-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathgoslim_metagenomics.obo
1995 lines (1871 loc) · 90.9 KB
/
goslim_metagenomics.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: go/2023-11-15/subsets/goslim_metagenomics.owl
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
subsetdef: goslim_agr "AGR slim"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_drosophila "Drosophila GO slim"
subsetdef: goslim_flybase_ribbon "FlyBase Drosophila GO ribbon slim"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_metagenomics "Metagenomics GO slim"
subsetdef: goslim_mouse "Mouse GO slim"
subsetdef: goslim_pir "PIR GO slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_pombe "Fission yeast GO slim"
subsetdef: goslim_synapse "synapse GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: prokaryote_subset "GO subset for prokaryotes"
synonymtypedef: syngo_official_label "label approved by the SynGO project"
synonymtypedef: systematic_synonym "Systematic synonym" EXACT
ontology: go/subsets/goslim_metagenomics
property_value: owl:versionInfo "2023-11-15" xsd:string
[Term]
id: GO:0000015
name: phosphopyruvate hydratase complex
namespace: cellular_component
def: "A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water." [GOC:jl, ISBN:0198506732]
subset: goslim_metagenomics
synonym: "enolase complex" EXACT []
is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0000150
name: DNA strand exchange activity
namespace: molecular_function
def: "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC:elh]
comment: Note that this term represents activities that do not break or form phosphodiester bonds, and is therefore not a parent of 'site-specific recombinase activity ; GO:0009009'.
subset: goslim_metagenomics
synonym: "RecA-family recombinase activity" RELATED []
synonym: "recombinase activity" EXACT []
synonym: "strand exchange activity" RELATED []
synonym: "strand transferase" NARROW []
xref: Reactome:R-HSA-912458 "Formation of meiotic heteroduplex"
is_a: GO:0003824 ! catalytic activity
relationship: part_of GO:0006259 ! DNA metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20964" xsd:anyURI
[Term]
id: GO:0000160
name: phosphorelay signal transduction system
namespace: biological_process
def: "A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins." [PMID:9191038]
subset: goslim_metagenomics
synonym: "histidyl-aspartyl phosphorelay" EXACT []
is_a: GO:0007165 ! signal transduction
relationship: occurs_in GO:0005622 ! intracellular anatomical structure
[Term]
id: GO:0000166
name: nucleotide binding
namespace: molecular_function
def: "Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC:mah, ISBN:0198547684]
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0003674
name: molecular_function
namespace: molecular_function
alt_id: GO:0005554
def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt]
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "molecular function" EXACT []
[Term]
id: GO:0003676
name: nucleic acid binding
namespace: molecular_function
alt_id: GO:0000496
def: "Binding to a nucleic acid." [GOC:jl]
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "base pairing" NARROW []
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0003700
name: DNA-binding transcription factor activity
namespace: molecular_function
alt_id: GO:0000130
alt_id: GO:0001071
alt_id: GO:0001130
alt_id: GO:0001131
alt_id: GO:0001151
alt_id: GO:0001199
alt_id: GO:0001204
def: "A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons." [GOC:txnOH-2018]
comment: Usage guidance: Most DNA-binding transcription factors do not have enzymatic activity. The presence of specific DNA-binding domains known to be present in DNA-binding transcription factors (HOX, GATA etc) should be used to help decide whether a protein is a DNA binding transcription factor or a coregulator. If a protein has an enzymatic activity (for example, ubiquitin ligase, histone acetyl transferase) and no known DNA binding domain, consider annotating to GO:0003712 transcription coregulator activity. Special care should be taken with proteins containing zinc fingers, Myb/SANT and ARID domains, since only a subset of proteins containing these domains directly and selectively bind to regulatory DNA motifs in cis-regulatory regions.
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_plant
subset: goslim_yeast
synonym: "bacterial-type DNA binding transcription factor activity" NARROW []
synonym: "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity" NARROW []
synonym: "bacterial-type RNA polymerase transcription enhancer sequence-specific DNA binding transcription factor activity" NARROW []
synonym: "bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding" NARROW []
synonym: "bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding" NARROW []
synonym: "DNA binding transcription factor activity" EXACT []
synonym: "gene-specific transcription factor activity" EXACT []
synonym: "metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity" NARROW []
synonym: "metal ion regulated sequence-specific DNA binding transcription factor activity" NARROW []
synonym: "nucleic acid binding transcription factor activity" BROAD []
synonym: "sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity" NARROW []
synonym: "sequence-specific DNA binding transcription factor activity" EXACT []
synonym: "transcription factor activity" BROAD []
synonym: "transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding" NARROW []
synonym: "transcription factor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding" NARROW []
synonym: "transcription factor activity, bacterial-type RNA polymerase transcription enhancer sequence-specific binding" NARROW []
synonym: "transcription factor activity, metal ion regulated sequence-specific DNA binding" NARROW []
is_a: GO:0003674 ! molecular_function
relationship: has_part GO:0003676 ! nucleic acid binding
relationship: part_of GO:0019222 ! regulation of metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15704" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16534" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20253" xsd:anyURI
created_by: krc
creation_date: 2010-10-21T04:37:54Z
[Term]
id: GO:0003735
name: structural constituent of ribosome
namespace: molecular_function
alt_id: GO:0003736
alt_id: GO:0003737
alt_id: GO:0003738
alt_id: GO:0003739
alt_id: GO:0003740
alt_id: GO:0003741
alt_id: GO:0003742
def: "The action of a molecule that contributes to the structural integrity of the ribosome." [GOC:mah]
comment: Note that this term may be used to annotate ribosomal RNAs as well as ribosomal proteins.
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_yeast
synonym: "ribosomal protein" BROAD []
synonym: "ribosomal RNA" RELATED []
is_a: GO:0003674 ! molecular_function
relationship: occurs_in GO:0005840 ! ribosome
[Term]
id: GO:0003824
name: catalytic activity
namespace: molecular_function
def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb]
xref: Wikipedia:Enzyme
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0004601
name: peroxidase activity
namespace: molecular_function
alt_id: GO:0016685
alt_id: GO:0016686
alt_id: GO:0016687
alt_id: GO:0016693
def: "Catalysis of the reaction: a donor + a peroxide = an oxidized donor + 2 H2O." [GOC:curators]
subset: goslim_metagenomics
synonym: "bacterial catalase-peroxidase activity" NARROW []
synonym: "donor:hydrogen-peroxide oxidoreductase activity" RELATED []
synonym: "eosinophil peroxidase activity" NARROW []
synonym: "extensin peroxidase" NARROW []
synonym: "guaiacol peroxidase" NARROW []
synonym: "heme peroxidase" NARROW []
synonym: "horseradish peroxidase (HRP)" NARROW []
synonym: "japanese radish peroxidase" NARROW []
synonym: "lactoperoxidase activity" NARROW []
synonym: "MPO" RELATED []
synonym: "myeloperoxidase activity" NARROW []
synonym: "oxyperoxidase activity" RELATED []
synonym: "peroxidase reaction" EXACT []
synonym: "protoheme peroxidase" NARROW []
synonym: "pyrocatechol peroxidase" NARROW []
synonym: "scopoletin peroxidase" NARROW []
synonym: "secretory plant peroxidase activity" NARROW []
synonym: "thiocyanate peroxidase" NARROW []
synonym: "verdoperoxidase" NARROW []
xref: EC:1.11.1.-
xref: KEGG_REACTION:R03532
xref: Reactome:R-HSA-1222346 "AhpC reduces H2O2"
xref: Reactome:R-HSA-140359 "PGG2 is reduced to PGH2 by PTGS1"
xref: Reactome:R-HSA-209815 "Tyrosine is monoiodinated"
xref: Reactome:R-HSA-209840 "Two DITs combine to form thyroxine"
xref: Reactome:R-HSA-209925 "DIT and MIT combine to form triiodothyronine"
xref: Reactome:R-HSA-209973 "Tyrosine is diiodinated"
xref: Reactome:R-HSA-2309773 "PGG2 is reduced to PGH2 by PTGS2"
xref: Reactome:R-HSA-2559639 "Collagen type IV sulfilimine cross-linking by peroxidasin"
xref: Reactome:R-HSA-3341296 "GPX7,8 catalyze peroxidation of P4HB (PDI)"
xref: Reactome:R-HSA-350901 "Iodide is organified"
xref: Reactome:R-HSA-5631885 "PRDX1 overoxidizes"
xref: Reactome:R-HSA-6789031 "Membrane-bound myeloperoxidase (MPO) produces hypochlorous acid (HOCl)"
xref: Reactome:R-HSA-6789126 "Myeloperoxidase (MPO) produces hypochlorous acid (HOCl)"
xref: Reactome:R-HSA-8855490 "Lactoperoxidase (LPO) produces OSCN-"
xref: Reactome:R-HSA-8933635 "Myeloperoxidase (MPO) catalyzes oxidation of nitrite to nitrogen dioxide"
xref: Wikipedia:Peroxidase
is_a: GO:0016209 ! antioxidant activity
is_a: GO:0016491 ! oxidoreductase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23121" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25776" xsd:anyURI
[Term]
id: GO:0004803
name: transposase activity
namespace: molecular_function
alt_id: GO:0004804
def: "Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element." [GOC:bm, ISBN:0198506732]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "P-element encoded transposase activity" NARROW []
is_a: GO:0003824 ! catalytic activity
[Term]
id: GO:0005215
name: transporter activity
namespace: molecular_function
alt_id: GO:0005478
def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC:ai, GOC:dgf]
comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: prokaryote_subset
synonym: "carrier" RELATED []
xref: Reactome:R-HSA-168313 "Virion-associated M2 protein mediated ion infusion"
xref: Reactome:R-HSA-178215 "SMAD7:SMURF1 complex is exported to the cytosol"
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0005515
name: protein binding
namespace: molecular_function
alt_id: GO:0001948
alt_id: GO:0045308
def: "Binding to a protein." [GOC:go_curators]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "glycoprotein binding" NARROW []
synonym: "protein amino acid binding" EXACT []
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0005575
name: cellular_component
namespace: cellular_component
alt_id: GO:0008372
def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt]
comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. 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 'no data' (ND), is used to indicate this.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "cell or subcellular entity" EXACT []
synonym: "cellular component" EXACT []
synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315]
xref: NIF_Subcellular:sao1337158144
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17729" xsd:anyURI
[Term]
id: GO:0005576
name: extracellular region
namespace: cellular_component
def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators]
comment: Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: prokaryote_subset
synonym: "extracellular" EXACT []
xref: Wikipedia:Extracellular
is_a: GO:0005575 ! cellular_component
[Term]
id: GO:0005618
name: cell wall
namespace: cellular_component
def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins." [GOC:giardia, ISBN:0198547684, PMID:15134259, Wikipedia:Microbial_cyst]
comment: Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for plants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).
subset: gocheck_do_not_annotate
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: prokaryote_subset
xref: Wikipedia:Cell_wall
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005575 ! cellular_component
property_value: RO:0002161 NCBITaxon:33208
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21669" xsd:anyURI
[Term]
id: GO:0005622
name: intracellular anatomical structure
namespace: cellular_component
def: "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732]
subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_plant
synonym: "internal to cell" EXACT []
synonym: "intracellular" EXACT []
synonym: "nucleocytoplasm" RELATED [GOC:mah]
synonym: "protoplasm" EXACT []
synonym: "protoplast" RELATED [GOC:mah]
xref: Wikipedia:Intracellular
is_a: GO:0005575 ! cellular_component
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17776" xsd:anyURI
[Term]
id: GO:0005634
name: nucleus
namespace: cellular_component
def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "cell nucleus" EXACT []
synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757]
xref: NIF_Subcellular:sao1702920020
xref: Wikipedia:Cell_nucleus
is_a: GO:0005575 ! cellular_component
relationship: has_part GO:0016020 ! membrane
relationship: part_of GO:0005622 ! intracellular anatomical structure
[Term]
id: GO:0005694
name: chromosome
namespace: cellular_component
def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684]
comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
subset: prokaryote_subset
synonym: "chromatid" RELATED []
synonym: "interphase chromosome" NARROW []
synonym: "prophase chromosome" NARROW []
xref: Wikipedia:Chromosome
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005622 ! intracellular anatomical structure
[Term]
id: GO:0005727
name: extrachromosomal circular DNA
namespace: cellular_component
def: "Circular DNA structures that are not part of a chromosome." [GOC:ai]
subset: goslim_metagenomics
is_a: GO:0005622 ! intracellular anatomical structure
relationship: part_of GO:0005622 ! intracellular anatomical structure
[Term]
id: GO:0005737
name: cytoplasm
namespace: cellular_component
def: "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: prokaryote_subset
xref: Wikipedia:Cytoplasm
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005622 ! intracellular anatomical structure
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI
[Term]
id: GO:0005839
name: proteasome core complex
namespace: cellular_component
alt_id: GO:0000503
def: "A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex." [GOC:rb, PMID:10806206]
subset: goslim_metagenomics
synonym: "20S core complex" NARROW []
synonym: "20S proteasome" NARROW [GOC:cjk]
synonym: "macropain" EXACT []
synonym: "PA28gamma-20S proteasome" NARROW [CORUM:194]
is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:1902494 ! catalytic complex
[Term]
id: GO:0005840
name: ribosome
namespace: cellular_component
alt_id: GO:0033279
def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: prokaryote_subset
synonym: "free ribosome" NARROW [NIF_Subcellular:sao1139385046]
synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653]
synonym: "ribosomal RNA" RELATED []
xref: NIF_Subcellular:sao1429207766
xref: Wikipedia:Ribosome
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005622 ! intracellular anatomical structure
[Term]
id: GO:0005874
name: microtubule
namespace: cellular_component
def: "Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle." [ISBN:0879693568]
subset: goslim_metagenomics
synonym: "microtubuli" EXACT []
synonym: "microtubulus" EXACT []
synonym: "neurotubule" NARROW [NIF_Subcellular:sao248349196]
xref: NIF_Subcellular:sao1846835077
xref: Wikipedia:Microtubule
is_a: GO:0005575 ! cellular_component
relationship: part_of GO:0005622 ! intracellular anatomical structure
[Term]
id: GO:0005886
name: plasma membrane
namespace: cellular_component
alt_id: GO:0005887
alt_id: GO:0005904
def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_plant
subset: goslim_yeast
subset: prokaryote_subset
synonym: "bacterial inner membrane" NARROW []
synonym: "cell membrane" EXACT []
synonym: "cellular membrane" EXACT [NIF_Subcellular:sao6433132645]
synonym: "cytoplasmic membrane" EXACT []
synonym: "inner endospore membrane" NARROW []
synonym: "integral component of plasma membrane" NARROW []
synonym: "integral to plasma membrane" NARROW []
synonym: "juxtamembrane" BROAD []
synonym: "plasma membrane lipid bilayer" NARROW [GOC:mah]
synonym: "plasmalemma" EXACT []
xref: NIF_Subcellular:sao1663586795
xref: Wikipedia:Cell_membrane
is_a: GO:0016020 ! membrane
relationship: part_of GO:0005575 ! cellular_component
[Term]
id: GO:0005975
name: carbohydrate metabolic process
namespace: biological_process
alt_id: GO:0044261
alt_id: GO:0044723
def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:mah, ISBN:0198506732]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
subset: prokaryote_subset
synonym: "carbohydrate metabolism" EXACT []
xref: Wikipedia:Carbohydrate_metabolism
is_a: GO:0008152 ! metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22880" xsd:anyURI
created_by: jl
creation_date: 2012-10-23T15:40:34Z
[Term]
id: GO:0006091
name: generation of precursor metabolites and energy
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." [GOC:jl]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
subset: prokaryote_subset
synonym: "energy pathways" BROAD []
synonym: "intermediary metabolism" RELATED [GOC:mah]
synonym: "metabolic energy generation" RELATED []
is_a: GO:0008152 ! 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_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "cellular DNA metabolism" EXACT []
synonym: "DNA metabolism" EXACT []
is_a: GO:0006807 ! nitrogen compound metabolic process
[Term]
id: GO:0006282
name: regulation of DNA repair
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA repair." [GOC:go_curators]
subset: goslim_metagenomics
is_a: GO:0019222 ! regulation of metabolic process
relationship: regulates GO:0006259 ! DNA metabolic process
relationship: regulates GO:0006950 ! response to stress
[Term]
id: GO:0006351
name: DNA-templated transcription
namespace: biological_process
alt_id: GO:0001121
alt_id: GO:0006350
alt_id: GO:0061018
alt_id: GO:0061022
def: "The synthesis of an RNA transcript from a DNA template." [GOC:jl, GOC:txnOH]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_pombe
subset: prokaryote_subset
synonym: "bacterial transcription" NARROW []
synonym: "cellular transcription" BROAD []
synonym: "DNA-dependent transcription" EXACT []
synonym: "transcription" BROAD []
synonym: "transcription from bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcription, DNA-dependent" EXACT [GOC:txnOH]
synonym: "transcription, DNA-templated" EXACT []
xref: Wikipedia:Transcription_(genetics)
is_a: GO:0009058 ! biosynthetic process
is_a: GO:0016070 ! RNA metabolic process
relationship: part_of GO:0009058 ! biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14854" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16737" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22258" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22555" xsd:anyURI
[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 or circRNA 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 or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: prokaryote_subset
synonym: "protein anabolism" EXACT []
synonym: "protein biosynthesis" EXACT []
synonym: "protein biosynthetic process" EXACT []
synonym: "protein formation" EXACT []
synonym: "protein synthesis" EXACT []
synonym: "protein translation" EXACT []
xref: Wikipedia:Translation_(genetics)
is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0009058 ! biosynthetic process
relationship: has_part GO:0009058 ! biosynthetic process
[Term]
id: GO:0006457
name: protein folding
namespace: biological_process
alt_id: GO:0007022
alt_id: GO:0007024
alt_id: GO:0007025
def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:go_curators, GOC:rb]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
subset: prokaryote_subset
synonym: "alpha-tubulin folding" NARROW [GOC:mah]
synonym: "beta-tubulin folding" NARROW [GOC:mah]
synonym: "chaperone activity" RELATED []
synonym: "chaperonin ATPase activity" RELATED []
synonym: "chaperonin-mediated tubulin folding" NARROW [GOC:mah]
synonym: "co-chaperone activity" RELATED []
synonym: "co-chaperonin activity" RELATED []
synonym: "glycoprotein-specific chaperone activity" RELATED []
synonym: "non-chaperonin molecular chaperone ATPase activity" RELATED []
synonym: "protein complex assembly, multichaperone pathway" RELATED []
xref: Wikipedia:Protein_folding
is_a: GO:0008150 ! biological_process
relationship: part_of GO:0006807 ! nitrogen compound metabolic process
relationship: part_of GO:0009058 ! biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25673" xsd:anyURI
[Term]
id: GO:0006508
name: proteolysis
namespace: biological_process
def: "The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds." [GOC:bf, GOC:mah]
comment: This term was intentionally placed under 'protein metabolic process ; GO:0019538' rather than 'protein catabolic process ; GO:0030163' to cover all processes centered on breaking peptide bonds, including those involved in protein processing.
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
synonym: "ATP-dependent proteolysis" NARROW [GOC:mah]
synonym: "peptidolysis" EXACT []
xref: Wikipedia:Proteolysis
is_a: GO:0006807 ! nitrogen compound metabolic process
[Term]
id: GO:0006629
name: lipid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
subset: prokaryote_subset
synonym: "lipid metabolism" EXACT []
xref: Wikipedia:Lipid_metabolism
is_a: GO:0008152 ! 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." [GOC:jl, ISBN:0198506732]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "nitrogen compound metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0006808
name: regulation of nitrogen utilization
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of nitrogen utilization." [GOC:go_curators]
subset: goslim_metagenomics
is_a: GO:0008150 ! biological_process
relationship: regulates GO:0008150 ! biological_process
[Term]
id: GO:0006810
name: transport
namespace: biological_process
alt_id: GO:0015457
alt_id: GO:0015460
alt_id: GO:0044765
def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
subset: gocheck_do_not_annotate
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: prokaryote_subset
synonym: "single-organism transport" RELATED []
is_a: GO:0008150 ! biological_process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI
created_by: jl
creation_date: 2012-12-13T16:25:32Z
[Term]
id: GO:0006950
name: response to stress
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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah]
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: gocheck_do_not_manually_annotate
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_plant
synonym: "response to abiotic stress" RELATED []
synonym: "response to biotic stress" RELATED []
is_a: GO:0008150 ! biological_process
[Term]
id: GO:0007155
name: cell adhesion
namespace: biological_process
alt_id: GO:0098602
def: "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." [GOC:hb, GOC:pf]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
subset: prokaryote_subset
synonym: "cell adhesion molecule activity" RELATED []
synonym: "single organism cell adhesion" RELATED []
xref: Wikipedia:Cell_adhesion
is_a: GO:0008150 ! biological_process
created_by: dos
creation_date: 2014-04-15T15:59:10Z
[Term]
id: GO:0007165
name: signal transduction
namespace: biological_process
alt_id: GO:0023014
alt_id: GO:0023015
alt_id: GO:0023016
alt_id: GO:0023033
alt_id: GO:0023045
def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11]
comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_plant
synonym: "signal transduction by cis-phosphorylation" NARROW []
synonym: "signal transduction by conformational transition" NARROW []
synonym: "signal transduction by protein phosphorylation" NARROW []
synonym: "signal transduction by trans-phosphorylation" NARROW []
synonym: "signaling cascade" NARROW []
synonym: "signaling pathway" RELATED []
synonym: "signalling cascade" NARROW []
synonym: "signalling pathway" RELATED [GOC:mah]
xref: Wikipedia:Signal_transduction
is_a: GO:0008150 ! biological_process
relationship: part_of GO:0008150 ! biological_process
[Term]
id: GO:0008134
name: transcription factor binding
namespace: molecular_function
def: "Binding to a transcription factor, a protein required to initiate or regulate transcription." [ISBN:0198506732]
comment: Note that this term should not be used for direct annotation. Please consier one of the more specific descendants, GO:0140297 ; DNA-binding transcription factor binding, GO:0140296 ; general transcription initiation factor binding or GO:0001221 ; transcription coregulator binding.
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_yeast
synonym: "TF binding" EXACT []
synonym: "transcription regulator binding" RELATED []
is_a: GO:0005515 ! protein binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19354" xsd:anyURI
[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
alt_id: GO:0000004
alt_id: GO:0007582
alt_id: GO:0044699
def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. 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 'no data' (ND), is used to indicate this.
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
synonym: "biological process" EXACT []
synonym: "physiological process" EXACT []
synonym: "single organism process" RELATED []
synonym: "single-organism process" RELATED []
xref: Wikipedia:Biological_process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI
created_by: jl
creation_date: 2012-09-19T15:05:24Z
[Term]
id: GO:0008152
name: metabolic process
namespace: biological_process
alt_id: GO:0044236
alt_id: GO:0044710
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: gocheck_do_not_manually_annotate
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
synonym: "metabolic process resulting in cell growth" NARROW []
synonym: "metabolism" EXACT []
synonym: "metabolism resulting in cell growth" NARROW []
synonym: "multicellular organism metabolic process" NARROW []
synonym: "single-organism metabolic process" RELATED []
xref: Wikipedia:Metabolism
is_a: GO:0008150 ! biological_process
created_by: jl
creation_date: 2012-10-17T15:46:40Z
[Term]
id: GO:0008218
name: bioluminescence
namespace: biological_process
def: "The production of light by certain enzyme-catalyzed reactions in cells." [ISBN:0198506732]
subset: goslim_chembl
subset: goslim_metagenomics
xref: Wikipedia:Bioluminescence
is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0008233
name: peptidase activity
namespace: molecular_function
alt_id: GO:0070010
alt_id: GO:0070011
def: "Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid." [GOC:jl, ISBN:0815332181]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
synonym: "hydrolase, acting on peptide bonds" EXACT []
synonym: "peptidase activity, acting on D-amino acid peptides" NARROW []
synonym: "peptidase activity, acting on L-amino acid peptides" NARROW []
synonym: "peptide hydrolase activity" EXACT []
synonym: "protease activity" EXACT []
synonym: "proteinase activity" NARROW []
xref: EC:3.4.-.-
xref: Reactome:R-HSA-205112 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6"
xref: Reactome:R-HSA-3000243 "Unknown lysosomal protease degrades CBLIF:RCbl to release Cbl"
xref: Reactome:R-HSA-3000263 "TCN2:RCbl is degraded to release RCbl"
xref: Reactome:R-HSA-3065958 "An unknown protease degrades ACACA"
xref: Reactome:R-HSA-3065959 "An unknown protease degrades hCBXs"
xref: Reactome:R-HSA-3139027 "Maturation of HIV Virion"
xref: Reactome:R-HSA-376149 "Proteolytic processing of SLIT"
xref: Reactome:R-HSA-4167501 "An unknown protease degrades ACACB"
xref: Reactome:R-HSA-448678 "CTSG cleaves CASP1(1-404)"
xref: Reactome:R-HSA-5655483 "USP1 autocleavage"
xref: Reactome:R-HSA-5684864 "NAPSA, CTSH, PGA3-5 cleave pro-SFTPB"
xref: Reactome:R-HSA-5685902 "NAPSA, CTSH, PGA3-5 cleave pro-SFTPC"
xref: Reactome:R-HSA-6803060 "DCD(63-110) is processed to DCD(63-109)"
is_a: GO:0016787 ! hydrolase activity
[Term]
id: GO:0008658
name: penicillin binding
namespace: molecular_function
def: "Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system." [GOC:ai]
subset: goslim_metagenomics
is_a: GO:0043167 ! ion binding
[Term]
id: GO:0009055
name: electron transfer activity
namespace: molecular_function
alt_id: GO:0009053
alt_id: GO:0009054
def: "Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient." [ISBN:0198506732]
comment: Note that this term should only be be used for electron transfer that generates a transmembrane electrochemical gradient, e.g. components of the respiratory or photosynthetic electron transport chain.
subset: goslim_metagenomics
subset: goslim_pir
synonym: "electron acceptor activity" NARROW []
synonym: "electron carrier" RELATED []
synonym: "electron donor activity" NARROW []
synonym: "electron transporter activity" RELATED []
xref: Reactome:R-HSA-169260 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF"
xref: Reactome:R-HSA-2564826 "4Fe-4S cluster assembles on NUBP2:NUBP1 scaffold"
is_a: GO:0016491 ! oxidoreductase activity
relationship: part_of GO:0006091 ! generation of precursor metabolites and energy
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21334" xsd:anyURI
[Term]
id: GO:0009058
name: biosynthetic process
namespace: biological_process
alt_id: GO:0044274
alt_id: GO:0044711
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_chembl
subset: goslim_metagenomics
subset: goslim_plant
synonym: "anabolism" EXACT []
synonym: "biosynthesis" EXACT []
synonym: "formation" BROAD []
synonym: "multicellular organismal biosynthetic process" NARROW []
synonym: "single-organism biosynthetic process" RELATED []
synonym: "synthesis" EXACT []
xref: Wikipedia:Anabolism
is_a: GO:0008152 ! metabolic process
created_by: jl
creation_date: 2012-10-17T15:52:18Z
[Term]
id: GO:0009276
name: Gram-negative-bacterium-type cell wall
namespace: cellular_component
def: "The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain." [GOC:mlg, ISBN:0815108893]
subset: goslim_metagenomics
synonym: "1-2nm peptidoglycan-based cell wall" EXACT []
synonym: "cell wall inner membrane" EXACT []
is_a: GO:0005618 ! cell wall
[Term]
id: GO:0009288
name: bacterial-type flagellum
namespace: cellular_component
def: "A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope." [GOC:cilia, GOC:jh2, GOC:krc, GOC:mtg_sensu, http:en.wikipedia.org/wiki/Flagellum#Bacterial, PMID:7787060]
subset: goslim_metagenomics
subset: goslim_pir