format-version: 1.2 data-version: go/2024-03-01/subsets/goslim_generic.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 "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_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_yeast "Yeast GO slim" synonymtypedef: syngo_official_label "label approved by the SynGO project" synonymtypedef: systematic_synonym "Systematic synonym" EXACT ontology: go/subsets/goslim_generic property_value: owl:versionInfo "2024-03-01" xsd:string [Term] id: GO:0000228 name: nuclear chromosome namespace: cellular_component def: "A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact." [GOC:dph, GOC:mah] subset: goslim_chembl subset: goslim_generic synonym: "nuclear interphase chromosome" NARROW [] is_a: GO:0005694 ! chromosome intersection_of: GO:0005694 ! chromosome intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000278 name: mitotic cell cycle namespace: biological_process alt_id: GO:0007067 def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_yeast synonym: "mitosis" RELATED [] xref: Wikipedia:Mitosis relationship: has_part GO:0140014 ! mitotic nuclear division [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:0001618 name: virus receptor activity namespace: molecular_function def: "Combining with a virus component and mediating entry of the virus into the cell." [GOC:bf, GOC:dph, PMID:7621403, UniProtKB-KW:KW-1183] subset: goslim_chembl subset: goslim_generic synonym: "viral receptor activity" EXACT [] [Term] id: GO:0002181 name: cytoplasmic translation namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein." [GOC:hjd] comment: Note that this term applies to translation performed by cytoplasmic ribosomes, which is distinct from translation performed by organellar ribosomes. For mitochondrial translation, consider GO:0032543 'mitochondrial translation' or its child terms. subset: goslim_generic subset: goslim_pombe subset: goslim_yeast created_by: hjd creation_date: 2011-06-09T03:11:53Z [Term] id: GO:0002376 name: immune system process namespace: biological_process def: "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." [GO_REF:0000022, GOC:add] comment: Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). subset: goslim_agr subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0003012 name: muscle system process namespace: biological_process def: "A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers." [GOC:mtg_cardio] subset: goslim_drosophila subset: goslim_generic synonym: "muscle physiological process" RELATED [] [Term] id: GO:0003013 name: circulatory system process namespace: biological_process def: "A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism." [GOC:mtg_cardio] subset: goslim_chembl subset: goslim_generic xref: Wikipedia:Circulatory_system [Term] id: GO:0003014 name: renal system process namespace: biological_process def: "A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila)." [GOC:cjm, GOC:mtg_cardio, GOC:mtg_kidney_jan10] subset: goslim_generic synonym: "excretory system process" EXACT [] synonym: "kidney system process" RELATED [] [Term] id: GO:0003016 name: respiratory system process namespace: biological_process alt_id: GO:0010802 def: "A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange." [GOC:dph, GOC:mtg_cardio, GOC:tb] subset: goslim_generic synonym: "respiratory gaseous exchange" EXACT [] [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_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_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: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_flybase_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] xref: Wikipedia:Enzyme [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_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, 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 subset: goslim_prokaryote_ribbon 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_prokaryote_ribbon 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 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_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cell_wall is_a: GO:0030312 ! external encapsulating structure property_value: RO:0002161 NCBITaxon:33208 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21669" xsd:anyURI [Term] id: GO:0005634 name: nucleus namespace: cellular_component def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "cell nucleus" EXACT [] synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757] xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043226 ! organelle [Term] id: GO:0005635 name: nuclear envelope namespace: cellular_component alt_id: GO:0005636 def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN:0198547684] subset: goslim_chembl subset: goslim_generic subset: goslim_plant xref: Wikipedia:Nuclear_envelope relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0005654 name: nucleoplasm namespace: cellular_component def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653] subset: goslim_chembl subset: goslim_generic subset: goslim_plant xref: NIF_Subcellular:sao661522542 xref: Wikipedia:Nucleoplasm relationship: part_of GO:0005634 ! nucleus [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:0005730 name: nucleolus namespace: cellular_component def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus is_a: GO:0043226 ! organelle relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0005739 name: mitochondrion namespace: cellular_component def: "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [GOC:giardia, ISBN:0198506732] comment: Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) 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_yeast synonym: "mitochondria" EXACT [] xref: NIF_Subcellular:sao1860313010 xref: Wikipedia:Mitochondrion is_a: GO:0043226 ! organelle [Term] id: GO:0005764 name: lysosome namespace: cellular_component def: "A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [GOC:mah, ISBN:0198506732] subset: goslim_chembl subset: goslim_generic subset: goslim_plant xref: NIF_Subcellular:sao585356902 xref: Wikipedia:Lysosome is_a: GO:0005773 ! vacuole property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0005768 name: endosome namespace: cellular_component def: "A vacuole to which materials ingested by endocytosis are delivered." [ISBN:0198506732, PMID:19696797] subset: goslim_agr subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant xref: NIF_Subcellular:sao1720343330 xref: Wikipedia:Endosome is_a: GO:0031410 ! cytoplasmic vesicle [Term] id: GO:0005773 name: vacuole namespace: cellular_component def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732] 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_yeast synonym: "vacuolar carboxypeptidase Y" RELATED [] xref: Wikipedia:Vacuole is_a: GO:0043226 ! organelle [Term] id: GO:0005777 name: peroxisome namespace: cellular_component alt_id: GO:0019818 def: "A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism." [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_plant subset: goslim_yeast synonym: "peroxisomal" RELATED [] synonym: "peroxisome vesicle" BROAD [] xref: NIF_Subcellular:sao499555322 xref: Wikipedia:Peroxisome is_a: GO:0043226 ! organelle [Term] id: GO:0005783 name: endoplasmic reticulum namespace: cellular_component def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "ER" EXACT [] xref: NIF_Subcellular:sao1036339110 xref: Wikipedia:Endoplasmic_reticulum is_a: GO:0043226 ! organelle [Term] id: GO:0005794 name: Golgi apparatus namespace: cellular_component def: "A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways." [ISBN:0198506732] comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "Golgi" BROAD [] synonym: "Golgi complex" EXACT [] synonym: "Golgi ribbon" NARROW [] xref: NIF_Subcellular:sao451912436 xref: Wikipedia:Golgi_apparatus is_a: GO:0043226 ! organelle [Term] id: GO:0005811 name: lipid droplet namespace: cellular_component def: "An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins." [GOC:mah, GOC:tb] comment: Note that this term does not refer to vesicles, but instead to structures in which lipids do not necessarily form bilayers. subset: goslim_chembl subset: goslim_generic synonym: "adiposome" EXACT [] synonym: "lipid body" EXACT [] synonym: "lipid particle" EXACT [] is_a: GO:0043226 ! organelle [Term] id: GO:0005815 name: microtubule organizing center namespace: cellular_component def: "An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides." [GOC:vw, ISBN:0815316194, PMID:17072892, PMID:17245416, Wikipedia:Microtubule_organizing_center] subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_yeast synonym: "microtubule organising centre" EXACT [] synonym: "MTOC" EXACT [] xref: Wikipedia:Microtubule_organizing_center relationship: part_of GO:0005856 ! cytoskeleton [Term] id: GO:0005829 name: cytosol namespace: cellular_component def: "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC:hjd, GOC:jl] subset: goslim_agr subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_plant xref: NIF_Subcellular:sao101633890 xref: Wikipedia:Cytosol [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_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: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_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:0005929 name: cilium namespace: cellular_component alt_id: GO:0072372 def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body." [GOC:cilia, GOC:curators, GOC:kmv, GOC:vw, ISBN:0198547684, PMID:16824949, PMID:17009929, PMID:20144998] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pir synonym: "eukaryotic flagellum" EXACT [] synonym: "flagellum" RELATED [] synonym: "microtubule-based flagellum" EXACT [] synonym: "primary cilium" NARROW [] xref: FMA:67181 xref: NIF_Subcellular:sao787716553 xref: Wikipedia:Cilium is_a: GO:0043226 ! organelle property_value: RO:0002161 NCBITaxon:3176 property_value: RO:0002161 NCBITaxon:3312 property_value: RO:0002161 NCBITaxon:3378 property_value: RO:0002161 NCBITaxon:3398 property_value: RO:0002161 NCBITaxon:4890 property_value: RO:0002161 NCBITaxon:5782 [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_prokaryote_ribbon 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 [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:0006325 name: chromatin organization namespace: biological_process alt_id: GO:0006333 alt_id: GO:0006336 alt_id: GO:0016568 alt_id: GO:0031497 alt_id: GO:0034724 def: "The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA." [PMID:20404130] subset: goslim_generic subset: goslim_pombe subset: goslim_yeast synonym: "chromatin assembly" NARROW [] synonym: "chromatin assembly or disassembly" RELATED [] synonym: "chromatin assembly/disassembly" RELATED [] synonym: "chromatin maintenance" BROAD [] synonym: "chromatin modification" RELATED [] synonym: "chromatin organisation" EXACT [GOC:mah] synonym: "DNA replication-independent chromatin assembly" NARROW [] synonym: "DNA replication-independent chromatin organization" NARROW [] synonym: "DNA replication-independent nucleosome organisation" NARROW [] synonym: "DNA replication-independent nuclesome assembly" NARROW [] synonym: "establishment of chromatin architecture" EXACT [GOC:mah] synonym: "establishment or maintenance of chromatin architecture" EXACT [GOC:mah] synonym: "transcription-coupled nucleosome assembly" NARROW [] property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22130" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23549" xsd:anyURI [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 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) 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:0006399 name: tRNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established." [ISBN:0198506732] subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pombe synonym: "tRNA metabolism" EXACT [] [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_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: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 [] 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_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 [] 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_prokaryote_ribbon subset: goslim_yeast synonym: "lipid metabolism" EXACT [] xref: Wikipedia:Lipid_metabolism [Term] id: GO:0006766 name: vitamin metabolic process namespace: biological_process def: "The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems." [GOC:ai] subset: goslim_candida subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_yeast synonym: "vitamin metabolism" EXACT [] [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: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] [Term] id: GO:0006913 name: nucleocytoplasmic transport namespace: biological_process alt_id: GO:0000063 def: "The directed movement of molecules between the nucleus and the cytoplasm." [GOC:go_curators] comment: Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed. subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pombe synonym: "nucleocytoplasmic shuttling" NARROW [] [Term] id: GO:0006914 name: autophagy namespace: biological_process alt_id: GO:0016238 def: "The cellular catabolic process in which cells digest cellular materials, such as organelles and other macromolecular constituents, or non-self materials such as intracellular pathogens. Autophagy serves to provide essential nutrients under conditions of cellular stress; or can remodel intracellular structures during cell differentiation." [GOC:autophagy, ISBN:0198547684, PMID:11099404, PMID:29455577, PMID:9412464] subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_pombe xref: Wikipedia:Autophagy_(cellular) property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25541#issuecomment-1740659745" xsd:anyURI [Term] id: GO:0006954 name: inflammatory response namespace: biological_process def: "The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages." [GO_REF:0000022, ISBN:0198506732] subset: goslim_generic synonym: "inflammation" BROAD [] xref: Wikipedia:Inflammation [Term] id: GO:0007005 name: mitochondrion 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 mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components." [GOC:dph, GOC:jl, GOC:mah, GOC:sgd_curators, PMID:9786946] subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_yeast synonym: "mitochondria organization" EXACT [GOC:mah] synonym: "mitochondrial biogenesis" EXACT [] synonym: "mitochondrial organization" EXACT [] synonym: "mitochondrion biogenesis" EXACT [] synonym: "mitochondrion morphogenesis" RELATED [] synonym: "mitochondrion organisation" EXACT [GOC:mah] synonym: "mitochondrion organization and biogenesis" RELATED [] [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:0007018 name: microtubule-based movement namespace: biological_process def: "A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." [GOC:cjm, ISBN:0815316194] subset: goslim_drosophila subset: goslim_generic [Term] id: GO:0007031 name: peroxisome 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 peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules." [GOC:mah] subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_yeast synonym: "peroxisome organisation" EXACT [] synonym: "peroxisome organization and biogenesis" RELATED [GOC:mah] [Term] id: GO:0007040 name: lysosome 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 lysosome. A lysosome is a cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases." [GOC:mah] subset: goslim_generic synonym: "lysosome organisation" EXACT [] synonym: "lysosome 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:0009536 name: plastid namespace: cellular_component def: "Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid." [GOC:jl, ISBN:0198547684] subset: goslim_chembl subset: goslim_generic subset: goslim_pir subset: goslim_plant xref: Wikipedia:Plastid is_a: GO:0043226 ! organelle property_value: RO:0002161 NCBITaxon:2 property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:28009 property_value: RO:0002161 NCBITaxon:33208 property_value: RO:0002161 NCBITaxon:4751 property_value: RO:0002161 NCBITaxon:554915 [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 subset: goslim_prokaryote_ribbon 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 subset: goslim_prokaryote_ribbon is_a: GO:0003824 ! catalytic activity [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 subset: goslim_prokaryote_ribbon xref: Wikipedia:Photosynthesis property_value: RO:0002161 NCBITaxon:33208 property_value: RO:0002161 NCBITaxon:4895 [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 [] [Term] id: GO:0016073 name: snRNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving snRNA, small nuclear RNA, any of various low-molecular-mass RNA molecules found in the eukaryotic nucleus as components of the small nuclear ribonucleoprotein." [ISBN:0198506732] subset: goslim_drosophila subset: goslim_generic subset: goslim_pombe synonym: "snRNA metabolism" EXACT [] [Term] id: GO:0016192 name: vesicle-mediated transport namespace: biological_process alt_id: GO:0006899 def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_pombe synonym: "nonselective vesicle transport" NARROW [] synonym: "protein sorting along secretory pathway" RELATED [] synonym: "vesicle trafficking" RELATED [] synonym: "vesicle transport" EXACT [] synonym: "vesicular transport" EXACT [GOC:mah] property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25421" xsd:anyURI [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 subset: goslim_prokaryote_ribbon 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_prokaryote_ribbon 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" is_a: GO:0003824 ! catalytic activity [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_prokaryote_ribbon 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" is_a: GO:0003824 ! catalytic activity [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_prokaryote_ribbon 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" is_a: GO:0003824 ! catalytic activity [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_prokaryote_ribbon 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)" is_a: GO:0003824 ! catalytic activity [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_prokaryote_ribbon subset: goslim_yeast synonym: "other isomerase activity" NARROW [] xref: EC:5.-.-.- xref: Reactome:R-HSA-6787623 "TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal" is_a: GO:0003824 ! catalytic activity [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_prokaryote_ribbon subset: goslim_yeast synonym: "synthetase activity" EXACT [GOC:jh2] xref: EC:6.-.-.- is_a: GO:0003824 ! catalytic activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19380" xsd:anyURI [Term] id: GO:0022414 name: reproductive process namespace: biological_process alt_id: GO:0044702 def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_pir subset: goslim_plant synonym: "single organism reproductive process" RELATED [] xref: Wikipedia:Reproduction property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI created_by: jl creation_date: 2012-09-19T15:56:06Z [Term] id: GO:0022600 name: digestive system process namespace: biological_process def: "A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [GOC:isa_complete, GOC:jid, GOC:mtg_cardio] subset: goslim_generic [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_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:0030154 name: cell differentiation namespace: biological_process def: "The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732] subset: goslim_agr subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_mouse subset: goslim_plant xref: Wikipedia:Cellular_differentiation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24390" 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:0030198 name: extracellular matrix 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 an extracellular matrix." [GOC:mah] subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic synonym: "extracellular matrix organisation" EXACT [] synonym: "extracellular matrix organization and biogenesis" RELATED [GOC:mah] [Term] id: GO:0030312 name: external encapsulating structure namespace: cellular_component def: "A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space." [GOC:go_curators] comment: The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'. subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_plant [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 is_a: GO:0030312 ! external encapsulating structure [Term] id: GO:0031047 name: regulatory ncRNA-mediated gene silencing namespace: biological_process def: "A process in which an regulatory non-coding RNA molecule reduces expression of target genes. This can occur pre-transcriptionally by assembly of heterochromatin and prevention of transcription or co- or post-transcriptionally by targeting RNAs for degradation or by interfering with splicing or translation. This process starts once the inhibitory RNA molecule has been transcribed, and includes processing of the RNA such as cleavage, modifications, transport from the nucleus to the cytoplasm, loading onto the RISC complex, and the effect on transcription or translation." [PMID:15020054] subset: goslim_drosophila subset: goslim_generic synonym: "gene silencing by RNA" RELATED [] synonym: "RNA-dependent gene silencing" EXACT [] synonym: "RNA-mediated gene silencing" RELATED [] property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22202" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22635" xsd:anyURI [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:0031410 name: cytoplasmic vesicle namespace: cellular_component alt_id: GO:0016023 def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_mouse subset: goslim_yeast synonym: "cytoplasmic membrane bounded vesicle" RELATED [] synonym: "cytoplasmic membrane-enclosed vesicle" RELATED [] synonym: "cytoplasmic, membrane-bounded vesicle" RELATED [] xref: NIF_Subcellular:sao180601769 is_a: GO:0043226 ! organelle [Term] id: GO:0032200 name: telomere 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 telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_generic subset: goslim_pombe subset: goslim_yeast synonym: "chromosome organization, telomeric" EXACT [] synonym: "organization of chromosome, telomeric region" EXACT [] synonym: "telomere organisation" EXACT [GOC:mah] synonym: "telomere organization and biogenesis" RELATED [GOC:mah] [Term] id: GO:0034330 name: cell junction 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 cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl subset: goslim_generic synonym: "cell junction assembly and maintenance" EXACT [] synonym: "cell junction biogenesis" RELATED [] synonym: "cell junction organisation" EXACT [GOC:mah] [Term] id: GO:0038024 name: cargo receptor activity namespace: molecular_function def: "Binding specifically to a substance (cargo) to deliver it to a transport vesicle. Cargo receptors span membranes (for instance the plasma membrane or the endoplasmic reticulum membrane), binding simultaneously to cargo molecules and coat adaptors, to efficiently recruit the cargo molecules to nascent vesicles." [PMID:15239958, PMID:27903609] comment: Notes: (1) For receptors binding a molecule but coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. (2) Cargo receptors transport substances by vesicular transport, not by transmembrane transport. For transmembrane transporters, consider instead the term 'transmembrane transporter activity ; GO:0022857'. subset: goslim_drosophila subset: goslim_generic synonym: "endocytic receptor activity" NARROW [GOC:signaling, ISBN:0123645387, PMID:12671190] synonym: "receptor activity" BROAD [] synonym: "receptor activity involved in receptor-mediated endocytosis" NARROW [GOC:bf] synonym: "transport receptor activity" BROAD [GOC:signaling] xref: Reactome:R-HSA-3000103 "CUBN:AMN binds CBLIF:RCbl" xref: Reactome:R-HSA-3000112 "CD320-mediated TCN2:RCbl uptake and delivery to lysosome" xref: Reactome:R-HSA-3000122 "CD320 binds extracellular TCN2:RCbl" xref: Reactome:R-HSA-3000137 "CUBN:AMN-mediated CBLIF:RCbl uptake and delivery to lysosome" xref: Reactome:R-HSA-350168 "LRP2-mediated uptake of extracellular CUBN:GC:25(OH)D" xref: Reactome:R-HSA-9759202 "LRP2-mediated TCN2:RCbl uptake and delivery to lysosome" xref: Reactome:R-HSA-9759209 "LRP2 binds extracellular TCN2:RCbl" relationship: has_part GO:0060090 ! molecular adaptor activity relationship: part_of GO:0016192 ! vesicle-mediated transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26872" xsd:anyURI created_by: bf creation_date: 2011-08-01T02:50:45Z [Term] id: GO:0042060 name: wound healing namespace: biological_process def: "The series of events that restore integrity to a damaged tissue, following an injury." [GOC:bf, PMID:15269788] subset: goslim_generic xref: Wikipedia:Wound_healing relationship: has_part GO:0048856 ! anatomical structure development [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: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: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: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:0044782 name: cilium 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 cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:cilia, GOC:jl] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. subset: goslim_drosophila subset: goslim_generic synonym: "microtubule-based flagellum organization" EXACT [] created_by: jl creation_date: 2013-03-27T15:09:58Z [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:0048018 name: receptor ligand activity namespace: molecular_function alt_id: GO:0071884 def: "The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands)." [GOC:kv, GOC:molecular_function_refactoring, GOC:pdt] subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic synonym: "receptor agonist activity" BROAD [GOC:molecular_function_refactoring] synonym: "signaling molecule" EXACT [] synonym: "signaling receptor ligand activity" EXACT [] synonym: "vitamin D receptor activator activity" NARROW [] is_a: GO:0098772 ! molecular function regulator activity relationship: part_of GO:0023052 ! signaling relationship: positively_regulates GO:0060089 ! molecular transducer activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14220" xsd:anyURI created_by: mah creation_date: 2010-09-13T04:51:59Z [Term] id: GO:0048856 name: anatomical structure development namespace: biological_process def: "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GO_REF:0000021] subset: gocheck_do_not_annotate subset: goslim_chembl subset: goslim_generic subset: goslim_plant synonym: "development of an anatomical structure" EXACT [] property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI [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:0050877 name: nervous system process namespace: biological_process def: "A organ system process carried out by any of the organs or tissues of neurological system." [GOC:ai, GOC:mtg_cardio] subset: goslim_agr subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_pir synonym: "neurological system process" EXACT [] synonym: "neurophysiological process" EXACT [] synonym: "pan-neural process" RELATED [] property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] id: GO:0050886 name: endocrine process namespace: biological_process def: "The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system." [ISBN:0721662544] subset: goslim_generic subset: goslim_pir synonym: "endocrine physiological process" EXACT [] synonym: "endocrine physiology" 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:0055085 name: transmembrane transport namespace: biological_process alt_id: GO:0090662 def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pombe subset: goslim_yeast synonym: "ATP hydrolysis coupled transmembrane transport" NARROW [] synonym: "membrane transport" EXACT [] created_by: tb creation_date: 2015-10-21T13:22:47Z [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 subset: goslim_prokaryote_ribbon synonym: "binding, bridging" EXACT [] synonym: "protein complex scaffold activity" RELATED [] synonym: "protein-containing complex scaffold activity" RELATED [] [Term] id: GO:0061007 name: hepaticobiliary system process namespace: biological_process def: "An system process carried out by any of the organs or tissues of the hepaticobiliary system. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins." [GOC:dph] subset: goslim_generic synonym: "hepatobiliary system process" EXACT [GOC:dph] created_by: dph creation_date: 2010-01-22T09:09:10Z [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_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: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:0072659 name: protein localization to plasma membrane namespace: biological_process alt_id: GO:0072661 alt_id: GO:0090002 def: "A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane." [GOC:mah] subset: goslim_generic subset: goslim_pombe synonym: "protein localisation in plasma membrane" RELATED [GOC:mah] synonym: "protein localization in plasma membrane" RELATED [] synonym: "protein targeting to plasma membrane" RELATED [] synonym: "protein-plasma membrane targeting" RELATED [GOC:mah] created_by: tb creation_date: 2009-07-10T10:29:23Z [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: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 [] 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 subset: goslim_prokaryote_ribbon [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 subset: goslim_prokaryote_ribbon 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:0120274 name: virus coreceptor activity namespace: molecular_function def: "Combining with a virus component, and in cooperation with a nearby primary receptor, initiating a change in cell activity." [GOC:ha, GOC:krc, PMID:16051304] subset: goslim_generic synonym: "viral coreceptor activity" EXACT [] property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20137" xsd:anyURI created_by: krc creation_date: 2020-10-20T18:32:45Z [Term] id: GO:0140013 name: meiotic nuclear division namespace: biological_process def: "One of the two nuclear divisions that occur as part of the meiotic cell cycle." [PMID:9334324] subset: goslim_generic synonym: "meiosis" EXACT [] is_a: GO:0022414 ! reproductive process relationship: part_of GO:0022414 ! reproductive process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI created_by: pg creation_date: 2017-03-23T09:40:00Z [Term] id: GO:0140014 name: mitotic nuclear division namespace: biological_process def: "A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." [ISBN:0198547684] subset: goslim_chembl subset: goslim_generic synonym: "mitosis" EXACT [] relationship: part_of GO:0000278 ! mitotic cell cycle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19910" xsd:anyURI created_by: pg creation_date: 2017-03-23T14:44:23Z [Term] id: GO:0140053 name: mitochondrial gene expression namespace: biological_process def: "The process in which a mitochondrial gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [PMID:27058308] subset: goslim_generic subset: goslim_pombe relationship: occurs_in GO:0005739 ! mitochondrion created_by: pg creation_date: 2017-06-26T10:57:45Z [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 is_a: GO:0003824 ! catalytic activity 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 is_a: GO:0003824 ! catalytic activity 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 is_a: GO:0003824 ! catalytic activity 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 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_flybase_ribbon subset: goslim_generic subset: goslim_plant 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_generic 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: RO:0002161 NCBITaxon:2 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: 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 subset: goslim_prokaryote_ribbon 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