format-version: 1.2 date: 25:09:2009 11:40 auto-generated-by: OBO-Edit 2.1-beta1 saved-by: jane synonymtypedef: systematic_synonym "Systematic synonym" EXACT subsetdef: goslim_candida "Candida GO slim" subsetdef: goslim_generic "Generic GO slim" subsetdef: goslim_goa "GOA and proteome slim" subsetdef: goslim_pir "PIR GO slim" subsetdef: goslim_plant "Plant GO slim" subsetdef: goslim_pombe "Fission yeast GO slim" subsetdef: goslim_yeast "Yeast GO slim" subsetdef: gosubset_prok "Prokaryotic GO subset" remark: cvs version: $Revision: 1.7 $ [Term] id: GO:0000003 name: reproduction namespace: biological_process alt_id: GO:0019952 alt_id: GO:0050876 def: "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [GOC:go_curators, GOC:isa_complete, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "reproductive physiological process" EXACT [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process [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 relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0000128 name: flocculation namespace: biological_process def: "The non-sexual aggregation of single-celled organisms." [GOC:jl] subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Flocculation is_a: GO:0051704 ! multi-organism process [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 relationship: part_of GO:0030427 ! site of polarized growth relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0000151 name: ubiquitin ligase complex namespace: cellular_component def: "A protein complex that includes a ubiquitin-protein ligase (E3) and other proteins that may confer substrate specificity on the complex." [PMID:9529603] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0000166 name: nucleotide binding namespace: molecular_function def: "Interacting selectively and non-covalently with 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 moiety." [GOC:mah, ISBN:0198547684] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0000178 name: exosome (RNase complex) namespace: cellular_component def: "Complex of 3'-5' exoribonucleases." [PMID:10465791] 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 [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0000267 name: cell fraction namespace: cellular_component def: "A generic term for parts of cells prepared by disruptive biochemical techniques." [GOC:ma] comment: Note that this term refers to disrupted cells, and does not necessarily correspond to any specific structure(s) in an intact cell. subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [Term] id: GO:0000280 name: nuclear division namespace: biological_process def: "A process by which a cell nucleus is divided 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 heterodimeric enzymes that contain a kinase catalytic subunit associated with a regulatory cyclin partner." [GOC:krc, PMID:11602261] subset: goslim_pir synonym: "CDK holoenzyme" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 [] relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0000441 name: SSL2-core TFIIH complex namespace: cellular_component def: "A complex which is part of both the general transcription factor TFIIH and the nucleotide-excision repair factor 3 complex. It is composed of the tightly associated 5 subunit core TFIIH subcomplex plus one additional, more loosely associated subunit. The subunits are well conserved from yeast to humans. In S. cerevisiae, the 5-subunit core is composed of Rad3, Tfb1, Tfb2, Ssl1, Tfb4 and the loosely associated subunit is Ssl2p (also called Rad25). In humans, the 5 subunit core is composed of ERCC2, p62, p55, p44, p34 and the loosely associated subunit is XPB." [GOC:krc, PMID:14500720, PMID:7813015] subset: goslim_pir is_a: GO:0043234 ! protein complex [Term] id: GO:0000502 name: proteasome complex namespace: cellular_component def: "A large multisubunit complex which catalyzes protein degradation. 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] subset: goslim_pir synonym: "26S proteasome" NARROW [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0000746 name: conjugation namespace: biological_process def: "The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms." [GOC:elh] subset: goslim_candida subset: goslim_pir subset: goslim_yeast subset: gosubset_prok xref: Wikipedia:Conjugation is_a: GO:0051704 ! multi-organism process [Term] id: GO:0000776 name: kinetochore namespace: cellular_component alt_id: GO:0005699 def: "A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules." [GOC:elh] subset: goslim_pir xref: Wikipedia:Kinetochore relationship: part_of GO:0005694 ! chromosome is_a: GO:0043232 ! intracellular non-membrane-bounded organelle is_a: GO:0043234 ! protein complex [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 subset: gosubset_prok is_a: GO:0032991 ! macromolecular complex is_a: GO:0044464 ! cell part relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0000786 name: nucleosome namespace: cellular_component 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 xref: Wikipedia:Nucleosome is_a: GO:0032991 ! macromolecular complex is_a: GO:0044464 ! cell part relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0000796 name: condensin complex namespace: cellular_component alt_id: GO:0005676 alt_id: GO:0008620 def: "A multisubunit protein complex that plays a central role in chromosome condensation." [GOC:elh] subset: goslim_pir synonym: "13S condensin complex" NARROW [] synonym: "SMC complex" RELATED [] relationship: part_of GO:0005694 ! chromosome is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 subset: gosubset_prok synonym: "ORC" EXACT [] synonym: "origin of replication recognition complex" EXACT [] xref: Wikipedia:Origin_recognition_complex relationship: part_of GO:0005694 ! chromosome is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 relationship: part_of GO:0005856 ! cytoskeleton is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0001534 name: radial spoke namespace: cellular_component def: "Protein complex that links the outer microtubule doublet of the ciliary or flagellum 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." [ISBN:0124325653, PMID:9450971] subset: goslim_pir xref: Wikipedia:Radial_spoke relationship: part_of GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0042995 ! cell projection is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0001775 name: cell activation namespace: biological_process def: "A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:mgi_curators] subset: goslim_pir is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0001816 name: cytokine production namespace: biological_process 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 "Fundamental Immunology"] comment: Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules. subset: goslim_pir is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0001871 name: pattern binding namespace: molecular_function def: "Interacting selectively and non-covalently with a repeating or polymeric structure, such as a polysaccharide or peptidoglycan." [PMID:12072369, PMID:12225919, PMID:12507420, PMID:12925128, PMID:14523544] comment: Note that this term and its child terms are intended for annotation of gene products which function to recognize (bind) the repeating structural units such as polysaccharides or peptidoglycans commonly found in microbial cell walls and virions. If such binding is coupled to signal transduction, use 'pattern recognition receptor activity ; GO:0008329' instead. subset: goslim_pir subset: gosubset_prok synonym: "pattern recognition activity" BROAD [] is_a: GO:0005488 ! binding [Term] id: GO:0001882 name: nucleoside binding namespace: molecular_function def: "Interacting selectively and non-covalently with a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose." [GOC:hjd] subset: goslim_pir subset: gosubset_prok 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 subset: gosubset_prok 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 relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [Term] id: GO:0002054 name: nucleobase binding namespace: molecular_function def: "Interacting selectively and non-covalently with a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases." [GOC:hjd] subset: goslim_pir subset: gosubset_prok 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, GOC:mtg_15nov05] comment: This term was added by GO_REF:0000022. subset: goslim_pir xref: Wikipedia:Immune_syntem is_a: GO:0008150 ! biological_process [Term] id: GO:0003674 name: molecular_function namespace: molecular_function alt_id: GO:0005554 def: "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that 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 ND, no data, is used to indicate this. subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "molecular function" EXACT [] synonym: "molecular function unknown" NARROW [] [Term] id: GO:0003676 name: nucleic acid binding namespace: molecular_function def: "Interacting selectively and non-covalently with any nucleic acid." [GOC:jl] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0003682 name: chromatin binding namespace: molecular_function def: "Interacting selectively and non-covalently with chromatin, the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_pir subset: goslim_plant synonym: "lamin/chromatin binding" BROAD [] synonym: "microtubule/chromatin interaction" RELATED [] synonym: "nuclear membrane vesicle binding to chromatin" NARROW [] is_a: GO:0005488 ! binding [Term] id: GO:0003774 name: motor activity namespace: molecular_function def: "Catalysis of movement along a polymeric molecule such as a microfilament or microtubule, coupled to the hydrolysis of a nucleoside triphosphate." [GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0003823 name: antigen binding namespace: molecular_function def: "Interacting selectively and non-covalently with 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." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology", ISBN:0721662544 "Dorland's Illustrated Medical Dictionary"] subset: goslim_pir synonym: "B cell receptor activity" RELATED [] synonym: "antibody" RELATED [] synonym: "immunoglobulin" RELATED [] synonym: "opsonin activity" RELATED [] is_a: GO:0005488 ! binding [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." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] xref: Wikipedia:Enzyme is_a: GO:0003674 ! molecular_function [Term] id: GO:0004133 name: glycogen debranching enzyme activity namespace: molecular_function def: "Catalysis of the cleavage of branch points in branched glycogen polymers." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004386 name: helicase activity namespace: molecular_function def: "Catalysis of the reaction: NTP + H2O = NDP + phosphate to drive the unwinding of a DNA or RNA helix." [GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that most helicases catalyze processive duplex unwinding. subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok xref: Reactome:7001 "helicase activity" is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0004497 name: monooxygenase activity namespace: molecular_function def: "Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water." [http://www.onelook.com/, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok xref: Reactome:9021 "monooxygenase activity" is_a: GO:0016491 ! oxidoreductase activity [Term] id: GO:0004803 name: transposase activity namespace: molecular_function def: "Catalysis of the transposition of transposable elements or transposons. Transposases are involved in site-specific DNA recombination required for transposition in bacteria and other organisms." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004871 name: signal transducer activity namespace: molecular_function def: "Mediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok is_a: GO:0060089 ! molecular transducer 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 or assembly within or outside a cell." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok is_a: GO:0003674 ! molecular_function [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, within or between cells." [GOC:ai, GOC:df] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "small-molecule carrier or transporter" RELATED [] xref: Reactome:1391 "transporter activity" is_a: GO:0003674 ! molecular_function [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 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "ligand" NARROW [] xref: Wikipedia:Binding_(molecular) is_a: GO:0003674 ! molecular_function [Term] id: GO:0005496 name: steroid binding namespace: molecular_function def: "Interacting selectively and non-covalently with 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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok is_a: GO:0008289 ! lipid binding [Term] id: GO:0005515 name: protein binding namespace: molecular_function alt_id: GO:0045308 def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "alpha-2 macroglobulin receptor-associated protein activity" RELATED [] synonym: "protein amino acid binding" EXACT [] synonym: "protein degradation tagging activity" RELATED [] synonym: "protein folding chaperone" NARROW [GOC:dph, GOC:mah, GOC:tb] synonym: "protein tagging activity" RELATED [] xref: Reactome:6125 "protein binding" is_a: GO:0005488 ! binding [Term] id: GO:0005549 name: odorant binding namespace: molecular_function def: "Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell." [GOC:jl, ISBN:0721662544 "Dorland's Illustrated Medical Dictionary"] subset: goslim_pir subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 def: "The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that 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 ND, no data, is used to indicate this. subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "cellular component" EXACT [] synonym: "cellular component unknown" NARROW [] [Term] id: GO:0005576 name: extracellular region namespace: cellular_component def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators] comment: Note that this term is intended to annotate gene products that are not uniformly 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_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular is_a: GO:0005575 ! cellular_component [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, and most prokaryotic cells, 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." [ISBN:0198547684] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok xref: Wikipedia:Cell_wall relationship: part_of GO:0005575 ! cellular_component is_a: GO:0030312 ! external encapsulating structure [Term] id: GO:0005622 name: intracellular namespace: cellular_component def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "internal to cell" EXACT [] synonym: "protoplasm" EXACT [] xref: Wikipedia:Intracellular relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [Term] id: GO:0005634 name: nucleus namespace: cellular_component def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "cell nucleus" EXACT [] xref: Wikipedia:Cell_nucleus relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [Term] id: GO:0005643 name: nuclear pore namespace: cellular_component alt_id: GO:0005644 def: "Any of the numerous similar discrete openings 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 [] xref: Wikipedia:Nuclear_pore relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0005663 name: DNA replication factor C complex namespace: cellular_component def: "A complex of five polypeptides in eukaryotes, and two in prokaryotes, that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase." [PMID:14614842, PMID:14646196, PMID:16172520] subset: goslim_pir subset: gosubset_prok synonym: "RFC complex" EXACT [] synonym: "activator 1 complex" EXACT [] relationship: part_of GO:0005694 ! chromosome is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0005667 name: transcription factor complex namespace: cellular_component def: "A protein complex, distinct from RNA polymerase, that associates with DNA at promoters or at cis-acting regulatory sequences, by direct binding or by interaction with other DNA-binding polypeptides or complexes, and regulates transcription." [GOC:mah] subset: goslim_pir relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0005681 name: spliceosomal complex namespace: cellular_component def: "Any of a series of ribonucleoprotein complexes that contain RNA and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the splicing of a messenger RNA primary transcript to excise an intron." [GOC:mah, ISBN:0198547684, PMID:19239890] subset: goslim_pir synonym: "spliceosome complex" EXACT [] xref: Wikipedia:Spliceosome relationship: part_of GO:0005634 ! nucleus is_a: GO:0030529 ! ribonucleoprotein complex [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] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome relationship: part_of GO:0005622 ! intracellular is_a: GO:0043232 ! intracellular non-membrane-bounded 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 relationship: part_of GO:0005634 ! nucleus is_a: GO:0030529 ! ribonucleoprotein complex [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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast xref: Wikipedia:Nucleolus relationship: part_of GO:0005634 ! nucleus is_a: GO:0043232 ! intracellular non-membrane-bounded organelle [Term] id: GO:0005732 name: small nucleolar ribonucleoprotein complex namespace: cellular_component def: "A ribonucleoprotein complex that contains a small nucleolar RNA (snoRNA) and associated proteins, and is found in eukaryotic cells. Most are involved in a step of processing of rRNA: cleavage, 2'-O-methylation, or pseudouridylation. The majority, though not all, fall into one of two classes, box C/D type or box H/ACA type." [GOC:krc, GOC:mah, ISBN:0879695897] subset: goslim_pir synonym: "small nucleolar ribonucleoprotein" EXACT [] synonym: "snoRNP" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0030529 ! ribonucleoprotein complex [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." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "mitochondria" EXACT [] xref: Wikipedia:Mitochondrion relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [Term] id: GO:0005744 name: mitochondrial inner membrane presequence translocase complex namespace: cellular_component def: "The protein transport machinery of the mitochondrial inner membrane that 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." [EC:3.6.3.51, PMID:8851659] comment: See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'. subset: goslim_pir synonym: "Tim23 complex" NARROW [] synonym: "mitochondrial inner membrane pre-sequence translocase complex" EXACT [] synonym: "mitochondrial inner membrane translocase complex" EXACT [] relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0005739 ! mitochondrion is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0005768 name: endosome namespace: cellular_component def: "A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_pir subset: goslim_plant xref: Wikipedia:Endosome relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "vacuolar carboxypeptidase Y" RELATED [] xref: Wikipedia:Vacuole relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [Term] id: GO:0005783 name: endoplasmic reticulum namespace: cellular_component def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "ER" EXACT [] xref: Wikipedia:Endoplasmic_reticulum relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [Term] id: GO:0005784 name: translocon complex namespace: cellular_component def: "A translocation complex that constitutes the specific site of protein translocation across the endoplasmic reticulum, which involves the signal recognition particle receptor. Composed of a heterotetramer of alpha, beta, gamma and delta subunits (translocon-associated proteins or TRAPs). In yeast it is a heterotrimeric complex consisting of Sec61p, Sbh1p, and Sss1p. The Sec61 complex functions in cotranslational and posttranslational translocation events." [GOC:rb, ISBN:0198599471] subset: goslim_pir synonym: "sec61 complex" NARROW [] relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0005783 ! endoplasmic reticulum is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0005794 name: Golgi apparatus namespace: cellular_component def: "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] 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_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "Golgi" BROAD [] synonym: "Golgi complex" EXACT [] synonym: "Golgi ribbon" NARROW [] xref: Wikipedia:Golgi_apparatus relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [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 relationship: part_of GO:0005856 ! cytoskeleton is_a: GO:0043232 ! intracellular non-membrane-bounded organelle [Term] id: GO:0005835 name: fatty acid synthase complex namespace: cellular_component def: "A multienzyme complex required to convert carbohydrates to fatty acids, specifically acetyl CoA to palmitate." [GOC:sgd_curators, ISBN:0716746840] subset: goslim_pir subset: gosubset_prok synonym: "FAS complex" EXACT [] synonym: "fatty acid synthetase complex" EXACT [] synonym: "holo-[acyl-carrier-protein] synthase complex" RELATED [] xref: Wikipedia:Fatty_acid_synthetase_complex relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0005840 name: ribosome namespace: cellular_component 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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "ribosomal RNA" RELATED [] xref: Wikipedia:Ribosome relationship: part_of GO:0005622 ! intracellular is_a: GO:0030529 ! ribonucleoprotein complex is_a: GO:0043232 ! intracellular non-membrane-bounded organelle [Term] id: GO:0005844 name: polysome namespace: cellular_component def: "Several ribosomes bound to one mRNA." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir synonym: "polyribosome" EXACT [] xref: Wikipedia:Polysome relationship: part_of GO:0005622 ! intracellular is_a: GO:0030529 ! ribonucleoprotein complex [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 relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0005856 name: cytoskeleton namespace: cellular_component def: "Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces 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, ISBN:0198547684, PMID:16959967] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok xref: Wikipedia:Cytoskeleton relationship: part_of GO:0005622 ! intracellular is_a: GO:0043232 ! intracellular non-membrane-bounded 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 [] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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:0813516194] 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 xref: Wikipedia:Microvillus relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [Term] id: GO:0005903 name: brush border namespace: cellular_component def: "Dense covering of microvilli on the apical surface of epithelial cells 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 relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [Term] id: GO:0005929 name: cilium namespace: cellular_component def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:kmv, ISBN:0198547684] subset: goslim_generic subset: goslim_pir xref: Wikipedia:Cilium relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [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 relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [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 [] relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [Term] id: GO:0005942 name: phosphoinositide 3-kinase complex namespace: cellular_component def: "A complex containing a heterodimer of a catalytic subunit and a regulatory (adaptor) subunit of any phosphoinositide 3-kinase (PI3K)." [GOC:bf] subset: goslim_pir synonym: "1-phosphatidylinositol 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] synonym: "phosphatidylinositol 3-kinase complex" EXACT [CORUM:429] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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, MetaCyc:GCVMULTI-CPLX] subset: goslim_pir subset: gosubset_prok 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 relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0005975 name: carbohydrate metabolic process namespace: biological_process def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: gosubset_prok synonym: "carbohydrate metabolism" EXACT [] xref: Reactome:448487 "Metabolism of carbohydrates" xref: Reactome:469617 "Metabolism of carbohydrates" xref: Reactome:487336 "Metabolism of carbohydrates" xref: Reactome:507287 "Metabolism of carbohydrates" xref: Reactome:517301 "Metabolism of carbohydrates" xref: Reactome:526186 "Metabolism of carbohydrates" xref: Reactome:531076 "Metabolism of carbohydrates" xref: Reactome:536449 "Metabolism of carbohydrates" xref: Reactome:542153 "Metabolism of carbohydrates" xref: Reactome:547511 "Metabolism of carbohydrates" xref: Reactome:552109 "Metabolism of carbohydrates" xref: Reactome:557702 "Metabolism of carbohydrates" xref: Reactome:568311 "Metabolism of carbohydrates" xref: Reactome:581513 "Metabolism of carbohydrates" xref: Reactome:585745 "Metabolism of carbohydrates" xref: Reactome:592407 "Metabolism of carbohydrates" xref: Reactome:595291 "Metabolism of carbohydrates" xref: Reactome:597267 "Metabolism of carbohydrates" xref: Reactome:598076 "Metabolism of carbohydrates" xref: Reactome:599604 "Metabolism of carbohydrates" xref: Reactome:600550 "Metabolism of carbohydrates" xref: Reactome:602409 "Metabolism of carbohydrates" xref: Reactome:71387 "Metabolism of carbohydrates" xref: Wikipedia:Carbohydrate_metabolism is_a: GO:0044238 ! primary metabolic process [Term] id: GO:0005976 name: polysaccharide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving polysaccharides, a polymer of more than 20 monosaccharide residues joined by glycosidic linkages." [ISBN:0198547684] subset: goslim_pir subset: gosubset_prok synonym: "glycan metabolic process" EXACT [] synonym: "glycan metabolism" EXACT [] synonym: "polysaccharide metabolism" EXACT [] is_a: GO:0005975 ! carbohydrate metabolic process is_a: GO:0043283 ! biopolymer 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." [ChEBI:30879, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "alcohol metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006081 name: cellular 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:go_curators, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "aldehyde metabolism" EXACT [] synonym: "alkanal metabolic process" EXACT [] synonym: "alkanal metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006082 name: organic acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "organic acid metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [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_generic subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "energy pathways" BROAD [] synonym: "intermediary metabolism" RELATED [GOC:mah] synonym: "metabolic energy generation" RELATED [] is_a: GO:0044237 ! cellular 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 subset: gosubset_prok synonym: "energy reserve metabolism" EXACT [] xref: Reactome:163685 "Integration of energy metabolism" xref: Reactome:448491 "Integration of energy metabolism" xref: Reactome:469621 "Integration of energy metabolism" xref: Reactome:487340 "Integration of energy metabolism" xref: Reactome:507291 "Integration of energy metabolism" xref: Reactome:517305 "Integration of energy metabolism" xref: Reactome:526190 "Integration of energy metabolism" xref: Reactome:531080 "Integration of energy metabolism" xref: Reactome:536453 "Integration of energy metabolism" xref: Reactome:542157 "Integration of energy metabolism" xref: Reactome:547515 "Integration of energy metabolism" xref: Reactome:552152 "Integration of energy metabolism" xref: Reactome:557694 "Integration of energy metabolism" xref: Reactome:568315 "Integration of energy metabolism" xref: Reactome:581517 "Integration of energy metabolism" xref: Reactome:585777 "Integration of energy metabolism" xref: Reactome:592453 "Integration of energy metabolism" xref: Reactome:595323 "Integration of energy metabolism" xref: Reactome:597293 "Integration of energy metabolism" xref: Reactome:598102 "Integration of energy metabolism" xref: Reactome:599599 "Integration of energy metabolism" xref: Reactome:600582 "Integration of energy metabolism" xref: Reactome:602450 "Integration of energy metabolism" is_a: GO:0006091 ! generation of precursor metabolites and energy [Term] id: GO:0006113 name: fermentation namespace: biological_process def: "The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, to other compounds, especially to ethyl alcohol, yielding energy in the form of adenosine triphosphate (ATP)." [http://cancerweb.ncl.ac.uk/] subset: goslim_pir subset: gosubset_prok xref: MetaCyc:FERMENTATION-PWY xref: Wikipedia:Fermentation_(biochemistry) is_a: GO:0006091 ! generation of precursor metabolites and energy [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 "Oxford Dictionary of Biochemistry and Molecular Biology", ISBN:0471331309 "Biochemical Pathways"] subset: goslim_pir subset: gosubset_prok synonym: "respiratory-chain phosphorylation" EXACT [] xref: Wikipedia:Oxidative_phosphorylation is_a: GO:0006091 ! generation of precursor metabolites and energy is_a: GO:0006793 ! phosphorus metabolic process [Term] id: GO:0006139 name: nucleobase, nucleoside, nucleotide and nucleic acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0044238 ! primary metabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006259 name: DNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving DNA, deoxyribonucleic acid, 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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "DNA metabolism" EXACT [] is_a: GO:0043283 ! biopolymer metabolic process is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0006260 name: DNA replication namespace: biological_process def: "The process whereby new strands of DNA are synthesized. The template for replication can either be an existing DNA molecule or RNA." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'. subset: goslim_pir subset: goslim_pombe subset: gosubset_prok synonym: "DNA biosynthesis" RELATED [] synonym: "DNA biosynthetic process" RELATED [] synonym: "DNA synthesis" RELATED [] xref: Reactome:176101 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:176116 "Recruitment and activation of Chk1" xref: Reactome:176175 "Stalling of DNA replication fork and RPA binding" xref: Reactome:176187 "Activation of ATR in response to replication stress" xref: Reactome:176250 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:176264 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:176298 "Activation of claspin" xref: Reactome:176318 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:429125 "Activation of claspin" xref: Reactome:433202 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:442012 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:446069 "Recruitment and activation of Chk1" xref: Reactome:446123 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:446153 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:447074 "Stalling of DNA replication fork and RPA binding" xref: Reactome:448696 "Activation of ATR in response to replication stress" xref: Reactome:463715 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:467450 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:467477 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:468344 "Stalling of DNA replication fork and RPA binding" xref: Reactome:470298 "Activation of ATR in response to replication stress" xref: Reactome:472164 "Activation of claspin" xref: Reactome:475516 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:482185 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:485413 "Recruitment and activation of Chk1" xref: Reactome:485440 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:485461 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:486163 "Stalling of DNA replication fork and RPA binding" xref: Reactome:487512 "Activation of ATR in response to replication stress" xref: Reactome:490390 "Activation of claspin" xref: Reactome:502397 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:505179 "Recruitment and activation of Chk1" xref: Reactome:507473 "Activation of ATR in response to replication stress" xref: Reactome:514771 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:516172 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:517816 "Activation of ATR in response to replication stress" xref: Reactome:525168 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:526692 "Activation of ATR in response to replication stress" xref: Reactome:531467 "Activation of ATR in response to replication stress" xref: Reactome:536852 "Activation of ATR in response to replication stress" xref: Reactome:541523 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:542605 "Activation of ATR in response to replication stress" xref: Reactome:546964 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:547923 "Activation of ATR in response to replication stress" xref: Wikipedia:DNA_replication is_a: GO:0043284 ! biopolymer biosynthetic process is_a: GO:0006259 ! DNA metabolic process [Term] id: GO:0006266 name: DNA ligation namespace: biological_process def: "The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [ISBN:0815316194] subset: goslim_pir subset: gosubset_prok is_a: GO:0006259 ! DNA metabolic process [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 subset: gosubset_prok is_a: GO:0009987 ! cellular 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_pir subset: goslim_pombe subset: gosubset_prok xref: Reactome:448579 "DNA Repair" xref: Reactome:449225 "DNA Damage Reversal" xref: Reactome:469708 "DNA Repair" xref: Reactome:470344 "DNA Damage Reversal" xref: Reactome:487420 "DNA Repair" xref: Reactome:488024 "DNA Damage Reversal" xref: Reactome:507375 "DNA Repair" xref: Reactome:507985 "DNA Damage Reversal" xref: Reactome:517374 "DNA Repair" xref: Reactome:526250 "DNA Repair" xref: Reactome:531127 "DNA Repair" xref: Reactome:536499 "DNA Repair" xref: Reactome:542209 "DNA Repair" xref: Reactome:542599 "DNA Damage Reversal" xref: Reactome:547563 "DNA Repair" xref: Reactome:552173 "DNA Repair" xref: Reactome:557757 "DNA Repair" xref: Reactome:558121 "DNA Damage Reversal" xref: Reactome:568370 "DNA Repair" xref: Reactome:568747 "DNA Damage Reversal" xref: Reactome:581572 "DNA Repair" xref: Reactome:581951 "DNA Damage Reversal" xref: Reactome:585783 "DNA Repair" xref: Reactome:592468 "DNA Repair" xref: Reactome:595411 "DNA Repair" xref: Reactome:597351 "DNA Repair" xref: Reactome:598160 "DNA Repair" xref: Reactome:599712 "DNA Repair" xref: Reactome:600616 "DNA Repair" xref: Reactome:600694 "DNA Damage Reversal" xref: Reactome:602518 "DNA Repair" xref: Reactome:602608 "DNA Damage Reversal" xref: Reactome:73894 "DNA Repair" xref: Reactome:73942 "DNA Damage Reversal" xref: Wikipedia:DNA_repair is_a: GO:0050896 ! response to stimulus is_a: GO:0006259 ! DNA metabolic process [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 subset: gosubset_prok is_a: GO:0043412 ! biopolymer modification is_a: GO:0006259 ! DNA metabolic process [Term] id: GO:0006323 name: DNA packaging namespace: biological_process def: "Any process by which DNA and associated proteins are formed into a compact, orderly structure." [GOC:mah, ISBN:0815316194] subset: goslim_pir synonym: "DNA organisation" EXACT [GOC:curators] synonym: "DNA organization" EXACT [GOC:curators] is_a: GO:0016043 ! cellular component organization is_a: GO:0009987 ! cellular process [Term] id: GO:0006350 name: transcription namespace: biological_process def: "The synthesis of either RNA on a template of DNA or DNA on a template of RNA." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok xref: Reactome:448636 "Transcription" xref: Reactome:469764 "Transcription" xref: Reactome:487521 "Transcription" xref: Reactome:507482 "Transcription" xref: Reactome:517466 "Transcription" xref: Reactome:526339 "Transcription" xref: Reactome:531172 "Transcription" xref: Reactome:536547 "Transcription" xref: Reactome:542268 "Transcription" xref: Reactome:547614 "Transcription" xref: Reactome:552218 "Transcription" xref: Reactome:557808 "Transcription" xref: Reactome:568425 "Transcription" xref: Reactome:581627 "Transcription" xref: Reactome:585958 "Transcription" xref: Reactome:592524 "Transcription" xref: Reactome:595359 "Transcription" xref: Reactome:74159 "Transcription" xref: Wikipedia:Transcription_(genetics) relationship: part_of GO:0043170 ! macromolecule metabolic process is_a: GO:0043284 ! biopolymer biosynthetic process is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0006354 name: RNA elongation namespace: biological_process def: "The extension of an RNA molecule after transcription initiation by the addition of ribonucleotides catalyzed by an RNA polymerase." [GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "transcription elongation" BROAD [] synonym: "transcriptional elongation" BROAD [] relationship: part_of GO:0016070 ! RNA metabolic process relationship: part_of GO:0006350 ! transcription is_a: GO:0016070 ! RNA metabolic process [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_pir subset: gosubset_prok xref: Wikipedia:Post-transcriptional_modification relationship: part_of GO:0043170 ! macromolecule metabolic process is_a: 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 by which a protein is formed, using the sequence of a mature mRNA 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. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "protein anabolism" EXACT [] synonym: "protein biosynthesis" EXACT [] synonym: "protein formation" EXACT [] synonym: "protein synthesis" EXACT [] synonym: "protein translation" EXACT [] xref: Reactome:448800 "Translation" xref: Reactome:469916 "Translation" xref: Reactome:487622 "Translation" xref: Reactome:507577 "Translation" xref: Reactome:517550 "Translation" xref: Reactome:526417 "Translation" xref: Reactome:531240 "Translation" xref: Reactome:536611 "Translation" xref: Reactome:542335 "Translation" xref: Reactome:547676 "Translation" xref: Reactome:552260 "Translation" xref: Reactome:557879 "Translation" xref: Reactome:568477 "Translation" xref: Reactome:581688 "Translation" xref: Reactome:585834 "Translation" xref: Reactome:592595 "Translation" xref: Reactome:595406 "Translation" xref: Reactome:597395 "Translation" xref: Reactome:598177 "Translation" xref: Reactome:599776 "Translation" xref: Reactome:72766 "Translation" xref: Wikipedia:Translation_(genetics) relationship: part_of GO:0043170 ! macromolecule metabolic process is_a: GO:0043284 ! biopolymer biosynthetic process is_a: GO:0019538 ! protein metabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006457 name: protein folding namespace: biological_process alt_id: GO:0007022 alt_id: GO:0007024 alt_id: GO:0007025 def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:go_curators, GOC:rb] subset: goslim_candida subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok 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:389960 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:389967 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:390466 "Chaperonin-mediated protein folding" xref: Reactome:392033 "Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding" xref: Reactome:448640 "Chaperonin-mediated protein folding" xref: Reactome:448770 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:469768 "Chaperonin-mediated protein folding" xref: Reactome:469885 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:487587 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:487589 "Chaperonin-mediated protein folding" xref: Reactome:507422 "Chaperonin-mediated protein folding" xref: Reactome:507545 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:517425 "Chaperonin-mediated protein folding" xref: Reactome:517525 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:526299 "Chaperonin-mediated protein folding" xref: Reactome:526394 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:531205 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:531207 "Chaperonin-mediated protein folding" xref: Reactome:536535 "Chaperonin-mediated protein folding" xref: Reactome:536580 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:542256 "Chaperonin-mediated protein folding" xref: Reactome:542306 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:547600 "Chaperonin-mediated protein folding" xref: Reactome:547647 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:552207 "Chaperonin-mediated protein folding" xref: Reactome:552239 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:557798 "Chaperonin-mediated protein folding" xref: Reactome:557852 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:568411 "Chaperonin-mediated protein folding" xref: Reactome:568446 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:581613 "Chaperonin-mediated protein folding" xref: Reactome:581659 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:585812 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:585814 "Chaperonin-mediated protein folding" xref: Reactome:592510 "Chaperonin-mediated protein folding" xref: Reactome:592570 "Formation of tubulin folding intermediates by CCT/TriC" xref: Reactome:595349 "Chaperonin-mediated protein folding" xref: Reactome:595388 "Formation of tubulin folding intermediates by CCT/TriC" xref: Wikipedia:Protein_folding is_a: GO:0019538 ! protein metabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006464 name: protein modification process namespace: biological_process 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:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "process resulting in protein modification" RELATED [] synonym: "protein tagging activity" RELATED [] xref: Reactome:163841 "Post-translational protein modification" xref: Reactome:448468 "Post-translational protein modification" xref: Reactome:469598 "Post-translational protein modification" xref: Reactome:487317 "Post-translational protein modification" xref: Reactome:507268 "Post-translational protein modification" xref: Reactome:517285 "Post-translational protein modification" xref: Reactome:526163 "Post-translational protein modification" xref: Reactome:531060 "Post-translational protein modification" xref: Reactome:536442 "Post-translational protein modification" xref: Reactome:542137 "Post-translational protein modification" xref: Reactome:547504 "Post-translational protein modification" xref: Reactome:552404 "Post-translational protein modification" xref: Reactome:557675 "Post-translational protein modification" xref: Reactome:568295 "Post-translational protein modification" xref: Reactome:581497 "Post-translational protein modification" xref: Reactome:585741 "Post-translational protein modification" xref: Reactome:592394 "Post-translational protein modification" xref: Reactome:595284 "Post-translational protein modification" xref: Reactome:597401 "Post-translational protein modification" xref: Reactome:598181 "Post-translational protein modification" is_a: GO:0019538 ! protein metabolic process is_a: GO:0043412 ! biopolymer modification is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006508 name: proteolysis namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with the hydrolysis of peptide bonds." [GOC:jsg, GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "ATP-dependent proteolysis" NARROW [GOC:mah] synonym: "peptidolysis" EXACT [] xref: Reactome:159782 "Removal of aminoterminal propeptides from gamma-carboxylated proteins" xref: Reactome:449259 "Removal of aminoterminal propeptides from gamma-carboxylated proteins" xref: Reactome:470378 "Removal of aminoterminal propeptides from gamma-carboxylated proteins" xref: Reactome:488060 "Removal of aminoterminal propeptides from gamma-carboxylated proteins" xref: Reactome:508017 "Removal of aminoterminal propeptides from gamma-carboxylated proteins" xref: Reactome:517878 "Removal of aminoterminal propeptides from gamma-carboxylated proteins" xref: Wikipedia:Proteolysis is_a: GO:0043285 ! biopolymer catabolic process 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:go_curators, http://cancerweb.ncl.ac.uk/] subset: goslim_pir subset: gosubset_prok synonym: "peptide metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006519 name: cellular amino acid and derivative metabolic process namespace: biological_process def: "The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents, and compounds derived from amino acids, as carried out by individual cells." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "amino acid and derivative metabolism" EXACT [] is_a: GO:0044238 ! primary metabolic process is_a: GO:0044237 ! cellular metabolic process [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_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: gosubset_prok synonym: "lipid metabolism" EXACT [] xref: Reactome:448458 "Metabolism of lipids and lipoproteins" xref: Reactome:469588 "Metabolism of lipids and lipoproteins" xref: Reactome:487307 "Metabolism of lipids and lipoproteins" xref: Reactome:507258 "Metabolism of lipids and lipoproteins" xref: Reactome:517280 "Metabolism of lipids and lipoproteins" xref: Reactome:526158 "Metabolism of lipids and lipoproteins" xref: Reactome:531055 "Metabolism of lipids and lipoproteins" xref: Reactome:536437 "Metabolism of lipids and lipoproteins" xref: Reactome:542134 "Metabolism of lipids and lipoproteins" xref: Reactome:547525 "Metabolism of lipids and lipoproteins" xref: Reactome:552094 "Metabolism of lipids and lipoproteins" xref: Reactome:557672 "Metabolism of lipids and lipoproteins" xref: Reactome:568290 "Metabolism of lipids and lipoproteins" xref: Reactome:581492 "Metabolism of lipids and lipoproteins" xref: Reactome:585774 "Metabolism of lipids and lipoproteins" xref: Reactome:592389 "Metabolism of lipids and lipoproteins" xref: Reactome:595297 "Metabolism of lipids and lipoproteins" xref: Reactome:597258 "Metabolism of lipids and lipoproteins" xref: Reactome:598099 "Metabolism of lipids and lipoproteins" xref: Reactome:599584 "Metabolism of lipids and lipoproteins" xref: Reactome:600579 "Metabolism of lipids and lipoproteins" xref: Reactome:602390 "Metabolism of lipids and lipoproteins" xref: Reactome:73923 "Metabolism of lipids and lipoproteins" xref: Wikipedia:Lipid_metabolism is_a: GO:0044238 ! primary metabolic process [Term] id: GO:0006662 name: glycerol ether metabolic process namespace: biological_process def: "The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol." [GOC:ai, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "glycerol ether metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006725 name: cellular aromatic compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." [GOC:ai, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "aromatic compound metabolism" EXACT [] synonym: "aromatic hydrocarbon metabolic process" NARROW [] synonym: "aromatic hydrocarbon metabolism" NARROW [] is_a: GO:0044237 ! cellular 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 subset: gosubset_prok 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:0044237 ! cellular 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_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "vitamin metabolism" EXACT [] xref: Reactome:196854 "Metabolism of vitamins and cofactors" xref: Reactome:448501 "Metabolism of vitamins and cofactors" xref: Reactome:469631 "Metabolism of vitamins and cofactors" xref: Reactome:487350 "Metabolism of vitamins and cofactors" xref: Reactome:507301 "Metabolism of vitamins and cofactors" xref: Reactome:517315 "Metabolism of vitamins and cofactors" xref: Reactome:526200 "Metabolism of vitamins and cofactors" xref: Reactome:531086 "Metabolism of vitamins and cofactors" xref: Reactome:536459 "Metabolism of vitamins and cofactors" xref: Reactome:542163 "Metabolism of vitamins and cofactors" xref: Reactome:547521 "Metabolism of vitamins and cofactors" xref: Reactome:552114 "Metabolism of vitamins and cofactors" xref: Reactome:557706 "Metabolism of vitamins and cofactors" xref: Reactome:568321 "Metabolism of vitamins and cofactors" xref: Reactome:581523 "Metabolism of vitamins and cofactors" xref: Reactome:585808 "Metabolism of vitamins and cofactors" xref: Reactome:592410 "Metabolism of vitamins and cofactors" xref: Reactome:595340 "Metabolism of vitamins and cofactors" xref: Reactome:597308 "Metabolism of vitamins and cofactors" xref: Reactome:598109 "Metabolism of vitamins and cofactors" xref: Reactome:599609 "Metabolism of vitamins and cofactors" xref: Reactome:600553 "Metabolism of vitamins and cofactors" xref: Reactome:602413 "Metabolism of vitamins and cofactors" is_a: GO:0044237 ! cellular 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, usually in the form of a phosphate group (PO4)." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "phosphorus metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006800 name: oxygen and reactive oxygen species metabolic process namespace: biological_process def: "The chemical reactions and pathways involving dioxygen (O2), or any of the reactive oxygen species, e.g. superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (-OH)." [GOC:jl, PMID:12115731] subset: goslim_pir subset: gosubset_prok synonym: "oxygen and AOS metabolism" EXACT [] synonym: "oxygen and ROI metabolism" EXACT [] synonym: "oxygen and ROS metabolic process" EXACT [] synonym: "oxygen and ROS metabolism" EXACT [] synonym: "oxygen and active oxygen species metabolism" EXACT [] synonym: "oxygen and reactive oxidative species metabolism" EXACT [] synonym: "oxygen and reactive oxygen intermediate metabolism" EXACT [] synonym: "oxygen and reactive oxygen species metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006805 name: xenobiotic metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide." [GOC:cab2] subset: goslim_pir subset: gosubset_prok synonym: "xenobiotic metabolism" EXACT [] xref: Reactome:140191 "Phase 1 functionalization" xref: Reactome:156580 "Phase II conjugation" xref: Reactome:156587 "Amino Acid conjugation" xref: Reactome:159424 "Conjugation of carboxylic acids" xref: Reactome:177128 "Conjugation of salicylate with glycine" xref: Reactome:177135 "Conjugation of benzoate with glycine" xref: Reactome:177162 "Conjugation of phenylacetate with glutamine" xref: Reactome:211859 "Biological oxidations" xref: Reactome:211945 "Phase 1 - Functionalization of compounds" xref: Reactome:448504 "Phase 1 - Functionalization of compounds" xref: Reactome:448505 "Biological oxidations" xref: Reactome:448574 "Phase II conjugation" xref: Reactome:448625 "Phase 1 functionalization" xref: Reactome:448895 "Conjugation of benzoate with glycine" xref: Reactome:448896 "Conjugation of carboxylic acids" xref: Reactome:448897 "Amino Acid conjugation" xref: Reactome:449231 "Conjugation of phenylacetate with glutamine" xref: Reactome:449280 "Conjugation of salicylate with glycine" xref: Reactome:469634 "Phase 1 - Functionalization of compounds" xref: Reactome:469635 "Biological oxidations" xref: Reactome:469703 "Phase II conjugation" xref: Reactome:469753 "Phase 1 functionalization" xref: Reactome:470012 "Conjugation of benzoate with glycine" xref: Reactome:470013 "Conjugation of carboxylic acids" xref: Reactome:470014 "Amino Acid conjugation" xref: Reactome:470350 "Conjugation of phenylacetate with glutamine" xref: Reactome:470400 "Conjugation of salicylate with glycine" xref: Reactome:487410 "Phase 1 - Functionalization of compounds" xref: Reactome:487411 "Biological oxidations" xref: Reactome:487415 "Phase II conjugation" xref: Reactome:487594 "Phase 1 functionalization" xref: Reactome:487713 "Conjugation of benzoate with glycine" xref: Reactome:487714 "Conjugation of carboxylic acids" xref: Reactome:487715 "Amino Acid conjugation" xref: Reactome:488030 "Conjugation of phenylacetate with glutamine" xref: Reactome:488078 "Conjugation of salicylate with glycine" xref: Reactome:507362 "Phase 1 - Functionalization of compounds" xref: Reactome:507363 "Biological oxidations" xref: Reactome:507370 "Phase II conjugation" xref: Reactome:507549 "Phase 1 functionalization" xref: Reactome:517378 "Phase II conjugation" xref: Reactome:517379 "Biological oxidations" xref: Reactome:517417 "Phase 1 - Functionalization of compounds" xref: Reactome:517528 "Phase 1 functionalization" xref: Reactome:526254 "Phase II conjugation" xref: Reactome:526255 "Biological oxidations" xref: Reactome:526291 "Phase 1 - Functionalization of compounds" xref: Reactome:526397 "Phase 1 functionalization" xref: Reactome:531155 "Phase 1 - Functionalization of compounds" xref: Reactome:531156 "Biological oxidations" xref: Reactome:531211 "Phase 1 functionalization" xref: Reactome:531414 "Phase II conjugation" xref: Reactome:536526 "Phase 1 - Functionalization of compounds" xref: Reactome:536527 "Biological oxidations" xref: Reactome:536583 "Phase 1 functionalization" xref: Reactome:536785 "Phase II conjugation" xref: Reactome:542213 "Phase II conjugation" xref: Reactome:542214 "Biological oxidations" xref: Reactome:542229 "Phase 1 - Functionalization of compounds" xref: Reactome:542246 "Phase 1 functionalization" xref: Reactome:547567 "Phase II conjugation" xref: Reactome:547568 "Biological oxidations" xref: Reactome:547592 "Phase 1 - Functionalization of compounds" xref: Reactome:547852 "Phase 1 functionalization" xref: Reactome:552168 "Phase 1 - Functionalization of compounds" xref: Reactome:552169 "Biological oxidations" xref: Reactome:552242 "Phase 1 functionalization" xref: Reactome:552443 "Phase II conjugation" xref: Reactome:557761 "Phase II conjugation" xref: Reactome:557762 "Biological oxidations" xref: Reactome:557790 "Phase 1 - Functionalization of compounds" xref: Reactome:557855 "Phase 1 functionalization" xref: Reactome:568374 "Phase II conjugation" xref: Reactome:568375 "Biological oxidations" xref: Reactome:568403 "Phase 1 - Functionalization of compounds" xref: Reactome:568449 "Phase 1 functionalization" xref: Reactome:581576 "Phase II conjugation" xref: Reactome:581577 "Biological oxidations" xref: Reactome:581605 "Phase 1 - Functionalization of compounds" xref: Reactome:581662 "Phase 1 functionalization" xref: Reactome:586030 "Phase II conjugation" xref: Reactome:586031 "Biological oxidations" xref: Reactome:592501 "Phase 1 - Functionalization of compounds" xref: Reactome:592502 "Biological oxidations" xref: Reactome:592573 "Phase 1 functionalization" xref: Reactome:592642 "Conjugation of benzoate with glycine" xref: Reactome:592643 "Conjugation of carboxylic acids" xref: Reactome:592644 "Amino Acid conjugation" xref: Reactome:592645 "Phase II conjugation" xref: Reactome:592861 "Conjugation of phenylacetate with glutamine" xref: Reactome:592886 "Conjugation of salicylate with glycine" xref: Reactome:595434 "Phase 1 - Functionalization of compounds" xref: Reactome:595435 "Biological oxidations" xref: Reactome:595529 "Phase II conjugation" xref: Reactome:597324 "Phase 1 - Functionalization of compounds" xref: Reactome:597325 "Biological oxidations" xref: Reactome:597365 "Conjugation of benzoate with glycine" xref: Reactome:597366 "Conjugation of carboxylic acids" xref: Reactome:597367 "Amino Acid conjugation" xref: Reactome:597368 "Phase II conjugation" xref: Reactome:597439 "Conjugation of phenylacetate with glutamine" xref: Reactome:597448 "Conjugation of salicylate with glycine" xref: Reactome:598121 "Phase 1 - Functionalization of compounds" xref: Reactome:598122 "Biological oxidations" xref: Reactome:598212 "Phase II conjugation" xref: Reactome:599669 "Phase 1 - Functionalization of compounds" xref: Reactome:599670 "Biological oxidations" xref: Reactome:599771 "Phase II conjugation" xref: Reactome:600624 "Phase 1 - Functionalization of compounds" xref: Reactome:600625 "Biological oxidations" xref: Reactome:600690 "Phase II conjugation" xref: Reactome:602454 "Phase II conjugation" xref: Reactome:602455 "Biological oxidations" xref: Reactome:602485 "Phase 1 - Functionalization of compounds" xref: Reactome:602505 "Phase 1 functionalization" xref: Wikipedia:Xenobiotic_metabolism relationship: part_of GO:0050896 ! response to stimulus is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006807 name: nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds; includes nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium." [GOC:go_curators, GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that amino acid and derivative metabolism should not be annotated here. Instead use the 'amino acid and derivative metabolism' node. subset: goslim_pir subset: gosubset_prok synonym: "nitrogen compound metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006810 name: transport namespace: biological_process def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells, or within a multicellular organism." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "small molecule transport" NARROW [] synonym: "solute:solute exchange" NARROW [] relationship: part_of GO:0051179 ! localization is_a: GO:0051234 ! establishment of localization [Term] id: GO:0006811 name: ion transport namespace: biological_process def: "The directed movement of charged atoms or small charged molecules into, out of, within or between cells." [GOC:ai] subset: goslim_generic subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0006818 name: hydrogen transport namespace: biological_process def: "The directed movement of hydrogen (H2 or H+), into, out of, within or between cells." [GOC:jl] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization 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, within or between cells. 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 [] relationship: part_of GO:0051179 ! localization 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, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "amino acid transmembrane transport" EXACT [GOC:mah] xref: Reactome:352230 "Amino acid transport across the plasma membrane" xref: Reactome:449281 "Amino acid transport across the plasma membrane" xref: Reactome:470401 "Amino acid transport across the plasma membrane" xref: Reactome:488079 "Amino acid transport across the plasma membrane" xref: Reactome:508045 "Amino acid transport across the plasma membrane" xref: Reactome:517899 "Amino acid transport across the plasma membrane" xref: Reactome:526725 "Amino acid transport across the plasma membrane" xref: Reactome:531498 "Amino acid transport across the plasma membrane" xref: Reactome:536887 "Amino acid transport across the plasma membrane" xref: Reactome:542637 "Amino acid transport across the plasma membrane" xref: Reactome:547953 "Amino acid transport across the plasma membrane" xref: Reactome:552527 "Amino acid transport across the plasma membrane" xref: Reactome:558149 "Amino acid transport across the plasma membrane" xref: Reactome:568776 "Amino acid transport across the plasma membrane" xref: Reactome:581979 "Amino acid transport across the plasma membrane" xref: Reactome:586032 "Amino acid transport across the plasma membrane" xref: Reactome:592887 "Amino acid transport across the plasma membrane" xref: Reactome:597449 "Amino acid transport across the plasma membrane" xref: Reactome:598213 "Amino acid transport across the plasma membrane" xref: Reactome:599782 "Amino acid transport across the plasma membrane" xref: Reactome:602616 "Amino acid transport across the plasma membrane" relationship: part_of GO:0051179 ! localization is_a: GO:0015849 ! organic acid transport is_a: GO:0009987 ! cellular process is_a: GO:0015837 ! amine transport [Term] id: GO:0006869 name: lipid transport namespace: biological_process def: "The directed movement of lipids into, out of, within or between cells. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok xref: Reactome:383186 "lipid transport" relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0006914 name: autophagy namespace: biological_process def: "The process by which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation." [ISBN:0198547684, PMID:11099404, PMID:9412464] subset: goslim_pir xref: Wikipedia:Autophagy_(cellular) is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006928 name: cell motion namespace: biological_process def: "Any process involved in the controlled movement of a cell." [GOC:dgh, GOC:dph, GOC:jl, GOC:mlg] subset: goslim_goa subset: goslim_pir subset: gosubset_prok synonym: "cell locomotion" RELATED [] synonym: "cell movement" EXACT [] relationship: part_of GO:0051179 ! localization is_a: GO:0009987 ! cellular process [Term] id: GO:0006936 name: muscle contraction namespace: biological_process def: "A process whereby 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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir xref: Wikipedia:Muscle_contraction is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0006949 name: syncytium formation namespace: biological_process def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir relationship: part_of GO:0032502 ! developmental process is_a: GO:0032502 ! developmental process is_a: GO:0009987 ! cellular process [Term] id: GO:0006996 name: organelle organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an 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] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: gosubset_prok synonym: "organelle organisation" EXACT [GOC:curators] synonym: "organelle organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization is_a: GO:0009987 ! cellular process [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_pir subset: goslim_yeast synonym: "nuclear morphology" RELATED [] synonym: "nuclear organisation" EXACT [GOC:curators] synonym: "nuclear organization" EXACT [GOC:curators] 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_generic subset: goslim_pir subset: goslim_pombe subset: goslim_yeast synonym: "mitochondria organization" EXACT [GOC:mah] synonym: "mitochondrion organisation" EXACT [GOC:mah] synonym: "mitochondrion organization and biogenesis" RELATED [GOC:curators] 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_generic subset: goslim_pir subset: gosubset_prok synonym: "cytoplasm organisation" EXACT [GOC:curators] synonym: "cytoplasm organization and biogenesis" RELATED [GOC:mah] is_a: GO:0016043 ! cellular component organization is_a: GO:0009987 ! cellular process [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: "ER organisation" EXACT [GOC:curators] synonym: "ER organization and biogenesis" RELATED [GOC:mah] synonym: "endoplasmic reticulum morphology" RELATED [] synonym: "endoplasmic reticulum organisation" EXACT [GOC:curators] synonym: "endoplasmic reticulum organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle 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 organisation" EXACT [GOC:curators] synonym: "Golgi organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle 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_pir subset: goslim_pombe subset: goslim_yeast synonym: "peroxisome organisation" EXACT [GOC:curators] synonym: "peroxisome organization and biogenesis" RELATED [GOC:mah] synonym: "peroxisome-assembly ATPase activity" RELATED [] 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 [GOC:curators] synonym: "endosome organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization [Term] id: GO:0007033 name: vacuole 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 vacuole." [GOC:mah] subset: goslim_pir subset: goslim_pombe subset: goslim_yeast synonym: "vacuolar assembly" EXACT [] synonym: "vacuole organisation" EXACT [GOC:curators] synonym: "vacuole organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization [Term] id: GO:0007047 name: cell wall 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 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:dph, GOC:jl, GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "cell wall organisation" EXACT [GOC:curators] synonym: "cell wall organization and biogenesis" RELATED [GOC:mah] is_a: GO:0045229 ! external encapsulating structure 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:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "cell-division cycle" EXACT [] xref: Wikipedia:Cell_cycle is_a: GO:0009987 ! cellular process [Term] id: GO:0007059 name: chromosome segregation namespace: biological_process def: "The process by which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets." [GOC:ai] subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "chromosome division" EXACT [] synonym: "chromosome transmission" RELATED [] xref: Wikipedia:Chromosome_segregation is_a: GO:0009987 ! cellular process [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_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Cell_signaling is_a: GO:0009987 ! cellular process [Term] id: GO:0007155 name: cell adhesion namespace: biological_process 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_pir subset: goslim_pombe subset: gosubset_prok synonym: "cell adhesion molecule activity" RELATED [] xref: Wikipedia:Cell_adhesion is_a: GO:0022610 ! biological adhesion is_a: GO:0009987 ! cellular process [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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir 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: goslim_pir xref: Wikipedia:Excretion relationship: part_of GO:0051179 ! localization is_a: GO:0032501 ! multicellular organismal process is_a: GO:0046903 ! secretion [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:heartdev_mtg, 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 relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0008037 name: cell recognition namespace: biological_process def: "The process by which a cell in a multicellular organism interprets its surroundings." [GOC:go_curators] subset: goslim_generic subset: goslim_pir is_a: GO:0009987 ! cellular process [Term] id: GO:0008144 name: drug binding namespace: molecular_function def: "Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0008150 name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that 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 ND, no data, is used to indicate this. subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "biological process" EXACT [] synonym: "biological process unknown" NARROW [] synonym: "physiological process" EXACT [] xref: Wikipedia:Biological_process [Term] id: GO:0008152 name: metabolic process namespace: biological_process def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] synonym: "metabolism resulting in cell growth" NARROW [] xref: Wikipedia:Metabolism is_a: GO:0008150 ! biological_process [Term] id: GO:0008233 name: peptidase activity namespace: molecular_function 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." [GOC:jl, ISBN:0815332181] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "hydrolase, acting on peptide bonds" EXACT [] synonym: "peptide hydrolase activity" EXACT [] synonym: "protease activity" EXACT [] synonym: "proteinase activity" EXACT [] xref: EC:3.4 xref: Reactome:1687 "peptidase activity" is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0008278 name: cohesin complex namespace: cellular_component alt_id: GO:0008279 def: "A protein complex required for sister chromatid cohesion in eukaryotes." [PMID:9887095] subset: goslim_pir synonym: "14S cohesin" NARROW [] synonym: "SMC complex" RELATED [] relationship: part_of GO:0005694 ! chromosome is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0008283 name: cell proliferation namespace: biological_process def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb] subset: goslim_generic subset: goslim_pir subset: gosubset_prok is_a: GO:0009987 ! cellular 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 subset: gosubset_prok relationship: part_of GO:0005575 ! cellular_component is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0008289 name: lipid binding namespace: molecular_function def: "Interacting selectively and non-covalently with a lipid." [GOC:ai] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok 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 a 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:go_curators, ISBN:0198599560] subset: goslim_pir relationship: part_of GO:0005856 ! cytoskeleton is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0008367 name: bacterial binding namespace: molecular_function def: "Interacting selectively and non-covalently with any part of a bacterial cell." [GOC:jl] subset: goslim_pir subset: gosubset_prok synonym: "bacterium binding" EXACT [] synonym: "binding to bacterium" EXACT [] is_a: GO:0005488 ! binding [Term] id: GO:0008641 name: small protein 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: "ubiquitin-like activating enzyme activity" NARROW [] is_a: GO:0003824 ! catalytic activity [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, within or between cells. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "sugar transport" NARROW [] relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0008655 name: pyrimidine salvage namespace: biological_process def: "Any process that generates a pyrimidine, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis." [GOC:jl] subset: goslim_pir subset: gosubset_prok is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:0046483 ! heterocycle metabolic process is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process is_a: GO:0043094 ! cellular metabolic compound salvage [Term] id: GO:0008907 name: integrase activity namespace: molecular_function def: "Catalysis of the integration of lambdoid phage DNA during establishment, probably by forming a transient DNA-protein link." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_goa subset: goslim_pir subset: gosubset_prok is_a: GO:0003824 ! catalytic activity [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 DNA target sequences." [GOC:elh] comment: Consider also annotating to the molecular function term 'double-stranded DNA binding ; GO:0003690'. 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 subset: gosubset_prok is_a: GO:0003824 ! catalytic activity [Term] id: GO:0009055 name: electron carrier activity namespace: molecular_function alt_id: GO:0009053 alt_id: GO:0009054 def: "Any molecular entity that serves as an electron acceptor and electron donor in an electron transport system." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: gosubset_prok synonym: "2Fe-2S electron transfer carrier" NARROW [] synonym: "3Fe-4S/4Fe-4S electron transfer carrier" NARROW [] synonym: "adrenodoxin-type ferredoxin" NARROW [] synonym: "amicyanin" NARROW [] synonym: "azurin" NARROW [] synonym: "bacterial-type ferredoxin" NARROW [] synonym: "chloroplast-type ferredoxin" NARROW [] synonym: "copper electron carrier" NARROW [] synonym: "dicluster bacterial-type ferredoxin" NARROW [] synonym: "electron acceptor activity" NARROW [] synonym: "electron carrier, chlorophyll electron transport system" RELATED [] synonym: "electron donor activity" NARROW [] synonym: "electron transfer flavoprotein" NARROW [] synonym: "electron transfer flavoprotein, group I" NARROW [] synonym: "electron transfer flavoprotein, group II" NARROW [] synonym: "electron transporter activity" EXACT [] synonym: "high-potential iron-sulfur carrier" NARROW [] synonym: "iron-sulfur electron transfer carrier" NARROW [] synonym: "monocluster bacterial-type ferredoxin" NARROW [] synonym: "mononuclear iron electron carrier" NARROW [] synonym: "polyferredoxin" NARROW [] synonym: "redox-active disulfide bond electron carrier" NARROW [] synonym: "rubredoxin" NARROW [] synonym: "small blue copper electron carrier" NARROW [] synonym: "thioredoxin-like 2Fe-2S ferredoxin" NARROW [] xref: Reactome:20046 "electron carrier activity" is_a: GO:0003674 ! molecular_function [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 (ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleotide), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine)." [GOC:ma] subset: goslim_pir subset: gosubset_prok synonym: "nucleoside metabolism" EXACT [] is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid 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 subset: gosubset_prok synonym: "nucleotide metabolism" EXACT [] is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0009225 name: nucleotide-sugar metabolic process namespace: biological_process def: "The chemical reactions and pathways involving nucleotide-sugars, any nucleotide in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "nucleotide-sugar metabolism" EXACT [] is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [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] subset: goslim_pir subset: gosubset_prok synonym: "fimbria" EXACT [] synonym: "fimbriae" EXACT [] synonym: "fimbrium" EXACT [] synonym: "pili" EXACT [] xref: Wikipedia:Pilus relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [Term] id: GO:0009292 name: genetic transfer namespace: biological_process def: "In the absence of a sexual life cycle, the process involved in the introduction of genetic information to create a genetically different individual." [GOC:clt] subset: goslim_pir subset: gosubset_prok synonym: "genetic exchange" BROAD [] is_a: GO:0051704 ! multi-organism process [Term] id: GO:0009308 name: amine metabolic process namespace: biological_process 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, as carried out by individual cells. 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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "amine metabolism" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process [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, UniProtKB:P24182] subset: goslim_pir subset: gosubset_prok synonym: "ACCase complex" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0009372 name: quorum sensing namespace: biological_process def: "The process by which single-celled organisms monitor their population density by detecting the concentration of small, diffusible signal molecules produced by the cells themselves." [PMID:15716452, PMID:8288518] subset: goslim_pir subset: gosubset_prok synonym: "quorum sensing system" EXACT [] xref: Wikipedia:Quorum_sensing is_a: GO:0051704 ! multi-organism process is_a: GO:0065007 ! biological regulation [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 subset: gosubset_prok synonym: "toxin metabolism" EXACT [] relationship: part_of GO:0050896 ! response to stimulus is_a: GO:0044237 ! cellular metabolic process 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 subset: gosubset_prok synonym: "reaction center" NARROW [] synonym: "reaction centre" NARROW [] xref: Wikipedia:Photosystem relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0009579 ! thylakoid is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Plastid relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "photosynthetic membrane" RELATED [] xref: Wikipedia:Thylakoid relationship: part_of GO:0005622 ! intracellular is_a: GO:0044464 ! cell part [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 [GOC:curators] 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, within or between cells." [GOC:tb] subset: goslim_pir relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport is_a: GO:0065007 ! biological regulation [Term] id: GO:0009975 name: cyclase activity namespace: molecular_function def: "Catalysis of a ring closure reaction." [ISBN:0198547684] subset: goslim_pir subset: gosubset_prok 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_goa subset: goslim_pir subset: gosubset_prok synonym: "cell associated" EXACT [] synonym: "cell bound" EXACT [] relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [Term] id: GO:0009987 name: cellular process namespace: biological_process alt_id: GO:0008151 alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "cell growth and/or maintenance" NARROW [] synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] is_a: GO:0008150 ! biological_process [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:0009987 ! cellular process [Term] id: GO:0010191 name: mucilage metabolic process namespace: biological_process def: "The chemical reactions and pathways involving mucilage, a gelatinous substance secreted by plants." [GOC:sm] subset: goslim_pir synonym: "mucilage metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic 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:0043234 ! protein complex [Term] id: GO:0015031 name: protein transport namespace: biological_process alt_id: GO:0015831 def: "The directed movement of proteins into, out of, within or between cells." [GOC:ai] subset: goslim_generic subset: goslim_pir subset: gosubset_prok synonym: "enzyme transport" NARROW [] relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0015074 name: DNA integration namespace: biological_process def: "The process by which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome." [GOC:mah] subset: goslim_pir subset: gosubset_prok is_a: GO:0006259 ! DNA metabolic process [Term] id: GO:0015457 name: auxiliary transport protein activity namespace: molecular_function def: "Facilitates transport across one or more biological membranes but do not themselves participate directly as transporters. These proteins always function in conjunction with one or more established transport systems. They may provide a function connected with energy coupling to transport, play a structural role in complex formation, serve a biogenic or stability function or function in regulation." [TC:8.A.-.-.-] subset: goslim_pir subset: gosubset_prok is_a: GO:0003674 ! molecular_function [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, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0015791 name: polyol transport namespace: biological_process def: "The directed movement of polyols, any polyhydric alcohol, into, out of, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok is_a: GO:0006810 ! transport relationship: part_of GO:0051179 ! localization [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, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization 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, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "murein transport" EXACT [] relationship: part_of GO:0051179 ! localization 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, within or between cells." [GOC:ai, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "amine/polyamine transport" RELATED [] relationship: part_of GO:0051179 ! localization 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, within or between cells." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0015891 name: siderophore transport namespace: biological_process def: "The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "siderochrome transport" NARROW [] relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0015893 name: drug transport namespace: biological_process def: "The directed movement of a drug, a substance used in the diagnosis, treatment or prevention of a disease, into, out of, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization relationship: part_of GO:0050896 ! response to stimulus is_a: GO:0006810 ! transport [Term] id: GO:0015920 name: lipopolysaccharide transport namespace: biological_process def: "The directed movement of lipopolysaccharides into, out of, within or between cells. 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 subset: gosubset_prok synonym: "LPS transport" EXACT [] relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0015931 name: nucleobase, nucleoside, nucleotide and nucleic acid transport namespace: biological_process def: "The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization 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 subset: gosubset_prok synonym: "ribosomal small subunit" EXACT [] relationship: part_of GO:0005840 ! ribosome is_a: GO:0030529 ! ribonucleoprotein complex [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_pir subset: gosubset_prok synonym: "methane biosynthesis" EXACT [] synonym: "methane biosynthetic process" EXACT [] xref: UM-BBD_pathwayID:meth xref: Wikipedia:Methanogenesis is_a: GO:0045333 ! cellular respiration is_a: GO:0043446 ! cellular alkane metabolic process [Term] id: GO:0015949 name: nucleobase, nucleoside and nucleotide interconversion namespace: biological_process def: "The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide is synthesized from another nucleobase, nucleoside or nucleotide." [GOC:mah, ISBN:0306444747, ISBN:0471394831] subset: goslim_pir subset: gosubset_prok xref: MetaCyc:P1-PWY is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0015976 name: carbon utilization namespace: biological_process subset: goslim_pir subset: gosubset_prok is_a: GO:0008152 ! metabolic process [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_pir subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Photosynthesis is_a: GO:0044237 ! cellular 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 [] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0016020 name: membrane namespace: cellular_component def: "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:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok xref: Wikipedia:Biological_membrane relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [Term] id: GO:0016028 name: rhabdomere namespace: cellular_component def: "The specialized microvillar organelle on the apical surfaces of a photoreceptor cell containing the visual pigment rhodopsin and most of the proteins involved in phototransduction." [GOC:hb, PMID:8646774] subset: goslim_pir relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [Term] id: GO:0016032 name: viral reproduction namespace: biological_process def: "The process by which a virus reproduces. Usually, this is by 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:mah] comment: See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'. subset: goslim_generic subset: goslim_pir synonym: "viral infection" RELATED [] synonym: "viral life cycle" EXACT [] synonym: "viral replication cycle" EXACT [] synonym: "virulence" RELATED [] xref: Reactome:162587 "HIV Life Cycle" xref: Reactome:162906 "HIV Infection" xref: Reactome:168255 "Influenza Life Cycle" xref: Wikipedia:Viral_life_cycle is_a: GO:0008150 ! biological_process [Term] id: GO:0016043 name: cellular component 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 cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "cell organisation" EXACT [] synonym: "cell organization and biogenesis" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process [Term] id: GO:0016044 name: membrane 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 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:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_candida subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "membrane organisation" EXACT [GOC:curators] synonym: "membrane organization and biogenesis" RELATED [GOC:mah] xref: Reactome:199991 "Membrane Trafficking" xref: Reactome:448815 "Membrane Trafficking" xref: Reactome:469931 "Membrane Trafficking" xref: Reactome:487634 "Membrane Trafficking" xref: Reactome:507593 "Membrane Trafficking" xref: Reactome:517561 "Membrane Trafficking" xref: Reactome:526427 "Membrane Trafficking" xref: Reactome:531244 "Membrane Trafficking" xref: Reactome:536615 "Membrane Trafficking" xref: Reactome:542339 "Membrane Trafficking" xref: Reactome:547680 "Membrane Trafficking" xref: Reactome:552334 "Membrane Trafficking" xref: Reactome:557889 "Membrane Trafficking" xref: Reactome:568487 "Membrane Trafficking" xref: Reactome:581698 "Membrane Trafficking" xref: Reactome:585888 "Membrane Trafficking" xref: Reactome:592605 "Membrane Trafficking" xref: Reactome:595446 "Membrane Trafficking" is_a: GO:0016043 ! cellular component organization is_a: GO:0009987 ! cellular process [Term] id: GO:0016049 name: cell growth namespace: biological_process def: "The process by which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:ai] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok 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 [] relationship: part_of GO:0065007 ! biological regulation is_a: GO:0009987 ! cellular process 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 [GOC:curators] 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 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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "RNA metabolism" EXACT [] is_a: GO:0043283 ! biopolymer metabolic process is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0016192 name: vesicle-mediated transport namespace: biological_process alt_id: GO:0006899 def: "The directed movement of substances into, out of or within a cell by a cellular process that begins with the formation of membrane-bounded vesicles in which the transported substances are enclosed or located in the vesicle membrane. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] subset: goslim_candida subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok 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] relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport is_a: GO:0009987 ! cellular process [Term] id: GO:0016209 name: antioxidant activity namespace: molecular_function def: "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: gosubset_prok is_a: GO:0003674 ! molecular_function [Term] id: GO:0016458 name: gene silencing namespace: biological_process def: "Any transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:jic, GOC:tb] comment: Note that this process is the opposite of long-term maintenance of gene activation. subset: goslim_pir synonym: "long-term maintenance of gene inactivation" RELATED [] xref: Wikipedia:Gene_silencing is_a: GO:0009987 ! cellular process is_a: GO:0065007 ! biological regulation relationship: negatively_regulates GO:0043170 ! macromolecule metabolic process [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_pir subset: gosubset_prok synonym: "hydrogen-transporting two-sector ATPase complex" EXACT [] synonym: "vacuolar hydrogen-transporting ATPase" RELATED [] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 [] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0016491 name: oxidoreductase activity namespace: molecular_function def: "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC:go_curators] comment: Note that enzymes of class EC:1.97.-.- should also be annotated to this term. subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "oxidoreductase activity, acting on other substrates" NARROW [] synonym: "redox activity" EXACT [] xref: EC:1 xref: Reactome:95 "oxidoreductase activity" is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016530 name: metallochaperone activity namespace: molecular_function def: "Assists in the delivery of metal ions to target proteins or compartments." [GOC:jl, PMID:11739376] subset: goslim_pir subset: gosubset_prok is_a: GO:0003674 ! molecular_function [Term] id: GO:0016585 name: chromatin remodeling complex namespace: cellular_component alt_id: GO:0005679 def: "Any complex that mediates dynamic changes in eukaryotic chromatin." [GOC:mah] subset: goslim_pir synonym: "chromatin remodelling complex" EXACT [] synonym: "nucleosome remodeling complex" EXACT [] relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0016591 name: DNA-directed RNA polymerase II, holoenzyme namespace: cellular_component def: "Large protein complex composed of the RNA polymerase core complex and a variety of other proteins including transcription factor complexes TFIIA, D, E, F, and H which are required for promoter recognition, and the Mediator subcomplex. Catalyzes the synthesis of eukaryotic pre-mRNA." [GOC:jl, PMID:15196470, Wikipedia:Rna_polymerase_ii] subset: goslim_pir relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0016597 name: amino acid binding namespace: molecular_function def: "Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents." [GOC:ai] subset: goslim_pir subset: gosubset_prok is_a: GO:0031406 ! carboxylic acid binding is_a: GO:0043176 ! amine 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." [EC:1.18.6.1, MetaCyc:CPLX-186, MetaCyc:CPLX-525] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0016740 name: transferase activity namespace: molecular_function def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok xref: EC:2 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016787 name: hydrolase activity namespace: molecular_function def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok xref: EC:3 xref: Reactome:450 "hydrolase activity" is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016829 name: lyase activity namespace: molecular_function def: "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC:4.-.-.-, ISBN:0198547684] comment: Note that enzymes of class EC:4.99.-.- should also be annotated to this term. subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "other lyase activity" NARROW [] xref: EC:4 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016853 name: isomerase activity namespace: molecular_function def: "Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that enzymes of class EC:5.99.-.- should also be annotated to this term. subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "other isomerase activity" NARROW [] xref: EC:5 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016874 name: ligase activity namespace: molecular_function def: "Catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok xref: EC:6 is_a: GO:0003824 ! catalytic activity [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 [] relationship: part_of GO:0005576 ! extracellular region is_a: GO:0043234 ! protein complex [Term] id: GO:0017053 name: transcriptional repressor complex namespace: cellular_component def: "A protein complex that possesses activity that prevents or downregulates transcription." [GOC:mah] subset: goslim_pir relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0017144 name: drug metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice." [GOC:cab2] subset: goslim_pir subset: gosubset_prok synonym: "drug metabolism" EXACT [] xref: Reactome:428314 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI)" xref: Reactome:450647 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI)" xref: Reactome:537533 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI)" xref: Reactome:76397 "Acetaminophen oxidised to N-acetylbenzoquinoneimine (NAPQI)" xref: Wikipedia:Drug_metabolism is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0018942 name: organometal metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organometals, any metal-containing organic compound, especially one in which the metal atom is linked directly to one of more carbon atoms." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "organometal metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0019012 name: virion namespace: cellular_component def: "The complete fully infectious extracellular virus particle." [ISBN:0781718325] subset: goslim_pir synonym: "complete virus particle" EXACT [] xref: Wikipedia:Virus is_a: GO:0005575 ! cellular_component [Term] id: GO:0019213 name: deacetylase activity namespace: molecular_function def: "Catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule." [GOC:jl] subset: goslim_pir subset: gosubset_prok is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0019239 name: deaminase activity namespace: molecular_function def: "Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3)." [GOC:jl, http://cancerweb.ncl.ac.uk/] subset: goslim_pir subset: gosubset_prok is_a: GO:0003824 ! catalytic activity [Term] id: GO:0019538 name: protein metabolic process namespace: biological_process alt_id: GO:0006411 def: "The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification." [GOC:ma] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "protein metabolic process and modification" EXACT [] synonym: "protein metabolism" EXACT [] synonym: "protein metabolism and modification" EXACT [] xref: Wikipedia:Protein_metabolism is_a: GO:0043283 ! biopolymer metabolic process is_a: GO:0044238 ! primary metabolic process [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:go_curators] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "secondary metabolism" EXACT [] xref: Wikipedia:Secondary_metabolism is_a: GO:0008152 ! metabolic process [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 is_a: GO:0043234 ! protein complex [Term] id: GO:0019825 name: oxygen binding namespace: molecular_function def: "Interacting selectively and non-covalently with oxygen (O2)." [GOC:jl] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "cytochrome P450" NARROW [] synonym: "cytochrome P450 activity" RELATED [] xref: Reactome:4477 "oxygen binding" is_a: GO:0005488 ! binding [Term] id: GO:0019840 name: isoprenoid binding namespace: molecular_function def: "Interacting selectively and non-covalently with any 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 subset: gosubset_prok is_a: GO:0008289 ! lipid binding [Term] id: GO:0019842 name: vitamin binding namespace: molecular_function def: "Interacting selectively and non-covalently with 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_pir subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0019861 name: flagellum namespace: cellular_component alt_id: GO:0008223 def: "Long whiplike or feathery structures borne either singly or in groups by the motile cells of many bacteria and unicellular eukaryotes and by the motile male gametes of many eukaryotic organisms, which propel the cell through a liquid medium." [SP_KW:KW-0282] subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Flagellum relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [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 relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [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] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [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] subset: goslim_pir is_a: GO:0009987 ! cellular process [Term] id: GO:0022411 name: cellular component disassembly namespace: biological_process def: "A cellular process that results in the breakdown of a part of the cell." [GOC:isa_complete] subset: goslim_pir subset: gosubset_prok synonym: "cell structure disassembly" EXACT [] is_a: GO:0016043 ! cellular component organization [Term] id: GO:0022607 name: cellular component assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_pir subset: gosubset_prok synonym: "cell structure assembly" EXACT [] relationship: part_of GO:0008150 ! biological_process is_a: GO:0016043 ! cellular component organization [Term] id: GO:0022610 name: biological adhesion namespace: biological_process def: "The attachment of a cell or organism to a substrate or other organism." [GOC:isa_complete] subset: goslim_pir subset: gosubset_prok is_a: GO:0008150 ! biological_process [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 subset: gosubset_prok synonym: "antenna complex" RELATED [] xref: Wikipedia:Light-harvesting_complex relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0030112 name: glycocalyx namespace: cellular_component def: "A viscous, carbohydrate rich layer at the outermost periphery of a cell." [GOC:mlg, ISBN:0815316208] subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Glycocalyx relationship: part_of GO:0005575 ! cellular_component 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 subset: gosubset_prok xref: Wikipedia:S-layer relationship: part_of GO:0005575 ! cellular_component 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 [] relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0043234 ! protein complex relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0030175 name: filopodium namespace: cellular_component alt_id: GO:0030028 def: "Thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone; usually approximately 0.1 um wide, 5-10 um long, can be up to 50 um long in axon growth cones; contains a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward." [GOC:mah, ISBN:0815316194] subset: goslim_pir synonym: "microspike" EXACT [] xref: Wikipedia:Filopodia relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [Term] id: GO:0030234 name: enzyme regulator activity namespace: molecular_function def: "Modulates the activity of an enzyme." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "catalytic regulator activity" EXACT [GOC:dph] synonym: "enzyme modulator" EXACT [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0030246 name: carbohydrate binding namespace: molecular_function def: "Interacting selectively and non-covalently with any carbohydrate, any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:mah] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "selectin" RELATED [] 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." [GOC:go_curators] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [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_generic subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Cell_envelope is_a: GO:0005575 ! cellular_component [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 relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [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 subset: gosubset_prok synonym: "cross wall" EXACT [] synonym: "septum" BROAD [] relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [Term] id: GO:0030431 name: sleep namespace: biological_process def: "Any process by 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:0050896 ! response to stimulus 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) relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [Term] id: GO:0030528 name: transcription regulator activity namespace: molecular_function def: "Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "transcriptional regulator activity" EXACT [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0030529 name: ribonucleoprotein complex namespace: cellular_component def: "A macromolecular complex containing both protein and RNA molecules." [GOC:krc] subset: goslim_pir subset: gosubset_prok synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] synonym: "protein-RNA complex" EXACT [] synonym: "ribonucleoprotein" EXACT [] xref: Wikipedia:Ribonucleoprotein relationship: part_of GO:0005622 ! intracellular is_a: GO:0032991 ! macromolecular complex is_a: GO:0044464 ! cell part [Term] id: GO:0030532 name: small nuclear ribonucleoprotein complex namespace: cellular_component def: "A complex composed of RNA of the small nuclear RNA (snRNA) class and protein, found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP or U4/U6 snRNP. Many, but not all, of these complexes are involved in splicing of nuclear mRNAs." [GOC:krc, GOC:mah, ISBN:0879695897] subset: goslim_pir synonym: "small nuclear ribonucleoprotein" EXACT [] synonym: "snRNP" EXACT [] xref: Wikipedia:SnRNP relationship: part_of GO:0005634 ! nucleus is_a: GO:0030529 ! ribonucleoprotein complex [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 subset: gosubset_prok synonym: "RNase P complex" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0030529 ! 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 relationship: part_of GO:0005622 ! intracellular is_a: GO:0030529 ! 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: 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 relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 subset: gosubset_prok synonym: "multisubunit RNA polymerase" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 subset: gosubset_prok 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 relationship: part_of GO:0005694 ! chromosome is_a: GO:0032991 ! macromolecular complex is_a: GO:0044464 ! cell part [Term] id: GO:0030904 name: retromer complex namespace: cellular_component def: "A conserved multimeric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. For example, the budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p." [PMID:9700157] subset: goslim_pir relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 catalyses 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 subset: gosubset_prok synonym: "Complex I" EXACT [] 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 relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0030990 name: intraflagellar transport particle namespace: cellular_component def: "A nonmembrane-bound oliogmeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules." [GOC:kmv, PMID:14570576] subset: goslim_pir relationship: part_of GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0042995 ! cell projection is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0031012 name: extracellular matrix namespace: cellular_component def: "A structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals) or be part of the cell (as in plants)." [GOC:mah] subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Extracellular_matrix is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005576 ! extracellular region [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 [GOC:curators] synonym: "microtubule organizing center organization and biogenesis" RELATED [GOC:mah] relationship: part_of GO:0006996 ! organelle organization is_a: 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 subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0031049 name: programmed DNA elimination namespace: biological_process def: "The DNA metabolic process by which micronuclear-limited sequences, internal eliminated sequences (IES) and breakage eliminated sequences (BES) are removed from the developing macronucleus (anlage) of a ciliate." [GOC:mah, GOC:ns] subset: goslim_pir is_a: GO:0006259 ! DNA metabolic process [Term] id: GO:0031074 name: nucleocytoplasmic shuttling 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: goslim_pir relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [Term] id: GO:0031105 name: septin complex namespace: cellular_component def: "Any of several heterooligomeric complexes containing multiple septins." [GOC:mah, PMID:15385632] subset: goslim_pir relationship: part_of GO:0005856 ! cytoskeleton is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir synonym: "pseudopod" EXACT [] xref: Wikipedia:Pseudopod relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [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:12158317, PMID:14617809] subset: goslim_pir relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0005783 ! endoplasmic reticulum is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 [] relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [Term] id: GO:0031254 name: 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 [] relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [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." [PMID:12628743, PMID:12655293] subset: goslim_pir synonym: "DISC" EXACT [] synonym: "death-inducing signalling complex" EXACT [] xref: Wikipedia:Death-inducing_signaling_complex relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 relationship: part_of GO:0005622 ! intracellular is_a: GO:0030529 ! 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 [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0031386 name: protein tag namespace: molecular_function def: "Acting as an indicator or marker to facilitate recognition by other molecules in the cell. Recognition of the tag, which can be covalently attached to the target molecule, may result in modification, sequestration, transport or degradation of the molecule in question." [GOC:go_curators] subset: goslim_generic subset: goslim_pir synonym: "protein tagging activity" RELATED [] synonym: "ubiquitin" RELATED [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0031406 name: carboxylic acid binding namespace: molecular_function def: "Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0031409 name: pigment binding namespace: molecular_function def: "Interacting selectively and non-covalently with a pigment, any general or particular coloring matter in living organisms, e.g. melanin." [GOC:mah] subset: goslim_pir subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0031469 name: polyhedral organelle 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] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043232 ! intracellular non-membrane-bounded organelle [Term] id: GO:0031501 name: mannosyltransferase complex namespace: cellular_component def: "A complex that posseses mannosyltransferase activity." [GOC:mah] subset: goslim_pir relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 [] relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0031640 name: killing of cells of another organism namespace: biological_process alt_id: GO:0001908 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 subset: gosubset_prok synonym: "killing of cells of another, non-host, organism" NARROW [] is_a: GO:0001906 ! cell killing is_a: GO:0051704 ! multi-organism process [Term] id: GO:0031647 name: regulation of protein stability namespace: biological_process def: "Any process that affects the structure and integrity of a protein by altering the likelihood of its degradation or aggregation." [GOC:dph, GOC:mah, GOC:tb] subset: goslim_pir subset: gosubset_prok relationship: regulates GO:0043170 ! macromolecule metabolic process is_a: GO:0019538 ! protein metabolic process is_a: GO:0065007 ! biological regulation [Term] id: GO:0031982 name: vesicle namespace: cellular_component def: "Any small, fluid-filled, spherical organelle enclosed by membrane or protein." [GOC:mah, GOC:pz] subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Vesicle_(biology) is_a: GO:0043226 ! organelle [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:go_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 characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusions." [PMID:12083798, PMID:16624291] subset: goslim_pir xref: Wikipedia:Bleb_(cell_biology) relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [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. The cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane. The mitotic, or meiotic, spindle is aligned perpendicular to the division plane." [GOC:krc, GOC:ns, PMID:12101122, PMID:15380095] subset: goslim_pir synonym: "cell division plane" EXACT [] relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [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 relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [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." [GOC:jp, ISBN:1555812090] subset: goslim_candida subset: goslim_pir subset: goslim_yeast subset: gosubset_prok xref: Wikipedia:Transposon is_a: GO:0009987 ! cellular 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 relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0032392 name: DNA geometric change namespace: biological_process def: "The process by 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:0006259 ! DNA metabolic process [Term] id: GO:0032421 name: stereocilium bundle namespace: cellular_component def: "An actin-based, cross-linked cellular protrusion on the apical surface of auditory and vestibular hair cells. 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 [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043232 ! intracellular non-membrane-bounded organelle [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: decaprenyl diphosphate synthase complex namespace: cellular_component def: "A complex that possesses di-trans,poly-cis-decaprenylcistransferase activity; involved in ubiquinone biosynthesis." [GOC:mah, PMID:14519123] subset: goslim_pir is_a: GO:0043234 ! protein complex [Term] id: GO:0032501 name: multicellular organismal process namespace: biological_process 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] subset: goslim_goa subset: goslim_pir synonym: "organismal physiological process" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0032502 name: developmental process namespace: biological_process 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_pir subset: gosubset_prok synonym: "development" NARROW [] is_a: GO:0008150 ! biological_process [Term] id: GO:0032989 name: cellular component morphogenesis namespace: biological_process def: "The process by which cellular structures, including whole cells or cell parts, are generated and organized. Morphogenesis pertains to the creation of form." [GOC:dph, GOC:mah, GOC:tb] subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "cellular structure morphogenesis" EXACT [GOC:dph, GOC:tb] relationship: part_of GO:0032502 ! developmental process is_a: GO:0032502 ! developmental process is_a: GO:0016043 ! cellular component organization is_a: GO:0009987 ! cellular process [Term] id: GO:0032991 name: macromolecular complex namespace: cellular_component def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together." [GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "macromolecule complex" EXACT [] is_a: GO:0005575 ! cellular_component [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 "Fundamental Immunology"] subset: goslim_pir synonym: "Fc-receptor complex" EXACT [] synonym: "FcR complex" EXACT [] synonym: "immunoglobulin receptor complex" BROAD [] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0033061 name: DNA recombinase mediator complex namespace: cellular_component def: "A protein complex that promotes nucleoprotein filament formation during homologous recombination; most known examples contain two or more RecA family proteins (often Rad51 paralogs)." [GOC:elh, GOC:mah, GOC:vw] subset: goslim_pir relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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." [http://authors.library.caltech.edu/3529/, PMID:11325545, PMID:12003948] subset: goslim_pir relationship: part_of GO:0005622 ! intracellular 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_pir subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0033218 name: amide binding namespace: molecular_function def: "Interacting selectively and non-covalently with an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [ChEBI:32988, GOC:mah] subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0033256 name: I-kappaB/NF-kappaB complex namespace: cellular_component def: "A protein complex containing an I-kappaB protein and one or more copies of an NF-kappaB protein; mediates regulation of NF-kappaB activity by I-kappaB." [GOC:mah, PMID:9407099] subset: goslim_pir relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0034622 name: cellular macromolecular complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a complex, carried out at the cellular level." [GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "cellular macromolecule complex assembly" EXACT [] relationship: part_of GO:0008150 ! biological_process is_a: GO:0009987 ! cellular process is_a: GO:0065003 ! macromolecular complex assembly [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 relationship: part_of GO:0005634 ! nucleus is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [Term] id: GO:0035273 name: phthalate binding namespace: molecular_function def: "Interacting selectively and non-covalently with a phthalate, any ester or salt of phthalic acid." [http://umbbd.ahc.umn.edu/pth/pth_map.html] subset: goslim_pir subset: gosubset_prok is_a: GO:0043167 ! ion binding [Term] id: GO:0040007 name: growth namespace: biological_process 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: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "growth pattern" RELATED [] 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_pir subset: gosubset_prok 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, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization 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:go_curators, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "attractant" BROAD [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0042133 name: neurotransmitter metabolic process namespace: biological_process def: "The chemical reactions and pathways involving neurotransmitters, any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell." [GOC:jl, http://cancerweb.ncl.ac.uk/] subset: goslim_pir synonym: "neurotransmitter metabolism" EXACT [] xref: Reactome:374909 "Metabolism of Noradrenaline" xref: Reactome:442356 "Metabolism of Noradrenaline" xref: Reactome:464108 "Metabolism of Noradrenaline" xref: Reactome:482514 "Metabolism of Noradrenaline" xref: Reactome:502734 "Metabolism of Noradrenaline" xref: Reactome:540906 "Metabolism of Noradrenaline" xref: Reactome:590858 "Metabolism of Noradrenaline" xref: Reactome:602013 "Metabolism of Noradrenaline" relationship: part_of GO:0007154 ! cell communication relationship: part_of GO:0050877 ! neurological system process is_a: GO:0044237 ! cellular metabolic process is_a: GO:0065007 ! biological regulation [Term] id: GO:0042165 name: neurotransmitter binding namespace: molecular_function def: "Interacting selectively and non-covalently with a neurotransmitter, any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir is_a: GO:0005488 ! binding [Term] id: GO:0042180 name: cellular 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 subset: gosubset_prok synonym: "ketone metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0042254 name: ribosome biogenesis namespace: biological_process alt_id: GO:0007046 def: "The process of the formation of the constituents of the ribosome subunits, their assembly, and their transport to the sites of protein synthesis." [GOC:ma] subset: goslim_candida subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "ribosomal chaperone activity" RELATED [] synonym: "ribosome biogenesis and assembly" EXACT [] xref: Wikipedia:Ribosome_biogenesis is_a: GO:0009987 ! cellular process [Term] id: GO:0042277 name: peptide binding namespace: molecular_function def: "Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds." [GOC:jl] subset: goslim_pir subset: gosubset_prok 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 "Oxford Dictionary of Biochemistry and Molecular Biology"] 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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "pigment metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0042445 name: hormone metabolic process namespace: biological_process 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, http://cancerweb.ncl.ac.uk/] subset: goslim_pir subset: gosubset_prok synonym: "hormone metabolism" EXACT [] xref: Reactome:436289 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:458699 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:478024 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:497682 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:512826 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:521993 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:528938 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:534163 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:539659 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:550173 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:555346 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:564263 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:576523 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:589474 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:601556 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" xref: Reactome:76521 "Dehydrogenation of Testosterone to form 6-Dehydrotestosterone" is_a: GO:0008152 ! metabolic process is_a: GO:0065007 ! biological regulation [Term] id: GO:0042562 name: hormone binding namespace: molecular_function def: "Interacting selectively and non-covalently with any hormone, naturally occurring substances secreted by specialized cells that affect the metabolism or behavior of other cells possessing functional receptors for the hormone." [GOC:jl, http://cancerweb.ncl.ac.uk/] 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 relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [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, http://cancerweb.ncl.ac.uk/, PMID:12045093] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir xref: Wikipedia:Microbody relationship: part_of GO:0005622 ! intracellular is_a: GO:0043231 ! intracellular membrane-bounded organelle [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 inner membrane and cell wall (Fungi)." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "periplasm" EXACT [] relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [Term] id: GO:0042600 name: chorion namespace: cellular_component def: "A protective, noncellular membrane that surrounds the eggs of various animals including insects and fish." [GOC:jl, http://cancerweb.ncl.ac.uk/, ISBN:0721662544 "Dorland's Illustrated Medical Dictionary"] 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 relationship: part_of GO:0005575 ! cellular_component 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 "Fundamental Immunology", PMID:15928678, PMID:16153240] subset: goslim_pir relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 subset: gosubset_prok synonym: "PHA metabolic process" BROAD [] synonym: "PHA metabolism" BROAD [] synonym: "poly(3-hydroxyalkanoate) metabolism" EXACT [] is_a: GO:0043283 ! biopolymer metabolic process [Term] id: GO:0042710 name: biofilm formation namespace: biological_process def: "A process whereby microorganisms irreversibly attach to and grow on a surface and produce extracellular polymers that facilitate attachment and matrix formation, resulting in an alteration in the phenotype of the organisms with respect to growth rate and gene transcription." [PMID:11932229] subset: goslim_candida subset: goslim_pir subset: gosubset_prok is_a: GO:0051704 ! multi-organism process [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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "pheromone metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process is_a: GO:0019748 ! secondary 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 relationship: part_of GO:0005783 ! endoplasmic reticulum is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0042886 name: amide transport namespace: biological_process def: "The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of, within or between cells." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0042908 name: xenobiotic transport namespace: biological_process def: "The directed movement of a xenobiotic, a compound foreign to living organisms, into, out of, within or between cells." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0042995 name: cell projection namespace: cellular_component def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [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, http://www.cogsci.princeton.edu/~wn/] subset: goslim_pir synonym: "neurite" NARROW [] synonym: "neuronal cell projection" EXACT [] relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [Term] id: GO:0043021 name: ribonucleoprotein binding namespace: molecular_function def: "Interacting selectively and non-covalently with any complex of RNA and protein." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "RNP binding" EXACT [] is_a: GO:0005488 ! binding [Term] id: GO:0043025 name: cell soma namespace: cellular_component def: "The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections." [GOC:go_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: "cell body" EXACT [] xref: Wikipedia:Soma_(biology) relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [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 subset: gosubset_prok synonym: "debranching enzyme complex" BROAD [] is_a: GO:0043234 ! protein 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_goa subset: goslim_pir subset: gosubset_prok synonym: "extracellular structure organisation" EXACT [GOC:curators] synonym: "extracellular structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization is_a: GO:0009987 ! cellular process [Term] id: GO:0043094 name: cellular 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 subset: gosubset_prok is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0043101 name: purine salvage namespace: biological_process def: "Any process that generates a purine, 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 subset: gosubset_prok is_a: GO:0046483 ! heterocycle metabolic process is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process is_a: GO:0043094 ! cellular 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 subset: gosubset_prok synonym: "cell envelope organisation" EXACT [GOC:curators] 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: "Interacting selectively and non-covalently with ions, charged atoms or groups of atoms." [GOC:jl] subset: goslim_pir subset: gosubset_prok synonym: "atom binding" RELATED [] is_a: GO:0005488 ! binding [Term] id: GO:0043170 name: macromolecule metabolic process namespace: biological_process 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." [ChEBI:33839, GOC:mah] subset: goslim_goa subset: goslim_pir subset: gosubset_prok synonym: "macromolecule metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0043176 name: amine binding namespace: molecular_function def: "Interacting selectively and non-covalently with any organic compound that is weakly basic in character and contains an amino or a substituted amino group." [GOC:jl] subset: goslim_pir subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0043178 name: alcohol binding namespace: molecular_function def: "Interacting selectively and non-covalently with an alcohol, any of a class of alkyl compounds containing a hydroxyl group." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok 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_pir subset: gosubset_prok synonym: "ABC-type efflux permease activity" NARROW [] synonym: "ABC-type efflux porter activity" NARROW [] synonym: "ABC-type uptake permease activity" NARROW [] synonym: "ATP-binding cassette (ABC) transporter activity" RELATED [] synonym: "mating pheromone exporter" NARROW [] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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. Excludes the plasma membrane." [GOC:go_curators] subset: goslim_generic subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Organelle is_a: GO:0005575 ! cellular_component [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:go_curators] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043226 ! organelle is_a: GO:0044464 ! cell part [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 subset: gosubset_prok relationship: part_of GO:0005576 ! extracellular region is_a: GO:0043226 ! organelle [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:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "intracellular membrane-enclosed organelle" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043229 ! intracellular organelle [Term] id: GO:0043232 name: intracellular non-membrane-bounded 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:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "intracellular non-membrane-enclosed organelle" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043229 ! intracellular organelle [Term] id: GO:0043234 name: protein complex namespace: cellular_component def: "Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or carbohydrate groups." [GOC:go_curators] comment: Note that although at some level almost all cellular components can be thought of as protein complexes, this term is intended to exclude structures composed of the same repeating subunit or subunits, for example microtubules. Protein complexes encompassed by this term are generally not structural, and usually have a defined set of subunits. subset: goslim_generic subset: goslim_pir subset: gosubset_prok synonym: "protein-protein complex" EXACT [] xref: Wikipedia:Protein_complex is_a: GO:0032991 ! macromolecular complex [Term] id: GO:0043235 name: receptor complex namespace: cellular_component def: "Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok is_a: GO:0043234 ! protein complex [Term] id: GO:0043256 name: laminin complex 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." [GOC:jl, http://www.sdbonline.org/fly/newgene/laminna1.htm, PMID:10842354] subset: goslim_pir relationship: part_of GO:0031012 ! extracellular matrix is_a: GO:0043234 ! protein complex [Term] id: GO:0043283 name: biopolymer metabolic process namespace: biological_process def: "The chemical reactions and pathways involving biopolymers, long, repeating chains of monomers found in nature, such as polysaccharides and proteins." [GOC:jl, Wikipedia:Biopolymer] subset: goslim_pir subset: gosubset_prok synonym: "biopolymer metabolism" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process [Term] id: GO:0043284 name: biopolymer biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of biopolymers, long, repeating chains of monomers found in nature e.g. polysaccharides and proteins." [GOC:jl, Wikipedia:Biopolymer] subset: goslim_pir subset: gosubset_prok synonym: "biopolymer anabolism" EXACT [] synonym: "biopolymer biosynthesis" EXACT [] synonym: "biopolymer formation" EXACT [] synonym: "biopolymer synthesis" EXACT [] is_a: GO:0043283 ! biopolymer metabolic process [Term] id: GO:0043285 name: biopolymer catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of biopolymers, long, repeating chains of monomers found in nature e.g. polysaccharides and proteins." [GOC:jl, Wikipedia:Biopolymer] subset: goslim_pir subset: gosubset_prok synonym: "biopolymer breakdown" EXACT [] synonym: "biopolymer catabolism" EXACT [] synonym: "biopolymer degradation" EXACT [] is_a: GO:0043283 ! biopolymer metabolic process [Term] id: GO:0043364 name: catalysis of free radical formation namespace: molecular_function def: "Catalysis of a reaction that generates a free radical, a highly reactive molecule with an unsatisfied electron valence pair." [GOC:jl, http://cancerweb.ncl.ac.uk/] subset: goslim_pir synonym: "catalysis of free radical generation" EXACT [] synonym: "catalysis of free-radical biosynthesis" EXACT [] synonym: "catalysis of free-radical formation" EXACT [] synonym: "catalysis of free-radical generation" EXACT [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0043412 name: biopolymer modification namespace: biological_process def: "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer, resulting in a change in its properties." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok is_a: GO:0043283 ! biopolymer metabolic process [Term] id: GO:0043446 name: cellular alkane metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an alkane, any acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, as carried out by individual cells." [ChEBI:18310, GOC:jl, Wikipedia:Alkane] subset: goslim_pir subset: gosubset_prok synonym: "alkane metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0043449 name: cellular alkene metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an alkene, any cyclic branched or unbranched hydrocarbon having one carbon-carbon double bond and the general formula CnH2n, as carried out by individual cells." [ChEBI:32878, GOC:jl, Wikipedia:Alkene] subset: goslim_pir subset: gosubset_prok synonym: "alkene metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0043452 name: cellular alkyne metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an alkyne, any cyclic branched or unbranched hydrocarbon having a carbon-carbon triple bond and the general formula CnH2n-2, as carried out by individual cells." [ChEBI:22339, GOC:jl, Wikipedia:Alkyne] subset: goslim_pir subset: gosubset_prok synonym: "alkyne metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0043473 name: pigmentation namespace: biological_process def: "The deposition or aggregation of coloring matter in an organism, tissue or cell." [GOC:jl] subset: goslim_pir subset: gosubset_prok is_a: GO:0008150 ! biological_process [Term] id: GO:0043498 name: cell surface binding namespace: molecular_function def: "Interacting selectively and non-covalently with any component on the surface of a cell." [GOC:jl] subset: goslim_pir subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0043500 name: muscle adaptation namespace: biological_process def: "A process by 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 [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 relationship: part_of GO:0005576 ! extracellular region is_a: GO:0043234 ! protein complex [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] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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:go_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] relationship: part_of GO:0005575 ! cellular_component is_a: GO:0005618 ! cell wall [Term] id: GO:0043603 name: cellular amide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells." [ChEBI:32988] subset: goslim_pir subset: gosubset_prok synonym: "amide metabolism" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0044237 name: cellular metabolic process namespace: biological_process def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "cellular metabolism" EXACT [] synonym: "intermediary metabolism" RELATED [GOC:mah] is_a: GO:0008152 ! metabolic process is_a: GO:0009987 ! cellular process [Term] id: GO:0044238 name: primary metabolic process namespace: biological_process def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] subset: goslim_generic subset: goslim_pir subset: gosubset_prok synonym: "primary metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0044255 name: cellular lipid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving lipids, as carried out by individual cells." [GOC:jl] subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "cellular lipid metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process is_a: GO:0006629 ! lipid metabolic process [Term] id: GO:0044419 name: interspecies interaction between organisms namespace: biological_process def: "Any process by which an organism has an effect on an organism of a different species." [GOC:cc] subset: goslim_candida subset: goslim_pir subset: gosubset_prok synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0051704 ! multi-organism process [Term] id: GO:0044464 name: cell part namespace: cellular_component def: "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005575 ! cellular_component is_a: GO:0005575 ! cellular_component [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 relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [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:bmah, ISBN:0185316194] subset: goslim_pir relationship: part_of GO:0005575 ! cellular_component is_a: GO:0044464 ! cell part [Term] id: GO:0045182 name: translation regulator activity namespace: molecular_function def: "Any substance involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "translation factor activity" EXACT [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0045202 name: synapse namespace: cellular_component def: "The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending 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 nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir synonym: "synaptic junction" EXACT [] xref: Wikipedia:Chemical_synapse is_a: GO:0005575 ! cellular_component [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 subset: gosubset_prok synonym: "external encapsulating structure organisation" EXACT [GOC:curators] synonym: "external encapsulating structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization is_a: GO:0009987 ! cellular process [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 subset: gosubset_prok synonym: "capsule organisation" EXACT [GOC:curators] 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 subset: gosubset_prok synonym: "slime layer organisation" EXACT [GOC:curators] 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 enzyme complex namespace: cellular_component def: "Any of the heteromeric enzymes that act in the TCA cycle." [GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "TCA cycle enzyme complex" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0045251 name: electron transfer flavoprotein complex namespace: cellular_component def: "A protein complex containing flavin adenine dinucleotide (FAD) and acyl-CoA dehydrogenase, which form a system that oxidizes an acyl-CoA molecule and reduces ubiquinone and other acceptors in the mitochondrial electron transport system." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0045252 name: oxoglutarate dehydrogenase complex namespace: cellular_component def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) ; EC:1.2.4.2 (E1), dihydrolipoamide S-succinyltransferase ; EC:2.3.1.61 (E2) and dihydrolipoamide dehydrogenase ; EC:1.8.1.4 (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2)." [UniProtKB:Q60597] comment: See also the molecular functions term 'oxoglutarate dehydrogenase (succinyl-transferring) activity ; GO:0004591', 'dihydrolipoyllysine-residue succinyltransferase activity ; GO:0004149' and 'dihydrolipoyl dehydrogenase activity ; GO:0004148'. subset: goslim_pir subset: gosubset_prok synonym: "dihydrolipoamide S-succinyltransferase complex" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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." [UniProtKB:P35816] comment: See also the cellular component term 'cytosolic pyruvate dehydrogenase complex ; GO:0045250'. subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0045254 name: pyruvate dehydrogenase complex namespace: cellular_component alt_id: GO:0009364 def: "Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA; comprises subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3)." [ISBN:0716720094] 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 functions of this complex are represented by the molecular function terms 'pyruvate dehydrogenase (lipoamide) activity ; GO:0004739', 'dihydrolipoamide S-acetyltransferase activity ; GO:0004742', and 'dihydrolipoamide dehydrogenase activity ; GO:0004148'. subset: goslim_pir subset: gosubset_prok synonym: "dihydrolipoyl dehydrogenase complex" BROAD [] synonym: "pyruvate dehydrogenase complex (lipoamide)" EXACT [] xref: Wikipedia:Pyruvate_dehydrogenase_complex relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0045273 name: respiratory chain complex II 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 subset: gosubset_prok synonym: "electron transport complex II" RELATED [] relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 subset: gosubset_prok synonym: "complex III" EXACT [] 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 relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 subset: gosubset_prok synonym: "cytochrome c oxidase complex" EXACT [] synonym: "electron transport complex IV" RELATED [] relationship: part_of GO:0016020 ! membrane relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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." [http://www.ejbiotechnology.info/content/vol1/issue1/full/4/, PMID:11564867, PMID:12139607] subset: goslim_pir synonym: "editosome" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0045333 name: cellular respiration namespace: biological_process def: "The enzymatic release of energy from organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration)." [ISBN:0140513590, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_pir subset: goslim_yeast subset: gosubset_prok 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:dph, GOC:go_curators, GOC:jl, GOC:mah] subset: goslim_pir synonym: "fusome organisation" EXACT [GOC:curators] synonym: "fusome organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization [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 subset: gosubset_prok synonym: "chemorepellant activity" EXACT [] is_a: GO:0003674 ! molecular_function [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: gosubset_prok synonym: "storage protein" RELATED [] synonym: "storage protein of fat body" RELATED [] synonym: "yolk protein" RELATED [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0046483 name: heterocycle metabolic process namespace: biological_process def: "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "heterocycle metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok 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:0044255 ! cellular lipid 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 relationship: part_of GO:0005634 ! nucleus relationship: part_of GO:0005694 ! chromosome is_a: GO:0032991 ! macromolecular complex is_a: GO:0044464 ! cell part [Term] id: GO:0046794 name: virion transport namespace: biological_process def: "The directed movement of a virion into, out of, or within a host cell." [GOC:ai] subset: goslim_pir relationship: part_of GO:0000003 ! reproduction relationship: part_of GO:0051179 ! localization relationship: part_of GO:0044419 ! interspecies interaction between organisms relationship: part_of GO:0016032 ! viral reproduction is_a: GO:0006810 ! transport is_a: GO:0044419 ! interspecies interaction between organisms [Term] id: GO:0046812 name: host cell surface binding namespace: molecular_function def: "Interacting selectively and non-covalently with the surface of a host cell." [GOC:ai] subset: goslim_pir subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0046864 name: isoprenoid transport namespace: biological_process def: "The directed movement of isoprenoids into, out of, within or between cells. Isoprenoids comprise a group of compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [GOC:ai] subset: goslim_pir relationship: part_of GO:0051179 ! localization 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, a group of cells, or a tissue." [GOC:ai] subset: goslim_goa subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0046906 name: tetrapyrrole binding namespace: molecular_function def: "Interacting selectively and non-covalently with a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position." [http://cancerweb.ncl.ac.uk/, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "porphyrin binding" NARROW [] is_a: GO:0005488 ! binding [Term] id: GO:0046950 name: cellular ketone body metabolic process namespace: biological_process def: "The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok synonym: "ketone body metabolism" EXACT [] xref: Reactome:448513 "Ketone body metabolism" xref: Reactome:469643 "Ketone body metabolism" xref: Reactome:487355 "Ketone body metabolism" xref: Reactome:507306 "Ketone body metabolism" xref: Reactome:517320 "Ketone body metabolism" xref: Reactome:526203 "Ketone body metabolism" xref: Reactome:531089 "Ketone body metabolism" xref: Reactome:536462 "Ketone body metabolism" xref: Reactome:542166 "Ketone body metabolism" xref: Reactome:547524 "Ketone body metabolism" xref: Reactome:552117 "Ketone body metabolism" xref: Reactome:557709 "Ketone body metabolism" xref: Reactome:568324 "Ketone body metabolism" xref: Reactome:581526 "Ketone body metabolism" xref: Reactome:592413 "Ketone body metabolism" xref: Reactome:595296 "Ketone body metabolism" xref: Reactome:597271 "Ketone body metabolism" xref: Reactome:598125 "Ketone body metabolism" xref: Reactome:599612 "Ketone body metabolism" xref: Reactome:602416 "Ketone body metabolism" xref: Reactome:74182 "Ketone body metabolism" is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0048037 name: cofactor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok 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:go_curators, http://www.mercksource.com, http://www.stedmans.com/] 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 relationship: part_of GO:0005576 ! extracellular region is_a: GO:0043234 ! protein complex [Term] id: GO:0048196 name: middle lamella-containing extracellular matrix namespace: cellular_component def: "The matrix external to the cell, composed of the cell wall and middle lamella." [GOC:jic, GOC:mtg_sensu, http://cancerweb.ncl.ac.uk] comment: Note that this term does not have 'extracellular region ; GO:0005576' as a parent because in plants the extracellular matrix is considered part of the cell. subset: goslim_pir relationship: part_of GO:0005576 ! extracellular region is_a: GO:0031012 ! extracellular matrix is_a: GO:0030312 ! external encapsulating structure [Term] id: GO:0048284 name: organelle fusion namespace: biological_process def: "The creation of a single organelle from two or more organelles." [GOC:jic] subset: goslim_pir 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:jic] subset: goslim_pir 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:jic] subset: goslim_pir is_a: GO:0006996 ! organelle organization [Term] id: GO:0048469 name: cell maturation namespace: biological_process def: "A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "functional differentiation" RELATED [GOC:dph] relationship: part_of GO:0032502 ! developmental process relationship: part_of GO:0009987 ! cellular process is_a: GO:0032502 ! developmental process is_a: GO:0009987 ! cellular process [Term] id: GO:0048476 name: Holliday junction resolvase complex namespace: cellular_component def: "A protein complex that mediates the conversion of a Holliday junction into two separate duplex DNA molecules; the complex includes a single- or multisubunit helicase that catalyzes the extension of heteroduplex DNA by branch migration and a nuclease that resolves the junction by nucleolytic cleavage." [PMID:11207366, PMID:12374758] subset: goslim_pir synonym: "Mus81-Eme1 complex" NARROW [] synonym: "resolvasome" EXACT [PMID:11207366] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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 subset: gosubset_prok synonym: "RubisCO complex" EXACT [] relationship: part_of GO:0005622 ! intracellular is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [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_pir subset: gosubset_prok xref: Wikipedia:Signal_recognition_particle relationship: part_of GO:0005622 ! intracellular is_a: GO:0030529 ! ribonucleoprotein complex [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:jic] subset: goslim_pir subset: gosubset_prok 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 [GOC:curators] synonym: "pigment granule organization and biogenesis" RELATED [GOC:mah] relationship: part_of GO:0043473 ! pigmentation relationship: part_of GO:0009987 ! cellular process is_a: GO:0016050 ! vesicle organization [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 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:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "depsipeptide metabolism" EXACT [] is_a: GO:0006518 ! peptide metabolic process [Term] id: GO:0050817 name: coagulation namespace: biological_process def: "The process by which a fluid solution, or part of it, changes into a solid or semisolid mass." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir synonym: "clotting" EXACT [] is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0050824 name: water binding namespace: molecular_function def: "Interacting selectively and non-covalently with water (H2O)." [GOC:ai] subset: goslim_pir subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0050840 name: extracellular matrix binding namespace: molecular_function def: "Interacting selectively and non-covalently with a component of the extracellular matrix." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "adhesive extracellular matrix constituent" RELATED [] synonym: "extracellular matrix constituent binding" EXACT [] is_a: GO:0005488 ! binding [Term] id: GO:0050877 name: neurological system process namespace: biological_process def: "A organ system process carried out by any of the organs or tissues of neurological system." [GOC:ai, GOC:mtg_cardio] subset: goslim_pir synonym: "neurophysiological process" EXACT [] synonym: "pan-neural process" RELATED [] is_a: GO:0032501 ! multicellular organismal process [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:0032501 ! multicellular organismal process is_a: GO:0065007 ! biological regulation [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: "Any of the hormonal, neural, and secretory processes that release products into the blood or lymph. These products have specific effects on other organs." [ISBN:0721662544 "Dorland's Illustrated Medical Dictionary"] 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: "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." [GOC:ai] subset: goslim_goa subset: goslim_pir subset: gosubset_prok synonym: "physiological response to stimulus" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0051179 name: localization namespace: biological_process def: "Any process by which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location." [GOC:ai] subset: goslim_pir subset: gosubset_prok 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 [] is_a: GO:0008150 ! biological_process [Term] id: GO:0051180 name: vitamin transport namespace: biological_process def: "The directed movement of vitamins into, out of, within or between cells. 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 subset: gosubset_prok synonym: "vitamin or cofactor transport" BROAD [] relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0051181 name: cofactor transport namespace: biological_process def: "The directed movement of a cofactor into, out of, within or between cells. A cofactor is a substance that is required for the activity of an enzyme or other protein." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "vitamin or cofactor transport" BROAD [] relationship: part_of GO:0051179 ! localization is_a: GO:0006810 ! transport [Term] id: GO:0051186 name: cofactor metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate." [GOC:ai] subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "cofactor metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [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 subset: gosubset_prok synonym: "coenzyme and prosthetic group metabolic process" BROAD [] synonym: "coenzyme and prosthetic group metabolism" BROAD [] synonym: "prosthetic group metabolism" EXACT [] relationship: part_of GO:0019538 ! protein metabolic process relationship: part_of GO:0044237 ! cellular metabolic process is_a: GO:0051186 ! cofactor metabolic process [Term] id: GO:0051213 name: dioxygenase activity namespace: molecular_function def: "Catalysis of the incorporation of both atoms of oxygen from one molecule of O2 into the (reduced) substrate." [http://www.onelook.com/] subset: goslim_pir subset: gosubset_prok is_a: GO:0016491 ! oxidoreductase activity [Term] id: GO:0051234 name: establishment of localization namespace: biological_process def: "The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location." [GOC:ai] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0051179 ! localization is_a: GO:0008150 ! biological_process [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 subset: gosubset_prok synonym: "protein polymer biosynthesis" EXACT [] synonym: "protein polymer biosynthetic process" EXACT [] synonym: "protein polymer formation" EXACT [] relationship: part_of GO:0008150 ! biological_process is_a: GO:0034622 ! cellular macromolecular complex assembly [Term] id: GO:0051261 name: protein depolymerization namespace: biological_process def: "The process by 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 subset: gosubset_prok 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 is_a: GO:0009987 ! cellular process [Term] id: GO:0051276 name: chromosome organization namespace: biological_process 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." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "chromosome organisation" EXACT [] synonym: "chromosome organization and biogenesis" RELATED [GOC:mah] synonym: "maintenance of genome integrity" RELATED [] synonym: "nuclear genome maintenance" RELATED [] is_a: GO:0006996 ! organelle organization [Term] id: GO:0051301 name: cell division namespace: biological_process def: "The process resulting in the physical partitioning and separation of a cell into daughter cells." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Cell_division is_a: GO:0009987 ! cellular process [Term] id: GO:0051540 name: metal cluster binding namespace: molecular_function def: "Interacting selectively and non-covalently with 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 subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0051604 name: protein maturation namespace: biological_process def: "The process leading to the attainment of the full functional capacity of a protein." [GOC:ai] subset: goslim_pir subset: gosubset_prok relationship: part_of GO:0043170 ! macromolecule metabolic process is_a: GO:0019538 ! protein metabolic 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 subset: gosubset_prok 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 by which an organelle is transported to, and/or maintained in, a specific location." [GOC:ai] subset: goslim_pir synonym: "establishment and maintenance of organelle localization" EXACT [] is_a: GO:0051641 ! cellular localization [Term] id: GO:0051641 name: cellular localization namespace: biological_process def: "Any process by which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within or in the membrane of a cell." [GOC:ai] subset: goslim_pir subset: gosubset_prok 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 [] is_a: GO:0051179 ! localization is_a: GO:0009987 ! cellular process [Term] id: GO:0051703 name: intraspecies interaction between organisms namespace: biological_process def: "Any process by which an organism has an effect on an organism of the same species." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "intraspecies interaction with other organisms" EXACT [] is_a: GO:0051704 ! multi-organism process [Term] id: GO:0051704 name: multi-organism process namespace: biological_process alt_id: GO:0051706 def: "Any process by which an organism has an effect on another organism of the same or different species." [GOC:ai] subset: goslim_goa subset: goslim_pir subset: gosubset_prok synonym: "interaction between organisms" EXACT [] synonym: "physiological interaction between organisms" EXACT [] synonym: "physiological interaction with other organism" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0051705 name: behavioral interaction between organisms namespace: biological_process def: "Any process by which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] subset: goslim_pir synonym: "behavioral interaction with other organism" EXACT [] synonym: "behavioural interaction between organisms" EXACT [] synonym: "behavioural interaction with other organism" EXACT [] is_a: GO:0050896 ! response to stimulus is_a: GO:0051704 ! multi-organism process [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 subset: gosubset_prok synonym: "phytoalexin metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0055044 name: symplast namespace: cellular_component def: "The interconnected protoplasts of a plant. The interconnections occur via the plasmodesmata." [GOC:mtg_sensu] subset: goslim_pir xref: Wikipedia:Symplast is_a: GO:0005575 ! cellular_component [Term] id: GO:0060089 name: molecular transducer activity namespace: molecular_function def: "The molecular function that accepts an input of one form and creates an output of a different form." [GOC:mtg_MIT_16mar07] subset: goslim_pir subset: gosubset_prok is_a: GO:0003674 ! molecular_function [Term] id: GO:0060090 name: molecular adaptor activity namespace: molecular_function def: "The binding activity of a molecule that brings together two or more molecules, permitting those molecules to function in a coordinated way." [GOC:mtg_MIT_16mar07] subset: goslim_pir subset: gosubset_prok is_a: GO:0005488 ! binding [Term] id: GO:0065003 name: macromolecular complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a complex." [GOC:jl] subset: goslim_pir subset: gosubset_prok synonym: "macromolecule complex assembly" EXACT [] relationship: part_of GO:0008150 ! biological_process is_a: GO:0022607 ! cellular component assembly [Term] id: GO:0065007 name: biological regulation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of any biological process, quality or function." [GOC:isa_complete] subset: goslim_pir subset: gosubset_prok synonym: "regulation" BROAD [] is_a: GO:0008150 ! biological_process [Term] id: GO:0070020 name: transforming growth factor beta1-type II receptor complex namespace: cellular_component def: "A protein complex that consists of a dimeric transforming growth factor beta (TGF-beta) type II receptor bound to a TGF-beta1 dimer." [Reactome:REACT_7218] subset: goslim_pir synonym: "TGF-beta receptor II-TGF-beta1 complex" EXACT [] synonym: "TGF-beta1-type II receptor complex" EXACT [Reactome:REACT_7218] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0070021 name: transforming growth factor beta1-type II receptor-type I receptor complex namespace: cellular_component def: "A protein complex that is formed by the association of a ligand-bound TGF-beta type II receptor dimer with a TGF-beta type I receptor dimer." [Reactome:REACT_7425] subset: goslim_pir synonym: "TGF-beta 1:type II receptor:type I receptor complex" EXACT [Reactome:REACT_7425] synonym: "TGF-beta receptor II-TGF-beta receptor I-TGF-beta1 complex" EXACT [] synonym: "TGF-beta1-type II receptor-type I receptor complex" EXACT [] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0070023 name: interleukin12-interleukin-12 receptor complex namespace: cellular_component def: "A protein complex that is formed by the association of a heterodimeric interleukin-12 receptor complex with an interleukin-12 heterodimer." [PMID:11900991] subset: goslim_pir synonym: "IL12-IL12 receptor complex" EXACT [] synonym: "IL12B-IL12RB1-IL12RB2 complex" NARROW [CORUM:2020] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0070024 name: CD19-Vav-PIK3R1 complex namespace: cellular_component def: "A protein complex that contains the cell surface signaling molecule CD19, the Ras guanine nucleotide exchange factor Vav, and the regulatory subunit alpha of phosphatidylinositol 3-kinase (PI3K)." [PMID:7528218] subset: goslim_pir synonym: "CD19-Vav-PI 3-kinase (p85 subunit) complex" EXACT [CORUM:2574] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0070450 name: interleukin4-interleukin-4 receptor complex namespace: cellular_component def: "A protein complex that is formed by the association of a heterodimeric interleukin-4 receptor complex with an interleukin-4 molecule." [GOC:mah, PMID:10358772] subset: goslim_pir synonym: "IL4-IL4 receptor complex" EXACT [GOC:mah] synonym: "IL4-IL4R-IL2RG complex" NARROW [CORUM:1515] relationship: part_of GO:0016020 ! membrane is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0070451 name: cell hair namespace: cellular_component def: "A long, thin cell projection that contains F-actin and tubulin, with microtubules centrally located and F-actin peripherally located." [PMID:11526084] subset: goslim_pir synonym: "imaginal disc-derived wing hair" NARROW [GOC:mah] synonym: "non-sensory hair" EXACT [GOC:bf] xref: Wikipedia:Membrane_nanotube relationship: part_of GO:0005575 ! cellular_component is_a: GO:0042995 ! cell projection [Term] id: GO:0070517 name: DNA replication factor C core complex namespace: cellular_component def: "A protein complex containing three of the five subunits of eukaryotic replication factor C, those corresponding to human p40, p38, and p37." [PMID:8692848, PMID:9228079, PMID:9582326] subset: goslim_pir subset: gosubset_prok synonym: "RFC core complex" EXACT [CORUM:278] relationship: part_of GO:0005663 ! DNA replication factor C complex relationship: part_of GO:0005634 ! nucleus relationship: part_of GO:0030894 ! replisome is_a: GO:0043234 ! protein complex is_a: GO:0044464 ! cell part [Term] id: GO:0070565 name: telomere-telomerase complex namespace: cellular_component def: "A complex of DNA and protein located at the end of a linear chromosome that enables replication of the telomeric repeat sequences at the end of a linear chromosome." [GOC:pde, PMID:19179534] 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 subset: gosubset_prok is_a: GO:0032991 ! macromolecular complex is_a: GO:0044464 ! cell part relationship: part_of GO:0005694 ! chromosome [Typedef] id: has_part name: has_part namespace: gene_ontology is_transitive: true [Typedef] id: negatively_regulates name: negatively_regulates namespace: gene_ontology is_a: regulates ! regulates [Typedef] id: part_of name: part_of namespace: gene_ontology xref: OBO_REL:part_of is_transitive: true [Typedef] id: positively_regulates name: positively_regulates namespace: gene_ontology is_a: regulates ! regulates [Typedef] id: regulates name: regulates namespace: gene_ontology