format-version: 1.2
data-version: go/2024-10-21/subsets/goslim_prokaryote_ribbon.owl
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_obsoletion_candidate "Terms planned for obsoletion"
subsetdef: goslim_agr "AGR slim"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_drosophila "Drosophila GO slim"
subsetdef: goslim_euk_cellular_processes_ribbon "GO ribbon for eukaroytic cellular processes"
subsetdef: goslim_flybase_ribbon "Insecta GO ribbon slim"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_metagenomics "Metagenomics GO slim"
subsetdef: goslim_mouse "Mouse GO slim"
subsetdef: goslim_pir "PIR GO slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_plant_ribbon "Plant GO ribbon"
subsetdef: goslim_pombe "Fission yeast GO slim"
subsetdef: goslim_prokaryote "GO subset for prokaryotes"
subsetdef: goslim_prokaryote_ribbon "Prokaryote GO ribbon slim"
subsetdef: goslim_synapse "synapse GO slim"
subsetdef: goslim_virus "GO subset for viruses"
subsetdef: goslim_yeast "Yeast GO slim"
synonymtypedef: syngo_official_label "label approved by the SynGO project"
synonymtypedef: systematic_synonym "Systematic synonym" EXACT
ontology: go/subsets/goslim_prokaryote_ribbon
property_value: owl:versionInfo "2024-10-21" xsd:string

[Term]
id: GO:0003677
name: DNA binding
namespace: molecular_function
alt_id: GO:0043566
def: "Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "microtubule/chromatin interaction" RELATED []
synonym: "plasmid binding" NARROW []
synonym: "structure specific DNA binding" RELATED []
synonym: "structure-specific DNA binding" RELATED []

[Term]
id: GO:0003723
name: RNA binding
namespace: molecular_function
alt_id: GO:0000498
alt_id: GO:0044822
def: "Binding to an RNA molecule or a portion thereof." [GOC:jl, GOC:mah]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "base pairing with RNA" NARROW []
synonym: "poly(A) RNA binding" RELATED []
synonym: "poly(A)-RNA binding" RELATED []
synonym: "poly-A RNA binding" RELATED []
xref: Reactome:R-HSA-203922 "Exportin-5 recognizes 3' overhang of pre-miRNA"

[Term]
id: GO:0003774
name: cytoskeletal motor activity
namespace: molecular_function
def: "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)." [GOC:mah, GOC:vw, PMID:11242086, PMID:29716949]
subset: goslim_candida
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "motor activity" BROAD []
xref: Reactome:R-HSA-1861595 "Extension of pseudopodia by myosin-X in a PI3K dependent manner"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19590" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21756" xsd:anyURI

[Term]
id: GO:0003824
name: catalytic activity
namespace: molecular_function
def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote_ribbon
synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb]
xref: Wikipedia:Enzyme

[Term]
id: GO:0005198
name: structural molecule activity
namespace: molecular_function
def: "The action of a molecule that contributes to the structural integrity of a complex." [GOC:mah, GOC:vw]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24130" xsd:anyURI

[Term]
id: GO:0005215
name: transporter activity
namespace: molecular_function
alt_id: GO:0005478
def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells." [GOC:ai, GOC:dgf]
comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "carrier" RELATED []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27621" xsd:anyURI

[Term]
id: GO:0005515
name: protein binding
namespace: molecular_function
alt_id: GO:0001948
alt_id: GO:0045308
def: "Binding to a protein." [GOC:go_curators]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote_ribbon
synonym: "glycoprotein binding" NARROW []
synonym: "protein amino acid binding" EXACT []

[Term]
id: GO:0005576
name: extracellular region
namespace: cellular_component
def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators]
comment: Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "extracellular" EXACT []
xref: Wikipedia:Extracellular

[Term]
id: GO:0005618
name: cell wall
namespace: cellular_component
def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins." [GOC:giardia, ISBN:0198547684, PMID:15134259, Wikipedia:Microbial_cyst]
comment: Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for plants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).
subset: gocheck_do_not_annotate
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
xref: Wikipedia:Cell_wall
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21669" xsd:anyURI

[Term]
id: GO:0005694
name: chromosome
namespace: cellular_component
def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684]
comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "chromatid" RELATED []
synonym: "interphase chromosome" NARROW []
synonym: "prophase chromosome" NARROW []
xref: Wikipedia:Chromosome
is_a: GO:0043226 ! organelle

[Term]
id: GO:0005737
name: cytoplasm
namespace: cellular_component
def: "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
xref: Wikipedia:Cytoplasm
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI

[Term]
id: GO:0005840
name: ribosome
namespace: cellular_component
alt_id: GO:0033279
def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "free ribosome" NARROW [NIF_Subcellular:sao1139385046]
synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653]
synonym: "ribosomal RNA" RELATED []
xref: NIF_Subcellular:sao1429207766
xref: Wikipedia:Ribosome
is_a: GO:0043226 ! organelle

[Term]
id: GO:0005886
name: plasma membrane
namespace: cellular_component
alt_id: GO:0005887
alt_id: GO:0005904
def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "bacterial inner membrane" NARROW []
synonym: "cell membrane" EXACT []
synonym: "cellular membrane" EXACT [NIF_Subcellular:sao6433132645]
synonym: "cytoplasmic membrane" EXACT []
synonym: "inner endospore membrane" NARROW []
synonym: "integral component of plasma membrane" NARROW []
synonym: "integral to plasma membrane" NARROW []
synonym: "juxtamembrane" BROAD []
synonym: "plasma membrane lipid bilayer" NARROW [GOC:mah]
synonym: "plasmalemma" EXACT []
xref: NIF_Subcellular:sao1663586795
xref: Wikipedia:Cell_membrane

[Term]
id: GO:0006091
name: generation of precursor metabolites and energy
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." [GOC:jl]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "energy pathways" BROAD []
synonym: "intermediary metabolism" RELATED [GOC:mah]
synonym: "metabolic energy generation" RELATED []
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0006259
name: DNA metabolic process
namespace: biological_process
alt_id: GO:0055132
def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote_ribbon
synonym: "cellular DNA metabolism" EXACT []
synonym: "DNA metabolism" EXACT []
is_a: GO:0044238 ! primary metabolic process

[Term]
id: GO:0006351
name: DNA-templated transcription
namespace: biological_process
alt_id: GO:0001121
alt_id: GO:0006350
alt_id: GO:0061018
alt_id: GO:0061022
def: "The synthesis of an RNA transcript from a DNA template." [GOC:jl, GOC:txnOH]
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "bacterial transcription" NARROW []
synonym: "cellular transcription" BROAD []
synonym: "DNA-dependent transcription" EXACT []
synonym: "transcription" BROAD []
synonym: "transcription from bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcription, DNA-dependent" EXACT [GOC:txnOH]
synonym: "transcription, DNA-templated" EXACT []
xref: Wikipedia:Transcription_(genetics)
is_a: GO:0044238 ! primary metabolic process
relationship: part_of GO:0008152 ! metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14854" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16737" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22258" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22555" xsd:anyURI

[Term]
id: GO:0006355
name: regulation of DNA-templated transcription
namespace: biological_process
alt_id: GO:0032583
alt_id: GO:0045449
alt_id: GO:0061019
def: "Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "regulation of cellular transcription, DNA-dependent" EXACT []
synonym: "regulation of gene-specific transcription" RELATED []
synonym: "regulation of transcription, DNA-dependent" EXACT [GOC:txnOH]
synonym: "regulation of transcription, DNA-templated" EXACT []
synonym: "transcriptional control" BROAD []
relationship: regulates GO:0006351 ! DNA-templated transcription
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25256" xsd:anyURI

[Term]
id: GO:0006412
name: translation
namespace: biological_process
alt_id: GO:0006416
alt_id: GO:0006453
alt_id: GO:0043037
def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "protein anabolism" EXACT []
synonym: "protein biosynthesis" EXACT []
synonym: "protein biosynthetic process" EXACT []
synonym: "protein formation" EXACT []
synonym: "protein synthesis" EXACT []
synonym: "protein translation" EXACT []
xref: Wikipedia:Translation_(genetics)
is_a: GO:0044238 ! primary metabolic process

[Term]
id: GO:0006457
name: protein folding
namespace: biological_process
alt_id: GO:0007022
alt_id: GO:0007024
alt_id: GO:0007025
def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:go_curators, GOC:rb]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "alpha-tubulin folding" NARROW [GOC:mah]
synonym: "beta-tubulin folding" NARROW [GOC:mah]
synonym: "chaperone activity" RELATED []
synonym: "chaperonin ATPase activity" RELATED []
synonym: "chaperonin-mediated tubulin folding" NARROW [GOC:mah]
synonym: "co-chaperone activity" RELATED []
synonym: "co-chaperonin activity" RELATED []
synonym: "glycoprotein-specific chaperone activity" RELATED []
synonym: "non-chaperonin molecular chaperone ATPase activity" RELATED []
synonym: "protein complex assembly, multichaperone pathway" RELATED []
xref: Wikipedia:Protein_folding
relationship: part_of GO:0044238 ! primary metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25673" xsd:anyURI

[Term]
id: GO:0006520
name: amino acid metabolic process
namespace: biological_process
alt_id: GO:0006519
def: "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups." [ISBN:0198506732]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "amino acid and derivative metabolism" RELATED []
synonym: "cellular amino acid and derivative metabolic process" RELATED []
synonym: "cellular amino acid metabolic process" EXACT []
synonym: "cellular amino acid metabolism" EXACT []
is_a: GO:0044238 ! primary metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17904" xsd:anyURI

[Term]
id: GO:0006629
name: lipid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "lipid metabolism" EXACT []
xref: Wikipedia:Lipid_metabolism
is_a: GO:0044238 ! primary metabolic process

[Term]
id: GO:0006810
name: transport
namespace: biological_process
alt_id: GO:0015457
alt_id: GO:0015460
alt_id: GO:0044765
def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
subset: gocheck_do_not_annotate
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "single-organism transport" RELATED []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI
created_by: jl
creation_date: 2012-12-13T16:25:32Z

[Term]
id: GO:0008152
name: metabolic process
namespace: biological_process
alt_id: GO:0044236
alt_id: GO:0044710
def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well  macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684]
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote_ribbon
synonym: "metabolism" EXACT []
xref: Wikipedia:Metabolism
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI
created_by: jl
creation_date: 2012-10-17T15:46:40Z

[Term]
id: GO:0008289
name: lipid binding
namespace: molecular_function
def: "Binding to a lipid." [GOC:ai]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast

[Term]
id: GO:0009279
name: cell outer membrane
namespace: cellular_component
def: "A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures." [GOC:md, GOC:mtg_sensu, ISBN:0135712254]
comment: To annotate the plasma (cytoplasmic) membrane, see instead GO:0005886.
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "outer membrane of cell" EXACT []

[Term]
id: GO:0009579
name: thylakoid
namespace: cellular_component
def: "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." [GOC:ds, GOC:mtg_sensu, ISBN:0198506732]
comment: A thylakoid is not considered an organelle, but some thylakoids are part of organelles.
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "photosynthetic membrane" RELATED []
xref: Wikipedia:Thylakoid
is_a: GO:0043226 ! organelle
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13958" xsd:anyURI

[Term]
id: GO:0015979
name: photosynthesis
namespace: biological_process
def: "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." [ISBN:0198547684]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
xref: Wikipedia:Photosynthesis
is_a: GO:0008152 ! metabolic process

[Term]
id: GO:0016209
name: antioxidant activity
namespace: molecular_function
def: "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage." [ISBN:0198506732]
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
relationship: part_of GO:0098754 ! detoxification

[Term]
id: GO:0023052
name: signaling
namespace: biological_process
alt_id: GO:0023046
alt_id: GO:0044700
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_agr
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "biological signaling" EXACT []
synonym: "signaling process" EXACT []
synonym: "signalling" EXACT []
synonym: "signalling process" RELATED [GOC:mah]
synonym: "single organism signaling" RELATED []
created_by: jl
creation_date: 2010-02-16T09:30:50Z

[Term]
id: GO:0036094
name: small molecule binding
namespace: molecular_function
def: "Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:pm]
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
subset: goslim_agr
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_plant_ribbon
subset: goslim_prokaryote_ribbon
created_by: bf
creation_date: 2012-01-17T04:20:34Z

[Term]
id: GO:0042254
name: ribosome biogenesis
namespace: biological_process
alt_id: GO:0007046
def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis." [GOC:ma, PMID:26404467, Wikipedia:Ribosome_biogenesis]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "ribosome biogenesis and assembly" EXACT []

[Term]
id: GO:0042597
name: periplasmic space
namespace: cellular_component
alt_id: GO:0005620
def: "The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria)." [GOC:go_curators, GOC:md]
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "periplasm" EXACT []

[Term]
id: GO:0042995
name: cell projection
namespace: cellular_component
def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917]
subset: goslim_agr
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_mouse
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "cell process" BROAD []
synonym: "cellular process" BROAD []
synonym: "cellular projection" EXACT []

[Term]
id: GO:0043226
name: organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
xref: NIF_Subcellular:sao1539965131
xref: Wikipedia:Organelle

[Term]
id: GO:0043590
name: bacterial nucleoid
namespace: cellular_component
def: "The region of a bacterial cell to which the DNA is confined." [GOC:jl]
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
is_a: GO:0043226 ! organelle

[Term]
id: GO:0044238
name: primary metabolic process
namespace: biological_process
def: "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." [GOC:go_curators]
subset: gocheck_do_not_annotate
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_pir
subset: goslim_plant_ribbon
subset: goslim_prokaryote_ribbon
synonym: "primary metabolism" EXACT []
xref: Wikipedia:Primary_metabolite
is_a: GO:0008152 ! metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI

[Term]
id: GO:0044283
name: small molecule biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw]
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "small molecule biosynthesis" EXACT []
is_a: GO:0008152 ! metabolic process
created_by: jl
creation_date: 2010-01-26T12:06:49Z

[Term]
id: GO:0045182
name: translation regulator activity
namespace: molecular_function
def: "Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai]
subset: goslim_candida
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "translation factor activity" EXACT []

[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. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_flybase_ribbon
subset: goslim_mouse
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "physiological response to stimulus" EXACT []

[Term]
id: GO:0060090
name: molecular adaptor activity
namespace: molecular_function
alt_id: GO:0032947
def: "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." [GOC:mtg_MIT_16mar07, GOC:vw]
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "binding, bridging" EXACT []
synonym: "protein complex scaffold activity" BROAD []
synonym: "protein-containing complex scaffold activity" BROAD []

[Term]
id: GO:0071554
name: cell wall organization or biogenesis
namespace: biological_process
alt_id: GO:0070882
def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cell wall." [GOC:mah]
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
subset: goslim_yeast
synonym: "cell wall organisation or biogenesis" EXACT [GOC:mah]
synonym: "cell wall organization or biogenesis at cellular level" EXACT [GOC:mah]
synonym: "cellular cell wall organisation or biogenesis" EXACT [GOC:mah]
synonym: "cellular cell wall organization or biogenesis" EXACT []
created_by: mah
creation_date: 2010-01-13T03:19:38Z

[Term]
id: GO:0090729
name: toxin activity
namespace: molecular_function
alt_id: GO:0050827
def: "Interacting selectively with one or more biological molecules in another (target) organism, initiating pathogenesis (leading to an abnormal, generally detrimental state) in the target organism. The activity should refer to an evolved function of the active gene product, i.e. one that was selected for. Examples include the activity of botulinum toxin, and snake venom." [GOC:pt]
subset: goslim_generic
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "toxin receptor binding" EXACT []
xref: Wikipedia:Toxin
created_by: tb
creation_date: 2016-12-19T15:23:27Z

[Term]
id: GO:0098754
name: detoxification
namespace: biological_process
def: "Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." [GOC:dos]
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
relationship: part_of GO:0050896 ! response to stimulus

[Term]
id: GO:0098772
name: molecular function regulator activity
namespace: molecular_function
def: "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." [GOC:dos, GOC:pt]
subset: gocheck_do_not_annotate
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "molecular function regulator" EXACT []
relationship: has_part GO:0005515 ! protein binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20854" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20862" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25165" xsd:anyURI

[Term]
id: GO:0140104
name: molecular carrier activity
namespace: molecular_function
def: "Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location." [GOC:molecular_function_refactoring, GOC:pdt]
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.
subset: gocheck_do_not_annotate
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14221" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20848" xsd:anyURI
created_by: pg
creation_date: 2017-09-19T13:10:18Z

[Term]
id: GO:0140110
name: transcription regulator activity
namespace: molecular_function
def: "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." [GOC:pg, GOC:txnOH-2018, Wikipedia:Transcription_factor]
subset: gocheck_do_not_annotate
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_plant
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13588" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23609" xsd:anyURI
created_by: pg
creation_date: 2017-10-18T07:05:44Z

[Term]
id: GO:0140223
name: general transcription initiation factor activity
namespace: molecular_function
def: "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." [GOC:txnOH-2018]
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.
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_plant_ribbon
subset: goslim_prokaryote_ribbon
synonym: "basal transcription factor activity" EXACT []
synonym: "general transcription factor activity" EXACT []
synonym: "GTF activity" EXACT []
relationship: part_of GO:0006351 ! DNA-templated transcription
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20253" xsd:anyURI
created_by: pg
creation_date: 2018-05-24T07:51:23Z

[Term]
id: GO:0140299
name: molecular sensor activity
namespace: molecular_function
def: "Binding to a molecule and eliciting a change in the protein's activity in response to the intracellular level of that molecule." [PMID:26328879]
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "small molecular sensor activity" EXACT []
synonym: "small molecule sensing activity" EXACT []
synonym: "small molecule sensor activity" NARROW []
is_a: GO:0098772 ! molecular function regulator activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28772" xsd:anyURI
created_by: pg
creation_date: 2018-12-10T14:30:28Z

[Term]
id: GO:0140313
name: molecular sequestering activity
namespace: molecular_function
def: "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." [PMID:13130076]
subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_generic
subset: goslim_plant_ribbon
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
xref: Reactome:R-HSA-3245898 "TCN1 binds correnoids in the circulation"
created_by: pg
creation_date: 2019-03-28T10:00:25Z

[Typedef]
id: ends_during
name: ends during
namespace: external
xref: RO:0002093

[Typedef]
id: happens_during
name: happens during
namespace: external
xref: RO:0002092
is_transitive: true
is_a: ends_during ! ends during

[Typedef]
id: has_ontology_root_term
name: has ontology root term
namespace: external
xref: IAO:0000700
is_metadata_tag: true
is_class_level: true

[Typedef]
id: has_part
name: has part
namespace: external
xref: BFO:0000051
is_transitive: true

[Typedef]
id: negatively_regulates
name: negatively regulates
namespace: external
xref: RO:0002212
is_a: regulates ! regulates

[Typedef]
id: occurs_in
name: occurs in
namespace: external
xref: BFO:0000066
transitive_over: part_of ! part of

[Typedef]
id: part_of
name: part of
namespace: external
xref: BFO:0000050
is_transitive: true
inverse_of: has_part ! has part

[Typedef]
id: positively_regulates
name: positively regulates
namespace: external
xref: RO:0002213
holds_over_chain: negatively_regulates negatively_regulates
is_a: regulates ! regulates

[Typedef]
id: regulates
name: regulates
namespace: external
xref: RO:0002211
is_transitive: true

[Typedef]
id: starts_during
name: starts during
namespace: external
xref: RO:0002091

[Typedef]
id: term_tracker_item
name: term tracker item
namespace: external
xref: IAO:0000233
is_metadata_tag: true
is_class_level: true