Mercurial > repos > iuc > goslimmer

comparison test-data/go.obo @ 0:294de027cb5d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
author iuc
date Fri, 11 Jan 2019 06:18:00 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:294de027cb5d
1 format-version: 1.2
2 data-version: releases/2018-04-30
3 subsetdef: goantislim_grouping "Grouping classes that can be excluded"
4 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
5 subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
6 subsetdef: goslim_agr "AGR slim"
7 subsetdef: goslim_aspergillus "Aspergillus GO slim"
8 subsetdef: goslim_candida "Candida GO slim"
9 subsetdef: goslim_chembl "ChEMBL protein targets summary"
10 subsetdef: goslim_generic "Generic GO slim"
11 subsetdef: goslim_goa "GOA and proteome slim"
12 subsetdef: goslim_metagenomics "Metagenomics GO slim"
13 subsetdef: goslim_mouse "Mouse GO slim"
14 subsetdef: goslim_pir "PIR GO slim"
15 subsetdef: goslim_plant "Plant GO slim"
16 subsetdef: goslim_pombe "Fission yeast GO slim"
17 subsetdef: goslim_synapse "synapse GO slim"
18 subsetdef: goslim_virus "Viral GO slim"
19 subsetdef: goslim_yeast "Yeast GO slim"
20 subsetdef: gosubset_prok "Prokaryotic GO subset"
21 subsetdef: mf_needs_review "Catalytic activity terms in need of attention"
22 subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors"
23 subsetdef: virus_checked "Viral overhaul terms"
24 synonymtypedef: syngo_official_label "label approved by the SynGO project"
25 synonymtypedef: systematic_synonym "Systematic synonym" EXACT
26 default-namespace: gene_ontology
27 remark: cvs version: $Revision: 38972$
28 remark: Includes Ontology(OntologyID(Anonymous-35)) [Axioms: 230 Logical Axioms: 228]
29 remark: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/never_in_taxon.owl>))) [Axioms: 18 Logical Axioms: 0]
30 ontology: go
31 property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/licenses/by/4.0/
32
33 [Term]
34 id: GO:0000003
35 name: reproduction
36 namespace: biological_process
37 alt_id: GO:0019952
38 alt_id: GO:0050876
39 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]
40 subset: goslim_agr
41 subset: goslim_chembl
42 subset: goslim_generic
43 subset: goslim_pir
44 subset: goslim_plant
45 subset: gosubset_prok
46 synonym: "reproductive physiological process" EXACT []
47 xref: Wikipedia:Reproduction
48 is_a: GO:0008150 ! biological_process
49 disjoint_from: GO:0044848 ! biological phase
50
51 [Term]
52 id: GO:0001906
53 name: cell killing
54 namespace: biological_process
55 def: "Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." [GOC:add]
56 subset: goslim_pir
57 subset: gosubset_prok
58 synonym: "necrosis" RELATED []
59 is_a: GO:0008150 ! biological_process
60 disjoint_from: GO:0044848 ! biological phase
61
62 [Term]
63 id: GO:0002376
64 name: immune system process
65 namespace: biological_process
66 def: "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05]
67 comment: Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022.
68 subset: goslim_agr
69 subset: goslim_chembl
70 subset: goslim_generic
71 subset: goslim_mouse
72 subset: goslim_pir
73 xref: Wikipedia:Immune_system
74 is_a: GO:0008150 ! biological_process
75 disjoint_from: GO:0044848 ! biological phase
76
77 [Term]
78 id: GO:0003674
79 name: molecular_function
80 namespace: molecular_function
81 alt_id: GO:0005554
82 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt]
83 comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use 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.
84 subset: goslim_aspergillus
85 subset: goslim_candida
86 subset: goslim_chembl
87 subset: goslim_generic
88 subset: goslim_metagenomics
89 subset: goslim_pir
90 subset: goslim_plant
91 subset: goslim_yeast
92 subset: gosubset_prok
93 synonym: "molecular function" EXACT []
94
95 [Term]
96 id: GO:0003824
97 name: catalytic activity
98 namespace: molecular_function
99 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]
100 subset: goslim_chembl
101 subset: goslim_metagenomics
102 subset: goslim_pir
103 subset: goslim_plant
104 subset: gosubset_prok
105 synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb]
106 xref: Wikipedia:Enzyme
107 is_a: GO:0003674 ! molecular_function
108
109 [Term]
110 id: GO:0005198
111 name: structural molecule activity
112 namespace: molecular_function
113 def: "The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell." [GOC:mah, GOC:vw]
114 subset: goslim_agr
115 subset: goslim_aspergillus
116 subset: goslim_candida
117 subset: goslim_chembl
118 subset: goslim_generic
119 subset: goslim_pir
120 subset: goslim_plant
121 subset: goslim_yeast
122 subset: gosubset_prok
123 is_a: GO:0003674 ! molecular_function
124
125 [Term]
126 id: GO:0005215
127 name: transporter activity
128 namespace: molecular_function
129 alt_id: GO:0005478
130 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]
131 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.
132 subset: goslim_agr
133 subset: goslim_aspergillus
134 subset: goslim_candida
135 subset: goslim_chembl
136 subset: goslim_metagenomics
137 subset: goslim_mouse
138 subset: goslim_pir
139 subset: goslim_plant
140 subset: gosubset_prok
141 synonym: "carrier" RELATED []
142 xref: Reactome:REACT_6315 "Virion-associated M2 protein mediated ion infusion, Homo sapiens"
143 is_a: GO:0003674 ! molecular_function
144
145 [Term]
146 id: GO:0005488
147 name: binding
148 namespace: molecular_function
149 def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732]
150 comment: Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
151 subset: gocheck_do_not_manually_annotate
152 subset: goslim_pir
153 subset: goslim_plant
154 subset: gosubset_prok
155 synonym: "ligand" NARROW []
156 xref: Wikipedia:Binding_(molecular)
157 is_a: GO:0003674 ! molecular_function
158
159 [Term]
160 id: GO:0005575
161 name: cellular_component
162 namespace: cellular_component
163 alt_id: GO:0008372
164 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." [GOC:pdt, NIF_Subcellular:sao-1337158144]
165 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. 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.
166 subset: goslim_aspergillus
167 subset: goslim_candida
168 subset: goslim_chembl
169 subset: goslim_generic
170 subset: goslim_metagenomics
171 subset: goslim_pir
172 subset: goslim_plant
173 subset: goslim_yeast
174 subset: gosubset_prok
175 synonym: "cell or subcellular entity" EXACT []
176 synonym: "cellular component" EXACT []
177 synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315]
178 xref: NIF_Subcellular:sao-1337158144
179 xref: NIF_Subcellular:sao1337158144
180
181 [Term]
182 id: GO:0005576
183 name: extracellular region
184 namespace: cellular_component
185 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]
186 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'.
187 subset: goslim_agr
188 subset: goslim_aspergillus
189 subset: goslim_candida
190 subset: goslim_chembl
191 subset: goslim_generic
192 subset: goslim_metagenomics
193 subset: goslim_mouse
194 subset: goslim_pir
195 subset: goslim_plant
196 subset: goslim_yeast
197 subset: gosubset_prok
198 synonym: "extracellular" EXACT []
199 xref: Wikipedia:Extracellular
200 is_a: GO:0005575 ! cellular_component
201
202 [Term]
203 id: GO:0005623
204 name: cell
205 namespace: cellular_component
206 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]
207 subset: goslim_chembl
208 subset: goslim_generic
209 subset: goslim_plant
210 subset: gosubset_prok
211 xref: NIF_Subcellular:sao1813327414
212 xref: Wikipedia:Cell_(biology)
213 is_a: GO:0005575 ! cellular_component
214 property_value: IAO:0000589 "cell and encapsulating structures" xsd:string
215
216 [Term]
217 id: GO:0006791
218 name: sulfur utilization
219 namespace: biological_process
220 def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary sulfur sources and then activates genes to scavenge the last traces of the primary sulfur source and to transport and metabolize alternate sulfur sources. The utilization process begins when the cell or organism detects sulfur levels, includes the activation of genes whose products detect, transport or metabolize sulfur-containing compounds, and ends when the sulfur is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg]
221 subset: gosubset_prok
222 synonym: "sulphur utilization" EXACT []
223 is_a: GO:0008150 ! biological_process
224
225 [Term]
226 id: GO:0006794
227 name: phosphorus utilization
228 namespace: biological_process
229 def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary phosphorus source and then activates genes to scavenge the last traces of the primary phosphorus source and to transport and metabolize alternative phosphorus sources. The utilization process begins when the cell or organism detects phosphorus levels, includes the phosphorus-containing substances, and ends when phosphorus is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg]
230 subset: gosubset_prok
231 is_a: GO:0008150 ! biological_process
232
233 [Term]
234 id: GO:0007610
235 name: behavior
236 namespace: biological_process
237 alt_id: GO:0044708
238 def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973]
239 comment: 1. 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 reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
240 subset: gocheck_do_not_manually_annotate
241 subset: goslim_agr
242 subset: goslim_plant
243 subset: gosubset_prok
244 synonym: "behavioral response to stimulus" EXACT []
245 synonym: "behaviour" EXACT []
246 synonym: "behavioural response to stimulus" EXACT []
247 synonym: "single-organism behavior" RELATED []
248 xref: Wikipedia:Behavior
249 is_a: GO:0008150 ! biological_process
250 disjoint_from: GO:0032502 ! developmental process
251 created_by: janelomax
252 creation_date: 2012-09-20T14:06:08Z
253
254 [Term]
255 id: GO:0008150
256 name: biological_process
257 namespace: biological_process
258 alt_id: GO:0000004
259 alt_id: GO:0007582
260 alt_id: GO:0044699
261 def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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]
262 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. 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.
263 subset: goslim_aspergillus
264 subset: goslim_candida
265 subset: goslim_chembl
266 subset: goslim_generic
267 subset: goslim_metagenomics
268 subset: goslim_pir
269 subset: goslim_plant
270 subset: goslim_pombe
271 subset: goslim_yeast
272 subset: gosubset_prok
273 synonym: "biological process" EXACT []
274 synonym: "physiological process" EXACT []
275 synonym: "single organism process" RELATED []
276 synonym: "single-organism process" RELATED []
277 xref: Wikipedia:Biological_process
278 created_by: janelomax
279 creation_date: 2012-09-19T15:05:24Z
280
281 [Term]
282 id: GO:0008152
283 name: metabolic process
284 namespace: biological_process
285 alt_id: GO:0044236
286 alt_id: GO:0044710
287 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]
288 comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
289 subset: gocheck_do_not_manually_annotate
290 subset: goslim_chembl
291 subset: goslim_metagenomics
292 subset: goslim_pir
293 subset: goslim_plant
294 subset: gosubset_prok
295 synonym: "metabolic process resulting in cell growth" NARROW []
296 synonym: "metabolism" EXACT []
297 synonym: "metabolism resulting in cell growth" NARROW []
298 synonym: "multicellular organism metabolic process" NARROW []
299 synonym: "single-organism metabolic process" RELATED []
300 xref: Wikipedia:Metabolism
301 is_a: GO:0008150 ! biological_process
302 disjoint_from: GO:0044848 ! biological phase
303 created_by: janelomax
304 creation_date: 2012-10-17T15:46:40Z
305
306 [Term]
307 id: GO:0008283
308 name: cell proliferation
309 namespace: biological_process
310 def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb]
311 comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.
312 subset: goslim_agr
313 subset: goslim_chembl
314 subset: goslim_generic
315 subset: goslim_mouse
316 subset: goslim_pir
317 subset: gosubset_prok
318 is_a: GO:0008150 ! biological_process
319
320 [Term]
321 id: GO:0009295
322 name: nucleoid
323 namespace: cellular_component
324 def: "The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined." [GOC:bm, GOC:ma, ISBN:3540076689]
325 subset: gosubset_prok
326 xref: Wikipedia:Nucleoid
327 is_a: GO:0005575 ! cellular_component
328
329 [Term]
330 id: GO:0009758
331 name: carbohydrate utilization
332 namespace: biological_process
333 alt_id: GO:0007587
334 def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbohydrate sources,usually glucose, and then activates genes to scavenge the last traces of the primary carbohydrate source and to transport and metabolize alternate carbohydrate sources. The utilization process begins when the cell or organism detects carbohydrate levels, includes the activation of genes whose products detect, transport or metabolize carbohydrates, and ends when the carbohydrate is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mcc2, GOC:mlg]
335 synonym: "sugar utilization" NARROW [GOC:mcc2]
336 is_a: GO:0008150 ! biological_process
337
338 [Term]
339 id: GO:0009987
340 name: cellular process
341 namespace: biological_process
342 alt_id: GO:0008151
343 alt_id: GO:0044763
344 alt_id: GO:0050875
345 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]
346 subset: goslim_pir
347 subset: goslim_plant
348 subset: gosubset_prok
349 synonym: "cell growth and/or maintenance" NARROW []
350 synonym: "cell physiology" EXACT []
351 synonym: "cellular physiological process" EXACT []
352 synonym: "single-organism cellular process" RELATED []
353 is_a: GO:0008150 ! biological_process
354 disjoint_from: GO:0044848 ! biological phase
355 created_by: janelomax
356 creation_date: 2012-12-11T16:56:55Z
357
358 [Term]
359 id: GO:0015976
360 name: carbon utilization
361 namespace: biological_process
362 alt_id: GO:0015978
363 def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg]
364 subset: goslim_chembl
365 subset: goslim_pir
366 subset: gosubset_prok
367 synonym: "carbon utilization by utilization of organic compounds" EXACT [GOC:mah]
368 synonym: "heterotrophy" EXACT []
369 xref: Wikipedia:Heterotroph
370 is_a: GO:0008150 ! biological_process
371
372 [Term]
373 id: GO:0016020
374 name: membrane
375 namespace: cellular_component
376 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it." [GOC:dos, GOC:mah, ISBN:0815316194]
377 subset: goslim_aspergillus
378 subset: goslim_candida
379 subset: goslim_chembl
380 subset: goslim_metagenomics
381 subset: goslim_pir
382 subset: goslim_plant
383 subset: goslim_yeast
384 subset: gosubset_prok
385 xref: Wikipedia:Biological_membrane
386 is_a: GO:0005575 ! cellular_component
387
388 [Term]
389 id: GO:0016209
390 name: antioxidant activity
391 namespace: molecular_function
392 def: "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage." [ISBN:0198506732]
393 subset: goslim_metagenomics
394 subset: goslim_pir
395 subset: gosubset_prok
396 is_a: GO:0003674 ! molecular_function
397
398 [Term]
399 id: GO:0019012
400 name: virion
401 namespace: cellular_component
402 def: "The complete fully infectious extracellular virus particle." [ISBN:0781718325]
403 subset: goslim_chembl
404 subset: goslim_metagenomics
405 subset: goslim_pir
406 synonym: "complete virus particle" EXACT []
407 xref: Wikipedia:Virus
408 is_a: GO:0005575 ! cellular_component
409
410 [Term]
411 id: GO:0019740
412 name: nitrogen utilization
413 namespace: biological_process
414 def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary nitrogen source, usually ammonia, and then activates genes to scavenge the last traces of the primary nitrogen source and to transport and metabolize alternative nitrogen sources. The utilization process begins when the cell or organism detects nitrogen levels, includes the activation of genes whose products detect, transport or metabolize nitrogen-containing substances, and ends when nitrogen is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg]
415 subset: gosubset_prok
416 is_a: GO:0008150 ! biological_process
417
418 [Term]
419 id: GO:0022414
420 name: reproductive process
421 namespace: biological_process
422 alt_id: GO:0044702
423 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete]
424 subset: gosubset_prok
425 synonym: "single organism reproductive process" RELATED []
426 is_a: GO:0008150 ! biological_process
427 intersection_of: GO:0008150 ! biological_process
428 intersection_of: part_of GO:0000003 ! reproduction
429 disjoint_from: GO:0044848 ! biological phase
430 relationship: part_of GO:0000003 ! reproduction
431 created_by: janelomax
432 creation_date: 2012-09-19T15:56:06Z
433
434 [Term]
435 id: GO:0022610
436 name: biological adhesion
437 namespace: biological_process
438 def: "The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions." [GOC:isa_complete]
439 subset: goslim_pir
440 subset: gosubset_prok
441 is_a: GO:0008150 ! biological_process
442 disjoint_from: GO:0044848 ! biological phase
443
444 [Term]
445 id: GO:0023052
446 name: signaling
447 namespace: biological_process
448 alt_id: GO:0023046
449 alt_id: GO:0044700
450 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling]
451 comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
452 subset: goslim_agr
453 subset: goslim_mouse
454 subset: goslim_pombe
455 subset: goslim_yeast
456 synonym: "biological signaling" EXACT []
457 synonym: "signaling process" EXACT []
458 synonym: "signalling" EXACT []
459 synonym: "signalling process" RELATED [GOC:mah]
460 synonym: "single organism signaling" RELATED []
461 is_a: GO:0008150 ! biological_process
462 disjoint_from: GO:0044848 ! biological phase
463 created_by: janelomax
464 creation_date: 2010-02-16T09:30:50Z
465
466 [Term]
467 id: GO:0030054
468 name: cell junction
469 namespace: cellular_component
470 def: "A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix." [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732]
471 subset: goslim_agr
472 xref: Wikipedia:Cell_junction
473 is_a: GO:0005575 ! cellular_component
474
475 [Term]
476 id: GO:0031386
477 name: protein tag
478 namespace: molecular_function
479 def: "A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation." [GOC:dos, GOC:go_curators, PMID:19028679, PMID:20054389, PMID:6305978]
480 comment: Use this term to annotate conjugated tags, not for conjugating enzymes. At the time of writing, all known gene products with this activity are ubiquitin-like, either based on overall sequence similarity or the presence of common motifs and structures.
481 subset: goslim_pir
482 synonym: "covalent modifier" RELATED [GOC:vw]
483 synonym: "protein tagging activity" RELATED []
484 synonym: "ubiquitin" RELATED []
485 synonym: "ubiquitin-like protein modifier" EXACT []
486 is_a: GO:0003674 ! molecular_function
487
488 [Term]
489 id: GO:0031974
490 name: membrane-enclosed lumen
491 namespace: cellular_component
492 def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah]
493 is_a: GO:0005575 ! cellular_component
494
495 [Term]
496 id: GO:0032501
497 name: multicellular organismal process
498 namespace: biological_process
499 alt_id: GO:0044707
500 alt_id: GO:0050874
501 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb]
502 subset: goslim_pir
503 synonym: "organismal physiological process" EXACT []
504 synonym: "single-multicellular organism process" RELATED []
505 is_a: GO:0008150 ! biological_process
506 disjoint_from: GO:0044848 ! biological phase
507 created_by: janelomax
508 creation_date: 2012-09-19T16:07:47Z
509
510 [Term]
511 id: GO:0032502
512 name: developmental process
513 namespace: biological_process
514 alt_id: GO:0044767
515 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]
516 subset: goslim_agr
517 subset: goslim_aspergillus
518 subset: goslim_pir
519 subset: gosubset_prok
520 synonym: "development" NARROW []
521 synonym: "single-organism developmental process" RELATED []
522 is_a: GO:0008150 ! biological_process
523 disjoint_from: GO:0044848 ! biological phase
524 created_by: janelomax
525 creation_date: 2012-12-19T12:21:31Z
526
527 [Term]
528 id: GO:0032991
529 name: protein-containing complex
530 namespace: cellular_component
531 alt_id: GO:0043234
532 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah]
533 comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
534 subset: goslim_agr
535 subset: goslim_chembl
536 subset: goslim_generic
537 subset: goslim_pir
538 subset: gosubset_prok
539 synonym: "macromolecular complex" EXACT []
540 synonym: "macromolecule complex" EXACT []
541 synonym: "protein complex" NARROW []
542 synonym: "protein containing complex" EXACT []
543 synonym: "protein-protein complex" NARROW []
544 is_a: GO:0005575 ! cellular_component
545
546 [Term]
547 id: GO:0038024
548 name: cargo receptor activity
549 namespace: molecular_function
550 def: "Combining selectively with an extracellular substance and delivering the substance into the cell via endocytosis." [GOC:bf, GOC:signaling, PMID:15239958]
551 comment: Note that this term and its child terms are intended for receptors that bind to and internalize molecules by receptor-mediated endocytosis. For receptors that are coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children.
552 synonym: "endocytic receptor activity" EXACT [GOC:signaling, ISBN:0123645387, PMID:12671190]
553 synonym: "receptor activity" BROAD []
554 synonym: "receptor activity involved in ligand uptake" EXACT [PMID:12671190]
555 synonym: "receptor activity involved in receptor-mediated endocytosis" EXACT [GOC:bf]
556 synonym: "transport receptor activity" BROAD [GOC:signaling]
557 is_a: GO:0003674 ! molecular_function
558 created_by: rfoulger
559 creation_date: 2011-08-01T02:50:45Z
560
561 [Term]
562 id: GO:0040007
563 name: growth
564 namespace: biological_process
565 alt_id: GO:0048590
566 def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma]
567 comment: See also the biological process term 'cell growth ; GO:0016049'.
568 subset: goslim_chembl
569 subset: goslim_generic
570 subset: goslim_pir
571 subset: goslim_plant
572 subset: gosubset_prok
573 synonym: "growth pattern" RELATED []
574 synonym: "non-developmental growth" RELATED [GOC:mah]
575 is_a: GO:0008150 ! biological_process
576 disjoint_from: GO:0044848 ! biological phase
577
578 [Term]
579 id: GO:0040011
580 name: locomotion
581 namespace: biological_process
582 def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh]
583 subset: goslim_chembl
584 subset: goslim_generic
585 subset: goslim_pir
586 subset: gosubset_prok
587 is_a: GO:0008150 ! biological_process
588 disjoint_from: GO:0044848 ! biological phase
589
590 [Term]
591 id: GO:0043226
592 name: organelle
593 namespace: cellular_component
594 def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators]
595 subset: goslim_chembl
596 subset: goslim_generic
597 subset: goslim_pir
598 subset: gosubset_prok
599 xref: NIF_Subcellular:sao1539965131
600 xref: Wikipedia:Organelle
601 is_a: GO:0005575 ! cellular_component
602
603 [Term]
604 id: GO:0043473
605 name: pigmentation
606 namespace: biological_process
607 def: "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." [GOC:jl]
608 subset: goslim_chembl
609 subset: goslim_generic
610 subset: goslim_pir
611 subset: gosubset_prok
612 is_a: GO:0008150 ! biological_process
613
614 [Term]
615 id: GO:0044215
616 name: other organism
617 namespace: cellular_component
618 def: "A secondary organism with which the first organism is interacting." [GOC:jl]
619 comment: We plan to obsolete this branch of GO and replace its usage in annotation with a system for multi-organism annotation.
620 is_a: GO:0005575 ! cellular_component
621 created_by: jane
622 creation_date: 2009-11-12T01:04:58Z
623
624 [Term]
625 id: GO:0044217
626 name: other organism part
627 namespace: cellular_component
628 def: "Any constituent part of a secondary organism with which the first organism is interacting." [GOC:jl]
629 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.
630 subset: gocheck_do_not_annotate
631 is_a: GO:0005575 ! cellular_component
632 intersection_of: GO:0005575 ! cellular_component
633 intersection_of: part_of GO:0044215 ! other organism
634 relationship: part_of GO:0044215 ! other organism
635 created_by: jane
636 creation_date: 2009-11-12T01:18:21Z
637
638 [Term]
639 id: GO:0044421
640 name: extracellular region part
641 namespace: cellular_component
642 def: "Any constituent part of the extracellular region, 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 constituent parts of the host cell environment outside an intracellular parasite." [GOC:jl]
643 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.
644 subset: goantislim_grouping
645 subset: gocheck_do_not_annotate
646 subset: gosubset_prok
647 synonym: "extracellular structure" RELATED [NIF_Subcellular:sao9117790637]
648 xref: NIF_Subcellular:sao9117790637
649 is_a: GO:0005575 ! cellular_component
650 intersection_of: GO:0005575 ! cellular_component
651 intersection_of: part_of GO:0005576 ! extracellular region
652 relationship: part_of GO:0005576 ! extracellular region
653
654 [Term]
655 id: GO:0044422
656 name: organelle part
657 namespace: cellular_component
658 def: "Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane." [GOC:jl]
659 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.
660 subset: goantislim_grouping
661 subset: gocheck_do_not_annotate
662 subset: gosubset_prok
663 is_a: GO:0005575 ! cellular_component
664 intersection_of: GO:0005575 ! cellular_component
665 intersection_of: part_of GO:0043226 ! organelle
666 relationship: part_of GO:0043226 ! organelle
667
668 [Term]
669 id: GO:0044423
670 name: virion part
671 namespace: cellular_component
672 def: "Any constituent part of a virion, a complete fully infectious extracellular virus particle." [GOC:jl]
673 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.
674 subset: goantislim_grouping
675 subset: gocheck_do_not_annotate
676 is_a: GO:0005575 ! cellular_component
677 intersection_of: GO:0005575 ! cellular_component
678 intersection_of: part_of GO:0019012 ! virion
679 relationship: part_of GO:0019012 ! virion
680
681 [Term]
682 id: GO:0044425
683 name: membrane part
684 namespace: cellular_component
685 def: "Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:jl]
686 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.
687 subset: goantislim_grouping
688 subset: gocheck_do_not_annotate
689 subset: gosubset_prok
690 is_a: GO:0005575 ! cellular_component
691 intersection_of: GO:0005575 ! cellular_component
692 intersection_of: part_of GO:0016020 ! membrane
693 relationship: part_of GO:0016020 ! membrane
694
695 [Term]
696 id: GO:0044456
697 name: synapse part
698 namespace: cellular_component
699 def: "Any constituent part of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell." [GOC:jl]
700 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.
701 subset: goantislim_grouping
702 subset: gocheck_do_not_annotate
703 synonym: "synaptic component" RELATED [NIF_Subcellular:sao1784069613]
704 xref: NIF_Subcellular:sao1784069613
705 is_a: GO:0005575 ! cellular_component
706 intersection_of: GO:0005575 ! cellular_component
707 intersection_of: part_of GO:0045202 ! synapse
708 relationship: part_of GO:0045202 ! synapse
709
710 [Term]
711 id: GO:0044464
712 name: cell part
713 namespace: cellular_component
714 def: "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl]
715 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.
716 subset: goantislim_grouping
717 subset: gocheck_do_not_annotate
718 subset: goslim_pir
719 subset: gosubset_prok
720 synonym: "cellular subcomponent" EXACT [NIF_Subcellular:sao628508602]
721 synonym: "protoplast" RELATED [GOC:mah]
722 xref: NIF_Subcellular:sao628508602
723 is_a: GO:0005575 ! cellular_component
724 intersection_of: GO:0005575 ! cellular_component
725 intersection_of: part_of GO:0005623 ! cell
726 relationship: part_of GO:0005623 ! cell
727
728 [Term]
729 id: GO:0044848
730 name: biological phase
731 namespace: biological_process
732 def: "A distinct period or stage in a biological process or cycle." [GOC:jl]
733 comment: Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase.
734 subset: gocheck_do_not_manually_annotate
735 is_a: GO:0008150 ! biological_process
736 disjoint_from: GO:0048511 ! rhythmic process
737 disjoint_from: GO:0050896 ! response to stimulus
738 disjoint_from: GO:0051179 ! localization
739 disjoint_from: GO:0051704 ! multi-organism process
740 disjoint_from: GO:0071840 ! cellular component organization or biogenesis
741 disjoint_from: GO:0098743 ! cell aggregation
742 created_by: janelomax
743 creation_date: 2014-07-16T13:12:40Z
744
745 [Term]
746 id: GO:0045182
747 name: translation regulator activity
748 namespace: molecular_function
749 def: "Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai]
750 subset: goslim_aspergillus
751 subset: goslim_candida
752 subset: goslim_pir
753 subset: goslim_plant
754 subset: gosubset_prok
755 synonym: "translation factor activity" EXACT []
756 is_a: GO:0003674 ! molecular_function
757
758 [Term]
759 id: GO:0045202
760 name: synapse
761 namespace: cellular_component
762 def: "The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." [ISBN:0198506732]
763 subset: goslim_agr
764 subset: goslim_mouse
765 subset: goslim_pir
766 subset: goslim_synapse
767 synonym: "electrotonic synapse" RELATED [NIF_Subcellular:sao1311109124]
768 synonym: "mixed synapse" NARROW [NIF_Subcellular:sao1506103497]
769 synonym: "synaptic junction" EXACT []
770 xref: NIF_Subcellular:sao914572699
771 xref: Wikipedia:Chemical_synapse
772 is_a: GO:0005575 ! cellular_component
773
774 [Term]
775 id: GO:0045735
776 name: nutrient reservoir activity
777 namespace: molecular_function
778 def: "Functions in the storage of nutritious substrates." [GOC:ai]
779 comment: Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'.
780 subset: goslim_pir
781 subset: gosubset_prok
782 synonym: "storage protein" RELATED []
783 synonym: "storage protein of fat body" RELATED []
784 synonym: "yolk protein" RELATED []
785 is_a: GO:0003674 ! molecular_function
786
787 [Term]
788 id: GO:0048511
789 name: rhythmic process
790 namespace: biological_process
791 def: "Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism." [GOC:jid]
792 subset: goslim_pir
793 subset: gosubset_prok
794 synonym: "rhythm" RELATED []
795 is_a: GO:0008150 ! biological_process
796
797 [Term]
798 id: GO:0050896
799 name: response to stimulus
800 namespace: biological_process
801 alt_id: GO:0051869
802 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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf]
803 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.
804 subset: gocheck_do_not_manually_annotate
805 subset: goslim_agr
806 subset: goslim_mouse
807 subset: goslim_pir
808 subset: gosubset_prok
809 synonym: "physiological response to stimulus" EXACT []
810 is_a: GO:0008150 ! biological_process
811
812 [Term]
813 id: GO:0051179
814 name: localization
815 namespace: biological_process
816 alt_id: GO:1902578
817 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos]
818 subset: goslim_pir
819 subset: gosubset_prok
820 synonym: "establishment and maintenance of cellular component location" NARROW []
821 synonym: "establishment and maintenance of localization" EXACT []
822 synonym: "establishment and maintenance of position" EXACT []
823 synonym: "establishment and maintenance of substance location" NARROW []
824 synonym: "establishment and maintenance of substrate location" NARROW []
825 synonym: "localisation" EXACT [GOC:mah]
826 synonym: "single organism localization" RELATED [GOC:TermGenie]
827 synonym: "single-organism localization" RELATED []
828 is_a: GO:0008150 ! biological_process
829 created_by: jl
830 creation_date: 2013-12-18T13:51:04Z
831
832 [Term]
833 id: GO:0051704
834 name: multi-organism process
835 namespace: biological_process
836 alt_id: GO:0051706
837 def: "A biological process which involves another organism of the same or different species." [GOC:jl]
838 subset: goslim_pir
839 subset: gosubset_prok
840 synonym: "interaction between organisms" EXACT []
841 synonym: "physiological interaction between organisms" EXACT []
842 synonym: "physiological interaction with other organism" EXACT []
843 is_a: GO:0008150 ! biological_process
844
845 [Term]
846 id: GO:0055044
847 name: symplast
848 namespace: cellular_component
849 def: "The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata." [GOC:mtg_sensu]
850 subset: goslim_pir
851 xref: Wikipedia:Symplast
852 is_a: GO:0005575 ! cellular_component
853
854 [Term]
855 id: GO:0060089
856 name: molecular transducer activity
857 namespace: molecular_function
858 def: "A compound molecular function in which an effector function is controlled by one or more regulatory components." [GOC:dos, GOC:pdt]
859 subset: gocheck_do_not_manually_annotate
860 subset: goslim_pir
861 subset: gosubset_prok
862 is_a: GO:0003674 ! molecular_function
863
864 [Term]
865 id: GO:0065007
866 name: biological regulation
867 namespace: biological_process
868 def: "Any process that modulates a measurable attribute of any biological process, quality or function." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw]
869 subset: gocheck_do_not_annotate
870 subset: goslim_pir
871 subset: gosubset_prok
872 synonym: "regulation" BROAD []
873 is_a: GO:0008150 ! biological_process
874
875 [Term]
876 id: GO:0071840
877 name: cellular component organization or biogenesis
878 namespace: biological_process
879 alt_id: GO:0071841
880 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah]
881 subset: goslim_metagenomics
882 synonym: "cellular component organisation or biogenesis" EXACT [GOC:mah]
883 synonym: "cellular component organisation or biogenesis at cellular level" EXACT [GOC:mah]
884 synonym: "cellular component organization or biogenesis at cellular level" EXACT []
885 is_a: GO:0008150 ! biological_process
886 created_by: midori
887 creation_date: 2010-09-10T01:39:16Z
888
889 [Term]
890 id: GO:0090729
891 name: toxin activity
892 namespace: molecular_function
893 alt_id: GO:0050827
894 def: "Interacting selectively with one or more biological molecules in another organism (the \"target\" organism), initiating pathogenesis (leading to an abnormal, generally detrimental state) in the target organism. The activity should refer to an evolved function of the active gene product, i.e. one that was selected for. Examples include the activity of botulinum toxin, and snake venom." [GOC:pt]
895 synonym: "toxin receptor binding" EXACT []
896 xref: Wikipedia:Toxin
897 is_a: GO:0003674 ! molecular_function
898 created_by: tanyaberardini
899 creation_date: 2016-12-19T15:23:27Z
900
901 [Term]
902 id: GO:0097423
903 name: mitochondrion-associated adherens complex
904 namespace: cellular_component
905 def: "An organelle arrangement comprised of the following elements: a mitochondrion positioned near the presynaptic membrane; an electron-dense mitochondrial plaque adjacent to the outer mitochondrial membrane that faces the presynaptic membrane; filament-like elements appearing to link the mitochondrial plaque to a cell-cell junction region (sometimes termed punctum adherens); tubular or vesicular-appearing membrane (also called vesicular chain) interposed among the filaments. Mitochondrion-associated adherens complexes were initially described in the dorsal horn of the spinal cord. They are found in calyces and other large terminals of the auditory brainstem, and in a variety of mammalian species including humans." [NIF_Subcellular:sao1933817066, PMID:20089910]
906 synonym: "MAC" RELATED []
907 synonym: "mitochondrial adhaerens complex" EXACT []
908 xref: NIF_Subcellular:sao1933817066
909 is_a: GO:0005575 ! cellular_component
910 created_by: paola
911 creation_date: 2012-11-07T13:38:50Z
912
913 [Term]
914 id: GO:0098743
915 name: cell aggregation
916 namespace: biological_process
917 def: "The clustering together and adhesion of initially separate cells to form an aggregate. Examples include the clustering of unicellular organisms or blood cells in suspension and the condensation of mesenchymal cells during cartilage formation." [GOC:dos]
918 is_a: GO:0008150 ! biological_process
919
920 [Term]
921 id: GO:0098754
922 name: detoxification
923 namespace: biological_process
924 def: "Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." [GOC:dos]
925 subset: goslim_pombe
926 is_a: GO:0008150 ! biological_process
927
928 [Term]
929 id: GO:0098772
930 name: molecular function regulator
931 namespace: molecular_function
932 def: "A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators." [GOC:dos, GOC:pt]
933 is_a: GO:0003674 ! molecular_function
934 relationship: regulates GO:0003674 ! molecular_function
935
936 [Term]
937 id: GO:0099080
938 name: supramolecular complex
939 namespace: cellular_component
940 def: "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." [GOC:dos]
941 is_a: GO:0005575 ! cellular_component
942
943 [Term]
944 id: GO:0104005
945 name: hijacked molecular function
946 namespace: molecular_function
947 def: "A function that was not selected for in the evolution of an organism, but arises from co-option by another organism, e.g. a human protein used as a virus receptor." [GOC:pdt]
948 is_a: GO:0003674 ! molecular_function
949 created_by: dos
950 creation_date: 2017-08-04T02:12:09Z
951
952 [Term]
953 id: GO:0140104
954 name: molecular carrier activity
955 namespace: molecular_function
956 def: "Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location." [GOC:pdt]
957 comment: https://github.com/geneontology/go-ontology/issues/14221
958 subset: gocheck_do_not_annotate
959 is_a: GO:0003674 ! molecular_function
960 created_by: pg
961 creation_date: 2017-09-19T13:10:18Z
962
963 [Term]
964 id: GO:0140110
965 name: transcription regulator activity
966 namespace: molecular_function
967 def: "A molecular function that controls the rate, timing and/or magnitude of transcription of genetic information. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism." [GOC:pg, GOC:txnOH-2018, Wikipedia:Transcription_factor]
968 comment: https://github.com/geneontology/go-ontology/issues/13588
969 subset: gocheck_do_not_annotate
970 is_a: GO:0003674 ! molecular_function
971 created_by: pg
972 creation_date: 2017-10-18T07:05:44Z
973
974 [Typedef]
975 id: ends_during
976 name: ends_during
977 namespace: external
978 xref: RO:0002093
979
980 [Typedef]
981 id: happens_during
982 name: happens_during
983 namespace: external
984 xref: RO:0002092
985 is_transitive: true
986 is_a: ends_during ! ends_during
987
988 [Typedef]
989 id: has_part
990 name: has_part
991 namespace: external
992 xref: BFO:0000051
993 is_transitive: true
994
995 [Typedef]
996 id: negatively_regulates
997 name: negatively regulates
998 namespace: external
999 xref: RO:0002212
1000 is_a: regulates ! regulates
1001 transitive_over: part_of ! part of
1002
1003 [Typedef]
1004 id: never_in_taxon
1005 name: never_in_taxon
1006 namespace: external
1007 xref: RO:0002161
1008 expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y" []
1009 is_metadata_tag: true
1010 is_class_level: true
1011
1012 [Typedef]
1013 id: occurs_in
1014 name: occurs in
1015 namespace: external
1016 xref: BFO:0000066
1017 holds_over_chain: part_of occurs_in
1018 transitive_over: part_of ! part of
1019
1020 [Typedef]
1021 id: part_of
1022 name: part of
1023 namespace: external
1024 xref: BFO:0000050
1025 is_transitive: true
1026 inverse_of: has_part ! has_part
1027
1028 [Typedef]
1029 id: positively_regulates
1030 name: positively regulates
1031 namespace: external
1032 xref: RO:0002213
1033 holds_over_chain: negatively_regulates negatively_regulates
1034 is_a: regulates ! regulates
1035 transitive_over: part_of ! part of
1036
1037 [Typedef]
1038 id: regulates
1039 name: regulates
1040 namespace: external
1041 xref: RO:0002211
1042 is_transitive: true
1043 transitive_over: part_of ! part of
1044
1045 [Typedef]
1046 id: starts_during
1047 name: starts_during
1048 namespace: external
1049 xref: RO:0002091
1050