From gocvs at genome.stanford.edu Mon Mar 3 21:30:47 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Mon, 3 Mar 2008 21:30:47 -0800 (PST) Subject: [Go-diff] GO update 03/03/2008 Message-ID: <200803040530.VAA12020@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.719 by 5.720 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Changed name of GO:0001659 from "thermoregulation" to "temperature homeostasis" * Added synonym "thermoregulation" to GO:0001659 * Added general dbxref GOC:tb to synonym thermoregulation of GO:0001659 * Added general dbxref GOC:dph to synonym thermoregulation of GO:0001659 * Changed synonym scope of GO:0001659 from "Related" to "Exact" * Changed name of GO:0001895 from "retinal homeostasis" to "retina homeostasis" * Added definition dbxref GOC:dph to GO:0001895 * Added definition dbxref GOC:tb to GO:0001895 * Changed name of GO:0001977 from "renal regulation of blood volume" to "regulation of blood volume by renal system process" * Added definition dbxref GOC:dph to GO:0001977 * Added definition dbxref GOC:tb to GO:0001977 * Added synonym "renal regulation of blood volume" to GO:0001977 * Added general dbxref GOC:tb to synonym renal regulation of blood volume of GO:0001977 * Added general dbxref GOC:dph to synonym renal regulation of blood volume of GO:0001977 * Copied GO:0001977 to GO:0050878 with type OBO_REL:is_a * Changed name of GO:0002006 from "vasopressin mediated vasoconstriction involved in systemic arterial blood pressure control" to "vasoconstriction by vasopressin involved in systemic arterial blood pressure control" * Added definition dbxref GOC:dph to GO:0002006 * Added definition dbxref GOC:tb to GO:0002006 * Added synonym "vasopressin mediated vasoconstriction involved in systemic arterial blood pressure control" to GO:0002006 * Added general dbxref GOC:tb to synonym vasopressin mediated vasoconstriction involved in systemic arterial blood pressure control of GO:0002006 * Added general dbxref GOC:dph to synonym vasopressin mediated vasoconstriction involved in systemic arterial blood pressure control of GO:0002006 * Changed synonym scope of GO:0002006 from "Related" to "Exact" * Changed name of GO:0002017 from "renal regulation of blood volume by aldosterone" to "regulation of blood volume by renal aldosterone" * Added synonym "renal regulation of blood volume by aldosterone" to GO:0002017 * Added general dbxref GOC:tb to synonym renal regulation of blood volume by aldosterone of GO:0002017 * Added general dbxref GOC:dph to synonym renal regulation of blood volume by aldosterone of GO:0002017 * Changed synonym scope of GO:0002017 from "Related" to "Exact" * Copied GO:0002085 to GO:0045596 with type OBO_REL:is_a * Changed name of GO:0003072 from "renal regulation of systemic arterial blood pressure by control of peripheral vascular resistence" to "regulation of systemic arterial blood pressure by renal control of peripheral vascular resistence" * Added synonym "renal regulation of systemic arterial blood pressure by control of peripheral vascular resistence" to GO:0003072 * Added general dbxref GOC:tb to synonym renal regulation of systemic arterial blood pressure by control of peripheral vascular resistence of GO:0003072 * Added general dbxref GOC:dph to synonym renal regulation of systemic arterial blood pressure by control of peripheral vascular resistence of GO:0003072 * Changed synonym scope of GO:0003072 from "Related" to "Exact" * Changed name of GO:0003075 from "renal regulation of systemic arterial blood pressure by vasodilation of the peripheral vascular system" to "regulation of systemic arterial blood pressure by renal vasodilation of the peripheral vascular system" * Added synonym "renal regulation of systemic arterial blood pressure by vasodilation of the peripheral vascular system" to GO:0003075 * Added general dbxref GOC:tb to synonym renal regulation of systemic arterial blood pressure by vasodilation of the peripheral vascular system of GO:0003075 * Added general dbxref GOC:dph to synonym renal regulation of systemic arterial blood pressure by vasodilation of the peripheral vascular system of GO:0003075 * Changed synonym scope of GO:0003075 from "Related" to "Exact" * Changed name of GO:0006588 from "tryptophan hydroxylase activation" to "activation of tryptophan 5-monooxygenase activity" * Changed definition of GO:0006588 from "The process by which the tryptophan hydroxylase enzyme is changed so that is can carry out its enzymatic activity." to "The process by which the tryptophan 5-monooxygenase enzyme is changed so that it can carry out its enzymatic activity." * Added definition dbxref GOC:tb to GO:0006588 * Added synonym "tryptophan hydroxylase activation" to GO:0006588 * Added general dbxref GOC:tb to synonym tryptophan hydroxylase activation of GO:0006588 * Added general dbxref GOC:dph to synonym tryptophan hydroxylase activation of GO:0006588 * Deleted GO:0006588 --OBO_REL:is_a--> GO:0048554 * Copied GO:0006588 to GO:0032770 with type OBO_REL:is_a * Changed name of GO:0006933 from "substrate-bound cell migration, cell release from substrate" to "negative regulation of cell adhesion involved in substrate-bound cell migration" * Added definition dbxref GOC:dph to GO:0006933 * Added definition dbxref GOC:tb to GO:0006933 * Added synonym "substrate-bound cell migration, cell release from substrate" to GO:0006933 * Added general dbxref GOC:tb to synonym substrate-bound cell migration, cell release from substrate of GO:0006933 * Added general dbxref GOC:dph to synonym substrate-bound cell migration, cell release from substrate of GO:0006933 * Changed synonym scope of GO:0006933 from "Related" to "Exact" * Changed name of GO:0006987 from "unfolded protein response, activation of signaling protein activity" to "activation of signaling protein activity involved in unfolded protein response" * Added definition dbxref GOC:dph to GO:0006987 * Added definition dbxref GOC:tb to GO:0006987 * Added synonym "unfolded protein response, activation of signaling protein activity" to GO:0006987 * Added general dbxref GOC:tb to synonym unfolded protein response, activation of signaling protein activity of GO:0006987 * Added general dbxref GOC:dph to synonym unfolded protein response, activation of signaling protein activity of GO:0006987 * Changed synonym scope of GO:0006987 from "Related" to "Exact" * Changed name of GO:0006994 from "sterol depletion response, SREBP target gene transcriptional activation" to "positive regulation of sterol regulatory element binding protein target gene transcription involved in sterol depletion response" * Added synonym "sterol depletion response, SREBP target gene transcriptional activation" to GO:0006994 * Added general dbxref GOC:mtg_lung to synonym sterol depletion response, SREBP target gene transcriptional activation of GO:0006994 * Added general dbxref GOC:dph to synonym sterol depletion response, SREBP target gene transcriptional activation of GO:0006994 * Changed synonym scope of GO:0006994 from "Related" to "Exact" * Deleted GO:0006994 --OBO_REL:is_a--> GO:0032569 * Changed name of GO:0007171 from "transmembrane receptor protein tyrosine kinase activation (dimerization)" to "activation of transmembrane receptor protein tyrosine kinase activity" * Set definition of GO:0007171 to "Any process that initiates the activity of the inactive transmembrane receptor protein tyrosine kinase activity." * Added definition dbxref GOC:dph to GO:0007171 * Added definition dbxref GOC:tb to GO:0007171 * Added synonym "transmembrane receptor protein tyrosine kinase activation" to GO:0007171 * Added general dbxref GOC:tb to synonym transmembrane receptor protein tyrosine kinase activation of GO:0007171 * Added general dbxref GOC:dph to synonym transmembrane receptor protein tyrosine kinase activation of GO:0007171 * Added synonym "transmembrane receptor protein tyrosine kinase dimerization" to GO:0007171 * Added general dbxref GOC:mtg_lung to synonym transmembrane receptor protein tyrosine kinase dimerization of GO:0007171 * Added general dbxref GOC:dph to synonym transmembrane receptor protein tyrosine kinase dimerization of GO:0007171 * Deleted GO:0007171 --OBO_REL:is_a--> GO:0045860 * Copied GO:0007171 to GO:0032147 with type OBO_REL:is_a * Changed definition of GO:0008360 from "Any process that modulates the shape of a cell." to "Any process that modulates the surface configuration of a cell." * Added definition dbxref GOC:dph to GO:0008360 * Added definition dbxref GOC:tb to GO:0008360 * Changed name of GO:0014808 from "release of sequestered calcium ion by sarcoplasmic reticulum into cytosol" to "release of sequestered calcium ion into cytosol by sarcoplasmic reticulum" * Added synonym "release of sequestered calcium ion by sarcoplasmic reticulum into cytosol" to GO:0014808 * Added general dbxref GOC:tb to synonym release of sequestered calcium ion by sarcoplasmic reticulum into cytosol of GO:0014808 * Added general dbxref GOC:dph to synonym release of sequestered calcium ion by sarcoplasmic reticulum into cytosol of GO:0014808 * Changed name of GO:0014834 from "satellite cell compartment self-renewal involved in skeletal muscle regeneration" to "satellite cell maintenance involved in skeletal muscle regeneration" * Changed definition of GO:0014834 from "The process essential to mantain a ready source of satellite cells. It consists in the return of activated satellite cells to a quiescent state after proliferation to replenish the satellite cell pool. Satellite cells are quiescent cells that are located between the basal lamina and the plasmalemma of the muscle fibre, which are the main contributors to postnatal muscle growth. In adult muscle, satellite cells become activated to divide and differentiate in response to muscle damage." to "The process essential to mantain a ready source of satellite cells. It consists of the return of activated satellite cells to a quiescent state after proliferation to replenish the satellite cell pool. Satellite cells are quiescent cells that are located between the basal lamina and the plasmalemma of the muscle fibre, which are the main contributors to postnatal muscle growth. In adult muscle, satellite cells become activated to divide and differentiate in response to muscle damage." * Added definition dbxref GOC:dph to GO:0014834 * Added definition dbxref GOC:tb to GO:0014834 * Added synonym "satellite cell compartment self-renewal involved in skeletal muscle regeneration" to GO:0014834 * Added general dbxref GOC:tb to synonym satellite cell compartment self-renewal involved in skeletal muscle regeneration of GO:0014834 * Added general dbxref GOC:dph to synonym satellite cell compartment self-renewal involved in skeletal muscle regeneration of GO:0014834 * Changed synonym scope of GO:0014834 from "Related" to "Exact" * Deleted GO:0014834 --OBO_REL:is_a--> GO:0045596 * Copied GO:0014834 to GO:0035019 with type OBO_REL:is_a * Changed name of GO:0016476 from "shape changes of embryonic cells" to "regulation of embryonic cell shape" * Set definition of GO:0016476 to "Any process that modulates the surface configuration of an embryonic cell." * Added definition dbxref GOC:dph to GO:0016476 * Added definition dbxref GOC:tb to GO:0016476 * Added synonym "shape changes of embryonic cells" to GO:0016476 * Added general dbxref GOC:tb to synonym shape changes of embryonic cells of GO:0016476 * Added general dbxref GOC:dph to synonym shape changes of embryonic cells of GO:0016476 * Copied GO:0016476 to GO:0045995 with type OBO_REL:is_a * Changed name of GO:0021875 from "fibroblast growth factor receptor signaling pathway in forebrain neuroblast division" to "fibroblast growth factor receptor signaling pathway involved in forebrain neuroblast division" * Changed name of GO:0021907 from "fibroblast growth factor receptor signaling pathway in spinal cord anterior-posterior patterning" to "fibroblast growth factor receptor signaling pathway involved in spinal cord anterior-posterior patterning" * Changed name of GO:0022002 from "Wnt receptor signaling involved in negative regulation of anterior neural cell fate commitment of the neural plate" to "Wnt receptor signaling pathway involved in negative regulation of anterior neural cell fate commitment of the neural plate" * Copied GO:0022002 to GO:0016055 with type OBO_REL:is_a * Changed name of GO:0022003 from "Fgf receptor signaling involved in negative regulation of anterior neural cell fate commitment of the neural plate" to "fibroblast growth factor receptor signaling pathway involved in negative regulation of anterior neural cell fate commitment of the neural plate" * Copied GO:0022003 to GO:0008543 with type OBO_REL:is_a * Changed name of GO:0031047 from "RNA-mediated gene silencing" to "gene silencing by RNA" * Added definition dbxref GOC:dph to GO:0031047 * Added definition dbxref GOC:tb to GO:0031047 * Added synonym "RNA-mediated gene silencing" to GO:0031047 * Added general dbxref GOC:tb to synonym RNA-mediated gene silencing of GO:0031047 * Added general dbxref GOC:dph to synonym RNA-mediated gene silencing of GO:0031047 * Changed synonym scope of GO:0031047 from "Related" to "Exact" * Changed name of GO:0031048 from "small RNA-mediated chromatin silencing" to "chromatin silencing by small RNA" * Added definition dbxref GOC:dph to GO:0031048 * Added definition dbxref GOC:mtg_lung to GO:0031048 * Added general dbxref GOC:tb to synonym RNA-mediated chromatin silencing of GO:0031048 * Added general dbxref GOC:dph to synonym RNA-mediated chromatin silencing of GO:0031048 * Changed name of GO:0031556 from "ribosome-mediated transcriptional attenuation" to "transcriptional attenuation by ribosome" * Added synonym "ribosome-mediated transcriptional " to GO:0031556 * Added general dbxref GOC:tb to synonym ribosome-mediated transcriptional of GO:0031556 * Added general dbxref GOC:dph to synonym ribosome-mediated transcriptional of GO:0031556 * Changed synonym scope of GO:0031556 from "Related" to "Exact" * Changed name of GO:0033562 from "small RNA-mediated cotranscriptional gene silencing" to "cotranscriptional gene silencing by small RNA" * Added synonym "small RNA-mediated cotranscriptional gene silencing" to GO:0033562 * Added general dbxref GOC:tb to synonym small RNA-mediated cotranscriptional gene silencing of GO:0033562 * Added general dbxref GOC:dph to synonym small RNA-mediated cotranscriptional gene silencing of GO:0033562 * Changed synonym scope of GO:0033562 from "Related" to "Exact" * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Changed name of GO:0035194 from "RNA-mediated posttranscriptional gene silencing" to "posttranscriptional gene silencing by RNA" * Added synonym "RNA-mediated posttranscriptional gene silencing" to GO:0035194 * Added general dbxref GOC:tb to synonym RNA-mediated posttranscriptional gene silencing of GO:0035194 * Added general dbxref GOC:dph to synonym RNA-mediated posttranscriptional gene silencing of GO:0035194 * Changed synonym scope of GO:0035194 from "Related" to "Exact" * Changed name of GO:0035195 from "miRNA-mediated gene silencing" to "gene silencing by miRNA" * Added synonym "miRNA-mediated gene silencing" to GO:0035195 * Added general dbxref GOC:tb to synonym miRNA-mediated gene silencing of GO:0035195 * Added general dbxref GOC:dph to synonym miRNA-mediated gene silencing of GO:0035195 * Changed synonym scope of GO:0035195 from "Related" to "Exact" * Changed name of GO:0035196 from "miRNA-mediated gene silencing, production of miRNAs" to "gene silencing by miRNA, production of miRNAs" * Added definition dbxref GOC:dph to GO:0035196 * Added definition dbxref GOC:tb to GO:0035196 * Added synonym "miRNA-mediated gene silencing, production of miRNAs" to GO:0035196 * Added general dbxref GOC:tb to synonym miRNA-mediated gene silencing, production of miRNAs of GO:0035196 * Added general dbxref GOC:dph to synonym miRNA-mediated gene silencing, production of miRNAs of GO:0035196 * Changed synonym scope of GO:0035196 from "Related" to "Exact" * Changed name of GO:0035278 from "miRNA-mediated gene silencing, negative regulation of translation" to "gene silencing by miRNA, negative regulation of translation" * Added synonym "miRNA-mediated gene silencing, negative regulation of translation" to GO:0035278 * Added general dbxref GOC:tb to synonym miRNA-mediated gene silencing, negative regulation of translation of GO:0035278 * Added general dbxref GOC:dph to synonym miRNA-mediated gene silencing, negative regulation of translation of GO:0035278 * Changed name of GO:0035279 from "miRNA-mediated gene silencing, mRNA cleavage" to "gene silencing by miRNA, mRNA cleavage" * Added definition dbxref GOC:dph to GO:0035279 * Added definition dbxref GOC:mtg_lung to GO:0035279 * Added synonym "miRNA-mediated gene silencing, mRNA cleavage" to GO:0035279 * Added general dbxref GOC:tb to synonym miRNA-mediated gene silencing, mRNA cleavage of GO:0035279 * Added general dbxref GOC:dph to synonym miRNA-mediated gene silencing, mRNA cleavage of GO:0035279 * Changed synonym scope of GO:0035279 from "Related" to "Exact" * Changed name of GO:0035280 from "miRNA-mediated gene silencing, miRNA loading onto RISC" to "gene silencing by miRNA, miRNA loading onto RISC" * Added synonym "miRNA-mediated gene silencing, miRNA loading onto RISC" to GO:0035280 * Added general dbxref GOC:tb to synonym miRNA-mediated gene silencing, miRNA loading onto RISC of GO:0035280 * Added general dbxref GOC:dph to synonym miRNA-mediated gene silencing, miRNA loading onto RISC of GO:0035280 * Changed synonym scope of GO:0035280 from "Related" to "Exact" * Changed name of GO:0048876 from "retinal chemical homeostasis" to "chemical homeostasis within retina" * Changed name of GO:0048877 from "homeostasis of number of retinal cells" to "homeostasis of number of retina cells" * Added definition dbxref GOC:dph to GO:0048877 * Added definition dbxref GOC:tb to GO:0048877 * Added definition dbxref GOC:dph to GO:0051209 * Added definition dbxref GOC:mtg_lung to GO:0051209 * Changed definition of GO:0051606 from "The series of events in which a stimulus is received by a cell and converted into a molecular signal." to "The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal." * Added definition dbxref GOC:add to GO:0051606 * Added definition dbxref GOC:dph to GO:0051606 * Added definition dbxref GOC:mah to GO:0051606 * Deleted GO:0051606 --OBO_REL:is_a--> GO:0009987 * Changed name of GO:0060086 from "circadian thermoregulation" to "circadian temperature homeostasis" * Added definition dbxref GOC:tb to GO:0060086 * Added synonym "circadian thermoregulation" to GO:0060086 * Added general dbxref GOC:tb to synonym circadian thermoregulation of GO:0060086 * Added general dbxref GOC:dph to synonym circadian thermoregulation of GO:0060086 * Changed synonym scope of GO:0060086 from "Related" to "Exact" From gocvs at genome.stanford.edu Wed Mar 5 21:30:44 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Wed, 5 Mar 2008 21:30:44 -0800 (PST) Subject: [Go-diff] GO update 03/05/2008 Message-ID: <200803060530.VAA02607@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.720 by 5.723 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0010556 * Created object of type obo:TERM with id GO:0010557 * Created object of type obo:TERM with id GO:0010558 * Created object of type obo:TERM with id GO:0010559 * Created object of type obo:TERM with id GO:0010560 * Created object of type obo:TERM with id GO:0010561 * Populated new object GO:0010556 (macro) * Changed name of GO:0010556 from "" to "regulation of macromolecule biosynthetic process" * Set definition of GO:0010556 to "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." * Added definition dbxref GOC:dph to GO:0010556 * Added definition dbxref GOC:tb to GO:0010556 * Copied GO:0010556 to GO:0009059 with type part_of * Copied GO:0010556 to GO:0009889 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010556 * Populated new object GO:0010557 (macro) * Changed name of GO:0010557 from "" to "positive regulation of macromolecule biosynthetic process" * Set definition of GO:0010557 to "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." * Added definition dbxref GOC:dph to GO:0010557 * Added definition dbxref GOC:tb to GO:0010557 * Copied GO:0010557 to GO:0009891 with type OBO_REL:is_a * Copied GO:0010557 to GO:0010556 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010557 * Populated new object GO:0010558 (macro) * Changed name of GO:0010558 from "" to "negative regulation of macromolecule biosynthetic process" * Set definition of GO:0010558 to "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." * Added definition dbxref GOC:dph to GO:0010558 * Added definition dbxref GOC:tb to GO:0010558 * Copied GO:0010558 to GO:0010556 with type OBO_REL:is_a * Copied GO:0010558 to GO:0009890 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010558 * Populated new object GO:0010559 (macro) * Changed name of GO:0010559 from "" to "regulation of glycoprotein biosynthetic process" * Set definition of GO:0010559 to "Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues other than as a moiety of nucleic acid; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." * Added definition dbxref GOC:dph to GO:0010559 * Added definition dbxref GOC:tb to GO:0010559 * Copied GO:0010559 to GO:0010556 with type OBO_REL:is_a * Copied GO:0010559 to GO:0009101 with type part_of * Assigned namespace "biological_process" to GO:0010559 * Populated new object GO:0010560 (macro) * Changed name of GO:0010560 from "" to "positive regulation of glycoprotein biosynthetic process" * Set definition of GO:0010560 to "Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues other than as a moiety of nucleic acid; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." * Added definition dbxref GOC:dph to GO:0010560 * Added definition dbxref GOC:tb to GO:0010560 * Copied GO:0010560 to GO:0010557 with type OBO_REL:is_a * Copied GO:0010560 to GO:0010559 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010560 * Populated new object GO:0010561 (macro) * Changed name of GO:0010561 from "" to "negative regulation of glycoprotein biosynthetic process" * Set definition of GO:0010561 to "Any process that decreases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues other than as a moiety of nucleic acid; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." * Added definition dbxref GOC:dph to GO:0010561 * Added definition dbxref GOC:tb to GO:0010561 * Copied GO:0010561 to GO:0010558 with type OBO_REL:is_a * Copied GO:0010561 to GO:0010559 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010561 * Deleted GO:0002640 --OBO_REL:is_a--> GO:0006417 * Copied GO:0002640 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0002641 --OBO_REL:is_a--> GO:0017148 * Copied GO:0002641 to GO:0010558 with type OBO_REL:is_a * Deleted GO:0002642 --OBO_REL:is_a--> GO:0045727 * Copied GO:0002642 to GO:0010557 with type OBO_REL:is_a * Copied GO:0006417 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0014062 --OBO_REL:is_a--> GO:0046928 * Copied GO:0014062 to GO:0051046 with type OBO_REL:is_a * Deleted GO:0014063 --OBO_REL:is_a--> GO:0046929 * Copied GO:0014063 to GO:0051048 with type OBO_REL:is_a * Deleted GO:0014064 --OBO_REL:is_a--> GO:0001956 * Copied GO:0014064 to GO:0051047 with type OBO_REL:is_a * Copied GO:0017148 to GO:0010558 with type OBO_REL:is_a * Deleted GO:0032803 --OBO_REL:is_a--> GO:0006417 * Copied GO:0032803 to GO:0031329 with type OBO_REL:is_a * Copied GO:0032964 to GO:0006412 with type OBO_REL:is_a * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Deleted GO:0042035 --OBO_REL:is_a--> GO:0006417 * Copied GO:0042035 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0042036 --OBO_REL:is_a--> GO:0017148 * Copied GO:0042036 to GO:0010558 with type OBO_REL:is_a * Deleted GO:0042108 --OBO_REL:is_a--> GO:0045727 * Copied GO:0042108 to GO:0010557 with type OBO_REL:is_a * Deleted GO:0042984 --OBO_REL:is_a--> GO:0006417 * Copied GO:0042984 to GO:0010559 with type OBO_REL:is_a * Copied GO:0042985 to GO:0010561 with type OBO_REL:is_a * Copied GO:0042986 to GO:0010560 with type OBO_REL:is_a * Deleted GO:0045113 --OBO_REL:is_a--> GO:0006417 * Copied GO:0045113 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0045219 --OBO_REL:is_a--> GO:0006417 * Copied GO:0045219 to GO:0010559 with type OBO_REL:is_a * Copied GO:0045220 to GO:0010560 with type OBO_REL:is_a * Copied GO:0045221 to GO:0010561 with type OBO_REL:is_a * Deleted GO:0045223 --OBO_REL:is_a--> GO:0006417 * Copied GO:0045223 to GO:0010559 with type OBO_REL:is_a * Copied GO:0045224 to GO:0010560 with type OBO_REL:is_a * Copied GO:0045225 to GO:0010561 with type OBO_REL:is_a * Deleted GO:0045343 --OBO_REL:is_a--> GO:0006417 * Copied GO:0045343 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0045344 --OBO_REL:is_a--> GO:0017148 * Copied GO:0045344 to GO:0010558 with type OBO_REL:is_a * Deleted GO:0045345 --OBO_REL:is_a--> GO:0045727 * Copied GO:0045345 to GO:0010557 with type OBO_REL:is_a * Deleted GO:0045346 --OBO_REL:is_a--> GO:0006417 * Copied GO:0045346 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0045347 --OBO_REL:is_a--> GO:0017148 * Copied GO:0045347 to GO:0010558 with type OBO_REL:is_a * Deleted GO:0045348 --OBO_REL:is_a--> GO:0045727 * Copied GO:0045348 to GO:0010557 with type OBO_REL:is_a * Deleted GO:0045560 --OBO_REL:is_a--> GO:0006417 * Copied GO:0045560 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0045563 --OBO_REL:is_a--> GO:0017148 * Copied GO:0045563 to GO:0010558 with type OBO_REL:is_a * Deleted GO:0045564 --OBO_REL:is_a--> GO:0045727 * Copied GO:0045564 to GO:0010557 with type OBO_REL:is_a * Deleted GO:0045720 --OBO_REL:is_a--> GO:0017148 * Copied GO:0045720 to GO:0010558 with type OBO_REL:is_a * Deleted GO:0045726 --OBO_REL:is_a--> GO:0045727 * Copied GO:0045726 to GO:0010557 with type OBO_REL:is_a * Copied GO:0045727 to GO:0010557 with type OBO_REL:is_a * Deleted GO:0046984 --OBO_REL:is_a--> GO:0006417 * Copied GO:0046984 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0046985 --OBO_REL:is_a--> GO:0045727 * Copied GO:0046985 to GO:0010557 with type OBO_REL:is_a * Deleted GO:0046986 --OBO_REL:is_a--> GO:0017148 * Copied GO:0046986 to GO:0010558 with type OBO_REL:is_a * Deleted GO:0050758 --OBO_REL:is_a--> GO:0006417 * Copied GO:0050758 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0050759 --OBO_REL:is_a--> GO:0045727 * Copied GO:0050759 to GO:0010557 with type OBO_REL:is_a * Deleted GO:0050760 --OBO_REL:is_a--> GO:0017148 * Copied GO:0050760 to GO:0010558 with type OBO_REL:is_a * Deleted GO:0051543 --OBO_REL:is_a--> GO:0006417 * Copied GO:0051543 to GO:0010559 with type OBO_REL:is_a * Copied GO:0051544 to GO:0010560 with type OBO_REL:is_a * Copied GO:0051545 to GO:0010561 with type OBO_REL:is_a * Deleted GO:0051769 --OBO_REL:is_a--> GO:0006417 * Copied GO:0051769 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0051770 --OBO_REL:is_a--> GO:0045727 * Copied GO:0051770 to GO:0010557 with type OBO_REL:is_a * Deleted GO:0051771 --OBO_REL:is_a--> GO:0017148 * Copied GO:0051771 to GO:0010558 with type OBO_REL:is_a * Deleted GO:0051772 --OBO_REL:is_a--> GO:0006417 * Copied GO:0051772 to GO:0010556 with type OBO_REL:is_a * Deleted GO:0051773 --OBO_REL:is_a--> GO:0045727 * Copied GO:0051773 to GO:0010557 with type OBO_REL:is_a * Deleted GO:0051774 --OBO_REL:is_a--> GO:0017148 * Copied GO:0051774 to GO:0010558 with type OBO_REL:is_a From gocvs at genome.stanford.edu Thu Mar 6 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Thu, 6 Mar 2008 21:30:45 -0800 (PST) Subject: [Go-diff] GO update 03/06/2008 Message-ID: <200803070530.VAA21428@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.723 by 5.724 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034290 * Created object of type obo:TERM with id GO:0034291 * Created object of type obo:TERM with id GO:0034292 * Populated new object GO:0034290 (macro) * Changed name of GO:0034290 from "" to "holin activity" * Set definition of GO:0034290 to "Catalysis of the temporally-regulated formation of a transmembrane protein hole that directly or indirectly allows murein hydrolyases to access their cell wall substrate." * Added definition dbxref GOC:jh2 to GO:0034290 * Added definition dbxref PMID:1406491 to GO:0034290 * Copied GO:0034290 to GO:0015267 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034290 * Populated new object GO:0034291 (macro) * Changed name of GO:0034291 from "" to "canonical holin activity" * Set definition of GO:0034291 to "Catalysis of the temporally-regulated formation of a non-specific transmembrane protein hole that allows release of a fully-folded phage-encoded endolysin (murein-degradase) from the cell." * Added definition dbxref GOC:jh2 to GO:0034291 * Added definition dbxref GOC:mah to GO:0034291 * Added definition dbxref PMID:1406491 to GO:0034291 * Copied GO:0034291 to GO:0034290 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034291 * Populated new object GO:0034292 (macro) * Changed name of GO:0034292 from "" to "pinholin activity" * Set definition of GO:0034292 to "Catalysis of the temporally-regulated formation of a transmembrane protein hole that allows the passage of ions, causing a lethal, irreversible depolarization of the cell membrane." * Added definition dbxref GOC:jh2 to GO:0034292 * Added definition dbxref GOC:mah to GO:0034292 * Added definition dbxref PMID:1406491 to GO:0034292 * Copied GO:0034292 to GO:0034290 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034292 * Changed definition of GO:0000045 from "The formation of a double membrane-bound structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm." to "The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm." * Changed definition of GO:0000046 from "The fusion of an autophagic vacuole with a vacuole (yeast) or lysosome (e.g. mammals and insects). In the case of yeast, inner membrane-bound structures (autophagic bodies) appear in the vacuole." to "The fusion of an autophagic vacuole with a vacuole (yeast) or lysosome (e.g. mammals and insects). In the case of yeast, inner membrane-bounded structures (autophagic bodies) appear in the vacuole." * Changed definition of GO:0000324 from "The vacuole is a large, membrane-bound organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure." to "The vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure." * Changed definition of GO:0000327 from "A membrane-bound compartment containing crystals of phytic acid and proteins characteristic of a lytic vacuole, found within a storage vacuole." to "A membrane-bounded compartment containing crystals of phytic acid and proteins characteristic of a lytic vacuole, found within a storage vacuole." * added secondary id GO:0003889 to GO:0003887 * added secondary id GO:0003890 to GO:0003887 * added secondary id GO:0003891 to GO:0003887 * added secondary id GO:0003893 to GO:0003887 * added secondary id GO:0003894 to GO:0003887 * added secondary id GO:0003895 to GO:0003887 * added secondary id GO:0008723 to GO:0003887 * added secondary id GO:0015999 to GO:0003887 * added secondary id GO:0016000 to GO:0003887 * added secondary id GO:0016448 to GO:0003887 * added secondary id GO:0016449 to GO:0003887 * added secondary id GO:0016450 to GO:0003887 * added secondary id GO:0016451 to GO:0003887 * added secondary id GO:0016452 to GO:0003887 * added secondary id GO:0019984 to GO:0003887 * Added general dbxref EC:2.7.7.- to GO:0003887 * Added general dbxref Reactome:11738 to GO:0003887 * Added general dbxref Reactome:26112 to GO:0003887 * Added general dbxref Reactome:69114 to GO:0003887 * Added synonym "alpha DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "beta DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "delta DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "DNA polymerase alpha" to GO:0003887 * Added general dbxref EC:2.7.7.7 to synonym DNA polymerase alpha of GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "DNA polymerase beta" to GO:0003887 * Added general dbxref EC:2.7.7.7 to synonym DNA polymerase beta of GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "DNA polymerase gamma" to GO:0003887 * Added general dbxref EC:2.7.7.7 to synonym DNA polymerase gamma of GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "DNA polymerase V activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "epsilon DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "eta DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "gamma DNA-directed DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "iota DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "kappa DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "lambda DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "mu DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "nu DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "sigma DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "theta DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Added synonym "zeta DNA polymerase activity" to GO:0003887 * Changed synonym scope of GO:0003887 from "Related" to "Narrow" * Deleted GO:0003889 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0003889 * Deleted GO:0003890 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0003890 * Deleted GO:0003891 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0003891 * Deleted GO:0003893 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0003893 * Deleted GO:0003894 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0003894 * Deleted GO:0003895 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0003895 * added secondary id GO:0004785 to GO:0004784 * added secondary id GO:0008382 to GO:0004784 * added secondary id GO:0008383 to GO:0004784 * added secondary id GO:0016954 to GO:0004784 * Added synonym "copper, zinc superoxide dismutase activity" to GO:0004784 * Changed synonym scope of GO:0004784 from "Related" to "Narrow" * Added synonym "Cu,Zn-SOD" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym Cu,Zn-SOD of GO:0004784 * Added synonym "Cu-Zn superoxide dismutase activity activity" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym Cu-Zn superoxide dismutase activity activity of GO:0004784 * Changed synonym scope of GO:0004784 from "Related" to "Narrow" * Added synonym "cuprein" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym cuprein of GO:0004784 * Added synonym "cytocuprein" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym cytocuprein of GO:0004784 * Added synonym "erythrocuprein" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym erythrocuprein of GO:0004784 * Added synonym "Fe-SOD" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym Fe-SOD of GO:0004784 * Added synonym "ferrisuperoxide dismutase activity" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym ferrisuperoxide dismutase activity of GO:0004784 * Changed synonym scope of GO:0004784 from "Related" to "Narrow" * Added synonym "hemocuprein" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym hemocuprein of GO:0004784 * Added synonym "hepatocuprein" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym hepatocuprein of GO:0004784 * Added synonym "iron superoxide dismutase activity" to GO:0004784 * Changed synonym scope of GO:0004784 from "Related" to "Narrow" * Added synonym "iron superoxide oxidoreductase" to GO:0004784 * Added synonym "manganese superoxide dismutase activity" to GO:0004784 * Changed synonym scope of GO:0004784 from "Related" to "Narrow" * Added synonym "manganese superoxide oxidoreductase" to GO:0004784 * Added synonym "Mn-SOD" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym Mn-SOD of GO:0004784 * Added synonym "nickel superoxide dismutase activity" to GO:0004784 * Changed synonym scope of GO:0004784 from "Related" to "Narrow" * Added synonym "nickel superoxide oxidoreductase" to GO:0004784 * Added synonym "SOD-1" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym SOD-1 of GO:0004784 * Added synonym "SOD-2" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym SOD-2 of GO:0004784 * Added synonym "SOD-3" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym SOD-3 of GO:0004784 * Added synonym "SOD-4" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym SOD-4 of GO:0004784 * Added synonym "SODF" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym SODF of GO:0004784 * Added synonym "superoxide dismutase I" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym superoxide dismutase I of GO:0004784 * Added synonym "superoxide dismutase II" to GO:0004784 * Added general dbxref EC:1.15.1.1 to synonym superoxide dismutase II of GO:0004784 * Added synonym "zinc superoxide oxidoreductase" to GO:0004784 * Deleted GO:0004785 --OBO_REL:is_a--> GO:0004784 * Destroyed object GO:0004785 * Changed definition of GO:0005768 from "A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." to "A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." * Changed definition of GO:0006605 from "The process of targeting specific proteins to particular membrane-bound subcellular organelles. Usually requires an organelle specific protein sequence motif." to "The process of targeting specific proteins to particular membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif." * Deleted GO:0008382 --OBO_REL:is_a--> GO:0004784 * Destroyed object GO:0008382 * Deleted GO:0008383 --OBO_REL:is_a--> GO:0004784 * Destroyed object GO:0008383 * Deleted GO:0008723 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0008723 * Deleted GO:0008778 --OBO_REL:is_a--> GO:0016291 * Destroyed object GO:0008778 * added secondary id GO:0016948 to GO:0008901 * added secondary id GO:0016949 to GO:0008901 * added secondary id GO:0016950 to GO:0008901 * added secondary id GO:0016951 to GO:0008901 * Deleted definition dbxref EC:1.18.99.1 from GO:0008901 * Added definition dbxref EC:1.12.7.2 to GO:0008901 * Deleted synonym "1.18.99.1" from GO:0008901 * Added synonym "iron hydrogenase activity" to GO:0008901 * Changed synonym scope of GO:0008901 from "Related" to "Narrow" * Added synonym "iron-only hydrogenase activity" to GO:0008901 * Changed synonym scope of GO:0008901 from "Related" to "Narrow" * Added synonym "Ni-Fe hydrogenase activity" to GO:0008901 * Changed synonym scope of GO:0008901 from "Related" to "Narrow" * Added synonym "Ni-Fe-Se hydrogenase activity" to GO:0008901 * Changed synonym scope of GO:0008901 from "Related" to "Narrow" * Added synonym "nickel hydrogenase activity" to GO:0008901 * Changed synonym scope of GO:0008901 from "Related" to "Narrow" * Added synonym "nickel-iron hydrogenase activity" to GO:0008901 * Changed synonym scope of GO:0008901 from "Related" to "Narrow" * Added synonym "nickel-iron-selenium hydrogenase activity" to GO:0008901 * Changed synonym scope of GO:0008901 from "Related" to "Narrow" * Changed definition of GO:0009579 from "A membraneous cellular structure that bears the photosynthetic pigments in photosynthetic organisms. In prokaryotes the thylakoids are of various shapes and are attached to the plasma membrane. In eukaryotes they are flattened, membrane-bound disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." to "A membraneous cellular structure that bears the photosynthetic pigments in photosynthetic organisms. In prokaryotes the thylakoids are of various shapes and are attached to the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." * Deleted GO:0015999 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0015999 * Deleted GO:0016000 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0016000 * Changed name of GO:0016023 from "cytoplasmic membrane-bound vesicle" to "cytoplasmic membrane-bounded vesicle" * Changed definition of GO:0016023 from "A membrane-bound vesicle found in the cytoplasm of the cell." to "A membrane-bounded vesicle found in the cytoplasm of the cell." * Deleted synonym "cytoplasmic membrane bound vesicle" from GO:0016023 * Added synonym "cytoplasmic membrane bounded vesicle" to GO:0016023 * Changed synonym scope of GO:0016023 from "Related" to "Exact" * Added synonym "cytoplasmic membrane-enclosed vesicle" to GO:0016023 * Changed synonym scope of GO:0016023 from "Related" to "Exact" * Changed definition of GO:0016079 from "Fusion of intracellular membrane-bound vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft." to "Fusion of intracellular membrane-bounded vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft." * Changed definition of GO:0016197 from "The directed movement of substances into, out of or mediated by an endosome, a membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." to "The directed movement of substances into, out of or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." * added secondary id GO:0008778 to GO:0016291 * added secondary id GO:0016292 to GO:0016291 * Added synonym "acyl-CoA thioesterase I activity" to GO:0016291 * Changed synonym scope of GO:0016291 from "Related" to "Narrow" * Added synonym "acyl-CoA thioesterase II activity" to GO:0016291 * Changed synonym scope of GO:0016291 from "Related" to "Narrow" * Deleted GO:0016292 --OBO_REL:is_a--> GO:0016291 * Destroyed object GO:0016292 * Deleted GO:0016448 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0016448 * Deleted GO:0016449 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0016449 * Deleted GO:0016450 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0016450 * Deleted GO:0016451 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0016451 * Deleted GO:0016452 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0016452 * Deleted GO:0016948 --OBO_REL:is_a--> GO:0008901 * Destroyed object GO:0016948 * Deleted GO:0016949 --OBO_REL:is_a--> GO:0008901 * Deleted GO:0016951 --OBO_REL:is_a--> GO:0016949 * Deleted GO:0016950 --OBO_REL:is_a--> GO:0016949 * Destroyed object GO:0016949 * Deleted GO:0016950 --OBO_REL:is_a--> GO:0016949 * Destroyed object GO:0016950 * Deleted GO:0016951 --OBO_REL:is_a--> GO:0016949 * Destroyed object GO:0016951 * Deleted GO:0016954 --OBO_REL:is_a--> GO:0004784 * Destroyed object GO:0016954 * Deleted GO:0019984 --OBO_REL:is_a--> GO:0003887 * Destroyed object GO:0019984 * Changed definition of GO:0020015 from "Membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis." to "A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis." * Added synonym "cell wall-enclosed periplasmic space" to GO:0030287 * Changed synonym scope of GO:0030287 from "Related" to "Exact" * Added synonym "outer membrane-enclosed periplasmic space" to GO:0030288 * Changed synonym scope of GO:0030288 from "Related" to "Exact" * Changed name of GO:0031988 from "membrane-bound vesicle" to "membrane-bounded vesicle" * Added synonym "membrane-enclosed vesicle" to GO:0031988 * Changed synonym scope of GO:0031988 from "Related" to "Exact" * Changed definition of GO:0032046 from "A membrane-bound flattened sac that is formed during micropexophagy between the membrane tips of an engulfing vacuole, completing the engulfment and sequestration of peroxisomes from the cytosol, and forming a micropexophagic body within the lumen of the vacuole." to "A membrane-bounded flattened sac that is formed during micropexophagy between the membrane tips of an engulfing vacuole, completing the engulfment and sequestration of peroxisomes from the cytosol, and forming a micropexophagic body within the lumen of the vacuole." * Changed definition of GO:0032047 from "A double-membrane-bounde organelle that functions in iron-sulfur protein maturation; evolutionarily derived from mitochondria." to "A double-membrane-bounded organelle that functions in iron-sulfur protein maturation; evolutionarily derived from mitochondria." * Changed definition of GO:0032456 from "The directed movement of membrane-bound vesicles from recycling endosomes back to the plasma membrane where they are recycled for further rounds of transport." to "The directed movement of membrane-bounded vesicles from recycling endosomes back to the plasma membrane where they are recycled for further rounds of transport." * Changed definition of GO:0032457 from "The directed movement of membrane-bound vesicles from peripheral endocytic compartments back to the plasma membrane where they are recycled for further rounds of transport." to "The directed movement of membrane-bounded vesicles from peripheral endocytic compartments back to the plasma membrane where they are recycled for further rounds of transport." * Changed definition of GO:0032458 from "The directed movement of membrane-bound vesicles from deep (non-peripheral) compartments endocytic compartments back to the plasma membrane where they are recycled for further rounds of transport." to "The directed movement of membrane-bounded vesicles from deep (non-peripheral) compartments endocytic compartments back to the plasma membrane where they are recycled for further rounds of transport." * Changed name of GO:0033648 from "host intracellular membrane-bound organelle" to "host intracellular membrane-bounded organelle" * Added synonym "host intracellular membrane-enclosed organelle" to GO:0033648 * Changed synonym scope of GO:0033648 from "Related" to "Exact" * Changed definition of GO:0033675 from "A membrane-bound vesicle found near the apical, or pericanalicular, membrane of a hepatocyte; contains proteins involved in bile salt transport and other fluid and solute transport processes." to "A membrane-bounded vesicle found near the apical, or pericanalicular, membrane of a hepatocyte; contains proteins involved in bile salt transport and other fluid and solute transport processes." * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Changed definition of GO:0042588 from "A membrane-bound, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme." to "A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme." * Changed definition of GO:0042735 from "Membrane-bound plant organelle found in the developing endosperm, contains storage proteins." to "A membrane-bounded plant organelle found in the developing endosperm, contains storage proteins." * Changed name of GO:0043227 from "membrane-bound organelle" to "membrane-bounded organelle" * Added synonym "membrane-enclosed organelle" to GO:0043227 * Changed synonym scope of GO:0043227 from "Related" to "Exact" * Changed name of GO:0043228 from "non-membrane-bound organelle" to "non-membrane-bounded organelle" * Added synonym "non-membrane-enclosed organelle" to GO:0043228 * Changed synonym scope of GO:0043228 from "Related" to "Exact" * Changed name of GO:0043231 from "intracellular membrane-bound organelle" to "intracellular membrane-bounded organelle" * Added synonym "intracellular membrane-enclosed organelle" to GO:0043231 * Changed synonym scope of GO:0043231 from "Related" to "Exact" * Changed name of GO:0043232 from "intracellular non-membrane-bound organelle" to "intracellular non-membrane-bounded organelle" * Added synonym "intracellular non-membrane-enclosed organelle" to GO:0043232 * Changed synonym scope of GO:0043232 from "Related" to "Exact" * Changed name of GO:0043264 from "extracellular non-membrane-bound organelle" to "extracellular non-membrane-bounded organelle" * Added synonym "extracellular non-membrane-enclosed organelle" to GO:0043264 * Changed synonym scope of GO:0043264 from "Related" to "Exact" * Changed definition of GO:0044440 from "Any constituent part of an endosome, a membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." to "Any constituent part of an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." * Changed definition of GO:0045009 from "An intracellular membrane-bound particle found in fungi and containing chitin synthase; it synthesizes chitin microfibrils. Chitin synthase activity exists in chitosomes and they are proposed to act as a reservoir for regulated transport of chitin synthase enzymes to the division septum." to "An intracellular membrane-bounded particle found in fungi and containing chitin synthase; it synthesizes chitin microfibrils. Chitin synthase activity exists in chitosomes and they are proposed to act as a reservoir for regulated transport of chitin synthase enzymes to the division septum." * Changed definition of GO:0048489 from "The directed movement of substances in synaptic membrane-bound vesicles within the neuron along the cytoskeleton either toward or away from the neuronal cell body." to "The directed movement of substances in synaptic membrane-bounded vesicles within the neuron along the cytoskeleton either toward or away from the neuronal cell body." * Changed definition of GO:0048490 from "The directed movement of substances in synaptic membrane-bound vesicles within the neuron, along the cytoskeleton, away from the neuronal cell body." to "The directed movement of substances in synaptic membrane-bounded vesicles within the neuron, along the cytoskeleton, away from the neuronal cell body." * Changed definition of GO:0048491 from "The directed movement of substances in synaptic membrane-bound vesicles within the neuron, along the cytoskeleton, toward the neuronal cell body." to "The directed movement of substances in synaptic membrane-bounded vesicles within the neuron, along the cytoskeleton, toward the neuronal cell body." * Changed definition of GO:0048770 from "A small, subcellular membrane-bound vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes." to "A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes." * Changed definition of GO:0051036 from "Any process that modulates the volume of an endosome, a membrane-bound organelle that carries materials newly ingested by endocytosis." to "Any process that modulates the volume of an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis." * Changed definition of GO:0055107 from "The directed movement of proteins from the Golgi to a secretory granule. The secretory granule is a membrane-bound particle, usually protein, formed in the granular endoplasmic reticulum and the Golgi complex." to "The directed movement of proteins from the Golgi to a secretory granule. The secretory granule is a membrane-bounded particle, usually protein, formed in the granular endoplasmic reticulum and the Golgi complex." * Changed name of GO:0060205 from "cytoplasmic membrane-bound vesicle lumen" to "cytoplasmic membrane-bounded vesicle lumen" * Changed definition of GO:0060205 from "The volume enclosed by the membrane of a cytoplasmic membrane-bound vesicle." to "The volume enclosed by the membrane of a cytoplasmic membrane-bounded vesicle." * Added synonym "cytoplasmic membrane-enclosed vesicle lumen" to GO:0060205 * Changed synonym scope of GO:0060205 from "Related" to "Exact" * Changed name of GO:0065010 from "extracellular membrane-bound organelle" to "extracellular membrane-bounded organelle" * Added synonym "extracellular membrane-enclosed organelle" to GO:0065010 * Changed synonym scope of GO:0065010 from "Related" to "Exact" From gocvs at genome.stanford.edu Fri Mar 7 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Fri, 7 Mar 2008 21:30:45 -0800 (PST) Subject: [Go-diff] GO update 03/07/2008 Message-ID: <200803080530.VAA27451@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.724 by 5.726 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0010562 * Created object of type obo:TERM with id GO:0010563 * Created object of type obo:TERM with id GO:0010564 * Created object of type obo:TERM with id GO:0010565 * Created object of type obo:TERM with id GO:0010566 * Created object of type obo:TERM with id GO:0010567 * Created object of type obo:TERM with id GO:0034293 * Created object of type obo:TERM with id GO:0034294 * Created object of type obo:TERM with id GO:0034295 * Created object of type obo:TERM with id GO:0034296 * Created object of type obo:TERM with id GO:0034297 * Created object of type obo:TERM with id GO:0034298 * Created object of type obo:TERM with id GO:0034299 * Created object of type obo:TERM with id GO:0034300 * Created object of type obo:TERM with id GO:0034301 * Created object of type obo:TERM with id GO:0034302 * Created object of type obo:TERM with id GO:0034303 * Created object of type obo:TERM with id GO:0034304 * Created object of type obo:TERM with id GO:0034305 * Created object of type obo:TERM with id GO:0034306 * Created object of type obo:TERM with id GO:0034307 * Created object of type obo:TERM with id GO:0034308 * Created object of type obo:TERM with id GO:0034309 * Created object of type obo:TERM with id GO:0034310 * Created object of type obo:TERM with id GO:0034311 * Created object of type obo:TERM with id GO:0034312 * Created object of type obo:TERM with id GO:0034313 * Populated new object GO:0010562 (macro) * Changed name of GO:0010562 from "" to "positive regulation of phosphorus metabolic process" * Set definition of GO:0010562 to "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus." * Added definition dbxref GOC:dph to GO:0010562 * Added definition dbxref GOC:tb to GO:0010562 * Copied GO:0010562 to GO:0051174 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010562 * Populated new object GO:0010563 (macro) * Changed name of GO:0010563 from "" to "negative regulation of phosphorus metabolic process" * Set definition of GO:0010563 to "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus." * Added definition dbxref GOC:dph to GO:0010563 * Added definition dbxref GOC:tb to GO:0010563 * Copied GO:0010563 to GO:0051174 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010563 * Populated new object GO:0010564 (macro) * Changed name of GO:0010564 from "" to "regulation of cell cycle process" * Set definition of GO:0010564 to "Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events." * Added definition dbxref GOC:dph to GO:0010564 * Added definition dbxref GOC:tb to GO:0010564 * Copied GO:0010564 to GO:0050794 with type OBO_REL:is_a * Copied GO:0010564 to GO:0022402 with type part_of * Assigned namespace "biological_process" to GO:0010564 * Populated new object GO:0010565 (macro) * Changed name of GO:0010565 from "" to "regulation of ketone metabolic process" * Set definition of GO:0010565 to "Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." * Added definition dbxref GOC:dph to GO:0010565 * Added definition dbxref GOC:tb to GO:0010565 * Copied GO:0010565 to GO:0031323 with type OBO_REL:is_a * Copied GO:0010565 to GO:0042180 with type part_of * Assigned namespace "biological_process" to GO:0010565 * Populated new object GO:0010566 (macro) * Changed name of GO:0010566 from "" to "regulation of ketone biosynthetic process" * Set definition of GO:0010566 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells." * Added definition dbxref GOC:dph to GO:0010566 * Added definition dbxref GOC:tb to GO:0010566 * Copied GO:0010566 to GO:0010565 with type OBO_REL:is_a * Copied GO:0010566 to GO:0031326 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010566 * Populated new object GO:0010567 (macro) * Changed name of GO:0010567 from "" to "regulation of ketone catabolic process" * Set definition of GO:0010567 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells." * Added definition dbxref GOC:dph to GO:0010567 * Added definition dbxref GOC:tb to GO:0010567 * Copied GO:0010567 to GO:0031329 with type OBO_REL:is_a * Copied GO:0010567 to GO:0010565 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010567 * Populated new object GO:0034293 (macro) * Changed name of GO:0034293 from "" to "sexual sporulation" * Set definition of GO:0034293 to "The formation of spores derived from the products of meiosis." * Added definition dbxref GOC:mah to GO:0034293 * Added synonym "meiotic spore formation" to GO:0034293 * Changed synonym scope of GO:0034293 from "Related" to "Exact" * Added synonym "meiotic sporulation" to GO:0034293 * Changed synonym scope of GO:0034293 from "Related" to "Exact" * Added synonym "sexual spore formation" to GO:0034293 * Changed synonym scope of GO:0034293 from "Related" to "Exact" * Copied GO:0034293 to GO:0030435 with type OBO_REL:is_a * Copied GO:0034293 to GO:0048610 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034293 * Populated new object GO:0034294 (macro) * Changed name of GO:0034294 from "" to "sexual spore wall assembly" * Set definition of GO:0034294 to "The chemical reactions and pathways resulting in the formation of the specialized envelope lying outside the cell membrane of a spore derived from a product of meiosis." * Added definition dbxref GOC:mah to GO:0034294 * Added GO:0034294 to category gosubset_prok * Added synonym "sexual spore wall formation" to GO:0034294 * Changed synonym scope of GO:0034294 from "Related" to "Exact" * Copied GO:0034294 to GO:0030436 with type part_of * Copied GO:0034294 to GO:0042244 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034294 * Populated new object GO:0034295 (macro) * Changed name of GO:0034295 from "" to "basidiospore formation" * Set definition of GO:0034295 to "The process by which spores form outside a specialized end cell known as a basidium. Basidia are characteristic of the basidiomycete fungi (phylum Basidiomycota), and give rise to spores that each contain a haploid nucleus that is the product of meiosis. The spores are usually attached to the basidium by short spikes called sterigmata (singular: sterigma). In most basidiomycetes there are four sterigmata (and four spores) to a basidium." * Added definition dbxref GOC:ds to GO:0034295 * Added definition dbxref GOC:mah to GO:0034295 * Added definition dbxref http://www.gsbs.utmb.edu/microbook/ch073.htm to GO:0034295 * Added definition dbxref http://www.ilmyco.gen.chicago.il.us/Terms/basid133.html to GO:0034295 * Copied GO:0034295 to GO:0034293 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034295 * Populated new object GO:0034296 (macro) * Changed name of GO:0034296 from "" to "zygospore formation" * Set definition of GO:0034296 to "The process by which zygospores are formed. Zygospores are characteristic of the zygomycete fungi (phylum Zygomycota) thick-walled and darkly colored, and usually heavily ornamented as well, with many spines or ridges. It is formed between two specialized organs called suspensors, which are themselves usually heavily ornamented, one from each mating partner. The zygospore forms between them and then breaks away." * Added definition dbxref GOC:ds to GO:0034296 * Added definition dbxref GOC:mah to GO:0034296 * Added definition dbxref http://www.ilmyco.gen.chicago.il.us/Terms/zygos581.html to GO:0034296 * Copied GO:0034296 to GO:0034293 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034296 * Populated new object GO:0034297 (macro) * Changed name of GO:0034297 from "" to "oidium formation" * Set definition of GO:0034297 to "The process by which oidia, a type of asexual spore found in fungi, are formed. Oidia are borne a few at a time on very simple hyphae that protrude a short distance into the substrate, and are usually presumed not to constitute the main reproductive strategy of the fungus." * Added definition dbxref GOC:mah to GO:0034297 * Added definition dbxref http://www.ilmyco.gen.chicago.il.us/Terms/oidiu163.html to GO:0034297 * Copied GO:0034297 to GO:0030436 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034297 * Populated new object GO:0034298 (macro) * Changed name of GO:0034298 from "" to "arthrospore formation" * Set definition of GO:0034298 to "The formation of conidia by the conversion of a pre-existing hypha. An arthrospore is produced by the last cell on a hypha breaking off and dispersing. Usually the walls thicken and the cell(s) separates before swelling of each spore. Sometimes further septa form in each cell prior to disarticulation." * Added definition dbxref GOC:mah to GO:0034298 * Added definition dbxref http://bugs.bio.usyd.edu.au/Mycology/Glossary/glossary_a_b.shtml#arthrospore to GO:0034298 * Added definition dbxref http://www.ilmyco.gen.chicago.il.us/Terms/arthr620.html to GO:0034298 * Added synonym "arthroconidium formation" to GO:0034298 * Added general dbxref http://medical.merriam-webster.com/medical/medical?book=Medical&va=arthroconidium to synonym arthroconidium formation of GO:0034298 * Changed synonym scope of GO:0034298 from "Related" to "Exact" * Copied GO:0034298 to GO:0048315 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034298 * Populated new object GO:0034299 (macro) * Changed name of GO:0034299 from "" to "blastospore formation" * Set definition of GO:0034299 to "The formation of produced from a vegetative mother cell by budding. Blastospores are a type of asexual spore found in some fungi, including Candida species and the class Glomeromycota." * Added definition dbxref GOC:ds to GO:0034299 * Added definition dbxref ISBN:?? to GO:0034299 * Added synonym "blastoconidium formation" to GO:0034299 * Added general dbxref http://cancerweb.ncl.ac.uk/cgi-bin/omd?Blastoconidium to synonym blastoconidium formation of GO:0034299 * Changed synonym scope of GO:0034299 from "Related" to "Exact" * Copied GO:0034299 to GO:0048315 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034299 * Populated new object GO:0034300 (macro) * Changed name of GO:0034300 from "" to "sporangiospore formation" * Set definition of GO:0034300 to "The process by which sporangiospores, a type of asexual spore found in fungi, are formed. Sporangiospores are formed within sac-like structure, the sporangium, following the division of the cytoplasm" * Added definition dbxref GO:ds to GO:0034300 * Added definition dbxref GOC:mah to GO:0034300 * Added definition dbxref http://bugs.bio.usyd.edu.au/Mycology/Glossary/glossary_n_z.shtml to GO:0034300 * Copied GO:0034300 to GO:0030436 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034300 * Populated new object GO:0034301 (macro) * Changed name of GO:0034301 from "" to "endospore formation" * Set definition of GO:0034301 to "The process by which a cell gives rise to an endospore, a dormant, highly resistant spore with a thick wall that forms within the mother cell. Endospores are produced by some low G+C Gram-positive bacteria in response to harsh conditions." * Added definition dbxref GOC:ds to GO:0034301 * Added definition dbxref GOC:mah to GO:0034301 * Added definition dbxref http://howie.myweb.uga.edu/introduction.html to GO:0034301 * Copied GO:0034301 to GO:0030436 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034301 * Populated new object GO:0034302 (macro) * Changed name of GO:0034302 from "" to "akinete formation" * Set definition of GO:0034302 to "The process by which an akinete, a thick-walled (encysted) dormant cell derived from the enlargement of a vegetative cell, is formed. Akinetes typically have granular cytoplasm, are more resistant to environmental extremes than vegetative cells, and are characteristic of several groups of Cyanobacteria." * Added definition dbxref GOC:ds to GO:0034302 * Added definition dbxref GOC:mah to GO:0034302 * Added definition dbxref http://www.msu.edu/course/bot/423/algalglossary.htm#Reproductive to GO:0034302 * Added definition dbxref PMID:11948167 to GO:0034302 * Copied GO:0034302 to GO:0030436 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034302 * Populated new object GO:0034303 (macro) * Changed name of GO:0034303 from "" to "myxospore formation" * Set definition of GO:0034303 to "The process by which differentiated, resting cells are formed, usually within a fruiting body by Myxobacteria. The myxospore is more resistant to high temperature, dessication, and UV than vegetative myxobacteria." * Added definition dbxref GOC:ds to GO:0034303 * Added definition dbxref ISBN:0122268008 to GO:0034303 * Copied GO:0034303 to GO:0030436 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034303 * Populated new object GO:0034304 (macro) * Changed name of GO:0034304 from "" to "actinomycete-type spore formation" * Set definition of GO:0034304 to "The process by which differentiated, resting cells are formed from a substrate mycelium; characteristic of many members of the order Actinomycetales." * Added definition dbxref GOC:ds to GO:0034304 * Added definition dbxref ISBN:0122268008 to GO:0034304 * Copied GO:0034304 to GO:0030436 with type OBO_REL:is_a * Copied GO:0034304 to GO:0022413 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034304 * Populated new object GO:0034305 (macro) * Changed name of GO:0034305 from "" to "regulation of asexual sporulation" * Set definition of GO:0034305 to "Any process that modulates the frequency, rate or extent of spore formation from the products of mitosis." * Added definition dbxref GOC:mah to GO:0034305 * Added synonym "regulation of asexual spore formation" to GO:0034305 * Changed synonym scope of GO:0034305 from "Related" to "Exact" * Added synonym "regulation of mitotic spore formation" to GO:0034305 * Changed synonym scope of GO:0034305 from "Related" to "Exact" * Added synonym "regulation of mitotic sporulation" to GO:0034305 * Changed synonym scope of GO:0034305 from "Related" to "Exact" * Copied GO:0034305 to GO:0042173 with type OBO_REL:is_a * Copied GO:0034305 to GO:0030436 with type part_of * Assigned namespace "biological_process" to GO:0034305 * Populated new object GO:0034306 (macro) * Changed name of GO:0034306 from "" to "regulation of sexual sporulation" * Set definition of GO:0034306 to "Any process that modulates the frequency, rate or extent of spore formation from the products of meiosis." * Added definition dbxref GOC:mah to GO:0034306 * Added synonym "MAPKKK cascade during sporulation (sensu Fungi)" to GO:0034306 * Changed synonym scope of GO:0034306 from "Related" to "Narrow" * Added synonym "regulation of meiotic spore formation" to GO:0034306 * Changed synonym scope of GO:0034306 from "Related" to "Exact" * Added synonym "regulation of meiotic sporulation" to GO:0034306 * Changed synonym scope of GO:0034306 from "Related" to "Exact" * Added synonym "regulation of sexual spore formation" to GO:0034306 * Changed synonym scope of GO:0034306 from "Related" to "Exact" * Copied GO:0034306 to GO:0034293 with type part_of * Copied GO:0034306 to GO:0042173 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034306 * Populated new object GO:0034307 (macro) * Changed name of GO:0034307 from "" to "regulation of ascospore formation" * Set definition of GO:0034307 to "Any process that modulates the frequency, rate or extent of ascospore formation." * Added definition dbxref GOC:mah to GO:0034307 * Added synonym "MAPKKK cascade during sporulation (sensu Saccharomyces)" to GO:0034307 * Changed synonym scope of GO:0034307 from "Related" to "Narrow" * Copied GO:0034307 to GO:0034306 with type OBO_REL:is_a * Copied GO:0034307 to GO:0030437 with type part_of * Assigned namespace "biological_process" to GO:0034307 * Populated new object GO:0034308 (macro) * Changed name of GO:0034308 from "" to "monohydric alcohol metabolic process" * Set definition of GO:0034308 to "The chemical reactions and pathways involving alcohols, any of a class of compounds containing one hydroxyl group attached to a saturated carbon atom." * Added definition dbxref ChEBI:30879 to GO:0034308 * Added definition dbxref GOC:mah to GO:0034308 * Added synonym "monohydric alcohol metabolism" to GO:0034308 * Changed synonym scope of GO:0034308 from "Related" to "Exact" * Copied GO:0034308 to GO:0006066 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034308 * Populated new object GO:0034309 (macro) * Changed name of GO:0034309 from "" to "monohydric alcohol biosynthetic process" * Set definition of GO:0034309 to "The chemical reactions and pathways resulting in the formation of monohydric alcohols, any of a class of alkyl compounds containing a single hydroxyl group." * Added definition dbxref ChEBI:30879 to GO:0034309 * Added definition dbxref GOC:mah to GO:0034309 * Added GO:0034309 to category gosubset_prok * Added synonym "monohydric alcohol anabolism" to GO:0034309 * Changed synonym scope of GO:0034309 from "Related" to "Exact" * Added synonym "monohydric alcohol biosynthesis" to GO:0034309 * Changed synonym scope of GO:0034309 from "Related" to "Exact" * Added synonym "monohydric alcohol formation" to GO:0034309 * Changed synonym scope of GO:0034309 from "Related" to "Exact" * Added synonym "monohydric alcohol synthesis" to GO:0034309 * Changed synonym scope of GO:0034309 from "Related" to "Exact" * Copied GO:0034309 to GO:0046165 with type OBO_REL:is_a * Copied GO:0034309 to GO:0034308 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034309 * Populated new object GO:0034310 (macro) * Changed name of GO:0034310 from "" to "monohydric alcohol catabolic process" * Set definition of GO:0034310 to "The chemical reactions and pathways resulting in the breakdown of monohydric alcohols, any of a class of compounds containing a single hydroxyl group attached to a saturated carbon atom." * Added definition dbxref ChEBI:30879 to GO:0034310 * Added definition dbxref GOC:mah to GO:0034310 * Added GO:0034310 to category gosubset_prok * Added synonym "monohydric alcohol breakdown" to GO:0034310 * Changed synonym scope of GO:0034310 from "Related" to "Exact" * Added synonym "monohydric alcohol catabolism" to GO:0034310 * Changed synonym scope of GO:0034310 from "Related" to "Exact" * Added synonym "monohydric alcohol degradation" to GO:0034310 * Changed synonym scope of GO:0034310 from "Related" to "Exact" * Copied GO:0034310 to GO:0034308 with type OBO_REL:is_a * Copied GO:0034310 to GO:0046164 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034310 * Populated new object GO:0034311 (macro) * Changed name of GO:0034311 from "" to "diol metabolic process" * Set definition of GO:0034311 to "The chemical reactions and pathways involving a diol, any alcohol containing two hydroxyl groups attached to saturated carbon atoms." * Added definition dbxref ChEBI:23824 to GO:0034311 * Added definition dbxref GOC:mah to GO:0034311 * Added synonym "dihydric alcohol metabolic process" to GO:0034311 * Changed synonym scope of GO:0034311 from "Related" to "Exact" * Added synonym "diol metabolism" to GO:0034311 * Changed synonym scope of GO:0034311 from "Related" to "Exact" * Copied GO:0034311 to GO:0006066 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034311 * Populated new object GO:0034312 (macro) * Changed name of GO:0034312 from "" to "diol biosynthetic process" * Set definition of GO:0034312 to "The chemical reactions and pathways resulting in the formation of a diol, any alcohol containing two hydroxyl groups attached to saturated carbon atoms." * Added definition dbxref ChEBI:23824 to GO:0034312 * Added definition dbxref GOC:mah to GO:0034312 * Added synonym "dihydric alcohol biosynthetic process" to GO:0034312 * Changed synonym scope of GO:0034312 from "Related" to "Exact" * Added synonym "diol anabolism" to GO:0034312 * Changed synonym scope of GO:0034312 from "Related" to "Exact" * Added synonym "diol biosynthesis" to GO:0034312 * Changed synonym scope of GO:0034312 from "Related" to "Exact" * Added synonym "diol formation" to GO:0034312 * Changed synonym scope of GO:0034312 from "Related" to "Exact" * Added synonym "diol synthesis" to GO:0034312 * Changed synonym scope of GO:0034312 from "Related" to "Exact" * Copied GO:0034312 to GO:0046165 with type OBO_REL:is_a * Copied GO:0034312 to GO:0034311 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034312 * Populated new object GO:0034313 (macro) * Changed name of GO:0034313 from "" to "diol catabolic process" * Set definition of GO:0034313 to "The chemical reactions and pathways resulting in the breakdown of a diol, any alcohol containing two hydroxyl groups attached to saturated carbon atoms." * Added definition dbxref ChEBI:23824 to GO:0034313 * Added definition dbxref GOC:mah to GO:0034313 * Added synonym "dihydric alcohol catabolic process" to GO:0034313 * Changed synonym scope of GO:0034313 from "Related" to "Exact" * Added synonym "diol breakdown" to GO:0034313 * Changed synonym scope of GO:0034313 from "Related" to "Exact" * Added synonym "diol catabolism" to GO:0034313 * Changed synonym scope of GO:0034313 from "Related" to "Exact" * Added synonym "diol degradation" to GO:0034313 * Changed synonym scope of GO:0034313 from "Related" to "Exact" * Copied GO:0034313 to GO:0046164 with type OBO_REL:is_a * Copied GO:0034313 to GO:0034311 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034313 * Deleted GO:0001100 --OBO_REL:is_a--> GO:0048523 * Copied GO:0001100 to GO:0045839 with type OBO_REL:is_a * Deleted GO:0001953 --OBO_REL:is_a--> GO:0022408 * Copied GO:0001953 to GO:0007162 with type OBO_REL:is_a * Deleted GO:0002682 --OBO_REL:is_a--> GO:0051239 * Copied GO:0002682 to GO:0050789 with type OBO_REL:is_a * Deleted GO:0002683 --OBO_REL:is_a--> GO:0051241 * Copied GO:0002683 to GO:0048519 with type OBO_REL:is_a * Deleted GO:0002684 --OBO_REL:is_a--> GO:0051240 * Copied GO:0002684 to GO:0048518 with type OBO_REL:is_a * Changed definition of GO:0006066 from "The chemical reactions and pathways involving alcohols, any of a class of alkyl compounds containing a hydroxyl group." to "The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." * Added definition dbxref ChEBI:30879 to GO:0006066 * Deleted GO:0006067 --OBO_REL:is_a--> GO:0006066 * Copied GO:0006067 to GO:0034308 with type OBO_REL:is_a * Deleted GO:0006068 --OBO_REL:is_a--> GO:0046164 * Copied GO:0006068 to GO:0034310 with type OBO_REL:is_a * Deleted GO:0006070 --OBO_REL:is_a--> GO:0006066 * Copied GO:0006070 to GO:0034308 with type OBO_REL:is_a * Deleted GO:0006115 --OBO_REL:is_a--> GO:0046165 * Copied GO:0006115 to GO:0034309 with type OBO_REL:is_a * Deleted GO:0006715 --OBO_REL:is_a--> GO:0046165 * Copied GO:0006715 to GO:0034309 with type OBO_REL:is_a * Deleted GO:0006795 --OBO_REL:is_a--> GO:0019220 * Copied GO:0006795 to GO:0051174 with type OBO_REL:is_a * Copied GO:0007063 to GO:0010564 with type OBO_REL:is_a * Copied GO:0007088 to GO:0010564 with type OBO_REL:is_a * Copied GO:0007096 to GO:0010564 with type OBO_REL:is_a * Deleted GO:0007116 --OBO_REL:is_a--> GO:0050793 * Copied GO:0007553 to GO:0010565 with type OBO_REL:is_a * Copied GO:0007554 to GO:0010566 with type OBO_REL:is_a * Deleted GO:0008634 --OBO_REL:is_a--> GO:0048519 * Copied GO:0010389 to GO:0010564 with type OBO_REL:is_a * Copied GO:0010504 to GO:0010564 with type OBO_REL:is_a * Copied GO:0010520 to GO:0010564 with type OBO_REL:is_a * Deleted GO:0015945 --OBO_REL:is_a--> GO:0006066 * Copied GO:0015945 to GO:0034308 with type OBO_REL:is_a * Deleted GO:0016487 --OBO_REL:is_a--> GO:0006066 * Copied GO:0016487 to GO:0034308 with type OBO_REL:is_a * Deleted GO:0016488 --OBO_REL:is_a--> GO:0046164 * Copied GO:0016488 to GO:0034310 with type OBO_REL:is_a * Changed definition of GO:0019751 from "The chemical reactions and pathways involving a polyol, any polyhydric alcohol." to "The chemical reactions and pathways involving a polyol, any alcohol containing three or more hydroxyl groups attached to saturated carbon atoms." * Deleted definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) from GO:0019751 * Added definition dbxref ChEBI:26191 to GO:0019751 * Added synonym "polyhydric alcohol metabolic process" to GO:0019751 * Changed synonym scope of GO:0019751 from "Related" to "Exact" * Copied GO:0030071 to GO:0010564 with type OBO_REL:is_a * Changed definition of GO:0030435 from "The formation of spores." to "The process by which a relatively unspecialized cell acquires the specialized features of a spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction. Spores are usually unicellular and may develop into vegetative organisms or gametes. They may be produced asexually or sexually and are of many types." * Deleted definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) from GO:0030435 * Added definition dbxref GOC:mah to GO:0030435 * Added definition dbxref ISBN:0072992913 to GO:0030435 * Changed name of GO:0030436 from "sporulation (sensu Bacteria)" to "asexual sporulation" * Changed definition of GO:0030436 from "The formation of spores as in, but not restricted to, the Bacteria (Bacteria, ncbi_taxonomy_id:2)." to "The formation of spores derived from the products of mitosis." * Added definition dbxref PMID:9529886 to GO:0030436 * Changed synonym scope of GO:0030436 from "Exact" to "Narrow" * Added synonym "asexual spore formation" to GO:0030436 * Changed synonym scope of GO:0030436 from "Related" to "Exact" * Added synonym "mitotic spore formation" to GO:0030436 * Changed synonym scope of GO:0030436 from "Related" to "Exact" * Added synonym "mitotic sporulation" to GO:0030436 * Changed synonym scope of GO:0030436 from "Related" to "Exact" * Added synonym "sporulation (sensu Bacteria)" to GO:0030436 * Changed synonym scope of GO:0030436 from "Related" to "Narrow" * Changed name of GO:0030437 from "sporulation (sensu Fungi)" to "ascospore formation" * Changed definition of GO:0030437 from "The formation of spores as in, but not restricted to, the fungi (Fungi, ncbi_taxonomy_id:4751)." to "The process by which a diploid cell undergoes meiosis, and the meiotic products acquire the specialized features of ascospores. Ascospores are generally found in clusters of four or eight spores within a single mother cell, the ascus, and are characteristic of the ascomycete fungi (phylum Ascomycota)." * Added definition dbxref PMID:16339736 to GO:0030437 * Deleted synonym "ascospore formation" from GO:0030437 * Changed synonym scope of GO:0030437 from "Exact" to "Broad" * Added synonym "sporulation (sensu Fungi)" to GO:0030437 * Changed synonym scope of GO:0030437 from "Related" to "Broad" * Deleted GO:0030437 --OBO_REL:is_a--> GO:0048622 * Copied GO:0030437 to GO:0034293 with type OBO_REL:is_a * Changed name of GO:0030476 from "fungal-type spore wall assembly" to "ascospore wall assembly" * Changed definition of GO:0030476 from "Process by which the spore nucleus becomes surrounded by a specialized spore wall. Occurs by deposition of spore wall components in the lumenal space between the outer and inner leaflets of the prospore membrane." to "The process by which the ascospore nucleus becomes surrounded by a specialized spore wall. Occurs by deposition of spore wall components in the lumenal space between the outer and inner leaflets of the prospore membrane." * Changed name of GO:0031321 from "prospore formation" to "ascospore-type prospore formation" * Changed definition of GO:0031321 from "During fungal sporulation, the process by which each haploid nucleus becomes encapsulated by a double membrane." to "During ascospore formation, the process by which each haploid nucleus becomes encapsulated by a double membrane." * Changed name of GO:0031322 from "prospore-specific spindle pole body modification" to "ascospore-type prospore-specific spindle pole body modification" * Changed definition of GO:0031322 from "Structural modification of the spindle pole body that takes place during the second meiotic division; includes the recruitment of sporulation-specific proteins to the outer plaque to form the meiotic outer plaque (MOP)." to "Structural modification of the spindle pole body that takes place during the second meiotic division during ascospore formation; includes the recruitment of sporulation-specific proteins to the outer plaque to form the meiotic outer plaque (MOP)." * Deleted GO:0031536 --OBO_REL:is_a--> GO:0048522 * Copied GO:0031536 to GO:0045840 with type OBO_REL:is_a * Changed name of GO:0032120 from "prospore membrane formation" to "ascospore-type prospore membrane formation" * Copied GO:0032887 to GO:0010564 with type OBO_REL:is_a * Deleted GO:0033020 --OBO_REL:is_a--> GO:0006066 * Copied GO:0033020 to GO:0034308 with type OBO_REL:is_a * Deleted GO:0033021 --OBO_REL:is_a--> GO:0046165 * Copied GO:0033021 to GO:0034309 with type OBO_REL:is_a * Deleted GO:0033022 --OBO_REL:is_a--> GO:0046164 * Copied GO:0033022 to GO:0034310 with type OBO_REL:is_a * Copied GO:0033045 to GO:0010564 with type OBO_REL:is_a * Copied GO:0033261 to GO:0010564 with type OBO_REL:is_a * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Deleted GO:0034077 --OBO_REL:is_a--> GO:0019751 * Copied GO:0034077 to GO:0034311 with type OBO_REL:is_a * Deleted GO:0034078 --OBO_REL:is_a--> GO:0046174 * Copied GO:0034078 to GO:0034313 with type OBO_REL:is_a * Deleted GO:0034079 --OBO_REL:is_a--> GO:0046173 * Copied GO:0034079 to GO:0034312 with type OBO_REL:is_a * Copied GO:0034091 to GO:0010564 with type OBO_REL:is_a * Changed name of GO:0034217 from "spore wall chitin biosynthetic process" to "ascospore wall chitin biosynthetic process" * Changed definition of GO:0034217 from "The chemical reactions and pathways resulting in the formation of spore wall chitin, a linear polysaccharide consisting of P-1,4-linked N-acetyl-D-glucosamine residues, found in the walls of fungal-type spores." to "The chemical reactions and pathways resulting in the formation of ascospore wall chitin, a linear polysaccharide consisting of P-1,4-linked N-acetyl-D-glucosamine residues, found in the walls of ascospores." * Deleted synonym "spore wall chitin anabolism" from GO:0034217 * Deleted synonym "spore wall chitin biosynthesis" from GO:0034217 * Deleted synonym "spore wall chitin formation" from GO:0034217 * Deleted synonym "spore wall chitin synthesis" from GO:0034217 * Added synonym "ascospore wall chitin anabolism" to GO:0034217 * Changed synonym scope of GO:0034217 from "Related" to "Exact" * Added synonym "ascospore wall chitin biosynthesis" to GO:0034217 * Changed synonym scope of GO:0034217 from "Related" to "Exact" * Added synonym "ascospore wall chitin formation" to GO:0034217 * Changed synonym scope of GO:0034217 from "Related" to "Exact" * Added synonym "ascospore wall chitin synthesis" to GO:0034217 * Changed synonym scope of GO:0034217 from "Related" to "Exact" * Changed name of GO:0034218 from "spore wall chitin metabolic process" to "ascospore wall chitin metabolic process" * Changed definition of GO:0034218 from "The chemical reactions and pathways involving spore wall chitin, a linear polysaccharide consisting of P-1,4-linked N-acetyl-D-glucosamine residues, found in the walls of fungal-type spores." to "The chemical reactions and pathways involving ascospore wall chitin, a linear polysaccharide consisting of P-1,4-linked N-acetyl-D-glucosamine residues, found in the walls of ascospores." * Deleted synonym "spore wall chitin metabolism" from GO:0034218 * Added synonym "ascospore wall chitin metabolism" to GO:0034218 * Changed synonym scope of GO:0034218 from "Related" to "Exact" * Changed name of GO:0034223 from "regulation of spore wall chitin biosynthetic process" to "regulation of ascospore wall chitin biosynthetic process" * Changed definition of GO:0034223 from "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of spore wall chitin." to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ascospore wall chitin." * Deleted synonym "regulation of spore wall chitin anabolism" from GO:0034223 * Deleted synonym "regulation of spore wall chitin biosynthesis" from GO:0034223 * Deleted synonym "regulation of spore wall chitin formation" from GO:0034223 * Deleted synonym "regulation of spore wall chitin synthesis" from GO:0034223 * Added synonym "regulation of ascospore wall chitin anabolism" to GO:0034223 * Changed synonym scope of GO:0034223 from "Related" to "Exact" * Added synonym "regulation of ascospore wall chitin biosynthesis" to GO:0034223 * Changed synonym scope of GO:0034223 from "Related" to "Exact" * Added synonym "regulation of ascospore wall chitin formation" to GO:0034223 * Changed synonym scope of GO:0034223 from "Related" to "Exact" * Added synonym "regulation of ascospore wall chitin synthesis" to GO:0034223 * Changed synonym scope of GO:0034223 from "Related" to "Exact" * Changed name of GO:0034232 from "spore wall chitin catabolic process" to "ascospore wall chitin catabolic process" * Changed definition of GO:0034232 from "The chemical reactions and pathways resulting in the breakdown of spore wall chitin, a linear polysaccharide consisting of P-1,4-linked N-acetyl-D-glucosamine residues, found in the walls of fungal-type spores." to "The chemical reactions and pathways resulting in the breakdown of ascospore wall chitin, a linear polysaccharide consisting of P-1,4-linked N-acetyl-D-glucosamine residues, found in the walls of ascospores." * Deleted synonym "spore wall chitin breakdown" from GO:0034232 * Deleted synonym "spore wall chitin catabolism" from GO:0034232 * Deleted synonym "spore wall chitin degradation" from GO:0034232 * Added synonym "ascospore wall chitin breakdown" to GO:0034232 * Changed synonym scope of GO:0034232 from "Related" to "Exact" * Added synonym "ascospore wall chitin catabolism" to GO:0034232 * Changed synonym scope of GO:0034232 from "Related" to "Exact" * Added synonym "ascospore wall chitin degradation" to GO:0034232 * Changed synonym scope of GO:0034232 from "Related" to "Exact" * Changed name of GO:0034234 from "regulation of spore wall chitin catabolic process" to "regulation of ascospore wall chitin catabolic process" * Changed definition of GO:0034234 from "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of spore wall chitin." to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of ascospore wall chitin." * Deleted synonym "regulation of spore wall chitin breakdown" from GO:0034234 * Deleted synonym "regulation of spore wall chitin catabolism" from GO:0034234 * Deleted synonym "regulation of spore wall chitin degradation" from GO:0034234 * Added synonym "regulation of ascospore wall chitin breakdown" to GO:0034234 * Changed synonym scope of GO:0034234 from "Related" to "Exact" * Added synonym "regulation of ascospore wall chitin catabolism" to GO:0034234 * Changed synonym scope of GO:0034234 from "Related" to "Exact" * Added synonym "regulation of ascospore wall chitin degradation" to GO:0034234 * Changed synonym scope of GO:0034234 from "Related" to "Exact" * Copied GO:0040020 to GO:0010564 with type OBO_REL:is_a * Deleted synonym "MAPKKK cascade during sporulation (sensu Fungi)" from GO:0042173 * Deleted synonym "MAPKKK cascade during sporulation (sensu Saccharomyces)" from GO:0042173 * Changed name of GO:0042243 from "spore wall assembly (sensu Bacteria)" to "asexual spore wall assembly" * Changed definition of GO:0042243 from "The chemical reactions and pathways resulting in the formation of the specialized envelope lying outside the cell membrane of a spore, as in, but not restricted to, the Bacteria (Bacteria, ncbi_taxonomy_id:2)." to "The chemical reactions and pathways resulting in the formation of the specialized envelope lying outside the cell membrane of a spore derived from a product of mitosis." * Added synonym "asexual spore wall formation" to GO:0042243 * Changed synonym scope of GO:0042243 from "Related" to "Exact" * Added synonym "spore wall assembly (sensu Bacteria)" to GO:0042243 * Changed synonym scope of GO:0042243 from "Related" to "Narrow" * Deleted GO:0042243 --OBO_REL:is_a--> GO:0030436 * Copied GO:0042243 to GO:0030436 with type part_of * Added synonym "spore wall formation" to GO:0042244 * Changed synonym scope of GO:0042244 from "Related" to "Exact" * Changed name of GO:0042763 from "immature spore" to "intracellular immature spore" * Changed name of GO:0042764 from "prospore" to "ascospore-type prospore" * Changed definition of GO:0042764 from "An immature spore, of the type seen in some species of fungi and protist, undergoing development, usually consisting of nucleic acid, prospore membrane(s) that encase the nucleic acid, and ultimately a cell wall that covers the membrane(s)." to "An immature spore, of the type observed in ascopore-forming fungi, undergoing development; usually consists of nucleic acid, prospore membrane(s) that encase the nucleic acid, and ultimately a cell wall that covers the membrane(s)." * Changed synonym scope of GO:0042764 from "Exact" to "Broad" * Deleted GO:0042844 --OBO_REL:is_a--> GO:0006066 * Copied GO:0042844 to GO:0034311 with type OBO_REL:is_a * Deleted GO:0042845 --OBO_REL:is_a--> GO:0046165 * Copied GO:0042845 to GO:0034312 with type OBO_REL:is_a * Deleted GO:0042846 --OBO_REL:is_a--> GO:0046164 * Copied GO:0042846 to GO:0034313 with type OBO_REL:is_a * Deleted GO:0042985 --OBO_REL:is_a--> GO:0009890 * Deleted GO:0042986 --OBO_REL:is_a--> GO:0009891 * Copied GO:0045456 to GO:0045455 with type OBO_REL:is_a * Deleted GO:0045781 --OBO_REL:is_a--> GO:0051093 * Deleted GO:0045782 --OBO_REL:is_a--> GO:0051094 * Deleted GO:0045942 --OBO_REL:is_a--> GO:0045936 * Copied GO:0045942 to GO:0010563 with type OBO_REL:is_a * Deleted GO:0045949 --OBO_REL:is_a--> GO:0045937 * Copied GO:0045949 to GO:0010562 with type OBO_REL:is_a * Deleted GO:0046017 --part_of--> GO:0045896 * Copied GO:0046017 to GO:0045896 with type OBO_REL:is_a * Deleted GO:0046021 --part_of--> GO:0045896 * Copied GO:0046021 to GO:0045896 with type OBO_REL:is_a * Deleted GO:0046023 --part_of--> GO:0045896 * Copied GO:0046023 to GO:0045896 with type OBO_REL:is_a * Changed definition of GO:0046164 from "The chemical reactions and pathways resulting in the breakdown of alcohols, any of a class of alkyl compounds containing a hydroxyl group." to "The chemical reactions and pathways resulting in the breakdown of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." * Added definition dbxref ChEBI:30879 to GO:0046164 * Changed definition of GO:0046165 from "The chemical reactions and pathways resulting in the formation of alcohols, any of a class of alkyl compounds containing a hydroxyl group." to "The chemical reactions and pathways resulting in the formation of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." * Added definition dbxref ChEBI:30879 to GO:0046165 * Deleted GO:0046169 --OBO_REL:is_a--> GO:0046165 * Copied GO:0046169 to GO:0034309 with type OBO_REL:is_a * Deleted GO:0046170 --OBO_REL:is_a--> GO:0046164 * Copied GO:0046170 to GO:0034310 with type OBO_REL:is_a * Deleted GO:0046171 --OBO_REL:is_a--> GO:0046165 * Copied GO:0046171 to GO:0034309 with type OBO_REL:is_a * Deleted GO:0046172 --OBO_REL:is_a--> GO:0046164 * Copied GO:0046172 to GO:0034310 with type OBO_REL:is_a * Changed definition of GO:0046173 from "The chemical reactions and pathways resulting in the formation of a polyol, any polyhydric alcohol." to "The chemical reactions and pathways resulting in the formation of a polyol, any alcohol containing three or more hydroxyl groups attached to saturated carbon atoms." * Deleted definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) from GO:0046173 * Added definition dbxref ChEBI:26191 to GO:0046173 * Added synonym "polyhydric alcohol biosynthetic process" to GO:0046173 * Changed synonym scope of GO:0046173 from "Related" to "Exact" * Changed definition of GO:0046174 from "The chemical reactions and pathways resulting in the breakdown of a polyol, any polyhydric alcohol." to "The chemical reactions and pathways resulting in the breakdown of a polyol, any alcohol containing three or more hydroxyl groups attached to saturated carbon atoms." * Deleted definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) from GO:0046174 * Added definition dbxref ChEBI:26191 to GO:0046174 * Added synonym "polyhydric alcohol catabolic process" to GO:0046174 * Changed synonym scope of GO:0046174 from "Related" to "Exact" * Copied GO:0046344 to GO:0045455 with type OBO_REL:is_a * Deleted GO:0046454 --OBO_REL:is_a--> GO:0006066 * Copied GO:0046454 to GO:0034311 with type OBO_REL:is_a * Copied GO:0046599 to GO:0010564 with type OBO_REL:is_a * Copied GO:0046605 to GO:0010564 with type OBO_REL:is_a * Deleted GO:0048315 --part_of--> GO:0030437 * Copied GO:0048315 to GO:0030436 with type OBO_REL:is_a * Added comment "This term was made obsolete because it was ambiguously defined and incorrectly placed in the ontology." * Changed definition of GO:0048622 from "The formation of reproductive spores." to "OBSOLETE. The formation of reproductive spores." * Deleted GO:0048622 --OBO_REL:is_a--> GO:0030435 * Deleted GO:0048622 --OBO_REL:is_a--> GO:0022413 * org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 1db2025 * Deleted GO:0051143 --OBO_REL:is_a--> GO:0019751 * Copied GO:0051143 to GO:0034311 with type OBO_REL:is_a * Deleted GO:0051144 --OBO_REL:is_a--> GO:0046174 * Copied GO:0051144 to GO:0034313 with type OBO_REL:is_a From gocvs at genome.stanford.edu Mon Mar 10 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Mon, 10 Mar 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 03/10/2008 Message-ID: <200803110430.VAA27985@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.726 by 5.727 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Deleted GO:0001781 --OBO_REL:is_a--> GO:0006915 * Copied GO:0001781 to GO:0033028 with type OBO_REL:is_a * Copied GO:0006085 to GO:0009108 with type OBO_REL:is_a * Deleted GO:0006091 --OBO_REL:is_a--> GO:0008152 * Copied GO:0006091 to GO:0044237 with type OBO_REL:is_a * Copied GO:0007446 to GO:0035265 with type OBO_REL:is_a * Copied GO:0007533 to GO:0006259 with type OBO_REL:is_a * Deleted GO:0008154 --OBO_REL:is_a--> GO:0044260 * Copied GO:0008154 to GO:0044267 with type OBO_REL:is_a * Deleted GO:0008610 --OBO_REL:is_a--> GO:0044255 * Deleted GO:0009998 --OBO_REL:is_a--> GO:0042683 * Copied GO:0009998 to GO:0009996 with type OBO_REL:is_a * Deleted GO:0010109 --OBO_REL:is_a--> GO:0019222 * Deleted GO:0010109 --OBO_REL:is_a--> GO:0050794 * Copied GO:0010109 to GO:0031323 with type OBO_REL:is_a * Deleted GO:0010337 --OBO_REL:is_a--> GO:0032350 * Copied GO:0010337 to GO:0031323 with type OBO_REL:is_a * Deleted GO:0015979 --OBO_REL:is_a--> GO:0008152 * Copied GO:0015979 to GO:0044237 with type OBO_REL:is_a * Deleted GO:0030997 --OBO_REL:is_a--> GO:0051493 * Copied GO:0030997 to GO:0032886 with type OBO_REL:is_a * Deleted GO:0031135 --OBO_REL:is_a--> GO:0048523 * Copied GO:0031135 to GO:0048519 with type OBO_REL:is_a * Deleted GO:0031136 --OBO_REL:is_a--> GO:0048522 * Copied GO:0031136 to GO:0048518 with type OBO_REL:is_a * Deleted GO:0031494 --OBO_REL:is_a--> GO:0050793 * Copied GO:0031494 to GO:0045595 with type OBO_REL:is_a * Deleted GO:0031495 --OBO_REL:is_a--> GO:0051093 * Copied GO:0031495 to GO:0045596 with type OBO_REL:is_a * Deleted GO:0031496 --OBO_REL:is_a--> GO:0051094 * Copied GO:0031496 to GO:0045597 with type OBO_REL:is_a * Deleted GO:0032804 --OBO_REL:is_a--> GO:0017148 * Copied GO:0032804 to GO:0032269 with type OBO_REL:is_a * Copied GO:0032804 to GO:0031330 with type OBO_REL:is_a * Deleted GO:0032805 --OBO_REL:is_a--> GO:0017148 * Copied GO:0032805 to GO:0031331 with type OBO_REL:is_a * Copied GO:0032885 to GO:0010556 with type OBO_REL:is_a * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Deleted GO:0035020 --OBO_REL:is_a--> GO:0035023 * Copied GO:0035020 to GO:0046578 with type OBO_REL:is_a * Deleted GO:0042673 --OBO_REL:is_a--> GO:0042682 * Copied GO:0042673 to GO:0042659 with type OBO_REL:is_a * Deleted GO:0043155 --OBO_REL:is_a--> GO:0048523 * Deleted GO:0043155 --OBO_REL:is_a--> GO:0009892 * Copied GO:0043155 to GO:0031324 with type OBO_REL:is_a * Deleted GO:0043255 --OBO_REL:is_a--> GO:0031326 * Copied GO:0043255 to GO:0009889 with type OBO_REL:is_a * Copied GO:0043471 to GO:0044275 with type part_of * Deleted GO:0045304 --OBO_REL:is_a--> GO:0050793 * Copied GO:0045304 to GO:0050789 with type OBO_REL:is_a * Copied GO:0045713 to GO:0006412 with type OBO_REL:is_a * Deleted GO:0046889 --OBO_REL:is_a--> GO:0031328 * Copied GO:0046889 to GO:0009891 with type OBO_REL:is_a * Deleted GO:0046890 --OBO_REL:is_a--> GO:0031326 * Copied GO:0046890 to GO:0009889 with type OBO_REL:is_a * Copied GO:0046949 to GO:0006633 with type OBO_REL:is_a * Deleted GO:0046999 --OBO_REL:is_a--> GO:0050794 * Copied GO:0046999 to GO:0050789 with type OBO_REL:is_a * Deleted GO:0051049 --OBO_REL:is_a--> GO:0050794 * Copied GO:0051049 to GO:0032879 with type OBO_REL:is_a * Deleted GO:0051050 --OBO_REL:is_a--> GO:0048522 * Copied GO:0051050 to GO:0048518 with type OBO_REL:is_a * Deleted GO:0051051 --OBO_REL:is_a--> GO:0048523 * Copied GO:0051051 to GO:0048519 with type OBO_REL:is_a * Deleted GO:0051055 --OBO_REL:is_a--> GO:0031327 * Copied GO:0051055 to GO:0009890 with type OBO_REL:is_a From gocvs at genome.stanford.edu Wed Mar 12 21:30:44 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Wed, 12 Mar 2008 21:30:44 -0700 (PDT) Subject: [Go-diff] GO update 03/12/2008 Message-ID: <200803130430.VAA08629@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.727 by 5.732 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0000947 * Created object of type obo:TERM with id GO:0000948 * Created object of type obo:TERM with id GO:0000949 * Created object of type obo:TERM with id GO:0000950 * Created object of type obo:TERM with id GO:0000951 * Created object of type obo:TERM with id GO:0000952 * Created object of type obo:TERM with id GO:0000953 * Created object of type obo:TERM with id GO:0000954 * Created object of type obo:TERM with id GO:0000955 * Populated new object GO:0000947 (macro) * Changed name of GO:0000947 from "" to "amino acid catabolic process to alcohol via Ehrlich pathway" * Set definition of GO:0000947 to "The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." * Added definition dbxref GOC:krc to GO:0000947 * Added definition dbxref PMID:18281432 to GO:0000947 * Copied GO:0000947 to GO:0046165 with type OBO_REL:is_a * Copied GO:0000947 to GO:0000955 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0000947 * Populated new object GO:0000948 (macro) * Changed name of GO:0000948 from "" to "amino acid catabolic process to carboxylic acid via Ehrlich pathway" * Set definition of GO:0000948 to "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." * Added definition dbxref GOC:krc to GO:0000948 * Added definition dbxref PMID:18281432 to GO:0000948 * Copied GO:0000948 to GO:0046394 with type OBO_REL:is_a * Copied GO:0000948 to GO:0000955 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0000948 * Populated new object GO:0000949 (macro) * Changed name of GO:0000949 from "" to "aromatic amino acid family catabolic process to alcohol via Ehrlich pathway" * Set definition of GO:0000949 to "The chemical reactions and pathways involving the catabolism of aromatic amino acids to produce aromatic alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanol, 4-hydroxyphenylethanol, or tryptophol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." * Added definition dbxref GOC:krc to GO:0000949 * Added definition dbxref PMID:18281432 to GO:0000949 * Copied GO:0000949 to GO:0009074 with type OBO_REL:is_a * Copied GO:0000949 to GO:0000947 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0000949 * Populated new object GO:0000950 (macro) * Changed name of GO:0000950 from "" to "branched chain family amino acid catabolic process to alcohol via Ehrlich pathway" * Set definition of GO:0000950 to "The chemical reactions and pathways involving the catabolism of branched chain amino acids to produce branched chain alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When a branched chain family amino acid, leucine, isoleucine, or valine, is used as the substrate, 3-methylbutanol, 2-methylbutanol, or 2-methylpropanol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." * Added definition dbxref GOC:krc to GO:0000950 * Added definition dbxref PMID:18281432 to GO:0000950 * Copied GO:0000950 to GO:0000947 with type OBO_REL:is_a * Copied GO:0000950 to GO:0009083 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0000950 * Populated new object GO:0000951 (macro) * Changed name of GO:0000951 from "" to "methionine catabolic process to 3-methylthiopropanol" * Set definition of GO:0000951 to "The chemical reactions and pathways involving the catabolism of branched chain amino acids to produce branched chain alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When methionine is used as the substrate, 3-methylthiopropanol is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." * Added definition dbxref GOC:krc to GO:0000951 * Added definition dbxref PMID:18281432 to GO:0000951 * Copied GO:0000951 to GO:0000947 with type OBO_REL:is_a * Copied GO:0000951 to GO:0009087 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0000951 * Populated new object GO:0000952 (macro) * Changed name of GO:0000952 from "" to "aromatic amino acid family catabolic process to carboxylic acid via Ehrlich pathway" * Set definition of GO:0000952 to "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanoate, 4-hydroxyphenylethanoate, or 2-(Indol-3-yl)-ethanoate, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." * Added definition dbxref GOC:krc to GO:0000952 * Added definition dbxref PMID:18281432 to GO:0000952 * Copied GO:0000952 to GO:0009074 with type OBO_REL:is_a * Copied GO:0000952 to GO:0000948 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0000952 * Populated new object GO:0000953 (macro) * Changed name of GO:0000953 from "" to "branched chain family amino acid catabolic process to carboxylic acid via Ehrlich pathway" * Set definition of GO:0000953 to "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When a branched chain family amino acid, leucine, isoleucine, or valine, is used as the substrate, 3-methylbutanoate, 2-methylbutanoate, or 2-methylpropanoate, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." * Added definition dbxref GOC:krc to GO:0000953 * Added definition dbxref PMID:18281432 to GO:0000953 * Copied GO:0000953 to GO:0009083 with type OBO_REL:is_a * Copied GO:0000953 to GO:0000948 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0000953 * Populated new object GO:0000954 (macro) * Changed name of GO:0000954 from "" to "methionine catabolic process to 3-methylthiopropanoate" * Set definition of GO:0000954 to "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When methionine is used as the substrate, 3-methylthiopropanoate is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." * Added definition dbxref GOC:krc to GO:0000954 * Added definition dbxref PMID:18281432 to GO:0000954 * Copied GO:0000954 to GO:0009087 with type OBO_REL:is_a * Copied GO:0000954 to GO:0000948 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0000954 * Populated new object GO:0000955 (macro) * Changed name of GO:0000955 from "" to "amino acid catabolic process via Ehrlich pathway" * Set definition of GO:0000955 to "The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols or carboxylic acids containing one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives, sometimes referred to as fusel acids, may be produced instead of alcohols." * Added definition dbxref GOC:krc to GO:0000955 * Added definition dbxref PMID:18281432 to GO:0000955 * Copied GO:0000955 to GO:0009063 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0000955 * Changed comment from "Note that this term should not be confused with 'response to anoxia ; GO:0034059'." to "Note that this term should not be confused with 'response to anoxia ; GO:0034059'. Note that in laboratory studies, hypoxia is typically studied at O2 concentrations ranging from 0.1 - 5%." * Changed definition of GO:0001666 from "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 stimulus indicating lowered oxygen tension." to "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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level." * Deleted GO:0006275 --part_of--> GO:0006261 * Copied GO:0006275 to GO:0006260 with type part_of * Changed definition of GO:0007275 from "The biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." to "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." * Added definition dbxref GOC:dph to GO:0007275 * Added definition dbxref GOC:tb to GO:0007275 * Added definition dbxref ChEBI:28494 to GO:0032048 * Deleted GO:0032048 --OBO_REL:is_a--> GO:0006650 * Copied GO:0032048 to GO:0046471 with type OBO_REL:is_a * Added definition dbxref ChEBI:28494 to GO:0032049 * Copied GO:0032049 to GO:0006655 with type OBO_REL:is_a * Changed definition of GO:0032501 from "The biological processes, occurring at the level of the organism, pertinent to the function of the organism." to "The biological processes, occurring at the level of a multicellular organism, pertinent to its function." * Added definition dbxref GOC:dph to GO:0032501 * Added definition dbxref GOC:tb to GO:0032501 * Changed definition of GO:0032880 from "Any process that modulates the frequency, rate or extent of any process by which a cell, a protein is transported to, or maintained in, a specific location." to "Any process that modulates the frequency, rate or extent of any process by which a protein is transported to, or maintained in, a specific location." * Added definition dbxref GOC:dph to GO:0032880 * Added definition dbxref GOC:tb to GO:0032880 * Copied GO:0032880 to GO:0008104 with type part_of * Changed synonym scope of GO:0033920 from "Broad" to "Exact" * Changed definition of GO:0034059 from "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 stimulus indicating oxygen deprivation." to "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 stimulus indicating a decline in oxygen levels to trace amounts, <0.1%." * Deleted GO:0045185 --part_of--> GO:0008104 * Copied GO:0045185 to GO:0032880 with type OBO_REL:is_a * Deleted GO:0045607 --OBO_REL:is_a--> GO:0045604 * Deleted GO:0045608 --OBO_REL:is_a--> GO:0045605 * Deleted GO:0045609 --OBO_REL:is_a--> GO:0045606 * Deleted GO:0045808 --OBO_REL:is_a--> GO:0051093 * Copied GO:0045808 to GO:0048519 with type OBO_REL:is_a * Deleted GO:0045809 --OBO_REL:is_a--> GO:0051094 * Copied GO:0045809 to GO:0048518 with type OBO_REL:is_a * Changed name of GO:0048086 from "negative regulation of pigmentation" to "negative regulation of pigmentation during development" * Changed definition of GO:0048086 from "Any process that stops, prevents or reduces the rate or extent of color pattern formation in an organ or organism." to "Any process that stops, prevents or reduces the deposition of coloring matter occurring during development." * Added definition dbxref GOC:dph to GO:0048086 * Added definition dbxref GOC:tb to GO:0048086 * Changed name of GO:0048087 from "positive regulation of pigmentation" to "positive regulation of pigmentation during development" * Changed definition of GO:0048087 from "Any process that activates or increases the rate or extent of color pattern formation in an organ or organism." to "Any process that activates or increases the deposition of coloring matter occurring during development." * Added definition dbxref GOC:dph to GO:0048087 * Added definition dbxref GOC:tb to GO:0048087 * Changed definition of GO:0048609 from "The process, occurring above the cellular level, that is pertinent to the reproductive function of an organism. This includes the integrated processes at the level of tissues and organs." to "The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs." * Added definition dbxref GOC:tb to GO:0048609 * Deleted GO:0050865 --OBO_REL:is_a--> GO:0051239 * Changed definition of GO:0050879 from "Physiological processes involved in changing the position of an organism or an anatomical part of an organism." to "Physiological processes involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism." * Added definition dbxref GOC:tb to GO:0050879 * Changed definition of GO:0051108 from "Catalysis of the reaction: D-carnitine + CoA = D-carnitinyl-CoA." to "Catalysis of the reaction: D-carnitine + CoA + ATP = AMP + diphosphate + D-carnitinyl-CoA." * Changed definition of GO:0051109 from "Catalysis of the reaction: CoA + crotono-betaine = crotonobetainyl-CoA." to "Catalysis of the reaction: CoA + crotono-betaine + ATP = AMP + diphosphate + crotonobetainyl-CoA." * Deleted GO:0051235 --part_of--> GO:0051179 * Deleted GO:0051235 --OBO_REL:is_a--> GO:0008150 * Copied GO:0051235 to GO:0032879 with type OBO_REL:is_a * Changed definition of GO:0051239 from "Any process that modulates the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." to "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs." * Added definition dbxref GOC:dph to GO:0051239 * Added definition dbxref GOC:tb to GO:0051239 * Deleted GO:0051270 --OBO_REL:is_a--> GO:0040012 * Deleted GO:0051271 --OBO_REL:is_a--> GO:0040013 * Deleted GO:0051272 --OBO_REL:is_a--> GO:0040017 From gocvs at genome.stanford.edu Thu Mar 13 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Thu, 13 Mar 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 03/13/2008 Message-ID: <200803140430.VAA03533@bread.Stanford.EDU> OBODIFF of gene_ontology_edit.obo version 5.732 by 5.733 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034314 * Created object of type obo:TERM with id GO:0034315 * Created object of type obo:TERM with id GO:0034316 * Created object of type obo:TERM with id GO:0034317 * Created object of type obo:TERM with id GO:0034318 * Created object of type obo:TERM with id GO:0034319 * Created object of type obo:TERM with id GO:0034320 * Created object of type obo:TERM with id GO:0034321 * Created object of type obo:TERM with id GO:0034322 * Created object of type obo:TERM with id GO:0034323 * Created object of type obo:TERM with id GO:0034324 * Created object of type obo:TERM with id GO:0034325 * Created object of type obo:TERM with id GO:0034326 * Created object of type obo:TERM with id GO:0034327 * Created object of type obo:TERM with id GO:0034328 * Populated new object GO:0034314 (macro) * Changed name of GO:0034314 from "" to "Arp2/3 complex-mediated actin nucleation" * Set definition of GO:0034314 to "The initial step in the formation of an actin filament, in which actin monomers combine to form a new filament, mediated by the Arp2/3 protein complex and its interaction with other proteins." * Added definition dbxref GOC:mah to GO:0034314 * Added definition dbxref PMID:16959963 to GO:0034314 * Copied GO:0034314 to GO:0045010 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034314 * Populated new object GO:0034315 (macro) * Changed name of GO:0034315 from "" to "regulation of Arp2/3 complex-mediated actin nucleation" * Set definition of GO:0034315 to "Any process that modulates the frequency, rate or extent of actin nucleation mediated by the Arp2/3 complex and interacting proteins." * Added definition dbxref GOC:mah to GO:0034315 * Copied GO:0034315 to GO:0034314 with type part_of * Copied GO:0034315 to GO:0051125 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034315 * Populated new object GO:0034316 (macro) * Changed name of GO:0034316 from "" to "negative regulation of Arp2/3 complex-mediated actin nucleation" * Set definition of GO:0034316 to "Any process that stops, prevents, or reduces the frequency, rate or extent of actin nucleation mediated by the Arp2/3 complex and interacting proteins." * Added definition dbxref GOC:mah to GO:0034316 * Added definition dbxref PMID:16959963 to GO:0034316 * Copied GO:0034316 to GO:0051126 with type OBO_REL:is_a * Copied GO:0034316 to GO:0034315 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034316 * Populated new object GO:0034317 (macro) * Changed name of GO:0034317 from "" to "nicotinic acid riboside kinase activity" * Set definition of GO:0034317 to "Catalysis of the reaction: ATP + nicotinic acid riboside (NaR) = ADP + nicotinic acid mononucleotide (NaMN)." * Added definition dbxref PMID:17914902 to GO:0034317 * Copied GO:0034317 to GO:0019206 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034317 * Populated new object GO:0034318 (macro) * Changed name of GO:0034318 from "" to "alcohol O-acyltransferase activity" * Set definition of GO:0034318 to "Catalysis of the transfer of an acyl group to an oxygen atom on an alcohol acceptor molecule." * Added definition dbxref GOC:mah to GO:0034318 * Added synonym "acyl-CoA:alcohol O-acyltransferase activity" to GO:0034318 * Changed synonym scope of GO:0034318 from "Related" to "Exact" * Added synonym "acyl-CoA:ethanol O-acyltransferase" to GO:0034318 * Changed synonym scope of GO:0034318 from "Related" to "Narrow" * Added synonym "acyl-coenzymeA:alcohol O-acyltransferase activity" to GO:0034318 * Changed synonym scope of GO:0034318 from "Related" to "Exact" * Added synonym "acyl-coenzymeA:ethanol O-acyltransferase activity" to GO:0034318 * Changed synonym scope of GO:0034318 from "Related" to "Narrow" * Added synonym "AEATase activity" to GO:0034318 * Changed synonym scope of GO:0034318 from "Related" to "Narrow" * Added synonym "alcohol acyltransferase activity" to GO:0034318 * Changed synonym scope of GO:0034318 from "Related" to "Exact" * Copied GO:0034318 to GO:0008374 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034318 * Populated new object GO:0034319 (macro) * Changed name of GO:0034319 from "" to "alcohol O-butanoyltransferase activity" * Set definition of GO:0034319 to "Catalysis of the reaction: butanoyl-CoA + an alcohol = CoA + a butyl ester." * Added definition dbxref GOC:mah to GO:0034319 * Added definition dbxref PMID:16361250 to GO:0034319 * Copied GO:0034319 to GO:0034323 with type OBO_REL:is_a * Copied GO:0034319 to GO:0034318 with type OBO_REL:is_a * Copied GO:0034319 to GO:0016413 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034319 * Populated new object GO:0034320 (macro) * Changed name of GO:0034320 from "" to "alcohol O-hexanoyltransferase activity" * Set definition of GO:0034320 to "Catalysis of the reaction: hexanoyl-CoA + an alcohol = CoA + a hexyl ester." * Added definition dbxref GOC:mah to GO:0034320 * Added definition dbxref PMID:16361250 to GO:0034320 * Copied GO:0034320 to GO:0016413 with type OBO_REL:is_a * Copied GO:0034320 to GO:0034324 with type OBO_REL:is_a * Copied GO:0034320 to GO:0034318 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034320 * Populated new object GO:0034321 (macro) * Changed name of GO:0034321 from "" to "alcohol O-octanoyltransferase activity" * Set definition of GO:0034321 to "Catalysis of the reaction: octanoyl-CoA + an alcohol = CoA + an octyl ester." * Added definition dbxref GOC:mah to GO:0034321 * Added definition dbxref PMID:16361250 to GO:0034321 * Copied GO:0034321 to GO:0016413 with type OBO_REL:is_a * Copied GO:0034321 to GO:0034318 with type OBO_REL:is_a * Copied GO:0034321 to GO:0016414 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034321 * Populated new object GO:0034322 (macro) * Changed name of GO:0034322 from "" to "alcohol O-decanoyltransferase activity" * Set definition of GO:0034322 to "Catalysis of the reaction: decanoyl-CoA + an alcohol = CoA + a decyl ester." * Added definition dbxref GOC:mah to GO:00343