comparison test-data/ontologizer/test.obo @ 8:00a5ede354a0

Uploaded

8:00a5ede354a0

format-version: 1.2
ontology: go
subsetdef: Cross-product_review "Involved_in"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_metagenomics "Metagenomics GO slim"
subsetdef: goslim_pir "PIR GO slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_pombe "Fission yeast GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"
subsetdef: high_level_annotation_qc "High-level terms not to be used for direct annotation"
subsetdef: mf_needs_review "Catalytic activity terms in need of attention"
subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors"
subsetdef: virus_checked "Viral overhaul terms"
synonymtypedef: systematic_synonym "Systematic synonym" EXACT

[Term]
id: GO:0007154
name: cell communication
namespace: biological_process
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]
subset: goslim_metagenomics  ! Metagenomics GO slim
subset: goslim_pir  ! PIR GO slim
subset: goslim_plant  ! Plant GO slim
subset: gosubset_prok  ! Prokaryotic GO subset
xref: Wikipedia:Cell_signaling
is_a: GO:0044763  ! single-organism cellular process

[Term]
id: GO:0007165
name: signal transduction
namespace: biological_process
alt_id: GO:0023033
def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11]
comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
subset: goslim_aspergillus  ! Aspergillus GO slim
subset: goslim_candida  ! Candida GO slim
subset: goslim_generic  ! Generic GO slim
subset: goslim_metagenomics  ! Metagenomics GO slim
subset: goslim_plant  ! Plant GO slim
subset: gosubset_prok  ! Prokaryotic GO subset
synonym: "signaling cascade" NARROW []
synonym: "signaling pathway" RELATED []
synonym: "signalling cascade" NARROW []
synonym: "signalling pathway" RELATED [GOC:mah]
xref: Reactome:REACT_100624
xref: Reactome:REACT_102354
xref: Reactome:REACT_112130
xref: Reactome:REACT_112549
xref: Reactome:REACT_113151
xref: Reactome:REACT_113601
xref: Reactome:REACT_113964
xref: Reactome:REACT_114657
xref: Reactome:REACT_114690
xref: Reactome:REACT_114820
xref: Reactome:REACT_114910
xref: Reactome:REACT_115037
xref: Reactome:REACT_115147
xref: Reactome:REACT_12478
xref: Reactome:REACT_31232
xref: Reactome:REACT_78535
xref: Reactome:REACT_89740
xref: Reactome:REACT_93680
xref: Reactome:REACT_98872
xref: Wikipedia:Signal_transduction
is_a: GO:0050794  ! regulation of cellular process
is_a: GO:0051716  ! cellular response to stimulus
relationship: part_of GO:0007154 ! cell communication
relationship: part_of GO:0044700 ! single organism signaling

[Term]
id: GO:0007166
name: cell surface receptor signaling pathway
namespace: biological_process
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]
subset: gosubset_prok  ! Prokaryotic GO subset
synonym: "cell surface receptor linked signal transduction" EXACT []
synonym: "cell surface receptor linked signaling pathway" EXACT [GOC:bf]
synonym: "cell surface receptor linked signalling pathway" EXACT [GOC:mah]
xref: Reactome:REACT_6290
is_a: GO:0007165  ! signal transduction

[Term]
id: GO:0007167
name: enzyme linked receptor protein signaling pathway
namespace: biological_process
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]
synonym: "enzyme linked receptor protein signalling pathway" EXACT []
is_a: GO:0007166  ! cell surface receptor signaling pathway

[Term]
id: GO:0007169
name: transmembrane receptor protein tyrosine kinase signaling pathway
namespace: biological_process
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]
synonym: "transmembrane receptor protein tyrosine kinase signalling pathway" EXACT []
xref: Reactome:REACT_101238
xref: Reactome:REACT_104074
xref: Reactome:REACT_106114
xref: Reactome:REACT_106720
xref: Reactome:REACT_108494
xref: Reactome:REACT_11064
xref: Reactome:REACT_29786
xref: Reactome:REACT_82296
xref: Reactome:REACT_90767
xref: Reactome:REACT_97816
is_a: GO:0007167  ! enzyme linked receptor protein signaling pathway

[Term]
id: GO:0007224
name: smoothened signaling pathway
namespace: biological_process
def: "A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened." [GOC:mah, PMID:15205520]
synonym: "Shh signaling pathway" RELATED [GOC:dph]
synonym: "Sonic hedgehog signaling pathway" NARROW [GOC:dph]
synonym: "hedgehog signaling pathway" EXACT []
synonym: "hh signaling pathway" NARROW []
synonym: "hh signalling pathway" NARROW []
synonym: "smoothened signalling pathway" EXACT []
xref: Wikipedia:Hedgehog_signaling_pathway
is_a: GO:0007166  ! cell surface receptor signaling pathway

[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
alt_id: GO:0000004
alt_id: GO:0007582
def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
subset: goslim_aspergillus  ! Aspergillus GO slim
subset: goslim_candida  ! Candida GO slim
subset: goslim_generic  ! Generic GO slim
subset: goslim_metagenomics  ! Metagenomics GO slim
subset: goslim_pir  ! PIR GO slim
subset: goslim_plant  ! Plant GO slim
subset: goslim_pombe  ! Fission yeast GO slim
subset: goslim_yeast  ! Yeast GO slim
subset: gosubset_prok  ! Prokaryotic GO subset
synonym: "biological process" EXACT []
synonym: "biological process unknown" NARROW []
synonym: "physiological process" EXACT []
xref: Wikipedia:Biological_process

[Term]
id: GO:0008589
name: regulation of smoothened signaling pathway
namespace: biological_process
alt_id: GO:0007226
alt_id: GO:0043109
def: "Any process that modulates the frequency, rate or extent of smoothened signaling." [GOC:go_curators]
synonym: "regulation of hedgehog signaling pathway" EXACT [GOC:bf, GOC:ecd]
synonym: "regulation of hh signaling pathway" EXACT [GOC:bf, GOC:ecd]
synonym: "regulation of smoothened activity" RELATED []
synonym: "regulation of smoothened by patched" RELATED []
synonym: "regulation of smoothened receptor activity by patched" RELATED []
synonym: "regulation of smoothened signalling pathway" EXACT []
is_a: GO:0009966  ! regulation of signal transduction
relationship: regulates GO:0007224 ! smoothened signaling pathway
intersection_of: GO:0065007  ! biological regulation
intersection_of: regulates GO:0007224 ! smoothened signaling pathway

[Term]
id: GO:0009966
name: regulation of signal transduction
namespace: biological_process
alt_id: GO:0035466
def: "Any process that modulates the frequency, rate or extent of signal transduction." [GOC:sm]
subset: gosubset_prok  ! Prokaryotic GO subset
synonym: "regulation of signaling pathway" RELATED []
synonym: "regulation of signalling pathway" RELATED [GOC:mah]
is_a: GO:0010646  ! regulation of cell communication
is_a: GO:0023051  ! regulation of signaling
is_a: GO:0048583  ! regulation of response to stimulus
relationship: regulates GO:0007165 ! signal transduction
intersection_of: GO:0065007  ! biological regulation
intersection_of: regulates GO:0007165 ! signal transduction

[Term]
id: GO:0009987
name: cellular process
namespace: biological_process
alt_id: GO:0008151
alt_id: GO:0050875
def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete]
subset: goslim_pir  ! PIR GO slim
subset: goslim_plant  ! Plant GO slim
subset: gosubset_prok  ! Prokaryotic GO subset
synonym: "cell growth and/or maintenance" NARROW []
synonym: "cell physiology" EXACT []
synonym: "cellular physiological process" EXACT []
is_a: GO:0008150  ! biological_process

[Term]
id: GO:0010646
name: regulation of cell communication
namespace: biological_process
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]
is_a: GO:0050794  ! regulation of cellular process
relationship: regulates GO:0007154 ! cell communication
intersection_of: GO:0065007  ! biological regulation
intersection_of: regulates GO:0007154 ! cell communication

[Term]
id: GO:0023051
name: regulation of signaling
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of a signaling process." [GOC:mtg_signal]
synonym: "regulation of signaling process" RELATED [GOC:bf]
synonym: "regulation of signalling process" RELATED [GOC:mah]
is_a: GO:0050789  ! regulation of biological process
relationship: regulates GO:0044700 ! single organism signaling
intersection_of: GO:0065007  ! biological regulation
intersection_of: regulates GO:0023052 ! signaling

[Term]
id: GO:0023052
name: signaling
namespace: biological_process
alt_id: GO:0023046
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]
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.
subset: goslim_pombe  ! Fission yeast GO slim
subset: goslim_yeast  ! Yeast GO slim
synonym: "biological signaling" EXACT []
synonym: "signaling process" EXACT []
synonym: "signalling" EXACT []
synonym: "signalling process" RELATED [GOC:mah]
is_a: GO:0008150  ! biological_process

[Term]
id: GO:0044699
name: single-organism process
namespace: biological_process
def: "A biological process that involves only one organism." [GOC:jl]
synonym: "single organism process" EXACT []
is_a: GO:0008150  ! biological_process

[Term]
id: GO:0044700
name: single organism signaling
namespace: biological_process
def: "A signaling process occurring within a single organism." [GOC:jl]
is_a: GO:0023052  ! signaling
is_a: GO:0044699  ! single-organism process

[Term]
id: GO:0044763
name: single-organism cellular process
namespace: biological_process
def: "Any process that is carried out at the cellular level, occurring within a single organism." [GOC:jl]
is_a: GO:0009987  ! cellular process
is_a: GO:0044699  ! single-organism process

[Term]
id: GO:0048009
name: insulin-like growth factor receptor signaling pathway
namespace: biological_process
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]
synonym: "IGF receptor signaling pathway" EXACT []
synonym: "IGF receptor signalling pathway" EXACT []
is_a: GO:0007169  ! transmembrane receptor protein tyrosine kinase signaling pathway

[Term]
id: GO:0048583
name: regulation of response to stimulus
namespace: biological_process
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]
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.
subset: gosubset_prok  ! Prokaryotic GO subset
subset: high_level_annotation_qc  ! High-level terms not to be used for direct annotation
is_a: GO:0050789  ! regulation of biological process
relationship: regulates GO:0050896 ! response to stimulus
intersection_of: GO:0065007  ! biological regulation
intersection_of: regulates GO:0050896 ! response to stimulus

[Term]
id: GO:0050789
name: regulation of biological process
namespace: biological_process
alt_id: GO:0050791
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]
subset: goslim_aspergillus  ! Aspergillus GO slim
subset: goslim_candida  ! Candida GO slim
subset: gosubset_prok  ! Prokaryotic GO subset
synonym: "regulation of physiological process" EXACT []
is_a: GO:0065007  ! biological regulation
relationship: regulates GO:0008150 ! biological_process
intersection_of: GO:0065007  ! biological regulation
intersection_of: regulates GO:0008150 ! biological_process

[Term]
id: GO:0050794
name: regulation of cellular process
namespace: biological_process
alt_id: GO:0051244
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]
subset: gosubset_prok  ! Prokaryotic GO subset
synonym: "regulation of cellular physiological process" EXACT []
is_a: GO:0050789  ! regulation of biological process
relationship: regulates GO:0009987 ! cellular process
intersection_of: GO:0065007  ! biological regulation
intersection_of: regulates GO:0009987 ! cellular process

[Term]
id: GO:0050896
name: response to stimulus
namespace: biological_process
alt_id: GO:0051869
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]
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.
subset: goslim_pir  ! PIR GO slim
subset: gosubset_prok  ! Prokaryotic GO subset
subset: high_level_annotation_qc  ! High-level terms not to be used for direct annotation
synonym: "physiological response to stimulus" EXACT []
is_a: GO:0008150  ! biological_process

[Term]
id: GO:0051716
name: cellular response to stimulus
namespace: biological_process
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]
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.
subset: gosubset_prok  ! Prokaryotic GO subset
subset: high_level_annotation_qc  ! High-level terms not to be used for direct annotation
is_a: GO:0044763  ! single-organism cellular process
is_a: GO:0050896  ! response to stimulus

[Term]
id: GO:0065007
name: biological regulation
namespace: biological_process
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]
subset: goslim_pir  ! PIR GO slim
subset: gosubset_prok  ! Prokaryotic GO subset
synonym: "regulation" BROAD []
is_a: GO:0008150  ! biological_process

[Typedef]
id: part_of
name: part_of
namespace: gene_ontology
is_transitive: true
xref: BFO:0000050
xref: OBO_REL:part_of

[Typedef]
id: regulates
name: regulates
namespace: gene_ontology
xref: RO:0002211
transitive_over: part_of  ! part_of