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8
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1 format-version: 1.2
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2 ontology: go
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3 subsetdef: Cross-product_review "Involved_in"
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4 subsetdef: goslim_aspergillus "Aspergillus GO slim"
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5 subsetdef: goslim_candida "Candida GO slim"
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6 subsetdef: goslim_generic "Generic GO slim"
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7 subsetdef: goslim_metagenomics "Metagenomics GO slim"
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8 subsetdef: goslim_pir "PIR GO slim"
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9 subsetdef: goslim_plant "Plant GO slim"
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10 subsetdef: goslim_pombe "Fission yeast GO slim"
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11 subsetdef: goslim_yeast "Yeast GO slim"
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12 subsetdef: gosubset_prok "Prokaryotic GO subset"
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13 subsetdef: high_level_annotation_qc "High-level terms not to be used for direct annotation"
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14 subsetdef: mf_needs_review "Catalytic activity terms in need of attention"
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15 subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors"
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16 subsetdef: virus_checked "Viral overhaul terms"
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17 synonymtypedef: systematic_synonym "Systematic synonym" EXACT
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18
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19 [Term]
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20 id: GO:0007154
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21 name: cell communication
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22 namespace: biological_process
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23 def: "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:mah]
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24 subset: goslim_metagenomics ! Metagenomics GO slim
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25 subset: goslim_pir ! PIR GO slim
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26 subset: goslim_plant ! Plant GO slim
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27 subset: gosubset_prok ! Prokaryotic GO subset
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28 xref: Wikipedia:Cell_signaling
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29 is_a: GO:0044763 ! single-organism cellular process
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30
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31 [Term]
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32 id: GO:0007165
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33 name: signal transduction
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34 namespace: biological_process
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35 alt_id: GO:0023033
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36 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]
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37 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.
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38 subset: goslim_aspergillus ! Aspergillus GO slim
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39 subset: goslim_candida ! Candida GO slim
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40 subset: goslim_generic ! Generic GO slim
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41 subset: goslim_metagenomics ! Metagenomics GO slim
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42 subset: goslim_plant ! Plant GO slim
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43 subset: gosubset_prok ! Prokaryotic GO subset
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44 synonym: "signaling cascade" NARROW []
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45 synonym: "signaling pathway" RELATED []
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46 synonym: "signalling cascade" NARROW []
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47 synonym: "signalling pathway" RELATED [GOC:mah]
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48 xref: Reactome:REACT_100624
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49 xref: Reactome:REACT_102354
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50 xref: Reactome:REACT_112130
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51 xref: Reactome:REACT_112549
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52 xref: Reactome:REACT_113151
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53 xref: Reactome:REACT_113601
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54 xref: Reactome:REACT_113964
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55 xref: Reactome:REACT_114657
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56 xref: Reactome:REACT_114690
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57 xref: Reactome:REACT_114820
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58 xref: Reactome:REACT_114910
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59 xref: Reactome:REACT_115037
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60 xref: Reactome:REACT_115147
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61 xref: Reactome:REACT_12478
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62 xref: Reactome:REACT_31232
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63 xref: Reactome:REACT_78535
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64 xref: Reactome:REACT_89740
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65 xref: Reactome:REACT_93680
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66 xref: Reactome:REACT_98872
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67 xref: Wikipedia:Signal_transduction
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68 is_a: GO:0050794 ! regulation of cellular process
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69 is_a: GO:0051716 ! cellular response to stimulus
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70 relationship: part_of GO:0007154 ! cell communication
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71 relationship: part_of GO:0044700 ! single organism signaling
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72
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73 [Term]
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74 id: GO:0007166
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75 name: cell surface receptor signaling pathway
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76 namespace: biological_process
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77 def: "A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
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78 subset: gosubset_prok ! Prokaryotic GO subset
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79 synonym: "cell surface receptor linked signal transduction" EXACT []
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80 synonym: "cell surface receptor linked signaling pathway" EXACT [GOC:bf]
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81 synonym: "cell surface receptor linked signalling pathway" EXACT [GOC:mah]
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82 xref: Reactome:REACT_6290
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83 is_a: GO:0007165 ! signal transduction
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84
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85 [Term]
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86 id: GO:0007167
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87 name: enzyme linked receptor protein signaling pathway
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88 namespace: biological_process
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89 def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, ISBN:0185316194]
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90 synonym: "enzyme linked receptor protein signalling pathway" EXACT []
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91 is_a: GO:0007166 ! cell surface receptor signaling pathway
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92
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93 [Term]
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94 id: GO:0007169
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95 name: transmembrane receptor protein tyrosine kinase signaling pathway
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96 namespace: biological_process
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97 def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:ceb, GOC:signaling]
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98 synonym: "transmembrane receptor protein tyrosine kinase signalling pathway" EXACT []
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99 xref: Reactome:REACT_101238
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100 xref: Reactome:REACT_104074
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101 xref: Reactome:REACT_106114
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102 xref: Reactome:REACT_106720
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103 xref: Reactome:REACT_108494
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104 xref: Reactome:REACT_11064
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105 xref: Reactome:REACT_29786
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106 xref: Reactome:REACT_82296
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107 xref: Reactome:REACT_90767
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108 xref: Reactome:REACT_97816
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109 is_a: GO:0007167 ! enzyme linked receptor protein signaling pathway
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110
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111 [Term]
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112 id: GO:0007224
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113 name: smoothened signaling pathway
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114 namespace: biological_process
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115 def: "A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened." [GOC:mah, PMID:15205520]
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116 synonym: "Shh signaling pathway" RELATED [GOC:dph]
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117 synonym: "Sonic hedgehog signaling pathway" NARROW [GOC:dph]
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118 synonym: "hedgehog signaling pathway" EXACT []
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119 synonym: "hh signaling pathway" NARROW []
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120 synonym: "hh signalling pathway" NARROW []
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121 synonym: "smoothened signalling pathway" EXACT []
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122 xref: Wikipedia:Hedgehog_signaling_pathway
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123 is_a: GO:0007166 ! cell surface receptor signaling pathway
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124
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125 [Term]
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126 id: GO:0008150
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127 name: biological_process
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128 namespace: biological_process
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129 alt_id: GO:0000004
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130 alt_id: GO:0007582
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131 def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete]
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132 comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
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133 subset: goslim_aspergillus ! Aspergillus GO slim
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134 subset: goslim_candida ! Candida GO slim
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135 subset: goslim_generic ! Generic GO slim
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136 subset: goslim_metagenomics ! Metagenomics GO slim
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137 subset: goslim_pir ! PIR GO slim
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138 subset: goslim_plant ! Plant GO slim
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139 subset: goslim_pombe ! Fission yeast GO slim
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140 subset: goslim_yeast ! Yeast GO slim
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141 subset: gosubset_prok ! Prokaryotic GO subset
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142 synonym: "biological process" EXACT []
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143 synonym: "biological process unknown" NARROW []
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144 synonym: "physiological process" EXACT []
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145 xref: Wikipedia:Biological_process
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146
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147 [Term]
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148 id: GO:0008589
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149 name: regulation of smoothened signaling pathway
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150 namespace: biological_process
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151 alt_id: GO:0007226
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152 alt_id: GO:0043109
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153 def: "Any process that modulates the frequency, rate or extent of smoothened signaling." [GOC:go_curators]
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154 synonym: "regulation of hedgehog signaling pathway" EXACT [GOC:bf, GOC:ecd]
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155 synonym: "regulation of hh signaling pathway" EXACT [GOC:bf, GOC:ecd]
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156 synonym: "regulation of smoothened activity" RELATED []
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157 synonym: "regulation of smoothened by patched" RELATED []
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158 synonym: "regulation of smoothened receptor activity by patched" RELATED []
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159 synonym: "regulation of smoothened signalling pathway" EXACT []
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160 is_a: GO:0009966 ! regulation of signal transduction
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161 relationship: regulates GO:0007224 ! smoothened signaling pathway
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162 intersection_of: GO:0065007 ! biological regulation
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163 intersection_of: regulates GO:0007224 ! smoothened signaling pathway
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164
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165 [Term]
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166 id: GO:0009966
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167 name: regulation of signal transduction
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168 namespace: biological_process
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169 alt_id: GO:0035466
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170 def: "Any process that modulates the frequency, rate or extent of signal transduction." [GOC:sm]
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171 subset: gosubset_prok ! Prokaryotic GO subset
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172 synonym: "regulation of signaling pathway" RELATED []
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173 synonym: "regulation of signalling pathway" RELATED [GOC:mah]
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174 is_a: GO:0010646 ! regulation of cell communication
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175 is_a: GO:0023051 ! regulation of signaling
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176 is_a: GO:0048583 ! regulation of response to stimulus
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177 relationship: regulates GO:0007165 ! signal transduction
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178 intersection_of: GO:0065007 ! biological regulation
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179 intersection_of: regulates GO:0007165 ! signal transduction
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180
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181 [Term]
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182 id: GO:0009987
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183 name: cellular process
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184 namespace: biological_process
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185 alt_id: GO:0008151
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186 alt_id: GO:0050875
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187 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]
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188 subset: goslim_pir ! PIR GO slim
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189 subset: goslim_plant ! Plant GO slim
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190 subset: gosubset_prok ! Prokaryotic GO subset
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191 synonym: "cell growth and/or maintenance" NARROW []
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192 synonym: "cell physiology" EXACT []
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193 synonym: "cellular physiological process" EXACT []
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194 is_a: GO:0008150 ! biological_process
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195
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196 [Term]
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197 id: GO:0010646
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198 name: regulation of cell communication
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199 namespace: biological_process
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200 def: "Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:dph, GOC:tb]
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201 is_a: GO:0050794 ! regulation of cellular process
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202 relationship: regulates GO:0007154 ! cell communication
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203 intersection_of: GO:0065007 ! biological regulation
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204 intersection_of: regulates GO:0007154 ! cell communication
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205
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206 [Term]
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207 id: GO:0023051
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208 name: regulation of signaling
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209 namespace: biological_process
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210 def: "Any process that modulates the frequency, rate or extent of a signaling process." [GOC:mtg_signal]
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211 synonym: "regulation of signaling process" RELATED [GOC:bf]
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212 synonym: "regulation of signalling process" RELATED [GOC:mah]
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213 is_a: GO:0050789 ! regulation of biological process
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214 relationship: regulates GO:0044700 ! single organism signaling
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215 intersection_of: GO:0065007 ! biological regulation
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216 intersection_of: regulates GO:0023052 ! signaling
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217
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218 [Term]
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219 id: GO:0023052
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220 name: signaling
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221 namespace: biological_process
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222 alt_id: GO:0023046
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223 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]
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224 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.
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225 subset: goslim_pombe ! Fission yeast GO slim
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226 subset: goslim_yeast ! Yeast GO slim
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227 synonym: "biological signaling" EXACT []
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228 synonym: "signaling process" EXACT []
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229 synonym: "signalling" EXACT []
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230 synonym: "signalling process" RELATED [GOC:mah]
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231 is_a: GO:0008150 ! biological_process
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232
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233 [Term]
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234 id: GO:0044699
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235 name: single-organism process
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236 namespace: biological_process
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237 def: "A biological process that involves only one organism." [GOC:jl]
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238 synonym: "single organism process" EXACT []
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239 is_a: GO:0008150 ! biological_process
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240
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241 [Term]
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242 id: GO:0044700
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243 name: single organism signaling
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244 namespace: biological_process
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245 def: "A signaling process occurring within a single organism." [GOC:jl]
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246 is_a: GO:0023052 ! signaling
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247 is_a: GO:0044699 ! single-organism process
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248
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249 [Term]
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250 id: GO:0044763
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251 name: single-organism cellular process
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252 namespace: biological_process
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253 def: "Any process that is carried out at the cellular level, occurring within a single organism." [GOC:jl]
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254 is_a: GO:0009987 ! cellular process
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255 is_a: GO:0044699 ! single-organism process
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256
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257 [Term]
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258 id: GO:0048009
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259 name: insulin-like growth factor receptor signaling pathway
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260 namespace: biological_process
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261 def: "The series of molecular signals generated as a consequence of the insulin-like growth factor receptor binding to one of its physiological ligands." [GOC:ceb]
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262 synonym: "IGF receptor signaling pathway" EXACT []
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263 synonym: "IGF receptor signalling pathway" EXACT []
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264 is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway
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265
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266 [Term]
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267 id: GO:0048583
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268 name: regulation of response to stimulus
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269 namespace: biological_process
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270 def: "Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is 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." [GOC:jid]
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271 comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC.
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272 subset: gosubset_prok ! Prokaryotic GO subset
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273 subset: high_level_annotation_qc ! High-level terms not to be used for direct annotation
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274 is_a: GO:0050789 ! regulation of biological process
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275 relationship: regulates GO:0050896 ! response to stimulus
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276 intersection_of: GO:0065007 ! biological regulation
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277 intersection_of: regulates GO:0050896 ! response to stimulus
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278
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279 [Term]
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280 id: GO:0050789
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281 name: regulation of biological process
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282 namespace: biological_process
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283 alt_id: GO:0050791
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284 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators]
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285 subset: goslim_aspergillus ! Aspergillus GO slim
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286 subset: goslim_candida ! Candida GO slim
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287 subset: gosubset_prok ! Prokaryotic GO subset
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288 synonym: "regulation of physiological process" EXACT []
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289 is_a: GO:0065007 ! biological regulation
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290 relationship: regulates GO:0008150 ! biological_process
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291 intersection_of: GO:0065007 ! biological regulation
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292 intersection_of: regulates GO:0008150 ! biological_process
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293
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294 [Term]
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295 id: GO:0050794
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296 name: regulation of cellular process
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297 namespace: biological_process
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298 alt_id: GO:0051244
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299 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are 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]
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300 subset: gosubset_prok ! Prokaryotic GO subset
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301 synonym: "regulation of cellular physiological process" EXACT []
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302 is_a: GO:0050789 ! regulation of biological process
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303 relationship: regulates GO:0009987 ! cellular process
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304 intersection_of: GO:0065007 ! biological regulation
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305 intersection_of: regulates GO:0009987 ! cellular process
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306
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307 [Term]
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308 id: GO:0050896
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309 name: response to stimulus
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310 namespace: biological_process
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311 alt_id: GO:0051869
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312 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]
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313 comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC.
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314 subset: goslim_pir ! PIR GO slim
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315 subset: gosubset_prok ! Prokaryotic GO subset
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316 subset: high_level_annotation_qc ! High-level terms not to be used for direct annotation
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317 synonym: "physiological response to stimulus" EXACT []
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318 is_a: GO:0008150 ! biological_process
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319
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320 [Term]
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321 id: GO:0051716
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322 name: cellular response to stimulus
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323 namespace: biological_process
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324 def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell." [GOC:bf, GOC:jl]
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325 comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC.
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326 subset: gosubset_prok ! Prokaryotic GO subset
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327 subset: high_level_annotation_qc ! High-level terms not to be used for direct annotation
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328 is_a: GO:0044763 ! single-organism cellular process
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329 is_a: GO:0050896 ! response to stimulus
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330
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331 [Term]
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332 id: GO:0065007
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333 name: biological regulation
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334 namespace: biological_process
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335 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]
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336 subset: goslim_pir ! PIR GO slim
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337 subset: gosubset_prok ! Prokaryotic GO subset
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338 synonym: "regulation" BROAD []
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339 is_a: GO:0008150 ! biological_process
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340
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341 [Typedef]
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342 id: part_of
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343 name: part_of
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344 namespace: gene_ontology
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345 is_transitive: true
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346 xref: BFO:0000050
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347 xref: OBO_REL:part_of
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348
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349 [Typedef]
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350 id: regulates
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351 name: regulates
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352 namespace: gene_ontology
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353 xref: RO:0002211
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354 transitive_over: part_of ! part_of
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355
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356
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