OBO-Edit 2.0 25:01:2011 12:46 file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt 1.2 cmattin definition CTD CODE Candida GO slim Generic GO slim GOA and proteome slim PIR GO slim Plant GO slim Fission yeast GO slim Yeast GO slim Prokaryotic GO subset Systematic synonym subset_property synonym_type_property has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_scope has_synonym_type in_subset The abundance of a chemical (if chemical synthesis is not known). abu file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:1 abundance CTDI:1 The abundance of a chemical (if chemical synthesis is not known). CTDI:ctd_curators abu A biochemical event resulting in a new chemical product. csy file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:10 chemical synthesis CTDI:10 A biochemical event resulting in a new chemical product. CTDI:ctd_curators csy The addition of an ethyl group. eth file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:11 ethylation CTDI:11 The addition of an ethyl group. CTDI:ctd_curators eth The movement of a molecule out of a cell (by more specific means than secretion). ext file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:12 export CTDI:12 The movement of a molecule out of a cell (by more specific means than secretion). CTDI:ctd_curators ext The bending and positioning of a molecule to achieve conformational integrity. fol file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:13 folding CTDI:13 fol The bending and positioning of a molecule to achieve conformational integrity. CTDI:ctd_curators The addition of a geranoyl group. ger file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:14 geranoylation CTDI:14 The addition of a geranoyl group. CTDI:ctd_curators ger The non-enzymatic addition of a sugar. gyc file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:15 glycation CTDI:15 The non-enzymatic addition of a sugar. CTDI:ctd_curators gyc The addition of a hydroxy group. hdx file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:16 hydroxylation CTDI:16 The addition of a hydroxy group. CTDI:ctd_curators hdx The splitting of a molecule via the specific use of water. hyd file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:17 hydrolysis CTDI:17 The splitting of a molecule via the specific use of water. CTDI:ctd_curators hyd The movement of a molecule into a cell (by more specific means than uptake). imt file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:18 import CTDI:18 The movement of a molecule into a cell (by more specific means than uptake). CTDI:ctd_curators imt The genetic alteration of a gene product. mut file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:19 mutagenesis CTDI:19 The genetic alteration of a gene product. CTDI:ctd_curators mut The addition of an acetyl group. ace file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:2 acetylation CTDI:2 The addition of an acetyl group. CTDI:ctd_curators ace The loss of electrons. oxd file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:20 oxidation CTDI:20 The loss of electrons. CTDI:ctd_curators oxd The gain of electrons. red file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:21 reduction CTDI:21 The gain of electrons. CTDI:ctd_curators red The addition of a ribosyl group. rib file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:22 ribosylation CTDI:22 The addition of a ribosyl group. CTDI:ctd_curators rib Any general biochemical or molecular event. rxn file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:23 reaction CTDI:23 Any general biochemical or molecular event. CTDI:ctd_curators rxn Overall propensity of molecules to degradation. sta file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:24 stability CTDI:24 Overall propensity of molecules to degradation. CTDI:ctd_curators sta The movement of a molecule into a cell (by less specific means than import). upt file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:25 uptake CTDI:25 The movement of a molecule into a cell (by less specific means than import). CTDI:ctd_curators upt Involving the use of two or more chemicals simultaneously. w file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:26 cotreatment CTDI:26 Involving the use of two or more chemicals simultaneously. CTDI:ctd_curators w An elemental function of a molecule. act file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:3 activity CTDI:3 An elemental function of a molecule. CTDI:ctd_curators act The addition of an acyl group. acy file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:4 acylation CTDI:4 The addition of an acyl group. CTDI:ctd_curators acy The addition of an alkyl group. alk file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:5 alkylation CTDI:5 The addition of an alkyl group. CTDI:ctd_curators alk The addition of an amine group. ami file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:6 amination CTDI:6 The addition of an amine group. CTDI:ctd_curators ami The addition of a ADP-ribosyl group. arb file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:7 ADP-ribosylation CTDI:7 The addition of a ADP-ribosyl group. CTDI:ctd_curators arb The processing or splitting of a molecule, not necessarily leading to the destruction of the molecule. clv file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:8 cleavage CTDI:8 The processing or splitting of a molecule, not necessarily leading to the destruction of the molecule. CTDI:ctd_curators clv The addition of a carboxyl group. cox file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt CTDI:9 carboxylation CTDI:9 The addition of a carboxyl group. CTDI:ctd_curators cox The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) b molecular_function GO:0005488 For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. binding GO:0005488 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 b true GO:0006395 true GO:0006485 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 ngl protein amino acid N-linked glycosylation biological_process N-glycan biosynthesis N-glycan metabolism GO:0006487 protein N-linked glycosylation GO:0006487 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 ngl protein amino acid N-linked glycosylation GOC:bf 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. RESID:AA0153 RESID:AA0154 RESID:AA0155 RESID:AA0157 RESID:AA0212 ogl protein amino acid O-linked glycosylation biological_process GO:0006493 protein O-linked glycosylation GO:0006493 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 ogl protein amino acid O-linked glycosylation GOC:bf The covalent attachment of lipid groups to an amino acid in a protein. GO:0042050 RESID:AA0059 RESID:AA0060 RESID:AA0077 RESID:AA0078 RESID:AA0079 RESID:AA0080 RESID:AA0102 RESID:AA0103 RESID:AA0104 RESID:AA0106 RESID:AA0107 RESID:AA0158 RESID:AA0159 RESID:AA0160 RESID:AA0161 RESID:AA0162 RESID:AA0163 RESID:AA0166 RESID:AA0223 RESID:AA0290 RESID:AA0307 RESID:AA0308 RESID:AA0309 RESID:AA0316 lip lipid:protein modification protein amino acid lipidation protein lipidation biological_process GO:0006497 For non-covalent interactions with a lipid, consider instead the term 'lipid binding ; GO:0008289' and its children. protein lipidation GO:0006497 The covalent attachment of lipid groups to an amino acid in a protein. GOC:jl lip protein amino acid lipidation GOC:bf 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. GO:0015457 GO:0015460 trt small molecule transport solute:solute exchange biological_process auxiliary transport protein activity transport accessory protein activity GO:0006810 transport GO:0006810 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 trt auxiliary transport protein activity GOC:mah transport accessory protein activity GOC:mah 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. met file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process GO:0008152 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 met 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. GO:0006395 Reactome:1006447 Reactome:1051751 Reactome:1076708 Reactome:1097222 Reactome:1116507 Reactome:1140327 Reactome:1170576 Reactome:1192393 Reactome:1206583 Reactome:1221220 Reactome:1239204 Reactome:1246834 Reactome:1252579 Reactome:1258368 Reactome:1262057 Reactome:72172 Reactome:979854 Wikipedia:RNA_splicing spl biological_process pre-mRNA splicing factor activity GO:0008380 RNA splicing GO:0008380 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 Reactome:1006447 mRNA Splicing Reactome:1051751 mRNA Splicing Reactome:1076708 mRNA Splicing Reactome:1097222 mRNA Splicing Reactome:1116507 mRNA Splicing Reactome:1140327 mRNA Splicing Reactome:1170576 mRNA Splicing Reactome:1192393 mRNA Splicing Reactome:1206583 mRNA Splicing Reactome:1221220 mRNA Splicing Reactome:1239204 mRNA Splicing Reactome:1246834 mRNA Splicing Reactome:1252579 mRNA Splicing Reactome:1258368 mRNA Splicing Reactome:1262057 mRNA Splicing Reactome:72172 mRNA Splicing Reactome:979854 mRNA Splicing spl 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. Wikipedia:Catabolism deg biological_process GO:0009056 catabolic process GO:0009056 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 deg 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. Reactome:1006441 Reactome:1024783 Reactome:1051745 Reactome:1076702 Reactome:1097220 Reactome:1116505 Reactome:1140321 Reactome:1170570 Reactome:1192387 Reactome:1206581 Reactome:1221214 Reactome:1239198 Reactome:1246779 Reactome:1252532 Reactome:1258323 Reactome:1262022 Reactome:1264209 Reactome:1265616 Reactome:1266830 Reactome:74160 Reactome:979848 Wikipedia:Gene_expression exp biological_process GO:0010467 gene expression GO:0010467 Reactome:1192387 Gene Expression Reactome:1206581 Gene Expression Reactome:1221214 Gene Expression Reactome:1239198 Gene Expression Reactome:1246779 Gene Expression Reactome:1252532 Gene Expression Reactome:1258323 Gene Expression Reactome:1262022 Gene Expression Reactome:1264209 Gene Expression Reactome:1265616 Gene Expression Reactome:1266830 Gene Expression Reactome:74160 Gene Expression Reactome:979848 Gene Expression exp 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 Reactome:1006441 Gene Expression Reactome:1024783 Gene Expression Reactome:1051745 Gene Expression Reactome:1076702 Gene Expression Reactome:1097220 Gene Expression Reactome:1116505 Gene Expression Reactome:1140321 Gene Expression Reactome:1170570 Gene Expression The protein modification process in which a glutathione molecule is added to a protein amino acid through a disulfide linkage. glt protein amino acid glutathionylation biological_process GO:0010731 protein glutathionylation GO:0010731 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 glt protein amino acid glutathionylation GOC:bf true GO:0015457 true GO:0015460 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. Wikipedia:Phosphorylation pho biological_process GO:0016310 phosphorylation GO:0016310 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 pho The process in which one or more ubiquitin groups are added to a protein. protein ubiquitinylation protein ubiquitylation ubq biological_process GO:0016567 protein ubiquitination GO:0016567 The process in which one or more ubiquitin groups are added to a protein. GOC:ai ubq 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. GO:0006485 GO:0016927 Wikipedia:SUMO_protein SUMO-protein conjugation protein sumolation small ubiquitin-related protein 1 conjugation sum sumoylation biological_process GO:0016925 protein sumoylation GO:0016925 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 sum true GO:0016927 The covalent addition of a nitric oxide group to an amino acid within a protein. nit protein amino acid nitrosylation biological_process GO:0017014 protein nitrosylation GO:0017014 The covalent addition of a nitric oxide group to an amino acid within a protein. GOC:ai PMID:20972426 nit protein amino acid nitrosylation GOC:bf The addition of a nucleotide to a protein amino acid. nuc protein amino acid nucleotidylation biological_process GO:0018175 protein nucleotidylation GO:0018175 The addition of a nucleotide to a protein amino acid. GOC:ai nuc protein amino acid nucleotidylation GOC:bf true GO:0018318 true GO:0018319 The covalent attachment of a prenyl group to a protein; geranyl, farnesyl, or geranylgeranyl groups may be added. GO:0018346 pre protein amino acid prenylation C-terminal protein prenylation biological_process GO:0018342 protein prenylation GO:0018342 The covalent attachment of a prenyl group to a protein; geranyl, farnesyl, or geranylgeranyl groups may be added. ISBN:0198506732 pre protein amino acid prenylation GOC:bf The covalent attachment of a farnesyl group to a protein. GO:0018347 far protein amino acid farnesylation C-terminal protein farnesylation biological_process GO:0018343 protein farnesylation GO:0018343 The covalent attachment of a farnesyl group to a protein. GOC:jl far protein amino acid farnesylation GOC:bf The covalent attachment of a palmitoyl group to a protein. GO:0018318 GO:0018349 pal protein amino acid palmitoylation biological_process <pal> GO:0018345 protein palmitoylation GO:0018345 The covalent attachment of a palmitoyl group to a protein. GOC:jl PMID:15520806 pal protein amino acid palmitoylation GOC:bf true GO:0018346 true GO:0018347 true GO:0018349 The covalent attachment of a myristoyl group to a protein. GO:0018319 myr protein amino acid myristoylation biological_process GO:0018377 protein myristoylation GO:0018377 The covalent attachment of a myristoyl group to a protein. GOC:ai myr protein amino acid myristoylation GOC:bf The modification of a protein by amino acid glucuronidation. glc protein amino acid glucuronidation biological_process GO:0018411 protein glucuronidation GO:0018411 The modification of a protein by amino acid glucuronidation. GOC:ai glc protein amino acid glucuronidation GOC:bf The process in which a methyl group is covalently attached to a molecule. Reactome:1006567 Reactome:1024884 Reactome:1051871 Reactome:1076824 Reactome:1097328 Reactome:1116621 Reactome:1140446 Reactome:1170691 Reactome:1192489 Reactome:1206864 Reactome:1221409 Reactome:1239392 Reactome:1246869 Reactome:1252723 Reactome:1258533 Reactome:1262147 Reactome:1264263 Reactome:1265699 Reactome:156581 Reactome:979970 Wikipedia:Methylation myl biological_process GO:0032259 methylation GO:0032259 The process in which a methyl group is covalently attached to a molecule. GOC:mah Reactome:1006567 Methylation Reactome:1024884 Methylation Reactome:1051871 Methylation Reactome:1076824 Methylation Reactome:1097328 Methylation Reactome:1116621 Methylation Reactome:1140446 Methylation Reactome:1170691 Methylation Reactome:1192489 Methylation Reactome:1206864 Methylation Reactome:1221409 Methylation Reactome:1239392 Methylation Reactome:1246869 Methylation Reactome:1252723 Methylation Reactome:1258533 Methylation Reactome:1262147 Methylation Reactome:1264263 Methylation Reactome:1265699 Methylation Reactome:156581 Methylation Reactome:979970 Methylation myl true GO:0042050 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. rec response to chemical substance biological_process GO:0042221 response to chemical stimulus GO:0042221 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 rec The controlled release of a substance by a cell, a group of cells, or a tissue. sec biological_process GO:0046903 secretion GO:0046903 The controlled release of a substance by a cell, a group of cells, or a tissue. GOC:ai sec The addition of a carbamoyl group to a protein amino acid. A carbamoyl group is the acyl group -CO-NH2. car protein amino acid carbamoylation biological_process GO:0046944 protein carbamoylation GO:0046944 The addition of a carbamoyl group to a protein amino acid. A carbamoyl group is the acyl group -CO-NH2. GOC:ai car protein amino acid carbamoylation GOC:bf 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. establishment and maintenance of localization establishment and maintenance of position loc localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process GO:0051179 localization GO:0051179 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 loc localisation GOC:mah The addition of a sulfate group to a molecule. phase II metabolism sul sulfonation sulfur addition sulphation sulphur addition biological_process GO:0051923 sulfation GO:0051923 The addition of a sulfate group to a molecule. http://www.onelook.com phase II metabolism PMID:20056724 sul The covalent attachment of a glycosyl residue to a substrate molecule. Wikipedia:Glycosylation gly biological_process GO:0070085 glycosylation GO:0070085 The covalent attachment of a glycosyl residue to a substrate molecule. GOC:mah gly OBO-Edit 2.0 25:01:2011 12:46 file:/Users/cmattin/Documents/stuff_work/projects/ixn_ontology.txt 1.2 cmattin