format-version: 1.2 date: 25:01:2011 12:46 saved-by: cmattin auto-generated-by: OBO-Edit 2.0 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" synonymtypedef: CTDCODE "CTD CODE" EXACT synonymtypedef: systematic_synonym "Systematic synonym" EXACT default-namespace: file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt [Term] id: CTDI:1 name: abundance def: "The abundance of a chemical (if chemical synthesis is not known)." [CTDI:ctd_curators] synonym: "abu" EXACT CTDCODE [] [Term] id: CTDI:10 name: chemical synthesis def: "A biochemical event resulting in a new chemical product." [CTDI:ctd_curators] synonym: "csy" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:11 name: ethylation def: "The addition of an ethyl group." [CTDI:ctd_curators] synonym: "eth" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:12 name: export def: "The movement of a molecule out of a cell (by more specific means than secretion)." [CTDI:ctd_curators] synonym: "ext" EXACT CTDCODE [] is_a: GO:0046903 ! secretion [Term] id: CTDI:13 name: folding def: "The bending and positioning of a molecule to achieve conformational integrity." [CTDI:ctd_curators] synonym: "fol" EXACT CTDCODE [] [Term] id: CTDI:14 name: geranoylation def: "The addition of a geranoyl group." [CTDI:ctd_curators] synonym: "ger" EXACT CTDCODE [] is_a: GO:0006497 ! protein lipidation [Term] id: CTDI:15 name: glycation def: "The non-enzymatic addition of a sugar." [CTDI:ctd_curators] synonym: "gyc" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:16 name: hydroxylation def: "The addition of a hydroxy group." [CTDI:ctd_curators] synonym: "hdx" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:17 name: hydrolysis def: "The splitting of a molecule via the specific use of water." [CTDI:ctd_curators] synonym: "hyd" EXACT CTDCODE [] is_a: CTDI:000008 [Term] id: CTDI:18 name: import def: "The movement of a molecule into a cell (by more specific means than uptake)." [CTDI:ctd_curators] synonym: "imt" EXACT CTDCODE [] is_a: CTDI:000023 [Term] id: CTDI:19 name: mutagenesis def: "The genetic alteration of a gene product." [CTDI:ctd_curators] synonym: "mut" EXACT CTDCODE [] [Term] id: CTDI:2 name: acetylation def: "The addition of an acetyl group." [CTDI:ctd_curators] synonym: "ace" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:20 name: oxidation def: "The loss of electrons." [CTDI:ctd_curators] synonym: "oxd" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:21 name: reduction def: "The gain of electrons." [CTDI:ctd_curators] synonym: "red" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:22 name: ribosylation def: "The addition of a ribosyl group." [CTDI:ctd_curators] synonym: "rib" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:23 name: reaction def: "Any general biochemical or molecular event." [CTDI:ctd_curators] synonym: "rxn" EXACT CTDCODE [] [Term] id: CTDI:24 name: stability def: "Overall propensity of molecules to degradation." [CTDI:ctd_curators] synonym: "sta" EXACT CTDCODE [] [Term] id: CTDI:25 name: uptake def: "The movement of a molecule into a cell (by less specific means than import)." [CTDI:ctd_curators] synonym: "upt" EXACT CTDCODE [] is_a: GO:0006810 ! transport [Term] id: CTDI:26 name: cotreatment def: "Involving the use of two or more chemicals simultaneously." [CTDI:ctd_curators] synonym: "w" EXACT CTDCODE [] [Term] id: CTDI:3 name: activity def: "An elemental function of a molecule." [CTDI:ctd_curators] synonym: "act" EXACT CTDCODE [] [Term] id: CTDI:4 name: acylation def: "The addition of an acyl group." [CTDI:ctd_curators] synonym: "acy" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:5 name: alkylation def: "The addition of an alkyl group." [CTDI:ctd_curators] synonym: "alk" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:6 name: amination def: "The addition of an amine group." [CTDI:ctd_curators] synonym: "ami" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: CTDI:7 name: ADP-ribosylation def: "The addition of a ADP-ribosyl group." [CTDI:ctd_curators] synonym: "arb" EXACT CTDCODE [] is_a: CTDI:000021 [Term] id: CTDI:8 name: cleavage def: "The processing or splitting of a molecule, not necessarily leading to the destruction of the molecule." [CTDI:ctd_curators] synonym: "clv" EXACT CTDCODE [] is_a: GO:0009056 ! catabolic process [Term] id: CTDI:9 name: carboxylation def: "The addition of a carboxyl group." [CTDI:ctd_curators] synonym: "cox" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [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. synonym: "b" EXACT CTDCODE [] xref: Wikipedia:Binding_(molecular) [Term] id: GO:0006487 name: protein N-linked glycosylation namespace: biological_process def: "A protein glycosylation process in which a sugar unit is added to a protein via the N4 atom of peptidyl-asparagine, the omega-N of arginine, or the N1' atom peptidyl-tryptophan." [RESID:AA0151, RESID:AA0156, RESID:AA0327] subset: gosubset_prok synonym: "N-glycan biosynthesis" RELATED [] synonym: "N-glycan metabolism" RELATED [] synonym: "ngl" EXACT CTDCODE [] synonym: "protein amino acid N-linked glycosylation" EXACT [GOC:bf] xref: RESID:AA0151 xref: RESID:AA0156 xref: RESID:AA0327 is_a: id: [Term] id: GO:0006493 name: protein O-linked glycosylation namespace: biological_process def: "A protein glycosylation process in which a sugar unit is added to a protein via the hydroxyl group of peptidyl-serine, peptidyl-threonine, peptidyl-hydroxylysine, or peptidyl-hydroxyproline, or via the phenol group of peptidyl-tyrosine, forming an O-glycan." [ISBN:0879695595, RESID:AA0153, RESID:AA0154, RESID:AA0155, RESID:AA0157, RESID:AA0212] subset: gosubset_prok synonym: "ogl" EXACT CTDCODE [] synonym: "protein amino acid O-linked glycosylation" EXACT [GOC:bf] xref: RESID:AA0153 xref: RESID:AA0154 xref: RESID:AA0155 xref: RESID:AA0157 xref: RESID:AA0212 is_a: id: [Term] id: GO:0006497 name: protein lipidation namespace: biological_process alt_id: GO:0042050 def: "The covalent attachment of lipid groups to an amino acid in a protein." [GOC:jl] comment: For non-covalent interactions with a lipid, consider instead the term 'lipid binding ; GO:0008289' and its children. subset: gosubset_prok synonym: "lip" EXACT CTDCODE [] synonym: "lipid:protein modification" EXACT [] synonym: "protein amino acid lipidation" EXACT [GOC:bf] synonym: "protein lipidation" EXACT [] xref: RESID:AA0059 xref: RESID:AA0060 xref: RESID:AA0077 xref: RESID:AA0078 xref: RESID:AA0079 xref: RESID:AA0080 xref: RESID:AA0102 xref: RESID:AA0103 xref: RESID:AA0104 xref: RESID:AA0106 xref: RESID:AA0107 xref: RESID:AA0158 xref: RESID:AA0159 xref: RESID:AA0160 xref: RESID:AA0161 xref: RESID:AA0162 xref: RESID:AA0163 xref: RESID:AA0166 xref: RESID:AA0223 xref: RESID:AA0290 xref: RESID:AA0307 xref: RESID:AA0308 xref: RESID:AA0309 xref: RESID:AA0316 is_a: GO:0008152 ! metabolic 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_goa subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast 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] synonym: "trt" EXACT CTDCODE [] [Term] id: GO:0008152 name: metabolic 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. synonym: "met" EXACT CTDCODE [] [Term] id: GO:0008380 name: RNA splicing namespace: biological_process alt_id: GO:0006395 def: "The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA." [GOC:krc, GOC:mah] subset: gosubset_prok synonym: "pre-mRNA splicing factor activity" RELATED [] synonym: "spl" EXACT CTDCODE [] xref: Reactome:1006447 "mRNA Splicing" xref: Reactome:1051751 "mRNA Splicing" xref: Reactome:1076708 "mRNA Splicing" xref: Reactome:1097222 "mRNA Splicing" xref: Reactome:1116507 "mRNA Splicing" xref: Reactome:1140327 "mRNA Splicing" xref: Reactome:1170576 "mRNA Splicing" xref: Reactome:1192393 "mRNA Splicing" xref: Reactome:1206583 "mRNA Splicing" xref: Reactome:1221220 "mRNA Splicing" xref: Reactome:1239204 "mRNA Splicing" xref: Reactome:1246834 "mRNA Splicing" xref: Reactome:1252579 "mRNA Splicing" xref: Reactome:1258368 "mRNA Splicing" xref: Reactome:1262057 "mRNA Splicing" xref: Reactome:72172 "mRNA Splicing" xref: Reactome:979854 "mRNA Splicing" xref: Wikipedia:RNA_splicing [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] synonym: "deg" EXACT CTDCODE [] xref: Wikipedia:Catabolism is_a: GO:0008152 ! metabolic process [Term] id: GO:0010467 name: gene expression namespace: biological_process def: "The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] subset: gosubset_prok synonym: "exp" EXACT CTDCODE [] xref: Reactome:1006441 "Gene Expression" xref: Reactome:1024783 "Gene Expression" xref: Reactome:1051745 "Gene Expression" xref: Reactome:1076702 "Gene Expression" xref: Reactome:1097220 "Gene Expression" xref: Reactome:1116505 "Gene Expression" xref: Reactome:1140321 "Gene Expression" xref: Reactome:1170570 "Gene Expression" xref: Reactome:1192387 "Gene Expression" xref: Reactome:1206581 "Gene Expression" xref: Reactome:1221214 "Gene Expression" xref: Reactome:1239198 "Gene Expression" xref: Reactome:1246779 "Gene Expression" xref: Reactome:1252532 "Gene Expression" xref: Reactome:1258323 "Gene Expression" xref: Reactome:1262022 "Gene Expression" xref: Reactome:1264209 "Gene Expression" xref: Reactome:1265616 "Gene Expression" xref: Reactome:1266830 "Gene Expression" xref: Reactome:74160 "Gene Expression" xref: Reactome:979848 "Gene Expression" xref: Wikipedia:Gene_expression [Term] id: GO:0010731 name: protein glutathionylation namespace: biological_process def: "The protein modification process in which a glutathione molecule is added to a protein amino acid through a disulfide linkage." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb] synonym: "glt" EXACT CTDCODE [] synonym: "protein amino acid glutathionylation" EXACT [GOC:bf] is_a: GO:0008152 ! metabolic process [Term] id: GO:0016310 name: phosphorylation namespace: biological_process def: "The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok synonym: "pho" EXACT CTDCODE [] xref: Wikipedia:Phosphorylation is_a: GO:0008152 ! metabolic process [Term] id: GO:0016567 name: protein ubiquitination namespace: biological_process def: "The process in which one or more ubiquitin groups are added to a protein." [GOC:ai] synonym: "protein ubiquitinylation" EXACT [] synonym: "protein ubiquitylation" EXACT [] synonym: "ubq" EXACT CTDCODE [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0016925 name: protein sumoylation namespace: biological_process alt_id: GO:0006485 alt_id: GO:0016927 def: "The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein." [GOC:jl, PMID:11265250] synonym: "protein sumolation" EXACT [] synonym: "small ubiquitin-related protein 1 conjugation" EXACT [] synonym: "sum" EXACT CTDCODE [] synonym: "SUMO-protein conjugation" EXACT [] synonym: "sumoylation" EXACT [] xref: Wikipedia:SUMO_protein is_a: GO:0008152 ! metabolic process [Term] id: GO:0017014 name: protein nitrosylation namespace: biological_process def: "The covalent addition of a nitric oxide group to an amino acid within a protein." [GOC:ai, PMID:20972426] subset: gosubset_prok synonym: "nit" EXACT CTDCODE [] synonym: "protein amino acid nitrosylation" EXACT [GOC:bf] is_a: GO:0008152 ! metabolic process [Term] id: GO:0018175 name: protein nucleotidylation namespace: biological_process def: "The addition of a nucleotide to a protein amino acid." [GOC:ai] subset: gosubset_prok synonym: "nuc" EXACT CTDCODE [] synonym: "protein amino acid nucleotidylation" EXACT [GOC:bf] is_a: GO:0008152 ! metabolic process [Term] id: GO:0018342 name: protein prenylation namespace: biological_process alt_id: GO:0018346 def: "The covalent attachment of a prenyl group to a protein; geranyl, farnesyl, or geranylgeranyl groups may be added." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok synonym: "C-terminal protein prenylation" NARROW [] synonym: "pre" EXACT CTDCODE [] synonym: "protein amino acid prenylation" EXACT [GOC:bf] is_a: GO:0006497 ! protein lipidation [Term] id: GO:0018343 name: protein farnesylation namespace: biological_process alt_id: GO:0018347 def: "The covalent attachment of a farnesyl group to a protein." [GOC:jl] subset: gosubset_prok synonym: "C-terminal protein farnesylation" NARROW [] synonym: "far" EXACT CTDCODE [] synonym: "protein amino acid farnesylation" EXACT [GOC:bf] is_a: GO:0006497 ! protein lipidation [Term] id: GO:0018345 name: protein palmitoylation namespace: biological_process alt_id: GO:0018318 alt_id: GO:0018349 def: "The covalent attachment of a palmitoyl group to a protein." [GOC:jl, PMID:15520806] subset: gosubset_prok synonym: "" RELATED [] synonym: "pal" EXACT CTDCODE [] synonym: "protein amino acid palmitoylation" EXACT [GOC:bf] is_a: GO:0006497 ! protein lipidation is_a: GO:0043543 [Term] id: GO:0018377 name: protein myristoylation namespace: biological_process alt_id: GO:0018319 def: "The covalent attachment of a myristoyl group to a protein." [GOC:ai] subset: gosubset_prok synonym: "myr" EXACT CTDCODE [] synonym: "protein amino acid myristoylation" EXACT [GOC:bf] is_a: CTDI:000004 is_a: GO:0006497 ! protein lipidation [Term] id: GO:0018411 name: protein glucuronidation namespace: biological_process def: "The modification of a protein by amino acid glucuronidation." [GOC:ai] subset: gosubset_prok synonym: "glc" EXACT CTDCODE [] synonym: "protein amino acid glucuronidation" EXACT [GOC:bf] is_a: GO:0070085 ! glycosylation [Term] id: GO:0032259 name: methylation namespace: biological_process def: "The process in which a methyl group is covalently attached to a molecule." [GOC:mah] synonym: "myl" EXACT CTDCODE [] xref: Reactome:1006567 "Methylation" xref: Reactome:1024884 "Methylation" xref: Reactome:1051871 "Methylation" xref: Reactome:1076824 "Methylation" xref: Reactome:1097328 "Methylation" xref: Reactome:1116621 "Methylation" xref: Reactome:1140446 "Methylation" xref: Reactome:1170691 "Methylation" xref: Reactome:1192489 "Methylation" xref: Reactome:1206864 "Methylation" xref: Reactome:1221409 "Methylation" xref: Reactome:1239392 "Methylation" xref: Reactome:1246869 "Methylation" xref: Reactome:1252723 "Methylation" xref: Reactome:1258533 "Methylation" xref: Reactome:1262147 "Methylation" xref: Reactome:1264263 "Methylation" xref: Reactome:1265699 "Methylation" xref: Reactome:156581 "Methylation" xref: Reactome:979970 "Methylation" xref: Wikipedia:Methylation is_a: GO:0008152 ! metabolic process [Term] id: GO:0042221 name: response to chemical 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 chemical stimulus." [GOC:jl] subset: goslim_candida subset: goslim_yeast subset: gosubset_prok synonym: "rec" EXACT CTDCODE [] synonym: "response to chemical substance" EXACT [] [Term] id: GO:0046903 name: secretion namespace: biological_process def: "The controlled release of a substance by a cell, a group of cells, or a tissue." [GOC:ai] subset: goslim_goa subset: goslim_pir subset: gosubset_prok synonym: "sec" EXACT CTDCODE [] is_a: GO:0006810 ! transport [Term] id: GO:0046944 name: protein carbamoylation namespace: biological_process def: "The addition of a carbamoyl group to a protein amino acid. A carbamoyl group is the acyl group -CO-NH2." [GOC:ai] subset: gosubset_prok synonym: "car" EXACT CTDCODE [] synonym: "protein amino acid carbamoylation" EXACT [GOC:bf] is_a: GO:0008152 ! metabolic process [Term] id: GO:0051179 name: localization namespace: biological_process def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "establishment and maintenance of cellular component location" NARROW [] synonym: "establishment and maintenance of localization" EXACT [] synonym: "establishment and maintenance of position" EXACT [] synonym: "establishment and maintenance of substance location" NARROW [] synonym: "establishment and maintenance of substrate location" NARROW [] synonym: "loc" EXACT CTDCODE [] synonym: "localisation" EXACT [GOC:mah] [Term] id: GO:0051923 name: sulfation namespace: biological_process def: "The addition of a sulfate group to a molecule." [http://www.onelook.com] subset: gosubset_prok synonym: "phase II metabolism" BROAD [PMID:20056724] synonym: "sul" EXACT CTDCODE [] synonym: "sulfonation" EXACT [] synonym: "sulfur addition" EXACT [] synonym: "sulphation" EXACT [] synonym: "sulphur addition" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0070085 name: glycosylation namespace: biological_process def: "The covalent attachment of a glycosyl residue to a substrate molecule." [GOC:mah] synonym: "gly" EXACT CTDCODE [] xref: Wikipedia:Glycosylation is_a: GO:0008152 ! metabolic process