[go-diff] GO update 02/25/2008

Mon Feb 25 21:30:44 PST 2008

OBODIFF of gene_ontology_edit.obo version 5.705 by 5.707

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Changed definition of GO:0005234 from "Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts." to "Catalysis of the transmembrane transfer of an ion by a channel that opens when extracellular glutamate has been bound by the channel complex or one of its constituent parts."
* Changed synonym scope of GO:0005840 from "Narrow" to "Related"
* Changed definition of GO:0008068 from "Catalysis of the transmembrane transfer of a chloride ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts." to "Catalysis of the transmembrane transfer of a chloride ion by a channel that opens when extracellular glutamate has been bound by the channel complex or one of its constituent parts."
* Changed definition of GO:0008579 from "Catalysis of the reaction: MAP kinase serine/threonine/tyrosine phosphate + H2O = MAP kinase serine/threonine/tyrosine + phosphate." to "Catalysis of the reaction: JUN kinase serine/threonine/tyrosine phosphate + H2O = JUN kinase serine/threonine/tyrosine + phosphate."
* Changed comment from "Note that this function was formely EC 1.12.1.1, EC 1.12.7.1, EC 1.98.1.1, EC 1.18.3.1 and EC 1.18.99.1." to "Note that this function was formerly EC 1.12.1.1, EC 1.12.7.1, EC 1.98.1.1, EC 1.18.3.1 and EC 1.18.99.1."
* Changed definition of GO:0009198 from "The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleoside diphosphate, a glycosamine consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with diphosphate on its glycose moiety." to "The chemical reactions and pathways resulting in the breakdown of pyrimidine deoxynucleoside diphosphate, a glycosamine consisting of a pyrimidine base linked to a deoxyribose sugar esterified with diphosphate on its glycose moiety."
* Changed definition of GO:0010493 from "The chemical reactions and pathways resulting in the formation of a K antigen, a capsular polysaccharide antigen carried on the surface of bacterial capsules that masks somatic (O) antigens." to "The chemical reactions and pathways resulting in the formation of a Lewis a epitope, a trisaccharide (Fuc-alpha-1->4(Gal-beta-1->3)GlcNAc) characteristic of plant protein N-linked oligosaccharides."
* Changed definition of GO:0010524 from "Any process that decreases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." to "Any process that increases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components."
* Changed definition of GO:0010530 from "Any process that decreases the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites." to "Any process that increases the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites."
* Deleted GO:0015394 --OBO_REL:is_a--> GO:0015536
* Copied GO:0015394 to GO:0015506 with type OBO_REL:is_a
* Changed definition of GO:0015503 from "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: K+(in) + H+(out) = K+(out) + H+(in)." to "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: K+(in) + H+(out) = K+(out) + H+(in), where glutathione maintains the closed state."
* Added definition dbxref PMID:11053405 to GO:0015503
* added secondary id GO:0015536 to GO:0015506
* Added definition dbxref TC:2.A.1.10.1 to GO:0015506
* Added synonym "nucleoside permease activity" to GO:0015506
* Added synonym "nucleoside:hydrogen ion symporter activity" to GO:0015506
* Changed synonym scope of GO:0015506 from "Related" to "Exact"
* Copied GO:0015506 to GO:0005337 with type OBO_REL:is_a
* Copied GO:0015506 to GO:0015293 with type OBO_REL:is_a
* Deleted GO:0015536 --OBO_REL:is_a--> GO:0015293
* Deleted GO:0015536 --OBO_REL:is_a--> GO:0005337
* Deleted GO:0015537 --OBO_REL:is_a--> GO:0015536
* Deleted GO:0015394 --OBO_REL:is_a--> GO:0015536
* Destroyed object GO:0015536
* Deleted GO:0015537 --OBO_REL:is_a--> GO:0015536
* Copied GO:0015537 to GO:0015506 with type OBO_REL:is_a
* Changed definition of GO:0015764 from "Catalysis of the transfer of N-acetylglucosamine from one side of the membrane to the other. The D isomer of N-acetylglucosamine is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide moiety of a glycoprotein." to "The directed movement of N-acetylglucosamine into, out of, within or between cells."
* Deleted definition dbxref GOC:ai from GO:0015764
* Added definition dbxref GOC:mah to GO:0015764
* Changed definition of GO:0015835 from "Enables the directed movement of peptidoglycans, a class of glycoconjugates found in bacterial cell walls, into, out of, within or between cells." to "The directed movement of peptidoglycans, a class of glycoconjugates found in bacterial cell walls, into, out of, within or between cells."
* Changed name of GO:0016058 from "maintenance of membrane potential involved in rhodopsin mediated signaling" to "maintenance of membrane potential in photoreceptor cell by rhodopsin mediated signaling"
* Changed definition of GO:0016058 from "Maintenance of the excited state of a photoreceptor cell to produce a steady state current." to "Maintenance of the excited state of a photoreceptor cell to produce a steady state current as a result of signals generated by rhodopsin activation by a photon."
* Deleted GO:0016058 --OBO_REL:is_a--> GO:0042391
* Deleted GO:0016058 --part_of--> GO:0016056
* Copied GO:0016058 to GO:0016057 with type OBO_REL:is_a
* Changed definition of GO:0016933 from "Catalysis of the transmembrane transfer of an ion by a channel that opens when glycine has been bound by the channel complex or one of its constituent parts." to "Catalysis of the transmembrane transfer of an ion by a channel that opens when extracellular glycine has been bound by the channel complex or one of its constituent parts."
* Changed definition of GO:0016934 from "Catalysis of the transmembrane transfer of a chloride ion by a channel that opens when glycine has been bound by the channel complex or one of its constituent parts." to "Catalysis of the transmembrane transfer of a chloride ion by a channel that opens when extracellular glycine has been bound by the channel complex or one of its constituent parts."
* Changed name of GO:0019057 from "modification by virus of host cell mRNA translation" to "regulation of host cell mRNA translation by virus"
* Added synonym "modification by virus of host cell mRNA translation" to GO:0019057
* Changed synonym scope of GO:0019057 from "Related" to "Exact"
* Changed definition of GO:0019141 from "Catalysis of the reaction: (R)-pantolactone + NADP+ = 2-dehydropantolactone + NADPH + H+." to "Catalysis of the reaction: (R)-pantolactone + NADP+ = 2-dehydropantolactone + NADPH + H+. The reaction is B-specific (i.e. the pro-S hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NADP+."
* Changed definition of GO:0019323 from "The chemical reactions and pathways resulting in the formation of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule." to "The chemical reactions and pathways resulting in the breakdown of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule."
* Changed definition of GO:0021780 from "The process whereby a cell becomes capable of differentiating autonomously into an oligodendrocyte in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed." to "The process whereby a cell becomes capable of differentiating autonomously into a glial cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed."
* Changed definition of GO:0022824 from "Catalysis of the transmembrane transfer of a solute by a channel that opens when a specific neurotransmitter has been bound by the channel complex or one of its constituent parts." to "Catalysis of the transmembrane transfer of an ion by a channel that opens when a specific neurotransmitter has been bound by the channel complex or one of its constituent parts."
* Changed synonym scope of GO:0030533 from "Exact" to "Related"
* Changed synonym scope of GO:0030533 from "Exact" to "Related"
* Changed definition of GO:0030706 from "The process whereby one relatively unspecialized immature cystocyte of the germ-line cyst acquires the specialized features of an oocyte." to "The process whereby one relatively unspecialized immature cystocyte of the germ-line cyst in the germarium acquires the specialized features of an oocyte."
* Changed definition of GO:0030708 from "Formation of a single follicular epithelium around the germ-line derived cells of a cyst formed in the female gonad." to "Formation of a single follicular epithelium around the germ-line derived cells of a cyst formed in the germarium."
* Changed definition of GO:0030727 from "Formation of a cluster of germ-line cells, in the female gonad, derived from a single founder cell (cystoblast)." to "Formation of a cluster of germ-line cells, in the germarium, derived from a single founder cell (cystoblast)."
* Changed definition of GO:0030738 from "Catalysis of the reaction: S-adenosyl-L-methionine + an amine = S-adenosyl-L-homocysteine + a methylated amine." to "Catalysis of the reaction: S-adenosyl-L-methionine + tyramine = S-adenosyl-L-homocysteine + N-methyltyramine."
* Deleted definition dbxref EC:2.1.1.49 from GO:0030738
* Changed definition of GO:0030747 from "Catalysis of the reaction: S-adenosyl-L-methionine + isoflavone = S-adenosyl-L-homocysteine + 4'-O-methylisoflavone." to "Catalysis of the reaction: S-adenosyl-L-methionine + (indol-3-yl)pyruvate = S-adenosyl-L-homocysteine + (S)-3-(indol-3-yl)-2-oxobutanoate."
* Changed definition of GO:0030751 from "Catalysis of the reaction: S-adenosyl-L-methionine + putrescine = S-adenosyl-L-homocysteine + N-methylputrescine." to "Catalysis of the reaction: S-adenosyl-L-methionine + licodione = S-adenosyl-L-homocysteine + 2'-O-methyllicodione."
* Changed definition of GO:0030927 from "The incorporation of calcium into a 4Mn-Ca-4O complex by bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide as in the photosystem II catalytic site." to "The incorporation of manganese into a 4Mn-Ca-4O complex by bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide as in the photosystem II catalytic site."
* Changed definition of GO:0032003 from "Interacting selectively with the interleukin-27 receptor." to "Interacting selectively with the interleukin-28 receptor."
* Changed definition of GO:0032327 from "The chemical reactions and pathways resulting in the formation of the W-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear tungsten ion (W) coordinated by one or two molybdopterin ligands." to "The chemical reactions and pathways resulting in the breakdown of the W-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear tungsten ion (W) coordinated by one or two molybdopterin ligands."
* Changed definition of GO:0032482 from "Any process that modulates the frequency, rate or extent of Rab protein signal transduction." to "A series of molecular signals within the cell that are mediated by a member of the Rab family of proteins switching to a GTP-bound active state."
* Changed definition of GO:0032802 from "The chemical reactions and pathways resulting in the breakdown of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." to "The chemical reactions and pathways resulting in the breakdown of a low-density lipoprotein receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function."
* Changed definition of GO:0032861 from "Any process that initiates the activity of an inactive GTPase of the Ran family through the replacement of GDP by GTP." to "Any process that initiates the activity of an inactive GTPase of the Rap family through the replacement of GDP by GTP."
* Changed definition of GO:0032947 from "Functions to provide a physical suport for the assembly of a multiprotein receptor signaling complex." to "Functions to provide a physical suport for the assembly of a multiprotein complex."
* Changed definition of GO:0033231 from "The directed movement of amino acids out of a cell or organelle." to "The directed movement of carbohydrates out of a cell or organelle."
* Changed definition of GO:0033396 from "The chemical reactions and pathways resulting in the formation of beta-alanine via the intermediate 3-hydroxypropionate." to "The chemical reactions and pathways resulting in the formation of beta-alanine via the intermediate 3-ureidopropionate."
* Changed definition of GO:0033587 from "The chemical reactions and pathways resulting in the breakdown of shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid." to "The chemical reactions and pathways resulting in the formation of shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid."
* Changed definition of GO:0033871 from "Catalysis of the reaction: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-glucosamine 3-sulfate." to "Catalysis of the reaction: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-glucosamine 3-sulfate; modifies selected glucosamine residues preceded by GlcA2S."
* Changed synonym scope of GO:0033920 from "Broad" to "Exact"
* Changed definition of GO:0034035 from "The chemical reactions and pathways involving a ribonucleoside bisphosphate, a glycosamine consisting of a base linked to a ribose sugar esterified with one phosphate group attached to each of two different hydroxyl groups on its glycose moiety." to "The chemical reactions and pathways involving a purine ribonucleoside bisphosphate, a glycosamine consisting of a purine base linked to a ribose sugar esterified with one phosphate group attached to each of two different hydroxyl groups on its glycose moiety."
* Changed definition of GO:0034056 from "Interacting selectively with the sterol response element (SRE), a nonpalindromic sequence found in the promoters of genes involved in lipid metabolism." to "Interacting selectively with the estrogen response element (ERE), a conserved sequence found in the promoters of genes whose expression is regulated in response to estrogen."
* Changed definition of GO:0034209 from "The addition of an acetyl group to a steroid molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." to "The addition of an acetyl group to a sterol molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid."
* Changed definition of GO:0034210 from "The removal of an acetyl group from a steroid molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." to "The removal of an acetyl group from a sterol molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid."
* Changed definition of GO:0042895 from "The directed movement of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms, into, out of, within or between cells." to "Enables the directed movement of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms, into, out of, within or between cells."
* Changed definition of GO:0043322 from "Any process that stops, prevents, or reduces the rate of mast cell degranulation." to "Any process that stops, prevents, or reduces the rate of natural killer cell degranulation."
* Changed definition of GO:0043371 from "Any process that modulates the frequency, rate, or extent of CD4-positive, alpha beta T cell differentiation." to "Any process that stops, prevents or reduces the frequency, rate, or extent of CD4-positive, alpha beta T cell differentiation."
* Changed definition of GO:0043561 from "Any process that activates or increases the frequency, rate or extent of translation initiation, as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell." to "Any process that modulates the frequency, rate or extent of translation initiation, as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell."
* Changed definition of GO:0043724 from "Catalysis of the reaction: 2-keto-3-deoxygluconate = D-glyceraldehyde + pyruvate." to "Catalysis of the reaction: 2-keto-3-deoxygalactonate = D-glyceraldehyde + pyruvate."
* Changed definition of GO:0043780 from "Catalysis of the reaction: cobalt-precorrin 5A + H2O = cobalt-precorrin 5B + acetaldehyde." to "Catalysis of the reaction: cobalt-precorrin 5B + S-adenosylmethionine = S-adenosylhomocysteine + cobalt-precorrin 6A."
* Deleted definition dbxref MetaCyc:RXN-8763 from GO:0043780
* Added definition dbxref MetaCyc:RXN-8764 to GO:0043780
* Deleted general dbxref MetaCyc:RXN-8763 from GO:0043780
* Added general dbxref MetaCyc:RXN-8764 to GO:0043780
* Changed synonym scope of GO:0043780 from "Related" to "Exact"
* Changed definition of GO:0045796 from "Any process that activates or increases the frequency, rate or extent of uptake of cholesterol into the blood by absorption from the intestine." to "Any process that stops, prevents or reduces the frequency, rate or extent of uptake of cholesterol into the blood by absorption from the intestine."
* Changed definition of GO:0046562 from "Catalysis of the reaction: beta-D-glucose + O2 = D-glucono-1,5-lactone + H2O2." to "Catalysis of the reaction: a hexose + O2 = a hexno-1,5-lactone + H2O2; includes beta-D-glucose + O2 = D-glucono-1,5-lactone + H2O2."
* Added definition dbxref GOC:mah to GO:0046562
* Changed definition of GO:0047011 from "Catalysis of the reaction: (R)-pantolactone + NADP+ = 2-dehydropantolactone + NADPH + H+." to "Catalysis of the reaction: (R)-pantolactone + NADP+ = 2-dehydropantolactone + NADPH + H+. The reaction is A-specific (i.e. the pro-R hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NADP+."
* Changed definition of GO:0047379 from "Catalysis of the reaction: H2O + acyl-CoA = an acid + CoA." to "Catalysis of the reaction: H2O + a short-chain acyl-CoA = a short-chain carboxylate + CoA."
* Changed definition of GO:0047380 from "Catalysis of the reaction: H2O + acyl-CoA = an acid + CoA." to "Catalysis of the reaction: H2O + a t
medium-chain acyl-CoA = a medium-chain carboxylate + CoA."
* Changed definition of GO:0047514 from "Catalysis of the reaction: 1,3-beta-D-glucosyl(n) + phosphate = 1,3-beta-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate." to "Catalysis of the reaction: 1,3-beta-D-glucosyl(n) + phosphate = 1,3-beta-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate; substrates include laminarin."
* Changed definition of GO:0047515 from "Catalysis of the reaction: 1,3-beta-D-glucosyl(n) + phosphate = 1,3-beta-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate." to "Catalysis of the reaction: oligomeric 1,3-beta-D-glucosyl(n) + phosphate = 1,3-beta-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate."
* Changed definition of GO:0047821 from "Catalysis of the reaction: D-glutamate + H2O + O2 = 2-oxoglutarate + NH3 + H2O2." to "Catalysis of the reaction: D-glutamate + H2O + O2 = 2-oxoglutarate + NH3 + H2O2; D-aspartate + H2O = oxaloacetate + NH3 + H2O2."
* Added definition dbxref BRENDA:1.4.3.15 to GO:0047821
* Changed definition of GO:0048905 from "The process whereby a relatively unspecialized cell acquires specialized features of a neuromast mantle cell. Mantle cells are non-sensory cells that surround the sensory strip, separating the neuromast from the epidermis. Mantle cells secrete the cupula in which the ciliary bundles of all of the hair cells are embedded." to "The process whereby a relatively unspecialized cell acquires specialized features of an anterior lateral line neuromast mantle cell. Mantle cells are non-sensory cells that surround the sensory strip, separating the neuromast from the epidermis. Mantle cells secrete the cupula in which the ciliary bundles of all of the hair cells are embedded."
* Changed definition of GO:0051142 from "Any process that stops, prevents or reduces the frequency, rate or extent of natural killer T cell proliferation." to "Any process that activates or increases the frequency, rate or extent of natural killer T cell proliferation."
* Changed definition of GO:0051166 from "The chemical reactions and pathways involving 2,5-dihydroxypyridine." to "The chemical reactions and pathways resulting in the breakdown of 2,5-dihydroxypyridine."
* Changed definition of GO:0051534 from "Any process that modulates the frequency, rate or extent of the movement of an NFAT protein from the cytoplasm to the nucleus." to "Any process that stops, prevents or reduces the frequency, rate or extent of the movement of an NFAT protein from the cytoplasm to the nucleus."
* Changed definition of GO:0051696 from "The removal of capping protein from the barbed (or plus) end of actin filaments to free the ends for addition, exchange or removal of further actin subunits." to "The removal of capping protein from the pointed (or minus) end of actin filaments to free the ends for addition, exchange or removal of further actin subunits."
* Changed definition of GO:0051737 from "Catalysis of the reaction: GTP + 5'-dephospho-RNA = GDP + 5'-phospho-RNA." to "Catalysis of the reaction: GTP + 5'-dephospho-DNA = GDP + 5'-phospho-DNA."
* Changed definition of GO:0052105 from "Any process by which an organism activates, maintains or increases the frequency, rate or extent of host processes resulting in the thickening of its cell walls, occurring as part of the defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." to "The activation by an organism of host processes resulting in the thickening of its cell walls, occurring as part of the defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction."
* Changed definition of GO:0052118 from "The directed movement of a motile cell or organism on, within or near its host organism towards a lower level of a physical stimulus involved in energy generation, such as light, oxygen, and oxidizable substrates. The host is defined as the larger of the organisms involved in a symbiotic interaction." to "The directed movement of a motile cell or organism on, within or near its host organism towards a higher level of a physical stimulus involved in energy generation, such as light, oxygen, and oxidizable substrates. The host is defined as the larger of the organisms involved in a symbiotic interaction."
* Changed definition of GO:0052158 from "Any process by which an organism activates, maintains or increases the frequency, rate or extent of the resistance gene-dependent defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." to "Any process by which an organism modulates the frequency, rate or extent of the resistance gene-dependent defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction."
* Changed definition of GO:0052218 from "The directed movement of a motile cell or organism on, within or near a second organism towards a lower level of a physical stimulus involved in energy generation, such as light, oxygen, and oxidizable substrates, where the two organisms are in a symbiotic interaction." to "The directed movement of a motile cell or organism on, within or near a second organism towards a higher level of a physical stimulus involved in energy generation, such as light, oxygen, and oxidizable substrates, where the two organisms are in a symbiotic interaction."
* Changed definition of GO:0052290 from "Any process by which an organism activates, maintains or increases the frequency, rate or extent of the thickening of cell walls that occurs as part of the defense response of a second organism, where the two organisms are in a symbiotic interaction." to "The activation by an organism of the thickening of cell walls that occurs as part of the defense response of a second organism, where the two organisms are in a symbiotic interaction."
* Changed definition of GO:0060092 from "Any process that stops or decreases the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine." to "Any process that modulates the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine."