[Go-diff] GO update 03/12/2008

[Remote CVS for Gene Ontology]

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 "<new term>" 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 "<new term>" 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 "<new term>" 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 "<new term>" 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 "<new term>" 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 "<new term>" 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 "<new term>" 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 "<new term>" 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 "<new term>" 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