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: "<pal>" 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