goslim plant ribbon.owl
type: Ontology
version IRI: goslim plant ribbon.owl
version info: 2024-10-21

definition
type: AnnotationProperty

term tracker item
type: AnnotationProperty
database_cross_reference: IAO:0000233
has_obo_namespace: external
id: term_tracker_item
is class level: true
is metadata tag: true
shorthand: term_tracker_item

has ontology root term
type: AnnotationProperty
database_cross_reference: IAO:0000700
has_obo_namespace: external
id: has_ontology_root_term
is class level: true
is metadata tag: true
shorthand: has_ontology_root_term

term replaced by
type: AnnotationProperty

chebi ph7 3
type: AnnotationProperty
comment: Rhea list of ChEBI terms representing the major species at pH 7.3.
sub property of: subset_property

gocheck do not annotate
type: AnnotationProperty
comment: Term not to be used for direct annotation
sub property of: subset_property

gocheck obsoletion candidate
type: AnnotationProperty
comment: Terms planned for obsoletion
sub property of: subset_property

goslim agr
type: AnnotationProperty
comment: AGR slim
sub property of: subset_property

goslim aspergillus
type: AnnotationProperty
comment: Aspergillus GO slim
sub property of: subset_property

goslim candida
type: AnnotationProperty
comment: Candida GO slim
sub property of: subset_property

goslim chembl
type: AnnotationProperty
comment: ChEMBL protein targets summary
sub property of: subset_property

goslim drosophila
type: AnnotationProperty
comment: Drosophila GO slim
sub property of: subset_property

goslim euk cellular processes ribbon
type: AnnotationProperty
comment: GO ribbon for eukaroytic cellular processes
sub property of: subset_property

goslim flybase ribbon
type: AnnotationProperty
comment: Insecta GO ribbon slim
sub property of: subset_property

goslim generic
type: AnnotationProperty
comment: Generic GO slim
sub property of: subset_property

goslim metagenomics
type: AnnotationProperty
comment: Metagenomics GO slim
sub property of: subset_property

goslim mouse
type: AnnotationProperty
comment: Mouse GO slim
sub property of: subset_property

goslim pir
type: AnnotationProperty
comment: PIR GO slim
sub property of: subset_property

goslim plant
type: AnnotationProperty
comment: Plant GO slim
sub property of: subset_property

goslim plant ribbon
type: AnnotationProperty
comment: Plant GO ribbon
sub property of: subset_property

goslim pombe
type: AnnotationProperty
comment: Fission yeast GO slim
sub property of: subset_property

goslim prokaryote
type: AnnotationProperty
comment: GO subset for prokaryotes
sub property of: subset_property

goslim prokaryote ribbon
type: AnnotationProperty
comment: Prokaryote GO ribbon slim
sub property of: subset_property

goslim synapse
type: AnnotationProperty
comment: synapse GO slim
sub property of: subset_property

goslim virus
type: AnnotationProperty
comment: GO subset for viruses
sub property of: subset_property

goslim yeast
type: AnnotationProperty
comment: Yeast GO slim
sub property of: subset_property

label approved by the SynGO project
type: AnnotationProperty
sub property of: synonym_type_property

Systematic synonym
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

subset_property
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

consider
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_scope
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty
database_cross_reference: BFO:0000050
has_obo_namespace: external
id: part_of
shorthand: part_of

has part
type: ObjectProperty
type: TransitiveProperty
database_cross_reference: BFO:0000051
has_obo_namespace: external
id: has_part
shorthand: has_part

occurs in
type: ObjectProperty
property chain axiom: part of
database_cross_reference: BFO:0000066
has_obo_namespace: external
id: occurs_in
shorthand: occurs_in

starts during
type: ObjectProperty
database_cross_reference: RO:0002091
has_obo_namespace: external
id: starts_during
shorthand: starts_during

happens during
type: ObjectProperty
sub property of: ends during
type: TransitiveProperty
database_cross_reference: RO:0002092
has_obo_namespace: external
id: happens_during
shorthand: happens_during

ends during
type: ObjectProperty
database_cross_reference: RO:0002093
has_obo_namespace: external
id: ends_during
shorthand: ends_during

regulates
type: ObjectProperty
type: TransitiveProperty
database_cross_reference: RO:0002211
has_obo_namespace: external
id: regulates
shorthand: regulates

negatively regulates
type: ObjectProperty
sub property of: regulates
database_cross_reference: RO:0002212
has_obo_namespace: external
id: negatively_regulates
shorthand: negatively_regulates

positively regulates
type: ObjectProperty
sub property of: regulates
property chain axiom: negatively regulates
database_cross_reference: RO:0002213
has_obo_namespace: external
id: positively_regulates
shorthand: positively_regulates

DNA binding
type: Class
definition: Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
has_alternative_id: GO:0043566
has_narrow_synonym: plasmid binding
has_obo_namespace: molecular_function
has_related_synonym: microtubule/chromatin interaction
has_related_synonym: structure specific DNA binding
has_related_synonym: structure-specific DNA binding
id: GO:0003677
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: DNA binding
annotated property: definition
annotated target: Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:tb
database_cross_reference: GOC:vw

RNA binding
type: Class
definition: Binding to an RNA molecule or a portion thereof.
has_alternative_id: GO:0000498
has_alternative_id: GO:0044822
database_cross_reference: Reactome:R-HSA-203922
has_narrow_synonym: base pairing with RNA
has_obo_namespace: molecular_function
has_related_synonym: poly(A) RNA binding
has_related_synonym: poly(A)-RNA binding
has_related_synonym: poly-A RNA binding
id: GO:0003723
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: RNA binding
annotated property: definition
annotated target: Binding to an RNA molecule or a portion thereof.
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Exportin-5 recognizes 3' overhang of pre-miRNA
type: Axiom
annotated source: RNA binding
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-203922

cytoskeletal motor activity
type: Class
definition: Generation of force resulting in movement, for example along a microfilament or microtubule, or in torque resulting in membrane scission or rotation of a flagellum. The energy required is obtained either from the hydrolysis of a nucleoside triphosphate or by an electrochemical proton gradient (proton-motive force).
term tracker item: https://github.com/geneontology/go-ontology/issues/19590
term tracker item: https://github.com/geneontology/go-ontology/issues/21756
has_broad_synonym: motor activity
database_cross_reference: Reactome:R-HSA-1861595
has_obo_namespace: molecular_function
id: GO:0003774
in_subset: goslim candida
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: cytoskeletal motor activity
annotated property: definition
annotated target: Generation of force resulting in movement, for example along a microfilament or microtubule, or in torque resulting in membrane scission or rotation of a flagellum. The energy required is obtained either from the hydrolysis of a nucleoside triphosphate or by an electrochemical proton gradient (proton-motive force).
database_cross_reference: GOC:mah
database_cross_reference: GOC:vw
database_cross_reference: PMID:11242086
database_cross_reference: PMID:29716949

Extension of pseudopodia by myosin-X in a PI3K dependent manner
type: Axiom
annotated source: cytoskeletal motor activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-1861595

catalytic activity
type: Class
definition: 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.
database_cross_reference: Wikipedia:Enzyme
has_exact_synonym: enzyme activity
has_obo_namespace: molecular_function
id: GO:0003824
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote ribbon

Axiom
annotated source: catalytic activity
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:vw
database_cross_reference: ISBN:0198506732

Axiom
annotated source: catalytic activity
annotated property: has_exact_synonym
annotated target: enzyme activity
database_cross_reference: GOC:dph
database_cross_reference: GOC:tb

structural molecule activity
type: Class
definition: The action of a molecule that contributes to the structural integrity of a complex.
term tracker item: https://github.com/geneontology/go-ontology/issues/24130
has_obo_namespace: molecular_function
id: GO:0005198
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: structural molecule activity
annotated property: definition
annotated target: The action of a molecule that contributes to the structural integrity of a complex.
database_cross_reference: GOC:mah
database_cross_reference: GOC:vw

transporter activity
type: Class
definition: Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells.
term tracker item: https://github.com/geneontology/go-ontology/issues/27621
has_alternative_id: GO:0005478
has_obo_namespace: molecular_function
has_related_synonym: carrier
id: GO:0005215
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
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.

Axiom
annotated source: transporter activity
annotated property: definition
annotated target: Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells.
database_cross_reference: GOC:ai
database_cross_reference: GOC:dgf

protein binding
type: Class
definition: Binding to a protein.
has_alternative_id: GO:0001948
has_alternative_id: GO:0045308
has_exact_synonym: protein amino acid binding
has_narrow_synonym: glycoprotein binding
has_obo_namespace: molecular_function
id: GO:0005515
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote ribbon

Axiom
annotated source: protein binding
annotated property: definition
annotated target: Binding to a protein.
database_cross_reference: GOC:go_curators

extracellular region
type: Class
definition: 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.
database_cross_reference: Wikipedia:Extracellular
has_exact_synonym: extracellular
has_obo_namespace: cellular_component
id: GO:0005576
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast
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'.

Axiom
annotated source: extracellular region
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:go_curators

cell wall
type: Class
definition: The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
term tracker item: https://github.com/geneontology/go-ontology/issues/21669
database_cross_reference: Wikipedia:Cell_wall
has_obo_namespace: cellular_component
id: GO:0005618
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast
comment: Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for plants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).

Axiom
annotated source: cell wall
annotated property: definition
annotated target: The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
database_cross_reference: GOC:giardia
database_cross_reference: ISBN:0198547684
database_cross_reference: PMID:15134259
database_cross_reference: Wikipedia:Microbial_cyst

nucleus
type: Class
definition: A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
database_cross_reference: NIF_Subcellular:sao1702920020
database_cross_reference: Wikipedia:Cell_nucleus
has_exact_synonym: cell nucleus
has_narrow_synonym: horsetail nucleus
has_obo_namespace: cellular_component
id: GO:0005634
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast

Axiom
annotated source: nucleus
annotated property: definition
annotated target: A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
database_cross_reference: GOC:go_curators

Axiom
annotated source: nucleus
annotated property: has_narrow_synonym
annotated target: horsetail nucleus
database_cross_reference: GOC:al
database_cross_reference: GOC:mah
database_cross_reference: GOC:vw
database_cross_reference: PMID:15030757

cytoplasm
type: Class
definition: The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
term tracker item: https://github.com/geneontology/go-ontology/issues/23023
database_cross_reference: Wikipedia:Cytoplasm
has_obo_namespace: cellular_component
id: GO:0005737
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: cytoplasm
annotated property: definition
annotated target: The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
database_cross_reference: ISBN:0198547684

mitochondrion
type: Class
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
database_cross_reference: NIF_Subcellular:sao1860313010
database_cross_reference: Wikipedia:Mitochondrion
has_exact_synonym: mitochondria
has_obo_namespace: cellular_component
id: GO:0005739
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast
comment: Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)

Axiom
annotated source: mitochondrion
annotated property: definition
annotated target: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
database_cross_reference: GOC:giardia
database_cross_reference: ISBN:0198506732

endosome
type: Class
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A vacuole to which materials ingested by endocytosis are delivered.
database_cross_reference: NIF_Subcellular:sao1720343330
database_cross_reference: Wikipedia:Endosome
has_obo_namespace: cellular_component
id: GO:0005768
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: endosome
annotated property: definition
annotated target: A vacuole to which materials ingested by endocytosis are delivered.
database_cross_reference: ISBN:0198506732
database_cross_reference: PMID:19696797

vacuole
type: Class
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
database_cross_reference: Wikipedia:Vacuole
has_obo_namespace: cellular_component
has_related_synonym: vacuolar carboxypeptidase Y
id: GO:0005773
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast

Axiom
annotated source: vacuole
annotated property: definition
annotated target: A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
database_cross_reference: GOC:mtg_sensu
database_cross_reference: ISBN:0198506732

peroxisome
type: Class
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
has_alternative_id: GO:0019818
has_broad_synonym: peroxisome vesicle
database_cross_reference: NIF_Subcellular:sao499555322
database_cross_reference: Wikipedia:Peroxisome
has_obo_namespace: cellular_component
has_related_synonym: peroxisomal
id: GO:0005777
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast

Axiom
annotated source: peroxisome
annotated property: definition
annotated target: A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
database_cross_reference: GOC:pm
database_cross_reference: PMID:9302272
database_cross_reference: UniProtKB-KW:KW-0576

endoplasmic reticulum
type: Class
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
database_cross_reference: NIF_Subcellular:sao1036339110
database_cross_reference: Wikipedia:Endoplasmic_reticulum
has_exact_synonym: ER
has_obo_namespace: cellular_component
id: GO:0005783
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast

Axiom
annotated source: endoplasmic reticulum
annotated property: definition
annotated target: The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
database_cross_reference: ISBN:0198506732

Golgi apparatus
type: Class
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
has_broad_synonym: Golgi
database_cross_reference: NIF_Subcellular:sao451912436
database_cross_reference: Wikipedia:Golgi_apparatus
has_exact_synonym: Golgi complex
has_narrow_synonym: Golgi ribbon
has_obo_namespace: cellular_component
id: GO:0005794
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast
comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.

Axiom
annotated source: Golgi apparatus
annotated property: definition
annotated target: A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
database_cross_reference: ISBN:0198506732

ribosome
type: Class
definition: An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
has_alternative_id: GO:0033279
database_cross_reference: NIF_Subcellular:sao1429207766
database_cross_reference: Wikipedia:Ribosome
has_narrow_synonym: free ribosome
has_narrow_synonym: membrane bound ribosome
has_obo_namespace: cellular_component
has_related_synonym: ribosomal RNA
id: GO:0005840
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: ribosome
annotated property: definition
annotated target: An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
database_cross_reference: ISBN:0198506732

Axiom
annotated source: ribosome
annotated property: has_narrow_synonym
annotated target: free ribosome
database_cross_reference: NIF_Subcellular:sao1139385046

Axiom
annotated source: ribosome
annotated property: has_narrow_synonym
annotated target: membrane bound ribosome
database_cross_reference: NIF_Subcellular:sao1291545653

cytoskeleton
type: Class
definition: A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
database_cross_reference: Wikipedia:Cytoskeleton
has_obo_namespace: cellular_component
id: GO:0005856
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: cytoskeleton
annotated property: definition
annotated target: A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
database_cross_reference: GOC:mah
database_cross_reference: PMID:16959967
database_cross_reference: PMID:27419875

plasma membrane
type: Class
definition: The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
has_alternative_id: GO:0005887
has_alternative_id: GO:0005904
has_broad_synonym: juxtamembrane
database_cross_reference: NIF_Subcellular:sao1663586795
database_cross_reference: Wikipedia:Cell_membrane
has_exact_synonym: cell membrane
has_exact_synonym: cellular membrane
has_exact_synonym: cytoplasmic membrane
has_exact_synonym: plasmalemma
has_narrow_synonym: bacterial inner membrane
has_narrow_synonym: inner endospore membrane
has_narrow_synonym: integral component of plasma membrane
has_narrow_synonym: integral to plasma membrane
has_narrow_synonym: plasma membrane lipid bilayer
has_obo_namespace: cellular_component
id: GO:0005886
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: plasma membrane
annotated property: definition
annotated target: The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
database_cross_reference: ISBN:0716731363

Axiom
annotated source: plasma membrane
annotated property: has_exact_synonym
annotated target: cellular membrane
database_cross_reference: NIF_Subcellular:sao6433132645

Axiom
annotated source: plasma membrane
annotated property: has_narrow_synonym
annotated target: plasma membrane lipid bilayer
database_cross_reference: GOC:mah

carbohydrate metabolic process
type: Class
subclass of: primary metabolic process
definition: The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
term tracker item: https://github.com/geneontology/go-ontology/issues/22880
created by: jl
creation date: 2012-10-23T15:40:34Z
has_alternative_id: GO:0044261
has_alternative_id: GO:0044723
database_cross_reference: Wikipedia:Carbohydrate_metabolism
has_exact_synonym: carbohydrate metabolism
has_obo_namespace: biological_process
id: GO:0005975
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim yeast

Axiom
annotated source: carbohydrate metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
database_cross_reference: GOC:mah
database_cross_reference: ISBN:0198506732

generation of precursor metabolites and energy
type: Class
definition: The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
has_broad_synonym: energy pathways
has_obo_namespace: biological_process
has_related_synonym: intermediary metabolism
has_related_synonym: metabolic energy generation
id: GO:0006091
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: generation of precursor metabolites and energy
annotated property: definition
annotated target: The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
database_cross_reference: GOC:jl

Axiom
annotated source: generation of precursor metabolites and energy
annotated property: has_related_synonym
annotated target: intermediary metabolism
database_cross_reference: GOC:mah

DNA metabolic process
type: Class
subclass of: primary metabolic process
definition: Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
has_alternative_id: GO:0055132
has_exact_synonym: DNA metabolism
has_exact_synonym: cellular DNA metabolism
has_obo_namespace: biological_process
id: GO:0006259
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote ribbon

Axiom
annotated source: DNA metabolic process
annotated property: definition
annotated target: Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
database_cross_reference: ISBN:0198506732

lipid metabolic process
type: Class
subclass of: primary metabolic process
definition: The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
database_cross_reference: Wikipedia:Lipid_metabolism
has_exact_synonym: lipid metabolism
has_obo_namespace: biological_process
id: GO:0006629
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim pombe
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: lipid metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
database_cross_reference: GOC:ma

transport
type: Class
definition: The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
term tracker item: https://github.com/geneontology/go-ontology/issues/20292
created by: jl
creation date: 2012-12-13T16:25:32Z
has_alternative_id: GO:0015457
has_alternative_id: GO:0015460
has_alternative_id: GO:0044765
has_obo_namespace: biological_process
has_related_synonym: single-organism transport
id: GO:0006810
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.

Axiom
annotated source: transport
annotated property: definition
annotated target: The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
database_cross_reference: GOC:dos
database_cross_reference: GOC:dph
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

response to stress
type: Class
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
term tracker item: https://github.com/geneontology/go-ontology/issues/26810
has_obo_namespace: biological_process
has_related_synonym: response to abiotic stress
has_related_synonym: response to biotic stress
id: GO:0006950
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim metagenomics
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: response to stress
annotated property: definition
annotated target: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
database_cross_reference: GOC:mah

cell cycle
type: Class
definition: The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
database_cross_reference: Wikipedia:Cell_cycle
has_exact_synonym: cell-division cycle
has_obo_namespace: biological_process
id: GO:0007049
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: cell cycle
annotated property: definition
annotated target: The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:mtg_cell_cycle

signal transduction
type: Class
definition: 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.
has_alternative_id: GO:0023014
has_alternative_id: GO:0023015
has_alternative_id: GO:0023016
has_alternative_id: GO:0023033
has_alternative_id: GO:0023045
database_cross_reference: Wikipedia:Signal_transduction
has_narrow_synonym: signaling cascade
has_narrow_synonym: signalling cascade
has_obo_namespace: biological_process
has_related_synonym: signaling pathway
has_related_synonym: signalling pathway
id: GO:0007165
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim plant
in_subset: goslim plant ribbon
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.

Axiom
annotated source: signal transduction
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:go_curators
database_cross_reference: GOC:mtg_signaling_feb11

circadian rhythm
type: Class
definition: Any biological process in an organism that recurs with a regularity of approximately 24 hours.
has_alternative_id: GO:0050895
database_cross_reference: Wikipedia:Circadian_rhythm
has_exact_synonym: circadian process
has_obo_namespace: biological_process
has_related_synonym: circadian response
has_related_synonym: response to circadian rhythm
id: GO:0007623
in_subset: goslim drosophila
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: circadian rhythm
annotated property: definition
annotated target: Any biological process in an organism that recurs with a regularity of approximately 24 hours.
database_cross_reference: GOC:bf
database_cross_reference: GOC:go_curators

lipid binding
type: Class
definition: Binding to a lipid.
has_obo_namespace: molecular_function
id: GO:0008289
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
in_subset: goslim yeast

Axiom
annotated source: lipid binding
annotated property: definition
annotated target: Binding to a lipid.
database_cross_reference: GOC:ai

catabolic process
type: Class
definition: A cellular process consisting of the biochemical pathways by which a living organism breaks down substances. This includes the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
term tracker item: https://github.com/geneontology/go-ontology/issues/28921
term tracker item: https://github.com/geneontology/go-ontology/issues/28932
created by: jl
creation date: 2012-10-17T15:52:35Z
has_alternative_id: GO:0044243
has_alternative_id: GO:0044712
database_cross_reference: Wikipedia:Catabolism
has_exact_synonym: breakdown of chemical
has_exact_synonym: breakdown of molecule
has_exact_synonym: breakdown of substance
has_exact_synonym: catabolism
has_exact_synonym: degradation
has_obo_namespace: biological_process
id: GO:0009056
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: catabolic process
annotated property: definition
annotated target: A cellular process consisting of the biochemical pathways by which a living organism breaks down substances. This includes the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
database_cross_reference: ISBN:0198547684

biosynthetic process
type: Class
definition: A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
term tracker item: https://github.com/geneontology/go-ontology/issues/28932
created by: jl
creation date: 2012-10-17T15:52:18Z
has_alternative_id: GO:0044274
has_alternative_id: GO:0044711
has_broad_synonym: formation
database_cross_reference: Wikipedia:Anabolism
has_exact_synonym: anabolism
has_exact_synonym: biosynthesis
has_exact_synonym: synthesis
has_narrow_synonym: multicellular organismal biosynthetic process
has_obo_namespace: biological_process
has_related_synonym: single-organism biosynthetic process
id: GO:0009058
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: biosynthetic process
annotated property: definition
annotated target: A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
database_cross_reference: GOC:curators
database_cross_reference: ISBN:0198547684

chloroplast
type: Class
subclass of: plastid
definition: A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
database_cross_reference: Wikipedia:Chloroplast
has_obo_namespace: cellular_component
id: GO:0009507
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: chloroplast
annotated property: definition
annotated target: A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
database_cross_reference: ISBN:0471245208

plastid
type: Class
subclass of: Restriction
  on property: part of
  some values from: cytoplasm
definition: Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
database_cross_reference: Wikipedia:Plastid
has_obo_namespace: cellular_component
id: GO:0009536
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: plastid
annotated property: definition
annotated target: Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0198547684

thylakoid
type: Class
definition: A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
term tracker item: https://github.com/geneontology/go-ontology/issues/13958
database_cross_reference: Wikipedia:Thylakoid
has_obo_namespace: cellular_component
has_related_synonym: photosynthetic membrane
id: GO:0009579
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
comment: A thylakoid is not considered an organelle, but some thylakoids are part of organelles.

Axiom
annotated source: thylakoid
annotated property: definition
annotated target: A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
database_cross_reference: GOC:ds
database_cross_reference: GOC:mtg_sensu
database_cross_reference: ISBN:0198506732

pollination
type: Class
subclass of: reproductive process
definition: The cascade of biological processes occurring in plants beginning when the pollen lands on the female reproductive organs of a plant and continuing up to, but not including, fertilization, as defined by sperm-egg cell fusion.
database_cross_reference: Wikipedia:Pollination
has_obo_namespace: biological_process
id: GO:0009856
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: pollination
annotated property: definition
annotated target: The cascade of biological processes occurring in plants beginning when the pollen lands on the female reproductive organs of a plant and continuing up to, but not including, fertilization, as defined by sperm-egg cell fusion.
database_cross_reference: GOC:tb
database_cross_reference: PMID:10973091

flower development
type: Class
subclass of: reproductive process
subclass of: anatomical structure development
subclass of: Restriction
  on property: part of
  some values from: anatomical structure development
definition: The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem.
has_alternative_id: GO:0048409
has_obo_namespace: biological_process
id: GO:0009908
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: flower development
annotated property: definition
annotated target: The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem.
database_cross_reference: GOC:tb
database_cross_reference: ISBN:0879015322

regulation of gene expression
type: Class
subclass of: Restriction
  on property: regulates
  some values from: biosynthetic process
definition: Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).
term tracker item: https://github.com/geneontology/go-ontology/issues/22557
database_cross_reference: Wikipedia:Regulation_of_gene_expression
has_narrow_synonym: regulation of protein expression
has_obo_namespace: biological_process
has_related_synonym: gene regulation
has_related_synonym: regulation of gene product expression
id: GO:0010468
in_subset: goslim euk cellular processes ribbon
in_subset: goslim plant ribbon
comment: This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.

Axiom
annotated source: regulation of gene expression
annotated property: definition
annotated target: Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).
database_cross_reference: GOC:txnOH-2018

Axiom
annotated source: regulation of gene expression
annotated property: has_related_synonym
annotated target: gene regulation
database_cross_reference: GOC:cjm

programmed cell death
type: Class
subclass of: Restriction
  on property: has part
  some values from: signal transduction
definition: A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
term tracker item: https://github.com/geneontology/go-ontology/issues/24835
has_alternative_id: GO:0016244
has_broad_synonym: regulated cell death
database_cross_reference: Wikipedia:Programmed_cell_death
has_narrow_synonym: caspase-independent cell death
has_narrow_synonym: non-apoptotic programmed cell death
has_narrow_synonym: nonapoptotic programmed cell death
has_obo_namespace: biological_process
has_related_synonym: PCD
has_related_synonym: RCD
has_related_synonym: caspase-independent apoptosis
id: GO:0012501
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children.

Axiom
annotated source: programmed cell death
annotated property: definition
annotated target: A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
database_cross_reference: GOC:lr
database_cross_reference: GOC:mtg_apoptosis

photosynthesis
type: Class
definition: The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
database_cross_reference: Wikipedia:Photosynthesis
has_obo_namespace: biological_process
id: GO:0015979
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: photosynthesis
annotated property: definition
annotated target: The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
database_cross_reference: ISBN:0198547684

cellular component organization
type: Class
definition: A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
has_alternative_id: GO:0044235
has_alternative_id: GO:0071842
has_exact_synonym: cell organisation
has_exact_synonym: cellular component organisation at cellular level
has_exact_synonym: cellular component organisation in other organism
has_exact_synonym: cellular component organization at cellular level
has_exact_synonym: cellular component organization in other organism
has_obo_namespace: biological_process
has_related_synonym: cell organization and biogenesis
id: GO:0016043
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: cellular component organization
annotated property: definition
annotated target: A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
database_cross_reference: GOC:ai
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization
annotated property: has_exact_synonym
annotated target: cellular component organisation at cellular level
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization
annotated property: has_exact_synonym
annotated target: cellular component organisation in other organism
database_cross_reference: GOC:mah

Axiom
annotated source: cellular component organization
annotated property: has_related_synonym
annotated target: cell organization and biogenesis
database_cross_reference: GOC:mah

antioxidant activity
type: Class
subclass of: Restriction
  on property: part of
  some values from: response to chemical
definition: 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.
has_obo_namespace: molecular_function
id: GO:0016209
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: antioxidant activity
annotated property: definition
annotated target: 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.
database_cross_reference: ISBN:0198506732

kinase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: Reactome:R-HSA-6788855
database_cross_reference: Reactome:R-HSA-6788867
has_exact_synonym: phosphokinase activity
has_obo_namespace: molecular_function
id: GO:0016301
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim metagenomics
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.

Axiom
annotated source: kinase activity
annotated property: definition
annotated target: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: ISBN:0198506732

FN3KRP phosphorylates PsiAm, RibAm
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788855

FN3K phosphorylates ketosamines
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788867

protein metabolic process
type: Class
subclass of: primary metabolic process
definition: The chemical reactions and pathways involving a protein. Includes protein modification.
term tracker item: https://github.com/geneontology/go-ontology/issues/23112
term tracker item: https://github.com/geneontology/go-ontology/issues/27189
has_alternative_id: GO:0006411
has_alternative_id: GO:0044267
has_alternative_id: GO:0044268
database_cross_reference: Wikipedia:Protein_metabolism
has_exact_synonym: cellular protein metabolic process
has_exact_synonym: cellular protein metabolism
has_exact_synonym: protein metabolic process and modification
has_exact_synonym: protein metabolism
has_exact_synonym: protein metabolism and modification
has_narrow_synonym: multicellular organismal protein metabolic process
has_obo_namespace: biological_process
id: GO:0019538
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim flybase ribbon
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
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.

Axiom
annotated source: protein metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving a protein. Includes protein modification.
database_cross_reference: GOC:ma

secondary metabolic process
type: Class
definition: The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients.
database_cross_reference: Wikipedia:Secondary_metabolism
has_exact_synonym: secondary metabolism
has_exact_synonym: secondary metabolite metabolic process
has_exact_synonym: secondary metabolite metabolism
has_obo_namespace: biological_process
id: GO:0019748
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim pombe

Axiom
annotated source: secondary metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients.
database_cross_reference: GOC:go_curators

reproductive process
type: Class
definition: 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.
term tracker item: https://github.com/geneontology/go-ontology/issues/27054
created by: jl
creation date: 2012-09-19T15:56:06Z
has_alternative_id: GO:0044702
database_cross_reference: Wikipedia:Reproduction
has_obo_namespace: biological_process
has_related_synonym: single organism reproductive process
id: GO:0022414
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: reproductive process
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:dph
database_cross_reference: GOC:isa_complete

cell differentiation
type: Class
definition: The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
term tracker item: https://github.com/geneontology/go-ontology/issues/24390
database_cross_reference: Wikipedia:Cellular_differentiation
has_obo_namespace: biological_process
id: GO:0030154
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: cell differentiation
annotated property: definition
annotated target: The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
database_cross_reference: ISBN:0198506732

enzyme regulator activity
type: Class
subclass of: molecular function regulator activity
subclass of: Restriction
  on property: regulates
  some values from: catalytic activity
definition: Binds to and modulates the activity of an enzyme.
has_alternative_id: GO:0010576
has_exact_synonym: catalytic regulator activity
has_exact_synonym: enzyme modulator
has_narrow_synonym: metalloenzyme regulator activity
has_obo_namespace: molecular_function
id: GO:0030234
in_subset: goslim agr
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast
comment: This term should only be used in cases when the regulator directly interacts with the enzyme.

Axiom
annotated source: enzyme regulator activity
annotated property: definition
annotated target: Binds to and modulates the activity of an enzyme.
database_cross_reference: GOC:dph
database_cross_reference: GOC:mah
database_cross_reference: GOC:tb

Axiom
annotated source: enzyme regulator activity
annotated property: has_exact_synonym
annotated target: catalytic regulator activity
database_cross_reference: GOC:dph

carbohydrate binding
type: Class
definition: Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
has_alternative_id: GO:0005529
has_exact_synonym: sugar binding
has_obo_namespace: molecular_function
has_related_synonym: selectin
id: GO:0030246
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim flybase ribbon
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: carbohydrate binding
annotated property: definition
annotated target: Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
database_cross_reference: GOC:mah

small molecule binding
type: Class
definition: Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule.
created by: bf
creation date: 2012-01-17T04:20:34Z
has_obo_namespace: molecular_function
id: GO:0036094
in_subset: goslim agr
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim plant ribbon
in_subset: goslim prokaryote ribbon
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.

Axiom
annotated source: small molecule binding
annotated property: definition
annotated target: Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule.
database_cross_reference: GOC:curators
database_cross_reference: GOC:pde
database_cross_reference: GOC:pm

signaling receptor activity
type: Class
definition: Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
created by: bf
creation date: 2011-08-01T02:45:27Z
has_alternative_id: GO:0004872
has_alternative_id: GO:0019041
has_broad_synonym: receptor activity
has_exact_synonym: receptor activity involved in signal transduction
has_exact_synonym: signalling receptor activity
has_obo_namespace: molecular_function
id: GO:0038023
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim drosophila
in_subset: goslim flybase ribbon
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: signaling receptor activity
annotated property: definition
annotated target: Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
database_cross_reference: GOC:bf
database_cross_reference: GOC:signaling

Axiom
annotated source: signaling receptor activity
annotated property: has_exact_synonym
annotated target: receptor activity involved in signal transduction
database_cross_reference: GOC:bf

response to chemical
type: Class
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
has_exact_synonym: response to chemical stimulus
has_exact_synonym: response to chemical substance
has_obo_namespace: biological_process
id: GO:0042221
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim drosophila
in_subset: goslim metagenomics
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim yeast
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.

Axiom
annotated source: response to chemical
annotated property: definition
annotated target: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
database_cross_reference: GOC:jl

Axiom
annotated source: response to chemical
annotated property: has_exact_synonym
annotated target: response to chemical stimulus
database_cross_reference: GOC:dos

primary metabolic process
type: Class
definition: The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
term tracker item: https://github.com/geneontology/go-ontology/issues/26424
database_cross_reference: Wikipedia:Primary_metabolite
has_exact_synonym: primary metabolism
has_obo_namespace: biological_process
id: GO:0044238
in_subset: gocheck do not annotate
in_subset: goslim euk cellular processes ribbon
in_subset: goslim pir
in_subset: goslim plant ribbon
in_subset: goslim prokaryote ribbon

Axiom
annotated source: primary metabolic process
annotated property: definition
annotated target: The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
database_cross_reference: GOC:go_curators

translation regulator activity
type: Class
subclass of: Restriction
  on property: part of
  some values from: regulation of gene expression
definition: Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
has_exact_synonym: translation factor activity
has_obo_namespace: molecular_function
id: GO:0045182
in_subset: goslim candida
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: translation regulator activity
annotated property: definition
annotated target: Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
database_cross_reference: GOC:ai

anatomical structure development
type: Class
definition: The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
term tracker item: https://github.com/geneontology/go-ontology/issues/26424
has_exact_synonym: development of an anatomical structure
has_obo_namespace: biological_process
id: GO:0048856
in_subset: gocheck do not annotate
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: anatomical structure development
annotated property: definition
annotated target: The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
database_cross_reference: GO_REF:0000021

molecular adaptor activity
type: Class
definition: The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
has_alternative_id: GO:0032947
has_broad_synonym: protein complex scaffold activity
has_broad_synonym: protein-containing complex scaffold activity
has_exact_synonym: binding, bridging
has_obo_namespace: molecular_function
id: GO:0060090
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: molecular adaptor activity
annotated property: definition
annotated target: The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
database_cross_reference: GOC:mtg_MIT_16mar07
database_cross_reference: GOC:vw

molecular function regulator activity
type: Class
subclass of: Restriction
  on property: has part
  some values from: protein binding
definition: A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition.
term tracker item: https://github.com/geneontology/go-ontology/issues/20854
term tracker item: https://github.com/geneontology/go-ontology/issues/20862
term tracker item: https://github.com/geneontology/go-ontology/issues/25165
has_exact_synonym: molecular function regulator
has_obo_namespace: molecular_function
id: GO:0098772
in_subset: gocheck do not annotate
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: molecular function regulator activity
annotated property: definition
annotated target: A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition.
database_cross_reference: GOC:dos
database_cross_reference: GOC:pt

molecular carrier activity
type: Class
definition: Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location.
term tracker item: https://github.com/geneontology/go-ontology/issues/14221
term tracker item: https://github.com/geneontology/go-ontology/issues/20848
created by: pg
creation date: 2017-09-19T13:10:18Z
has_obo_namespace: molecular_function
id: GO:0140104
in_subset: gocheck do not annotate
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon
comment: Note that a carrier moves with its substrate/cargo, while a transporter does not move with the cargo, but facilitates the change in localization.

Axiom
annotated source: molecular carrier activity
annotated property: definition
annotated target: Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location.
database_cross_reference: GOC:molecular_function_refactoring
database_cross_reference: GOC:pdt

transcription regulator activity
type: Class
definition: A molecular function that controls the rate, timing and/or magnitude of gene transcription. 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. Genes are transcriptional units, and include bacterial operons.
term tracker item: https://github.com/geneontology/go-ontology/issues/13588
term tracker item: https://github.com/geneontology/go-ontology/issues/23609
created by: pg
creation date: 2017-10-18T07:05:44Z
has_obo_namespace: molecular_function
id: GO:0140110
in_subset: gocheck do not annotate
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim plant
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: transcription regulator activity
annotated property: definition
annotated target: A molecular function that controls the rate, timing and/or magnitude of gene transcription. 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. Genes are transcriptional units, and include bacterial operons.
database_cross_reference: GOC:pg
database_cross_reference: GOC:txnOH-2018
database_cross_reference: Wikipedia:Transcription_factor

general transcription initiation factor activity
type: Class
subclass of: Restriction
  on property: part of
  some values from: biosynthetic process
subclass of: Restriction
  on property: part of
  some values from: primary metabolic process
definition: A molecular function required for core promoter activity that mediates the assembly of the RNA polymerase holoenzyme at promoter DNA to form the pre-initiation complex (PIC). General transcription factors (GTFs) bind to and open promoter DNA, initiate RNA synthesis and stimulate the escape of the polymerase from the promoter. Not all subunits of the general transcription factor are necessarily present at all promoters to initiate transcription. GTFs act at each promoter, although the exact subunit composition at individual promoters may vary.
term tracker item: https://github.com/geneontology/go-ontology/issues/20253
created by: pg
creation date: 2018-05-24T07:51:23Z
has_exact_synonym: GTF activity
has_exact_synonym: basal transcription factor activity
has_exact_synonym: general transcription factor activity
has_obo_namespace: molecular_function
id: GO:0140223
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim plant ribbon
in_subset: goslim prokaryote ribbon
comment: Usage guidance: The distinction between general transcription factors and DNA-binding transcription factors is that the latter modulate the selection of which genes are expressed under specific conditions, while general transcription factors are the constitutive machinery required for transcription initiation.

Axiom
annotated source: general transcription initiation factor activity
annotated property: definition
annotated target: A molecular function required for core promoter activity that mediates the assembly of the RNA polymerase holoenzyme at promoter DNA to form the pre-initiation complex (PIC). General transcription factors (GTFs) bind to and open promoter DNA, initiate RNA synthesis and stimulate the escape of the polymerase from the promoter. Not all subunits of the general transcription factor are necessarily present at all promoters to initiate transcription. GTFs act at each promoter, although the exact subunit composition at individual promoters may vary.
database_cross_reference: GOC:txnOH-2018

molecular sensor activity
type: Class
subclass of: molecular function regulator activity
definition: Binding to a molecule and eliciting a change in the protein's activity in response to the intracellular level of that molecule.
term tracker item: https://github.com/geneontology/go-ontology/issues/28772
created by: pg
creation date: 2018-12-10T14:30:28Z
has_exact_synonym: small molecular sensor activity
has_exact_synonym: small molecule sensing activity
has_narrow_synonym: small molecule sensor activity
has_obo_namespace: molecular_function
id: GO:0140299
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: molecular sensor activity
annotated property: definition
annotated target: Binding to a molecule and eliciting a change in the protein's activity in response to the intracellular level of that molecule.
database_cross_reference: PMID:26328879

molecular sequestering activity
type: Class
definition: Binding to a specific molecule to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active.
created by: pg
creation date: 2019-03-28T10:00:25Z
database_cross_reference: Reactome:R-HSA-3245898
has_obo_namespace: molecular_function
id: GO:0140313
in_subset: goslim drosophila
in_subset: goslim euk cellular processes ribbon
in_subset: goslim generic
in_subset: goslim plant ribbon
in_subset: goslim prokaryote
in_subset: goslim prokaryote ribbon

Axiom
annotated source: molecular sequestering activity
annotated property: definition
annotated target: Binding to a specific molecule to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active.
database_cross_reference: PMID:13130076

TCN1 binds correnoids in the circulation
type: Axiom
annotated source: molecular sequestering activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-3245898