format-version: 1.2
data-version: go/2024-01-04/subsets/goslim_prokaryote.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_do_not_manually_annotate "Term not to be used for direct manual annotation"
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_flybase_ribbon "FlyBase Drosophila 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_pombe "Fission yeast GO slim"
subsetdef: goslim_prokaryote "GO subset for prokaryotes"
subsetdef: goslim_synapse "synapse GO slim"
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
property_value: owl:versionInfo "2024-01-04" xsd:string

[Term]
id: GO:0000910
name: cytokinesis
namespace: biological_process
alt_id: GO:0007104
alt_id: GO:0016288
alt_id: GO:0033205
def: "The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells." [GOC:mtg_cell_cycle]
comment: Note that this term should not be used for direct annotation. When annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use 'FtsZ-dependent cytokinesis ; GO:0043093' or Cdv-dependent cytokinesis ; GO:0061639. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other.
subset: gocheck_do_not_manually_annotate
subset: goslim_candida
subset: goslim_generic
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "cell cycle cytokinesis" EXACT []
synonym: "cytokinesis involved in cell cycle" EXACT [GOC:dph, GOC:tb]
xref: Wikipedia:Cytokinesis
relationship: has_part GO:0061024 ! membrane organization

[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_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_prokaryote
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_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_prokaryote
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_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
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:0003924
name: GTPase activity
namespace: molecular_function
alt_id: GO:0061745
def: "Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate." [PMID:26832457, PMID:27218782]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "ARF small monomeric GTPase activity" NARROW []
synonym: "dynamin GTPase activity" NARROW []
synonym: "GTPase activity, coupled" RELATED []
synonym: "heterotrimeric G-protein GTPase activity" NARROW []
synonym: "heterotrimeric G-protein GTPase, alpha-subunit" RELATED []
synonym: "heterotrimeric G-protein GTPase, beta-subunit" RELATED []
synonym: "heterotrimeric G-protein GTPase, gamma-subunit" RELATED []
synonym: "hydrolase activity, acting on acid anhydrides, acting on GTP, involved in cellular and subcellular movement" BROAD []
synonym: "protein-synthesizing GTPase activity" NARROW []
synonym: "protein-synthesizing GTPase activity, elongation" NARROW []
synonym: "protein-synthesizing GTPase activity, initiation" NARROW []
synonym: "protein-synthesizing GTPase activity, termination" NARROW []
synonym: "Rab small monomeric GTPase activity" NARROW []
synonym: "Ran small monomeric GTPase activity" NARROW []
synonym: "Ras small monomeric GTPase activity" NARROW []
synonym: "RHEB small monomeric GTPase activity" NARROW []
synonym: "Rho small monomeric GTPase activity" NARROW []
synonym: "Sar small monomeric GTPase activity" NARROW []
synonym: "signal-recognition-particle GTPase activity" NARROW []
synonym: "small monomeric GTPase activity" NARROW []
synonym: "tubulin GTPase activity" NARROW []
xref: MetaCyc:RXN0-5462
xref: Reactome:R-HSA-1445143 "RAB8A,10,13,14 hydrolyze GTP"
xref: Reactome:R-HSA-1458485 "RALA hydrolyzes GTP"
xref: Reactome:R-HSA-156923 "Hydrolysis of eEF1A:GTP"
xref: Reactome:R-HSA-164381 "G alpha (s) auto-inactivates by hydrolysing GTP to GDP"
xref: Reactome:R-HSA-165055 "Hydrolysis of Ran:GTP to Ran:GDP"
xref: Reactome:R-HSA-167415 "G-protein alpha subunit is inactivated"
xref: Reactome:R-HSA-170666 "Adenylate cyclase increases the GTPase activity of G alpha-olf"
xref: Reactome:R-HSA-170685 "Adenylaye cyclase increases the GTPase activity of G alpha-olf"
xref: Reactome:R-HSA-170686 "Adenylate cyclase increases the GTPase activity of Gi alpha"
xref: Reactome:R-HSA-177501 "Endocytosis (internalization) of clathrin-coated vesicle"
xref: Reactome:R-HSA-203973 "Vesicle budding"
xref: Reactome:R-HSA-2130641 "Translocation of TGN-lysosome vesicle to lysosome"
xref: Reactome:R-HSA-2130725 "Internalization of MHC II:Ii clathrin coated vesicle"
xref: Reactome:R-HSA-2584246 "GNAT1-GTP hydrolyses its bound GTP to GDP"
xref: Reactome:R-HSA-380979 "RHEB in mTORC1:RHEB:GTP hydrolyses GTP"
xref: Reactome:R-HSA-392133 "G alpha (z) auto-inactivates by hydrolysing GTP to GDP"
xref: Reactome:R-HSA-392212 "G alpha (i) auto-inactivates by hydrolysing GTP to GDP"
xref: Reactome:R-HSA-418574 "G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP"
xref: Reactome:R-HSA-418582 "G alpha (q) auto-inactivates by hydrolysing GTP to GDP"
xref: Reactome:R-HSA-421835 "trans-Golgi Network Vesicle Scission"
xref: Reactome:R-HSA-428941 "P2Y purinoceptor 1 activates MAP kinase p38 alpha"
xref: Reactome:R-HSA-432707 "trans-Golgi Network Lysosomal Vesicle Scission"
xref: Reactome:R-HSA-5333615 "80S:Met-tRNAi:mRNA:SECISBP2:Sec-tRNA(Sec):EEFSEC:GTP is hydrolysed to 80S:Met-tRNAi:mRNA:SECISBP2:Sec and EEFSEC:GDP by EEFSEC"
xref: Reactome:R-HSA-5389839 "39S subunit binds 28S subunit:mRNA:fMet-tRNA"
xref: Reactome:R-HSA-5389842 "TUFM hydrolyzes GTP and TUFM:GDP dissociates from 55S ribosome"
xref: Reactome:R-HSA-5419273 "Hydrolysis of GTP and dissociation of 28S and 39S subunits"
xref: Reactome:R-HSA-5419279 "Translocation of peptidyl-tRNA from A-site to P-site (and translocation of 55S ribosome by 3 bases along mRNA)"
xref: Reactome:R-HSA-555065 "Formation of clathrin coated vesicle"
xref: Reactome:R-HSA-5623513 "ASAP1 stimulates GTPase activity of ARF4"
xref: Reactome:R-HSA-5638006 "ARL3 hydrolyzes GTP"
xref: Reactome:R-HSA-5658231 "RAS GAPs stimulate RAS GTPase activity"
xref: Reactome:R-HSA-5665809 "SRGAP2 stimulates RAC1 GTP-ase activity and ends FMNL1-mediated elongation of actin filaments"
xref: Reactome:R-HSA-5672017 "Rheb in the MTORC1 complex hydrolyses GTP"
xref: Reactome:R-HSA-5694527 "Loss of SAR1B GTPase"
xref: Reactome:R-HSA-6807877 "ARFGAPs stimulate ARF GTPase activity"
xref: Reactome:R-HSA-6814833 "TBC1D20 stimulates GTPase activity of RAB1, resulting in hydrolysis of GTP"
xref: Reactome:R-HSA-8847534 "RAB43 hydrolyses GTP"
xref: Reactome:R-HSA-8847883 "CYTH proteins stimulate ARF1 GTPase activity"
xref: Reactome:R-HSA-8849082 "ARHGAP35 stimulates RHOA GTPase activity"
xref: Reactome:R-HSA-8854173 "TBC RabGAPs accelerate GTP hydrolysis by RAB35"
xref: Reactome:R-HSA-8854255 "TBC1D2A accelerates GTP hydrolysis by RAB7"
xref: Reactome:R-HSA-8854329 "TBC1D15 accelerates GTP hydrolysis by RAB7"
xref: Reactome:R-HSA-8854604 "TBC1D16 accelerates GTP hydrolysis by RAB4A"
xref: Reactome:R-HSA-8854612 "TBC1D25 accelerates GTP hydrolysis by RAB33B"
xref: Reactome:R-HSA-8868661 "Dynamin-mediated GTP hydrolysis promotes vesicle scission"
xref: Reactome:R-HSA-8981353 "RASA1 stimulates RAS GTPase activity"
xref: Reactome:R-HSA-8982020 "G alpha (i)i1/i2/i3 in G (i):RGS complex is inactivated"
xref: Reactome:R-HSA-8982021 "G alpha (z) in G alpha (z):RGS complex is inactivated"
xref: Reactome:R-HSA-8982025 "G alpha (q) in G (q):RGS complex is inactivated"
xref: Reactome:R-HSA-9018814 "RHOT1 hydrolyzes GTP"
xref: Reactome:R-HSA-9018826 "RHOT2 hydrolyzes GTP"
xref: Reactome:R-HSA-9640195 "RRAGA,B hydrolyzes GTP"
xref: Reactome:R-HSA-9645598 "RRAGC,D hydrolyzes GTP"
xref: Reactome:R-HSA-9649736 "RAS intrinsic GTPase activity hydrolyzes GTP to GDP"
xref: Reactome:R-HSA-983422 "Disassembly of COPII coated vesicle"
xref: RHEA:19669
is_a: GO:0016787 ! hydrolase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19078" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26014" xsd:anyURI
created_by: dph
creation_date: 2015-11-11T12:47:56Z

[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_flybase_ribbon
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
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, or 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_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
synonym: "carrier" RELATED []

[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_flybase_ribbon
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "extracellular" EXACT []
xref: Wikipedia:Extracellular

[Term]
id: GO:0005615
name: extracellular space
namespace: cellular_component
def: "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684]
comment: Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term.
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
synonym: "intercellular space" RELATED []
xref: NIF_Subcellular:sao1425028079
relationship: part_of GO:0005576 ! extracellular region

[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_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
subset: goslim_yeast
xref: Wikipedia:Cell_wall
property_value: RO:0002161 NCBITaxon:33208
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_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_prokaryote
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_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
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:0005856
name: cytoskeleton
namespace: cellular_component
def: "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." [GOC:mah, PMID:16959967, PMID:27419875]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
subset: goslim_yeast
xref: Wikipedia:Cytoskeleton
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_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_plant
subset: goslim_prokaryote
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:0005975
name: carbohydrate metabolic process
namespace: biological_process
alt_id: GO:0044261
alt_id: GO:0044723
def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:mah, ISBN:0198506732]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "carbohydrate metabolism" EXACT []
xref: Wikipedia:Carbohydrate_metabolism
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22880" xsd:anyURI
created_by: jl
creation_date: 2012-10-23T15:40:34Z

[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_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "energy pathways" BROAD []
synonym: "intermediary metabolism" RELATED [GOC:mah]
synonym: "metabolic energy generation" RELATED []

[Term]
id: GO:0006260
name: DNA replication
namespace: biological_process
alt_id: GO:0055133
def: "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC:mah]
comment: DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'.
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast
xref: Wikipedia:DNA_replication
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/10596" xsd:anyURI

[Term]
id: GO:0006281
name: DNA repair
namespace: biological_process
def: "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID:11563486]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast
xref: Wikipedia:DNA_repair
is_a: GO:0050896 ! response to stimulus

[Term]
id: GO:0006310
name: DNA recombination
namespace: biological_process
def: "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN:0198506732]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast

[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_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
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:0016070 ! RNA 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
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_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
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)

[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_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
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:0051604 ! protein maturation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25673" xsd:anyURI

[Term]
id: GO:0006486
name: protein glycosylation
namespace: biological_process
alt_id: GO:0065006
def: "A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins." [GOC:curators, GOC:pr]
subset: goslim_generic
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "protein amino acid glycosylation" EXACT [GOC:bf]
synonym: "protein-carbohydrate complex assembly" RELATED []
is_a: GO:0036211 ! protein modification process
relationship: part_of GO:1901135 ! carbohydrate derivative metabolic process

[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_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 []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17904" xsd:anyURI

[Term]
id: GO:0006575
name: cellular modified amino acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents." [GOC:ai]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
synonym: "amino acid derivative metabolic process" EXACT []
synonym: "cellular amino acid derivative metabolic process" EXACT []
synonym: "cellular amino acid derivative metabolism" EXACT []
synonym: "cellular modified amino acid metabolism" EXACT [GOC:mah]
synonym: "modified amino acid metabolic process" EXACT [GOC:mah]
synonym: "modified amino acid metabolism" EXACT [GOC:mah]

[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_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "lipid metabolism" EXACT []
xref: Wikipedia:Lipid_metabolism

[Term]
id: GO:0006790
name: sulfur compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:ai]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
synonym: "sulfur metabolism" EXACT []
synonym: "sulphur metabolic process" EXACT []
synonym: "sulphur metabolism" EXACT []
xref: Wikipedia:Sulfur_metabolism

[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_prokaryote
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:0006886
name: intracellular protein transport
namespace: biological_process
alt_id: GO:0032779
def: "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell." [GOC:mah]
subset: goslim_generic
subset: goslim_prokaryote
synonym: "copper-induced intracellular protein transport" RELATED [GOC:al]
is_a: GO:0006810 ! transport

[Term]
id: GO:0007010
name: cytoskeleton organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:dph, GOC:jl, GOC:mah]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "cytoskeletal organization and biogenesis" RELATED [GOC:mah]
synonym: "cytoskeletal regulator activity" RELATED []
synonym: "cytoskeleton organisation" EXACT []
synonym: "cytoskeleton organization and biogenesis" RELATED [GOC:mah]

[Term]
id: GO:0007059
name: chromosome segregation
namespace: biological_process
def: "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." [GOC:jl, GOC:mah, GOC:mtg_cell_cycle, GOC:vw]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "chromosome division" EXACT []
synonym: "chromosome transmission" RELATED []
xref: Wikipedia:Chromosome_segregation

[Term]
id: GO:0007155
name: cell adhesion
namespace: biological_process
alt_id: GO:0098602
def: "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." [GOC:hb, GOC:pf]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
synonym: "cell adhesion molecule activity" RELATED []
synonym: "single organism cell adhesion" RELATED []
xref: Wikipedia:Cell_adhesion
created_by: dos
creation_date: 2014-04-15T15:59:10Z

[Term]
id: GO:0007163
name: establishment or maintenance of cell polarity
namespace: biological_process
alt_id: GO:0030012
alt_id: GO:0030467
def: "Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns." [GOC:mah]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
subset: goslim_prokaryote
synonym: "cell polarity" RELATED [GOC:mah, GOC:vw]
synonym: "establishment and/or maintenance of cell polarity" RELATED []
synonym: "establishment and/or maintenance of cell polarization" RELATED []

[Term]
id: GO:0008092
name: cytoskeletal protein binding
namespace: molecular_function
def: "Binding to a protein component of a cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton)." [GOC:mah]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_prokaryote
subset: goslim_yeast

[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_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
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
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_prokaryote
synonym: "photosynthetic membrane" RELATED []
xref: Wikipedia:Thylakoid
is_a: GO:0043226 ! organelle
property_value: RO:0002161 NCBITaxon:33208
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13958" xsd:anyURI

[Term]
id: GO:0009975
name: cyclase activity
namespace: molecular_function
def: "Catalysis of a ring closure reaction." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_pir
subset: goslim_prokaryote

[Term]
id: GO:0012501
name: programmed cell death
namespace: biological_process
alt_id: GO:0016244
def: "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." [GOC:lr, GOC:mtg_apoptosis]
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.
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_prokaryote
synonym: "caspase-independent apoptosis" RELATED []
synonym: "caspase-independent cell death" NARROW []
synonym: "non-apoptotic programmed cell death" NARROW []
synonym: "nonapoptotic programmed cell death" NARROW []
synonym: "PCD" RELATED []
synonym: "RCD" RELATED []
synonym: "regulated cell death" BROAD []
xref: Wikipedia:Programmed_cell_death
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24835" 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_prokaryote
xref: Wikipedia:Photosynthesis
property_value: RO:0002161 NCBITaxon:33208
property_value: RO:0002161 NCBITaxon:4895

[Term]
id: GO:0016070
name: RNA metabolic process
namespace: biological_process
def: "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732]
subset: goslim_agr
subset: goslim_candida
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_prokaryote
synonym: "RNA metabolism" EXACT []

[Term]
id: GO:0016071
name: mRNA metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes." [ISBN:0198506732]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
subset: goslim_prokaryote
synonym: "mRNA metabolism" EXACT []
is_a: GO:0016070 ! RNA 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_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_prokaryote
relationship: part_of GO:0098754 ! detoxification

[Term]
id: GO:0016491
name: oxidoreductase activity
namespace: molecular_function
def: "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC:go_curators]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "oxidoreductase activity, acting on other substrates" NARROW []
synonym: "redox activity" EXACT []
xref: EC:1.-.-.-
xref: Reactome:R-HSA-1614362 "SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases"
xref: Reactome:R-HSA-209921 "Monoiodinated tyrosine can be deiodinated"
xref: Reactome:R-HSA-209960 "Diiodinated tyrosine can be deiodinated"
xref: Reactome:R-HSA-3095889 "MMACHC dealkylates RCbl"
xref: Reactome:R-HSA-390425 "FAR1 reduces PalmCoA to HXOL"
xref: Reactome:R-HSA-390438 "FAR2 reduces PalmCoA to HXOL"
xref: Reactome:R-HSA-5662660 "Dopachrome is transformed to DHICA by DCT"
xref: Reactome:R-HSA-8878581 "TYRP1 oxidises DHICA to IQCA"
xref: Reactome:R-HSA-8936442 "MARC1,MARC2 reduce N-hydroxylated compounds"
xref: Reactome:R-HSA-9020249 "Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6"
xref: Reactome:R-HSA-9020260 "Hydroperoxy reducatse reduces 7(S)-Hp-17(S)-HDHA to RvD5"
xref: Reactome:R-HSA-9024624 "Hydroperoxy reductase reduces 4(S)-Hp-17(R)-HDHA to AT-RvD6"
xref: Reactome:R-HSA-9024630 "Hydroperoxy reductase reduces 7(S)-Hp-17(R)-HDHA to AT-RvD5"
xref: Reactome:R-HSA-9025007 "Hydroperoxy reductase reduces 7(S),14(S)-diHp-DHA to 7-epi-MaR1"
xref: Reactome:R-HSA-9026001 "Hydroperoxy reductase reduces 7,17-diHp-DPAn-3 to RvD5n-3DPA"
xref: Reactome:R-HSA-9026917 "Lipoxygenase dehydrogenates 7(S),17(S)-diHp-DHA to 7S(8)-epoxy-17(S)-HDHA"
xref: Reactome:R-HSA-9027033 "Hydroperoxy reducatase reduces 14(S)-Hp-DHA to 14(S)-HDHA"
xref: Reactome:R-HSA-9693722 "Unknown sepiapterin synthase transforms PTHP to sepiapterin"

[Term]
id: GO:0016740
name: transferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
subset: goslim_yeast
xref: EC:2.-.-.-
xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2"
xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1"
xref: Reactome:R-HSA-5668414 "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK"
xref: Reactome:R-HSA-8868783 "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248"

[Term]
id: GO:0016787
name: hydrolase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc." [ISBN:0198506732]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
subset: goslim_yeast
xref: EC:3.-.-.-
xref: Reactome:R-HSA-1236938 "Partial proteolysis of antigen in phagolysosomes"
xref: Reactome:R-HSA-2029475 "Production of AA by iPLA2 upon FCGR activation"
xref: Reactome:R-HSA-5694583 "ABHD4 hydrolyses NAPE"
xref: Reactome:R-HSA-5695964 "ABHD14B hydrolyses PNPB"
xref: Reactome:R-HSA-6786190 "CMBL hydrolyses OM to OLMS"
xref: Reactome:R-HSA-6788295 "HDHD1:Mg2+ dephosphorylates PURIDP"
xref: Reactome:R-HSA-8938314 "ENPPs hydrolyse CoA-SH to PPANT, PAP"
xref: Reactome:R-HSA-8952137 "Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate"

[Term]
id: GO:0016829
name: lyase activity
namespace: molecular_function
def: "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [ISBN:0198547684]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_yeast
xref: EC:4.-.-.-
xref: Reactome:R-HSA-5696408 "PXLP-K278-PHYKPL tetramer hydrolyses 5PHL"
xref: Reactome:R-HSA-6782895 "TYW1:FMN:4Fe-4S  transforms 1-methylguanosine yielding yW-187 (4-demethylwyosine) at nucleotide 37 of tRNA(Phe)"

[Term]
id: GO:0016853
name: isomerase activity
namespace: molecular_function
def: "Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5." [ISBN:0198506732]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "other isomerase activity" NARROW []
xref: EC:5.-.-.-
xref: Reactome:R-HSA-6787623 "TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal"

[Term]
id: GO:0016874
name: ligase activity
namespace: molecular_function
def: "Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient." [GOC:mah]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "synthetase activity" EXACT [GOC:jh2]
xref: EC:6.-.-.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19380" xsd:anyURI

[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_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_pombe
subset: goslim_prokaryote
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:0030030
name: cell projection organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/]
subset: goslim_prokaryote
synonym: "cell projection organisation" EXACT []
synonym: "cell projection organization and biogenesis" RELATED [GOC:mah]
synonym: "cell surface structure organization and biogenesis" RELATED [GOC:mah]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26279" xsd:anyURI

[Term]
id: GO:0030163
name: protein catabolic process
namespace: biological_process
alt_id: GO:0044254
alt_id: GO:0044257
def: "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:mah]
comment: This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children.
subset: goslim_candida
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
subset: goslim_prokaryote
synonym: "cellular protein breakdown" EXACT []
synonym: "cellular protein catabolic process" EXACT []
synonym: "cellular protein catabolism" EXACT []
synonym: "cellular protein degradation" EXACT []
synonym: "multicellular organismal protein catabolic process" NARROW []
synonym: "pheromone catabolic process" RELATED []
synonym: "pheromone catabolism" RELATED []
synonym: "protein breakdown" EXACT []
synonym: "protein catabolism" EXACT []
synonym: "protein degradation" EXACT []
xref: Wikipedia:Protein_catabolism
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI

[Term]
id: GO:0031012
name: extracellular matrix
namespace: cellular_component
alt_id: GO:0005578
def: "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." [GOC:BHF, GOC:mah, GOC:rph, NIF_Subcellular:nlx_subcell_20090513, PMID:21123617, PMID:28089324]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_prokaryote
synonym: "matrisome" NARROW []
synonym: "proteinaceous extracellular matrix" EXACT []
xref: NIF_Subcellular:nlx_subcell_20090513
xref: Wikipedia:Extracellular_matrix

[Term]
id: GO:0031386
name: protein tag activity
namespace: molecular_function
def: "A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation." [GOC:dos, PMID:19028679, PMID:20054389, PMID:6305978]
comment: Use this term to annotate conjugated tags, not for conjugating enzymes. At the time of writing, all known gene products with this activity are ubiquitin-like, either based on overall sequence similarity or the presence of common motifs and structures.
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_prokaryote
synonym: "covalent modifier" BROAD [GOC:vw]
synonym: "protein tag" EXACT []
synonym: "protein tagging activity" RELATED []
synonym: "ubiquitin" RELATED []
synonym: "ubiquitin-like protein modifier" EXACT []

[Term]
id: GO:0033013
name: tetrapyrrole metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next." [GOC:mah]
subset: goslim_pombe
subset: goslim_prokaryote
synonym: "tetrapyrrole metabolism" EXACT []

[Term]
id: GO:0036211
name: protein modification process
namespace: biological_process
alt_id: GO:0006464
def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:bf, GOC:jl]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
synonym: "cellular protein modification process" EXACT []
synonym: "process resulting in protein modification" EXACT []
synonym: "protein modification" EXACT [GOC:bf]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI
created_by: bf
creation_date: 2012-04-26T01:47:12Z

[Term]
id: GO:0036386
name: bacterial nucleoid packaging
namespace: biological_process
def: "A process in which chromosomal DNA and associated proteins organize into a compact, orderly bacterial nucleoid. Often resulting in DNA supercoiling." [GOC:bf, GOC:bhm, PMID:17097674, PMID:17360520]
subset: goslim_prokaryote
synonym: "bacterial nucleoid DNA packaging" EXACT []
synonym: "chromosomal compaction" BROAD [PMID:17097674]
synonym: "nucleoid compaction" BROAD [PMID:17097674]
synonym: "prokaryotic DNA condensation" BROAD [Wikipedia:DNA_condensation]
relationship: occurs_in GO:0043590 ! bacterial nucleoid
created_by: bf
creation_date: 2013-05-30T10:41:08Z

[Term]
id: GO:0040033
name: sRNA-mediated post-transcriptional gene silencing
namespace: biological_process
def: "A post-transcriptional gene silencing pathway mediated by the action of small regulatory non-coding RNAs (sRNAs). sRNAs are 20-500 nucleotides in length and found in bacteria." [PMID:12460531, PMID:2468565, PMID:33963446]
comment: It is postulated that there 3 mechanisms of sRNA-mediated gene silencing: (i) translation inhibition, (ii) RNA destabilization, and (iii) transcription termination loop formation (as this is common when looking at riboswitches). sRNA mediated gene silencing is sometimes referred to as 'regulation of riboswitch'.
subset: goslim_prokaryote
synonym: "downregulation of mRNA translation, ncRNA-mediated" BROAD []
synonym: "inhibition of mRNA translation, ncRNA-mediated" BROAD []
synonym: "RNA-mediated gene silencing by inhibition of translation" BROAD []
synonym: "small RNA-mediated gene silencing" EXACT []
synonym: "sRNA-mediated gene silencing" BROAD []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22860" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22863" xsd:anyURI

[Term]
id: GO:0042178
name: xenobiotic catabolic process
namespace: biological_process
alt_id: GO:0042737
alt_id: GO:0042738
def: "The chemical reactions and pathways resulting in the breakdown of a xenobiotic compound, a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:jl, GOC:krc]
subset: goslim_prokaryote
synonym: "drug breakdown" RELATED []
synonym: "drug catabolic process" RELATED []
synonym: "drug catabolism" RELATED []
synonym: "drug degradation" RELATED []
synonym: "exogenous drug breakdown" RELATED []
synonym: "exogenous drug catabolic process" RELATED []
synonym: "exogenous drug catabolism" RELATED []
synonym: "exogenous drug degradation" RELATED []
synonym: "xenobiotic breakdown" EXACT []
synonym: "xenobiotic catabolism" EXACT []
synonym: "xenobiotic degradation" EXACT []
relationship: part_of GO:0050896 ! response to stimulus
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19460" xsd:anyURI

[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
synonym: "ribosome biogenesis and assembly" EXACT []

[Term]
id: GO:0042393
name: histone binding
namespace: molecular_function
def: "Binding to a histone, any of a group of water-soluble proteins found in association with the DNA of eukaryotic or archaeal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in gene regulation and DNA replication. They may be chemically modified (methylated, acetlyated and others) to regulate gene transcription." [GOC:jl, PMID:16209651, PMID:30212449, PMID:9305837]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "histone-specific chaperone activity" RELATED []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23106" xsd:anyURI

[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
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, http://www.cogsci.princeton.edu/~wn/]
subset: goslim_agr
subset: goslim_flybase_ribbon
subset: goslim_mouse
subset: goslim_pir
subset: goslim_prokaryote
synonym: "cell process" BROAD []
synonym: "cellular process" BROAD []
synonym: "cellular projection" EXACT []

[Term]
id: GO:0043062
name: extracellular structure organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in 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, and also covers the host cell environment outside an intracellular parasite." [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
subset: goslim_pir
subset: goslim_prokaryote
synonym: "extracellular structure organisation" EXACT []
synonym: "extracellular structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah]

[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
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
is_a: GO:0043226 ! organelle

[Term]
id: GO:0044183
name: protein folding chaperone
namespace: molecular_function
def: "Binding to a protein or a protein-containing complex to assist the protein folding process." [GOC:mtg_cambridge_2009]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
synonym: "chaperone activity" BROAD []
synonym: "protein binding involved in protein folding" EXACT []
xref: Reactome:R-HSA-9018785 "RHOBTB2 binds GTP"
relationship: part_of GO:0006457 ! protein folding
created_by: jl
creation_date: 2009-09-25T11:33:48Z

[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
synonym: "small molecule biosynthesis" EXACT []
created_by: jl
creation_date: 2010-01-26T12:06:49Z

[Term]
id: GO:0044550
name: secondary metabolite biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of secondary metabolites, the compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon." [GOC:jl]
subset: goslim_prokaryote
synonym: "secondary metabolite biosynthesis" EXACT []
created_by: jl
creation_date: 2012-03-29T01:55:18Z

[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_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_prokaryote
synonym: "translation factor activity" EXACT []

[Term]
id: GO:0045735
name: nutrient reservoir activity
namespace: molecular_function
def: "Functions in the storage of nutritious substrates." [GOC:ai]
comment: Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'.
subset: goslim_generic
subset: goslim_pir
subset: goslim_prokaryote
synonym: "storage protein" RELATED []
synonym: "storage protein of fat body" RELATED []
synonym: "yolk protein" RELATED []

[Term]
id: GO:0048870
name: cell motility
namespace: biological_process
def: "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another." [GOC:dgh, GOC:dph, GOC:isa_complete, GOC:mlg]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
synonym: "cell locomotion" EXACT []
synonym: "cell movement" RELATED []
synonym: "movement of a cell" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI

[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_manually_annotate
subset: goslim_agr
subset: goslim_flybase_ribbon
subset: goslim_mouse
subset: goslim_pir
subset: goslim_prokaryote
synonym: "physiological response to stimulus" EXACT []

[Term]
id: GO:0051604
name: protein maturation
namespace: biological_process
def: "Any process leading to the attainment of the full functional capacity of a protein." [GOC:ai]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast

[Term]
id: GO:0055086
name: nucleobase-containing small molecule metabolic process
namespace: biological_process
def: "The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide." [GOC:vw]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED []
synonym: "nucleobase, nucleoside and nucleotide metabolism" EXACT []

[Term]
id: GO:0060089
name: molecular transducer activity
namespace: molecular_function
def: "A compound molecular function in which an effector function is controlled by one or more regulatory components." [GOC:dos, GOC:pdt]
subset: gocheck_do_not_manually_annotate
subset: goslim_generic
subset: goslim_pir
subset: goslim_prokaryote

[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_generic
subset: goslim_pir
subset: goslim_prokaryote
synonym: "binding, bridging" EXACT []
synonym: "protein complex scaffold activity" RELATED []
synonym: "protein-containing complex scaffold activity" RELATED []

[Term]
id: GO:0061024
name: membrane organization
namespace: biological_process
alt_id: GO:0016044
alt_id: GO:0044802
def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
synonym: "cellular membrane organisation" EXACT []
synonym: "cellular membrane organization" EXACT []
synonym: "membrane organisation" EXACT [GOC:mah]
synonym: "membrane organization and biogenesis" RELATED [GOC:mah]
synonym: "single-organism membrane organization" RELATED []
created_by: jl
creation_date: 2010-02-08T02:43:11Z

[Term]
id: GO:0065003
name: protein-containing complex assembly
namespace: biological_process
alt_id: GO:0006461
alt_id: GO:0034622
alt_id: GO:0043623
def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
subset: goslim_prokaryote
synonym: "cellular macromolecule complex assembly" RELATED []
synonym: "cellular protein complex assembly" EXACT []
synonym: "cellular protein-containing complex assembly" RELATED []
synonym: "chaperone activity" RELATED []
synonym: "macromolecular complex assembly" RELATED []
synonym: "macromolecule complex assembly" RELATED []
synonym: "protein complex assembly" RELATED []
synonym: "protein complex formation" RELATED []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI

[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_generic
subset: goslim_pombe
subset: goslim_prokaryote
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:0071941
name: nitrogen cycle metabolic process
namespace: biological_process
def: "A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization." [GOC:mah, PMID:16675690, Wikipedia:Nitrogen_cycle]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pombe
subset: goslim_prokaryote
xref: Wikipedia:Nitrogen_cycle
created_by: mah
creation_date: 2010-09-30T05:21:03Z

[Term]
id: GO:0072657
name: protein localization to membrane
namespace: biological_process
def: "A process in which a protein is transported to, or maintained in, a specific location in a membrane." [GOC:mah]
subset: goslim_prokaryote
synonym: "protein localisation in membrane" EXACT [GOC:mah]
synonym: "protein localization in membrane" EXACT []
created_by: mah
creation_date: 2011-02-14T02:35:18Z

[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
synonym: "toxin receptor binding" EXACT []
xref: Wikipedia:Toxin
created_by: tb
creation_date: 2016-12-19T15:23:27Z

[Term]
id: GO:0098542
name: defense response to other organism
namespace: biological_process
alt_id: GO:0009814
def: "Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism." [GOC:dos]
subset: goslim_generic
subset: goslim_prokaryote
synonym: "defence response incompatible interaction" NARROW []
synonym: "defence response to pathogen, incompatible interaction" NARROW []
synonym: "defense response, incompatible interaction" NARROW []
synonym: "resistance response to pathogen" NARROW []
is_a: GO:0050896 ! response to stimulus
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22173" xsd:anyURI
created_by: dos
creation_date: 2013-11-11T12:59:11Z

[Term]
id: GO:0098631
name: cell adhesion mediator activity
namespace: molecular_function
def: "The binding by a cell-adhesion protein on a cell surface to an adhesion molecule on another cell surface or an external substrate, to mediate adhesion of the cell to the external substrate or to another cell." [GOC:vw, Wikipedia:Cell_adhesion]
subset: goslim_generic
subset: goslim_prokaryote
synonym: "cell adhesion molecule" EXACT []
synonym: "protein binding involved in cell adhesion" EXACT []
relationship: part_of GO:0007155 ! cell adhesion
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22959" xsd:anyURI

[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_generic
subset: goslim_pombe
subset: goslim_prokaryote
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_flybase_ribbon
subset: goslim_generic
subset: goslim_prokaryote
synonym: "molecular function regulator" EXACT []
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:0140096
name: catalytic activity, acting on a protein
namespace: molecular_function
def: "Catalytic activity that acts to modify a protein." [GOC:molecular_function_refactoring, GOC:pdt]
subset: goslim_generic
subset: goslim_prokaryote
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI
created_by: pg
creation_date: 2017-09-14T10:32:59Z

[Term]
id: GO:0140097
name: catalytic activity, acting on DNA
namespace: molecular_function
def: "Catalytic activity that acts to modify DNA." [GOC:molecular_function_refactoring, GOC:pdt]
subset: goslim_generic
subset: goslim_prokaryote
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI
created_by: pg
creation_date: 2017-09-14T12:03:51Z

[Term]
id: GO:0140098
name: catalytic activity, acting on RNA
namespace: molecular_function
def: "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis." [GOC:molecular_function_refactoring, GOC:pdt]
subset: goslim_generic
subset: goslim_prokaryote
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14225" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21612" xsd:anyURI
created_by: pg
creation_date: 2017-09-14T12:05:21Z

[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_generic
subset: goslim_prokaryote
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:0140299
name: small molecule sensor activity
namespace: molecular_function
def: "Binding to a small molecule and eliciting a change in the protein's activity in response to the intracellular level of that small molecule." [PMID:26328879]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
synonym: "small molecular sensor activity" EXACT []
synonym: "small molecule sensing activity" EXACT []
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_generic
subset: goslim_prokaryote
xref: Reactome:R-HSA-3245898 "TCN1 binds correnoids in the circulation"
created_by: pg
creation_date: 2019-03-28T10:00:25Z

[Term]
id: GO:0140657
name: ATP-dependent activity
namespace: molecular_function
def: "A molecular function characterized by the coupling of ATP hydrolysis to other steps of a reaction mechanism to make the reaction energetically favorable, for example to catalyze a reaction or drive transport against a concentration gradient." [PMID:24878343, PMID:25750732, PMID:32933017, PMID:33818025, PMID:33873056, PMID:33988324]
comment: Note that this term represents a grouping class that includes all proteins that use ATP hydrolysis to drive a reaction; it is not meant to capture the ATP hydrolysis reaction itself. To annotate ATP hydrolysis, please use 'ATP hydrolysis activity ; GO:0016887'.
subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "ATP hydrolysis-dependent activity" EXACT []
synonym: "ATPase activity" EXACT []
synonym: "ATPase activity, coupled" EXACT []
synonym: "ATPase-dependent activity" EXACT []
relationship: has_part GO:0016787 ! hydrolase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21612" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22371" xsd:anyURI
created_by: pg
creation_date: 2021-06-15T07:35:06Z

[Term]
id: GO:1901135
name: carbohydrate derivative metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving carbohydrate derivative." [GOC:TermGenie]
subset: goslim_agr
subset: goslim_generic
subset: goslim_mouse
subset: goslim_prokaryote
synonym: "carbohydrate derivative metabolism" EXACT [GOC:TermGenie]
created_by: bf
creation_date: 2012-07-12T04:05:09Z

[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