-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathomp-edit.obo
21878 lines (19505 loc) · 929 KB
/
omp-edit.obo
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
format-version: 1.2
data-version: releases/2015-02-19
date: 13:04:2021 14:52
saved-by: siegele
auto-generated-by: OBO-Edit 2.3.1
subsetdef: abnormal_slim "Abnormal/normal slim"
subsetdef: absent_slim "Absent/present slim"
subsetdef: attribute_slim "Attribute slim"
subsetdef: cell_quality "cell_quality"
subsetdef: Cross_product_review "Involved_in"
subsetdef: disposition_slim "Disposition slim"
subsetdef: goantislim_grouping "Grouping classes that can be excluded"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_goa "GOA and proteome slim"
subsetdef: goslim_metagenomics "Metagenomics GO slim"
subsetdef: goslim_pir "PIR GO slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_pombe "Fission yeast GO slim"
subsetdef: goslim_virus "Viral GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"
subsetdef: hpo_slim "Human phenotype slim"
subsetdef: mf_needs_review "Catalytic activity terms in need of attention"
subsetdef: mpath_slim "Pathology slim"
subsetdef: qc_do_not_annotate "Term not to be used for direct annotation"
subsetdef: qc_do_not_manually_annotate "Term not to be used for direct manual annotation"
subsetdef: relational_slim "Relational slim: types of quality that require an additional entity in order to exist"
subsetdef: scalar_slim "Scalar slim"
subsetdef: SOFA "SO feature annotation"
subsetdef: value_slim "Value slim"
subsetdef: virus_checked "Viral overhaul terms"
synonymtypedef: BRAND_NAME "BRAND NAME"
synonymtypedef: FORMULA "FORMULA"
synonymtypedef: InChI "InChI"
synonymtypedef: InChIKey "InChIKey"
synonymtypedef: INN "INN"
synonymtypedef: IUPAC_NAME "IUPAC NAME"
synonymtypedef: SMILES "SMILES"
synonymtypedef: systematic_synonym "Systematic synonym" EXACT
default-namespace: microbial_phenotype
remark: select is_a closure
ontology: omp
ontology: go
ontology: pato
[Term]
id: CHEBI:24431
name: chemical entity
namespace: chebi_ontology
def: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." [CHEBI:Team]
[Term]
id: CHEBI:24432
name: biological role
namespace: chebi_ontology
def: "A role played by the molecular entity or part thereof within a biological context." [CHEBI:Team]
is_a: CHEBI:50906 ! role
[Term]
id: CHEBI:25944
name: pesticide
namespace: chebi_ontology
def: "Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests." [CHEBI:Team]
xref: Wikipedia:Pesticide
is_a: CHEBI:33232 ! application
[Term]
id: CHEBI:33232
name: application
namespace: chebi_ontology
def: "Intended use of the molecular entity or part thereof by humans." [CHEBI:Team]
is_a: CHEBI:50906 ! role
[Term]
id: CHEBI:33281
name: antimicrobial agent
namespace: chebi_ontology
def: "A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans." [CHEBI:Team]
synonym: "antimicrobial" RELATED []
synonym: "microbiocides" RELATED []
is_a: CHEBI:24432 ! biological role
is_a: CHEBI:25944 ! pesticide
[Term]
id: CHEBI:50906
name: role
namespace: chebi_ontology
def: "A role is a particular behaviour which a material entity may exhibit." [CHEBI:Team]
[Term]
id: GO:0000003
name: reproduction
namespace: biological_process
alt_id: GO:0019952
alt_id: GO:0050876
def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732]
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: gosubset_prok
synonym: "reproductive physiological process" EXACT []
xref: Wikipedia:Reproduction
is_a: GO:0008150 ! biological_process
[Term]
id: GO:0001539
name: cilium or flagellum-dependent cell motility
namespace: biological_process
def: "Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella." [GOC:cilia, GOC:hjd, GOC:krc]
comment: Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent, while the bacterial- and archaeal-type flagella have a different structure. The former are microtubule-based structures that lash back and forth and are present only in eukaryotes, while the latter achieve motility by rotation. Bacterial- and archaeal-type flagella are superficially similar but have a different molecular composition and fine structure. These three structures never co-exist in the same organism. Therefore, GO:0001539 'cilium or flagellum-dependent cell motility' is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term. Direct annotations to GO:0001539 'cilium or flagellum-dependent cell motility' may be amended during annotation QC.
subset: gosubset_prok
subset: qc_do_not_manually_annotate
synonym: "ciliary or bacterial-type flagellar motility" RELATED []
synonym: "ciliary/flagellar motility" EXACT []
is_a: GO:0048870 ! cell motility
[Term]
id: GO:0005575
name: cellular_component
namespace: cellular_component
alt_id: GO:0008372
def: "The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators, NIF_Subcellular:sao-1337158144]
comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
synonym: "cellular component" EXACT []
synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315]
xref: NIF_Subcellular:sao1337158144
[Term]
id: GO:0005623
name: cell
namespace: cellular_component
def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
xref: NIF_Subcellular:sao1813327414
xref: Wikipedia:Cell_(biology)
is_a: GO:0005575 ! cellular_component
[Term]
id: GO:0006139
name: nucleobase-containing compound metabolic process
namespace: biological_process
alt_id: GO:0055134
def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai]
subset: goslim_pir
subset: goslim_plant
subset: gosubset_prok
synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT []
synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT []
synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb]
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT []
is_a: GO:0006725 ! cellular aromatic compound metabolic process
is_a: GO:0034641 ! cellular nitrogen compound metabolic process
is_a: GO:0044238 ! primary metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
[Term]
id: GO:0006259
name: DNA metabolic process
namespace: biological_process
alt_id: GO:0055132
def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: gosubset_prok
synonym: "cellular DNA metabolism" EXACT []
synonym: "DNA metabolism" EXACT []
is_a: GO:0044260 ! cellular macromolecule metabolic process
is_a: GO:0090304 ! nucleic acid metabolic process
[Term]
id: GO:0006260
name: DNA replication
namespace: biological_process
alt_id: GO:0055133
def: "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC:mah]
comment: See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'.
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
subset: gosubset_prok
xref: Reactome:REACT_100559 "Activation of ATR in response to replication stress, Mus musculus"
xref: Reactome:REACT_101280 "Activation of claspin, Xenopus tropicalis"
xref: Reactome:REACT_101497 "Activation of claspin, Bos taurus"
xref: Reactome:REACT_102679 "Activation of ATR in response to replication stress, Gallus gallus"
xref: Reactome:REACT_103614 "Stalling of DNA replication fork and RPA binding, Taeniopygia guttata"
xref: Reactome:REACT_104547 "Recruitment and activation of Chk1, Gallus gallus"
xref: Reactome:REACT_105292 "Activation of ATR in response to replication stress, Xenopus tropicalis"
xref: Reactome:REACT_105467 "Loading of claspin onto DNA during replication origin firing, Danio rerio"
xref: Reactome:REACT_105835 "Stalling of DNA replication fork and RPA binding, Gallus gallus"
xref: Reactome:REACT_106018 "Recruitment of Rad17-RFC complex to DNA, Gallus gallus"
xref: Reactome:REACT_106104 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Bos taurus"
xref: Reactome:REACT_106382 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Drosophila melanogaster"
xref: Reactome:REACT_106434 "Activation of claspin, Canis familiaris"
xref: Reactome:REACT_106732 "Recruitment and activation of Chk1, Canis familiaris"
xref: Reactome:REACT_107075 "Activation of ATR in response to replication stress, Danio rerio"
xref: Reactome:REACT_107423 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Caenorhabditis elegans"
xref: Reactome:REACT_108461 "Recruitment and activation of Chk1, Bos taurus"
xref: Reactome:REACT_108634 "Loading of claspin onto DNA during replication origin firing, Mus musculus"
xref: Reactome:REACT_108739 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Xenopus tropicalis"
xref: Reactome:REACT_108768 "Activation of ATR in response to replication stress, Bos taurus"
xref: Reactome:REACT_108929 "Activation of ATR in response to replication stress, Drosophila melanogaster"
xref: Reactome:REACT_109137 "Stalling of DNA replication fork and RPA binding, Rattus norvegicus"
xref: Reactome:REACT_112472 "Activation of ATR in response to replication stress, Saccharomyces cerevisiae"
xref: Reactome:REACT_113703 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Gallus gallus"
xref: Reactome:REACT_29423 "Activation of ATR in response to replication stress, Schizosaccharomyces pombe"
xref: Reactome:REACT_29444 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Taeniopygia guttata"
xref: Reactome:REACT_29691 "Activation of ATR in response to replication stress, Rattus norvegicus"
xref: Reactome:REACT_29764 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Taeniopygia guttata"
xref: Reactome:REACT_30149 "Activation of claspin, Rattus norvegicus"
xref: Reactome:REACT_31024 "Recruitment of Rad17-RFC complex to DNA, Xenopus tropicalis"
xref: Reactome:REACT_31919 "Loading of claspin onto DNA during replication origin firing, Rattus norvegicus"
xref: Reactome:REACT_32546 "Recruitment of Rad17-RFC complex to DNA, Mus musculus"
xref: Reactome:REACT_32932 "Recruitment and activation of Chk1, Taeniopygia guttata"
xref: Reactome:REACT_33572 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Dictyostelium discoideum"
xref: Reactome:REACT_33874 "Recruitment and activation of Chk1, Xenopus tropicalis"
xref: Reactome:REACT_50018 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Rattus norvegicus"
xref: Reactome:REACT_53588 "Loading of claspin onto DNA during replication origin firing, Canis familiaris"
xref: Reactome:REACT_6729 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Homo sapiens"
xref: Reactome:REACT_6738 "Loading of claspin onto DNA during replication origin firing, Homo sapiens"
xref: Reactome:REACT_6750 "Activation of claspin, Homo sapiens"
xref: Reactome:REACT_6769 "Activation of ATR in response to replication stress, Homo sapiens"
xref: Reactome:REACT_6798 "Recruitment of Rad17-RFC complex to DNA, Homo sapiens"
xref: Reactome:REACT_6869 "Recruitment and activation of Chk1, Homo sapiens"
xref: Reactome:REACT_6936 "Stalling of DNA replication fork and RPA binding, Homo sapiens"
xref: Reactome:REACT_6939 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Homo sapiens"
xref: Reactome:REACT_77532 "Stalling of DNA replication fork and RPA binding, Canis familiaris"
xref: Reactome:REACT_79188 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Canis familiaris"
xref: Reactome:REACT_79450 "Activation of ATR in response to replication stress, Dictyostelium discoideum"
xref: Reactome:REACT_80432 "Loading of claspin onto DNA during replication origin firing, Taeniopygia guttata"
xref: Reactome:REACT_80571 "Activation of claspin, Mus musculus"
xref: Reactome:REACT_80896 "Recruitment and activation of Chk1, Sus scrofa"
xref: Reactome:REACT_80988 "Loading of claspin onto DNA during replication origin firing, Bos taurus"
xref: Reactome:REACT_81803 "Recruitment of Rad17-RFC complex to DNA, Canis familiaris"
xref: Reactome:REACT_83095 "Recruitment of Rad17-RFC complex to DNA, Danio rerio"
xref: Reactome:REACT_84829 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Danio rerio"
xref: Reactome:REACT_85561 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Rattus norvegicus"
xref: Reactome:REACT_86410 "Stalling of DNA replication fork and RPA binding, Mus musculus"
xref: Reactome:REACT_86739 "Recruitment and activation of Chk1, Rattus norvegicus"
xref: Reactome:REACT_87233 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Canis familiaris"
xref: Reactome:REACT_87449 "Recruitment of Rad17-RFC complex to DNA, Rattus norvegicus"
xref: Reactome:REACT_87590 "Recruitment of Rad17-RFC complex to DNA, Bos taurus"
xref: Reactome:REACT_88085 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Gallus gallus"
xref: Reactome:REACT_88384 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Schizosaccharomyces pombe"
xref: Reactome:REACT_88529 "Activation of claspin, Gallus gallus"
xref: Reactome:REACT_89355 "Activation of claspin, Danio rerio"
xref: Reactome:REACT_89439 "Activation of ATR in response to replication stress, Sus scrofa"
xref: Reactome:REACT_89725 "Loading of claspin onto DNA during replication origin firing, Drosophila melanogaster"
xref: Reactome:REACT_90512 "Stalling of DNA replication fork and RPA binding, Bos taurus"
xref: Reactome:REACT_90809 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Danio rerio"
xref: Reactome:REACT_90838 "Recruitment of Rad17-RFC complex to DNA, Taeniopygia guttata"
xref: Reactome:REACT_91184 "Recruitment and activation of Chk1, Danio rerio"
xref: Reactome:REACT_91302 "Activation of ATR in response to replication stress, Canis familiaris"
xref: Reactome:REACT_92527 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Mus musculus"
xref: Reactome:REACT_92644 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Xenopus tropicalis"
xref: Reactome:REACT_92706 "Stalling of DNA replication fork and RPA binding, Danio rerio"
xref: Reactome:REACT_94983 "Stalling of DNA replication fork and RPA binding, Xenopus tropicalis"
xref: Reactome:REACT_95253 "Activation of ATR in response to replication stress, Taeniopygia guttata"
xref: Reactome:REACT_95329 "Activation of claspin, Taeniopygia guttata"
xref: Reactome:REACT_96115 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Mus musculus"
xref: Reactome:REACT_96804 "Recruitment and activation of Chk1, Mus musculus"
xref: Reactome:REACT_96998 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Bos taurus"
xref: Reactome:REACT_97204 "Loading of claspin onto DNA during replication origin firing, Gallus gallus"
xref: Reactome:REACT_97726 "Activation of ATR in response to replication stress, Caenorhabditis elegans"
xref: Reactome:REACT_99948 "Loading of claspin onto DNA during replication origin firing, Xenopus tropicalis"
xref: Wikipedia:DNA_replication
is_a: GO:0006259 ! DNA metabolic process
is_a: GO:0034645 ! cellular macromolecule biosynthetic process
[Term]
id: GO:0006351
name: transcription, DNA-templated
namespace: biological_process
alt_id: GO:0006350
alt_id: GO:0061018
alt_id: GO:0061022
def: "The cellular synthesis of RNA on a template of DNA." [GOC:jl, GOC:txnOH]
subset: goslim_aspergillus
subset: goslim_metagenomics
subset: goslim_pombe
subset: gosubset_prok
synonym: "cellular transcription" BROAD []
synonym: "cellular transcription, DNA-dependent" EXACT []
synonym: "DNA-dependent transcription" EXACT []
synonym: "transcription" BROAD []
synonym: "transcription regulator activity" RELATED []
synonym: "transcription, DNA-dependent" EXACT [GOC:txnOH]
xref: Wikipedia:Transcription_(genetics)
is_a: GO:0032774 ! RNA biosynthetic process
is_a: GO:0034645 ! cellular macromolecule biosynthetic process
relationship: part_of GO:0010467 ! gene expression
[Term]
id: GO:0006412
name: translation
namespace: biological_process
alt_id: GO:0006416
alt_id: GO:0006453
alt_id: GO:0043037
def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: gosubset_prok
synonym: "protein anabolism" EXACT []
synonym: "protein biosynthesis" EXACT []
synonym: "protein biosynthetic process" EXACT [GOC:curators]
synonym: "protein formation" EXACT []
synonym: "protein synthesis" EXACT []
synonym: "protein translation" EXACT []
xref: Reactome:REACT_100338 "Translation, Sus scrofa"
xref: Reactome:REACT_100851 "Translation, Saccharomyces cerevisiae"
xref: Reactome:REACT_101045 "Translation, Dictyostelium discoideum"
xref: Reactome:REACT_101324 "Translation, Canis familiaris"
xref: Reactome:REACT_1014 "Translation, Homo sapiens"
xref: Reactome:REACT_103420 "Translation, Plasmodium falciparum"
xref: Reactome:REACT_105544 "Translation, Arabidopsis thaliana"
xref: Reactome:REACT_29980 "Translation, Bos taurus"
xref: Reactome:REACT_33559 "Translation, Rattus norvegicus"
xref: Reactome:REACT_77710 "Translation, Drosophila melanogaster"
xref: Reactome:REACT_79784 "Translation, Danio rerio"
xref: Reactome:REACT_81734 "Translation, Schizosaccharomyces pombe"
xref: Reactome:REACT_81833 "Translation, Caenorhabditis elegans"
xref: Reactome:REACT_82171 "Translation, Xenopus tropicalis"
xref: Reactome:REACT_83429 "Translation, Taeniopygia guttata"
xref: Reactome:REACT_83530 "Translation, Gallus gallus"
xref: Reactome:REACT_86996 "Translation, Oryza sativa"
xref: Reactome:REACT_95535 "Translation, Mus musculus"
xref: Reactome:REACT_96394 "Translation, Escherichia coli"
xref: Wikipedia:Translation_(genetics)
is_a: GO:0034645 ! cellular macromolecule biosynthetic process
is_a: GO:0044267 ! cellular protein metabolic process
relationship: part_of GO:0010467 ! gene expression
[Term]
id: GO:0006725
name: cellular aromatic compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." [GOC:ai, ISBN:0198506732]
subset: goslim_pir
subset: gosubset_prok
synonym: "aromatic compound metabolism" EXACT []
synonym: "aromatic hydrocarbon metabolic process" NARROW []
synonym: "aromatic hydrocarbon metabolism" NARROW []
is_a: GO:0044237 ! cellular metabolic process
[Term]
id: GO:0006807
name: nitrogen compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium." [CHEBI:51143, GOC:go_curators, GOC:jl, ISBN:0198506732]
comment: Note that amino acid and derivative metabolism should not be annotated here. Instead use the 'amino acid and derivative metabolism' node.
subset: goslim_metagenomics
subset: goslim_pir
subset: gosubset_prok
synonym: "nitrogen compound metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0006928
name: cellular component movement
namespace: biological_process
def: "The directed, self-propelled movement of a cellular component without the involvement of an external agent such as a transporter or a pore." [GOC:dgh, GOC:dph, GOC:jl, GOC:mlg]
comment: Note that in GO cellular components include whole cells (cell is_a cellular component).
subset: goslim_pir
subset: gosubset_prok
synonym: "cell movement" RELATED []
synonym: "cellular component motion" EXACT [GOC:dph, GOC:jl]
is_a: GO:0044763 ! single-organism cellular process
[Term]
id: GO:0006935
name: chemotaxis
namespace: biological_process
def: "The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." [ISBN:0198506732]
subset: goslim_metagenomics
subset: gosubset_prok
synonym: "taxis in response to chemical stimulus" EXACT []
xref: Wikipedia:Chemotaxis
is_a: GO:0042221 ! response to chemical
is_a: GO:0042330 ! taxis
[Term]
id: GO:0007059
name: chromosome segregation
namespace: biological_process
def: "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." [GOC:jl, GOC:mah, GOC:mtg_cell_cycle, GOC:vw]
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
subset: gosubset_prok
synonym: "chromosome division" EXACT []
synonym: "chromosome transmission" RELATED []
xref: Wikipedia:Chromosome_segregation
is_a: GO:0044763 ! single-organism cellular process
[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
alt_id: GO:0000004
alt_id: GO:0007582
def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
subset: gosubset_prok
synonym: "biological process" EXACT []
synonym: "physiological process" EXACT []
xref: Wikipedia:Biological_process
[Term]
id: GO:0008152
name: metabolic process
namespace: biological_process
def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684]
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
subset: goslim_pir
subset: goslim_plant
subset: gosubset_prok
synonym: "metabolic process resulting in cell growth" NARROW []
synonym: "metabolism" EXACT []
synonym: "metabolism resulting in cell growth" NARROW []
xref: Wikipedia:Metabolism
is_a: GO:0008150 ! biological_process
[Term]
id: GO:0009058
name: biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684]
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_plant
subset: gosubset_prok
synonym: "anabolism" EXACT []
synonym: "biosynthesis" EXACT []
synonym: "formation" EXACT []
synonym: "synthesis" EXACT []
xref: Wikipedia:Anabolism
is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0009059
name: macromolecule biosynthetic process
namespace: biological_process
alt_id: GO:0043284
def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah]
subset: gosubset_prok
synonym: "biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09]
synonym: "macromolecule anabolism" EXACT []
synonym: "macromolecule biosynthesis" EXACT []
synonym: "macromolecule formation" EXACT []
synonym: "macromolecule synthesis" EXACT []
is_a: GO:0043170 ! macromolecule metabolic process
is_a: GO:1901576 ! organic substance biosynthetic process
[Term]
id: GO:0009453
name: energy taxis
namespace: biological_process
def: "The directed movement of a motile cell or organism in response to physical parameters involved in energy generation, such as light, oxygen, and oxidizable substrates." [GOC:jl, PMID:11029423]
subset: gosubset_prok
synonym: "energytaxis" EXACT []
synonym: "taxis in response to energy source" EXACT []
is_a: GO:0042330 ! taxis
[Term]
id: GO:0009454
name: aerotaxis
namespace: biological_process
def: "The directed movement of a motile cell or organism in response to environmental oxygen." [GOC:jl, ISBN:0192801023]
subset: gosubset_prok
synonym: "taxis in response to atmospheric oxygen" EXACT []
is_a: GO:0006935 ! chemotaxis
is_a: GO:0009453 ! energy taxis
[Term]
id: GO:0009605
name: response to external stimulus
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus." [GOC:hb]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: goslim_plant
subset: gosubset_prok
subset: qc_do_not_manually_annotate
synonym: "response to environmental stimulus" EXACT []
is_a: GO:0050896 ! response to stimulus
[Term]
id: GO:0009847
name: spore germination
namespace: biological_process
def: "The physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall)." [GOC:lr]
subset: gosubset_prok
is_a: GO:0032502 ! developmental process
[Term]
id: GO:0009892
name: negative regulation of metabolic process
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators]
subset: gosubset_prok
synonym: "down regulation of metabolic process" EXACT []
synonym: "down-regulation of metabolic process" EXACT []
synonym: "downregulation of metabolic process" EXACT []
synonym: "inhibition of metabolic process" NARROW []
synonym: "negative regulation of metabolism" EXACT []
is_a: GO:0019222 ! regulation of metabolic process
is_a: GO:0048519 ! negative regulation of biological process
relationship: negatively_regulates GO:0008152 ! metabolic process
[Term]
id: GO:0009987
name: cellular process
namespace: biological_process
alt_id: GO:0008151
alt_id: GO:0050875
def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete]
subset: goslim_pir
subset: goslim_plant
subset: gosubset_prok
synonym: "cell growth and/or maintenance" NARROW []
synonym: "cell physiology" EXACT []
synonym: "cellular physiological process" EXACT []
is_a: GO:0008150 ! biological_process
[Term]
id: GO:0010467
name: gene expression
namespace: biological_process
def: "The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb]
subset: gosubset_prok
xref: Reactome:REACT_100537 "Gene Expression, Xenopus tropicalis"
xref: Reactome:REACT_101147 "Gene Expression, Danio rerio"
xref: Reactome:REACT_101952 "Gene Expression, Sus scrofa"
xref: Reactome:REACT_105649 "Gene Expression, Drosophila melanogaster"
xref: Reactome:REACT_108313 "Gene Expression, Caenorhabditis elegans"
xref: Reactome:REACT_29068 "Gene Expression, Escherichia coli"
xref: Reactome:REACT_34240 "Gene Expression, Staphylococcus aureus N315"
xref: Reactome:REACT_71 "Gene Expression, Homo sapiens"
xref: Reactome:REACT_78136 "Gene Expression, Mus musculus"
xref: Reactome:REACT_78959 "Gene Expression, Taeniopygia guttata"
xref: Reactome:REACT_79662 "Gene Expression, Plasmodium falciparum"
xref: Reactome:REACT_85241 "Gene Expression, Oryza sativa"
xref: Reactome:REACT_85359 "Gene Expression, Gallus gallus"
xref: Reactome:REACT_86357 "Gene Expression, Canis familiaris"
xref: Reactome:REACT_89816 "Gene Expression, Mycobacterium tuberculosis"
xref: Reactome:REACT_91657 "Gene Expression, Arabidopsis thaliana"
xref: Reactome:REACT_91965 "Gene Expression, Rattus norvegicus"
xref: Reactome:REACT_93586 "Gene Expression, Dictyostelium discoideum"
xref: Reactome:REACT_93968 "Gene Expression, Bos taurus"
xref: Reactome:REACT_94814 "Gene Expression, Schizosaccharomyces pombe"
xref: Reactome:REACT_98256 "Gene Expression, Saccharomyces cerevisiae"
xref: Wikipedia:Gene_expression
is_a: GO:0043170 ! macromolecule metabolic process
[Term]
id: GO:0010468
name: regulation of gene expression
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb]
subset: gosubset_prok
synonym: "regulation of gene product expression" RELATED [GOC:curators]
synonym: "regulation of protein expression" NARROW [GOC:curators]
xref: Wikipedia:Regulation_of_gene_expression
is_a: GO:0060255 ! regulation of macromolecule metabolic process
relationship: regulates GO:0010467 ! gene expression
[Term]
id: GO:0010605
name: negative regulation of macromolecule metabolic process
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb]
is_a: GO:0009892 ! negative regulation of metabolic process
is_a: GO:0060255 ! regulation of macromolecule metabolic process
relationship: negatively_regulates GO:0043170 ! macromolecule metabolic process
[Term]
id: GO:0010629
name: negative regulation of gene expression
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb]
is_a: GO:0010468 ! regulation of gene expression
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
relationship: negatively_regulates GO:0010467 ! gene expression
[Term]
id: GO:0016070
name: RNA metabolic process
namespace: biological_process
def: "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_metagenomics
subset: goslim_pir
subset: gosubset_prok
synonym: "RNA metabolism" EXACT []
xref: Reactome:REACT_107259 "Metabolism of RNA, Sus scrofa"
xref: Reactome:REACT_107652 "Metabolism of RNA, Schizosaccharomyces pombe"
xref: Reactome:REACT_110289 "Metabolism of RNA, Danio rerio"
xref: Reactome:REACT_21257 "Metabolism of RNA, Homo sapiens"
xref: Reactome:REACT_30579 "Metabolism of RNA, Xenopus tropicalis"
xref: Reactome:REACT_31367 "Metabolism of RNA, Dictyostelium discoideum"
xref: Reactome:REACT_33720 "Metabolism of RNA, Plasmodium falciparum"
xref: Reactome:REACT_80071 "Metabolism of RNA, Caenorhabditis elegans"
xref: Reactome:REACT_83630 "Metabolism of RNA, Taeniopygia guttata"
xref: Reactome:REACT_84169 "Metabolism of RNA, Canis familiaris"
xref: Reactome:REACT_85788 "Metabolism of RNA, Oryza sativa"
xref: Reactome:REACT_88316 "Metabolism of RNA, Mus musculus"
xref: Reactome:REACT_89992 "Metabolism of RNA, Saccharomyces cerevisiae"
xref: Reactome:REACT_91556 "Metabolism of RNA, Bos taurus"
xref: Reactome:REACT_92152 "Metabolism of RNA, Drosophila melanogaster"
xref: Reactome:REACT_94876 "Metabolism of RNA, Arabidopsis thaliana"
xref: Reactome:REACT_99403 "Metabolism of RNA, Rattus norvegicus"
xref: Reactome:REACT_99885 "Metabolism of RNA, Gallus gallus"
is_a: GO:0044260 ! cellular macromolecule metabolic process
is_a: GO:0090304 ! nucleic acid metabolic process
[Term]
id: GO:0016458
name: gene silencing
namespace: biological_process
def: "Any transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:jid, GOC:tb]
comment: Note that this process is the opposite of long-term maintenance of gene activation.
subset: goslim_pir
synonym: "long-term maintenance of gene inactivation" RELATED []
xref: Wikipedia:Gene_silencing
is_a: GO:0010629 ! negative regulation of gene expression
is_a: GO:0044763 ! single-organism cellular process
[Term]
id: GO:0018130
name: heterocycle biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [ISBN:0198547684]
subset: gosubset_prok
synonym: "heterocycle anabolism" EXACT []
synonym: "heterocycle biosynthesis" EXACT []
synonym: "heterocycle formation" EXACT []
synonym: "heterocycle synthesis" EXACT []
is_a: GO:0044249 ! cellular biosynthetic process
is_a: GO:0046483 ! heterocycle metabolic process
[Term]
id: GO:0019222
name: regulation of metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators]
subset: gosubset_prok
synonym: "regulation of metabolism" EXACT []
is_a: GO:0050789 ! regulation of biological process
relationship: regulates GO:0008152 ! metabolic process
[Term]
id: GO:0019438
name: aromatic compound biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring." [GOC:ai]
subset: gosubset_prok
synonym: "aromatic compound anabolism" EXACT []
synonym: "aromatic compound biosynthesis" EXACT []
synonym: "aromatic compound formation" EXACT []
synonym: "aromatic compound synthesis" EXACT []
synonym: "aromatic hydrocarbon biosynthesis" NARROW []
synonym: "aromatic hydrocarbon biosynthetic process" NARROW []
is_a: GO:0006725 ! cellular aromatic compound metabolic process
is_a: GO:0044249 ! cellular biosynthetic process
[Term]
id: GO:0019538
name: protein metabolic process
namespace: biological_process
alt_id: GO:0006411
def: "The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification." [GOC:ma]
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: gosubset_prok
synonym: "protein metabolic process and modification" EXACT []
synonym: "protein metabolism" EXACT []
synonym: "protein metabolism and modification" EXACT []
xref: Wikipedia:Protein_metabolism
is_a: GO:0043170 ! macromolecule metabolic process
is_a: GO:0044238 ! primary metabolic process
[Term]
id: GO:0019954
name: asexual reproduction
namespace: biological_process
def: "The biological process in which new individuals are produced by either a single cell or a group of cells, in the absence of any sexual process." [ISBN:0387520546]
subset: gosubset_prok
xref: Wikipedia:Asexual_reproduction
is_a: GO:0000003 ! reproduction
[Term]
id: GO:0022402
name: cell cycle process
namespace: biological_process
def: "The cellular process that ensures successive accurate and complete genome replication and chromosome segregation." [GOC:isa_complete, GOC:mtg_cell_cycle]
subset: gosubset_prok
subset: qc_do_not_manually_annotate
is_a: GO:0044763 ! single-organism cellular process
[Term]
id: GO:0030154
name: cell differentiation
namespace: biological_process
def: "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
xref: Wikipedia:Cellular_differentiation
is_a: GO:0048869 ! cellular developmental process
[Term]
id: GO:0030435
name: sporulation resulting in formation of a cellular spore
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." [GOC:mah, GOC:pamgo_curators, ISBN:0072992913]
comment: Note that the synonym 'spore differentiation', like the term name and definition, refers to differentiation into a spore rather than any subsequent developmental changes that a spore may undergo.
subset: gosubset_prok
synonym: "cellular spore formation by sporulation" EXACT [GOC:dph, GOC:tb]
synonym: "spore biosynthesis" EXACT []
synonym: "spore differentiation" EXACT []
synonym: "spore formation" EXACT []
xref: Wikipedia:Sporogenesis
is_a: GO:0030154 ! cell differentiation
is_a: GO:0043934 ! sporulation
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
[Term]
id: GO:0030436
name: asexual sporulation
namespace: biological_process
def: "The formation of spores derived from the products of mitosis. Examples of this process are found in Bacterial species." [GOC:mah, PMID:9529886]
subset: goslim_aspergillus
subset: gosubset_prok
synonym: "asexual spore formation" EXACT []
synonym: "mitotic spore formation" EXACT []
synonym: "mitotic sporulation" EXACT []
is_a: GO:0019954 ! asexual reproduction
is_a: GO:0043934 ! sporulation
[Term]
id: GO:0031975
name: envelope
namespace: cellular_component
def: "A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers." [GOC:mah, GOC:pz]
subset: gosubset_prok
is_a: GO:0044464 ! cell part
[Term]
id: GO:0032196
name: transposition
namespace: biological_process
def: "Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites." [GOC:jp, ISBN:1555812090]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
subset: gosubset_prok
xref: Wikipedia:Transposon
is_a: GO:0044763 ! single-organism cellular process
[Term]
id: GO:0032502
name: developmental process
namespace: biological_process
def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete]
subset: goslim_aspergillus
subset: goslim_pir
subset: gosubset_prok
synonym: "development" NARROW []
is_a: GO:0008150 ! biological_process
[Term]
id: GO:0032774
name: RNA biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers." [GOC:mah]
synonym: "RNA anabolism" EXACT []
synonym: "RNA biosynthesis" EXACT []
synonym: "RNA formation" EXACT []
synonym: "RNA synthesis" EXACT []
is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0016070 ! RNA metabolic process
is_a: GO:0034654 ! nucleobase-containing compound biosynthetic process
[Term]
id: GO:0034301
name: endospore formation
namespace: biological_process
def: "The process in which a cell gives rise to an endospore, a dormant, highly resistant spore with a thick wall that forms within the mother cell. Endospores are produced by some low G+C Gram-positive bacteria in response to harsh conditions." [GOC:ds, GOC:mah, ISBN:0470090278]
is_a: GO:0043936 ! asexual sporulation resulting in formation of a cellular spore
[Term]
id: GO:0034303
name: myxospore formation
namespace: biological_process
def: "The process in which differentiated, resting cells are formed, usually within a fruiting body by Myxobacteria. The myxospore is more resistant to high temperature, dessication, and UV than vegetative myxobacteria." [GOC:ds, ISBN:0122268008]
is_a: GO:0043936 ! asexual sporulation resulting in formation of a cellular spore
[Term]
id: GO:0034641
name: cellular nitrogen compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah]
subset: goslim_generic
subset: gosubset_prok
synonym: "cellular nitrogen compound metabolism" EXACT []
xref: Reactome:REACT_102000 "Metabolism of amino acids and derivatives, Mycobacterium tuberculosis"
xref: Reactome:REACT_103710 "Metabolism of amino acids and derivatives, Escherichia coli"
xref: Reactome:REACT_107293 "Metabolism of amino acids and derivatives, Arabidopsis thaliana"
xref: Reactome:REACT_108179 "Metabolism of amino acids and derivatives, Xenopus tropicalis"
xref: Reactome:REACT_109042 "Metabolism of amino acids and derivatives, Sus scrofa"
xref: Reactome:REACT_13 "Metabolism of amino acids and derivatives, Homo sapiens"
xref: Reactome:REACT_28699 "Metabolism of amino acids and derivatives, Saccharomyces cerevisiae"
xref: Reactome:REACT_29108 "Metabolism of amino acids and derivatives, Caenorhabditis elegans"
xref: Reactome:REACT_32429 "Metabolism of amino acids and derivatives, Rattus norvegicus"
xref: Reactome:REACT_33347 "Metabolism of amino acids and derivatives, Mus musculus"
xref: Reactome:REACT_34326 "Metabolism of amino acids and derivatives, Staphylococcus aureus N315"
xref: Reactome:REACT_55564 "Metabolism of amino acids and derivatives, Gallus gallus"
xref: Reactome:REACT_77741 "Metabolism of amino acids and derivatives, Taeniopygia guttata"
xref: Reactome:REACT_82379 "Metabolism of amino acids and derivatives, Bos taurus"
xref: Reactome:REACT_86268 "Metabolism of amino acids and derivatives, Drosophila melanogaster"
xref: Reactome:REACT_90299 "Metabolism of amino acids and derivatives, Oryza sativa"
xref: Reactome:REACT_91959 "Metabolism of amino acids and derivatives, Plasmodium falciparum"
xref: Reactome:REACT_93580 "Metabolism of amino acids and derivatives, Danio rerio"
xref: Reactome:REACT_95666 "Metabolism of amino acids and derivatives, Canis familiaris"
xref: Reactome:REACT_98086 "Metabolism of amino acids and derivatives, Dictyostelium discoideum"
xref: Reactome:REACT_99241 "Metabolism of amino acids and derivatives, Schizosaccharomyces pombe"
is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0044237 ! cellular metabolic process
[Term]
id: GO:0034645
name: cellular macromolecule biosynthetic process
namespace: biological_process
alt_id: GO:0034961
def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells." [CHEBI:33694, GOC:mah]
synonym: "cellular biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09]
synonym: "cellular macromolecule anabolism" EXACT [GOC:mah]
synonym: "cellular macromolecule biosynthesis" EXACT [GOC:mah]
synonym: "cellular macromolecule formation" EXACT [GOC:mah]
synonym: "cellular macromolecule synthesis" EXACT [GOC:mah]
is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0044249 ! cellular biosynthetic process
is_a: GO:0044260 ! cellular macromolecule metabolic process
[Term]
id: GO:0034654
name: nucleobase-containing compound biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah]
subset: gosubset_prok
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid anabolism" EXACT []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis" EXACT []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid formation" EXACT []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid synthesis" NARROW []
is_a: GO:0006139 ! nucleobase-containing compound metabolic process
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0019438 ! aromatic compound biosynthetic process
is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
[Term]
id: GO:0040007
name: growth
namespace: biological_process
alt_id: GO:0048590
def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma]
comment: See also the biological process term 'cell growth ; GO:0016049'.
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: gosubset_prok
synonym: "growth pattern" RELATED []
synonym: "non-developmental growth" RELATED [GOC:mah]
is_a: GO:0008150 ! biological_process
[Term]
id: GO:0040011
name: locomotion
namespace: biological_process
def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh]
subset: goslim_generic
subset: goslim_pir
subset: gosubset_prok
is_a: GO:0008150 ! biological_process
[Term]
id: GO:0042221
name: response to chemical
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus." [GOC:jl]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_yeast
subset: gosubset_prok
subset: qc_do_not_manually_annotate
synonym: "response to chemical stimulus" EXACT [GOC:dos]
synonym: "response to chemical substance" EXACT []
is_a: GO:0050896 ! response to stimulus
[Term]
id: GO:0042330
name: taxis
namespace: biological_process
def: "The directed movement of a motile cell or organism in response to an external stimulus." [GOC:jl, ISBN:0192801023]
subset: gosubset_prok
synonym: "directed movement in response to stimulus" EXACT []
xref: Wikipedia:Taxis
is_a: GO:0009605 ! response to external stimulus
is_a: GO:0040011 ! locomotion
[Term]
id: GO:0042995
name: cell projection
namespace: cellular_component
def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/]
subset: goslim_pir
subset: gosubset_prok
synonym: "cell process" BROAD []
synonym: "cellular process" BROAD []
synonym: "cellular projection" EXACT []
is_a: GO:0044464 ! cell part
[Term]
id: GO:0043107
name: type IV pilus-dependent motility
namespace: biological_process
def: "Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility." [GOC:go_curators, PMID:12704238]
subset: gosubset_prok
synonym: "social gliding motility" NARROW []
synonym: "TFP-dependent motility" EXACT []
synonym: "TFP-dependent movement" EXACT []
synonym: "twitching motility" NARROW []
synonym: "type 4 pilus-dependent motility" EXACT []
synonym: "type four pilus-dependent motility" EXACT []
is_a: GO:0048870 ! cell motility
[Term]
id: GO:0043158
name: heterocyst differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized features of a heterocyst, a differentiated cell in certain cyanobacteria whose purpose is to fix nitrogen." [GOC:jl]
subset: gosubset_prok
synonym: "heterocyst biosynthesis" EXACT []
synonym: "heterocyst cell differentiation" EXACT []
synonym: "heterocyst formation" EXACT []
is_a: GO:0030154 ! cell differentiation
[Term]
id: GO:0043170
name: macromolecule metabolic process
namespace: biological_process
alt_id: GO:0043283
def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah]
subset: goslim_pir
subset: gosubset_prok
synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09]
synonym: "macromolecule metabolism" EXACT []
is_a: GO:0071704 ! organic substance metabolic process
[Term]
id: GO:0043934
name: sporulation
namespace: biological_process
def: "The process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure. A spore is a structure that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." [GOC:pamgo_curators]