format-version: 1.2 data-version: go/releases/2026-04-20/subsets/goslim_pir.owl subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3." subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_obsoletion_candidate "Terms planned for obsoletion" subsetdef: goslim_agr "AGR slim" subsetdef: goslim_aspergillus "Aspergillus GO slim" subsetdef: goslim_candida "Candida GO slim" subsetdef: goslim_chembl "ChEMBL protein targets summary" subsetdef: goslim_drosophila "Drosophila GO slim" subsetdef: goslim_euk_cellular_processes_ribbon "GO ribbon for eukaroytic cellular processes" subsetdef: goslim_flybase_ribbon "Insecta GO ribbon slim" subsetdef: goslim_generic "Generic GO slim" subsetdef: goslim_metagenomics "Metagenomics GO slim" subsetdef: goslim_mouse "Mouse GO slim" subsetdef: goslim_pir "PIR GO slim" subsetdef: goslim_plant "Plant GO slim" subsetdef: goslim_plant_ribbon "Plant GO ribbon" subsetdef: goslim_pombe "Fission yeast GO slim" subsetdef: goslim_prokaryote "GO subset for prokaryotes" subsetdef: goslim_prokaryote_ribbon "Prokaryote GO ribbon slim" subsetdef: goslim_synapse "synapse GO slim" subsetdef: goslim_virus "GO subset for viruses" subsetdef: goslim_yeast "Yeast GO slim" synonymtypedef: syngo_official_label "label approved by the SynGO project" synonymtypedef: systematic_synonym "Systematic synonym" EXACT ontology: go/subsets/goslim_pir property_value: owl:versionInfo "2026-04-20" xsd:string [Term] id: GO:0000109 name: nucleotide-excision repair complex namespace: cellular_component def: "Any complex formed of proteins that act in nucleotide-excision repair." [PMID:10915862] comment: Note that process information is included in the term and definition for the purpose of describing and distinguishing the complex. subset: goslim_pir synonym: "UvrB-UvrC complex" NARROW [PMID:12145219] synonym: "UvrBC complex" NARROW [GOC:bhm, PMID:12145219] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000128 name: flocculation namespace: biological_process alt_id: GO:0000501 alt_id: GO:0032128 alt_id: GO:0036281 alt_id: GO:0036282 alt_id: GO:0043689 alt_id: GO:0043690 def: "The reversible, non-sexual aggregation of single-celled organisms in suspension to form aggregates of many cells known as flocs." [GOC:jl, GOC:vw, PMID:11472912, PMID:21114594, PMID:8740415] comment: The word floc derives from the Latin word floccus, which means a tuft of wool. subset: goslim_pir synonym: "cell-cell adhesion involved in flocculation" EXACT [] synonym: "cell-cell adhesion involved in flocculation via cell wall protein-carbohydrate interaction" NARROW [] synonym: "co-flocculation" NARROW [PMID:10689163] synonym: "coflocculation" NARROW [] synonym: "coflocculation via lectin-mannose interaction" NARROW [PMID:11693916] synonym: "coflocculation via protein-carbohydrate interaction" NARROW [] synonym: "flocculation via cell wall protein-carbohydrate interaction" RELATED [] synonym: "flocculation via extracellular polymer" RELATED [] xref: Wikipedia:Flocculation is_a: GO:0007155 ! cell adhesion is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18785" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20192" xsd:anyURI created_by: bf creation_date: 2012-07-11T01:30:40Z [Term] id: GO:0000133 name: polarisome namespace: cellular_component def: "Protein complex that plays a role in determining cell polarity by directing the localized assembly of actin filaments at polarization sites; in Saccharomyces the polarisome includes Bni1p, Spa2p, Pea2p, and Bud6p." [PMID:14734532, PMID:14998522, PMID:9632790] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0030427 ! site of polarized growth [Term] id: GO:0000151 name: ubiquitin ligase complex namespace: cellular_component def: "A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex." [GOC:jh2, PMID:9529603] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0000166 name: nucleotide binding namespace: molecular_function def: "Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC:mah, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant is_a: GO:0005488 ! binding [Term] id: GO:0000178 name: exosome (RNase complex) namespace: cellular_component def: "A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured." [PMID:17174896, PMID:20531386, PMID:26726035] comment: Note that this term should not be confused with 'exosome' used in the context of vesicles released from multivesicular bodies. subset: goslim_pir synonym: "exosome (ribonucleasease complex)" EXACT [] synonym: "exosome multienzyme ribonuclease complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0110165 ! cellular anatomical structure [Term] id: GO:0000280 name: nuclear division namespace: biological_process def: "The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei." [GOC:mah] subset: goslim_pir synonym: "karyokinesis" RELATED [] is_a: GO:0048285 ! organelle fission [Term] id: GO:0000307 name: cyclin-dependent protein kinase holoenzyme complex namespace: cellular_component def: "Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner." [GOC:krc, PMID:11602261] subset: goslim_pir synonym: "CDK holoenzyme" EXACT [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0000346 name: transcription export complex namespace: cellular_component def: "The transcription export (TREX) complex couples transcription elongation by RNA polymerase II to mRNA export. The complex associates with the polymerase and travels with it along the length of the transcribed gene. TREX is composed of the THO transcription elongation complex as well as other proteins that couple THO to mRNA export proteins. The TREX complex is known to be found in a wide range of eukaryotes, including S. cerevisiae and metazoans." [GOC:krc, PMID:11979277] subset: goslim_pir synonym: "TREX complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000347 name: THO complex namespace: cellular_component def: "The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1p, Tho2p, Thp1p, and Mft1p, while the human complex is composed of 7 subunits." [GOC:krc, PMID:11060033, PMID:11979277, PMID:16983072] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000375 name: RNA splicing, via transesterification reactions namespace: biological_process alt_id: GO:0000385 alt_id: GO:0031202 def: "Splicing of RNA via a series of two transesterification reactions." [GOC:krc] comment: Note that nuclear mRNA, Group I, Group II, and Group III introns are all spliced by a series of two transesterification reactions that occur within the RNA itself, or between two RNAs in trans splicing. Some of these require one or more proteins to stabilize the catalytic conformation, while others are autocatalytic. Note that tRNA introns are spliced by a different catalytic mechanism. subset: goslim_pir synonym: "pre-mRNA splicing factor activity" RELATED [GOC:krc, GOC:mah] synonym: "RNA splicing factor activity, transesterification mechanism" RELATED [GOC:krc, GOC:mah] synonym: "spliceosomal catalysis" RELATED [] is_a: GO:0006396 ! RNA processing [Term] id: GO:0000439 name: transcription factor TFIIH core complex namespace: cellular_component alt_id: GO:0000441 def: "The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD." [GOC:ew, GOC:krc, PMID:14500720, PMID:17215295, PMID:22308316, PMID:22572993, PMID:23028141, PMID:7813015] subset: goslim_pir synonym: "core TFIIH complex" EXACT [] synonym: "SSL2-core TFIIH complex" EXACT [] is_a: GO:0005667 ! transcription regulator complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000502 name: proteasome complex namespace: cellular_component def: "A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core." [GOC:rb, Wikipedia:Proteasome] subset: goslim_pir synonym: "26S proteasome" NARROW [] synonym: "proteasome" EXACT [GOC:cjm] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0000747 name: conjugation with cellular fusion namespace: biological_process alt_id: GO:0007322 alt_id: GO:0007333 alt_id: GO:0030461 alt_id: GO:0030477 def: "A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae." [GOC:elh] subset: goslim_candida subset: goslim_pir subset: goslim_pombe subset: goslim_yeast synonym: "cell fusion" RELATED [] synonym: "mating" RELATED [] xref: Wikipedia:Conjugation is_a: GO:0022414 ! reproductive process relationship: has_part GO:0008150 ! biological_process [Term] id: GO:0000776 name: kinetochore namespace: cellular_component alt_id: GO:0000777 alt_id: GO:0000778 alt_id: GO:0005699 alt_id: GO:0031617 def: "A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules." [GOC:elh] comment: Note that the kinetochore overlaps the centromeric DNA, but centromeric DNA is not part of the kinetochore. subset: goslim_pir synonym: "condensed chromosome kinetochore" EXACT [] synonym: "condensed nuclear chromosome kinetochore" EXACT [] synonym: "NMS complex" NARROW [] xref: Wikipedia:Kinetochore is_a: GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21126" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23605" xsd:anyURI [Term] id: GO:0000782 name: telomere cap complex namespace: cellular_component def: "A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes a linear chromosome." [GOC:elh] comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome. subset: goslim_pir is_a: GO:0032993 ! protein-DNA complex relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0000786 name: nucleosome namespace: cellular_component alt_id: GO:0000787 alt_id: GO:0000788 alt_id: GO:0005718 def: "A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC:elh] subset: goslim_pir synonym: "cytoplasmic nucleosome" NARROW [] synonym: "nuclear nucleosome" NARROW [] xref: Wikipedia:Nucleosome is_a: GO:0032993 ! protein-DNA complex relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0000796 name: condensin complex namespace: cellular_component alt_id: GO:0000797 alt_id: GO:0000799 alt_id: GO:0005676 alt_id: GO:0008620 alt_id: GO:0008621 alt_id: GO:0061814 def: "A multisubunit protein complex that plays a central role in chromosome condensation in meiosis and mitosis." [GOC:elh, PMID:17268547, PMID:21795393] subset: goslim_pir synonym: "13S condensin complex" NARROW [] synonym: "8S condensin complex" NARROW [] synonym: "condensin core heterodimer" NARROW [] synonym: "condensin I complex" NARROW [] synonym: "nuclear condensin complex" NARROW [] synonym: "SMC complex" RELATED [] synonym: "Smc2-Smc4 complex" NARROW [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005694 ! chromosome property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12832" xsd:anyURI [Term] id: GO:0000808 name: origin recognition complex namespace: cellular_component def: "A multisubunit complex that is located at the replication origins of a chromosome." [GOC:elh] subset: goslim_pir synonym: "ORC" EXACT [] synonym: "origin of replication recognition complex" EXACT [] xref: Wikipedia:Origin_recognition_complex is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0000930 name: gamma-tubulin complex namespace: cellular_component def: "A multiprotein complex composed of gamma-tubulin and other non-tubulin proteins. Gamma-tubulin complexes are localized to microtubule organizing centers, and play an important role in the nucleation of microtubules. The number and complexity of non-tubulin proteins associated with these complexes varies between species." [GOC:clt, PMID:12134075] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005856 ! cytoskeleton [Term] id: GO:0001534 name: radial spoke namespace: cellular_component def: "Protein complex that links the outer microtubule doublet of a 9+2 type ciliary or flagellar axoneme with the sheath that surrounds the central pair of microtubules. Composed of a stalk that attaches to each doublet microtubule and a globular structure (spoke head) that projects toward the central pair of microtubules." [GOC:krc, ISBN:0124325653, PMID:22118931, PMID:25694453, PMID:34871179, PMID:9450971] comment: Radial spokes are involved in some types of beating motions of the cilium. The radial spoke is usually a T-shaped structure comprised of a short base that attaches to the A-microtubule of an axonemal outer microtubule doublet (MTD) of a cilium, an elongated stalk, a neck complex, and an orthogonal head structure that extends perpendicularly towards the inner sheath and the central pair (CP) microtubules. Groups of radial spokes (RSs) repeat along the MTD with regular spacing. In most organisms, each group of radial spokes is comprised of a triplet of spokes: RS1, RS2, and RS3. In some organisms (e.g. Chlamydomonas and Sarcophaga bullata), each group contains a doublet of radial spokes: RS1 and RS2, while RS3 is represented only as a stump (referred to as RS3S) attached to the A-microtubule but lacking the rest of the stalk structure and entirely lacking the head structure. {xref="PMID:9450971", xref="GOC:krc", xref="PMID:34871179", xref="PMID:25694453"} subset: goslim_pir xref: Wikipedia:Radial_spoke is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005930 ! axoneme property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25321" xsd:anyURI [Term] id: GO:0001775 name: cell activation namespace: biological_process def: "A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell." [GOC:mgi_curators] subset: goslim_pir is_a: GO:0032501 ! multicellular organismal process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24416" xsd:anyURI [Term] id: GO:0001816 name: cytokine production namespace: biological_process alt_id: GO:0042032 alt_id: GO:0042089 alt_id: GO:0042107 alt_id: GO:0050663 def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cytokine biosynthetic process" NARROW [] synonym: "cytokine metabolic process" NARROW [] synonym: "cytokine secretion" NARROW [] synonym: "interferon production" NARROW [GOC:add, GOC:mah] synonym: "interferon secretion" NARROW [GOC:add, GOC:mah] synonym: "interleukin production" NARROW [GOC:add, GOC:mah, http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F] synonym: "interleukin secretion" NARROW [GOC:add, GOC:mah, http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F] is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0032501 ! multicellular organismal process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19116" xsd:anyURI [Term] id: GO:0001882 name: nucleoside binding namespace: molecular_function def: "Binding to a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose." [GOC:hjd] subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0001906 name: cell killing namespace: biological_process def: "Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." [GOC:add] subset: goslim_pir synonym: "necrosis" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0001917 name: photoreceptor inner segment namespace: cellular_component def: "The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs." [GOC:add, PMID:12019563] subset: goslim_pir is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0002054 name: nucleobase binding namespace: molecular_function def: "Binding to a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases." [GOC:hjd] subset: goslim_pir is_a: GO:0005488 ! binding [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 is_a: GO:0008150 ! biological_process [Term] id: GO:0003674 name: molecular_function namespace: molecular_function alt_id: GO:0005554 def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "molecular function" EXACT [] [Term] id: GO:0003676 name: nucleic acid binding namespace: molecular_function alt_id: GO:0000496 def: "Binding to a nucleic acid." [GOC:jl] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "base pairing" NARROW [] is_a: GO:0005488 ! binding [Term] id: GO:0003682 name: chromatin binding namespace: molecular_function def: "Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732, PMID:20404130] subset: goslim_chembl subset: goslim_drosophila subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "lamin/chromatin binding" NARROW [] synonym: "microtubule/chromatin interaction" NARROW [] synonym: "nuclear membrane vesicle binding to chromatin" NARROW [] is_a: GO:0005488 ! binding [Term] id: GO:0003774 name: cytoskeletal motor activity namespace: molecular_function def: "Generation of force resulting in movement, for example along a microfilament or microtubule, or in torque resulting in membrane scission or rotation of a flagellum. The energy required is obtained either from the hydrolysis of a nucleoside triphosphate or by an electrochemical proton gradient (proton-motive force)." [GOC:mah, GOC:vw, PMID:11242086, PMID:29716949] subset: goslim_candida subset: goslim_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "motor activity" BROAD [] xref: Reactome:R-HSA-1861595 "Extension of pseudopodia by myosin-X in a PI3K dependent manner" is_a: GO:0003674 ! molecular_function 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:0003823 name: antigen binding namespace: molecular_function def: "Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. Antigen binding by an MHC protein complex allows the antigen to be displayed to a T cell or NK cell." [GOC:jl, ISBN:0198506732, ISBN:0721662544] subset: goslim_chembl subset: goslim_pir synonym: "antibody activity" RELATED [] synonym: "B cell receptor activity" NARROW [] synonym: "major histocompatibility complex activity" NARROW [] synonym: "major histocompatibility complex antigen display activity" NARROW [] synonym: "MHC activity" NARROW [] synonym: "opsonin activity" NARROW [] is_a: GO:0005488 ! binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25644" xsd:anyURI [Term] id: GO:0003824 name: catalytic activity namespace: molecular_function def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732] subset: goslim_agr subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] xref: Wikipedia:Enzyme is_a: GO:0003674 ! molecular_function [Term] id: GO:0004386 name: helicase activity namespace: molecular_function alt_id: GO:0008026 def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix." [GOC:jl] comment: Note that most helicases catalyze processive duplex unwinding. subset: goslim_candida subset: goslim_chembl subset: goslim_pir subset: goslim_yeast synonym: "ATP-dependent helicase activity" EXACT [] xref: Reactome:R-HSA-169461 "MCM8 mediated fork unwinding" xref: Reactome:R-HSA-169468 "MCM2-7 mediated fork unwinding" xref: Reactome:R-HSA-5686410 "BLM mediates dissolution of double Holliday junction" xref: Reactome:R-HSA-5690996 "ERCC2 and ERCC3 DNA helicases form an open bubble structure in damaged DNA" xref: Reactome:R-HSA-9922957 "NS3 melts (+)-RNA secondary structures" xref: Reactome:R-HSA-9923073 "NS3 unwinds dsRNA secondary structures" is_a: GO:0016853 ! isomerase activity relationship: has_part GO:0016787 ! hydrolase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21393" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29690" xsd:anyURI [Term] id: GO:0004497 name: monooxygenase activity namespace: molecular_function def: "Catalysis of the incorporation of one atom of molecular oxygen (O2) into the substrate and the reduction of the other atom of O2 to water." [PMID:1444267] subset: goslim_pir synonym: "hydroxylase activity" RELATED [GOC:mah, GOC:vk] synonym: "mixed-function oxidase" RELATED [GOC:sjm] xref: Reactome:R-HSA-143468 "MEOS oxidizes ethanol to acetaldehyde" xref: Reactome:R-HSA-156526 "CYP1A2,3A4,3A5,2A13 oxidise AFB1 to AFXBO" xref: Reactome:R-HSA-211882 "CYP3A7 can 6beta-hydroxylate testosterone" xref: Reactome:R-HSA-211904 "CYP4F12 18-hydroxylates ARA" xref: Reactome:R-HSA-211910 "CYP2C8 inactivates paclitaxel by 6alpha-hydroxylation" xref: Reactome:R-HSA-211919 "CYP4F8 19-hydroxylates PGH2" xref: Reactome:R-HSA-211924 "CYP4B1 12-hydroxylates ARA" xref: Reactome:R-HSA-211929 "CYP2C19 5-hydroxylates omeprazole" xref: Reactome:R-HSA-211948 "CYP3A4 can N-demethylate loperamide" xref: Reactome:R-HSA-211959 "CYP3A43 6b-hydroxylates TEST" xref: Reactome:R-HSA-211960 "CYP2U1 19-hydroxylates ARA" xref: Reactome:R-HSA-211962 "CYP4F11 16-hydroxylates 3OH-PALM" xref: Reactome:R-HSA-211968 "CYP2W1 oxidises INDOL" xref: Reactome:R-HSA-211988 "CYP2C9 inactivates tolbutamide by 4methyl-hydroxylation" xref: Reactome:R-HSA-211991 "Cyclophosphamide is 4-hydroxylated by CYP2B6" xref: Reactome:R-HSA-212004 "CYP2C18 initiates bioactivation of phenytoin by 4-hydroxylation" xref: Reactome:R-HSA-212005 "CYP2F1 dehydrogenates 3-methylindole" xref: Reactome:R-HSA-213175 "CYP3A4,5 oxidise AFB1 to AFXBO" xref: Reactome:R-HSA-215526 "CYP4F3 20-hydroxylates LTB4" xref: Reactome:R-HSA-2161795 "Arachidonate is hydroxylated to 16-HETE by CYP(1)" xref: Reactome:R-HSA-2161814 "Arachidonate is hydroxylated to 19-HETE by CYP(2)" xref: Reactome:R-HSA-2161890 "Arachidonate is epoxidated to 5,6-EET by CYP(4)" xref: Reactome:R-HSA-2161899 "Arachidonate is epoxidated to 8,9-EET by CYP(5)" xref: Reactome:R-HSA-2161940 "Arachidonate is hydroxylated to 20-HETE by CYP(3)" xref: Reactome:R-HSA-2162191 "Unknown enzyme hydroxylates DMPhOH" xref: Reactome:R-HSA-217258 "FMO2:FAD:Mg2+ S-oxidises MTZ" xref: Reactome:R-HSA-5423647 "CYP2A13 oxidises AFM1 to AFM1E" xref: Reactome:R-HSA-5423664 "CYP3A4,5 hydroxylates AFB1 to AFQ1" xref: Reactome:R-HSA-5423672 "CYP1A2, 3A4 oxidise AFB1 to AFNBO" xref: Reactome:R-HSA-5423678 "CYP1A2 hydroxylates AFB1 to AFM1" xref: Reactome:R-HSA-5602242 "Defective CYP2U1 does not omega-hydroxylate ARA" xref: Reactome:R-HSA-5602272 "Defective CYP4F22 does not 20-hydroxylate TrXA3" xref: Reactome:R-HSA-5602295 "CYP4F22 20-hydroxylates TrXA3" xref: Reactome:R-HSA-5605147 "Defective CYP1B1 does not 4-hydroxylate EST17b" xref: Reactome:R-HSA-76354 "Vinyl chloride is oxidized to 2-Chloroethylene oxide" xref: Reactome:R-HSA-76373 "N-hydroxylation of 4-aminobiphenyl" xref: Reactome:R-HSA-76386 "CYP1A2 S-demethylates 6MMP" xref: Reactome:R-HSA-76397 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI)" xref: Reactome:R-HSA-76416 "Benzene is hydroxylated to phenol" xref: Reactome:R-HSA-76426 "N-atom dealkylation of caffeine" xref: Reactome:R-HSA-76434 "Dehalogenation of carbon tetrachloride to form a free radical" xref: Reactome:R-HSA-76456 "O-atom dealkylation of dextromethorphan" xref: Reactome:R-HSA-76466 "CYP4A11 omega-hydroxylates DDCX" xref: Reactome:R-HSA-76472 "Ethylene is oxidized to Ethylene oxide by CYP1A1" xref: Reactome:R-HSA-76475 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide" xref: Reactome:R-HSA-8865107 "MICAL1 produces NADP+, H2O2" xref: Reactome:R-HSA-9018874 "CYP monooxygenates EPA to 18(S)-HpEPE" xref: Reactome:R-HSA-9027042 "CPY4 -oxidises 14(S)-HDHA to MaR-L1" xref: Reactome:R-HSA-9027043 "CYPs hydroxylate DHA to 14(R)-HDHA" xref: Reactome:R-HSA-9027044 "CYP4 -oxidises 14(R)-HDHA to MaR-L2" xref: Reactome:R-HSA-9027302 "CYP2E1 oxidises 14(S)-HDHA to 14(S),21(R)-diHDHA and 14(S),21(S)-diHDHA" xref: Reactome:R-HSA-9027321 "CYP2E1 oxidises 14(R)-HDHA to 14(R),21(R)-diHDHA and 14(R),21(S)-diHDHA" xref: Reactome:R-HSA-9037761 "CYP1, CYP2 hydroxylate (N)PD1 to 22-OH-(N)PD1" xref: Reactome:R-HSA-9749986 "CYP2,3 cytochromes hydroxylate ST to 2,3-DHBA" xref: Reactome:R-HSA-9750016 "CYP2,3 cytochromes hydroxylate ST to 2,5-DHBA" xref: Reactome:R-HSA-9753285 "CYP2E1 monooxygenates APAP to NAPQI" xref: Reactome:R-HSA-9756138 "CYP3A4 monooxygenates ATVL to 2-OH-ATVL" xref: Reactome:R-HSA-9756162 "CYP3A4 monooxygenates ATV to 4-OH-ATV" xref: Reactome:R-HSA-9756169 "CYP3A4 monooxygenates ATV to 2-OH-ATV" xref: Reactome:R-HSA-9756180 "CYP3A4 monooxygenates ATVL to 4-OH-ATVL" xref: Reactome:R-HSA-9915971 "Arachidonate is epoxidated to 11,12-EET by CYP(5)" xref: Reactome:R-HSA-9915992 "Arachidonate is hydroxylated to 17-HETE by CYP(1)" xref: Reactome:R-HSA-9915993 "Arachidonate is hydroxylated to 18-HETE by CYP(1)" xref: Reactome:R-HSA-9915997 "Arachidonate is epoxidated to 14,15-EET by CYP(5)" xref: Reactome:R-HSA-9971246 "Unknown CYP 450 omega-hydroxylates C10 fatty acid" is_a: GO:0016491 ! oxidoreductase activity property_value: broadMatch http://purl.uniprot.org/enzyme/1.-.-.- property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30165" xsd:anyURI [Term] id: GO:0004803 name: transposase activity namespace: molecular_function alt_id: GO:0004804 def: "Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element." [GOC:bm, ISBN:0198506732] subset: goslim_metagenomics subset: goslim_pir synonym: "P-element encoded transposase activity" NARROW [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0005198 name: structural molecule activity namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of a complex." [GOC:mah, GOC:vw] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast is_a: GO:0003674 ! molecular_function property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24130" xsd:anyURI [Term] id: GO:0005215 name: transporter activity namespace: molecular_function alt_id: GO:0005478 def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells." [GOC:ai, GOC:dgf] comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "carrier" RELATED [] is_a: GO:0003674 ! molecular_function property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27621" xsd:anyURI [Term] id: GO:0005488 name: binding namespace: molecular_function def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] subset: goslim_pir subset: goslim_plant synonym: "ligand" NARROW [] xref: Wikipedia:Binding_(molecular) is_a: GO:0003674 ! molecular_function [Term] id: GO:0005496 name: steroid binding namespace: molecular_function def: "Binding to a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene." [GOC:jl, ISBN:0198506732] subset: goslim_pir is_a: GO:0008289 ! lipid binding [Term] id: GO:0005515 name: protein binding namespace: molecular_function alt_id: GO:0001948 alt_id: GO:0045308 def: "Binding to a protein." [GOC:curators] subset: goslim_candida subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "glycoprotein binding" NARROW [] synonym: "protein amino acid binding" EXACT [] xref: Reactome:R-HSA-9866132 "Intermediate II binds CYC1, UQCRC1, UQCRC2, UQCRH" is_a: GO:0005488 ! binding [Term] id: GO:0005549 name: odorant binding namespace: molecular_function def: "Binding to an odorant, any substance capable of stimulating the sense of smell." [GOC:jl, ISBN:0721662544] subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." [GOC:pdt] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "cell or subcellular entity" EXACT [] synonym: "cellular component" EXACT [] synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315] xref: NIF_Subcellular:sao1337158144 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17729" xsd:anyURI [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: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_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005618 name: cell wall namespace: cellular_component def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins." [GOC:giardia, ISBN:0198547684, PMID:15134259, Wikipedia:Microbial_cyst] comment: Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for plants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995). subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cell_wall is_a: GO:0030312 ! external encapsulating structure 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:curators] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon 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:0043231 ! intracellular membrane-bounded organelle [Term] id: GO:0005643 name: nuclear pore namespace: cellular_component alt_id: GO:0005644 def: "A protein complex providing a discrete opening in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined." [ISBN:0198547684] subset: goslim_pir synonym: "NPC" EXACT [] synonym: "nuclear pore complex" EXACT [] synonym: "nuclear pore membrane protein" NARROW [] synonym: "nucleopore" EXACT [GOC:al, PMID:7603572] xref: NIF_Subcellular:sao220861693 xref: Wikipedia:Nuclear_pore is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0005663 name: DNA replication factor C complex namespace: cellular_component def: "A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides." [PMID:14614842, PMID:14646196, PMID:16172520] subset: goslim_pir synonym: "activator 1 complex" EXACT [] synonym: "RFC complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0005667 name: transcription regulator complex namespace: cellular_component alt_id: GO:0044797 alt_id: GO:0044798 def: "A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription." [GOC:jl] subset: goslim_pir synonym: "cytoplasmic transcription factor complex" RELATED [] synonym: "nuclear transcription factor complex" RELATED [] synonym: "transcription factor complex" RELATED [] is_a: GO:0032991 ! protein-containing complex created_by: jl creation_date: 2013-08-28T12:11:37Z [Term] id: GO:0005681 name: spliceosomal complex namespace: cellular_component def: "Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA." [GOC:editors, GOC:mah, ISBN:0198547684, PMID:19239890] subset: goslim_pir synonym: "spliceosome" BROAD [] synonym: "spliceosome complex" EXACT [] xref: Wikipedia:Spliceosome is_a: GO:1990904 ! ribonucleoprotein complex 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:0043232 ! intracellular membraneless organelle [Term] id: GO:0005697 name: telomerase holoenzyme complex namespace: cellular_component def: "Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits." [PMID:11884619] subset: goslim_pir is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005634 ! nucleus [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:0043232 ! intracellular membraneless organelle relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0005732 name: sno(s)RNA-containing ribonucleoprotein complex namespace: cellular_component def: "A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family and associated proteins. Many are involved in a step of processing of rRNA molecules: cleavage, 2'-O-methylation, or pseudouridylation, but other RNA types can be targets as well. The majority fall into one of two classes, box C/D type or box H/ACA type, which are conserved across eukaryotes and archaea. Other members include the telomerase RNA and the ribonuclease MRP RNA." [GOC:krc, GOC:mah, ISBN:0879695897, PMID:17284456] comment: Note that 'nucleolar' in the name acronym 'snoRNA' is part of the RNA family designation 'small nucleolar', and does not reflect the location of the complex. Both box C/D type and box H/ACA RNAs are found in Archaea (where they are referred to as sRNAs) as well as in Eukaryota. In eukaryotes, box H/ACA RNAs are found in both nucleolar-localized snoRNP complexes and in Cajal body-localized scaRNP complexes. subset: goslim_pir synonym: "small nucleolar ribonucleoprotein" NARROW [] synonym: "small nucleolar ribonucleoprotein complex" NARROW [] synonym: "small ribonucleoprotein" NARROW [] synonym: "small ribonucleoprotein protein complex" NARROW [] synonym: "snoRNP" NARROW [] synonym: "sRNP" NARROW [] is_a: GO:1990904 ! ribonucleoprotein complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20416" xsd:anyURI [Term] id: GO:0005737 name: cytoplasm namespace: cellular_component def: "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast xref: Wikipedia:Cytoplasm is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0110165 ! cellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI [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_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_yeast synonym: "mitochondria" EXACT [] xref: NIF_Subcellular:sao1860313010 xref: Wikipedia:Mitochondrion is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005744 name: TIM23 mitochondrial import inner membrane translocase complex namespace: cellular_component def: "The protein transport machinery of the mitochondrial inner membrane that typically transports proteins that possess a matrix-targeting N-terminal presequence. The TIM23 complex contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor." [PMID:27554484, PMID:8851659] comment: See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'. subset: goslim_pir synonym: "mitochondrial inner membrane pre-sequence translocase complex" EXACT [] synonym: "mitochondrial inner membrane presequence translocase complex" EXACT [] synonym: "mitochondrial inner membrane translocase complex" BROAD [] synonym: "Tim23 complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005739 ! mitochondrion relationship: part_of GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21246" xsd:anyURI [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_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon xref: NIF_Subcellular:sao1720343330 xref: Wikipedia:Endosome is_a: GO:0031982 ! vesicle is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm [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_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_yeast synonym: "vacuolar carboxypeptidase Y" RELATED [] xref: Wikipedia:Vacuole is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm [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_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_yeast synonym: "ER" EXACT [] xref: NIF_Subcellular:sao1036339110 xref: Wikipedia:Endoplasmic_reticulum is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm [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, PMID:9695800] 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_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon 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:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14798" xsd:anyURI [Term] id: GO:0005813 name: centrosome namespace: cellular_component def: "A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle." [GOC:mah, ISBN:0198547684] subset: goslim_pir xref: Wikipedia:Centrosome is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0043232 ! intracellular membraneless organelle relationship: part_of GO:0005856 ! cytoskeleton [Term] id: GO:0005835 name: fatty acid synthase complex namespace: cellular_component alt_id: GO:0031373 alt_id: GO:0031374 def: "A multienzyme complex that catalyses the synthesis of fatty acids from acetyl CoA." [GOC:pde, GOC:sgd_curators, ISBN:0716746840] subset: goslim_pir synonym: "cytosolic FAS complex" EXACT [] synonym: "cytosolic fatty acid synthase complex" EXACT [] synonym: "cytosolic type I FAS complex" EXACT [] synonym: "cytosolic type I fatty acid synthase complex" EXACT [] synonym: "FAS complex" EXACT [] synonym: "fatty acid synthetase complex" EXACT [] synonym: "holo-[acyl-carrier-protein] synthase complex" RELATED [] xref: Wikipedia:Fatty_acid_synthetase_complex is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0005840 name: ribosome namespace: cellular_component alt_id: GO:0033279 def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "free ribosome" NARROW [NIF_Subcellular:sao1139385046] synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653] synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome is_a: GO:0043232 ! intracellular membraneless organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17777" xsd:anyURI [Term] id: GO:0005849 name: mRNA cleavage factor complex namespace: cellular_component def: "Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules." [GOC:mah, PMID:10357856] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005634 ! nucleus [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_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_yeast xref: Wikipedia:Cytoskeleton is_a: GO:0043232 ! intracellular membraneless organelle [Term] id: GO:0005891 name: voltage-gated calcium channel complex namespace: cellular_component def: "A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential." [GOC:mah] subset: goslim_pir synonym: "voltage gated calcium channel complex" EXACT [] synonym: "voltage-dependent calcium channel complex" EXACT [] synonym: "voltage-sensitive calcium channel complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [Term] id: GO:0005902 name: microvillus namespace: cellular_component def: "Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells." [ISBN:0815316194] comment: Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta. subset: goslim_pir synonym: "microvilli" RELATED [NIF_Subcellular:sao671419673] xref: NIF_Subcellular:sao671419673 xref: Wikipedia:Microvillus is_a: GO:0042995 ! cell projection relationship: has_part GO:0016020 ! membrane relationship: part_of GO:0005856 ! cytoskeleton [Term] id: GO:0005903 name: brush border namespace: cellular_component def: "The dense covering of microvilli on the apical surface of an epithelial cell in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell." [GOC:sl, ISBN:0815316194] subset: goslim_pir xref: Wikipedia:Brush_border is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0005902 ! microvillus relationship: part_of GO:0045177 ! apical part of cell property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29939" xsd:anyURI [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:0042995 ! cell projection is_a: GO:0043226 ! organelle relationship: has_part GO:0016020 ! membrane relationship: has_part GO:0030990 ! intraciliary transport particle [Term] id: GO:0005930 name: axoneme namespace: cellular_component alt_id: GO:0035085 alt_id: GO:0035086 def: "The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." [GOC:bf, GOC:cilia, ISBN:0198547684] comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane. subset: goslim_pir synonym: "ciliary axoneme" EXACT [] synonym: "cilium axoneme" EXACT [] synonym: "flagellar axoneme" EXACT [] synonym: "flagellum axoneme" EXACT [] xref: Wikipedia:Axoneme is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005856 ! cytoskeleton relationship: part_of GO:0005929 ! cilium [Term] id: GO:0005933 name: cellular bud namespace: cellular_component def: "A protuberance from a cell of an organism that reproduces by budding, which will grow larger and become a separate daughter cell after nuclear division, cytokinesis, and cell wall formation (when appropriate). The daughter cell may completely separate from the mother cell, or the mother and daughter cells may remain associated." [GOC:sgd_curators] subset: goslim_candida subset: goslim_pir subset: goslim_yeast is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0005937 name: mating projection namespace: cellular_component def: "The projection formed by unicellular fungi in response to mating pheromone." [GOC:mcc] subset: goslim_pir synonym: "conjugation tube" NARROW [] synonym: "shmoo" NARROW [] is_a: GO:0042995 ! cell projection relationship: has_part GO:0016020 ! membrane [Term] id: GO:0005942 name: phosphatidylinositol 3-kinase complex namespace: cellular_component def: "A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too." [GOC:bf, PMID:24587488] comment: For discussion of membrane association, please see https://sourceforge.net/p/geneontology/ontology-requests/11559/ subset: goslim_pir synonym: "1-phosphatidylinositol 3-kinase complex" EXACT [] synonym: "phosphoinositide 3-kinase complex" EXACT [] synonym: "PI3-kinase p85-subunit alpha- PI3-kinase p110 complex" NARROW [CORUM:2575] synonym: "PI3K complex" EXACT [] synonym: "PIK3C3-PIK3R4 complex" NARROW [CORUM:429] synonym: "PIK3CA-PIK3R1 complex" NARROW [CORUM:439] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [Term] id: GO:0005960 name: glycine cleavage complex namespace: cellular_component alt_id: GO:0005961 alt_id: GO:0070015 def: "A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T." [GOC:mah] subset: goslim_pir synonym: "glycine cleavage system" EXACT [] synonym: "glycine decarboxylase complex" EXACT [] synonym: "glycine dehydrogenase (decarboxylating) complex" EXACT [] synonym: "glycine dehydrogenase complex (decarboxylating)" RELATED [] synonym: "glycine synthase complex" EXACT [] xref: Wikipedia:Glycine_decarboxylase_complex is_a: GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28865" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30262" xsd:anyURI [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_plant_ribbon subset: goslim_pombe subset: goslim_prokaryote subset: goslim_yeast synonym: "carbohydrate metabolism" EXACT [] xref: Wikipedia:Carbohydrate_metabolism is_a: GO:0044238 ! primary metabolic process 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:0005976 name: polysaccharide metabolic process namespace: biological_process alt_id: GO:0044263 def: "The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [ISBN:0198547684] subset: goslim_pir synonym: "glycan metabolic process" NARROW [] synonym: "glycan metabolism" NARROW [] synonym: "multicellular organismal polysaccharide metabolic process" NARROW [] synonym: "polysaccharide metabolism" EXACT [] is_a: GO:0005975 ! carbohydrate metabolic process is_a: GO:0043170 ! macromolecule metabolic process [Term] id: GO:0006066 name: alcohol metabolic process namespace: biological_process def: "The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [ISBN:0198506732] subset: gocheck_do_not_annotate subset: goslim_drosophila subset: goslim_pir synonym: "alcohol metabolism" EXACT [] is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI [Term] id: GO:0006081 name: aldehyde metabolic process namespace: biological_process def: "The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells." [GOC:curators, ISBN:0198506732] subset: goslim_pir synonym: "aldehyde metabolism" EXACT [] synonym: "alkanal metabolic process" EXACT [] synonym: "alkanal metabolism" EXACT [] is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0006091 name: generation of precursor metabolites and energy namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." [GOC:jl] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_pombe subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "energy pathways" BROAD [] synonym: "intermediary metabolism" RELATED [GOC:mah] synonym: "metabolic energy generation" RELATED [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006112 name: energy reserve metabolic process namespace: biological_process def: "The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen." [GOC:mah] subset: goslim_pir synonym: "energy reserve metabolism" EXACT [] is_a: GO:0006091 ! generation of precursor metabolites and energy [Term] id: GO:0006113 name: fermentation namespace: biological_process def: "The metabolic process that uses oxidation-reduction reactions of organic compounds and substrate-level phosphorylation for the generation of adenosine triphosphate (ATP), without consuming oxygen and is independent of electron transport chains." [PMID:25617754, PMID:38821505] comment: PMID:38821505 mentions exceptions regarding organic compounds and electron transport chain. Fermentation sub-processes exclude glycolysis to prevent redundancy with the glycolytic pathway. subset: gocheck_do_not_annotate subset: goslim_pir xref: MetaCyc:Fermentation xref: Wikipedia:Fermentation_(biochemistry) is_a: GO:0006091 ! generation of precursor metabolites and energy property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI [Term] id: GO:0006119 name: oxidative phosphorylation namespace: biological_process def: "The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis." [ISBN:0198506732, ISBN:0471331309] subset: goslim_pir synonym: "respiratory-chain phosphorylation" EXACT [] xref: Wikipedia:Oxidative_phosphorylation is_a: GO:0045333 ! cellular respiration relationship: has_part GO:0009117 ! nucleotide metabolic process [Term] id: GO:0006139 name: nucleobase-containing compound metabolic process namespace: biological_process alt_id: GO:0055134 def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai] subset: gocheck_do_not_annotate subset: goslim_pir subset: goslim_plant synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0044238 ! primary metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31498" xsd:anyURI [Term] id: GO:0006259 name: DNA metabolic process namespace: biological_process alt_id: GO:0055132 def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "cellular DNA metabolism" EXACT [] synonym: "DNA metabolism" EXACT [] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0043170 ! macromolecule metabolic process [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_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_prokaryote subset: goslim_yeast xref: Reactome:R-HSA-176187 "Activation of ATR in response to replication stress" xref: Reactome:R-HSA-69239 "Synthesis of DNA" xref: Wikipedia:DNA_replication is_a: GO:0006259 ! DNA metabolic process relationship: has_part GO:0006259 ! DNA metabolic process relationship: has_part GO:0009059 ! macromolecule biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/10596" xsd:anyURI [Term] id: GO:0006276 name: plasmid maintenance namespace: biological_process def: "The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division." [GOC:ai] subset: goslim_pir is_a: GO:0008150 ! biological_process [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_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_prokaryote subset: goslim_yeast xref: Reactome:R-HSA-73894 "DNA Repair" xref: Wikipedia:DNA_repair is_a: GO:0006259 ! DNA metabolic process is_a: GO:0050896 ! response to stimulus [Term] id: GO:0006304 name: DNA modification namespace: biological_process def: "The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties." [GOC:jl, GOC:ma] subset: goslim_pir is_a: GO:0006259 ! DNA metabolic process is_a: GO:0043412 ! macromolecule modification [Term] id: GO:0006351 name: DNA-templated transcription namespace: biological_process alt_id: GO:0001121 alt_id: GO:0006350 alt_id: GO:0061018 alt_id: GO:0061022 def: "The synthesis of an RNA transcript from a DNA template." [GOC:jl, GOC:txnOH] subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_pombe subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "bacterial transcription" NARROW [] synonym: "cellular transcription" BROAD [] synonym: "DNA-dependent transcription" EXACT [] synonym: "transcription" BROAD [] synonym: "transcription from bacterial-type RNA polymerase promoter" NARROW [] synonym: "transcription, DNA-dependent" EXACT [GOC:txnOH] synonym: "transcription, DNA-templated" EXACT [] xref: Reactome:R-HSA-2173793 "Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer" xref: Reactome:R-HSA-74160 "Gene expression (Transcription)" xref: Wikipedia:Transcription_(genetics) is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0016070 ! RNA metabolic process relationship: part_of GO:0009059 ! macromolecule biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14854" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16737" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22258" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22555" xsd:anyURI [Term] id: GO:0006354 name: DNA-templated transcription elongation namespace: biological_process alt_id: GO:0001124 def: "The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase." [GOC:mah, GOC:txnOH, PMID:15020047, PMID:18280161] subset: goslim_pir subset: goslim_yeast synonym: "DNA-dependent transcription, elongation" EXACT [GOC:txnOH] synonym: "DNA-templated transcription, elongation" EXACT [] synonym: "RNA elongation" BROAD [] synonym: "RNA elongation from bacterial-type RNA polymerase promoter" NARROW [] synonym: "transcription elongation from bacterial-type RNA polymerase promoter" NARROW [] synonym: "transcription elongation, DNA-dependent" EXACT [GOC:jh2] synonym: "transcriptional elongation, DNA-dependent" EXACT [] is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0016070 ! RNA metabolic process relationship: part_of GO:0006351 ! DNA-templated transcription property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23386" xsd:anyURI [Term] id: GO:0006396 name: RNA processing namespace: biological_process alt_id: GO:0006394 def: "Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules." [GOC:mah] subset: goslim_drosophila subset: goslim_pir xref: Wikipedia:Post-transcriptional_modification is_a: GO:0044238 ! primary metabolic process relationship: part_of GO:0009059 ! macromolecule biosynthetic process relationship: part_of GO:0016070 ! RNA metabolic process [Term] id: GO:0006412 name: translation namespace: biological_process alt_id: GO:0006416 alt_id: GO:0006453 alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:curators] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "protein translation" EXACT [] xref: Reactome:R-HSA-72766 "Translation" xref: Wikipedia:Translation_(genetics) is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0019538 ! protein metabolic process relationship: has_part GO:0009059 ! macromolecule biosynthetic process relationship: has_part GO:0016740 ! transferase activity relationship: has_part GO:0022411 ! cellular component disassembly relationship: has_part GO:0065003 ! protein-containing complex assembly relationship: part_of GO:0009059 ! macromolecule biosynthetic process relationship: part_of GO:0019538 ! protein metabolic process [Term] id: GO:0006457 name: protein folding namespace: biological_process alt_id: GO:0007022 alt_id: GO:0007024 alt_id: GO:0007025 def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:curators, GOC:rb] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_pombe subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "alpha-tubulin folding" NARROW [GOC:mah] synonym: "beta-tubulin folding" NARROW [GOC:mah] synonym: "chaperone activity" RELATED [] synonym: "chaperonin ATPase activity" RELATED [] synonym: "chaperonin-mediated tubulin folding" NARROW [GOC:mah] synonym: "co-chaperone activity" RELATED [] synonym: "co-chaperonin activity" RELATED [] synonym: "glycoprotein-specific chaperone activity" RELATED [] synonym: "non-chaperonin molecular chaperone ATPase activity" RELATED [] synonym: "protein complex assembly, multichaperone pathway" RELATED [] xref: Reactome:R-HSA-389960 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:R-HSA-390450 "Folding of actin by CCT/TriC" xref: Reactome:R-HSA-390466 "Chaperonin-mediated protein folding" xref: Reactome:R-HSA-532668 "N-glycan trimming in the ER and Calnexin/Calreticulin cycle" xref: Wikipedia:Protein_folding is_a: GO:0008150 ! biological_process 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:0006508 name: proteolysis namespace: biological_process def: "The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds." [GOC:bf, GOC:mah] comment: This term was intentionally placed under 'protein metabolic process ; GO:0019538' rather than 'protein catabolic process ; GO:0030163' to cover all processes centered on breaking peptide bonds, including those involved in protein processing. subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir synonym: "ATP-dependent proteolysis" NARROW [GOC:mah] synonym: "peptidolysis" EXACT [] xref: Wikipedia:Proteolysis is_a: GO:0019538 ! protein metabolic process [Term] id: GO:0006518 name: peptide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." [GOC:curators] subset: goslim_pir synonym: "peptide metabolism" EXACT [] xref: Reactome:R-HSA-2980736 "Peptide hormone metabolism" is_a: GO:0008152 ! 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 [] is_a: GO:0044238 ! primary metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17904" xsd:anyURI [Term] id: GO:0006629 name: lipid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_pombe subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "lipid metabolism" EXACT [] xref: Reactome:R-HSA-556833 "Metabolism of lipids" xref: Wikipedia:Lipid_metabolism is_a: GO:0044238 ! primary metabolic process [Term] id: GO:0006730 name: one-carbon metabolic process namespace: biological_process alt_id: GO:0019753 alt_id: GO:0019754 def: "The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states." [GOC:hjd, GOC:mah, GOC:pde] subset: goslim_pir synonym: "one carbon metabolic process" EXACT [GOC:mah] synonym: "one carbon metabolism" EXACT [GOC:mah] synonym: "one-carbon metabolism" EXACT [GOC:mah] synonym: "one-carbon transfer metabolic process" EXACT [GOC:mah] synonym: "one-carbon transfer metabolism" EXACT [GOC:mah] xref: UM-BBD_pathwayID:C1cyc is_a: GO:0008152 ! metabolic process [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 [] xref: Reactome:R-HSA-211916 "Vitamins" is_a: GO:0008152 ! metabolic process [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 is_a: GO:0008152 ! metabolic process [Term] id: GO:0006793 name: phosphorus metabolic process namespace: biological_process def: "The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus." [GOC:ai] subset: goslim_pir synonym: "phosphorus metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006805 name: xenobiotic metabolic process namespace: biological_process alt_id: GO:0017144 def: "The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:cab2, GOC:krc] subset: goslim_chembl subset: goslim_pir synonym: "drug metabolic process" RELATED [] synonym: "drug metabolism" RELATED [] synonym: "xenobiotic metabolism" EXACT [] xref: Reactome:R-HSA-211859 "Biological oxidations" xref: Reactome:R-HSA-211981 "Xenobiotics" xref: Reactome:R-HSA-2161541 "Abacavir metabolism" xref: Reactome:R-HSA-9748784 "Drug ADME" xref: Wikipedia:Drug_metabolism xref: Wikipedia:Xenobiotic_metabolism is_a: GO:0008152 ! metabolic process relationship: part_of GO:0050896 ! response to stimulus property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19460" xsd:anyURI [Term] id: GO:0006810 name: transport namespace: biological_process alt_id: GO:0015457 alt_id: GO:0015460 alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "single-organism transport" RELATED [] xref: Reactome:R-HSA-382551 "Transport of small molecules" is_a: GO:0051234 ! establishment of localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20292" xsd:anyURI created_by: jl creation_date: 2012-12-13T16:25:32Z [Term] id: GO:0006811 name: monoatomic ion transport namespace: biological_process def: "The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:ai] subset: goslim_drosophila subset: goslim_pir subset: goslim_yeast synonym: "ion transport" BROAD [] is_a: GO:0006810 ! transport [Term] id: GO:0006836 name: neurotransmitter transport namespace: biological_process def: "The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [GOC:ai] subset: goslim_pir synonym: "sodium:neurotransmitter transport" NARROW [] xref: Reactome:R-HSA-181429 "Serotonin Neurotransmitter Release Cycle" xref: Reactome:R-HSA-181430 "Norepinephrine Neurotransmitter Release Cycle" xref: Reactome:R-HSA-210500 "Glutamate Neurotransmitter Release Cycle" xref: Reactome:R-HSA-212676 "Dopamine Neurotransmitter Release Cycle" xref: Reactome:R-HSA-264642 "Acetylcholine Neurotransmitter Release Cycle" xref: Reactome:R-HSA-442660 "SLC-mediated transport of neurotransmitters" is_a: GO:0006810 ! transport [Term] id: GO:0006865 name: amino acid transport namespace: biological_process alt_id: GO:0006866 def: "The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir subset: goslim_yeast xref: Reactome:R-HSA-9958863 "SLC-mediated transport of amino acids" is_a: GO:0006810 ! transport [Term] id: GO:0006869 name: lipid transport namespace: biological_process def: "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN:0198506732] subset: goslim_drosophila subset: goslim_pir subset: goslim_yeast xref: Reactome:R-HSA-1369062 "ABC transporters in lipid homeostasis" is_a: GO:0006810 ! transport relationship: part_of GO:0051179 ! localization [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_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_pir subset: goslim_pombe xref: Reactome:R-HSA-9612973 "Autophagy" xref: Wikipedia:Autophagy_(cellular) is_a: GO:0008152 ! metabolic process relationship: has_part GO:0006810 ! transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25541" xsd:anyURI [Term] id: GO:0006936 name: muscle contraction namespace: biological_process def: "A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis." [GOC:ef, GOC:mtg_muscle, ISBN:0198506732] subset: goslim_pir xref: Reactome:R-HSA-445355 "Smooth Muscle Contraction" xref: Wikipedia:Muscle_contraction is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0006996 name: organelle organization namespace: biological_process alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_pir synonym: "organelle organisation" EXACT [] synonym: "organelle organization and biogenesis" RELATED [GOC:dph, GOC:jl, GOC:mah] synonym: "single organism organelle organization" EXACT [GOC:TermGenie] synonym: "single-organism organelle organization" RELATED [] xref: Reactome:R-HSA-1852241 "Organelle biogenesis and maintenance" is_a: GO:0016043 ! cellular component organization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] id: GO:0006997 name: nucleus organization namespace: biological_process alt_id: GO:0048287 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus." [GOC:dph, GOC:ems, GOC:jl, GOC:mah] subset: goslim_candida subset: goslim_drosophila subset: goslim_pir subset: goslim_yeast synonym: "nuclear morphology" RELATED [] synonym: "nuclear organisation" EXACT [] synonym: "nuclear organization" EXACT [] synonym: "nuclear organization and biogenesis" RELATED [GOC:mah] synonym: "nucleus organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization [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 [] xref: Reactome:R-HSA-1592230 "Mitochondrial biogenesis" is_a: GO:0006996 ! organelle organization [Term] id: GO:0007028 name: cytoplasm 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 the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [GOC:curators, GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir synonym: "cytoplasm organisation" EXACT [] synonym: "cytoplasm organization and biogenesis" RELATED [GOC:mah] is_a: GO:0016043 ! cellular component organization [Term] id: GO:0007029 name: endoplasmic reticulum 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 the endoplasmic reticulum." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir synonym: "endoplasmic reticulum morphology" RELATED [] synonym: "endoplasmic reticulum organisation" EXACT [] synonym: "endoplasmic reticulum organization and biogenesis" RELATED [GOC:mah] synonym: "ER organisation" EXACT [] synonym: "ER organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization relationship: part_of GO:0016043 ! cellular component organization [Term] id: GO:0007030 name: Golgi 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 the Golgi apparatus." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir synonym: "Golgi apparatus organization" EXACT [] synonym: "Golgi organisation" EXACT [] synonym: "Golgi organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization relationship: part_of GO:0016043 ! cellular component organization [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] is_a: GO:0006996 ! organelle organization [Term] id: GO:0007032 name: endosome 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 endosomes." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir synonym: "endosome organisation" EXACT [] synonym: "endosome organization and biogenesis" RELATED [GOC:mah] is_a: GO:0016050 ! vesicle organization relationship: part_of GO:0016043 ! cellular component organization [Term] id: GO:0007033 name: vacuole organization namespace: biological_process alt_id: GO:0044086 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole." [GOC:mah] subset: goslim_drosophila subset: goslim_pir subset: goslim_yeast synonym: "vacuolar assembly" NARROW [GOC:mah] synonym: "vacuole biogenesis" RELATED [GOC:mah] synonym: "vacuole organisation" EXACT [] synonym: "vacuole organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization [Term] id: GO:0007049 name: cell cycle namespace: biological_process def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:curators, GOC:mtg_cell_cycle] subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon synonym: "cell-division cycle" EXACT [] xref: Reactome:R-HSA-1640170 "Cell Cycle" xref: Wikipedia:Cell_cycle is_a: GO:0008150 ! biological_process [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 is_a: GO:0008150 ! biological_process relationship: part_of GO:0007049 ! cell cycle [Term] id: GO:0007154 name: cell communication namespace: biological_process def: "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:mah] subset: goslim_pir subset: goslim_plant xref: Wikipedia:Cell_signaling is_a: GO:0008150 ! biological_process [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_euk_cellular_processes_ribbon 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 is_a: GO:0008150 ! biological_process created_by: dos creation_date: 2014-04-15T15:59:10Z [Term] id: GO:0007586 name: digestion namespace: biological_process def: "The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [GOC:isa_complete, ISBN:0198506732] subset: goslim_chembl subset: goslim_pir xref: Reactome:R-HSA-8935690 "Digestion" xref: Wikipedia:Digestion is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0007588 name: excretion namespace: biological_process def: "The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds." [ISBN:0192801023] subset: gocheck_do_not_annotate subset: goslim_pir xref: Wikipedia:Excretion is_a: GO:0032501 ! multicellular organismal process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22368" xsd:anyURI [Term] id: GO:0008015 name: blood circulation namespace: biological_process alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0008023 name: transcription elongation factor complex namespace: cellular_component def: "Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation." [GOC:jl] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0008037 name: cell recognition namespace: biological_process def: "The process in which a cell in an organism interprets its surroundings." [GOC:curators] subset: goslim_pir synonym: "recognition of surroundings by cell" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0008150 name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process alt_id: GO:0044236 alt_id: GO:0044710 def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_annotate subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote_ribbon synonym: "metabolism" EXACT [] xref: Reactome:R-HSA-1430728 "Metabolism" xref: Wikipedia:Metabolism is_a: GO:0008150 ! biological_process disjoint_from: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28932" xsd:anyURI created_by: jl creation_date: 2012-10-17T15:46:40Z [Term] id: GO:0008233 name: peptidase activity namespace: molecular_function alt_id: GO:0070010 alt_id: GO:0070011 def: "Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid." [EC:3.4.-.-, GOC:jl] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_metagenomics subset: goslim_pir subset: goslim_yeast synonym: "hydrolase, acting on peptide bonds" EXACT [] synonym: "peptidase activity, acting on D-amino acid peptides" NARROW [] synonym: "peptidase activity, acting on L-amino acid peptides" NARROW [] synonym: "peptide hydrolase activity" EXACT [] synonym: "protease activity" EXACT [] synonym: "proteinase activity" NARROW [] xref: EC:3.4.-.- xref: Reactome:R-HSA-205112 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6" xref: Reactome:R-HSA-3000243 "Unknown lysosomal protease degrades CBLIF:RCbl to release Cbl" xref: Reactome:R-HSA-3000263 "TCN2:RCbl is degraded to release RCbl" xref: Reactome:R-HSA-3065958 "An unknown protease degrades ACACA" xref: Reactome:R-HSA-3065959 "An unknown protease degrades hCBXs" xref: Reactome:R-HSA-3139027 "Maturation of HIV Virion" xref: Reactome:R-HSA-376149 "Proteolytic processing of SLIT" xref: Reactome:R-HSA-4167501 "An unknown protease degrades ACACB" xref: Reactome:R-HSA-448678 "CTSG cleaves CASP1(1-404)" xref: Reactome:R-HSA-5655483 "USP1 autocleavage" xref: Reactome:R-HSA-5684864 "NAPSA, CTSH, PGA3-5 cleave pro-SFTPB" xref: Reactome:R-HSA-5685902 "NAPSA, CTSH, PGA3-5 cleave pro-SFTPC" xref: Reactome:R-HSA-6803060 "DCD(63-110) is processed to DCD(63-109)" xref: Reactome:R-HSA-9935547 "Lysosomal degradation of ubiquitinated CDH1" is_a: GO:0016787 ! hydrolase activity property_value: exactMatch http://purl.uniprot.org/enzyme/3.4.-.- property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI [Term] id: GO:0008278 name: cohesin complex namespace: cellular_component alt_id: GO:0000798 alt_id: GO:0008279 alt_id: GO:0008280 alt_id: GO:0043222 def: "A protein complex that is required for sister chromatid cohesion in eukaryotes. The cohesin complex forms a molecular ring complex, and is composed of structural maintenance of chromosomes (SMC) and kleisin proteins. For example, in yeast, the complex is composed of the SMC proteins Smc1p and Smc3p, and the kleisin protein Scc1p. In vertebrates, the complex is composed of the SMC1 (SMC1A or SMC1B) and SMC3 heterodimer attached via their hinge domains to a kleisin (RAD21, REC8 or RAD21L) which links them, and one STAG protein (STAG1, STAG2 or STAG3)." [GOC:jl, GOC:sp, GOC:vw, PMID:9887095] subset: goslim_pir synonym: "14S cohesin" NARROW [] synonym: "9S cohesin" NARROW [] synonym: "cohesin core heterodimer" RELATED [] synonym: "nuclear cohesin complex" RELATED [] synonym: "SMC complex" RELATED [] synonym: "SMC/kleisin ring complex" EXACT [] synonym: "Smc1-Smc3 complex" NARROW [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0008283 name: cell population proliferation namespace: biological_process def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb] comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms. subset: goslim_agr subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon subset: goslim_mouse subset: goslim_pir synonym: "cell proliferation" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0008287 name: protein serine/threonine phosphatase complex namespace: cellular_component def: "A complex, normally consisting of a catalytic and a regulatory subunit, which catalyzes the removal of a phosphate group from a serine or threonine residue of a protein." [GOC:bf] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0008289 name: lipid binding namespace: molecular_function def: "Binding to a lipid." [GOC:ai] subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_generic subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon subset: goslim_yeast is_a: GO:0005488 ! binding [Term] id: GO:0008290 name: F-actin capping protein complex namespace: cellular_component def: "A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments." [GOC:curators, ISBN:0198599560] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005856 ! cytoskeleton [Term] id: GO:0008641 name: ubiquitin-like modifier activating enzyme activity namespace: molecular_function alt_id: GO:0008642 def: "Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond." [GOC:jl, GOC:mah] subset: goslim_pir synonym: "small protein activating enzyme activity" NARROW [] is_a: GO:0016874 ! ligase activity relationship: has_part GO:0016787 ! hydrolase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14208" xsd:anyURI [Term] id: GO:0008643 name: carbohydrate transport namespace: biological_process alt_id: GO:0006861 alt_id: GO:0008644 def: "The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y." [GOC:ai] subset: goslim_pir subset: goslim_yeast synonym: "sugar transport" NARROW [] is_a: GO:0006810 ! transport [Term] id: GO:0008655 name: pyrimidine-containing compound salvage namespace: biological_process def: "Any process that generates a pyrimidine-containing compound, a nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis." [GOC:jl] subset: goslim_pir synonym: "pyrimidine salvage" RELATED [] is_a: GO:0043094 ! metabolic compound salvage [Term] id: GO:0008907 name: integrase activity namespace: molecular_function def: "Catalysis of the integration of one DNA segment into another." [GOC:mah] subset: goslim_pir xref: Reactome:R-HSA-164523 "Transesterification to connect viral DNA 3' ends to host DNA 5' ends" is_a: GO:0003824 ! catalytic activity relationship: part_of GO:0015074 ! DNA integration [Term] id: GO:0009009 name: site-specific recombinase activity namespace: molecular_function def: "Catalysis of the formation of new phosphodiester bonds between a pair of short, unique target DNA sequences." [GOC:elh, PMID:6286142] comment: Note that this term is not a child of 'recombinase activity ; GO:0000150' because the latter represents activities that do not break or form phosphodiester bonds. subset: goslim_pir synonym: "RecA-family recombinase activity" EXACT [] is_a: GO:0008907 ! integrase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22264" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/3917" xsd:anyURI [Term] id: GO:0009055 name: electron transfer activity namespace: molecular_function alt_id: GO:0009053 alt_id: GO:0009054 def: "A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways." [Wikipedia:Electron_transfer] subset: goslim_metagenomics subset: goslim_pir synonym: "electron acceptor activity" NARROW [] synonym: "electron carrier" RELATED [] synonym: "electron donor activity" NARROW [] synonym: "electron transporter activity" RELATED [] xref: Reactome:R-HSA-169260 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF" is_a: GO:0003674 ! molecular_function property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21334" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26572" xsd:anyURI [Term] id: GO:0009057 name: macromolecule catabolic process namespace: biological_process alt_id: GO:0043285 alt_id: GO:0044266 def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "cellular macromolecule catabolic process" RELATED [] synonym: "cellular macromolecule catabolism" RELATED [] synonym: "cellular macromolecule degradation" RELATED [] synonym: "macromolecule breakdown" EXACT [] synonym: "macromolecule catabolism" EXACT [] synonym: "macromolecule degradation" EXACT [] synonym: "multicellular organismal macromolecule catabolic process" NARROW [] is_a: GO:0043170 ! macromolecule metabolic process [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate subset: goslim_pir synonym: "biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI [Term] id: GO:0009116 name: nucleoside metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine)." [GOC:ma] subset: goslim_pir synonym: "nucleoside metabolism" EXACT [] is_a: GO:0006139 ! nucleobase-containing compound metabolic process [Term] id: GO:0009117 name: nucleotide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates)." [GOC:ma] subset: goslim_pir synonym: "nucleotide metabolism" EXACT [] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0006793 ! phosphorus metabolic process [Term] id: GO:0009225 name: nucleotide-sugar metabolic process namespace: biological_process def: "The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative." [ISBN:0198506732] subset: goslim_pir synonym: "nucleotide-sugar metabolism" EXACT [] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0006793 ! phosphorus metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14587" xsd:anyURI [Term] id: GO:0009288 name: bacterial-type flagellum namespace: cellular_component def: "A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope." [GOC:cilia, GOC:jh2, GOC:krc, GOC:mtg_sensu, PMID:7787060, Wikipedia:Flagellum#Bacterial] subset: goslim_metagenomics subset: goslim_pir synonym: "flagellin-based flagellum" EXACT [] xref: Wikipedia:Flagellum#Bacterial is_a: GO:0042995 ! cell projection is_a: GO:0043226 ! organelle [Term] id: GO:0009289 name: pilus namespace: cellular_component def: "A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter." [GOC:pamgo_curators, PMID:28496159] subset: goslim_pir synonym: "fimbria" EXACT [] synonym: "fimbriae" EXACT [] synonym: "fimbrium" EXACT [] synonym: "pili" EXACT [] xref: Wikipedia:Pilus is_a: GO:0042995 ! cell projection [Term] id: GO:0009291 name: unidirectional conjugation namespace: biological_process def: "The process of unidirectional (polarized) transfer of genetic information involving direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells. Some or all of the chromosome(s) of the donor cell is transferred into the recipient cell." [Wikipedia:Bacterial_conjugation] comment: Unidirectional conjugation is not a type of not sexual reproduction, since no exchange of gamete occurs and no generation of a new organism: instead an existing organism is transformed. subset: goslim_pir synonym: "bacterial conjugation" RELATED [] xref: Wikipedia:Bacterial_conjugation is_a: GO:0009292 ! horizontal gene transfer [Term] id: GO:0009292 name: horizontal gene transfer namespace: biological_process def: "The introduction of genetic information into a cell to create a genetically different individual, without production of new individuals." [PMID:26184597] subset: goslim_pir synonym: "genetic exchange" BROAD [] synonym: "genetic transfer" EXACT [] synonym: "lateral gene transfer" EXACT [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22952" xsd:anyURI [Term] id: GO:0009308 name: amine metabolic process namespace: biological_process alt_id: GO:0044106 def: "The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." [GOC:jl, ISBN:0198506732] subset: goslim_chembl subset: goslim_pir synonym: "amine metabolism" EXACT [] synonym: "cellular amine metabolic process" EXACT [] is_a: GO:0008152 ! metabolic process created_by: jl creation_date: 2009-07-15T11:55:44Z [Term] id: GO:0009317 name: acetyl-CoA carboxylase complex namespace: cellular_component def: "A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex." [GOC:jl, GOC:mah, PMID:12121720] subset: goslim_metagenomics subset: goslim_pir synonym: "ACCase complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0009368 name: endopeptidase Clp complex namespace: cellular_component def: "A protein complex comprised of members of the ClpX, ClpC, ClpD, ClpP or ClpR protein families. ClpPs are the proteolytic subunit of active complexes, and ClpA and ClpX form the regulatory subunits. Enzymatically active and inactive complexes can form." [GOC:mah, PMID:11352464] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0009372 name: quorum sensing namespace: biological_process alt_id: GO:0010699 alt_id: GO:0060247 def: "The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms." [GOC:krc, GOC:mlg, PMID:10607620, PMID:15716452, PMID:16497924, PMID:16630813, PMID:8288518] subset: goslim_metagenomics subset: goslim_pir synonym: "cell-cell signaling involved in quorum sensing" RELATED [] synonym: "detection of cell density by secreted molecule" RELATED [] synonym: "quorum sensing system" EXACT [] xref: Wikipedia:Quorum_sensing is_a: GO:0007154 ! cell communication is_a: GO:0050789 ! regulation of biological process is_a: GO:0051606 ! detection of stimulus property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17730" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18018" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18061" xsd:anyURI [Term] id: GO:0009404 name: toxin metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism." [GOC:cab2] subset: goslim_pir synonym: "toxin metabolism" EXACT [] is_a: GO:0019748 ! secondary metabolic process [Term] id: GO:0009521 name: photosystem namespace: cellular_component alt_id: GO:0030090 def: "A complex located in a photosynthetic membrane that consists of a photoreaction center associated with accessory pigments and electron carriers. Examples of this component are found in Arabidopsis thaliana and in photosynthetic bacterial and archaeal species." [GOC:ds, GOC:mah, ISBN:0140514031, PMID:9821949] subset: goslim_pir synonym: "reaction center" NARROW [] synonym: "reaction centre" NARROW [] xref: Wikipedia:Photosystem is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0009579 ! thylakoid relationship: part_of GO:0016020 ! membrane [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 subset: goslim_plant_ribbon xref: Wikipedia:Plastid is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0009579 name: thylakoid namespace: cellular_component def: "A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." [GOC:ds, GOC:mtg_sensu, ISBN:0198506732] comment: A thylakoid is not considered an organelle, but some thylakoids are part of organelles. subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "photosynthetic membrane" RELATED [] xref: Wikipedia:Thylakoid is_a: GO:0043232 ! intracellular membraneless organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13958" xsd:anyURI [Term] id: GO:0009657 name: plastid 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 plastid." [GOC:mah] subset: goslim_pir synonym: "plastid organisation" EXACT [] synonym: "plastid organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization [Term] id: GO:0009914 name: hormone transport namespace: biological_process def: "The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:tb] subset: goslim_pir is_a: GO:0006810 ! transport is_a: GO:0065008 ! regulation of biological quality [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 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0009986 name: cell surface namespace: cellular_component alt_id: GO:0009928 alt_id: GO:0009929 def: "The external part of the cell wall and/or plasma membrane." [GOC:jl, GOC:mtg_sensu, GOC:sm] comment: Note that this term is intended to annotate gene products that are attached (integrated or loosely bound) to the plasma membrane or cell wall. subset: goslim_pir synonym: "cell associated" EXACT [] synonym: "cell bound" EXACT [] is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0010118 name: stomatal movement namespace: biological_process def: "The process of opening or closing of stomata, which is directly related to the stomatal conductance (measuring rate of passage of either water vapor or carbon dioxide (CO2) through stomata)." [GOC:sm] subset: goslim_pir is_a: GO:0008150 ! biological_process [Term] id: GO:0010316 name: pyrophosphate-dependent phosphofructokinase complex namespace: cellular_component def: "Heterodimeric complex that catalyzes the pyrophosphate-dependent phosphorylation of D-fructose 6-phosphate into D-fructose 1,6-bisphosphate." [PMID:2170409] subset: goslim_pir synonym: "PFK complex" RELATED [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0015031 name: protein transport namespace: biological_process alt_id: GO:0015831 def: "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_chembl subset: goslim_pir subset: goslim_yeast synonym: "enzyme transport" NARROW [] is_a: GO:0006810 ! transport [Term] id: GO:0015074 name: DNA integration namespace: biological_process def: "The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome." [GOC:mah] subset: goslim_pir is_a: GO:0006259 ! DNA metabolic process [Term] id: GO:0015669 name: gas transport namespace: biological_process def: "The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir is_a: GO:0006810 ! transport [Term] id: GO:0015791 name: polyol transmembrane transport namespace: biological_process def: "The directed movement of polyols, any polyhydric alcohol, across a membrane." [GOC:ai] subset: goslim_pir is_a: GO:0006810 ! transport [Term] id: GO:0015833 name: peptide transport namespace: biological_process def: "The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir is_a: GO:0006810 ! transport [Term] id: GO:0015835 name: peptidoglycan transport namespace: biological_process def: "The directed movement of peptidoglycans, a class of glycoconjugates found in bacterial cell walls, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir synonym: "murein transport" EXACT [] is_a: GO:0006810 ! transport [Term] id: GO:0015837 name: amine transport namespace: biological_process def: "The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai, ISBN:0198506732] subset: goslim_pir synonym: "amine/polyamine transport" RELATED [] xref: Reactome:R-HSA-549127 "SLC-mediated transport of organic cations" is_a: GO:0006810 ! transport [Term] id: GO:0015849 name: organic acid transport namespace: biological_process def: "The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [ISBN:0198506732] subset: goslim_pir is_a: GO:0006810 ! transport [Term] id: GO:0015891 name: siderophore transport namespace: biological_process alt_id: GO:0015892 def: "The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir synonym: "iron-siderochrome transport" NARROW [] synonym: "iron-siderophore transport" EXACT [] synonym: "siderochrome transport" NARROW [] synonym: "siderophore-iron transport" EXACT [] is_a: GO:0006811 ! monoatomic ion transport [Term] id: GO:0015920 name: lipopolysaccharide transport namespace: biological_process alt_id: GO:0015921 def: "The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide." [GOC:ai] subset: goslim_pir synonym: "lipopolysaccharide export" NARROW [] synonym: "LPS export" NARROW [] synonym: "LPS transport" EXACT [] is_a: GO:0006869 ! lipid transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23034" xsd:anyURI [Term] id: GO:0015931 name: nucleobase-containing compound transport namespace: biological_process def: "The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir subset: goslim_yeast synonym: "nucleobase, nucleoside, nucleotide and nucleic acid transport" RELATED [GOC:dph, GOC:tb] is_a: GO:0006810 ! transport [Term] id: GO:0015935 name: small ribosomal subunit namespace: cellular_component def: "The smaller of the two subunits of a ribosome." [GOC:mah] subset: goslim_pir synonym: "ribosomal small subunit" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005840 ! ribosome [Term] id: GO:0015948 name: methanogenesis namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes." [GOC:ai] subset: goslim_metagenomics subset: goslim_pir synonym: "methane biosynthesis" EXACT [] synonym: "methane biosynthetic process" EXACT [] xref: UM-BBD_pathwayID:meth xref: Wikipedia:Methanogenesis is_a: GO:0045333 ! cellular respiration [Term] id: GO:0015949 name: nucleobase-containing small molecule interconversion namespace: biological_process def: "The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule." [GOC:mah, ISBN:0306444747, ISBN:0471394831] subset: goslim_pir xref: Reactome:R-HSA-499943 "Interconversion of nucleotide di- and triphosphates" is_a: GO:0006139 ! nucleobase-containing compound metabolic process [Term] id: GO:0015976 name: carbon utilization namespace: biological_process alt_id: GO:0015978 def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg] subset: goslim_chembl subset: goslim_pir synonym: "carbon utilization by utilization of organic compounds" EXACT [GOC:mah] synonym: "heterotrophy" EXACT [] xref: Wikipedia:Heterotroph is_a: GO:0050896 ! response to stimulus [Term] id: GO:0015979 name: photosynthesis namespace: biological_process def: "The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds." [ISBN:0198547684] subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: Wikipedia:Photosynthesis is_a: GO:0008152 ! metabolic process [Term] id: GO:0016010 name: dystrophin-associated glycoprotein complex namespace: cellular_component def: "A multiprotein complex that forms a strong mechanical link between the cytoskeleton and extracellular matrix; typical of, but not confined to, muscle cells. The complex is composed of transmembrane, cytoplasmic, and extracellular proteins, including dystrophin, sarcoglycans, dystroglycan, dystrobrevins, syntrophins, sarcospan, caveolin-3, and NO synthase." [PMID:15117830, PMID:16710609] subset: goslim_pir synonym: "DGC" EXACT [] synonym: "dystrophin glycoprotein complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [Term] id: GO:0016020 name: membrane namespace: cellular_component alt_id: GO:0016021 alt_id: GO:0098589 alt_id: GO:0098805 def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl subset: goslim_flybase_ribbon subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "integral component of membrane" NARROW [] synonym: "integral to membrane" NARROW [] synonym: "membrane region" NARROW [] synonym: "region of membrane" NARROW [] synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane xref: Wikipedia:Transmembrane_protein is_a: GO:0110165 ! cellular anatomical structure creation_date: 2014-03-06T11:37:54Z [Term] id: GO:0016028 name: rhabdomere namespace: cellular_component def: "The specialized microvilli-containing organelle on the apical surfaces of a photoreceptor cell containing the visual pigment rhodopsin and most of the proteins involved in phototransduction." [GOC:hb, GOC:sart, PMID:8646774] subset: goslim_pir is_a: GO:0042995 ! cell projection relationship: has_part GO:0016020 ! membrane [Term] id: GO:0016032 name: viral process namespace: biological_process alt_id: GO:0022415 def: "A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle." [GOC:bf, GOC:jl, GOC:mah] comment: See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'. subset: goslim_metagenomics subset: goslim_pir subset: goslim_virus synonym: "viral infection" RELATED [] synonym: "virulence" RELATED [] synonym: "virus process" EXACT [GOC:bf, GOC:jl] xref: Reactome:R-HSA-162906 "HIV Infection" xref: Wikipedia:Viral_life_cycle is_a: GO:0008150 ! biological_process [Term] id: GO:0016043 name: cellular component organization namespace: biological_process alt_id: GO:0044235 alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon synonym: "cell organisation" EXACT [] synonym: "cell organization and biogenesis" RELATED [GOC:mah] synonym: "cellular component organisation at cellular level" EXACT [GOC:mah] synonym: "cellular component organisation in other organism" EXACT [GOC:mah] synonym: "cellular component organization at cellular level" EXACT [] synonym: "cellular component organization in other organism" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0016049 name: cell growth namespace: biological_process alt_id: GO:0048591 def: "The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:ai] subset: gocheck_do_not_annotate subset: goslim_drosophila subset: goslim_pir subset: goslim_plant synonym: "cell expansion" RELATED [] synonym: "cellular growth" EXACT [] synonym: "growth of cell" EXACT [] synonym: "metabolic process resulting in cell growth" RELATED [] synonym: "metabolism resulting in cell growth" RELATED [] synonym: "non-developmental cell growth" RELATED [GOC:mah] synonym: "non-developmental growth of a unicellular organism" RELATED [GOC:mah] is_a: GO:0040007 ! growth [Term] id: GO:0016050 name: vesicle 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 vesicle." [GOC:mah] subset: goslim_pir subset: goslim_yeast synonym: "vesicle organisation" EXACT [] synonym: "vesicle organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization [Term] id: GO:0016070 name: RNA metabolic process namespace: biological_process def: "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732] subset: goslim_agr subset: goslim_candida subset: goslim_euk_cellular_processes_ribbon subset: goslim_metagenomics subset: goslim_pir subset: goslim_prokaryote synonym: "RNA metabolism" EXACT [] xref: Reactome:R-HSA-8953854 "Metabolism of RNA" is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0043170 ! macromolecule metabolic process [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_euk_cellular_processes_ribbon 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] is_a: GO:0006810 ! transport 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_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon is_a: GO:0003674 ! molecular_function relationship: part_of GO:0050896 ! response to stimulus [Term] id: GO:0016469 name: proton-transporting two-sector ATPase complex namespace: cellular_component def: "A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of protons across a membrane. The complex comprises a membrane sector (F0, V0, or A0) that carries out proton transport and a cytoplasmic compartment sector (F1, V1, or A1) that catalyzes ATP synthesis or hydrolysis. Two major types have been characterized: V-type ATPases couple ATP hydrolysis to the transport of protons across a concentration gradient, whereas F-type ATPases, also known as ATP synthases, normally run in the reverse direction to utilize energy from a proton concentration or electrochemical gradient to synthesize ATP. A third type, A-type ATPases have been found in archaea, and are closely related to eukaryotic V-type ATPases but are reversible." [GOC:mah, ISBN:0716743663, PMID:16691483] subset: goslim_metagenomics subset: goslim_pir synonym: "hydrogen-transporting two-sector ATPase complex" EXACT [] synonym: "vacuolar hydrogen-transporting ATPase" RELATED [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15936" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28017" xsd:anyURI [Term] id: GO:0016472 name: sodium ion-transporting two-sector ATPase complex namespace: cellular_component def: "A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of sodium ions across a membrane. The complex comprises a membrane sector (F0 or V0) that carries out ion transport and a cytoplasmic compartment sector (F1 or V1) that catalyzes ATP synthesis or hydrolysis." [GOC:mah, PMID:14656431] subset: goslim_pir synonym: "sodium-transporting two-sector ATPase complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [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." [EC:1.-.-.-] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_prokaryote subset: goslim_yeast synonym: "oxidoreductase activity, acting on other substrates" NARROW [] synonym: "redox activity" EXACT [] xref: EC:1.-.-.- xref: Reactome:R-HSA-1614362 "SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases" xref: Reactome:R-HSA-2161612 "PGH2 is reduced to PGF2a by FAM213B" xref: Reactome:R-HSA-265296 "Arachidonate is oxidised to 5S-HpETE by ALOX5" xref: Reactome:R-HSA-266051 "5S-HpETE is dehydrated to LTA4 by ALOX5" xref: Reactome:R-HSA-390425 "FAR1 reduces PalmCoA to HXOL" xref: Reactome:R-HSA-390438 "FAR2 reduces PalmCoA to HXOL" 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 reductase 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" xref: Reactome:R-HSA-9759549 "Cob(I)alamin bound to MMACHC is oxidized to cob(II)alamin" is_a: GO:0003824 ! catalytic activity property_value: exactMatch http://purl.uniprot.org/enzyme/1.-.-.- property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI [Term] id: GO:0016530 name: metallochaperone activity namespace: molecular_function def: "Binding to and delivering metal ions to a target protein." [PMID:11739376] subset: goslim_pir is_a: GO:0003674 ! molecular_function relationship: has_part GO:0043167 ! ion binding [Term] id: GO:0016591 name: RNA polymerase II, holoenzyme namespace: cellular_component def: "A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters." [GOC:jl, GOC:krc, PMID:16858867, Wikipedia:Rna_polymerase_ii] subset: goslim_pir synonym: "DNA-directed RNA polymerase II, holoenzyme" EXACT [] is_a: GO:0030880 ! RNA polymerase complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0016597 name: amino acid binding namespace: molecular_function def: "Binding to an amino acid, organic acids containing one or more amino substituents." [GOC:ai] subset: goslim_metagenomics subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0016610 name: nitrogenase complex namespace: cellular_component def: "An enzyme complex composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase is tetrameric with an alpha2-beta2 structure and nitrogenase reductase is a homodimer, and both are associated with metal ions, which differ between species. Both proteins are required for the enzyme activity of the complex, the formation of oxidized ferredoxin and ammonia from reduced ferredoxin and nitrogen." [PMID:10852721] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21246" xsd:anyURI [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." [EC:2.-.-.-] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote subset: goslim_yeast xref: EC:2.-.-.- xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2" xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1" xref: Reactome:R-HSA-5333607 "GSSeH combines with bGalNAc derivative to form GSSebGalNac" 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 property_value: exactMatch http://purl.uniprot.org/enzyme/2.-.-.- property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI [Term] id: GO:0016787 name: hydrolase activity namespace: molecular_function def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote subset: goslim_yeast xref: EC:3.-.-.- xref: Reactome:R-HSA-1236938 "Partial proteolysis of antigen in phagolysosomes" xref: Reactome:R-HSA-2029475 "Production of AA by iPLA2 upon FCGR activation" xref: Reactome:R-HSA-5694583 "ABHD4 hydrolyses NAPE" xref: Reactome:R-HSA-5695964 "ABHD14B hydrolyses PNPB" xref: Reactome:R-HSA-6786190 "CMBL hydrolyses OM to OLMS" xref: Reactome:R-HSA-6788295 "HDHD1:Mg2+ dephosphorylates PURIDP" xref: Reactome:R-HSA-8938314 "ENPPs hydrolyse CoA-SH to PPANT, PAP" xref: Reactome:R-HSA-8952137 "Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate" xref: Reactome:R-HSA-9942295 "QNG1 hydrolyzes queuosine 5'-monophosphate yielding queuine and ribose 5'-monophosphate" is_a: GO:0003824 ! catalytic activity property_value: exactMatch http://purl.uniprot.org/enzyme/3.-.-.- property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI [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." [EC:4.-.-.-] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_prokaryote subset: goslim_yeast xref: EC:4.-.-.- xref: Reactome:R-HSA-5696408 "PXLP-K278-PHYKPL tetramer hydrolyses 5PHL" xref: Reactome:R-HSA-6782895 "TYW1:FMN:4Fe-4S transforms 1-methylguanosine yielding yW-187 (4-demethylwyosine) at nucleotide 37 of tRNA(Phe)" is_a: GO:0003824 ! catalytic activity property_value: exactMatch http://purl.uniprot.org/enzyme/4.-.-.- property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI [Term] id: GO:0016853 name: isomerase activity namespace: molecular_function def: "Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5." [ISBN:0198506732] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_prokaryote subset: goslim_yeast synonym: "other isomerase activity" NARROW [] xref: EC:5.-.-.- xref: Reactome:R-HSA-2161666 "PGA2 is isomerised to PGC2" xref: Reactome:R-HSA-2161735 "PGC2 is isomerised to PGB2" xref: Reactome:R-HSA-6787623 "GFUS dimer epimerises GDP-DHDMan to GDP-KDGal" is_a: GO:0003824 ! catalytic activity property_value: exactMatch http://purl.uniprot.org/enzyme/5.-.-.- property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI [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." [EC:6.-.-.-] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_prokaryote subset: goslim_yeast synonym: "synthetase activity" EXACT [GOC:jh2] xref: EC:6.-.-.- is_a: GO:0003824 ! catalytic activity property_value: exactMatch http://purl.uniprot.org/enzyme/6.-.-.- property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19380" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI [Term] id: GO:0016942 name: insulin-like growth factor binding protein complex namespace: cellular_component def: "A complex of proteins which includes the insulin-like growth factor (IGF) and a number of IGF-binding proteins. The complex plays a role in growth and development." [GOC:jl] subset: goslim_pir synonym: "IGF binding protein complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005576 ! extracellular region [Term] id: GO:0017053 name: transcription repressor complex namespace: cellular_component alt_id: GO:0090568 alt_id: GO:0090569 def: "A protein complex that possesses activity that prevents or downregulates transcription." [GOC:mah] subset: goslim_pir synonym: "cytoplasmic transcriptional repressor complex" RELATED [] synonym: "nuclear transcriptional repressor complex" RELATED [] synonym: "transcription factor inhibitor complex" EXACT [GOC:bhm] synonym: "transcriptional repressor complex" EXACT [] is_a: GO:0005667 ! transcription regulator complex created_by: tb creation_date: 2014-05-09T13:23:51Z [Term] id: GO:0019213 name: deacetylase activity namespace: molecular_function def: "Catalysis of the hydrolysis of an acetyl group from a substrate molecule." [GOC:jl] subset: goslim_pir xref: Reactome:R-HSA-5689000 "AADAC deacetylates PHEN" is_a: GO:0003824 ! catalytic activity property_value: broadMatch http://purl.uniprot.org/enzyme/2.3.1.- property_value: broadMatch http://purl.uniprot.org/enzyme/3.1.1.- property_value: broadMatch http://purl.uniprot.org/enzyme/3.5.1.- property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28920" xsd:anyURI [Term] id: GO:0019239 name: deaminase activity namespace: molecular_function def: "Catalysis of the removal of an amino group from a substrate, producing a substituted or nonsubstituted ammonia (NH4+/NH2R)." [GOC:jl] subset: goslim_pir xref: Reactome:R-HSA-74241 "ADA catalyzes the deamination of (deoxy)adenosine" xref: Reactome:R-HSA-9734745 "Defective ADA does not deaminate (deoxy)adenosine" xref: Reactome:R-HSA-9754964 "ADA deamidates RBV" is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0019538 name: protein metabolic process namespace: biological_process alt_id: GO:0006411 alt_id: GO:0044267 alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_flybase_ribbon subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon synonym: "cellular protein metabolic process" EXACT [] synonym: "cellular protein metabolism" EXACT [] synonym: "multicellular organismal protein metabolic process" NARROW [] synonym: "protein metabolic process and modification" EXACT [] synonym: "protein metabolism" EXACT [] synonym: "protein metabolism and modification" EXACT [] xref: Reactome:R-HSA-392499 "Metabolism of proteins" xref: Wikipedia:Protein_metabolism is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044238 ! primary metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI [Term] id: GO:0019748 name: secondary metabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." [GOC:curators] subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_pombe synonym: "secondary metabolism" EXACT [] synonym: "secondary metabolite metabolic process" EXACT [] synonym: "secondary metabolite metabolism" EXACT [] xref: Wikipedia:Secondary_metabolism is_a: GO:0008152 ! metabolic process [Term] id: GO:0019787 name: ubiquitin-like protein transferase activity namespace: molecular_function alt_id: GO:0008639 alt_id: GO:0008640 def: "Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y = Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein." [GOC:mah, GOC:rn, PMID:10806345, PMID:10884686] subset: goslim_drosophila subset: goslim_pir synonym: "E2" BROAD [] synonym: "E3" RELATED [GOC:dph] synonym: "small conjugating protein ligase activity" NARROW [GOC:dph] synonym: "small conjugating protein transferase activity" EXACT [GOC:dph] synonym: "small protein conjugating enzyme activity" NARROW [] synonym: "ubiquitin-like conjugating enzyme activity" NARROW [] synonym: "ubiquitin-like-protein ligase activity" NARROW [] xref: Reactome:R-HSA-5678490 "ATG16L1 complex transfers LC3 from ATG3 to PE" xref: Reactome:R-HSA-688137 "RIP2 is K63 polyubiquitinated" is_a: GO:0016740 ! transferase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24697" xsd:anyURI [Term] id: GO:0019814 name: immunoglobulin complex namespace: cellular_component def: "A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, GOC:jl, ISBN:0781765196] comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. subset: goslim_pir synonym: "antibody" NARROW [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0019825 name: oxygen binding namespace: molecular_function def: "Binding to oxygen (O2)." [GOC:jl] subset: goslim_pir subset: goslim_plant synonym: "cytochrome P450" NARROW [] synonym: "cytochrome P450 activity" RELATED [] is_a: GO:0005488 ! binding [Term] id: GO:0019840 name: isoprenoid binding namespace: molecular_function def: "Binding to an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [GOC:jl] subset: goslim_pir is_a: GO:0008289 ! lipid binding [Term] id: GO:0019842 name: vitamin binding namespace: molecular_function def: "Binding to a vitamin, one of 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." [GOC:ai] subset: goslim_metagenomics subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0020015 name: glycosome namespace: cellular_component def: "A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis." [GOC:mb] subset: goslim_pir xref: Wikipedia:Glycosome is_a: GO:0042579 ! microbody [Term] id: GO:0020022 name: acidocalcisome namespace: cellular_component def: "An electron-dense acidic membrane-bounded organelle which contains a matrix of pyrophosphate and polyphosphates with bound calcium and other cations." [GOC:mb] subset: goslim_pir synonym: "metachromatic granule" EXACT [PMID:15738951] synonym: "polyphosphate vacuole" RELATED [PMID:15738951] synonym: "volutin granule" EXACT [PMID:15738951] is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0022406 name: membrane docking namespace: biological_process def: "The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere." [GOC:isa_complete, PMID:27875684] subset: goslim_pir is_a: GO:0008150 ! biological_process [Term] id: GO:0022411 name: cellular component disassembly namespace: biological_process alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cell structure disassembly" EXACT [] synonym: "cellular component disassembly at cellular level" EXACT [] is_a: GO:0016043 ! cellular component organization disjoint_from: GO:0022607 ! cellular component assembly property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI [Term] id: GO:0022414 name: reproductive process namespace: biological_process alt_id: GO:0019952 alt_id: GO:0044702 alt_id: GO:0050876 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 subset: goslim_plant_ribbon synonym: "single organism reproductive process" RELATED [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process 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:0022607 name: cellular component assembly namespace: biological_process alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: gocheck_do_not_annotate subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon subset: goslim_pir synonym: "cell structure assembly" EXACT [] synonym: "cellular component assembly at cellular level" EXACT [] is_a: GO:0016043 ! cellular component organization relationship: part_of GO:0044085 ! cellular component biogenesis [Term] id: GO:0022900 name: electron transport chain namespace: biological_process def: "A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors." [GOC:mtg_electron_transport] subset: goslim_pir xref: Wikipedia:Electron_transport_chain is_a: GO:0006091 ! generation of precursor metabolites and energy property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21455" xsd:anyURI [Term] id: GO:0030076 name: light-harvesting complex namespace: cellular_component def: "A protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center." [GOC:lr] subset: goslim_pir synonym: "antenna complex" RELATED [] xref: Wikipedia:Light-harvesting_complex is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0110165 ! cellular anatomical structure [Term] id: GO:0030112 name: glycocalyx namespace: cellular_component def: "A carbohydrate rich layer at the outermost periphery of a cell." [GOC:krc, GOC:mlg, ISBN:0815316208, PMID:28876829] subset: goslim_pir xref: Wikipedia:Glycocalyx is_a: GO:0030312 ! external encapsulating structure [Term] id: GO:0030115 name: S-layer namespace: cellular_component def: "A crystalline protein layer surrounding some bacteria." [GOC:mlg, ISBN:0815108893] subset: goslim_pir xref: Wikipedia:S-layer is_a: GO:0030312 ! external encapsulating structure [Term] id: GO:0030119 name: AP-type membrane coat adaptor complex namespace: cellular_component def: "Any of several heterotetrameric complexes that link clathrin (or another coat-forming molecule, as hypothesized for AP-3 and AP-4) to a membrane surface; they are found on coated pits and coated vesicles, and mediate sorting of cargo proteins into vesicles. Each AP complex contains two large (a beta and one of either an alpha, gamma, delta, or epsilon) subunits (110-130 kDa), a medium (mu) subunit (approximately 50 kDa), and a small (sigma) subunit (15-20 kDa)." [GOC:mah, PMID:10611976, PMID:15473838] subset: goslim_pir synonym: "clathrin adaptor" RELATED [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0032991 ! protein-containing complex [Term] id: GO:0030175 name: filopodium namespace: cellular_component alt_id: GO:0030028 def: "Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft." [GOC:mah, GOC:pr, ISBN:0815316194] comment: A filopodium may be approximately 0.1 um wide, 5-10 um long, and up to 50 um long in axon growth cones; contain a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward. Note that filopodia on dendritic shafts are distinct from other types of filopodia (even those found in dendritic growth cones) and may react differently to stimuli, as shown in PMID:12904473. subset: goslim_pir xref: NIF_Subcellular:sao1046371754 xref: Wikipedia:Filopodia is_a: GO:0042995 ! cell projection relationship: has_part GO:0016020 ! membrane relationship: part_of GO:0005856 ! cytoskeleton [Term] id: GO:0030234 name: enzyme regulator activity namespace: molecular_function alt_id: GO:0010576 def: "A molecular function regulator that modulates a catalytic activity." [GOC:pdt] comment: This term should only be used in cases when the regulator directly interacts with the enzyme, but does not result in a covalent modification. subset: goslim_agr subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_yeast synonym: "catalytic regulator activity" EXACT [GOC:dph] synonym: "enzyme modulator" EXACT [] synonym: "metalloenzyme regulator activity" NARROW [] is_a: GO:0003674 ! molecular_function relationship: has_part GO:0005515 ! protein binding relationship: regulates GO:0003824 ! catalytic activity [Term] id: GO:0030246 name: carbohydrate binding namespace: molecular_function alt_id: GO:0005529 def: "Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates." [GOC:mah] subset: goslim_agr subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon synonym: "selectin" RELATED [] synonym: "sugar binding" EXACT [] is_a: GO:0005488 ! binding [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: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 is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005576 ! extracellular region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI [Term] id: GO:0030313 name: cell envelope namespace: cellular_component def: "An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present." [GOC:ds, GOC:mlg, http://pathmicro.med.sc.edu/fox/cell_envelope.htm] subset: goslim_pir xref: Wikipedia:Cell_envelope is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0016020 ! membrane [Term] id: GO:0030427 name: site of polarized growth namespace: cellular_component alt_id: GO:0000134 alt_id: GO:0030483 def: "Any part of a cell where non-isotropic growth takes place." [GOC:mah] subset: goslim_candida subset: goslim_pir subset: goslim_yeast is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0030428 name: cell septum namespace: cellular_component def: "A structure composed of peptidoglycan and often chitin in addition to other materials. It usually forms perpendicular to the long axis of a cell or hypha and grows centripetally from the cell wall to the center of the cell and often functions in the compartmentalization of a cell into two daughter cells." [GOC:clt, ISBN:0471940526] subset: goslim_pir synonym: "cross wall" EXACT [] synonym: "septum" BROAD [] is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0030431 name: sleep namespace: biological_process def: "Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain." [ISBN:0192800981] subset: goslim_pir synonym: "diapause" RELATED [] synonym: "dormancy" RELATED [] synonym: "lethargus" RELATED [] xref: Wikipedia:Sleep is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0030496 name: midbody namespace: cellular_component def: "A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis." [ISBN:0815316194] subset: goslim_pir xref: Wikipedia:Midbody_(cell_biology) is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0030532 name: small nuclear ribonucleoprotein complex namespace: cellular_component def: "A ribonucleoprotein complex that contains at least one RNA of the small nuclear RNA (snRNA) class and as well as its associated proteins. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP, U4/U6 snRNP, or 7SK snRNP. Many, of these complexes become part of the spliceosome involved in splicing of nuclear mRNAs. Others are involved in regulation of transcription elongation or 3'-end processing of replication-dependent histone pre-mRNAs." [GOC:krc, GOC:mah, ISBN:0879695897] subset: goslim_pir synonym: "small nuclear ribonucleoprotein" EXACT [] synonym: "snRNP" EXACT [] xref: Wikipedia:SnRNP is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0030677 name: ribonuclease P complex namespace: cellular_component def: "A ribonucleoprotein complex that catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs." [GOC:mah, PMID:12045094] comment: Note that chloroplasts possess a complex that is called 'RNase P' because it catalyzes pre-tRNA cleavage, but the chloroplast complex appears not to contain RNA. subset: goslim_pir synonym: "RNase P complex" EXACT [] is_a: GO:1990904 ! ribonucleoprotein complex [Term] id: GO:0030684 name: preribosome namespace: cellular_component def: "Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis." [PMID:10567516] subset: goslim_pir is_a: GO:1990904 ! ribonucleoprotein complex [Term] id: GO:0030689 name: Noc complex namespace: cellular_component def: "Any of several heterodimers containing one or two Noc proteins, associated with preribosomal complexes; involved in ribosome biogenesis." [PMID:12446671] comment: Noc complexes exhibit a dynamic intranuclear location; consider also annotating to 'nucleolus ; GO:0005730' and/or 'nucleoplasm ; GO:0005654'. Note that the definition uses Saccharomyces gene product names because this complex has only been described in Saccharomyces cerevisiae and no other names have yet arisen; the term nevertheless can be used for analogous complexes in other eukaryotes, and the definition can be changed if better wording is found. subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0030880 name: RNA polymerase complex namespace: cellular_component def: "Any complex that possesses RNA polymerase activity; generally comprises a catalytic subunit and one or more additional subunits." [GOC:mah] subset: goslim_pir synonym: "multisubunit RNA polymerase" EXACT [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0030894 name: replisome namespace: cellular_component def: "A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins." [GOC:mah, GOC:vw] subset: goslim_pir synonym: "DNA synthesome complex" RELATED [CORUM:1001] synonym: "RC complex" RELATED [CORUM:309, PMID:12006500] synonym: "replication-competent complex" RELATED [CORUM:309, PMID:12006500] xref: Wikipedia:Replisome is_a: GO:0032993 ! protein-DNA complex relationship: has_part GO:0033202 ! DNA helicase complex relationship: has_part GO:0042575 ! DNA polymerase complex relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0030904 name: retromer complex namespace: cellular_component def: "A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35." [GOC:bf, PMID:26220253, PMID:27385586, PMID:9700157] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [Term] id: GO:0030929 name: ADPG pyrophosphorylase complex namespace: cellular_component def: "Complex that possesses ADPG pyrophosphorylase activity. In all organisms where it has been found, the complex is a tetramer. In bacteria, it is a homotetramer. In plants, the complex is a heterotetramer composed small and large subunits." [GOC:tb, PMID:9680965] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0030964 name: NADH dehydrogenase complex namespace: cellular_component alt_id: GO:0030025 alt_id: GO:0030966 alt_id: GO:0031675 alt_id: GO:0031677 alt_id: GO:0031678 alt_id: GO:0045280 def: "An integral membrane complex that possesses NADH oxidoreductase activity. The complex is one of the components of the electron transport chain. It catalyzes the transfer of a pair of electrons from NADH to a quinone." [GOC:mah] comment: Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function possessed by this complex is represented by the molecular function term 'NADH dehydrogenase (quinone) activity ; GO:0050136'. subset: goslim_pir synonym: "NADH dehydrogenase complex (plastoquinone)" NARROW [] synonym: "NADH dehydrogenase complex (quinone)" NARROW [] synonym: "NADH dehydrogenase complex (ubiquinone)" NARROW [] synonym: "NADH:plastoquinone reductase complex" NARROW [] synonym: "plastid NADH dehydrogenase complex (plastoquinone)" NARROW [] xref: Wikipedia:NADH_dehydrogenase is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [Term] id: GO:0030990 name: intraciliary transport particle namespace: cellular_component def: "A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules." [GOC:cilia, GOC:kmv, PMID:14570576, PMID:22118932, PMID:23945166] comment: Note that we deem cilia and microtubule-based flagella to be equivalent. subset: goslim_pir synonym: "IFT complex" RELATED [] synonym: "intraflagellar transport complex" EXACT [] synonym: "intraflagellar transport particle" EXACT [] is_a: GO:0032991 ! protein-containing complex [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, PMID:21123617, PMID:28089324, PMID:33605520] subset: goslim_chembl subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon 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:0031023 name: microtubule organizing center 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 microtubule organizing center, a structure from which microtubules grow." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir synonym: "microtubule organising center organisation" EXACT [] synonym: "microtubule organizing center organization and biogenesis" RELATED [GOC:mah] is_a: GO:0016043 ! cellular component organization relationship: part_of GO:0006996 ! organelle organization [Term] id: GO:0031026 name: glutamate synthase complex namespace: cellular_component def: "A complex that possesses glutamate synthase activity." [GOC:mah] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0031049 name: programmed DNA elimination namespace: biological_process def: "A process in which genomic fragments or entire chromosomes are eliminated from somatic cells or from micronuclei of ciliates. This process occurs in the developing macronucleus (anlage) of a ciliate, as well as in other species, including vertebrates and is an irreversible mechanism of gene silencing." [GOC:mah, GOC:ns, PMID:18708581, PMID:24886889, PMID:32986476] subset: goslim_pir is_a: GO:0050789 ! regulation of biological process relationship: negatively_regulates GO:0009059 ! macromolecule biosynthetic process relationship: regulates GO:0009059 ! macromolecule biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22815" xsd:anyURI [Term] id: GO:0031074 name: nucleocytoplasmic transport complex namespace: cellular_component def: "Any complex that acts to move proteins or RNAs into or out of the nucleus through nuclear pores." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "nucleocytoplasmic shuttling complex" NARROW [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0031082 name: BLOC complex namespace: cellular_component def: "Any of several protein complexes required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes, platelet dense granules, and other related organelles; acronym for biogenesis of lysosomal-related organelles complex." [PMID:15102850, PMID:15261680] subset: goslim_pir synonym: "BLOC-1 related complex" EXACT [PMID:25898167] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0031094 name: platelet dense tubular network namespace: cellular_component def: "A network of membrane-bounded compartments found in blood platelets, where they regulate platelet activation by sequestering or releasing calcium. The dense tubular network exists as thin elongated membranes in resting platelets, and undergoes a major ultrastructural change, to a rounded vesicular form, upon addition of thrombin." [PMID:1322202] subset: goslim_pir is_a: GO:0043231 ! intracellular membrane-bounded organelle [Term] id: GO:0031105 name: septin complex namespace: cellular_component def: "A protein complex containing septins. Typically, these complexes contain multiple septins and are oligomeric." [GOC:mah, PMID:15385632] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005856 ! cytoskeleton [Term] id: GO:0031143 name: pseudopodium namespace: cellular_component def: "A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding." [ISBN:0198506732] subset: goslim_pir synonym: "axopodium" NARROW [] synonym: "lobopodium" NARROW [] synonym: "pseudopod" EXACT [] synonym: "pseudopodial protrusion" EXACT [] synonym: "reticulopodium" NARROW [] xref: Wikipedia:Pseudopod is_a: GO:0042995 ! cell projection relationship: has_part GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21139" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21141" xsd:anyURI [Term] id: GO:0031205 name: endoplasmic reticulum Sec complex namespace: cellular_component def: "An endoplasmic reticulum membrane-associated complex involved in the translocation of proteins that are targeted to the ER. In yeast, this complex consists of two subcomplexes, namely, the Sec61 complex and the Sec62/Sec63 complex." [GOC:mtg_sensu, PMID:14617809] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: has_part GO:0071256 ! translocon complex relationship: part_of GO:0005783 ! endoplasmic reticulum relationship: part_of GO:0016020 ! membrane [Term] id: GO:0031248 name: protein acetyltransferase complex namespace: cellular_component def: "A complex that catalyzes the transfer of an acetyl group to a protein acceptor molecule." [GOC:bf] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0031252 name: cell leading edge namespace: cellular_component def: "The area of a motile cell closest to the direction of movement." [GOC:pg] subset: goslim_pir synonym: "front of cell" EXACT [] synonym: "leading edge of cell" EXACT [] is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0031254 name: cell trailing edge namespace: cellular_component def: "The area of a motile cell opposite to the direction of movement." [GOC:pg] subset: goslim_pir synonym: "back of cell" EXACT [] synonym: "trailing edge" EXACT [] is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0031264 name: death-inducing signaling complex namespace: cellular_component def: "A protein complex formed by the association of signaling proteins with a death receptor upon ligand binding. The complex includes procaspases and death domain-containing proteins in addition to the ligand-bound receptor, and may control the activation of caspases 8 and 10." [GOC:mtg_apoptosis, PMID:12628743, PMID:12655293, PMID:8521815] comment: Gene products that may be annotated to this term include: 1) ligand-bound receptors such as FAS/CD95 (though care should be taken because FAS can also act as a non-apoptotic signal transducer); 2) signaling molecules such as FADD (FAS-associated protein with a death domain), cIAPs (cellular inhibitor of apoptosis proteins), c-FLIPs and caspases 8 and 10. subset: goslim_pir synonym: "death receptor-induced signaling complex" EXACT [] synonym: "death receptor-induced signalling complex" EXACT [] synonym: "death-inducing signalling complex" EXACT [] synonym: "DISC" EXACT [] synonym: "DISC protein complex" EXACT [] xref: Wikipedia:Death-inducing_signaling_complex is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [Term] id: GO:0031332 name: RNAi effector complex namespace: cellular_component def: "Any protein complex that mediates the effects of small interfering RNAs on gene expression. Most known examples contain one or more members of the Argonaute family of proteins." [GOC:mah, PMID:14704433] subset: goslim_pir is_a: GO:1990904 ! ribonucleoprotein complex [Term] id: GO:0031371 name: ubiquitin conjugating enzyme complex namespace: cellular_component def: "Any complex that possesses ubiquitin conjugating enzyme activity." [GOC:mah] subset: goslim_pir synonym: "E2 complex" RELATED [] is_a: GO:0032991 ! protein-containing complex [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 [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0031406 name: carboxylic acid binding namespace: molecular_function def: "Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:mah, ISBN:0198506732] subset: goslim_pir is_a: GO:0043167 ! ion binding [Term] id: GO:0031409 name: pigment binding namespace: molecular_function def: "Binding to a pigment, a general or particular coloring matter in living organisms, e.g. melanin." [GOC:mah] subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0031469 name: bacterial microcompartment namespace: cellular_component def: "An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy." [GOC:js, PMID:10498708, PMID:11844753, PMID:12923081, PMID:34058518, PMID:34340100] subset: goslim_pir synonym: "BAC" BROAD [] synonym: "BMC" BROAD [] synonym: "MCP" BROAD [] synonym: "polyhedral organelle" RELATED [] is_a: GO:0043232 ! intracellular membraneless organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16852" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22465" xsd:anyURI [Term] id: GO:0031501 name: mannosyltransferase complex namespace: cellular_component def: "A complex that possesses mannosyltransferase activity." [GOC:mah] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0031519 name: PcG protein complex namespace: cellular_component def: "A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure." [PMID:9372908] subset: goslim_pir synonym: "Polycomb Group protein complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0031640 name: killing of cells of another organism namespace: biological_process alt_id: GO:0001908 alt_id: GO:0051852 def: "Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." [GOC:add] subset: goslim_pir synonym: "killing of cells of other organism" EXACT [] is_a: GO:0001906 ! cell killing is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms [Term] id: GO:0031647 name: regulation of protein stability namespace: biological_process def: "Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation." [GOC:dph, GOC:mah, GOC:tb] subset: goslim_pir is_a: GO:0065008 ! regulation of biological quality [Term] id: GO:0031982 name: vesicle namespace: cellular_component alt_id: GO:0031988 def: "Any small, fluid-filled, spherical organelle enclosed by membrane." [GOC:mah, GOC:pz, GOC:vesicles] subset: goslim_pir synonym: "membrane-bounded vesicle" RELATED [] synonym: "membrane-enclosed vesicle" RELATED [] xref: NIF_Subcellular:sao221389602 xref: Wikipedia:Vesicle_(biology) is_a: GO:0043226 ! organelle relationship: has_part GO:0016020 ! membrane [Term] id: GO:0031992 name: energy transducer activity namespace: molecular_function def: "The biological transducer activity that accepts energy and converts it to another form, often by transfer to another molecule within the cell." [GOC:curators] subset: goslim_pir synonym: "light harvesting activity" RELATED [] synonym: "photon capture" RELATED [] is_a: GO:0060089 ! molecular transducer activity [Term] id: GO:0032059 name: bleb namespace: cellular_component def: "A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses." [GOC:mtg_apoptosis, PMID:12083798, PMID:16624291, Wikipedia:Bleb_(cell_biology)] subset: goslim_pir synonym: "plasma membrane bleb" EXACT [GOC:pr] xref: Wikipedia:Bleb_(cell_biology) is_a: GO:0042995 ! cell projection relationship: has_part GO:0016020 ! membrane [Term] id: GO:0032153 name: cell division site namespace: cellular_component def: "The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles." [GOC:bf, GOC:imk, GOC:krc, GOC:ns, PMID:12101122, PMID:15380095, PMID:16983191, PMID:18165305] comment: Note that this term refers to the future site of division in a cell that has not yet divided. subset: goslim_pir synonym: "cell division plane" EXACT [] is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0032179 name: germ tube namespace: cellular_component def: "The slender tubular outgrowth first produced by most spores in germination." [ISBN:0877799148] subset: goslim_pir xref: Wikipedia:Germ_tube is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0032196 name: transposition namespace: biological_process def: "Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites. For elements that are transcribed as the first step of transposition, the process starts with the transcription of the transposable element, its translation and maturation, and ending with integration into DNA. For elements that are cut out, the process starts with the excision of the donor DNA and integrated into another site." [ISBN:1555812090, PMID:14682279, PMID:25893143] subset: goslim_candida subset: goslim_chembl subset: goslim_pir subset: goslim_yeast xref: Wikipedia:Transposon is_a: GO:0008150 ! biological_process [Term] id: GO:0032300 name: mismatch repair complex namespace: cellular_component def: "Any complex formed of proteins that act in mismatch repair." [GOC:mah] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0110165 ! cellular anatomical structure [Term] id: GO:0032392 name: DNA geometric change namespace: biological_process def: "The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases." [GOC:mah] comment: Note that DNA geometric change and DNA topological change (GO:0006265) are distinct, but are usually coupled in vivo. subset: goslim_pir is_a: GO:0051276 ! chromosome organization [Term] id: GO:0032421 name: stereocilium bundle namespace: cellular_component def: "A bundle of cross-linked stereocilia, arranged around a kinocilium on the apical surface of a sensory hair cell (e.g. a neuromast, auditory or vestibular hair cell). Stereocilium bundles act as mechanosensory organelles by responding to fluid motion or fluid pressure changes." [GOC:ecd, PMID:15661519, PMID:7840137] subset: goslim_pir synonym: "stereocilia bundle" EXACT [] is_a: GO:0110165 ! cellular anatomical structure relationship: has_part GO:0043005 ! neuron projection [Term] id: GO:0032451 name: demethylase activity namespace: molecular_function def: "Catalysis of the removal of a methyl group from a substrate." [GOC:mah] subset: goslim_pir is_a: GO:0003824 ! catalytic activity [Term] id: GO:0032476 name: polyprenyl diphosphate synthase complex namespace: cellular_component def: "A complex that possesses polyprenyl diphosphate synthase activity involved in the synthesis of the isoprenoid chain of ubiquinone whose length varies between organisms." [GOC:mah, PMID:14519123, PMID:16262699] subset: goslim_pir synonym: "decaprenyl diphosphate synthase complex" NARROW [] is_a: GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26833" xsd:anyURI [Term] id: GO:0032501 name: multicellular organismal process namespace: biological_process alt_id: GO:0044707 alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI created_by: jl creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_flybase_ribbon subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2012-12-19T12:21:31Z [Term] id: GO:0032989 name: cellular anatomical entity morphogenesis namespace: biological_process def: "The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system." [GOC:dph, GOC:mah, GOC:tb] subset: goslim_pir synonym: "cellular component morphogenesis" EXACT [] synonym: "cellular structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0016043 ! cellular component organization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25496" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26249" xsd:anyURI [Term] id: GO:0032991 name: protein-containing complex namespace: cellular_component alt_id: GO:0043234 def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr subset: goslim_chembl subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_mouse subset: goslim_pir synonym: "macromolecular complex" EXACT [] synonym: "macromolecule complex" EXACT [] synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component [Term] id: GO:0032993 name: protein-DNA complex namespace: cellular_component def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. subset: goslim_pir synonym: "DNA-protein complex" EXACT [GOC:mah] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0032997 name: Fc receptor complex namespace: cellular_component def: "A protein complex composed of a subunit or subunits capable of binding the Fc portion of an immunoglobulin with additional signaling components. The complex functions as a receptor for immunoglobulin." [GOC:add, ISBN:0781735149] subset: goslim_pir synonym: "Fc-receptor complex" EXACT [] synonym: "FcR complex" EXACT [] synonym: "immunoglobulin receptor complex" BROAD [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [Term] id: GO:0033061 name: DNA recombinase mediator complex namespace: cellular_component def: "A protein complex containing accessory proteins which bind a recombinase (e.g. Rad51) and bind single-stranded DNA (ssDNA), and promote nucleation of the recombinase onto ssDNA through facilitating recombinase-RPA exchange." [GOC:elh, GOC:mah, GOC:vw, InterPro:IPR003488, PMID:12912992, PMID:32414915] comment: Many paralogs of Rad51 act as recombinase mediators. These paralogs dimerize (or occasionally form tetramers) amongst themselves to form complexes with ssDNA-binding activity, and which act as mediators of Rad51 presynaptic filament assembly. subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0033099 name: attachment organelle namespace: cellular_component def: "A membrane-bounded extension of the cell, originally characterized in Mycoplasma species, that contains an electron-dense core that is part of the cytoskeleton and is oriented lengthwise and ends distally in a bulbous knob (terminal button). Required for adherence to host cells and involved in gliding motility and cell division." [PMID:11325545, PMID:12003948] subset: goslim_pir is_a: GO:0043231 ! intracellular membrane-bounded organelle [Term] id: GO:0033202 name: DNA helicase complex namespace: cellular_component def: "A protein complex that possesses DNA helicase activity." [GOC:mah] subset: goslim_metagenomics subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0033256 name: I-kappaB/NF-kappaB complex namespace: cellular_component def: "A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm." [GOC:bf, GOC:mah, PMID:9407099] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0035097 name: histone methyltransferase complex namespace: cellular_component def: "A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins." [GOC:bf] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0035230 name: cytoneme namespace: cellular_component def: "A long, thin, polarized cell projection that contains actin and can extend for distances many times the diameter of the cell. Cytonemes represent extensions of cell cytoplasm and typically have a diameter of approximately 0.2um." [PMID:10367889, PMID:10675901] subset: goslim_pir synonym: "membrane nanotube" EXACT [Wikipedia:Membrane_nanotube] xref: Wikipedia:Membrane_nanotube is_a: GO:0042995 ! cell projection relationship: has_part GO:0016020 ! membrane [Term] id: GO:0035273 name: phthalate binding namespace: molecular_function def: "Binding to a phthalate, any ester or salt of phthalic acid." [PMID:31116073] subset: goslim_pir is_a: GO:0031406 ! carboxylic acid binding [Term] id: GO:0036211 name: protein modification process namespace: biological_process alt_id: GO:0006464 def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:bf, GOC:jl] subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_chembl subset: goslim_pir subset: goslim_plant subset: goslim_prokaryote synonym: "cellular protein modification process" EXACT [] synonym: "process resulting in protein modification" EXACT [] synonym: "protein modification" EXACT [GOC:bf] is_a: GO:0019538 ! protein metabolic process is_a: GO:0043412 ! macromolecule modification property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI created_by: bf creation_date: 2012-04-26T01:47:12Z [Term] id: GO:0038023 name: signaling receptor activity namespace: molecular_function alt_id: GO:0004872 alt_id: GO:0019041 def: "Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:bf, GOC:signaling] subset: goslim_agr subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon synonym: "receptor activity" BROAD [] synonym: "receptor activity involved in signal transduction" EXACT [GOC:bf] synonym: "signalling receptor activity" EXACT [] is_a: GO:0060089 ! molecular transducer activity created_by: bf creation_date: 2011-08-01T02:45:27Z [Term] id: GO:0040007 name: growth namespace: biological_process alt_id: GO:0048590 def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] comment: See also the biological process term 'cell growth ; GO:0016049'. subset: gocheck_do_not_annotate subset: goslim_chembl subset: goslim_pir subset: goslim_plant synonym: "growth pattern" RELATED [] synonym: "non-developmental growth" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process [Term] id: GO:0040011 name: locomotion namespace: biological_process def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh] subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process [Term] id: GO:0042044 name: fluid transport namespace: biological_process def: "The directed movement of substances that are in liquid form in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir is_a: GO:0006810 ! transport [Term] id: GO:0042056 name: chemoattractant activity namespace: molecular_function def: "Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal." [GOC:curators, ISBN:0198506732] subset: goslim_chembl subset: goslim_pir synonym: "attractant" BROAD [] is_a: GO:0003674 ! molecular_function relationship: has_part GO:0005515 ! protein binding relationship: part_of GO:0007154 ! cell communication relationship: part_of GO:0040011 ! locomotion relationship: part_of GO:0050789 ! regulation of biological process relationship: part_of GO:0050896 ! response to stimulus relationship: positively_regulates GO:0038023 ! signaling receptor activity relationship: regulates GO:0038023 ! signaling receptor activity [Term] id: GO:0042180 name: ketone metabolic process namespace: biological_process def: "The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:jl, ISBN:0787650153] subset: goslim_pir synonym: "ketone metabolism" EXACT [] is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI [Term] id: GO:0042254 name: ribosome biogenesis namespace: biological_process alt_id: GO:0007046 def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis." [GOC:ma, PMID:26404467, Wikipedia:Ribosome_biogenesis] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "ribosome biogenesis and assembly" EXACT [] is_a: GO:0044085 ! cellular component biogenesis [Term] id: GO:0042277 name: peptide binding namespace: molecular_function def: "Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds." [GOC:jl] subset: goslim_chembl subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0042303 name: molting cycle namespace: biological_process def: "The periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin, etc." [GOC:jl, ISBN:0198506732] subset: goslim_drosophila subset: goslim_pir is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0042440 name: pigment metabolic process namespace: biological_process def: "The chemical reactions and pathways involving pigment, any general or particular coloring matter in living organisms, e.g. melanin." [GOC:jl, ISBN:0198506732] subset: goslim_drosophila subset: goslim_pir synonym: "pigment metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0042445 name: hormone metabolic process namespace: biological_process alt_id: GO:0034754 def: "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." [GOC:jl] subset: goslim_pir synonym: "cellular hormone metabolic process" RELATED [] synonym: "hormone metabolism" EXACT [] is_a: GO:0008152 ! metabolic process is_a: GO:0065008 ! regulation of biological quality property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23965" xsd:anyURI [Term] id: GO:0042562 name: hormone binding namespace: molecular_function def: "Binding to an hormone, a naturally occurring substance secreted by specialized cells that affect the metabolism or behavior of cells possessing functional receptors for the hormone. Hormones may be produced by the same, or different, cell as express the receptor." [GOC:jl] subset: goslim_chembl subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0042566 name: hydrogenosome namespace: cellular_component def: "A spherical, membrane-bounded organelle found in some anaerobic protozoa, which participates in ATP and molecular hydrogen formation." [GOC:jl, PMID:11197234, PMID:11293569] subset: goslim_pir xref: Wikipedia:Hydrogenosome is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0042575 name: DNA polymerase complex namespace: cellular_component def: "A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA." [GOC:jl, PMID:12045093] subset: goslim_metagenomics subset: goslim_pir is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0042579 name: microbody namespace: cellular_component def: "Cytoplasmic organelles, spherical or oval in shape, that are bounded by a single membrane and contain oxidative enzymes, especially those utilizing hydrogen peroxide (H2O2)." [ISBN:0198506732] subset: goslim_pir xref: Wikipedia:Microbody is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0042597 name: periplasmic space namespace: cellular_component alt_id: GO:0005620 def: "The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria)." [GOC:curators, GOC:md] subset: goslim_metagenomics subset: goslim_pir subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "periplasm" EXACT [] is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0005576 ! extracellular region property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI [Term] id: GO:0042600 name: egg chorion namespace: cellular_component def: "A protective, noncellular membrane that surrounds the eggs of various animals including insects and fish." [GOC:jl, ISBN:0721662544] comment: Note that this term does not refer to the extraembryonic membrane surrounding the embryo of amniote vertebrates as this is an anatomical structure and is therefore not covered by GO. subset: goslim_pir is_a: GO:0030312 ! external encapsulating structure [Term] id: GO:0042611 name: MHC protein complex namespace: cellular_component def: "A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen." [GOC:add, GOC:jl, ISBN:0781735149, PMID:15928678, PMID:16153240] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [Term] id: GO:0042620 name: poly(3-hydroxyalkanoate) metabolic process namespace: biological_process def: "The chemical reactions and pathways involving poly(3-hydroxyalkanoates), polyesters of 3-hydroxyacids produced as intracellular granules by a large variety of bacteria." [GOC:jl, PMID:9925580] subset: goslim_pir synonym: "PHA metabolic process" BROAD [] synonym: "PHA metabolism" BROAD [] synonym: "poly(3-hydroxyalkanoate) metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0042710 name: biofilm formation namespace: biological_process def: "A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription." [GOC:di, PMID:11932229] subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_pir xref: Reactome:R-HSA-9931953 "Biofilm formation" is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17727" xsd:anyURI [Term] id: GO:0042810 name: pheromone metabolic process namespace: biological_process def: "The chemical reactions and pathways involving pheromones, a substance that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process." [ISBN:0198506732] subset: goslim_pir synonym: "pheromone metabolism" EXACT [] is_a: GO:0019748 ! secondary metabolic process is_a: GO:0042445 ! hormone metabolic process [Term] id: GO:0042824 name: MHC class I peptide loading complex namespace: cellular_component def: "A large, multisubunit complex which consists of the MHC class I-beta 2 microglobulin dimer, the transporter associated with antigen presentation (TAP), tapasin (an MHC-encoded membrane protein), the chaperone calreticulin and the thiol oxidoreductase ERp57. Functions in the assembly of peptides with newly synthesized MHC class I molecules." [GOC:jl, PMID:10631934] comment: Note that although this complex is located in the endoplasmic reticulum, there is some evidence that it may also be found in the Golgi. subset: goslim_pir synonym: "peptide-loading complex" EXACT [GOC:bhm] synonym: "PLC" RELATED [GOC:bhm] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005783 ! endoplasmic reticulum relationship: part_of GO:0016020 ! membrane [Term] id: GO:0042908 name: xenobiotic transport namespace: biological_process alt_id: GO:0015893 def: "The directed movement of a xenobiotic into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:curators, GOC:krc] subset: goslim_pir synonym: "drug transport" RELATED [] is_a: GO:0006810 ! transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19460" xsd:anyURI [Term] id: GO:0042995 name: cell projection namespace: cellular_component def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917] subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_mouse subset: goslim_pir subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] is_a: GO:0110165 ! cellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23013" xsd:anyURI [Term] id: GO:0043005 name: neuron projection namespace: cellular_component def: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, PMID:3077060] subset: goslim_pir synonym: "nerve fiber" RELATED [GOC:dph] synonym: "neurite" NARROW [] synonym: "neuron process" EXACT [] synonym: "neuron protrusion" EXACT [NIF_Subcellular:sao250931889] synonym: "neuronal cell projection" EXACT [] xref: NIF_Subcellular:sao867568886 is_a: GO:0042995 ! cell projection relationship: has_part GO:0016020 ! membrane [Term] id: GO:0043021 name: ribonucleoprotein complex binding namespace: molecular_function def: "Binding to a complex of RNA and protein." [GOC:bf, GOC:curators, GOC:vk] subset: goslim_pir synonym: "protein-RNA complex binding" EXACT [GOC:bf, GOC:vk] synonym: "ribonucleoprotein binding" EXACT [GOC:bf, GOC:vk] synonym: "RNP binding" EXACT [] is_a: GO:0005488 ! binding [Term] id: GO:0043025 name: neuronal cell body namespace: cellular_component def: "The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites." [GOC:curators] comment: Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections. subset: goslim_pir synonym: "neuron cell body" EXACT [] synonym: "neuronal cell soma" EXACT [] xref: NIF_Subcellular:sao1044911821 xref: Wikipedia:Soma_(biology) is_a: GO:0110165 ! cellular anatomical structure relationship: part_of GO:0110165 ! cellular anatomical structure [Term] id: GO:0043033 name: isoamylase complex namespace: cellular_component def: "A protein complex whose composition varies amongst species; in rice it probably exists in a homo-tetramer to homo-hexamer form and in Gram-negative bacteria as a dimer. Functions in the hydrolysis of alpha-(1,6)-D-glucosidic branch linkages." [GOC:jl, PMID:10333591] subset: goslim_pir synonym: "debranching enzyme complex" BROAD [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0043062 name: extracellular structure organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir subset: goslim_prokaryote synonym: "extracellular structure organisation" EXACT [] synonym: "extracellular structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization [Term] id: GO:0043094 name: metabolic compound salvage namespace: biological_process def: "Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells." [GOC:mlg] subset: goslim_pir is_a: GO:0008152 ! metabolic process [Term] id: GO:0043101 name: purine-containing compound salvage namespace: biological_process def: "Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis." [GOC:jl] subset: goslim_pir synonym: "purine salvage" RELATED [] xref: Reactome:R-HSA-74217 "Purine salvage" is_a: GO:0043094 ! metabolic compound salvage [Term] id: GO:0043163 name: cell envelope 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 the cell envelope, everything external to, but not including, the cytoplasmic membrane of bacteria, encompassing the periplasmic space, cell wall, and outer membrane if present." [GOC:jl] subset: goslim_pir synonym: "cell envelope organisation" EXACT [] synonym: "cell envelope organization and biogenesis" RELATED [GOC:mah] is_a: GO:0045229 ! external encapsulating structure organization [Term] id: GO:0043167 name: ion binding namespace: molecular_function def: "Binding to an ion, a charged atoms or groups of atoms." [GOC:jl] subset: gocheck_do_not_annotate subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_yeast synonym: "atom binding" RELATED [] is_a: GO:0005488 ! binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI [Term] id: GO:0043170 name: macromolecule metabolic process namespace: biological_process alt_id: GO:0034960 alt_id: GO:0043283 alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule metabolism" EXACT [] synonym: "multicellular organismal macromolecule metabolic process" NARROW [] synonym: "organismal macromolecule metabolism" EXACT [] is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI [Term] id: GO:0043176 name: amine binding namespace: molecular_function def: "Binding to an amine, a weakly basic organic compound that contains an amino or a substituted amino group." [GOC:jl] subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0043178 name: alcohol binding namespace: molecular_function def: "Binding to an alcohol, any of a class of alkyl compounds containing a hydroxyl group." [GOC:jl, ISBN:0198506732] subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0043190 name: ATP-binding cassette (ABC) transporter complex namespace: cellular_component alt_id: GO:0043191 alt_id: GO:0043192 def: "A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter." [GOC:jl, GOC:mtg_sensu, PMID:11421269, PMID:15111107] subset: goslim_metagenomics subset: goslim_pir synonym: "ABC-type efflux permease complex" NARROW [] synonym: "ABC-type efflux porter complex" NARROW [] synonym: "ABC-type uptake permease complex" NARROW [] synonym: "mating pheromone exporter" NARROW [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [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:curators] subset: goslim_chembl subset: goslim_generic subset: goslim_pir subset: goslim_prokaryote subset: goslim_prokaryote_ribbon xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:curators] subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0043226 ! organelle relationship: part_of GO:0110165 ! cellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043230 name: extracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi." [GOC:jl, PMID:9914479] subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005576 ! extracellular region relationship: part_of GO:0005576 ! extracellular region [Term] id: GO:0043231 name: intracellular membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:curators] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "intracellular membrane-enclosed organelle" EXACT [] is_a: GO:0043229 ! intracellular organelle relationship: has_part GO:0016020 ! membrane [Term] id: GO:0043232 name: intracellular membraneless organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:curators] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "intracellular non-membrane-bounded organelle" EXACT [] synonym: "intracellular non-membrane-enclosed organelle" EXACT [] is_a: GO:0043229 ! intracellular organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29106" xsd:anyURI [Term] id: GO:0043235 name: signaling receptor complex namespace: cellular_component def: "Any protein complex that binds a signaling molecule such as a hormone, neurotransmitter, molecular pattern recognition receptor (PAMPs and DAMPS), or an intracellular messenger to initiate a change in cell function." [GOC:curators] subset: goslim_pir synonym: "receptor complex" BROAD [] is_a: GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31605" xsd:anyURI [Term] id: GO:0043256 name: laminin trimer namespace: cellular_component def: "A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural scaffolding of basement membranes." [PMID:15979864, PMID:21421915, PMID:23263632] subset: goslim_pir synonym: "laminin complex" BROAD [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0031012 ! extracellular matrix property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30807" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31490" xsd:anyURI [Term] id: GO:0043364 name: glycyl-radical enzyme activating activity namespace: molecular_function def: "Catalyzes the activation of an enzyme by generating an organic free radical on a glycine residue via a homolytic cleavage of S-adenosyl-L-methionine (SAM)." [GOC:jl, PMID:24486374] subset: goslim_pir synonym: "catalysis of free radical formation" BROAD [] xref: RHEA:19225 xref: RHEA:61976 is_a: GO:0016491 ! oxidoreductase activity property_value: exactMatch http://rdf.rhea-db.org/61976 property_value: narrowMatch http://rdf.rhea-db.org/19225 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14190" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30701" xsd:anyURI [Term] id: GO:0043412 name: macromolecule modification namespace: biological_process def: "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties." [GOC:curators] subset: gocheck_obsoletion_candidate subset: goslim_pir is_a: GO:0043170 ! macromolecule metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI [Term] id: GO:0043473 name: pigmentation namespace: biological_process def: "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." [GOC:jl] subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process [Term] id: GO:0043500 name: muscle adaptation namespace: biological_process def: "A process in which muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." [GOC:mtg_muscle, PMID:11181628, PMID:11449884, PMID:12605307] subset: goslim_pir synonym: "muscle plasticity" RELATED [] is_a: GO:0032501 ! multicellular organismal process is_a: GO:0050896 ! response to stimulus [Term] id: GO:0043511 name: inhibin complex namespace: cellular_component def: "Heterodimeric hormone composed of an inhibin alpha subunit complexed with either an inhibin beta-A subunit, to form inhibin A, or an inhibin beta-B subunit, to form inhibin B." [GOC:jl] comment: Note that the actions of the inhibin complex are the opposite of those of the activin complex, which is a dimer of an inhibin beta-A and/or inhibin beta-B subunit. See also the cellular component term 'activin complex ; GO:0048180'. subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005576 ! extracellular region [Term] id: GO:0043527 name: tRNA methyltransferase complex namespace: cellular_component def: "A multimeric protein complex involved in the methylation of specific nucleotides in tRNA." [GOC:jl, PMID:24904644, PMID:9851972] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0110165 ! cellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27929" xsd:anyURI [Term] id: GO:0043591 name: endospore external encapsulating structure namespace: cellular_component alt_id: GO:0055030 def: "The structures that lie outside the inner membrane and surround the entire endospore; consists of a peptidoglycan-containing inner layer (the endospore cortex) surrounded by a multilayered proteinaceous coat. An exosporium may be present as an extreme outer layer." [GOC:curators, PMID:15035041] subset: goslim_pir synonym: "endospore wall" EXACT [GOC:mah] synonym: "peptidoglycan-based spore wall" EXACT [GOC:mtg_sensu] synonym: "spore wall" BROAD [GOC:mtg_sensu] is_a: GO:0005618 ! cell wall [Term] id: GO:0044085 name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI [Term] id: GO:0044238 name: primary metabolic process namespace: biological_process def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:curators] subset: gocheck_do_not_annotate subset: goslim_euk_cellular_processes_ribbon subset: goslim_pir subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "primary metabolism" EXACT [] xref: Reactome:R-HSA-71291 "Metabolism of amino acids and derivatives" xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI [Term] id: GO:0044419 name: biological process involved in interspecies interaction between organisms namespace: biological_process def: "Any process evolved to enable an interaction with an organism of a different species." [GOC:cc] subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] xref: Reactome:R-HSA-9824443 "Parasitic Infection Pathways" is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] id: GO:0044423 name: virion component namespace: cellular_component alt_id: GO:0019012 def: "Any constituent part of a virion, a complete fully infectious extracellular virus particle." [GOC:jl] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir synonym: "complete virus particle" RELATED [] synonym: "virion" RELATED [] synonym: "virion part" EXACT [] xref: Wikipedia:Virus is_a: GO:0005575 ! cellular_component disjoint_from: GO:0110165 ! cellular anatomical structure [Term] id: GO:0045177 name: apical part of cell namespace: cellular_component def: "The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue." [GOC:mah, ISBN:0815316194] subset: goslim_pir synonym: "apical region of cell" EXACT [GOC:krc] is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0045178 name: basal part of cell namespace: cellular_component def: "The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue." [GOC:mah, ISBN:0815316194] subset: goslim_pir is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0045182 name: translation regulator activity namespace: molecular_function def: "Any molecular function involved in the regulation of initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai] subset: goslim_candida subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon is_a: GO:0003674 ! molecular_function relationship: part_of GO:0050789 ! regulation of biological process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29089" xsd:anyURI [Term] id: GO:0045202 name: synapse namespace: cellular_component def: "The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." [GOC:aruk, ISBN:0198506732, PMID:24619342, PMID:29383328, PMID:31998110] subset: goslim_agr subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon subset: goslim_mouse subset: goslim_pir subset: goslim_synapse synonym: "electrotonic synapse" RELATED [NIF_Subcellular:sao1311109124] synonym: "mixed synapse" NARROW [NIF_Subcellular:sao1506103497] synonym: "synaptic junction" EXACT [] xref: NIF_Subcellular:sao914572699 xref: Wikipedia:Chemical_synapse is_a: GO:0110165 ! cellular anatomical structure [Term] id: GO:0045229 name: external encapsulating structure organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir synonym: "external encapsulating structure organisation" EXACT [] synonym: "external encapsulating structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization [Term] id: GO:0045230 name: capsule 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 the capsule, a protective structure surrounding some species of bacteria and fungi." [GOC:ai] subset: goslim_pir synonym: "capsule organisation" EXACT [] synonym: "capsule organization and biogenesis" RELATED [] is_a: GO:0045229 ! external encapsulating structure organization [Term] id: GO:0045231 name: slime layer 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 slime layer. A slime layer is an easily removed, diffuse, unorganized layer of extracellular material that surrounds a cell." [GOC:ai] subset: goslim_pir synonym: "slime layer organisation" EXACT [] synonym: "slime layer organization and biogenesis" RELATED [GOC:mah] is_a: GO:0045229 ! external encapsulating structure organization [Term] id: GO:0045239 name: tricarboxylic acid cycle heteromeric enzyme complex namespace: cellular_component def: "Any of the heteromeric enzymes that act in the TCA cycle." [GOC:mah] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "TCA cycle enzyme complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0045251 name: electron transfer flavoprotein complex namespace: cellular_component def: "A protein complex facilitating the electron transfer from an acyl-CoA molecule to ubiquinone via its flavin adenine dinucleotide (FAD) cofactor. Usually contains an alpha and a beta subunit and the structural cofactor adenosine monophosphate (AMP). Part of a system that oxidizes an acyl-CoA molecule and reduces ubiquinone and other acceptors in the electron transport system." [GOC:bhm, ISBN:0198506732] subset: goslim_pir synonym: "ETF complex" EXACT [GOC:bhm] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0045252 name: oxoglutarate dehydrogenase complex namespace: cellular_component def: "A multi-enzyme complex that catalyzes the oxidative decarboxylation of alpha-ketoglutarate (also known as 2-oxoglutarate) to form succinyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present." [PMID:10672230] comment: The catalytic activities of the individual components of this complex are represented by the molecular function terms 'oxoglutarate dehydrogenase (succinyl-transferring) activity ; GO:0004591' (E1), 'dihydrolipoyllysine-residue succinyltransferase activity ; GO:0004149' (E2), and 'dihydrolipoyl dehydrogenase activity ; GO:0004148' (E3). subset: goslim_pir synonym: "alpha-ketoglutarate dehydrogenase complex" EXACT [] synonym: "dihydrolipoamide S-succinyltransferase complex" EXACT [] synonym: "KGDHC" EXACT [] xref: Wikipedia:Oxoglutarate_dehydrogenase_complex is_a: GO:0045239 ! tricarboxylic acid cycle heteromeric enzyme complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26122" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26881" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29951" xsd:anyURI [Term] id: GO:0045253 name: pyruvate dehydrogenase (lipoamide) phosphatase complex namespace: cellular_component def: "A complex of a regulatory and catalytic subunit that catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex." [PMID:9395502] comment: See also the cellular component term 'cytosolic pyruvate dehydrogenase complex ; GO:0045250'. subset: goslim_pir is_a: GO:0008287 ! protein serine/threonine phosphatase complex relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0045254 name: pyruvate dehydrogenase complex namespace: cellular_component alt_id: GO:0009364 def: "A multi-enzyme complex that catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: pyruvate dehydrogenase (E1, which may be a homodimer or a heterotetramer of two alpha and two beta subunits, depending on species), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present." [PMID:36863425] comment: The catalytic activities of the individual components of this complex are represented by the molecular function terms 'pyruvate dehydrogenase (acetyl-transferring) activity ; GO:0004739' (E1), 'dihydrolipoyllysine-residue acetyltransferase activity ; GO:0004742' (E2), and 'dihydrolipoyl dehydrogenase activity ; GO:0004148' (E3). subset: goslim_pir synonym: "pyruvate dehydrogenase complex (lipoamide)" EXACT [] xref: Wikipedia:Pyruvate_dehydrogenase_complex is_a: GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24350" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26122" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26881" xsd:anyURI [Term] id: GO:0045273 name: respiratory chain complex II (succinate dehydrogenase) namespace: cellular_component def: "A part of the respiratory chain, containing the four polypeptide subunits of succinate dehydrogenase, flavin-adenine dinucleotide and iron-sulfur. Catalyzes the oxidation of succinate by ubiquinone. Connects the TCA cycle with the respiratory chain." [ISBN:0198547684] subset: goslim_pir synonym: "electron transport complex II" RELATED [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27253" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28017" xsd:anyURI [Term] id: GO:0045275 name: respiratory chain complex III namespace: cellular_component alt_id: GO:0032842 alt_id: GO:0045285 def: "A protein complex that transfers electrons from ubiquinol to cytochrome c and translocates two protons across a membrane. The complex contains a core structure of three catalytic subunits: cytochrome b, the Rieske iron sulfur protein (ISP), and cytochrome c1, which are arranged in an integral membrane-bound dimeric complex; additional subunits are present, and vary among different species." [PMID:16228398, PMID:16352458, PMID:17200733] subset: goslim_pir synonym: "coenzyme Q-cytochrome c oxidoreductase complex" RELATED [] synonym: "coenzyme Q-cytochrome c reductase complex" RELATED [] synonym: "complex III" EXACT [] synonym: "CoQH2-cytochrome c reductase complex" RELATED [] synonym: "cytochrome bc(1) complex" EXACT [] synonym: "cytochrome bc1 complex" EXACT [] synonym: "electron transport complex III" RELATED [] synonym: "ubiquinol-cytochrome c oxidoreductase complex" EXACT [] synonym: "ubiquinol-cytochrome-c reductase complex" EXACT [] xref: Wikipedia:Coenzyme_Q_-_cytochrome_c_reductase is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane [Term] id: GO:0045277 name: respiratory chain complex IV namespace: cellular_component alt_id: GO:0045287 def: "A part of the respiratory chain, containing the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2)." [ISBN:0198547684] subset: goslim_pir synonym: "cytochrome c oxidase complex" EXACT [] synonym: "electron transport complex IV" RELATED [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0016020 ! membrane property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27727" xsd:anyURI [Term] id: GO:0045293 name: mRNA editing complex namespace: cellular_component def: "A protein complex that posttranscriptionally catalyzes insertion, deletion or substitution of nucleotides at multiple sites within nascent mRNA transcripts to produce mature mRNAs in eukaryotes." [PMID:11564867, PMID:12139607, PMID:24316715] subset: goslim_pir synonym: "editosome" EXACT [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0045333 name: cellular respiration namespace: biological_process def: "The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration)." [GOC:das, ISBN:0140513590, ISBN:0198506732] subset: goslim_candida subset: goslim_pir subset: goslim_yeast synonym: "oxidative metabolic process" EXACT [] synonym: "oxidative metabolism" EXACT [] synonym: "respiration" BROAD [] xref: Wikipedia:Cellular_respiration is_a: GO:0006091 ! generation of precursor metabolites and energy [Term] id: GO:0045478 name: fusome 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 the fusome, a large intracellular spectrin-rich structure found in insect germline cells and mammalian hematopoietic cells." [GOC:curators, GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir synonym: "fusome organisation" EXACT [] synonym: "fusome organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization is_a: GO:0022414 ! reproductive process [Term] id: GO:0045499 name: chemorepellent activity namespace: molecular_function def: "Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a lower concentration of that signal." [GOC:ai] subset: goslim_pir synonym: "chemorepellant activity" EXACT [] is_a: GO:0003674 ! molecular_function relationship: has_part GO:0005515 ! protein binding relationship: part_of GO:0007154 ! cell communication relationship: part_of GO:0040011 ! locomotion relationship: part_of GO:0050789 ! regulation of biological process relationship: part_of GO:0050896 ! response to stimulus relationship: positively_regulates GO:0038023 ! signaling receptor activity relationship: regulates GO:0038023 ! signaling receptor activity [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 [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0046490 name: isopentenyl diphosphate metabolic process namespace: biological_process def: "The chemical reactions and pathways involving isopentenyl diphosphate, an isomer of dimethylallyl diphosphate and the key precursor of all isoprenoids." [ISBN:0198506732] subset: goslim_pir synonym: "IPP metabolic process" EXACT [] synonym: "IPP metabolism" EXACT [] synonym: "isopentenyl diphosphate metabolism" EXACT [] synonym: "isopentenyl pyrophosphate metabolic process" EXACT [] synonym: "isopentenyl pyrophosphate metabolism" EXACT [] is_a: GO:0006629 ! lipid metabolic process is_a: GO:0006793 ! phosphorus metabolic process [Term] id: GO:0046536 name: dosage compensation complex namespace: cellular_component def: "A protein or protein-RNA complex that localizes to one or more of the sex chromosome(s), where it acts to normalize transcription between different sexes." [GOC:kmv, GOC:mah] subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005634 ! nucleus relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0046794 name: transport of virus namespace: biological_process def: "The directed movement of a virus, or part of a virus, into, out of, or within a host cell." [GOC:ai] subset: goslim_pir synonym: "viral transport" EXACT [GOC:bf, GOC:jl] synonym: "virion transport" NARROW [GOC:bf, GOC:jl] is_a: GO:0016032 ! viral process [Term] id: GO:0046812 name: host cell surface binding namespace: molecular_function def: "Binding to the surface of a host cell." [GOC:ai] subset: goslim_pir is_a: GO:0005488 ! binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21459" xsd:anyURI [Term] id: GO:0046864 name: isoprenoid transport namespace: biological_process def: "The directed movement of isoprenoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Isoprenoids comprise a group of compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [GOC:ai] subset: goslim_pir is_a: GO:0006869 ! lipid transport [Term] id: GO:0046903 name: secretion namespace: biological_process def: "The controlled release of a substance by a cell or a tissue." [GOC:ai] subset: goslim_pir is_a: GO:0006810 ! transport [Term] id: GO:0046906 name: tetrapyrrole binding namespace: molecular_function def: "Binding to a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position." [GOC:curators, ISBN:0198506732] subset: goslim_metagenomics subset: goslim_pir synonym: "porphyrin binding" NARROW [] is_a: GO:0005488 ! binding [Term] id: GO:0048180 name: activin complex namespace: cellular_component def: "A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits, inhibin beta-A and inhibin beta-B (sometimes known as activin beta or activin/inhibin beta). There are three forms of activin complex, activin A, which is composed of 2 inhibin beta-A subunits, activin B, which is composed of 2 inhibin beta-B subunits, and activin AB, which is composed of an inhibin beta-A and an inhibin beta-B subunit." [GOC:curators] comment: Note that the actions of the activin complex are the opposite of those of the inhibin complex, which is a dimer of an inhibin beta-A or inhibin beta-B subunit and a inhibin alpha subunit. See 'inhibin complex ; GO:0043511'. subset: goslim_pir is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005576 ! extracellular region [Term] id: GO:0048284 name: organelle fusion namespace: biological_process def: "The creation of a single organelle from two or more organelles." [GOC:jid] subset: goslim_pir subset: goslim_yeast is_a: GO:0006996 ! organelle organization [Term] id: GO:0048285 name: organelle fission namespace: biological_process def: "The creation of two or more organelles by division of one organelle." [GOC:jid] subset: goslim_pir subset: goslim_yeast is_a: GO:0006996 ! organelle organization [Term] id: GO:0048308 name: organelle inheritance namespace: biological_process def: "The partitioning of organelles between daughter cells at cell division." [GOC:jid] subset: goslim_pir subset: goslim_yeast is_a: GO:0006996 ! organelle organization [Term] id: GO:0048469 name: cell maturation namespace: biological_process def: "The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state." [GOC:curators] subset: goslim_pir synonym: "functional differentiation" RELATED [GOC:dph] is_a: GO:0032502 ! developmental process relationship: part_of GO:0032502 ! developmental process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24390" xsd:anyURI [Term] id: GO:0048476 name: Holliday junction resolvase complex namespace: cellular_component def: "An endodeoxyribonuclease complex that resolves the 4-way DNA intermediates of a Holliday junction into two separate duplex DNA molecules. Can be branch-migration associated." [PMID:11207366, PMID:12374758] subset: goslim_pir synonym: "Mus81-Eme1 complex" NARROW [] synonym: "Mus81-Eme1 holliday resolvase complex" NARROW [] synonym: "Mus81-Eme2 complex" NARROW [] synonym: "Mus81-Eme2 holliday resolvase complex" NARROW [] synonym: "resolvasome" EXACT [PMID:11207366] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0048492 name: ribulose bisphosphate carboxylase complex namespace: cellular_component def: "A complex containing either both large and small subunits or just small subunits which carries out the activity of producing 3-phosphoglycerate from carbon dioxide and ribulose-1,5-bisphosphate." [GOC:mlg] subset: goslim_pir synonym: "RubisCO complex" EXACT [] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0048500 name: signal recognition particle namespace: cellular_component def: "A complex of protein and RNA which facilitates translocation of proteins across membranes." [GOC:mlg] subset: goslim_metagenomics subset: goslim_pir xref: Wikipedia:Signal_recognition_particle is_a: GO:1990904 ! ribonucleoprotein complex relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0048511 name: rhythmic process namespace: biological_process def: "Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism." [GOC:jid] subset: goslim_pir synonym: "rhythm" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0048753 name: pigment granule 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 pigment granule." [GOC:rc] subset: goslim_pir synonym: "pigment granule organisation" EXACT [] synonym: "pigment granule organization and biogenesis" RELATED [GOC:mah] is_a: GO:0016050 ! vesicle organization relationship: part_of GO:0043473 ! pigmentation [Term] id: GO:0048771 name: tissue remodeling namespace: biological_process def: "The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling." [GOC:ebc] subset: goslim_pir synonym: "tissue remodelling" EXACT [] is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0050761 name: depsipeptide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving depsipeptides, a linear or cyclic compound composed of both amino acids and hydroxy acids in peptide and ester bonds respectively." [GOC:curators] subset: goslim_pir synonym: "depsipeptide metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0050789 name: regulation of biological process namespace: biological_process alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:curators] subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_pir synonym: "regulation of physiological process" EXACT [] is_a: GO:0065007 ! biological regulation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008150 ! biological_process relationship: regulates GO:0008150 ! biological_process [Term] id: GO:0050817 name: coagulation namespace: biological_process def: "The process in which a fluid solution, or part of it, changes into a solid or semisolid mass." [ISBN:0198506732] subset: goslim_pir synonym: "clotting" EXACT [] is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0050840 name: extracellular matrix binding namespace: molecular_function def: "Binding to a component of the extracellular matrix." [GOC:ai] subset: goslim_chembl subset: goslim_pir synonym: "adhesive extracellular matrix constituent" RELATED [] synonym: "extracellular matrix constituent binding" EXACT [] is_a: GO:0005488 ! binding [Term] id: GO:0050877 name: nervous system process namespace: biological_process def: "An organ system process carried out by any of the organs or tissues of the 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 [] is_a: GO:0032501 ! multicellular organismal process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] id: GO:0050878 name: regulation of body fluid levels namespace: biological_process def: "Any process that modulates the levels of body fluids." [GOC:ai, GOC:dph, GOC:tb] subset: goslim_pir is_a: GO:0065008 ! regulation of biological quality [Term] id: GO:0050879 name: multicellular organismal movement namespace: biological_process def: "Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism." [GOC:dph, GOC:mtg_muscle, GOC:tb] subset: goslim_pir is_a: GO:0032501 ! multicellular organismal process [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 [] is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0050896 name: response to stimulus namespace: biological_process alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_flybase_ribbon subset: goslim_mouse subset: goslim_pir subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "physiological response to stimulus" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0051179 name: localization namespace: biological_process alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "establishment and maintenance of cellular component location" NARROW [] synonym: "establishment and maintenance of localization" EXACT [] synonym: "establishment and maintenance of position" EXACT [] synonym: "establishment and maintenance of substance location" NARROW [] synonym: "establishment and maintenance of substrate location" NARROW [] synonym: "localisation" EXACT [GOC:mah] synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] id: GO:0051180 name: vitamin transport namespace: biological_process def: "The directed movement of vitamins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A vitamin is one of 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." [GOC:ai] subset: goslim_pir synonym: "vitamin or cofactor transport" BROAD [] is_a: GO:0006810 ! transport [Term] id: GO:0051189 name: prosthetic group metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a prosthetic group, the non-amino acid portion of certain protein molecules. Prosthetic groups may be inorganic or organic and are usually required for the biological activity of the protein." [GOC:ai] subset: goslim_pir synonym: "coenzyme and prosthetic group metabolic process" BROAD [] synonym: "coenzyme and prosthetic group metabolism" BROAD [] synonym: "prosthetic group metabolism" EXACT [] is_a: GO:0008152 ! metabolic process relationship: part_of GO:0019538 ! protein metabolic process [Term] id: GO:0051213 name: dioxygenase activity namespace: molecular_function def: "Catalysis of the incorporation of both atoms of molecular oxygen (O2) into the substrate." [PMID:1444267] subset: goslim_pir xref: Reactome:R-HSA-112120 "Oxidative demethylation of 3-meC damaged DNA by ALKBH2" xref: Reactome:R-HSA-112121 "Oxidative dealkylation of 1-etA damaged DNA By ALKBH2" xref: Reactome:R-HSA-112124 "Oxidative demethylation of 3-meC damaged DNA By ALKBH3" xref: Reactome:R-HSA-112125 "Oxidative dealkylation of 1-EtA damaged DNA by ABH3" is_a: GO:0016491 ! oxidoreductase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30165" xsd:anyURI [Term] id: GO:0051234 name: establishment of localization namespace: biological_process def: "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos] subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_flybase_ribbon subset: goslim_mouse subset: goslim_pir synonym: "establishment of localisation" EXACT [GOC:mah] is_a: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI [Term] id: GO:0051258 name: protein polymerization namespace: biological_process def: "The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein." [GOC:ai] subset: goslim_pir synonym: "protein polymer biosynthesis" EXACT [] synonym: "protein polymer biosynthetic process" EXACT [] synonym: "protein polymer formation" EXACT [] is_a: GO:0065003 ! protein-containing complex assembly [Term] id: GO:0051261 name: protein depolymerization namespace: biological_process def: "The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric protein." [GOC:ai] subset: goslim_pir synonym: "protein polymer breakdown" EXACT [] synonym: "protein polymer catabolic process" EXACT [] synonym: "protein polymer catabolism" EXACT [] synonym: "protein polymer degradation" EXACT [] is_a: GO:0022411 ! cellular component disassembly [Term] id: GO:0051276 name: chromosome organization namespace: biological_process alt_id: GO:0006323 alt_id: GO:0007001 alt_id: GO:0051277 def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl subset: goslim_drosophila subset: goslim_pir synonym: "chromosome organisation" EXACT [] synonym: "chromosome organization and biogenesis" RELATED [GOC:mah] synonym: "DNA condensation" EXACT [] synonym: "DNA packaging" NARROW [] synonym: "maintenance of genome integrity" RELATED [] synonym: "nuclear genome maintenance" RELATED [] is_a: GO:0006996 ! organelle organization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22811" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/4585" xsd:anyURI [Term] id: GO:0051301 name: cell division namespace: biological_process def: "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells." [GOC:curators, GOC:di, GOC:pr] comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. subset: goslim_chembl subset: goslim_drosophila subset: goslim_pir xref: Wikipedia:Cell_division is_a: GO:0008150 ! biological_process [Term] id: GO:0051540 name: metal cluster binding namespace: molecular_function def: "Binding to a cluster of atoms including both metal ions and nonmetal atoms, usually sulfur and oxygen. Examples include iron-sulfur clusters and nickel-iron-sulfur clusters." [GOC:jsg] subset: goslim_pir is_a: GO:0005488 ! binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21211" xsd:anyURI [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 xref: Reactome:R-HSA-9918432 "Maturation of DENV proteins" is_a: GO:0019538 ! protein metabolic process relationship: part_of GO:0009059 ! macromolecule biosynthetic process [Term] id: GO:0051606 name: detection of stimulus namespace: biological_process def: "The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal." [GOC:add, GOC:ai, GOC:dph, GOC:mah] subset: goslim_pir synonym: "perception of stimulus" RELATED [] synonym: "stimulus detection" EXACT [] synonym: "stimulus sensing" RELATED [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0051640 name: organelle localization namespace: biological_process def: "Any process in which an organelle is transported to, and/or maintained in, a specific location." [GOC:ai] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "establishment and maintenance of organelle localization" EXACT [] synonym: "organelle localisation" EXACT [GOC:mah] is_a: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI [Term] id: GO:0051641 name: cellular localization namespace: biological_process alt_id: GO:1902580 def: "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane." [GOC:tb, GOC:vw] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular localisation" EXACT [GOC:mah] synonym: "establishment and maintenance of cellular localization" EXACT [] synonym: "establishment and maintenance of localization in cell or cell membrane" EXACT [] synonym: "intracellular localization" NARROW [] synonym: "localization within cell" NARROW [] synonym: "single organism cellular localization" EXACT [GOC:TermGenie] synonym: "single-organism cellular localization" RELATED [] is_a: GO:0051179 ! localization property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI created_by: jl creation_date: 2013-12-18T14:04:32Z [Term] id: GO:0051703 name: biological process involved in intraspecies interaction between organisms namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "intraspecies interaction between organisms" EXACT [] synonym: "intraspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] id: GO:0052314 name: phytoalexin metabolic process namespace: biological_process def: "The chemical reactions and pathways involving phytoalexins, any of a range of substances produced by plants as part of their defense response." [Wikipedia:Phytoalexin] subset: goslim_pir synonym: "phytoalexin metabolism" EXACT [] is_a: GO:0009404 ! toxin metabolic process [Term] id: GO:0055044 name: symplast namespace: cellular_component def: "The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata." [GOC:mtg_sensu] subset: goslim_pir xref: Wikipedia:Symplast is_a: GO:0110165 ! cellular anatomical structure [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_annotate subset: goslim_generic subset: goslim_pir subset: goslim_prokaryote is_a: GO:0003674 ! molecular_function [Term] id: GO:0060090 name: molecular adaptor activity namespace: molecular_function alt_id: GO:0032947 def: "The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way." [GOC:mtg_MIT_16mar07, GOC:vw] subset: goslim_drosophila subset: goslim_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_pir subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "binding, bridging" EXACT [] xref: Reactome:R-HSA-2564826 "4Fe-4S cluster assembles on NUBP2:NUBP1 scaffold" is_a: GO:0003674 ! molecular_function relationship: has_part GO:0005488 ! binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31509" xsd:anyURI [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 [] xref: Reactome:R-HSA-199991 "Membrane Trafficking" is_a: GO:0016043 ! cellular component organization 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 [] is_a: GO:0022607 ! cellular component assembly property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI [Term] id: GO:0065007 name: biological regulation namespace: biological_process def: "Any process that modulates a measurable attribute of any biological process, quality or function." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "regulation" BROAD [] is_a: GO:0008150 ! biological_process [Term] id: GO:0065008 name: regulation of biological quality namespace: biological_process def: "Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "regulation of biological attribute" EXACT [] synonym: "regulation of biological characteristic" EXACT [] is_a: GO:0065007 ! biological regulation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30599" xsd:anyURI [Term] id: GO:0065009 name: regulation of molecular function namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GOC:isa_complete] subset: gocheck_obsoletion_candidate subset: goslim_pir subset: goslim_plant synonym: "regulation of a molecular function" EXACT [] is_a: GO:0065007 ! biological regulation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0003674 ! molecular_function relationship: regulates GO:0003674 ! molecular_function [Term] id: GO:0071256 name: translocon complex namespace: cellular_component alt_id: GO:0031206 def: "A protein complex that constitutes a specific site of protein translocation across the endoplasmic reticulum, which involves the signal recognition particle receptor. The complex contains a core heterotrimer of alpha, beta and gamma subunits, and may contain additional proteins." [GOC:mah, PMID:10611978, PMID:18166647, PMID:8612571] subset: goslim_pir synonym: "Sec complex-associated translocon complex" NARROW [GOC:mah] is_a: GO:0032991 ! protein-containing complex relationship: part_of GO:0005783 ! endoplasmic reticulum relationship: part_of GO:0016020 ! membrane created_by: mah creation_date: 2009-12-08T02:08:03Z [Term] id: GO:0071555 name: cell wall organization namespace: biological_process alt_id: GO:0007047 alt_id: GO:0044234 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis." [GOC:mah] subset: goslim_candida subset: goslim_pir synonym: "cell wall organisation" EXACT [] synonym: "cell wall organisation in other organism" EXACT [GOC:mah] synonym: "cell wall organization and biogenesis" RELATED [GOC:mah] synonym: "cell wall organization at cellular level" EXACT [GOC:mah] synonym: "cell wall organization in other organism" EXACT [] synonym: "cellular cell wall organisation" EXACT [] synonym: "cellular cell wall organization" EXACT [] is_a: GO:0045229 ! external encapsulating structure organization created_by: mah creation_date: 2010-01-13T03:33:07Z [Term] id: GO:0110165 name: cellular anatomical structure namespace: cellular_component def: "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses." [GOC:kmv] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular anatomical entity" EXACT [] is_a: GO:0005575 ! cellular_component property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24200" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28978" xsd:anyURI created_by: kmv creation_date: 2019-08-12T18:01:37Z [Term] id: GO:1902600 name: proton transmembrane transport namespace: biological_process alt_id: GO:0006818 alt_id: GO:0015991 alt_id: GO:0015992 def: "The directed movement of a proton across a membrane." [GO_REF:0000069, GOC:pr, GOC:TermGenie] subset: goslim_pir synonym: "ATP hydrolysis coupled proton transport" NARROW [] synonym: "hydrogen ion transmembrane transport" EXACT [] synonym: "hydrogen ion transport" RELATED [] synonym: "hydrogen transmembrane transport" EXACT [] synonym: "hydrogen transport" BROAD [] synonym: "passive proton transport, down the electrochemical gradient" NARROW [] synonym: "proton transport" BROAD [] xref: Reactome:R-HSA-167826 "The fatty acid cycling model" is_a: GO:0006811 ! monoatomic ion transport created_by: pr creation_date: 2013-12-20T11:08:37Z [Term] id: GO:1990904 name: ribonucleoprotein complex namespace: cellular_component alt_id: GO:0030529 alt_id: GO:1990903 def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] subset: goslim_pir synonym: "extracellular ribonucleoprotein complex" NARROW [] synonym: "intracellular ribonucleoprotein complex" NARROW [] synonym: "protein-RNA complex" EXACT [] synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! protein-containing complex created_by: pr creation_date: 2015-11-19T12:26:37Z [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