Gene Ontology Ontology Comparison Report ========================== Files used: - file 1 (old): go-2011-12-10.obo; date: 09:12:2011 12:27; CVS revision: 1.2428 - file 2 (new): go-2011-12-17.obo; date: 15:12:2011 15:48; CVS revision: 1.2455 NEW TERMS ========= ID name namespace GO:0036044 protein malonylation biological_process GO:0036045 peptidyl-lysine malonylation biological_process GO:0036046 protein demalonylation biological_process GO:0036047 peptidyl-lysine demalonylation biological_process GO:0036048 protein desuccinylation biological_process GO:0036049 peptidyl-lysine desuccinylation biological_process GO:0036050 peptidyl-lysine succinylation biological_process GO:0036051 protein localization to trailing edge biological_process GO:0036052 protein localization to uropod biological_process GO:0036053 glomerular endothelium fenestra cellular_component GO:0036054 protein-malonyllysine demalonylase activity molecular_function GO:0036055 protein-succinyllysine desuccinylase activity molecular_function GO:0036056 filtration diaphragm cellular_component GO:0036057 slit diaphragm cellular_component GO:0036058 filtration diaphragm assembly biological_process GO:0036059 nephrocyte diaphragm assembly biological_process GO:0036060 slit diaphragm assembly biological_process GO:0036061 muscle cell chemotaxis toward tendon cell biological_process GO:0036062 presynaptic periactive zone cellular_component GO:0036063 acroblast cellular_component GO:0036064 cilium basal body cellular_component GO:0036065 fucosylation biological_process GO:0036066 protein O-linked fucosylation biological_process GO:0036067 light-dependent chlorophyll biosynthetic process biological_process GO:0036068 light-independent chlorophyll biosynthetic process biological_process GO:0036069 light-dependent bacteriochlorophyll biosynthetic process biological_process GO:0036070 light-independent bacteriochlorophyll biosynthetic process biological_process GO:0036071 N-glycan fucosylation biological_process GO:0038055 BMP secretion biological_process GO:0044380 protein localization to cytoskeleton biological_process GO:0044382 CLRC ubiquitin ligase complex localization to heterochromatin biological_process GO:0044383 host chromosome cellular_component GO:0044384 host cell outer membrane cellular_component GO:0044385 integral to membrane of host cell cellular_component GO:0044386 integral to host endoplasmic reticulum membrane cellular_component GO:0044387 negative regulation of protein kinase activity by regulation of protein phosphorylation biological_process GO:0044388 small protein activating enzyme binding molecular_function GO:0044389 small conjugating protein ligase binding molecular_function GO:0044390 small protein conjugating enzyme binding molecular_function GO:0044391 ribosomal subunit cellular_component GO:0044392 peptidyl-lysine malonylation biological_process GO:0044393 microspike cellular_component GO:0044394 protein malonylation biological_process GO:0052866 phosphatidylinositol phosphate phosphatase activity molecular_function GO:0061392 regulation of transcription from RNA polymerase II promoter in response to osmotic stress biological_process GO:0061393 positive regulation of transcription from RNA polymerase II promoter in response to osmotic stress biological_process GO:0061394 regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance biological_process GO:0061395 positive regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance biological_process GO:0090420 naphthalene-containing compound metabolic process biological_process GO:0097199 cysteine-type endopeptidase activity involved in apoptotic signaling pathway molecular_function GO:0097200 cysteine-type endopeptidase activity involved in execution phase of apoptosis molecular_function GO:0097201 negative regulation of transcription from RNA polymerase II promoter in response to stress biological_process GO:2001253 regulation of histone H3-K36 trimethylation biological_process GO:2001254 negative regulation of histone H3-K36 trimethylation biological_process GO:2001255 positive regulation of histone H3-K36 trimethylation biological_process GO:2001256 regulation of store-operated calcium entry biological_process GO:2001257 regulation of cation channel activity biological_process GO:2001258 negative regulation of cation channel activity biological_process GO:2001259 positive regulation of cation channel activity biological_process GO:2001260 regulation of semaphorin-plexin signaling pathway biological_process GO:2001261 negative regulation of semaphorin-plexin signaling pathway biological_process GO:2001262 positive regulation of semaphorin-plexin signaling pathway biological_process GO:2001263 regulation of C-C chemokine binding biological_process GO:2001264 negative regulation of C-C chemokine binding biological_process GO:2001265 positive regulation of C-C chemokine binding biological_process GO:2001266 Roundabout signaling pathway involved in axon guidance biological_process GO:2001267 regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway biological_process GO:2001268 negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway biological_process GO:2001269 positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway biological_process GO:2001270 regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis biological_process GO:2001271 negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis biological_process GO:2001272 positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis biological_process GO:2001273 regulation of glucose import in response to insulin stimulus biological_process GO:2001274 negative regulation of glucose import in response to insulin stimulus biological_process GO:2001275 positive regulation of glucose import in response to insulin stimulus biological_process GO:2001276 regulation of leucine biosynthetic process biological_process GO:2001277 negative regulation of leucine biosynthetic process biological_process GO:2001278 positive regulation of leucine biosynthetic process biological_process GO:2001279 regulation of unsaturated fatty acid biosynthetic process biological_process GO:2001280 positive regulation of unsaturated fatty acid biosynthetic process biological_process GO:2001281 regulation of muscle cell chemotaxis toward tendon cell biological_process GO:2001282 negative regulation of muscle cell chemotaxis toward tendon cell biological_process GO:2001283 Roundabout signaling pathway involved in muscle cell chemotaxis toward tendon cell biological_process GO:2001284 regulation of BMP secretion biological_process GO:2001285 negative regulation of BMP secretion biological_process GO:2001286 regulation of caveolin-mediated endocytosis biological_process GO:2001287 negative regulation of caveolin-mediated endocytosis biological_process GO:2001288 positive regulation of caveolin-mediated endocytosis biological_process OBSOLETIONS =========== GO:0036043, microspike (cellular_component) This term was made obsolete because it accidentally reused an exisiting id. See replacement term GO:0044393. Replaced by: GO:0044393 TERM MERGES =========== None TERM CHANGES ============ GO:0001669 : acrosomal vesicle + synonym: "acrosomal granule" EXACT [GOC:sart] GO:0003948 : N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity - is_a: GO:0004067 + is_a: GO:0016811 GO:0005840 : ribosome - synonym: "ribosomal subunit" RELATED [GOC:mah, GOC:vw] GO:0005917 : nephrocyte diaphragm - name: nephrocyte junction + name: nephrocyte diaphragm - def: A tissue-specific adherens junction found between nephrocyte cells. A nephrocyte is an insect excretory cell that regulates hemolymph composition by filtration and filtrate endocytosis. + def: A specialized cell-cell junction found between nephrocytes of the insect kidney, which is adapted for filtration of hemolymph. The insect nephrocyte is anatomically and functionally similarity to the glomerular podocyte of vertebrates. + synonym: "nephrocyte junction" RELATED [PMID:8314002] - is_a: GO:0005913 + is_a: GO:0036056 GO:0008417 : fucosyltransferase activity + relationship: part_of GO:0036065 GO:0008418 : protein-N-terminal asparagine amidohydrolase activity - name: protein N-terminal asparagine amidohydrolase activity + name: protein-N-terminal asparagine amidohydrolase activity - def: Catalysis of the deamidation of an N-terminal asparagine residue in a peptide or protein. + def: Catalysis of the reaction: protein-L-asparagine + H2O = protein-L-aspartate + NH3. This reaction is the deamidation of an N-terminal asparagine residue in a peptide or protein. - is_a: GO:0004067 + is_a: GO:0016811 GO:0008424 : glycoprotein 6-alpha-L-fucosyltransferase activity + relationship: part_of GO:0036071 GO:0010045 : response to nickel cation - name: response to nickel ion + name: response to nickel cation - def: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nickel ion stimulus. + def: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nickel cation stimulus. GO:0010416 : arabinoxylan-containing compound metabolic process - name: arabinoxylan metabolic process + name: arabinoxylan-containing compound metabolic process - def: The chemical reactions and pathways involving xylan, a polymer containing a beta-1,4-linked D-xylose backbone decorated with arabinose side units. + def: The chemical reactions and pathways involving an arabinoxylan, a polymer containing a beta-1,4-linked D-xylose backbone decorated with arabinose side units. GO:0010462 : regulation of light-activated voltage-gated calcium channel activity + is_a: GO:2001257 GO:0015099 : nickel cation transmembrane transporter activity - name: nickel ion transmembrane transporter activity + name: nickel cation transmembrane transporter activity - def: Catalysis of the transfer of nickel (Ni) ions from one side of a membrane to the other. + def: Catalysis of the transfer of nickel (Ni) cations from one side of a membrane to the other. GO:0015416 : organic phosphonate transmembrane-transporting ATPase activity - name: phosphonate transmembrane-transporting ATPase activity + name: organic phosphonate transmembrane-transporting ATPase activity GO:0015604 : organic phosphonate transmembrane transporter activity - name: phosphonate transmembrane transporter activity + name: organic phosphonate transmembrane transporter activity GO:0015675 : nickel cation transport - name: nickel ion transport + name: nickel cation transport - def: The directed movement of nickel (Ni) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. + def: The directed movement of nickel (Ni) cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015716 : organic phosphonate transport - name: phosphonate transport + name: organic phosphonate transport GO:0015717 : triose phosphate transport + synonym: "aldotriose phosphate transport" EXACT [] GO:0015934 : large ribosomal subunit - is_a: GO:0030529 + is_a: GO:0044391 - relationship: part_of GO:0005840 GO:0015935 : small ribosomal subunit - is_a: GO:0030529 + is_a: GO:0044391 - relationship: part_of GO:0005840 GO:0016151 : nickel cation binding - name: nickel ion binding + name: nickel cation binding - def: Interacting selectively and non-covalently with nickel (Ni) ions. + def: Interacting selectively and non-covalently with nickel (Ni) cations. GO:0018062 : peptidyl-tryptophan succinylation + is_a: GO:0031365 GO:0018335 : protein succinylation - def: The modification of a protein amino acid by succinylation. + def: The modification of a protein by the addition of a succinyl group (CO-CH2-CH2-CO) to an amino acid residue. - is_a: GO:0006464 + is_a: GO:0043543 GO:0018931 : naphthalene metabolic process - is_a: GO:0042537 + is_a: GO:0090420 GO:0018984 : naphthalenesulfonate metabolic process - is_a: GO:0018931 + is_a: GO:0090420 GO:0019634 : organic phosphonate metabolic process - name: phosphonate metabolic process + name: organic phosphonate metabolic process - def: The chemical reactions and pathways involving of phosphonates, any organic compound containing one or more C-PO(OH)2 or C-PO(OR)2 (with R=alkyl, aryl) groups. Metabolism of phosphonic acid itself, an inorganic compound without the biochemically relevant C-P bond, is not included. + def: The chemical reactions and pathways involving phosphonates, any organic compounds containing one or more C-PO(OH)2 or C-PO(OR)2 (with R=alkyl, aryl) groups. Metabolism of phosphonic acid itself, an inorganic compound without the biochemically relevant C-P bond, is not included. GO:0019700 : organic phosphonate catabolic process - name: phosphonate catabolic process + name: organic phosphonate catabolic process GO:0031392 : regulation of prostaglandin biosynthetic process - is_a: GO:0042304 + is_a: GO:2001279 GO:0031394 : positive regulation of prostaglandin biosynthetic process - is_a: GO:0045723 + is_a: GO:2001280 GO:0031585 : regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity - is_a: GO:0032412 + is_a: GO:2001257 GO:0031586 : negative regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity - is_a: GO:0032413 + is_a: GO:2001258 GO:0031587 : positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity - is_a: GO:0032414 + is_a: GO:2001259 GO:0031624 : ubiquitin conjugating enzyme binding - is_a: GO:0019899 + is_a: GO:0044390 GO:0031625 : ubiquitin protein ligase binding - is_a: GO:0019899 + is_a: GO:0044389 GO:0032234 : regulation of calcium ion transport via store-operated calcium channel activity - is_a: GO:0032412 + is_a: GO:2001257 GO:0032235 : negative regulation of calcium ion transport via store-operated calcium channel activity - is_a: GO:0032413 + is_a: GO:2001258 GO:0032236 : positive regulation of calcium ion transport via store-operated calcium channel activity - is_a: GO:0032414 + is_a: GO:2001259 GO:0032923 : organic phosphonate biosynthetic process - name: phosphonate biosynthetic process + name: organic phosphonate biosynthetic process GO:0033134 : ubiquitin activating enzyme binding - is_a: GO:0019899 + is_a: GO:0044388 GO:0034593 : phosphatidylinositol bisphosphate phosphatase activity - is_a: GO:0016791 + is_a: GO:0052866 GO:0034594 : phosphatidylinositol trisphosphate phosphatase activity - is_a: GO:0016791 + is_a: GO:0052866 GO:0034595 : phosphatidylinositol phosphate 5-phosphatase activity - def: Catalysis of the removal the of the 5-phosphate group of a phosphatidylinositol phosphate. + def: Catalysis of the removal of the 5-phosphate group of a phosphatidylinositol phosphate. - is_a: GO:0016791 + is_a: GO:0052866 GO:0034596 : phosphatidylinositol phosphate 4-phosphatase activity - def: Catalysis of the removal the of the 4-phosphate group of a phosphatidylinositol phosphate. + def: Catalysis of the removal of the 4-phosphate group of a phosphatidylinositol phosphate. - is_a: GO:0016791 + is_a: GO:0052866 GO:0035372 : protein localization to microtubule - is_a: GO:0033365 + is_a: GO:0044380 GO:0035444 : nickel cation transmembrane transport - name: nickel ion transmembrane transport + name: nickel cation transmembrane transport - def: The directed movement of nickel (Ni) ions across a membrane by means of some agent such as a transporter or pore. + def: The directed movement of nickel (Ni) cations across a membrane by means of some agent such as a transporter or pore. GO:0035602 : fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow - name: fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow + name: fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow - def: The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands, which stops, prevents, or reduces the frequency, rate or extent of the occurrence or rate of cell death by apoptosis in the bone marrow. + def: The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands, which stops, prevents, or reduces the frequency, rate or extent of the occurrence or rate of cell death by apoptotic process in the bone marrow. + synonym: "fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow" NARROW [] GO:0035784 : nickel cation homeostasis - name: nickel ion homeostasis + name: nickel cation homeostasis - def: Any process involved in the maintenance of an internal steady state of nickel ions within an organism or cell. + def: Any process involved in the maintenance of an internal steady state of nickel cations within an organism or cell. GO:0035853 : chromosome passenger complex localization to spindle midzone - is_a: GO:0033365 + is_a: GO:0044380 GO:0036043 : microspike - def: A dynamic, actin-rich projection extending from the surface of a migrating animal cell. + def: OBSOLETE. A dynamic, actin-rich projection extending from the surface of a migrating animal cell. - comment: Although in some literature 'microspike' and 'filopodium' are used synonymously, in GO microspike refers to a cell projection that is distinct from a filopodium. See also 'filopodium ; GO:0030175'. + comment: This term was made obsolete because it accidentally reused an exisiting id. See replacement term GO:0044393. - is_a: GO:0042995 + is_obsolete: true + replaced_by: GO:0044393 GO:0042242 : cobyrinic acid a,c-diamide synthase activity + subset: mf_needs_review - is_a: GO:0004359 + is_a: GO:0016811 GO:0043635 : methylnaphthalene catabolic process + is_a: GO:0090420 GO:0044084 : host cell membrane pore complex - is_a: GO:0033644 + is_a: GO:0033643 + relationship: part_of GO:0033644 GO:0044161 : host cell cytoplasmic vesicle - is_a: GO:0033647 + is_a: GO:0033648 GO:0044163 : host cytoskeleton - is_a: GO:0033646 + is_a: GO:0033647 GO:0044193 : host cell mitochondrial outer membrane + is_a: GO:0044384 GO:0044202 : host cell nuclear outer membrane + is_a: GO:0044384 GO:0044379 : protein localization to actin cortical patch - is_a: GO:0033365 + is_a: GO:0044380 GO:0046922 : peptide-O-fucosyltransferase activity + relationship: part_of GO:0036066 GO:0050417 : glutamin-(asparagin-)ase activity + subset: mf_needs_review GO:0052744 : phosphatidylinositol monophosphate phosphatase activity - def: Catalysis of the reaction: phosphatidylinositol phosphate + H2O = phosphatidylinositol + phosphate. + def: Catalysis of the reaction: phosphatidylinositol monophosphate + H2O = phosphatidylinositol + phosphate. - is_a: GO:0016791 + is_a: GO:0052866 GO:0052849 : NADPH-dependent curcumin reductase activity - name: NADPH-dependent curcurmin reductase activity + name: NADPH-dependent curcumin reductase activity GO:0052850 : NADPH-dependent dihydrocurcumin reductase activity - name: NADPH-dependent dihydrocurcurmin reductase activity + name: NADPH-dependent dihydrocurcumin reductase activity - def: Catalysis of the reaction: dihydrocurcurmin + NADPH+ + H+ = tetrahydrocurcurmin + NADP+. + def: Catalysis of the reaction: dihydrocurcumin + NADPH+ + H+ = tetrahydrocurcumin + NADP+. - synonym: "dihydrocurcurmin reductase (NADPH) activity" EXACT [] + synonym: "dihydrocurcumin reductase (NADPH) activity" EXACT [] GO:0060314 : regulation of ryanodine-sensitive calcium-release channel activity - is_a: GO:0032412 + is_a: GO:2001257 GO:0060315 : negative regulation of ryanodine-sensitive calcium-release channel activity - is_a: GO:0032413 + is_a: GO:2001258 GO:0060316 : positive regulation of ryanodine-sensitive calcium-release channel activity - is_a: GO:0032414 + is_a: GO:2001259 GO:0070773 : protein-N-terminal glutamine amidohydrolase activity - name: protein N-terminal glutamine amidohydrolase activity + name: protein-N-terminal glutamine amidohydrolase activity - def: Catalysis of the deamidation of an N-terminal glutamin residue of a protein. + def: Catalysis of the reaction: protein-N-terminal-L-glutamine + H2O = protein-N-terminal-L-glutamate + NH3. This reaction is the deamidation of an N-terminal glutamine residue of a protein. + subset: mf_needs_review GO:0071539 : protein localization to centrosome - is_a: GO:0033365 + is_a: GO:0044380 GO:0071839 : apoptotic process in bone marrow - name: apoptosis in bone marrow + name: apoptotic process in bone marrow - def: The process of apoptosis in cells in the bone marrow. + def: The apoptotic process in cells in the bone marrow. + synonym: "apoptosis in bone marrow" NARROW [] GO:0071865 : regulation of apoptotic process in bone marrow - name: regulation of apoptosis in bone marrow + name: regulation of apoptotic process in bone marrow - def: Any process that modulates the occurrence or rate of cell death by apoptosis in the bone marrow. + def: Any process that modulates the occurrence or rate of cell death by apoptotic process in the bone marrow. + synonym: "regulation of apoptosis in bone marrow" NARROW [] GO:0071866 : negative regulation of apoptotic process in bone marrow - name: negative regulation of apoptosis in bone marrow + name: negative regulation of apoptotic process in bone marrow - def: Any process that stops, prevents, or reduces the frequency, rate or extent of the occurrence or rate of cell death by apoptosis in the bone marrow. + def: Any process that stops, prevents, or reduces the frequency, rate or extent of the occurrence or rate of cell death by apoptotic process in the bone marrow. + synonym: "negative regulation of apoptosis in bone marrow" NARROW [] GO:0071988 : protein localization to spindle pole body - is_a: GO:0033365 + is_a: GO:0044380 GO:2000764 : positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis - is_a: GO:0048522 - is_a: GO:0009967 + is_a: GO:2001262 GO:2000888 : arabinoxylan-containing compound catabolic process - name: arabinoxylan catabolic process + name: arabinoxylan-containing compound catabolic process GO:2000921 : regulation of arabinoxylan-containing compound catabolic process - name: regulation of arabinoxylan catabolic process + name: regulation of arabinoxylan-containing compound catabolic process - def: Any process that modulates the frequency, rate or extent of arabinoxylan catabolic process. + def: Any process that modulates the frequency, rate or extent of arabinoxylan-containing compound catabolic process. GO:2000922 : negative regulation of arabinoxylan-containing compound catabolic process - name: negative regulation of arabinoxylan catabolic process + name: negative regulation of arabinoxylan-containing compound catabolic process - def: Any process that stops, prevents or reduces the frequency, rate or extent of arabinoxylan catabolic process. + def: Any process that stops, prevents or reduces the frequency, rate or extent of arabinoxylan-containing compound catabolic process. GO:2000923 : positive regulation of arabinoxylan-containing compound catabolic process - name: positive regulation of arabinoxylan catabolic process + name: positive regulation of arabinoxylan-containing compound catabolic process - def: Any process that activates or increases the frequency, rate or extent of arabinoxylan catabolic process. + def: Any process that activates or increases the frequency, rate or extent of arabinoxylan-containing compound catabolic process. GO:2001115 : methanopterin-containing compound metabolic process - name: methanopterin metabolic process + name: methanopterin-containing compound metabolic process GO:2001116 : methanopterin-containing compound biosynthetic process - name: methanopterin biosynthetic process + name: methanopterin-containing compound biosynthetic process GO:2001118 : tetrahydromethanopterin biosynthetic process - is_a: GO:2001115 + is_a: GO:2001116 GO:2001120 : methanofuran biosynthetic process - is_a: GO:2001115 + is_a: GO:2001116 FILE STATS ========== Term counts for the old and new files Ontology Old file New file Change molecular function 9193 9201 +8 (9193 defined) (9201 defined) cellular component 2927 2938 +11 (2927 defined) (2938 defined) biological process 21664 21730 +66 (21664 defined) (21730 defined) Obsolete 1606 1609 +3 (4.5% of total) (4.5% of total) (+0.2%) Totals 33784 33869 +88 (+0.2%) 33784 (100.0%) defined 33869 (100.0%) defined 35390 inc. obs 35478 inc. obs