-
Notifications
You must be signed in to change notification settings - Fork 89
/
Copy pathdb-xrefs.yaml
3063 lines (3063 loc) · 113 KB
/
db-xrefs.yaml
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
# Metadata on databases and database prefixes of relevances to the GOC
# See the README.md in this directory for more details.
#
- database: AgBase
name: AgBase resource for functional analysis of agricultural plant and animal gene products
generic_urls:
- http://www.agbase.msstate.edu/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: P02264
url_syntax: https://agbase.arizona.edu/cgi-bin/getEntry.pl?db_pick=all&database=Swiss-Prot&gb_acc=[example_id]
- database: AGI_LocusCode
name: Arabidopsis Genome Initiative
description: Comprises TAIR, TIGR and MIPS
generic_urls:
- http://www.arabidopsis.org
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: A[Tt][MmCc0-5][Gg][0-9]{5}(\.[0-9]{1})?
url_syntax: http://arabidopsis.org/servlets/TairObject?type=locus&name=[example_id]
example_id: AGI_LocusCode:At2g17950
example_url: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=At2g17950
- database: AGRICOLA_ID
name: AGRICultural OnLine Access
generic_urls:
- http://agricola.nal.usda.gov/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: AGRICOLA_NAL:TP248.2 P76 v.14
- database: AGRICOLA_IND
name: AGRICultural OnLine Access
generic_urls:
- http://agricola.nal.usda.gov/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: AGRICOLA_IND:IND23252955
- database: Alzheimers_University_of_Toronto
name: Alzheimers Project at University of Toronto
generic_urls:
- http://www.ims.utoronto.ca/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: APweb
name: Angiosperm Phylogeny Website
generic_urls:
- http://www.mobot.org/mobot/research/apweb/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html
example_id: APweb:Glossary
example_url: http://www.mobot.org/mobot/research/apweb/top/glossarya_h.html
- database: ARUK-UCL
name: Alzheimers Research Gene Ontology Initiative
generic_urls:
- https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/neurological-gene-0
entity_types:
- type_name: entity
type_id: BET:0000000
- database: ASAP
name: A Systematic Annotation Package for Community Analysis of Genomes
generic_urls:
- https://asap.genetics.wisc.edu/asap/ASAP1.htm
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=[example_id]
example_id: ASAP:ABF-0014586
example_url: https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=ABF-0014586
- database: AspGD
name: Aspergillus Genome Database
synonyms:
- ASPGD
- AspGDID
generic_urls:
- http://www.aspergillusgenome.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ASPL[0-9]{10}
url_syntax: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=[example_id]
example_id: AspGD:ASPL0000067538
example_url: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=ASPL0000067538
- database: AspGD_LOCUS
name: Aspergillus Genome Database
rdf_uri_prefix: http://identifiers.org/aspgd.locus/
generic_urls:
- http://www.aspergillusgenome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=[example_id]
example_id: AspGD_LOCUS:AN10942
example_url: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=AN10942
- database: AspGD_REF
name: Aspergillus Genome Database
generic_urls:
- http://www.aspergillusgenome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]
example_id: AspGD_REF:90
example_url: http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=90
- database: BFO
name: Basic Formal Ontology
description: An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050)
rdf_uri_prefix: http://purl.obolibrary.org/obo/BFO_
generic_urls:
- http://purl.obolibrary.org/obo/bfo
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://purl.obolibrary.org/obo/BFO_[example_id]
example_id: BFO:0000066
example_url: http://purl.obolibrary.org/obo/BFO_0000066
- database: BHF-UCL
name: Cardiovascular Gene Ontology Annotation Initiative
description: The Cardiovascular Gene Ontology Annotation Initiative is supported by the British Heart Foundation (BHF) and located at University College London (UCL).
generic_urls:
- https://www.ucl.ac.uk/cardiovascular/research/pre-clinical-and-fundamental-science/functional-gene-annotation/cardiovascular-gene
entity_types:
- type_name: entity
type_id: BET:0000000
- database: BioCyc
name: BioCyc collection of metabolic pathway databases
generic_urls:
- http://biocyc.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=[example_id]
example_id: BioCyc:PWY-5271
example_url: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5271
- database: BIOMD
name: BioModels Database
synonyms:
- BIOMDID
generic_urls:
- https://www.ebi.ac.uk/biomodels/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://www.ebi.ac.uk/biomodels/[example_id]
example_id: BIOMD:BIOMD0000000045
example_url: https://www.ebi.ac.uk/biomodels/BIOMD0000000045
- database: bioRxiv
name: bioRxiv
synonyms:
- BIORXIV
generic_urls:
- https://www.biorxiv.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: '[0-9]+'
url_syntax: https://www.biorxiv.org/content/[example_id]
example_id: bioRxiv:10.1101/530881v2
example_url: https://www.biorxiv.org/content/10.1101/530881v2
- database: BRENDA
name: BRENDA, The Comprehensive Enzyme Information System
generic_urls:
- http://www.brenda-enzymes.info
entity_types:
- type_name: catalytic activity
type_id: GO:0003824
url_syntax: https://www.brenda-enzymes.info/enzyme.php?ecno=[example_id]
example_id: BRENDA:4.2.1.3
example_url: https://www.brenda-enzymes.info/enzyme.php?ecno=4.2.1.3
- database: BTO
name: BRENDA tissue / enzyme ontology
description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.
rdf_uri_prefix: http://purl.obolibrary.org/obo/BTO_
generic_urls:
- http://purl.obolibrary.org/obo/bto
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://purl.obolibrary.org/obo/BTO_[example_id]
example_id: BTO_0002164
example_url: http://purl.obolibrary.org/obo/BTO_0002164
- database: CACAO
name: Community Assessment of Community Annotation with Ontologies
description: The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition.
generic_urls:
- http://gowiki.tamu.edu/wiki/index.php/Category:CACAO
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://gowiki.tamu.edu/wiki/index.php/[example_id]
example_id: MYCS2:A0QNF5
example_url: https://gowiki.tamu.edu/wiki/index.php/MYCS2:A0QNF5
- database: CAFA
name: Critical Assessment of Protein Function Annotation
generic_urls:
- http://biofunctionprediction.org/cafa/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: CARO
name: Common Anatomy Reference Ontology
description: An upper ontology for anatomy used by OBO Foundry ontologies. Used to facilitate interoperability between existing anatomy ontologies for different species
rdf_uri_prefix: http://purl.obolibrary.org/obo/CARO_
generic_urls:
- http://purl.obolibrary.org/obo/caro
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://purl.obolibrary.org/obo/CARO_[example_id]
example_id: CARO:0020003
example_url: http://purl.obolibrary.org/obo/CARO_0020003
- database: CAS
name: CAS Chemical Registry
description: CAS REGISTRY is the most authoritative collection of disclosed chemical substance information, containing more than 54 million organic and inorganic substances and 62 million sequences. CAS REGISTRY covers substances identified from the scientific literature from 1957 to the present, with additional substances going back to the early 1900s.
rdf_uri_prefix: http://identifiers.org/cas/
generic_urls:
- http://www.cas.org/expertise/cascontent/registry/index.html
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: CAS:58-08-2
- database: CASGEN
name: Catalog of Fishes genus database
synonyms:
- CAS_GEN
generic_urls:
- https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?genid=[example_id]
example_id: CASGEN:1040
example_url: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?genid=1040
- database: CASREF
name: Catalog of Fishes publications database
generic_urls:
- https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/getref.asp?id=[example_id]
example_id: CASREF:2031
example_url: https://researcharchive.calacademy.org/research/ichthyology/catalog/getref.asp?id=2031
- database: CASSPC
name: Catalog of Fishes species database
synonyms:
- CAS_SPC
generic_urls:
- https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=[example_id]
example_url: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=1979
- database: CAZY
name: Carbohydrate Active EnZYmes
description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
generic_urls:
- http://www.cazy.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: (CE|GH|GT|PL)\d+
url_syntax: http://www.cazy.org/[example_id].html
example_id: CAZY:PL11
example_url: http://www.cazy.org/PL11.html
- database: DTU
name: DTU Health Tech Services
description: Formerly CBS (Center for Biological Sequence Analysis)
generic_urls:
- http://www.cbs.dtu.dk/services
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: CBS:TMHMM
example_url: http://www.cbs.dtu.dk/services/TMHMM/
- database: CDD
name: Conserved Domain Database at NCBI
generic_urls:
- https://www.ncbi.nlm.nih.gov/cdd
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=[example_id]
example_id: CDD:34222
example_url: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=34222
- database: CGD
name: Candida Genome Database
synonyms:
- CGDID
rdf_uri_prefix: http://identifiers.org/cgd/
generic_urls:
- http://www.candidagenome.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: (CAL|CAF)[0-9]{10}
url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=[example_id]
example_id: CGD:CAL0000179664
example_url: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=CAL0000179664
- database: CGD_LOCUS
name: Candida Genome Database
generic_urls:
- http://www.candidagenome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.candidagenome.org/cgi-bin/locus.pl?locus=[example_id]
example_id: CGD_LOCUS:HWP1
example_url: http://www.candidagenome.org/cgi-bin/locus.pl?locus=HWP1
- database: CGD_REF
name: Candida Genome Database
generic_urls:
- http://www.candidagenome.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]
example_id: CGD_REF:1490
example_url: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=1490
- database: CGSC
name: CGSC
generic_urls:
- http://cgsc.biology.yale.edu/
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: CGSC:rbsK
example_url: http://cgsc.biology.yale.edu/Site.php?ID=315
- database: CHEBI
name: Chemical Entities of Biological Interest
synonyms:
- ChEBI
rdf_uri_prefix: http://purl.obolibrary.org/obo/CHEBI_
generic_urls:
- http://www.ebi.ac.uk/chebi/
entity_types:
- type_name: chemical entity
type_id: CHEBI:24431
id_syntax: '[0-9]{1,6}'
url_syntax: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:[example_id]
example_id: CHEBI:17234
example_url: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17234
- database: CL
name: Cell Type Ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/CL_
generic_urls:
- http://cellontology.org
entity_types:
- type_name: cell
type_id: GO:0005623
id_syntax: '[0-9]{7}'
url_syntax: http://purl.obolibrary.org/obo/CL_[example_id]
example_id: CL:0000041
example_url: http://purl.obolibrary.org/obo/CL_0000041
- database: CO_125
name: Crop Ontology CGIAR Musa Anatomy
generic_urls:
- http://www.cropontology.org/ontology/CO_125:0000000/CGIAR_Musa_anatomy
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: CO_125:0000002
example_url: http://www.cropontology.org/ontology/CO_125:0000000
- database: COG
name: NCBI Clusters of Orthologous Groups
generic_urls:
- http://www.ncbi.nlm.nih.gov/COG/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: COG_Cluster
name: NCBI COG cluster
generic_urls:
- http://www.ncbi.nlm.nih.gov/COG/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=[example_id]
example_id: COG_Cluster:COG0001
example_url: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=COG0001
- database: COG_Function
name: NCBI COG function
generic_urls:
- http://www.ncbi.nlm.nih.gov/COG/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=[example_id]
example_id: COG_Function:H
example_url: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=H
- database: COG_Pathway
name: NCBI COG pathway
generic_urls:
- http://www.ncbi.nlm.nih.gov/COG/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=[example_id]
example_id: COG_Pathway:14
example_url: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=14
- database: CollecTF
name: Database of transcription factor binding sites (TFBS) in the Bacteria domain
generic_urls:
- http://www.collectf.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: ComplexPortal
name: Complex Portal database of macromolecular complexes
generic_urls:
- https://www.ebi.ac.uk/complexportal
entity_types:
- type_name: macromolecular complex
type_id: GO:0032991
id_syntax: CPX-[0-9]+
url_syntax: https://www.ebi.ac.uk/complexportal/complex/[example_id]
example_id: ComplexPortal:CPX-2158
example_url: https://www.ebi.ac.uk/complexportal/complex/CPX-2158
- database: CORIELL
name: Coriell Institute for Medical Research
description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.
generic_urls:
- http://ccr.coriell.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=[example_id]
example_id: GM07892
example_url: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07892
- database: CORUM
name: CORUM - the Comprehensive Resource of Mammalian protein complexes
generic_urls:
- https://mips.helmholtz-muenchen.de/corum/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://mips.helmholtz-muenchen.de/corum/?id=[example_id]
example_id: CORUM:837
example_url: https://mips.helmholtz-muenchen.de/corum/?id=837
- database: cribi_vitis
name: Vitis CRIBI database
generic_urls:
- http://genomes.cribi.unipd.it
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=[example_id]&release=v1
example_id: VIT_00s0173g00270
example_url: http://genomes.cribi.unipd.it/cgi-bin/pqs2/report.pl?gene_name=VIT_00s0173g00270&release=v1
- database: dbSNP
name: NCBI dbSNP
rdf_uri_prefix: http://identifiers.org/dbsnp/
generic_urls:
- http://www.ncbi.nlm.nih.gov/projects/SNP
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d+
url_syntax: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=[example_id]
example_id: dbSNP:rs3131969
example_url: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs3131969
- database: DDANAT
name: Dictyostelium discoideum anatomy
rdf_uri_prefix: http://purl.obolibrary.org/obo/DDANAT_
generic_urls:
- http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html
entity_types:
- type_name: anatomical entity
type_id: CARO:0000000
id_syntax: '[0-9]{7}'
example_id: DDANAT:0000068
- database: DDBJ
name: DNA Databank of Japan
generic_urls:
- https://www.ddbj.nig.ac.jp
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://getentry.ddbj.nig.ac.jp/getentry/na/[example_id]
example_id: DDBJ:AA816246
example_url: http://getentry.ddbj.nig.ac.jp/getentry/na/AA816246
- database: dictyBase
name: dictyBase
synonyms:
- DDB
- DictyBase
rdf_uri_prefix: http://identifiers.org/dictybase.gene/
generic_urls:
- http://dictybase.org
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: DDB_G[0-9]{7}
url_syntax: http://dictybase.org/gene/[example_id]
example_id: dictyBase:DDB_G0277859
example_url: http://dictybase.org/gene/DDB_G0277859
- database: dictyBase_gene_name
name: dictyBase
generic_urls:
- http://dictybase.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://dictybase.org/gene/[example_id]
example_id: dictyBase_gene_name:mlcE
example_url: http://dictybase.org/gene/mlcE
- database: dictyBase_REF
name: dictyBase literature references
synonyms:
- DDB_REF
generic_urls:
- http://dictybase.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://dictybase.org/publication/[example_id]
example_id: dictyBase_REF:10157
example_url: http://dictybase.org/publication/10157
- database: DisProt
name: DisProt
description: Database of intrinsically disordered proteins
generic_urls:
- https://www.disprot.org
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://www.disprot.org/[example_id]
example_id: DP00086
example_url: https://www.disprot.org/DP00086
- database: DOI
name: Digital Object Identifier
generic_urls:
- http://dx.doi.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: 10\.[0-9]+\/.*
url_syntax: http://dx.doi.org/[example_id]
example_id: DOI:10.1016/S0963-9969(99)00021-6
example_url: http://dx.doi.org/10.1016/S0963-9969(99)00021-6
- database: EC
name: Enzyme Commission
generic_urls:
- http://enzyme.expasy.org/
entity_types:
- type_name: catalytic activity
type_id: GO:0003824
url_syntax: https://enzyme.expasy.org/EC/[example_id]
example_id: EC:1.1.1.1
example_url: https://enzyme.expasy.org/EC/1.1.1.1
- database: EchoBASE
name: EchoBASE post-genomic database for Escherichia coli
generic_urls:
- https://www.york.ac.uk/res/thomas/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: EB[0-9]{4}
url_syntax: https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=[example_id]
example_id: EchoBASE:EB0231
example_url: https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=EB0231
- database: ECO
name: Evidence Code Ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/ECO_
generic_urls:
- http://www.evidenceontology.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d{7}
url_syntax: http://www.evidenceontology.org/browse/#ECO_[example_id]
example_id: ECO:0000315
example_url: http://www.evidenceontology.org/browse/#ECO_0000315
- database: EcoCyc
name: Scientific database for the bacterium Escherichia coli K-12 MG1655
generic_urls:
- https://ecocyc.org/
entity_types:
- type_name: biological_process
type_id: GO:0008150
id_syntax: ^[A-Za-z0-9+_.%-:]+$
url_syntax: https://ecocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=[example_id]
example_id: EcoCyc:P2-PWY
example_url: https://ecocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=P2-PWY
- database: EcoCyc_REF
name: Scientific database for the bacterium Escherichia coli K-12 MG1655
synonyms:
- ECOCYC_REF
generic_urls:
- https://ecocyc.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://ecocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=[example_id]
example_id: EcoCyc_REF:COLISALII
example_url: https://ecocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=COLISALII
- database: EcoCyc_GENE
name: Scientific database for the bacterium Escherichia coli K-12 MG1655
generic_urls:
- https://ecocyc.org/
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: ^[A-Za-z0-9+_.%-:]+$
url_syntax: https://ecocyc.org/gene?orgid=ECOLI&id=[example_id]
example_id: EcoCyc:RBSA-MONOMER
example_url: https://ecocyc.org/gene?orgid=ECOLI&id=RBSA-MONOMER
- type_name: ribonucleic acid
type_id: CHEBI:33697
id_syntax: ^[A-Za-z0-9+_.%-:]+$
url_syntax: https://ecocyc.org/gene?orgid=ECOLI&id=[example_id]
example_id: EcoCyc:EG30086
example_url: https://ecocyc.org/gene?orgid=ECOLI&id=EG30086
- type_name: protein-containing complex
type_id: GO:0032991
id_syntax: ^[A-Za-z0-9+_.%-:]+$
url_syntax: https://ecocyc.org/ECOLI/NEW-IMAGE?id=[example_id]
example_id: EcoCyc:ABC-28-CPLX
example_url: https://ecocyc.org/ECOLI/NEW-IMAGE?id=ABC-28-CPLX
- database: EcoliWiki
name: EcoliWiki from EcoliHub
description: EcoliHub\'s subsystem for community annotation of E. coli K-12
generic_urls:
- http://ecoliwiki.net/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: '[A-Za-z]{3,4}'
- database: EMAPA
name: Mouse gross anatomy and development, abstract
description: "A time-independent Mouse Anatomical Dictionary; part of Gene Expression Database"
rdf_uri_prefix: http://purl.obolibrary.org/obo/EMAPA_
generic_urls:
- http://emouseatlas.org/
entity_types:
- type_name: anatomical entity
type_id: CARO:0000000
id_syntax: '[0-9]{5}'
url_syntax: "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:[example_id]"
example_id: EMAPA:16032
example_url: http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16894
- database: EMBL
name: EMBL Nucleotide Sequence Database
description: International nucleotide sequence database collaboration, comprising EMBL-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank
generic_urls:
- http://www.ebi.ac.uk/embl/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9})
url_syntax: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=[example_id]
example_id: EMBL:AA816246
example_url: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=AA816246
- database: ENA
name: European Nucleotide Archive
description: ENA is made up of a number of distinct databases that includes EMBL-Bank, the newly established Sequence Read Archive (SRA) and the Trace Archive. International nucleotide sequence database collaboration, comprising ENA-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank
generic_urls:
- http://www.ebi.ac.uk/ena/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: ([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9})
url_syntax: http://www.ebi.ac.uk/ena/data/view/[example_id]
example_id: ENA:AA816246
example_url: http://www.ebi.ac.uk/ena/data/view/AA816246
- database: ENSEMBL
name: Ensembl database of automatically annotated genomic data
synonyms:
- Ensembl
- ensembl
rdf_uri_prefix: http://identifiers.org/ensembl/
generic_urls:
- http://www.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ENS[A-Z0-9]{10,17}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL:ENSP00000265949
example_url: http://www.ensembl.org/id/ENSP00000265949
- type_name: protein
type_id: PR:000000001
id_syntax: ENS[A-Z0-9]{10,17}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL:ENSP00000265949
example_url: http://www.ensembl.org/id/ENSP00000265949
- type_name: transcript
type_id: SO:0000673
id_syntax: ENS[A-Z0-9]{10,17}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL:ENSP00000265949
example_url: http://www.ensembl.org/id/ENSP00000265949
- database: ENSEMBL_GeneID
name: Ensembl database of automatically annotated genomic data
generic_urls:
- http://www.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ENSG[0-9]{9,16}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL_GeneID:ENSG00000126016
example_url: http://www.ensembl.org/id/ENSG00000126016
- database: ENSEMBL_ProteinID
name: Ensembl database of automatically annotated genomic data
generic_urls:
- http://www.ensembl.org/
entity_types:
- type_name: protein
type_id: PR:000000001
id_syntax: ENSP[0-9]{9,16}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL_ProteinID:ENSP00000361027
example_url: http://www.ensembl.org/id/ENSP00000361027
- database: ENSEMBL_TranscriptID
name: Ensembl database of automatically annotated genomic data
generic_urls:
- http://www.ensembl.org/
entity_types:
- type_name: transcript
type_id: SO:0000673
id_syntax: ENST[0-9]{9,16}
url_syntax: http://www.ensembl.org/id/[example_id]
example_id: ENSEMBL_TranscriptID:ENST00000371959
example_url: http://www.ensembl.org/id/ENST00000371959
- database: EnsemblFungi
name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.
generic_urls:
- http://fungi.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: http://www.ensemblgenomes.org/id/[example_id]
example_id: EnsemblFungi:YOR197W
example_url: http://www.ensemblgenomes.org/id/YOR197W
- database: EnsemblMetazoa
name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa.
generic_urls:
- http://metazoa.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: http://www.ensemblgenomes.org/id/[example_id]
example_id: EnsemblMetazoa:FBgn0052693
example_url: http://www.ensemblgenomes.org/id/FBgn0052693
- database: EnsemblPlants
name: Ensembl Plants, the Ensembl database for accessing genome-scale data from plants.
synonyms:
- EnsemblPlants/Gramene
generic_urls:
- http://plants.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: http://www.ensemblgenomes.org/id/[example_id]
example_id: EnsemblPlants:LOC_Os01g22954
example_url: http://www.ensemblgenomes.org/id/LOC_Os01g22954
- database: EnsemblProtists
name: Ensembl Protists, the Ensembl database for accessing genome-scale data from protists.
generic_urls:
- http://protists.ensembl.org/
entity_types:
- type_name: gene
type_id: SO:0000704
url_syntax: http://www.ensemblgenomes.org/id/[example_id]
example_id: EnsemblProtists:PFL2550w
example_url: http://www.ensemblgenomes.org/id/PFL2550w
- database: ENZYME
name: Swiss Institute of Bioinformatics enzyme database
generic_urls:
- https://enzyme.expasy.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://enzyme.expasy.org/EC/[example_id]
example_id: 1.1.1.1
example_url: https://enzyme.expasy.org/EC/1.1.1.1
- database: EO_GIT
name: GitHub Issue Tracker for EO
generic_urls:
- https://github.com/Planteome/plant-environment-ontology
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://github.com/Planteome/plant-environment-ontology/issues/[example_id]
example_id: EO_GIT:76
example_url: https://github.com/Planteome/plant-environment-ontology/issues/76
- database: EuPathDB
name: The Eukaryotic Pathogen Database
generic_urls:
- http://eupathdb.org
entity_types:
- type_name: gene
type_id: BET:0000000
url_syntax: http://eupathdb.org/gene/[example_id]
example_id: EuPathDB:LtaP17.1490
example_url: http://eupathdb.org/gene/LtaP17.1490
- database: Eurofung
name: Eurofungbase community annotation
generic_urls:
- http://www.eurofung.net/option=com_content&task=section&id=3&Itemid=4
entity_types:
- type_name: entity
type_id: BET:0000000
- database: FB
name: FlyBase
synonyms:
- FlyBase
- FLYBASE
rdf_uri_prefix: http://identifiers.org/flybase/
generic_urls:
- http://flybase.org/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: FBgn[0-9]{7}
url_syntax: http://flybase.org/reports/[example_id].html
example_id: FB:FBgn0000024
example_url: http://flybase.org/reports/FBgn0000024.html
- database: FBbt
name: Drosophila gross anatomy
rdf_uri_prefix: http://purl.obolibrary.org/obo/FBbt_
generic_urls:
- http://flybase.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:[example_id]
example_id: FBbt:00005177
example_url: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:00005177
- database: FMA
name: Foundational Model of Anatomy
rdf_uri_prefix: http://purl.obolibrary.org/obo/FMA_
generic_urls:
- http://sig.biostr.washington.edu/projects/fm/index.html
entity_types:
- type_name: entity
type_id: BET:0000000
example_id: FMA:61905
- database: FYPO
name: Fission Yeast Phenotype Ontology
rdf_uri_prefix: http://purl.obolibrary.org/obo/FYPO_
generic_urls:
- http://www.pombase.org/
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d{7}
example_id: FYPO:0000001
- database: GenBank
name: GenBank
description: The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.
synonyms:
- GB
generic_urls:
- http://www.ncbi.nlm.nih.gov/Genbank/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ([A-Z]{2}[0-9]{6})|([A-Z]{1}[0-9]{5})
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=[example_id]
example_id: GB:AA816246
example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246
- type_name: protein
type_id: PR:000000001
id_syntax: ([A-Z]{2}[0-9]{6})|([A-Z]{1}[0-9]{5})
url_syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=[example_id]
example_id: GB:AA816246
example_url: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246
- database: Gene3D
name: Domain Architecture Classification
generic_urls:
- http://gene3d.biochem.ucl.ac.uk/Gene3D/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=[example_id]
example_id: Gene3D:3.30.390.30
example_url: http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=3.30.390.30
- database: GeneDB
name: GeneDB
rdf_uri_prefix: http://identifiers.org/genedb/
generic_urls:
- http://www.genedb.org/gene/
entity_types:
- type_name: gene
type_id: SO:0000704
id_syntax: ((LmjF|LinJ|LmxM)\.[0-9]{2}\.[0-9]{4})|(PF3D7_[0-9]{7})|(Tb[0-9]+\.[A-Za-z0-9]+\.[0-9]+)|(TcCLB\.[0-9]{6}\.[0-9]+)
url_syntax: http://www.genedb.org/gene/[example_id]
example_id: PF3D7_1467300
example_url: http://www.genedb.org/gene/PF3D7_1467300
- database: Genesys-pgr
name: Gene DB, Genesys
generic_urls:
- https://www.genesys-pgr.org/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: https://www.genesys-pgr.org/acn/search?q=[example_id]
example_id: Genesys-pgr:CM1015-16
example_url: https://www.genesys-pgr.org/acn/search?q=CM1015-16
- database: GEO
name: NCBI Gene Expression Omnibus
generic_urls:
- http://www.ncbi.nlm.nih.gov/geo/
entity_types:
- type_name: entity
type_id: BET:0000000
url_syntax: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=[example_id]
example_id: GEO:GDS2223
example_url: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS2223
- database: GO
name: Gene Ontology Database
rdf_uri_prefix: http://purl.obolibrary.org/obo/GO_
generic_urls:
- http://amigo.geneontology.org/
entity_types:
- type_name: molecular_function
type_id: GO:0003674
id_syntax: \d{7}
url_syntax: http://amigo.geneontology.org/amigo/term/GO:[example_id]
example_id: GO:0004352
example_url: http://amigo.geneontology.org/amigo/term/GO:0004352
- type_name: biological_process
type_id: GO:0008150
id_syntax: \d{7}
url_syntax: http://amigo.geneontology.org/amigo/term/GO:[example_id]
example_id: GO:0044767
example_url: http://amigo.geneontology.org/amigo/term/GO:0044767
- type_name: cellular_component
type_id: GO:0005575
id_syntax: \d{7}
url_syntax: http://amigo.geneontology.org/amigo/term/GO:[example_id]
example_id: GO:0005634
example_url: http://amigo.geneontology.org/amigo/term/GO:0005634
- type_name: macromolecular complex
type_id: GO:0032991
id_syntax: \d{7}
url_syntax: http://amigo.geneontology.org/amigo/term/GO:[example_id]
example_id: GO:0044776
example_url: http://amigo.geneontology.org/amigo/term/GO:0044776
- database: GO_Central
name: GO Central
synonyms:
- GO_CENTRAL
description: Manual annotation from PAINT curators into the UniProt Protein2GO curation tool.
generic_urls:
- http://www.geneontology.org/GO.refgenome.shtml
entity_types:
- type_name: entity
type_id: BET:0000000
- database: GO_Noctua
name: GO Noctua
description: Manual annotation derived from LEGO annotations
generic_urls:
- https://github.com/geneontology/noctua-models
entity_types:
- type_name: entity
type_id: BET:0000000
- database: GO_REF
name: Gene Ontology Database references
generic_urls:
- http://current.geneontology.org/metadata/gorefs/index.html
entity_types:
- type_name: entity
type_id: BET:0000000
id_syntax: \d{7}
url_syntax: http://purl.obolibrary.org/obo/go/references/[example_id]
example_id: "0000001"
example_url: http://purl.obolibrary.org/obo/go/references/0000001
- database: gomodel
name: Gene Ontology Causal Activity Model Database
rdf_uri_prefix: http://model.geneontology.org/
generic_urls:
- http://www.geneontology.org/gocam
entity_types:
- type_name: model
type_id: BET:0000000
url_syntax: http://www.geneontology.org/gocam/[example_id]
example_id: gomodel:5ae3b0f600001522
example_url: http://www.geneontology.org/gocam/gomodel:5ae3b0f600001522
- database: GOC
name: Gene Ontology Consortium
generic_urls:
- http://www.geneontology.org/
entity_types:
- type_name: entity
type_id: BET:0000000
- database: GOC-OWL
name: Gene Ontology Consortium - Logical inferences
generic_urls:
- http://www.geneontology.org/
entity_types:
- type_name: entity