format-version: 1.2 date: 15:08:2011 17:04 auto-generated-by: OBO-Edit 2.0 ontology: go saved-by: kchris synonymtypedef: systematic_synonym "Systematic synonym" EXACT subsetdef: goslim_candida "Candida GO slim" subsetdef: goslim_generic "Generic GO 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" subsetdef: high_level_annotation_qc "High-level terms not to be used for direct annotation" subsetdef: unvetted "unvetted" remark: cvs version: $Revision: 1.864 $ [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] 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:0000228 name: nuclear chromosome namespace: cellular_component def: "A chromosome found in the nucleus of a eukaryotic cell." [GOC:mah] subset: goslim_generic synonym: "nuclear interphase chromosome" NARROW [] relationship: part_of GO:0005634 ! nucleus is_a: GO:0005575 ! cellular_component is_a: GO:0005694 ! chromosome [Term] id: GO:0000229 name: cytoplasmic chromosome namespace: cellular_component def: "A chromosome found in the cytoplasm." [GOC:mah] subset: goslim_generic subset: gosubset_prok synonym: "cytoplasmic interphase chromosome" NARROW [] relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0005575 ! cellular_component is_a: GO:0005694 ! chromosome [Term] id: GO:0000902 name: cell morphogenesis namespace: biological_process alt_id: GO:0007148 alt_id: GO:0045790 alt_id: GO:0045791 def: "The developmental process in which the size or shape of a cell is generated and organized." [GOC:clt, GOC:dph, GOC:go_curators, GOC:tb] subset: goslim_generic subset: goslim_yeast subset: gosubset_prok synonym: "cellular morphogenesis" EXACT [] is_a: GO:0008150 ! biological_process relationship: part_of GO:0048856 ! anatomical structure development [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: Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022. subset: goslim_generic subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process [Term] id: GO:0003013 name: circulatory system process namespace: biological_process def: "A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism." [GOC:mtg_cardio] subset: goslim_generic xref: Wikipedia:Circulatory_system is_a: GO:0008150 ! biological_process [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_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "cellular component" EXACT [] synonym: "cellular component unknown" NARROW [] xref: NIF_Subcellular:sao1337158144 disjoint_from: GO:0003674 ! molecular_function [Term] id: GO:0005576 name: extracellular region namespace: cellular_component def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators] comment: Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. subset: goslim_candida subset: goslim_generic 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:0005578 name: proteinaceous extracellular matrix namespace: cellular_component def: "A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus." [GOC:mtg_sensu, ISBN:0198547684] subset: goslim_generic subset: goslim_plant relationship: part_of GO:0005576 ! extracellular region is_a: GO:0005575 ! cellular_component [Term] id: GO:0005615 name: extracellular space namespace: cellular_component def: "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684] comment: Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term. subset: goslim_generic subset: goslim_plant synonym: "intercellular space" RELATED [] xref: NIF_Subcellular:sao1425028079 relationship: part_of GO:0005576 ! extracellular region 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 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] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "internal to cell" EXACT [] synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular relationship: part_of GO:0005623 ! cell is_a: GO:0005575 ! cellular_component [Term] id: GO:0005623 name: cell namespace: cellular_component def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators] subset: goslim_generic subset: goslim_plant subset: gosubset_prok xref: NIF_Subcellular:sao1813327414 xref: Wikipedia:Cell_(biology) is_a: GO:0005575 ! cellular_component [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_pir subset: goslim_plant subset: goslim_yeast synonym: "cell nucleus" EXACT [] xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus relationship: part_of GO:0005622 ! intracellular is_a: GO:0043226 ! organelle [Term] id: GO:0005635 name: nuclear envelope namespace: cellular_component alt_id: GO:0005636 def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN:0198547684] subset: goslim_generic subset: goslim_plant xref: Wikipedia:Nuclear_envelope relationship: part_of GO:0005634 ! nucleus is_a: GO:0005575 ! cellular_component [Term] id: GO:0005654 name: nucleoplasm namespace: cellular_component def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653] subset: goslim_generic subset: goslim_plant xref: NIF_Subcellular:sao661522542 xref: Wikipedia:Nucleoplasm relationship: part_of GO:0005634 ! nucleus is_a: GO:0005575 ! cellular_component [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_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:0043226 ! organelle [Term] id: GO:0005730 name: nucleolus namespace: cellular_component def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus relationship: part_of GO:0005634 ! nucleus is_a: GO:0043226 ! organelle [Term] id: GO:0005737 name: cytoplasm namespace: cellular_component def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok xref: Wikipedia:Cytoplasm relationship: part_of GO:0005622 ! intracellular is_a: GO:0005575 ! cellular_component [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] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "mitochondria" EXACT [] xref: NIF_Subcellular:sao1860313010 xref: Wikipedia:Mitochondrion relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0043226 ! organelle [Term] id: GO:0005764 name: lysosome namespace: cellular_component def: "A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [GOC:mah, ISBN:0198506732] subset: goslim_generic subset: goslim_plant xref: NIF_Subcellular:sao585356902 xref: Wikipedia:Lysosome is_a: GO:0005773 ! vacuole [Term] id: GO:0005768 name: endosome namespace: cellular_component def: "A membrane-bounded organelle to which materials ingested by endocytosis are delivered." [ISBN:0198506732, PMID:19696797] subset: goslim_generic subset: goslim_pir subset: goslim_plant xref: NIF_Subcellular:sao1720343330 xref: Wikipedia:Endosome relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0043226 ! 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] 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:0005737 ! cytoplasm is_a: GO:0043226 ! organelle [Term] id: GO:0005777 name: peroxisome namespace: cellular_component alt_id: GO:0019818 def: "A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [ISBN:0815316194] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast synonym: "peroxisome vesicle" BROAD [] xref: NIF_Subcellular:sao499555322 xref: Wikipedia:Peroxisome relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0043226 ! organelle [Term] id: GO:0005783 name: endoplasmic reticulum namespace: cellular_component def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "ER" EXACT [] xref: NIF_Subcellular:sao1036339110 xref: Wikipedia:Endoplasmic_reticulum relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0043226 ! organelle [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] 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: NIF_Subcellular:sao451912436 xref: Wikipedia:Golgi_apparatus relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0043226 ! organelle [Term] id: GO:0005811 name: lipid particle namespace: cellular_component def: "Any particle of coalesced lipids in the cytoplasm of a cell. May include associated proteins." [GOC:mah] comment: Note that this term does not refer to vesicles, but instead to structures in which lipids do not necessarily form bilayers. subset: goslim_generic synonym: "adiposome" EXACT [] synonym: "lipid body" EXACT [] synonym: "lipid droplet" EXACT [] relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0005575 ! cellular_component [Term] id: GO:0005815 name: microtubule organizing center namespace: cellular_component def: "A cytoplasmic structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides." [ISBN:0815316194, PMID:17245416] subset: goslim_candida subset: goslim_generic subset: goslim_yeast synonym: "MTOC" EXACT [] synonym: "microtubule organising centre" EXACT [] xref: Wikipedia:Microtubule_organizing_center is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005856 ! cytoskeleton relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005829 name: cytosol namespace: cellular_component def: "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC:hgd, GOC:jl] subset: goslim_generic subset: goslim_plant subset: gosubset_prok xref: NIF_Subcellular:sao101633890 xref: Wikipedia:Cytosol relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0005575 ! cellular_component [Term] id: GO:0005840 name: ribosome namespace: cellular_component alt_id: GO:0033279 def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "ribosomal RNA" RELATED [] synonym: "ribosomal subunit" RELATED [GOC:mah, GOC:vw] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0043226 ! organelle [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:0043226 ! organelle [Term] id: GO:0005886 name: plasma membrane namespace: cellular_component alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "bacterial inner membrane" NARROW [] synonym: "cell membrane" EXACT [] synonym: "cytoplasmic membrane" EXACT [] synonym: "inner endospore membrane" NARROW [] synonym: "juxtamembrane" BROAD [] synonym: "plasma membrane lipid bilayer" NARROW [GOC:mah] synonym: "plasmalemma" EXACT [] xref: NIF_Subcellular:sao1663586795 xref: Wikipedia:Cell_membrane relationship: part_of GO:0005623 ! cell is_a: GO:0005575 ! cellular_component [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: NIF_Subcellular:sao787716553 xref: Wikipedia:Cilium relationship: part_of GO:0005623 ! cell is_a: GO:0005575 ! cellular_component [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] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "carbohydrate metabolism" EXACT [] xref: Reactome:REACT_101193 ! Metabolism of carbohydrates, Sus scrofa xref: Reactome:REACT_102834 ! Metabolism of carbohydrates, Mus musculus xref: Reactome:REACT_103806 ! Metabolism of carbohydrates, Mycobacterium tuberculosis xref: Reactome:REACT_104502 ! Metabolism of carbohydrates, Gallus gallus xref: Reactome:REACT_105321 ! Metabolism of carbohydrates, Escherichia coli xref: Reactome:REACT_106046 ! Metabolism of carbohydrates, Drosophila melanogaster xref: Reactome:REACT_107409 ! Metabolism of carbohydrates, Caenorhabditis elegans xref: Reactome:REACT_28218 ! Metabolism of carbohydrates, Xenopus tropicalis xref: Reactome:REACT_32291 ! Metabolism of carbohydrates, Staphylococcus aureus N315 xref: Reactome:REACT_33141 ! Metabolism of carbohydrates, Taeniopygia guttata xref: Reactome:REACT_33953 ! Metabolism of carbohydrates, Rattus norvegicus xref: Reactome:REACT_34800 ! Metabolism of carbohydrates, Danio rerio xref: Reactome:REACT_474 ! Metabolism of carbohydrates, Homo sapiens xref: Reactome:REACT_77669 ! Metabolism of carbohydrates, Plasmodium falciparum xref: Reactome:REACT_81945 ! Metabolism of carbohydrates, Schizosaccharomyces pombe xref: Reactome:REACT_83038 ! Metabolism of carbohydrates, Arabidopsis thaliana xref: Reactome:REACT_83329 ! Metabolism of carbohydrates, Saccharomyces cerevisiae xref: Reactome:REACT_88330 ! Metabolism of carbohydrates, Bos taurus xref: Reactome:REACT_88558 ! Metabolism of carbohydrates, Canis familiaris xref: Reactome:REACT_96375 ! Metabolism of carbohydrates, Dictyostelium discoideum xref: Reactome:REACT_98394 ! Metabolism of carbohydrates, Oryza sativa xref: Wikipedia:Carbohydrate_metabolism is_a: GO:0008150 ! biological_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:0008150 ! biological_process [Term] id: GO:0006259 name: DNA metabolic process namespace: biological_process alt_id: GO:0055132 def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "DNA metabolism" EXACT [] synonym: "cellular DNA metabolism" EXACT [] is_a: GO:0034641 ! cellular nitrogen compound metabolic process [Term] id: GO:0006397 name: mRNA processing namespace: biological_process def: "Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide." [GOC:mah] subset: goslim_generic subset: goslim_yeast subset: gosubset_prok synonym: "mRNA maturation" RELATED [] xref: Reactome:REACT_100203 ! Processing of Capped Intronless Pre-mRNA, Dictyostelium discoideum xref: Reactome:REACT_107308 ! Processing of Capped Intronless Pre-mRNA, Xenopus tropicalis xref: Reactome:REACT_109953 ! Processing of Capped Intronless Pre-mRNA, Canis familiaris xref: Reactome:REACT_1768 ! Processing of Capped Intronless Pre-mRNA, Homo sapiens xref: Reactome:REACT_32742 ! Processing of Capped Intronless Pre-mRNA, Bos taurus xref: Reactome:REACT_33642 ! Processing of Capped Intronless Pre-mRNA, Caenorhabditis elegans xref: Reactome:REACT_82691 ! Processing of Capped Intronless Pre-mRNA, Gallus gallus xref: Reactome:REACT_90366 ! Processing of Capped Intronless Pre-mRNA, Drosophila melanogaster xref: Reactome:REACT_91511 ! Processing of Capped Intronless Pre-mRNA, Danio rerio xref: Reactome:REACT_93186 ! Processing of Capped Intronless Pre-mRNA, Sus scrofa xref: Reactome:REACT_94083 ! Processing of Capped Intronless Pre-mRNA, Taeniopygia guttata xref: Reactome:REACT_96661 ! Processing of Capped Intronless Pre-mRNA, Oryza sativa xref: Reactome:REACT_97412 ! Processing of Capped Intronless Pre-mRNA, Rattus norvegicus xref: Reactome:REACT_97436 ! Processing of Capped Intronless Pre-mRNA, Mus musculus relationship: part_of GO:0008150 ! biological_process is_a: GO:0034641 ! cellular nitrogen compound metabolic process [Term] id: GO:0006399 name: tRNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established." [ISBN:0198506732] subset: goslim_generic subset: goslim_pombe subset: gosubset_prok synonym: "tRNA metabolism" EXACT [] is_a: GO:0034641 ! cellular nitrogen compound metabolic process [Term] id: GO:0006412 name: translation namespace: biological_process alt_id: GO:0006416 alt_id: GO:0006453 alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA 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: gosubset_prok synonym: "protein anabolism" EXACT [] synonym: "protein biosynthesis" EXACT [] synonym: "protein biosynthetic process" EXACT [GOC:curators] synonym: "protein formation" EXACT [] synonym: "protein synthesis" EXACT [] synonym: "protein translation" EXACT [] xref: Reactome:REACT_100851 ! Translation, Saccharomyces cerevisiae xref: Reactome:REACT_101045 ! Translation, Dictyostelium discoideum xref: Reactome:REACT_101324 ! Translation, Canis familiaris xref: Reactome:REACT_1014 ! Translation, Homo sapiens xref: Reactome:REACT_103420 ! Translation, Plasmodium falciparum xref: Reactome:REACT_105544 ! Translation, Arabidopsis thaliana xref: Reactome:REACT_29980 ! Translation, Bos taurus xref: Reactome:REACT_33559 ! Translation, Rattus norvegicus xref: Reactome:REACT_77710 ! Translation, Drosophila melanogaster xref: Reactome:REACT_79784 ! Translation, Danio rerio xref: Reactome:REACT_81734 ! Translation, Schizosaccharomyces pombe xref: Reactome:REACT_81833 ! Translation, Caenorhabditis elegans xref: Reactome:REACT_82171 ! Translation, Xenopus tropicalis xref: Reactome:REACT_83429 ! Translation, Taeniopygia guttata xref: Reactome:REACT_83530 ! Translation, Gallus gallus xref: Reactome:REACT_84182 ! Translation, Sus scrofa xref: Reactome:REACT_86996 ! Translation, Oryza sativa xref: Reactome:REACT_95535 ! Translation, Mus musculus xref: Reactome:REACT_96394 ! Translation, Escherichia coli xref: Wikipedia:Translation_(genetics) relationship: part_of GO:0008150 ! biological_process is_a: GO:0009058 ! biosynthetic 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_generic 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:REACT_100411 ! Chaperonin-mediated protein folding, Arabidopsis thaliana xref: Reactome:REACT_104912 ! Chaperonin-mediated protein folding, Caenorhabditis elegans xref: Reactome:REACT_105663 ! Chaperonin-mediated protein folding, Rattus norvegicus xref: Reactome:REACT_106009 ! Chaperonin-mediated protein folding, Canis familiaris xref: Reactome:REACT_106427 ! Chaperonin-mediated protein folding, Mus musculus xref: Reactome:REACT_106894 ! Formation of tubulin folding intermediates by CCT/TriC, Canis familiaris xref: Reactome:REACT_106927 ! Chaperonin-mediated protein folding, Drosophila melanogaster xref: Reactome:REACT_107029 ! Formation of tubulin folding intermediates by CCT/TriC, Drosophila melanogaster xref: Reactome:REACT_108248 ! Chaperonin-mediated protein folding, Gallus gallus xref: Reactome:REACT_109411 ! Formation of tubulin folding intermediates by CCT/TriC, Bos taurus xref: Reactome:REACT_110417 ! Formation of tubulin folding intermediates by CCT/TriC, Rattus norvegicus xref: Reactome:REACT_16956 ! Formation of tubulin folding intermediates by CCT/TriC, Homo sapiens xref: Reactome:REACT_17001 ! Formation of tubulin folding intermediates by CCT/TriC, Mus musculus xref: Reactome:REACT_17004 ! Chaperonin-mediated protein folding, Homo sapiens xref: Reactome:REACT_17056 ! Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding, Bos taurus xref: Reactome:REACT_23878 ! N-glycan trimming in the ER and Calnexin/Calreticulin cycle, Homo sapiens xref: Reactome:REACT_30906 ! Chaperonin-mediated protein folding, Oryza sativa xref: Reactome:REACT_32155 ! Chaperonin-mediated protein folding, Saccharomyces cerevisiae xref: Reactome:REACT_32255 ! Chaperonin-mediated protein folding, Schizosaccharomyces pombe xref: Reactome:REACT_33395 ! Formation of tubulin folding intermediates by CCT/TriC, Mus musculus xref: Reactome:REACT_77627 ! Chaperonin-mediated protein folding, Plasmodium falciparum xref: Reactome:REACT_77963 ! Formation of tubulin folding intermediates by CCT/TriC, Saccharomyces cerevisiae xref: Reactome:REACT_78530 ! Formation of tubulin folding intermediates by CCT/TriC, Gallus gallus xref: Reactome:REACT_81155 ! Formation of tubulin folding intermediates by CCT/TriC, Caenorhabditis elegans xref: Reactome:REACT_83906 ! Chaperonin-mediated protein folding, Dictyostelium discoideum xref: Reactome:REACT_85492 ! Formation of tubulin folding intermediates by CCT/TriC, Sus scrofa xref: Reactome:REACT_85496 ! Formation of tubulin folding intermediates by CCT/TriC, Plasmodium falciparum xref: Reactome:REACT_86318 ! Formation of tubulin folding intermediates by CCT/TriC, Arabidopsis thaliana xref: Reactome:REACT_91676 ! Formation of tubulin folding intermediates by CCT/TriC, Schizosaccharomyces pombe xref: Reactome:REACT_92785 ! Formation of tubulin folding intermediates by CCT/TriC, Dictyostelium discoideum xref: Reactome:REACT_92961 ! Chaperonin-mediated protein folding, Xenopus tropicalis xref: Reactome:REACT_92981 ! Chaperonin-mediated protein folding, Taeniopygia guttata xref: Reactome:REACT_94123 ! Formation of tubulin folding intermediates by CCT/TriC, Taeniopygia guttata xref: Reactome:REACT_94443 ! Formation of tubulin folding intermediates by CCT/TriC, Danio rerio xref: Reactome:REACT_94772 ! Chaperonin-mediated protein folding, Sus scrofa xref: Reactome:REACT_96773 ! Chaperonin-mediated protein folding, Danio rerio xref: Reactome:REACT_97016 ! Chaperonin-mediated protein folding, Bos taurus xref: Reactome:REACT_97220 ! Formation of tubulin folding intermediates by CCT/TriC, Xenopus tropicalis xref: Reactome:REACT_98132 ! Formation of tubulin folding intermediates by CCT/TriC, Oryza sativa xref: Wikipedia:Protein_folding is_a: GO:0008150 ! biological_process [Term] id: GO:0006461 name: protein complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form a protein complex." [GOC:ai] subset: goslim_generic subset: goslim_pombe subset: gosubset_prok synonym: "chaperone activity" RELATED [] synonym: "protein complex formation" EXACT [] is_a: GO:0065003 ! macromolecular complex assembly is_a: GO:0008150 ! biological_process relationship: part_of GO:0008150 ! biological_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: gosubset_prok synonym: "process resulting in protein modification" RELATED [] synonym: "protein tagging activity" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0006520 name: cellular amino acid metabolic process namespace: biological_process alt_id: GO:0006519 def: "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells." [CHEBI:33709, GOC:curators, ISBN:0198506732] subset: goslim_generic subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "amino acid and derivative metabolism" EXACT [GOC:curators] synonym: "amino acid metabolic process" EXACT [GOC:curators] synonym: "cellular amino acid and derivative metabolic process" EXACT [] synonym: "cellular amino acid metabolism" EXACT [] is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0044281 ! small molecule metabolic process [Term] id: GO:0006605 name: protein targeting namespace: biological_process def: "The process of targeting specific proteins to particular membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif." [GOC:ma] subset: goslim_generic subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "nascent polypeptide association" RELATED [] synonym: "protein sorting along secretory pathway" NARROW [] xref: Wikipedia:Protein_targeting is_a: GO:0006810 ! transport relationship: occurs_in GO:0005623 ! occurs in cell relationship: occurs_in GO:0005622 ! occurs in intracellular [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: goslim_yeast subset: gosubset_prok synonym: "lipid metabolism" EXACT [] xref: Reactome:REACT_104930 ! Lipid digestion, mobilization, and transport, Drosophila melanogaster xref: Reactome:REACT_107479 ! Lipid digestion, mobilization, and transport, Xenopus tropicalis xref: Reactome:REACT_108775 ! Lipid digestion, mobilization, and transport, Canis familiaris xref: Reactome:REACT_28745 ! Lipid digestion, mobilization, and transport, Saccharomyces cerevisiae xref: Reactome:REACT_31395 ! Lipid digestion, mobilization, and transport, Sus scrofa xref: Reactome:REACT_32539 ! Lipid digestion, mobilization, and transport, Bos taurus xref: Reactome:REACT_33836 ! Lipid digestion, mobilization, and transport, Rattus norvegicus xref: Reactome:REACT_602 ! Lipid digestion, mobilization, and transport, Homo sapiens xref: Reactome:REACT_77176 ! Lipid digestion, mobilization, and transport, Danio rerio xref: Reactome:REACT_77191 ! Lipid digestion, mobilization, and transport, Arabidopsis thaliana xref: Reactome:REACT_79244 ! Lipid digestion, mobilization, and transport, Plasmodium falciparum xref: Reactome:REACT_81778 ! Lipid digestion, mobilization, and transport, Oryza sativa xref: Reactome:REACT_82512 ! Lipid digestion, mobilization, and transport, Taeniopygia guttata xref: Reactome:REACT_82723 ! Lipid digestion, mobilization, and transport, Escherichia coli xref: Reactome:REACT_90757 ! Lipid digestion, mobilization, and transport, Mus musculus xref: Reactome:REACT_94607 ! Lipid digestion, mobilization, and transport, Mycobacterium tuberculosis xref: Reactome:REACT_97906 ! Lipid digestion, mobilization, and transport, Gallus gallus xref: Reactome:REACT_98052 ! Lipid digestion, mobilization, and transport, Caenorhabditis elegans xref: Reactome:REACT_98129 ! Lipid digestion, mobilization, and transport, Schizosaccharomyces pombe xref: Reactome:REACT_99706 ! Lipid digestion, mobilization, and transport, Dictyostelium discoideum xref: Wikipedia:Lipid_metabolism is_a: GO:0008150 ! biological_process [Term] id: GO:0006790 name: sulfur compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:ai] subset: goslim_generic subset: gosubset_prok synonym: "sulfur metabolism" EXACT [] synonym: "sulphur metabolic process" EXACT [] synonym: "sulphur metabolism" EXACT [] xref: Reactome:REACT_27247 ! Sulfur compound metabolism, Mycobacterium tuberculosis xref: Wikipedia:Sulfur_metabolism is_a: GO:0008150 ! biological_process [Term] id: GO:0006810 name: transport namespace: biological_process alt_id: GO:0015457 alt_id: GO:0015460 def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "auxiliary transport protein activity" RELATED [GOC:mah] synonym: "small molecule transport" NARROW [] synonym: "solute:solute exchange" NARROW [] synonym: "transport accessory protein activity" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process relationship: part_of GO:0008150 ! biological_process [Term] id: GO:0006913 name: nucleocytoplasmic transport namespace: biological_process alt_id: GO:0000063 def: "The directed movement of molecules between the nucleus and the cytoplasm." [GOC:go_curators] subset: goslim_generic subset: goslim_pombe synonym: "nucleocytoplasmic shuttling" NARROW [] is_a: GO:0006810 ! transport relationship: occurs_in GO:0005623 ! occurs in cell relationship: occurs_in GO:0005622 ! occurs in intracellular [Term] id: GO:0006950 name: response to stress namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: high_level_annotation_qc synonym: "response to abiotic stress" RELATED [] synonym: "response to biotic stress" RELATED [] is_a: GO:0008150 ! biological_process [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:0008150 ! biological_process [Term] id: GO:0007009 name: plasma 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 the plasma membrane." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_generic subset: gosubset_prok synonym: "plasma membrane organisation" EXACT [GOC:curators] synonym: "plasma membrane organization and biogenesis" RELATED [GOC:mah] is_a: GO:0061024 ! membrane organization [Term] id: GO:0007010 name: cytoskeleton organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "cytoskeletal organization and biogenesis" RELATED [GOC:mah] synonym: "cytoskeletal regulator activity" RELATED [] synonym: "cytoskeleton organisation" EXACT [GOC:curators] synonym: "cytoskeleton organization and biogenesis" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process [Term] id: GO:0007034 name: vacuolar transport namespace: biological_process def: "The directed movement of substances into, out of or within a vacuole." [GOC:ai] subset: goslim_generic is_a: GO:0006810 ! transport relationship: occurs_in GO:0005623 ! occurs in cell relationship: occurs_in GO:0005622 ! occurs in intracellular [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: gosubset_prok synonym: "cell-division cycle" EXACT [] xref: Wikipedia:Cell_cycle is_a: GO:0008150 ! biological_process [Term] id: GO:0007059 name: chromosome segregation namespace: biological_process def: "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the alignment of chromosomes at the metaphase plate, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." [GOC:ai, GOC:mah] subset: goslim_generic 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:0008150 ! biological_process [Term] id: GO:0007067 name: mitosis namespace: biological_process def: "A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." [GOC:dph, GOC:ma, GOC:mah, ISBN:0198547684] subset: goslim_generic xref: Wikipedia:Mitosis is_a: GO:0008150 ! biological_process relationship: part_of GO:0007049 ! cell cycle [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_generic subset: goslim_pir subset: goslim_pombe subset: gosubset_prok synonym: "cell adhesion molecule activity" RELATED [] xref: Wikipedia:Cell_adhesion is_a: GO:0008150 ! biological_process [Term] id: GO:0007165 name: signal transduction namespace: biological_process alt_id: GO:0023033 def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal, e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light, and ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell, and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "signaling cascade" NARROW [] synonym: "signaling pathway" RELATED [] synonym: "signalling cascade" NARROW [] synonym: "signalling pathway" RELATED [GOC:mah] xref: Reactome:REACT_100624 ! EGFR interacts with phospholipase C-gamma, Gallus gallus xref: Reactome:REACT_102354 ! EGFR interacts with phospholipase C-gamma, Canis familiaris xref: Reactome:REACT_12478 ! EGFR interacts with phospholipase C-gamma, Homo sapiens xref: Reactome:REACT_31232 ! EGFR interacts with phospholipase C-gamma, Rattus norvegicus xref: Reactome:REACT_78535 ! EGFR interacts with phospholipase C-gamma, Xenopus tropicalis xref: Reactome:REACT_89740 ! EGFR interacts with phospholipase C-gamma, Taeniopygia guttata xref: Reactome:REACT_93680 ! EGFR interacts with phospholipase C-gamma, Danio rerio xref: Reactome:REACT_98872 ! EGFR interacts with phospholipase C-gamma, Mus musculus xref: Wikipedia:Signal_transduction relationship: regulates GO:0008150 ! biological_process relationship: part_of GO:0008150 ! biological_process is_a: GO:0008150 ! biological_process [Term] id: GO:0007267 name: cell-cell signaling namespace: biological_process def: "Any process that mediates the transfer of information from one cell to another." [GOC:mah] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "cell-cell signalling" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0007568 name: aging namespace: biological_process alt_id: GO:0016280 def: "The inherent decline over time, from the optimal fertility and viability of early maturity, that may precede death and may be preceded by other indications, such as sterility." [GOC:dph, GOC:ems] subset: goslim_generic synonym: "ageing" EXACT [] xref: Wikipedia:Aging is_a: GO:0008150 ! biological_process [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_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 disjoint_from: GO:0005575 ! cellular_component [Term] id: GO:0008219 name: cell death namespace: biological_process def: "A biological process that results in permanent cessation of all vital functions of a cell." [GOC:mah] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "necrosis" RELATED [] is_a: GO:0008150 ! biological_process [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] comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. subset: goslim_generic subset: goslim_pir subset: gosubset_prok is_a: GO:0008150 ! biological_process [Term] id: GO:0009056 name: catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "breakdown" EXACT [] synonym: "catabolism" EXACT [] synonym: "degradation" EXACT [] xref: Wikipedia:Catabolism is_a: GO:0008150 ! biological_process [Term] id: GO:0009058 name: biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "anabolism" EXACT [] synonym: "biosynthesis" EXACT [] synonym: "formation" EXACT [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008150 ! biological_process [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:0005737 ! cytoplasm is_a: GO:0043226 ! 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] comment: A thylakoid is not considered an organelle, but some thylakoids are part of organelles. 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:0005575 ! cellular_component [Term] id: GO:0009790 name: embryo development namespace: biological_process alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: goslim_generic subset: goslim_plant synonym: "embryogenesis" EXACT [] synonym: "embryogenesis and morphogenesis" BROAD [] synonym: "embryonal development" EXACT [] xref: Wikipedia:Embryogenesis relationship: part_of GO:0008150 ! biological_process is_a: GO:0008150 ! biological_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_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Photosynthesis is_a: GO:0008150 ! biological_process [Term] id: GO:0016023 name: cytoplasmic membrane-bounded vesicle namespace: cellular_component def: "A membrane-bounded vesicle found in the cytoplasm of the cell." [GOC:ai, GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_yeast subset: gosubset_prok synonym: "cytoplasmic membrane bounded vesicle" EXACT [] synonym: "cytoplasmic membrane-enclosed vesicle" EXACT [] relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0043226 ! organelle [Term] id: GO:0016192 name: vesicle-mediated transport namespace: biological_process alt_id: GO:0006899 def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_pombe 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] is_a: GO:0006810 ! transport [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:0008150 ! biological_process [Term] id: GO:0021700 name: developmental maturation namespace: biological_process def: "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] comment: This term was added by GO_REF:0000021. subset: goslim_generic is_a: GO:0008150 ! biological_process [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_generic subset: goslim_pir subset: gosubset_prok synonym: "cell structure assembly" EXACT [] is_a: GO:0008150 ! biological_process relationship: part_of GO:0008150 ! biological_process [Term] id: GO:0022618 name: ribonucleoprotein complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex." [GOC:jl] subset: goslim_generic subset: gosubset_prok synonym: "RNA-protein complex assembly" EXACT [] synonym: "RNP complex assembly" EXACT [] synonym: "protein-RNA complex assembly" EXACT [] is_a: GO:0065003 ! macromolecular complex assembly [Term] id: GO:0030154 name: cell differentiation namespace: biological_process def: "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732] subset: goslim_generic subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Cellular_differentiation is_a: GO:0008150 ! biological_process [Term] id: GO:0030198 name: extracellular matrix organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix." [GOC:mah] subset: goslim_generic subset: gosubset_prok synonym: "extracellular matrix organisation" EXACT [GOC:curators] synonym: "extracellular matrix organization and biogenesis" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process [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_pir subset: goslim_plant subset: gosubset_prok relationship: part_of GO:0005623 ! cell is_a: GO:0005575 ! cellular_component [Term] id: GO:0030705 name: cytoskeleton-dependent intracellular transport namespace: biological_process def: "The directed movement of substances along cytoskeletal elements such as microfilaments or microtubules within a cell." [GOC:mah] subset: goslim_generic subset: gosubset_prok is_a: GO:0006810 ! transport relationship: occurs_in GO:0005623 ! occurs in cell relationship: occurs_in GO:0005622 ! occurs in intracellular [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_generic subset: goslim_pir subset: goslim_yeast subset: gosubset_prok xref: Wikipedia:Transposon is_a: GO:0008150 ! biological_process [Term] id: GO:0034330 name: cell junction organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_generic synonym: "cell junction assembly and maintenance" EXACT [] synonym: "cell junction biogenesis" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0034641 name: cellular nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah] subset: goslim_generic subset: gosubset_prok synonym: "cellular nitrogen compound metabolism" EXACT [] xref: Reactome:REACT_102000 ! Metabolism of amino acids and derivatives, Mycobacterium tuberculosis xref: Reactome:REACT_102044 ! Metabolism of amino acids and derivatives, Sus scrofa xref: Reactome:REACT_103710 ! Metabolism of amino acids and derivatives, Escherichia coli xref: Reactome:REACT_107293 ! Metabolism of amino acids and derivatives, Arabidopsis thaliana xref: Reactome:REACT_108179 ! Metabolism of amino acids and derivatives, Xenopus tropicalis xref: Reactome:REACT_13 ! Metabolism of amino acids and derivatives, Homo sapiens xref: Reactome:REACT_28699 ! Metabolism of amino acids and derivatives, Saccharomyces cerevisiae xref: Reactome:REACT_29108 ! Metabolism of amino acids and derivatives, Caenorhabditis elegans xref: Reactome:REACT_32429 ! Metabolism of amino acids and derivatives, Rattus norvegicus xref: Reactome:REACT_33347 ! Metabolism of amino acids and derivatives, Mus musculus xref: Reactome:REACT_34326 ! Metabolism of amino acids and derivatives, Staphylococcus aureus N315 xref: Reactome:REACT_55564 ! Metabolism of amino acids and derivatives, Gallus gallus xref: Reactome:REACT_77741 ! Metabolism of amino acids and derivatives, Taeniopygia guttata xref: Reactome:REACT_82379 ! Metabolism of amino acids and derivatives, Bos taurus xref: Reactome:REACT_86268 ! Metabolism of amino acids and derivatives, Drosophila melanogaster xref: Reactome:REACT_90299 ! Metabolism of amino acids and derivatives, Oryza sativa xref: Reactome:REACT_91959 ! Metabolism of amino acids and derivatives, Plasmodium falciparum xref: Reactome:REACT_93580 ! Metabolism of amino acids and derivatives, Danio rerio xref: Reactome:REACT_95666 ! Metabolism of amino acids and derivatives, Canis familiaris xref: Reactome:REACT_98086 ! Metabolism of amino acids and derivatives, Dictyostelium discoideum xref: Reactome:REACT_99241 ! Metabolism of amino acids and derivatives, Schizosaccharomyces pombe is_a: GO:0008150 ! biological_process [Term] id: GO:0034655 name: nucleobase, nucleoside, nucleotide and nucleic acid catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] subset: goslim_generic subset: gosubset_prok synonym: "nucleobase, nucleoside, nucleotide and nucleic acid breakdown" EXACT [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolism" EXACT [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid degradation" EXACT [] is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0009056 ! catabolic process [Term] id: GO:0040007 name: growth namespace: biological_process alt_id: GO:0048590 def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] comment: See also the biological process term 'cell growth ; GO:0016049'. subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "growth pattern" RELATED [] synonym: "non-developmental growth" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process [Term] id: GO:0040011 name: locomotion namespace: biological_process def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh] subset: goslim_generic subset: goslim_pir subset: gosubset_prok is_a: GO:0008150 ! biological_process [Term] id: GO:0042254 name: ribosome biogenesis namespace: biological_process alt_id: GO:0007046 def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis." [GOC:ma] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: gosubset_prok synonym: "ribosomal chaperone activity" RELATED [] synonym: "ribosome biogenesis and assembly" EXACT [] xref: Wikipedia:Ribosome_biogenesis is_a: GO:0008150 ! biological_process [Term] id: GO:0042592 name: homeostatic process namespace: biological_process def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_generic subset: gosubset_prok synonym: "homeostasis" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0043226 name: organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators] subset: goslim_generic subset: goslim_pir subset: gosubset_prok xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle is_a: GO:0005575 ! cellular_component [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 other small molecules." [GOC:go_curators] subset: goslim_generic subset: goslim_pir subset: gosubset_prok synonym: "protein-protein complex" EXACT [] xref: Wikipedia:Protein_complex is_a: GO:0005575 ! cellular_component [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_generic subset: goslim_pir subset: gosubset_prok is_a: GO:0008150 ! biological_process [Term] id: GO:0044281 name: small molecule metabolic process namespace: biological_process def: "The chemical reactions and pathways involving small molecules, any monomeric molecule of small relative molecular mass." [GOC:curators, GOC:vw] subset: goslim_generic synonym: "small molecule metabolism" EXACT [] is_a: GO:0008150 ! biological_process created_by: jane creation_date: 2010-01-26T12:05:20Z [Term] id: GO:0044403 name: symbiosis, encompassing mutualism through parasitism namespace: biological_process alt_id: GO:0043298 alt_id: GO:0044404 def: "An interaction between two organisms living together in more or less intimate association. The term host is usually used for the larger (macro) of the two members of a symbiosis. The smaller (micro) member is called the symbiont organism. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs." [GOC:cc, http://www.free-definition.com] comment: Note that this term encompasses all symbiotic relationships between species along a continuum from mutualism through to parasitism, as outlined in the definition. subset: goslim_generic subset: gosubset_prok synonym: "host-pathogen interaction" RELATED [] synonym: "symbiosis" EXACT [] synonym: "symbiotic interaction" EXACT [] synonym: "symbiotic interaction between host and organism" RELATED [] synonym: "symbiotic interaction between organisms" EXACT [] synonym: "symbiotic interaction between species" EXACT [] synonym: "symbiotic interaction with other non-host organism" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0048646 name: anatomical structure formation involved in morphogenesis namespace: biological_process def: "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph, GOC:jid, GOC:tb] comment: Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. subset: goslim_generic synonym: "formation of an anatomical structure involved in morphogenesis" EXACT [GOC:tb, GOC:dph] is_a: GO:0008150 ! biological_process relationship: part_of GO:0048856 ! anatomical structure development [Term] id: GO:0048856 name: anatomical structure development namespace: biological_process def: "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GO_REF:0000021, GOC:mtg_15jun06] comment: This term was added by GO_REF:0000021. subset: goslim_generic synonym: "development of an anatomical structure" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0048870 name: cell motility namespace: biological_process def: "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another." [GOC:dgh, GOC:dph, GOC:isa_complete, GOC:mlg] subset: goslim_generic subset: gosubset_prok synonym: "cell locomotion" EXACT [] synonym: "cell movement" RELATED [] synonym: "movement of a cell" EXACT [] relationship: part_of GO:0008150 ! biological_process is_a: GO:0040011 ! locomotion [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_generic subset: goslim_pir synonym: "neurophysiological process" EXACT [] synonym: "pan-neural process" RELATED [] is_a: GO:0008150 ! biological_process [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_generic subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "cofactor metabolism" EXACT [] is_a: GO:0008150 ! biological_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_generic subset: goslim_pir subset: goslim_pombe 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:0008150 ! biological_process [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] comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis excludes nuclear division; in prokaryotes, there is little difference between cytokinesis and cell division. Note that there is no relationship between this term and 'nuclear division ; GO:0000280' because cell division can take place without nuclear division (as in prokaryotes) and vice versa (as in syncytium formation by mitosis without cytokinesis. subset: goslim_generic subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Cell_division is_a: GO:0008150 ! biological_process [Term] id: GO:0051604 name: protein maturation namespace: biological_process def: "Any process leading to the attainment of the full functional capacity of a protein." [GOC:ai] subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok is_a: GO:0008150 ! biological_process relationship: part_of GO:0008150 ! biological_process [Term] id: GO:0055085 name: transmembrane transport namespace: biological_process def: "The process in which a solute is transported from one side of a membrane to the other." [GOC:dph, GOC:jid] subset: goslim_generic subset: goslim_pombe subset: goslim_yeast xref: Reactome:REACT_100480 ! SLC-mediated transmembrane transport, Taeniopygia guttata xref: Reactome:REACT_101577 ! SLC-mediated transmembrane transport, Caenorhabditis elegans xref: Reactome:REACT_101877 ! SLC-mediated transmembrane transport, Escherichia coli xref: Reactome:REACT_102348 ! Transmembrane transport of small molecules, Staphylococcus aureus N315 xref: Reactome:REACT_102897 ! Transmembrane transport of small molecules, Caenorhabditis elegans xref: Reactome:REACT_102974 ! SLC-mediated transmembrane transport, Canis familiaris xref: Reactome:REACT_104555 ! SLC-mediated transmembrane transport, Xenopus tropicalis xref: Reactome:REACT_108243 ! SLC-mediated transmembrane transport, Staphylococcus aureus N315 xref: Reactome:REACT_109832 ! Transmembrane transport of small molecules, Plasmodium falciparum xref: Reactome:REACT_110770 ! ABC-family proteins mediated transport, Mus musculus xref: Reactome:REACT_15480 ! ABC-family proteins mediated transport, Homo sapiens xref: Reactome:REACT_15518 ! Transmembrane transport of small molecules, Homo sapiens xref: Reactome:REACT_19118 ! SLC-mediated transmembrane transport, Homo sapiens xref: Reactome:REACT_28801 ! Transmembrane transport of small molecules, Sus scrofa xref: Reactome:REACT_29093 ! ABC-family proteins mediated transport, Taeniopygia guttata xref: Reactome:REACT_29184 ! SLC-mediated transmembrane transport, Gallus gallus xref: Reactome:REACT_29635 ! Transmembrane transport of small molecules, Canis familiaris xref: Reactome:REACT_30969 ! ABC-family proteins mediated transport, Canis familiaris xref: Reactome:REACT_32055 ! Transmembrane transport of small molecules, Saccharomyces cerevisiae xref: Reactome:REACT_32223 ! Transmembrane transport of small molecules, Rattus norvegicus xref: Reactome:REACT_32423 ! SLC-mediated transmembrane transport, Bos taurus xref: Reactome:REACT_32562 ! SLC-mediated transmembrane transport, Sus scrofa xref: Reactome:REACT_32713 ! ABC-family proteins mediated transport, Sus scrofa xref: Reactome:REACT_33571 ! SLC-mediated transmembrane transport, Danio rerio xref: Reactome:REACT_61245 ! Transmembrane transport of small molecules, Bos taurus xref: Reactome:REACT_79086 ! SLC-mediated transmembrane transport, Plasmodium falciparum xref: Reactome:REACT_79921 ! SLC-mediated transmembrane transport, Saccharomyces cerevisiae xref: Reactome:REACT_80022 ! ABC-family proteins mediated transport, Bos taurus xref: Reactome:REACT_80510 ! ABC-family proteins mediated transport, Rattus norvegicus xref: Reactome:REACT_80848 ! ABC-family proteins mediated transport, Schizosaccharomyces pombe xref: Reactome:REACT_80977 ! ABC-family proteins mediated transport, Caenorhabditis elegans xref: Reactome:REACT_81024 ! Transmembrane transport of small molecules, Oryza sativa xref: Reactome:REACT_81153 ! SLC-mediated transmembrane transport, Mus musculus xref: Reactome:REACT_82725 ! SLC-mediated transmembrane transport, Rattus norvegicus xref: Reactome:REACT_83770 ! Transmembrane transport of small molecules, Escherichia coli xref: Reactome:REACT_86135 ! ABC-family proteins mediated transport, Oryza sativa xref: Reactome:REACT_86409 ! Transmembrane transport of small molecules, Drosophila melanogaster xref: Reactome:REACT_86576 ! Transmembrane transport of small molecules, Schizosaccharomyces pombe xref: Reactome:REACT_87124 ! SLC-mediated transmembrane transport, Oryza sativa xref: Reactome:REACT_88059 ! ABC-family proteins mediated transport, Xenopus tropicalis xref: Reactome:REACT_88521 ! Transmembrane transport of small molecules, Taeniopygia guttata xref: Reactome:REACT_88894 ! Transmembrane transport of small molecules, Gallus gallus xref: Reactome:REACT_89376 ! SLC-mediated transmembrane transport, Schizosaccharomyces pombe xref: Reactome:REACT_91272 ! ABC-family proteins mediated transport, Arabidopsis thaliana xref: Reactome:REACT_91803 ! SLC-mediated transmembrane transport, Mycobacterium tuberculosis xref: Reactome:REACT_92006 ! Transmembrane transport of small molecules, Mycobacterium tuberculosis xref: Reactome:REACT_92624 ! ABC-family proteins mediated transport, Gallus gallus xref: Reactome:REACT_93747 ! Transmembrane transport of small molecules, Dictyostelium discoideum xref: Reactome:REACT_94160 ! Transmembrane transport of small molecules, Mus musculus xref: Reactome:REACT_94393 ! ABC-family proteins mediated transport, Drosophila melanogaster xref: Reactome:REACT_94944 ! ABC-family proteins mediated transport, Danio rerio xref: Reactome:REACT_94972 ! SLC-mediated transmembrane transport, Dictyostelium discoideum xref: Reactome:REACT_96636 ! SLC-mediated transmembrane transport, Arabidopsis thaliana xref: Reactome:REACT_97365 ! Transmembrane transport of small molecules, Arabidopsis thaliana xref: Reactome:REACT_97867 ! ABC-family proteins mediated transport, Saccharomyces cerevisiae xref: Reactome:REACT_98509 ! Transmembrane transport of small molecules, Xenopus tropicalis xref: Reactome:REACT_98716 ! SLC-mediated transmembrane transport, Drosophila melanogaster xref: Reactome:REACT_99579 ! Transmembrane transport of small molecules, Danio rerio xref: Reactome:REACT_99829 ! ABC-family proteins mediated transport, Dictyostelium discoideum is_a: GO:0006810 ! transport [Term] id: GO:0061024 name: membrane organization namespace: biological_process def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb] subset: goslim_generic is_a: GO:0008150 ! biological_process created_by: dph creation_date: 2010-02-08T02:43:11Z [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_generic subset: goslim_pir subset: gosubset_prok synonym: "macromolecule complex assembly" EXACT [] is_a: GO:0022607 ! cellular component assembly [Term] id: GO:0071554 name: cell wall organization or biogenesis namespace: biological_process def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cell wall." [GOC:mah] subset: goslim_generic subset: goslim_yeast subset: gosubset_prok synonym: "cell wall organisation or biogenesis" EXACT [GOC:mah] is_a: GO:0008150 ! biological_process created_by: midori creation_date: 2010-01-13T03:19:38Z [Term] id: GO:0071941 name: nitrogen cycle metabolic process namespace: biological_process def: "A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization." [GOC:mah, PMID:16675690, Wikipedia:Nitrogen_cycle] subset: goslim_generic subset: goslim_pombe xref: Wikipedia:Nitrogen_cycle is_a: GO:0008150 ! biological_process created_by: midori creation_date: 2010-09-30T05:21:03Z [Typedef] id: has_part name: has_part namespace: gene_ontology xref: OBO_REL:has_part is_transitive: true created_by: midori creation_date: 2009-07-30T12:00:35Z [Typedef] id: negatively_regulates name: negatively_regulates namespace: gene_ontology [Typedef] id: occurs_in name: occurs in namespace: gene_ontology xref: BFO:0000066 [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 [Typedef] id: regulates name: regulates namespace: gene_ontology