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: 1.739 $ [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: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: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:0003677 name: DNA binding namespace: molecular_function def: "Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "microtubule/chromatin interaction" RELATED [] synonym: "plasmid binding" NARROW [] is_a: GO:0003676 ! nucleic acid 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:0003700 name: transcription factor activity namespace: molecular_function alt_id: GO:0000130 def: "The function of binding to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:curators] subset: goslim_generic subset: goslim_plant subset: gosubset_prok xref: Reactome:4325 "transcription factor activity" is_a: GO:0003677 ! DNA binding is_a: GO:0030528 ! transcription regulator activity [Term] id: GO:0003723 name: RNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA molecule or a portion thereof." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok xref: Reactome:1805 "RNA binding" is_a: GO:0003676 ! nucleic acid 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: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:0004518 name: nuclease activity namespace: molecular_function def: "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN:0198547684] comment: Consider also annotating to the molecular function term 'nucleic acid binding ; GO:0003676'. Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. subset: goslim_generic subset: goslim_plant subset: gosubset_prok xref: EC:3.1.-.- is_a: GO:0016787 ! hydrolase 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:0003674 ! molecular_function [Term] id: GO:0004872 name: receptor activity namespace: molecular_function def: "Combining with an extracellular or intracellular messenger to initiate a change in cell activity." [GOC:ceb, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok synonym: "receptor guanylate cyclase activity" NARROW [] is_a: GO:0004871 ! signal transducer activity [Term] id: GO:0005102 name: receptor binding namespace: molecular_function def: "Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:bf, GOC:ceb, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "receptor ligand" NARROW [] synonym: "receptor-associated protein activity" RELATED [] xref: Wikipedia:Ligand_(biochemistry) is_a: GO:0005515 ! protein binding [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: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: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: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_goa subset: goslim_plant is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005576 ! extracellular region [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 are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term. subset: goslim_generic subset: goslim_goa subset: goslim_plant synonym: "intercellular space" RELATED [] is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005576 ! extracellular region [Term] id: GO:0005618 name: cell wall namespace: cellular_component def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, 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:0005623 ! cell 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 is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005623 ! cell [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_goa subset: goslim_plant subset: gosubset_prok 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_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "cell nucleus" EXACT [] xref: Wikipedia:Cell_nucleus is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005622 ! intracellular [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 is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0005654 name: nucleoplasm namespace: cellular_component def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653] subset: goslim_generic subset: goslim_plant xref: Wikipedia:Nucleoplasm is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0005730 name: nucleolus namespace: cellular_component def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732 "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:0005575 ! cellular_component [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_goa 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 "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 is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005737 ! cytoplasm [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 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_plant xref: Wikipedia:Lysosome relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0005773 ! vacuole [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 is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005773 name: vacuole namespace: cellular_component def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732 "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 is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005737 ! cytoplasm [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: Wikipedia:Peroxisome is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005783 name: endoplasmic reticulum namespace: cellular_component def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732 "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 is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005737 ! cytoplasm [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 is_a: GO:0005575 ! cellular_component 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: Wikipedia:Cytosol relationship: part_of GO:0005737 ! cytoplasm is_a: GO:0005575 ! cellular_component [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 is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005737 ! cytoplasm [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:0005575 ! cellular_component [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: Wikipedia:Cell_membrane relationship: part_of GO:0005623 ! cell is_a: GO:0016020 ! membrane [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:0008152 ! 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:0008152 ! metabolic process is_a: GO:0009987 ! cellular 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:0008152 ! metabolic process is_a: GO:0009987 ! cellular 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:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic 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:0008152 ! metabolic process is_a: GO:0009058 ! biosynthetic process is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid 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:0008152 ! metabolic process is_a: GO:0009058 ! biosynthetic process is_a: GO:0019538 ! protein metabolic process is_a: GO:0009987 ! cellular 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:0009987 ! cellular 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:0008152 ! metabolic process is_a: GO:0009987 ! cellular 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: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 [] is_a: GO:0008150 ! biological_process relationship: part_of GO:0008150 ! biological_process [Term] id: GO:0006950 name: response to stress namespace: biological_process 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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "response to abiotic stress" RELATED [] synonym: "response to biotic stress" RELATED [] is_a: GO:0008150 ! biological_process [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: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:0007165 name: signal transduction namespace: biological_process def: "The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately effecting a change in the functioning of the cell." [GOC:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "signaling" EXACT [] synonym: "signaling cascade" EXACT [] synonym: "signalling" EXACT [] synonym: "signalling cascade" EXACT [] xref: Reactome:212718 "EGFR interacts with phospholipase C-gamma" xref: Reactome:448734 "EGFR interacts with phospholipase C-gamma" xref: Reactome:469856 "EGFR interacts with phospholipase C-gamma" xref: Reactome:487553 "EGFR interacts with phospholipase C-gamma" xref: Reactome:507509 "EGFR interacts with phospholipase C-gamma" xref: Wikipedia:Signal_transduction relationship: regulates GO:0009987 ! cellular process is_a: GO:0007154 ! cell communication [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:0007154 ! cell communication [Term] id: GO:0007275 name: multicellular organismal development namespace: biological_process def: "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb] comment: Note that this term was 'developmental process'. subset: goslim_generic subset: goslim_goa subset: goslim_plant is_a: GO:0008150 ! biological_process [Term] id: GO:0007610 name: behavior namespace: biological_process def: "The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [GOC:ems, ISBN:0395448956] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok synonym: "behavioral response to stimulus" EXACT [] synonym: "behaviour" EXACT [] synonym: "behavioural response to stimulus" EXACT [] xref: Wikipedia:Behavior is_a: GO:0008150 ! biological_process [Term] id: GO:0008135 name: translation factor activity, nucleic acid binding namespace: molecular_function def: "Functions during translation by binding nucleic acids during polypeptide synthesis at the ribosome." [GOC:ai] subset: goslim_generic subset: goslim_plant subset: gosubset_prok is_a: GO:0045182 ! translation regulator activity is_a: GO:0003676 ! nucleic acid 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:0008219 name: cell death namespace: biological_process def: "The specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:ems] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok synonym: "necrosis" RELATED [] is_a: GO:0016265 ! death is_a: GO:0009987 ! cellular process [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: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_goa subset: goslim_plant subset: gosubset_prok synonym: "breakdown" EXACT [] synonym: "catabolism" EXACT [] synonym: "degradation" EXACT [] xref: Wikipedia:Catabolism is_a: GO:0008152 ! metabolic 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_goa subset: goslim_plant subset: gosubset_prok synonym: "anabolism" EXACT [] synonym: "biosynthesis" EXACT [] synonym: "formation" EXACT [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic 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 is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0009579 name: thylakoid namespace: cellular_component def: "A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." [GOC:ds, GOC:mtg_sensu, ISBN:0198506732 "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 is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005622 ! intracellular [Term] id: GO:0009605 name: response to external stimulus namespace: biological_process 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 an external stimulus." [GOC:hb] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "response to environmental stimulus" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0009606 name: tropism namespace: biological_process def: "The movement of an organism, or part of an organism, in response to an external source of stimulus, usually toward or away from it." [GOC:jl, http://cancerweb.ncl.ac.uk/] subset: goslim_plant xref: Wikipedia:Tropism is_a: GO:0009605 ! response to external stimulus [Term] id: GO:0009607 name: response to biotic stimulus namespace: biological_process 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 biotic stimulus, a stimulus caused or produced by a living organism." [GOC:hb] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "response to biotic stress" NARROW [] is_a: GO:0008150 ! biological_process [Term] id: GO:0009628 name: response to abiotic stimulus namespace: biological_process 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 an abiotic (non-living) stimulus." [GOC:hb] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "response to abiotic stress" NARROW [] is_a: GO:0008150 ! biological_process [Term] id: GO:0009653 name: anatomical structure morphogenesis namespace: biological_process def: "The process by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:go_curators, ISBN:0521436125] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "anatomical structure organization" EXACT [] synonym: "embryogenesis and morphogenesis" BROAD [] synonym: "morphogenesis" EXACT [] xref: Wikipedia:Morphogenesis relationship: part_of GO:0008150 ! biological_process is_a: GO:0008150 ! biological_process [Term] id: GO:0009719 name: response to endogenous stimulus namespace: biological_process 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 arising within the organism." [GOC:sm] subset: goslim_generic subset: goslim_plant subset: gosubset_prok is_a: GO:0008150 ! biological_process [Term] id: GO:0009790 name: embryonic 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 is_a: GO:0008150 ! biological_process relationship: part_of GO:0007275 ! multicellular organismal development [Term] id: GO:0009791 name: post-embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." [GOC:go_curators] subset: goslim_plant is_a: GO:0008150 ! biological_process relationship: part_of GO:0007275 ! multicellular organismal development [Term] id: GO:0009835 name: ripening namespace: biological_process def: "The series of events causing changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) to make it more attractive to animals and/or aid in seed dispersal." [GOC:lr] subset: goslim_plant xref: Wikipedia:Ripening is_a: GO:0008150 ! biological_process relationship: part_of GO:0000003 ! reproduction relationship: part_of GO:0007275 ! multicellular organismal development [Term] id: GO:0009838 name: abscission namespace: biological_process def: "The controlled shedding of a body part." [ISBN:0140514031] subset: goslim_plant xref: Wikipedia:Abscission is_a: GO:0008150 ! biological_process relationship: part_of GO:0007275 ! multicellular organismal development [Term] id: GO:0009856 name: pollination namespace: biological_process def: "The cascade of biological processes occurring in plants beginning when the pollen lands on the stigma and continuing up to, but not including, fertilization, as defined by sperm-central cell fusion." [GOC:tb, PMID:10973091] subset: goslim_plant xref: Wikipedia:Pollination relationship: part_of GO:0000003 ! reproduction is_a: GO:0008150 ! biological_process [Term] id: GO:0009875 name: pollen-pistil interaction namespace: biological_process def: "The interaction between a pollen grain and pistil." [GOC:go_curators] subset: goslim_plant relationship: part_of GO:0009856 ! pollination is_a: GO:0007154 ! cell communication [Term] id: GO:0009908 name: flower development namespace: biological_process alt_id: GO:0048409 def: "The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem." [GOC:tb, ISBN:0879015322] subset: goslim_plant relationship: part_of GO:0000003 ! reproduction relationship: part_of GO:0007275 ! multicellular organismal development is_a: GO:0009791 ! post-embryonic development [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:0009991 name: response to extracellular stimulus namespace: biological_process 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 an extracellular stimulus." [GOC:go_curators] subset: goslim_plant subset: gosubset_prok is_a: GO:0009605 ! response to external stimulus [Term] id: GO:0015979 name: photosynthesis namespace: biological_process def: "The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds." [ISBN:0198547684] subset: goslim_pir subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Photosynthesis is_a: GO:0008152 ! metabolic process is_a: GO:0009987 ! cellular process [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:0005623 ! cell is_a: GO:0005575 ! cellular_component [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: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:0008150 ! biological_process is_a: GO:0009987 ! cellular process is_a: GO:0040007 ! growth [Term] id: GO:0016265 name: death namespace: biological_process def: "A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism." [GOC:mah, ISBN:0877797099] comment: See also the biological process term 'apoptosis ; GO:0006915'. subset: goslim_generic subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Death is_a: GO:0008150 ! biological_process [Term] id: GO:0016301 name: kinase activity namespace: molecular_function def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok synonym: "phosphokinase activity" EXACT [] xref: Reactome:1423 "kinase activity" is_a: GO:0016740 ! transferase activity [Term] id: GO:0016740 name: transferase activity namespace: molecular_function def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732 "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: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:0008152 ! metabolic process [Term] id: GO:0019725 name: cellular homeostasis namespace: biological_process def: "Any process involved in the maintenance of an internal equilibrium at the level of the cell." [GOC:isa_complete, GOC:jl, ISBN:0395825172] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok is_a: GO:0009987 ! cellular 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: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:0030154 name: cell differentiation namespace: biological_process def: "The process whereby 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." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Cellular_differentiation is_a: GO:0009987 ! cellular process [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:0005623 ! cell is_a: GO:0005575 ! cellular_component [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: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:0040029 name: regulation of gene expression, epigenetic namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [PMID:10521337, PMID:11498582] subset: goslim_generic subset: goslim_plant subset: gosubset_prok is_a: GO:0008150 ! biological_process relationship: regulates GO:0008152 ! metabolic process [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 [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