_id=76834&atid=974664
twitter: dictybase
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_phenotypes.obo'}
contact: {email: r-chisholm@northwestern.edu, label: Rex Chisholm}
description: A structured controlled vocabulary of phenotypes of the slime-mould
<i>Dictyostelium discoideum</i>.
domain: anatomy
homepage: http://dictybase.org/
id: ddpheno
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/ddpheno.owl
products:
- {id: ddpheno.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ddpheno.owl'}
taxon: {id: 'NCBITaxon:44689', label: Dictyostelium discoideum}
title: Dictyostelium discoideum phenotype
twitter: dictybase
- contact: {email: mbrochhausen@gmail.com, label: Mathias Brochhausen}
description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
Evidence Ontology
homepage: https://github.com/DIDEO/DIDEO
id: dideo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/dideo.owl
products:
- {id: dideo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/dideo.owl'}
title: Drug Interaction and Evidence Ontology
tracker: https://github.com/DIDEO/DIDEO/issues
- contact: {email: Maria Herrero, label: mhzazo@pa.uc3m.es}
homepage: https://code.google.com/p/dinto/
id: dinto
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/dinto.owl
products:
- {id: dinto.owl, ontology_purl: 'http://purl.obolibrary.org/obo/dinto.owl'}
title: The Drug-drug Interaction Ontology
- browsers:
- {label: DO, title: DO Browser, url: 'http://www.disease-ontology.org/'}
- {label: Monarch, title: Monarch Phenotype Page, url: 'http://monarchinitiative.org/phenotype/DOID:4'}
build: {infallible: 1, method: obo2owl, source_url: 'http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo?format=raw'}
contact: {email: lynn.schriml@gmail.com, label: Lynn Schriml}
description: An ontology for describing the classification of human diseases organized
by etiology.
domain: disease
facebook: https://www.facebook.com/diseaseontology
homepage: http://diseaseontology.sourceforge.net/
id: doid
in_foundry_order: 1
layout: ontology_detail
license: {label: CC-BY, 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/doid.owl
page: http://diseaseontology.sourceforge.net/
products:
- {id: doid.owl, ontology_purl: 'http://purl.obolibrary.org/obo/doid.owl'}
- {id: doid.obo, ontology_purl: 'http://purl.obolibrary.org/obo/doid.obo'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/?term=25348409', title: 'Disease Ontology
2015 update: an expanded and updated database of human diseases for linking
biomedical knowledge through disease data'}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Human Disease Ontology
tracker: http://sourceforge.net/tracker/?func=add&group_id=79168&atid=555739
twitter: diseaseontology
- browsers:
- {label: FB, title: FlyBase Browser, url: 'http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000347'}
build: {infallible: 0, method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/fbcv/dpo.owl'}
contact: {email: mmc46@gen.cam.ac.uk, label: Marta Costa}
description: An ontology of commonly encountered and/or high level Drosophila phenotypes.
domain: phenotype
homepage: http://purl.obolibrary.org/obo/fbcv
id: dpo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/dpo.owl
preferredPrefix: FBcv
products:
- {id: fbcv/dpo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbcv/dpo.owl'}
publications:
- {id: 'http://dx.doi.org/10.1186/2041-1480-4-30', title: The Drosophila phenotype
ontology.}
taxon: {id: 'NCBITaxon:7227', label: Drosophila}
title: Drosophila Phenotype Ontology
tracker: http://purl.obolibrary.org/obo/fbcv/tracker
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/dron.owl'}
contact: {email: hoganwr@gmail.com, label: William Hogan}
description: An ontology to support comparative effectiveness researchers studying
claims data.
domain: health
homepage: https://bitbucket.org/uamsdbmi/dron.git
id: dron
layout: ontology_detail
license: {label: CC-BY, 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/dron.owl
products:
- {id: dron.owl, ontology_purl: 'http://purl.obolibrary.org/obo/dron.owl'}
title: The Drug Ontology
tracker: https://ontology.atlassian.net/browse/DRON
- build: {infallible: 1, method: obo2owl, notes: switch to vcs, source_url: 'https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/eco.obo'}
contact: {email: MChibucos@som.umaryland.edu, label: 'Chibucos, Marcus'}
description: An ontology for experimental and other evidence statements.
domain: experiments
funded_by: ['http://www.nsf.gov/awardsearch/showAward?AWD_ID=1458400']
homepage: https://github.com/evidenceontology/evidenceontology/
id: eco
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/eco.owl
products:
- {id: eco.owl, ontology_purl: 'http://purl.obolibrary.org/obo/eco.owl'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/25052702', title: Standardized description
of scientific evidence using the Evidence Ontology (ECO)}
title: Evidence codes
tracker: https://github.com/evidenceontology/evidenceontology/issues
- contact: {email: Jonathan Bard, label: J.Bard@ed.ac.uk}
homepage: http://genex.hgu.mrc.ac.uk/
id: ehda
is_obsolete: true
layout: ontology_detail
replaced_by: ehdaa2
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Human developmental anatomy, timed version
- contact: {email: Jonathan Bard, label: J.Bard@ed.ac.uk}
homepage: null
id: ehdaa
is_obsolete: true
layout: ontology_detail
replaced_by: ehdaa2
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Human developmental anatomy, abstract version
- build: {checkout: 'git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git',
method: vcs, path: src/ontology, system: git}
contact: {email: J.Bard@ed.ac.uk, label: Jonathan Bard}
dependencies:
- {id: aeo}
- {id: caro}
- {id: cl}
description: A structured controlled vocabulary of stage-specific anatomical structures
of the developing human.
domain: anatomy
homepage: http://genex.hgu.mrc.ac.uk/
id: ehdaa2
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/ehdaa2.owl
products:
- {id: ehdaa2.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ehdaa2.owl'}
- {id: ehdaa2.obo, ontology_purl: 'http://purl.obolibrary.org/obo/ehdaa2.obo'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22973865', title: A new ontology (structured
hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages
1-20).}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Human developmental anatomy, abstract
tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
- build: {method: obo2owl, notes: new url soon, source_url: 'ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo'}
contact: {email: Terry.Hayamizu@jax.org, label: Terry Hayamizu}
description: A structured controlled vocabulary of stage-specific anatomical structures
of the mouse (Mus).
domain: anatomy
homepage: http://emouseatlas.org
id: emap
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/emap.owl
page: http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page
products:
- {id: emap.owl, ontology_purl: 'http://purl.obolibrary.org/obo/emap.owl'}
taxon: {id: 'NCBITaxon:10088', label: Mus}
title: Mouse gross anatomy and development, timed
used_by:
- {label: GXD, url: 'https://www.biosharing.org/biodbcore-000659'}
- build: {method: obo2owl, notes: new url soon, source_url: 'ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo'}
contact: {email: Terry.Hayamizu@jax.org, label: Terry Hayamizu}
description: Abstract (i.e. non-stage specific) stage-specific anatomical structures
of the mouse.
domain: anatomy
homepage: http://emouseatlas.org
id: emapa
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/emapa.owl
page: http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page
products:
- {id: emap.owl, ontology_purl: 'http://purl.obolibrary.org/obo/emap.owl'}
taxon: {id: 'NCBITaxon:10088', label: Mus}
title: Mouse gross anatomy and development, timed
used_by:
- {label: GXD, url: 'https://www.biosharing.org/biodbcore-000659'}
- build: {checkout: 'git clone https://github.com/EnvironmentOntology/envo.git', email_cc: cjmungall@lbl.gov,
infallible: 1, method: vcs, path: ., system: git}
contact: {email: p.buttigieg@googlemail.com, label: Pier Luigi Buttigieg}
dependencies:
- {id: uberon}
- {id: pco}
- {id: ro}
- {id: chebi}
- {id: ncbitaxon}
description: Ontology of environmental features and habitats
domain: environment
homepage: http://environmentontology.org/
id: envo
layout: ontology_detail
license: {label: CC-BY, 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/envo.owl
page: https://github.com/EnvironmentOntology/envo
products:
- {id: envo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/envo.owl'}
publications:
- {id: 'http://www.dx.doi.org/10.1186/2041-1480-4-43', title: 'The environment ontology:
contextualising biological and biomedical entities'}
title: Environment Ontology
tracker: https://github.com/EnvironmentOntology/envo/issues/
- build: {method: obo2owl, source_url: 'https://github.com/Planteome/plant-environment-ontology/blob/master/plant-environment-ontology.obo.owl'}
contact: {email: jaiswalp@science.oregonstate.edu, label: Pankaj Jaiswal}
description: "A structured, controlled vocabulary which \u2260\u2260describes the\
\ treatments, growing conditions, and/or study types used in various types of\
\ plant biology experiments."
domain: environment
homepage: http://planteome.org/
id: eo
layout: ontology_detail
license: {label: CC-BY, url: 'https://creativecommons.org/licenses/by/3.0/'}
ontology_purl: http://purl.obolibrary.org/obo/eo.owl
page: http://planteome.org/amigo/cgi-bin/crop_amigo/term_details?term=EO:0007359&session_id=815amigo1442021959
products:
- {id: eo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/eo.owl'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/22847540', title: Ontologies as integrative
tools for plant science.}
title: Plant Environment Ontology
tracker: https://github.com/Planteome/plant-environment-ontology/issues
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/epo.owl'}
description: An ontology designed to support the semantic annotation of epidemiology
resources
homepage: https://code.google.com/p/epidemiology-ontology/
id: epo
in_foundry: false
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/epo.owl
products:
- {id: epo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/epo.owl'}
title: Epidemiology Ontology
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/ero.owl'}
contact: {email: carlotorniai@gmail.com, label: Carlo Torniai}
description: An ontology of research resources such as instruments. protocols, reagents,
animal models and biospecimens.
documentation: http://code.google.com/p/eagle-i/wiki/Documentation
domain: resources
homepage: http://code.google.com/p/eagle-i/
id: ero
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/ero.owl
products:
- {id: ero.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ero.owl'}
title: eagle-i resource ontology
tracker: http://code.google.com/p/eagle-i/issues/list
- contact: {email: eVOC mailing list, label: evoc@sanbi.ac.za}
homepage: http://www.evocontology.org/
id: ev
is_obsolete: true
layout: ontology_detail
title: eVOC (Expressed Sequence Annotation for Humans)
- build: {method: obo2owl, source_url: 'http://ctdbase.org/reports/CTD_exposure_ontology.obo'}
description: Vocabularies for describing exposure data to inform understanding of
environmental health.
domain: health
homepage: http://ctdbase.org/downloads/#exposures
id: exo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/exo.owl
page: http://ctdbase.org/downloads/#exposures
products:
- {id: exo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/exo.owl'}
title: Exposure ontology
- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/fungi/fungal_anatomy.obo'}
contact: {email: maria@genome.stanford.edu, label: Maria Costanzo}
description: A structured controlled vocabulary for the anatomy of fungi.
domain: anatomy
homepage: http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/
id: fao
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/fao.owl
page: http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/#description
products:
- {id: fao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fao.owl'}
taxon: {id: 'NCBITaxon:4751', label: Fungal}
title: Fungal gross anatomy
- build: {method: obo2owl, source_url: 'https://raw.githubusercontent.com/dosumis/fbbi/master/src/ontology/fbbi.obo'}
contact: {email: dorloff@ncmir.ucsd.edu, label: David Orloff}
description: A structured controlled vocabulary of sample preparation, visualization
and imaging methods used in biomedical research.
domain: experiments
homepage: http://cellimagelibrary.org/
id: fbbi
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/fbbi.owl
products:
- {id: fbbi.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbbi.owl'}
title: Biological imaging methods
- browsers:
- {label: FB, title: FlyBase Browser, url: 'http://flybase.org/.bin/cvreport.html?cvterm=FBbt:10000000'}
- {label: VFB, title: Virtual Fly Brain, url: 'http://www.virtualflybrain.org/site/stacks/index.htm?add=FBbt:00007401'}
- {label: BioPortal, title: BioPortal Browser, url: 'http://bioportal.bioontology.org/ontologies/FB-BT?p=classes'}
build: {infallible: 1, method: owl2obo, source_url: 'http://svn.code.sf.net/p/fbbtdv/code/fbbt/releases/fbbt.owl'}
contact: {email: mmc46@gen.cam.ac.uk, label: Marta Costa}
description: An ontology representing the gross anatomy of Drosophila melanogaster.
domain: anatomy
homepage: http://purl.obolibrary.org/obo/fbbt
id: fbbt
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/fbbt.owl
preferredPrefix: FBbt
products:
- {id: fbbt.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbbt.owl'}
- {id: fbbt/fbbt-simple.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbbt/fbbt-simple.owl'}
- {id: fbbt/fbbt-simple.obo, ontology_purl: 'http://purl.obolibrary.org/obo/fbbt/fbbt-simple.obo'}
publications:
- {id: 'http://dx.doi.org/10.1186/2041-1480-4-32', title: 'The Drosophila anatomy
ontology. [Journal of Biomedical Semantics'}
- {id: 'http://dx.doi.org/10.1093/bioinformatics/bts113', title: A strategy for
building neuroanatomy ontologies}
- {id: 'http://dx.doi.org/10.1093/bioinformatics/btr677', title: The Virtual Fly
Brain Browser and Query Interface}
- {id: 'http://dx.doi.org/10.1093/nar/gkj068', title: 'FlyBase: anatomical data,
images and queries'}
taxon: {id: 'NCBITaxon:7227', label: Drosophila}
title: Drosophila gross anatomy
tracker: http://purl.obolibrary.org/obo/fbbt/tracker
- browsers:
- {label: FB, title: FlyBase Browser, url: 'http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000013'}
build: {method: obo2owl, source_url: 'http://sourceforge.net/p/fbcv/code-0/HEAD/tree/src/trunk/ontologies/fbcv-edit.obo?format=raw'}
contact: {email: mmc46@gen.cam.ac.uk, label: Marta Costa}
description: A structured controlled vocabulary used for various aspects of annotation
by FlyBase.
domain: null
homepage: http://purl.obolibrary.org/obo/fbcv
id: fbcv
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/fbcv.owl
preferredPrefix: FBcv
products:
- {id: fbcv.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbcv.owl'}
title: FlyBase Controlled Vocabulary
tracker: http://purl.obolibrary.org/obo/fbbt/tracker
- browsers:
- {label: FB, title: FlyBase Browser, url: 'http://flybase.org/.bin/cvreport.html?cvterm=FBdv:00007008'}
build: {infallible: 0, method: obo2owl, source_url: 'http://svn.code.sf.net/p/fbbtdv/code/fbdv/releases/fbdv.obo'}
contact: {email: mmc46@gen.cam.ac.uk, label: Marta Costa}
description: A structured controlled vocabulary of the development of Drosophila
melanogaster.
domain: development
homepage: http://purl.obolibrary.org/obo/fbdv
id: fbdv
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/fbdv.owl
preferredPrefix: FBdv
products:
- {id: fbdv.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbdv.owl'}
- {id: fbdv/fbdv-simple.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl'}
- {id: fbdv/fbbt-simple.obo, ontology_purl: 'http://purl.obolibrary.org/obo/fbdv/fbbt-simple.obo'}
taxon: {id: 'NCBITaxon:7227', label: Drosophila}
title: Drosophila development
tracker: http://purl.obolibrary.org/obo/fbdv/tracker
- build: {method: obo2owl, source_url: 'http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo'}
contact: {email: mmc46@gen.cam.ac.uk, label: Marta Costa}
description: The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli)
and of other taxa referred to in FlyBase.
domain: taxonomy
homepage: http://www.flybase.org/
id: fbsp
is_obsolete: true
layout: ontology_detail
products:
- {id: fbsp.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fbsp.owl'}
taxon: {id: 'NCBITaxon:7227', label: Drosophila}
title: Fly taxonomy
- contact: {email: hastings@ebi.ac.uk, label: Janna Hastings}
description: An ontology of physico-chemical methods and properties.
id: fix
in_foundry: false
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/fix.owl
products:
- {id: fix.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fix.owl'}
title: Physico-chemical methods and properties
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/flu.owl'}
contact: {email: burkesquires@gmail.com, label: Burke Squires}
domain: health
homepage: http://purl.obolibrary.org/obo/flu/
id: flu
in_foundry: false
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/flu.owl
products:
- {id: flu.owl, ontology_purl: 'http://purl.obolibrary.org/obo/flu.owl'}
title: Influenza Ontology
tracker: http://purl.obolibrary.org/obo/flu/tracker
- build: {method: obo2owl, source_url: 'http://svn.code.sf.net/p/obo/svn/fma-conversion/trunk/fma2_obo.obo'}
contact: {email: mejino@comcast.net, label: Onard Mejino}
description: This is currently a slimmed down version of FMA
domain: anatomy
homepage: http://sig.biostr.washington.edu/projects/fm/index.html
id: fma
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/fma.owl
page: http://en.wikipedia.org/wiki/Foundational_Model_of_Anatomy
products:
- {id: fma.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fma.owl'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/18688289'}
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/18360535'}
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/16779026'}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Foundational Model of Anatomy (subset)
tracker: https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/
- build: {infallible: 1, method: obo2owl, source_url: 'https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/releases/latest/fypo.obo?format=raw'}
contact: {email: mah79@cam.ac.uk, label: Midori Harris}
depicted_by: http://www.pombase.org/sites/pombase.org/files/images/fypo_logo_tiny.png
description: FYPO is a formal ontology of phenotypes observed in fission yeast.
domain: phenotype
homepage: https://github.com/pombase/fypo
id: fypo
layout: ontology_detail
license: {label: CC-BY, 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/fypo.owl
products:
- {id: fypo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/fypo.owl'}
taxon: {id: 'NCBITaxon:4896', label: S. pombe}
title: Fission Yeast Phenotype Ontology
tracker: https://github.com/pombase/fypo/issues
- build: {method: archive, path: archive, source_url: 'http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/*zip*/archive.zip'}
contact: {email: ma11@gen.cam.ac.uk, label: Michael Ashburner}
description: A gazetteer constructed on ontological principles
homepage: http://gensc.org/gc_wiki/index.php/GAZ_Project
id: gaz
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/gaz.owl
products:
- {id: gaz.owl, ontology_purl: 'http://purl.obolibrary.org/obo/gaz.owl'}
- {id: gaz.obo, ontology_purl: 'http://purl.obolibrary.org/obo/gaz.obo'}
title: Gazetteer
tracker: https://github.com/EnvironmentOntology/envo/issues/
- contact: {email: MBrochhausen@uams.edu, label: Mathias Brochhausen}
description: An ontology of geographical entities
homepage: https://code.google.com/p/ge-ontology/
id: geo
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/geo.owl
products:
- {id: geo.owl, ontology_purl: 'http://purl.obolibrary.org/obo/geo.owl'}
title: Geographical Entity Ontology
tracker: https://ontology.atlassian.net/browse/GEO#selectedTab=com.atlassian.jira.plugin.system.project%3Aissues-panel
- browsers:
- {label: AmiGO, title: Gene Ontology AmiGO 2 Browser, url: 'http://amigo.geneontology.org/amigo/term/GO:0008150#display-lineage-tab'}
build: {checkout: 'svn --ignore-externals co svn://ext.geneontology.org/trunk/ontology',
infallible: 1, method: vcs, system: svn}
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/sites/default/files/go-logo-icon.mini__0.png
description: An ontology for describing the function of genes and gene products
domain: biology
facebook: https://www.facebook.com/Gene-Ontology-305908656519/
id: go
in_foundry_order: 1
integration_server: http://build.berkeleybop.org/view/GO
label: GO
layout: ontology_detail
license: {label: CC-BY, 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/go.owl
products:
- {id: go.owl, ontology_purl: 'http://purl.obolibrary.org/obo/go.owl'}
- {description: The core ontology plus axioms connecting to select external ontologies,
id: go/extensions/go-plus.owl, ontology_purl: 'http://purl.obolibrary.org/obo/go/extensions/go-plus.owl',
title: GO-Plus}
- {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',
title: GO Taxon Groupings}
taxon: {id: 'NCBITaxon:1', label: All life}
termgenie: http://go.termgenie.org
title: Gene Ontology
tracker: https://github.com/geneontology/go-ontology/issues/
twitter: news4go
- contact: {email: Plant Ontology Administrators, label: po-discuss@plantontology.org}
homepage: http://www.gramene.org/plant_ontology/
id: gro
is_obsolete: true
layout: ontology_detail
title: Cereal Plant Gross Anatomy
- contact: {email: Peter Midford, label: peteremidford@yahoo.com}
homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html
id: habronattus
is_obsolete: true
layout: ontology_detail
title: Habronattus courtship
- build: {checkout: 'svn co http://obo.svn.sourceforge.net/svnroot/obo/ontologies/trunk/HAO',
method: vcs, system: svn}
contact: {email: diapriid@gmail.com, label: Matt Yoder}
description: A structured controlled vocabulary of the anatomy of the Hymenoptera
(bees, wasps, and ants)
domain: anatomy
homepage: http://hymao.org
id: hao
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/hao.owl
products:
- {id: hao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/hao.owl'}
taxon: {id: 'NCBITaxon:7399', label: Hymenoptera}
title: Hymenoptera Anatomy Ontology
- build: {checkout: 'git clone https://github.com/BgeeDB/homology-ontology.git', method: vcs,
path: src/ontology, system: git}
contact: {email: bgee@isb-sib.ch, label: BgeeDB}
description: This ontology represents concepts related to homology, as well as other
concepts used to describe similarity and non-homology.
homepage: http://bioinfo.unil.ch
id: hom
layout: ontology_detail
license: {label: CC-BY, 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/hom.owl
products:
- {id: hom.owl, ontology_purl: 'http://purl.obolibrary.org/obo/hom.owl'}
title: Homology Ontology
tracker: https://github.com/BgeeDB/homology-ontology/issues
- alternativePrefix: HPO
browsers:
- {label: HPO, title: Charite HPO Browser, url: 'http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000118'}
- {label: Monarch, title: Monarch Phenotype Page, url: 'http://monarchinitiative.org/phenotype/HP:0000118'}
build: {infallible: 1, method: archive, path: archive/hp, source_url: 'http://compbio.charite.de/hudson/job/hpo/lastSuccessfulBuild/artifact/*zip*/archive.zip'}
contact: {email: sebastian.koehler@charite.de, label: Sebastian Koehler}
description: A structured and controlled vocabulary for the phenotypic features
encountered in human hereditary and other disease.
domain: phenotype
homepage: http://www.human-phenotype-ontology.org/
id: hp
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/hp.owl
products:
- {id: hp.owl, ontology_purl: 'http://purl.obolibrary.org/obo/hp.owl'}
- {id: hp.obo, ontology_purl: 'http://purl.obolibrary.org/obo/hp.obo'}
publications:
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/18950739', title: 'The Human Phenotype
Ontology: a tool for annotating and analyzing human hereditary disease.'}
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/26119816', title: 'The Human Phenotype
Ontology: Semantic Unification of Common and Rare Disease.'}
- {id: 'http://www.ncbi.nlm.nih.gov/pubmed/24217912', title: 'The Human Phenotype
Ontology project: linking molecular biology and disease through phenotype data.'}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
termgenie: http://hp.termgenie.org
title: human phenotype ontology
tracker: https://github.com/obophenotype/human-phenotype-ontology/issues/
twitter: hp_ontology
- build: {infallible: 1, method: obo2owl, source_url: 'https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/hsapdv/hsapdv.obo'}
description: Life cycle stages for Human
homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv
id: hsapdv
layout: ontology_detail
license: {label: CC-BY, 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/hsapdv.owl
page: https://github.com/obophenotype/developmental-stage-ontologies
products:
- {id: hsapdv.owl, ontology_purl: 'http://purl.obolibrary.org/obo/hsapdv.owl'}
- {id: hsapdv.obo, ontology_purl: 'http://purl.obolibrary.org/obo/hsapdv.obo'}
title: Human Developmental Stages
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/iao.owl'}
contact: {email: alanruttenberg@gmail.com, label: Alan Ruttenberg}
depicted_by: https://avatars0.githubusercontent.com/u/13591168?v=3&s=200
description: An ontology of information entities.
domain: information
homepage: https://github.com/information-artifact-ontology/IAO/
id: iao
layout: ontology_detail
license: {label: CC-BY, 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/iao.owl
products:
- {id: iao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/iao.owl'}
- {id: iao/ontology-metadata.owl, ontology_purl: 'http://purl.obolibrary.org/obo/iao/ontology-metadata.owl',
page: 'https://github.com/information-artifact-ontology/IAO/wiki/OntologyMetadata',
title: IAO ontology metadata}
- {id: iao/dev/iao.owl, ontology_purl: 'http://purl.obolibrary.org/obo/iao/dev/iao.owl',
title: IAO dev}
- contact: {email: mbrochhausen@gmail.com, label: Mathias Brochhausen}
description: An ontology based on a theory of document acts describing what people
can do with documents
id: iao/d-acts.owl
ontology_purl: http://purl.obolibrary.org/obo/iao/d-acts.owl
title: ontology of document acts
title: Information Artifact Ontology
tracker: https://github.com/information-artifact-ontology/IAO/issues
- contact: {email: Yongqun Oliver He, label: yongqunh@med.umich.edu}
homepage: https://code.google.com/p/ico-ontology/
id: ico
layout: ontology_detail
title: Informed Consent Ontology
- build: {method: owl2obo, source_url: 'http://purl.obolibrary.org/obo/ido.owl'}
contact: {email: Lindsay.Cowell@utsouthwestern.edu, label: Lindsay Cowell}
domain: health
homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology
id: ido
layout: ontology_detail
ontology_purl: http://purl.obolibrary.org/obo/ido.owl
products:
- {id: ido.owl, ontology_purl: 'http://purl.obolibrary.org/obo/ido.owl'}
taxon: {id: 'NCBITaxon:9606', label: Homo sapiens}
title: Infectious disease
tracker: http://code.google.com/p/infectious-disease-ontology/issues/list