[Go-diff] GO update 03/09/2009

[Remote CVS for Gene Ontology]

OBODIFF of gene_ontology_write.obo version 1.467 by 1.469

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010908
* Created object of type obo:TERM with id GO:0010909
* Created object of type obo:TERM with id GO:0010910
* Created object of type obo:TERM with id GO:0010911
* Created object of type obo:TERM with id GO:0010912
* Created object of type obo:TERM with id GO:0010913
* Created object of type obo:TERM with id GO:0010914
* Populated new object GO:0010908 (macro)
  * Changed name of GO:0010908 from "<new term>" to "regulation of heparan sulfate proteoglycan biosynthetic process"
  * Set definition of GO:0010908 to "Any process that modulates the rate, frequency or extent of heparan sulfate proteoglycan biosynthesis. Heparan sulfate proteoglycan biosynthetic processes are the chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating (alpha1->4)-linked hexuronic acid and glucosamine residues."
  * Added definition dbxref GOC:dph to GO:0010908
  * Added definition dbxref GOC:tb to GO:0010908
  * Copied GO:0010908 to GO:0010675 with type OBO_REL:is_a
  * Copied GO:0010908 to GO:0015012 with type regulates
  * Copied GO:0010908 to GO:0042762 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010908
* Populated new object GO:0010909 (macro)
  * Changed name of GO:0010909 from "<new term>" to "positive regulation of heparan sulfate proteoglycan biosynthetic process"
  * Set definition of GO:0010909 to "Any process that increases the rate, frequency or extent of heparan sulfate proteoglycan biosynthesis. Heparan sulfate proteoglycan biosynthetic processes are the chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating (alpha1->4)-linked hexuronic acid and glucosamine residues."
  * Added definition dbxref GOC:dph to GO:0010909
  * Added definition dbxref GOC:tb to GO:0010909
  * Copied GO:0010909 to GO:0010908 with type OBO_REL:is_a
  * Copied GO:0010909 to GO:0010676 with type OBO_REL:is_a
  * Copied GO:0010909 to GO:0051176 with type OBO_REL:is_a
  * Copied GO:0010909 to GO:0015012 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010909
* Populated new object GO:0010910 (macro)
  * Changed name of GO:0010910 from "<new term>" to "positive regulation of heparan sulfate proteoglycan biosynthesis by positive regulation of epimerase activity"
  * Set definition of GO:0010910 to "Any process that increases the rate, frequency or extent of heparan sulfate proteoglycan biosynthesis by an increase in epimerase activity. This epimerase activity catalyzes the reaction that converts D-glucuronate into its diastereoisomer in heparan sulfate."
  * Added definition dbxref GOC:dph to GO:0010910
  * Added definition dbxref GOC:tb to GO:0010910
  * Copied GO:0010910 to GO:0010909 with type OBO_REL:is_a
  * Copied GO:0010910 to GO:0010912 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010910
* Populated new object GO:0010911 (macro)
  * Changed name of GO:0010911 from "<new term>" to "regulation of isomerase activity"
  * Set definition of GO:0010911 to "Any process that modulates the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5."
  * Added definition dbxref GOC:dph to GO:0010911
  * Added definition dbxref GOC:tb to GO:0010911
  * Copied GO:0010911 to GO:0016853 with type regulates
  * Copied GO:0010911 to GO:0050790 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010911
* Populated new object GO:0010912 (macro)
  * Changed name of GO:0010912 from "<new term>" to "positive regulation of isomerase activity"
  * Set definition of GO:0010912 to "Any process that increases the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5."
  * Added definition dbxref GOC:dph to GO:0010912
  * Added definition dbxref GOC:tb to GO:0010912
  * Copied GO:0010912 to GO:0010911 with type OBO_REL:is_a
  * Copied GO:0010912 to GO:0016853 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010912
* Populated new object GO:0010913 (macro)
  * Changed name of GO:0010913 from "<new term>" to "regulation of sterigmatocystin biosynthetic process"
  * Set definition of GO:0010913 to "Any process that modulates the rate, frequency, or extent of sterigmatocystin biosynthesis. Sterigmatocystin biosynthetic processes are the chemical reactions and pathways resulting in the formation of sterigmatocystin, a carcinogenic mycotoxin produced in high yields by strains of the common molds."
  * Added definition dbxref GOC:dph to GO:0010913
  * Added definition dbxref GOC:tb to GO:0010913
  * Copied GO:0010913 to GO:0031326 with type OBO_REL:is_a
  * Copied GO:0010913 to GO:0045461 with type regulates
  * Copied GO:0010913 to GO:0043455 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010913
* Populated new object GO:0010914 (macro)
  * Changed name of GO:0010914 from "<new term>" to "positive regulation of sterigmatocystin biosynthetic process"
  * Set definition of GO:0010914 to "Any process that increases the rate, frequency, or extent of sterigmatocystin biosynthesis. Sterigmatocystin biosynthetic processes are the chemical reactions and pathways resulting in the formation of sterigmatocystin, a carcinogenic mycotoxin produced in high yields by strains of the common molds."
  * Added definition dbxref GOC:dph to GO:0010914
  * Added definition dbxref GOC:tb to GO:0010914
  * Copied GO:0010914 to GO:0045461 with type positively_regulates
  * Copied GO:0010914 to GO:0031328 with type OBO_REL:is_a
  * Copied GO:0010914 to GO:0010913 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010914
* Changed definition of GO:0000737 from "The hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides." to "The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides."
* Added definition dbxref GOC:mah to GO:0000737
* Changed definition of GO:0000738 from "The hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides." to "The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides."
* Added definition dbxref GOC:mah to GO:0000738
* Set definition of GO:0006112 to "The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen."
* Added definition dbxref GOC:mah to GO:0006112
* Changed definition of GO:0006508 from "The hydrolysis of a peptide bond or bonds within a protein." to "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with the hydrolysis of peptide bonds."
* Added definition dbxref GOC:mah to GO:0006508
* Added definition dbxref ChEBI:16000 to GO:0006580
* Set definition of GO:0006733 to "The chemical reactions and pathways involving coenzymes that are required, in addition to an enzyme and a substrate, for an oxidoreductase reaction to proceed."
* Added definition dbxref GOC:mah to GO:0006733
* Changed definition of GO:0008362 from "Synthesis and deposition of a chitin-based embryonic cuticle by the underlying epidermal epithelium. This tough, waterproof layer is essential to provide structural integrity of the larval body." to "Synthesis, including the chemical reactions and pathways resulting in the formation of chitin and other components, and deposition of a chitin-based embryonic cuticle by the underlying epidermal epithelium. This tough, waterproof layer is essential to provide structural integrity of the larval body."
* Changed definition of GO:0010289 from "The formation from simpler components of the pectidic homogalacturonan, characterized by a backbone of 1,4-linked alpha-D-GalpA residues that can be methyl-esterified at C-6 and carry acetyl groups on O-2 and O-3." to "The chemical reactions and pathways resulting in the formation of the pectidic homogalacturonan, characterized by a backbone of 1,4-linked alpha-D-GalpA residues that can be methyl-esterified at C-6 and carry acetyl groups on O-2 and O-3."
* Changed definition of GO:0010304 from "Catabolism of one or more components of the light-harvesting complex of photosystem II." to "The chemical reactions and pathways resulting in the breakdown of one or more components of the light-harvesting complex of photosystem II."
* Added definition dbxref GOC:mah to GO:0010304
* Changed definition of GO:0010306 from "The formation from simpler components of rhamnogalacturonan II, a low molecular mass (5 - 10KDa) pectic polysaccharide, conserved in the primary walls of dicotyledenous and monocotyledenous plants and gymnosperms." to "The chemical reactions and pathways resulting in the formation of rhamnogalacturonan II, a low molecular mass (5 - 10KDa) pectic polysaccharide, conserved in the primary walls of dicotyledenous and monocotyledenous plants and gymnosperms."
* Changed definition of GO:0010310 from "Any process that modulates the frequency, rate or extent of the chemical reactions involving hydrogen peroxide." to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving hydrogen peroxide."
* Changed definition of GO:0010337 from "Any process that modulates the frequency, rate or extent of the chemical reactions involving salicylic acid." to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving salicylic acid."
* Changed definition of GO:0010364 from "Any process that modulates the frequency, rate, or extent of ethylene biosynthetic process." to "Any process that modulates the frequency, rate, or extent of an ethylene biosynthetic process."
* Changed definition of GO:0010365 from "Any process that activates or increases the frequency, rate or extent of ethylene biosynthetic process." to "Any process that activates or increases the frequency, rate or extent of an ethylene biosynthetic process."
* Changed definition of GO:0010366 from "Any process that stops, prevents or reduces the frequency, rate or extent of ethylene biosynthetic process." to "Any process that stops, prevents or reduces the frequency, rate or extent of an ethylene biosynthetic process."
* Changed definition of GO:0010550 from "Any process that modulates the catabolism of one or more components of the light-harvesting complex of photosystem II." to "Any process that modulates the chemical reactions and pathways resulting in the breakdown of one or more components of the light-harvesting complex of photosystem II."
* Changed definition of GO:0010597 from "The biosynthesis of volatile molecules emitted from green plants, such as hexenal, hexenol and hexenyl acetate, from linoleic acid or linolenic acid." to "The chemical reactions and pathways resulting in the formation of volatile molecules emitted from green plants, such as hexenal, hexenol and hexenyl acetate, from linoleic acid or linolenic acid."
* Changed definition of GO:0010726 from "Any process that increases the frequency, rate or extent of the chemical reactions involving hydrogen peroxide." to "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving hydrogen peroxide."
* Changed definition of GO:0010727 from "Any process that decreases the frequency, rate or extent of the chemical reactions involving hydrogen peroxide." to "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving hydrogen peroxide."
* Copied GO:0015013 to GO:0018242 with type OBO_REL:is_a
* Set definition of GO:0015975 to "The chemical reactions and pathways by which a cell derives energy from inorganic compounds; results in the oxidation of the compounds from which energy is released."
* Added definition dbxref GOC:mah to GO:0015975
* Set definition of GO:0015980 to "The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released."
* Added definition dbxref GOC:mah to GO:0015980
* Changed definition of GO:0018265 from "The formation of a C-terminal peptidyl-asparagine ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a asparaginyl-peptide bond in the carboxy-terminal region of a membrane-associated protein." to "The chemical reactions and pathways resulting in the formation of a C-terminal peptidyl-asparagine ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a asparaginyl-peptide bond in the carboxy-terminal region of a membrane-associated protein."
* Changed definition of GO:0018266 from "The formation of a C-terminal peptidyl-aspartic acid ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a aspartyl-peptide bond in the carboxy-terminal region of a membrane-associated protein." to "The chemical reactions and pathways resulting in the formation of a C-terminal peptidyl-aspartic acid ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a aspartyl-peptide bond in the carboxy-terminal region of a membrane-associated protein."
* Changed definition of GO:0018267 from "The formation of a C-terminal peptidyl-cysteine ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a cysteinyl-peptide bond in the carboxy-terminal region of a membrane-associated protein." to "The chemical reactions and pathways resulting in the formation of a C-terminal peptidyl-cysteine ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a cysteinyl-peptide bond in the carboxy-terminal region of a membrane-associated protein."
* Changed definition of GO:0018268 from "The formation of a C-terminal peptidyl-glycine ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a glycyl-peptide bond in the carboxy-terminal region of a membrane-associated protein." to "The chemical reactions and pathways resulting in the formation of a C-terminal peptidyl-glycine ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a glycyl-peptide bond in the carboxy-terminal region of a membrane-associated protein."
* Changed definition of GO:0018269 from "The formation of a C-terminal peptidyl-serine ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a seryl-peptide bond in the carboxy-terminal region of a membrane-associated protein." to "The chemical reactions and pathways resulting in the formation of a C-terminal peptidyl-serine ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a seryl-peptide bond in the carboxy-terminal region of a membrane-associated protein."
* Changed definition of GO:0018270 from "The formation of a C-terminal peptidyl-alanine ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of an alanyl-peptide bond in the carboxy-terminal region of a membrane-associated protein." to "The chemical reactions and pathways resulting in the formation of a C-terminal peptidyl-alanine ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of an alanyl-peptide bond in the carboxy-terminal region of a membrane-associated protein."
* Changed definition of GO:0019184 from "The process whereby peptide bond formation occurs in the absence of the translational machinery. Examples include the synthesis of antibiotic peptides, and glutathione." to "The biosynthetic process whereby peptide bond formation occurs in the absence of the translational machinery. Examples include the synthesis of antibiotic peptides, and glutathione."
* Changed definition of GO:0019243 from "The breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step." to "The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step."
* Set definition of GO:0019410 to "The metabolic process by which carbon monoxide (CO) is oxidized to carbon dioxide (CO2) to generate energy; energy conservation likely uses sodium ion gradients for ATP synthesis and is coupled to quantitative sulfide methylation."
* Added definition dbxref PMID:18024677 to GO:0019410
* Set definition of GO:0019411 to "The metabolic process by which ferrous ions (Fe2+) are oxidized to ferric ions (Fe3+) to generate energy, coupled to the reduction of carbon dioxide."
* Added definition dbxref ISBN:3131084111 to GO:0019411
* Changed definition of GO:0030995 from "Dissolution of the septum edging during cell separation." to "The chemical reactions and pathways resulting in the dissolution of the septum edging during cell separation."
* Added definition dbxref GOC:mah to GO:0030995
* Changed definition of GO:0033621 from "The selective degradation of meiosis-specific transcripts during vegetative growth, by a mechanism that requires determinant of selective removal (DSR) sequences in the targeted mRNAs and involves a YTH family protein." to "The chemical reactions and pathways resulting in the selective degradation of meiosis-specific transcripts during vegetative growth, by a mechanism that requires determinant of selective removal (DSR) sequences in the targeted mRNAs and involves a YTH family protein."
* Changed definition of GO:0042160 from "The enzymatic modification of a lipoprotein; any conjugated, water-soluble protein in which the nonprotein moiety consists of a lipid or lipids." to "The chemical reactions and pathways resulting in the covalent alteration of one or more amino acid or lipid residues occurring in a lipoprotein, any conjugated, water-soluble protein in which the nonprotein moiety consists of a lipid or lipids."
* Deleted definition dbxref GOC:jl from GO:0042160
* Added definition dbxref GOC:mah to GO:0042160
* Set definition of GO:0042439 to "The chemical reactions and pathways involving ethanolamine (2-aminoethanol) and compounds derived from it."
* Added definition dbxref ChEBI:16000 to GO:0042439
* Added definition dbxref GOC:mah to GO:0042439
* Changed definition of GO:0043455 from "Any process that modulates the frequency, rate or extent of secondary metabolism, the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon." to "Any process that modulates the frequency, rate or extent of secondary metabolism, the chemical reactions and pathways involving compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon."
* Changed definition of GO:0043633 from "Destruction of an RNA molecule, initiated by the covalent modification of the target RNA." to "The chemical reactions and pathways resulting in the breakdown of an RNA molecule, initiated by the covalent modification of the target RNA."
* Added definition dbxref GOC:mah to GO:0043633
* Changed definition of GO:0043643 from "The chemical reactions involving tetracycline, (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide, a broad-spectrum antibiotic produced by streptomyces bacteria that blocks binding of aminoacyl tRNA to the ribosomes of both Gram-positive and Gram-negative organisms (and those of organelles)." to "The chemical reactions and pathways involving tetracycline, (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide, a broad-spectrum antibiotic produced by streptomyces bacteria that blocks binding of aminoacyl tRNA to the ribosomes of both Gram-positive and Gram-negative organisms (and those of organelles)."
* Changed definition of GO:0043644 from "The formation from simpler components of tetracycline, (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide, a broad-spectrum antibiotic produced by streptomyces bacteria that blocks binding of aminoacyl tRNA to the ribosomes of both Gram-positive and Gram-negative organisms (and those of organelles)." to "The chemical reactions and pathways resulting in the formation of tetracycline, (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide, a broad-spectrum antibiotic produced by streptomyces bacteria that blocks binding of aminoacyl tRNA to the ribosomes of both Gram-positive and Gram-negative organisms (and those of organelles)."
* Changed definition of GO:0043645 from "The chemical reactions involving a cephalosporin, any of large class of tetracyclic triterpene broad-spectrum antibiotics similar both chemically and in their mode of action to penicillin, first isolated from the culture filtrates of mediterranean fungus acremonium (cephalosporium acremonium), and effective against gram-positive bacteria." to "The chemical reactions and pathways involving a cephalosporin, any of large class of tetracyclic triterpene broad-spectrum antibiotics similar both chemically and in their mode of action to penicillin, first isolated from the culture filtrates of mediterranean fungus acremonium (cephalosporium acremonium), and effective against gram-positive bacteria."
* Changed definition of GO:0043646 from "The formation from simpler components of a cephalosporin, any of large class of tetracyclic triterpene broad-spectrum antibiotics similar both chemically and in their mode of action to penicillin, first isolated from the culture filtrates of mediterranean fungus acremonium (cephalosporium acremonium), and effective against gram-positive bacteria." to "The chemical reactions and pathways resulting in the formation of a cephalosporin, any of large class of tetracyclic triterpene broad-spectrum antibiotics similar both chemically and in their mode of action to penicillin, first isolated from the culture filtrates of mediterranean fungus acremonium (cephalosporium acremonium), and effective against gram-positive bacteria."
* Changed definition of GO:0043705 from "The chemical reactions involving cyanophycin, a non-protein, non-ribosomally produced amino acid polymer composed of an aspartic acid backbone and arginine side groups." to "The chemical reactions and pathways involving cyanophycin, a non-protein, non-ribosomally produced amino acid polymer composed of an aspartic acid backbone and arginine side groups."
* Changed definition of GO:0050493 from "The formation of a C-terminal peptidyl-threonyl ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a threonyl-peptide bond in the carboxy-terminal region of a membrane-associated protein." to "The chemical reactions and pathways resulting in the formation of a C-terminal peptidyl-threonyl ethanolamide-linked glycosylphosphatidylinositol (GPI) anchor following hydrolysis of a threonyl-peptide bond in the carboxy-terminal region of a membrane-associated protein."
* Changed definition of GO:0050494 from "The formation of a C-terminal peptidyl-glycine ethanolamide-linked glycosylsphingolipidinositol (GSI) anchor following hydrolysis of a glycyl-peptide bond in the carboxy-terminal region of a membrane-associated protein." to "The chemical reactions and pathways resulting in the formation of a C-terminal peptidyl-glycine ethanolamide-linked glycosylsphingolipidinositol (GSI) anchor following hydrolysis of a glycyl-peptide bond in the carboxy-terminal region of a membrane-associated protein."
* Changed definition of GO:0050495 from "The formation of a C-terminal peptidyl-glycine ethanolamide-linked phosphatide following hydrolysis of a glycyl-peptide bond, as in the cleavage of arginine from the carboxy-terminal of Apg8 followed by its amidation with phosphatidylethanolamine." to "The chemical reactions and pathways resulting in the formation of a C-terminal peptidyl-glycine ethanolamide-linked phosphatide following hydrolysis of a glycyl-peptide bond, as in the cleavage of arginine from the carboxy-terminal of Apg8 followed by its amidation with phosphatidylethanolamine."