[go-diff] GO update 01/31/2008

Thu Jan 31 21:30:45 PST 2008

OBODIFF of gene_ontology_edit.obo version 5.674 by 5.676

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034221
* Created object of type obo:TERM with id GO:0034222
* Created object of type obo:TERM with id GO:0034223
* Created object of type obo:TERM with id GO:0034224
* Created object of type obo:TERM with id GO:0034225
* Created object of type obo:TERM with id GO:0034226
* Created object of type obo:TERM with id GO:0034227
* Created object of type obo:TERM with id GO:0034228
* Created object of type obo:TERM with id GO:0034229
* Populated new object GO:0034221 (macro)
  * Changed name of GO:0034221 from "<new term>" to "fungal-type cell wall chitin biosynthetic process"
  * Set definition of GO:0034221 to "The chemical reactions and pathways resulting in the formation of cell wall chitin, a linear polysaccharide consisting of P-1,4-linked N-acetyl-D-glucosamine residues, found in the walls of vegetatively growing fungal cells."
  * Added definition dbxref GOC:mah to GO:0034221
  * Added synonym "fungal-type cell wall chitin anabolism" to GO:0034221
  * Changed synonym scope of GO:0034221 from "Related" to "Exact"
  * Added synonym "fungal-type cell wall chitin biosynthesis" to GO:0034221
  * Changed synonym scope of GO:0034221 from "Related" to "Exact"
  * Added synonym "fungal-type cell wall chitin formation" to GO:0034221
  * Changed synonym scope of GO:0034221 from "Related" to "Exact"
  * Added synonym "fungal-type cell wall chitin synthesis" to GO:0034221
  * Changed synonym scope of GO:0034221 from "Related" to "Exact"
  * Copied GO:0034221 to GO:0006038 with type OBO_REL:is_a
  * Copied GO:0034221 to GO:0051278 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034221
* Populated new object GO:0034222 (macro)
  * Changed name of GO:0034222 from "<new term>" to "regulation of cell wall chitin metabolic process"
  * Set definition of GO:0034222 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving chitin in a cell wall."
  * Added definition dbxref GOC:mah to GO:0034222
  * Copied GO:0034222 to GO:0032882 with type OBO_REL:is_a
  * Copied GO:0034222 to GO:0006037 with type part_of
  * Assigned namespace "biological_process" to GO:0034222
* Populated new object GO:0034223 (macro)
  * Changed name of GO:0034223 from "<new term>" to "regulation of spore wall chitin biosynthetic process"
  * Set definition of GO:0034223 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of spore wall chitin."
  * Added definition dbxref GOC:mah to GO:0034223
  * Added synonym "regulation of spore wall chitin anabolism" to GO:0034223
  * Changed synonym scope of GO:0034223 from "Related" to "Exact"
  * Added synonym "regulation of spore wall chitin biosynthesis" to GO:0034223
  * Changed synonym scope of GO:0034223 from "Related" to "Exact"
  * Added synonym "regulation of spore wall chitin formation" to GO:0034223
  * Changed synonym scope of GO:0034223 from "Related" to "Exact"
  * Added synonym "regulation of spore wall chitin synthesis" to GO:0034223
  * Changed synonym scope of GO:0034223 from "Related" to "Exact"
  * Copied GO:0034223 to GO:0032884 with type OBO_REL:is_a
  * Copied GO:0034223 to GO:0051128 with type OBO_REL:is_a
  * Copied GO:0034223 to GO:0034217 with type part_of
  * Copied GO:0034223 to GO:0006038 with type part_of
  * Assigned namespace "biological_process" to GO:0034223
* Populated new object GO:0034224 (macro)
  * Changed name of GO:0034224 from "<new term>" to "cellular response to zinc ion starvation"
  * Set definition of GO:0034224 to "A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of zinc ions."
  * Added definition dbxref GOC:mah to GO:0034224
  * Added synonym "ellular response to zinc ion limitation" to GO:0034224
  * Changed synonym scope of GO:0034224 from "Related" to "Exact"
  * Copied GO:0034224 to GO:0009267 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034224
* Populated new object GO:0034225 (macro)
  * Changed name of GO:0034225 from "<new term>" to "regulation of transcription from RNA polymerase II promoter in response to zinc ion starvation"
  * Set definition of GO:0034225 to "Modulation of the frequency, rate or extent of transcription from an from RNA polymerase II promoter as a result of a stimulus indicating the organism is deprived of zinc ions."
  * Added definition dbxref GOC:mah to GO:0034225
  * Added synonym "regulation of transcription from RNA polymerase II promoter in response to zinc deficiency" to GO:0034225
  * Changed synonym scope of GO:0034225 from "Related" to "Exact"
  * Added synonym "regulation of transcription from RNA polymerase II promoter in response to zinc ion limitation" to GO:0034225
  * Changed synonym scope of GO:0034225 from "Related" to "Exact"
  * Copied GO:0034225 to GO:0043618 with type OBO_REL:is_a
  * Copied GO:0034225 to GO:0034224 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034225
* Populated new object GO:0034226 (macro)
  * Changed name of GO:0034226 from "<new term>" to "lysine import"
  * Set definition of GO:0034226 to "The directed movement of lysine, 2,6-diaminohexanoic acid, into a cell or organelle."
  * Added definition dbxref GOC:jl to GO:0034226
  * Added definition dbxref GOC:mah to GO:0034226
  * Added synonym "L-lysine import" to GO:0034226
  * Changed synonym scope of GO:0034226 from "Related" to "Narrow"
  * Added synonym "lysine uptake" to GO:0034226
  * Changed synonym scope of GO:0034226 from "Related" to "Exact"
  * Copied GO:0034226 to GO:0043090 with type OBO_REL:is_a
  * Copied GO:0034226 to GO:0015819 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034226
* Populated new object GO:0034227 (macro)
  * Changed name of GO:0034227 from "<new term>" to "tRNA thio-modification"
  * Set definition of GO:0034227 to "The addition a sulfur atom to a nucleotide in a tRNA molecule."
  * Added definition dbxref GOC:mcc to GO:0034227
  * Added definition dbxref PMID:12549933 to GO:0034227
  * Added definition dbxref PMID:14722066 to GO:0034227
  * Added GO:0034227 to category gosubset_prok
  * Copied GO:0034227 to GO:0006400 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034227
* Populated new object GO:0034228 (macro)
  * Changed name of GO:0034228 from "<new term>" to "ethanolamine transmembrane transporter activity"
  * Set definition of GO:0034228 to "Catalysis of the transfer of ethanolamine from one side of the membrane to the other. Ethanolamine (2-aminoethanol, monoethanolamine) is an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids, such as phosphatidylethanolamine."
  * Added definition dbxref GOC:rn to GO:0034228
  * Added definition dbxref PMID:3514579 to GO:0034228
  * Added GO:0034228 to category gosubset_prok
  * Added synonym "2-aminoethanol transmembrane transporter activity" to GO:0034228
  * Changed synonym scope of GO:0034228 from "Related" to "Exact"
  * Added synonym "ethanolamine permease activity" to GO:0034228
  * Changed synonym scope of GO:0034228 from "Related" to "Exact"
  * Added synonym "monoethanolamine transmembrane transporter activity" to GO:0034228
  * Changed synonym scope of GO:0034228 from "Related" to "Exact"
  * Copied GO:0034228 to GO:0005275 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034228
* Populated new object GO:0034229 (macro)
  * Changed name of GO:0034229 from "<new term>" to "ethanolamine transport"
  * Set definition of GO:0034229 to "The directed movement of ethanolamine into, out of, within or between cells. Ethanolamine (2-aminoethanol, monoethanolamine) is an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids, such as phosphatidylethanolamine."
  * Added definition dbxref GOC:rn to GO:0034229
  * Added definition dbxref PMID:3514579 to GO:0034229
  * Added synonym "2-aminoethanol transport" to GO:0034229
  * Changed synonym scope of GO:0034229 from "Related" to "Exact"
  * Added synonym "monoethanolamine transport" to GO:0034229
  * Changed synonym scope of GO:0034229 from "Related" to "Exact"
  * Copied GO:0034229 to GO:0006836 with type OBO_REL:is_a
  * Copied GO:0034229 to GO:0015837 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034229
* Deleted GO:0004012 --OBO_REL:is_a--> GO:0042626
* Copied GO:0004012 to GO:0043492 with type OBO_REL:is_a
* Deleted GO:0005619 --OBO_REL:is_a--> GO:0009277
* Deleted GO:0006038 --OBO_REL:is_a--> GO:0051278
* Deleted synonym "nonsense suppression" from GO:0006451
* Added synonym "natural nonsense suppression" to GO:0006451
* Deleted general dbxref EC:3.6.1..- from GO:0008413
* Added general dbxref EC:3.6.1.- to GO:0008413
* Changed name of GO:0009272 from "chitin- and beta-glucan-containing cell wall biogenesis" to "fungal-type cell wall biogenesis"
* Changed definition of GO:0009272 from "The chemical reactions and pathways resulting in the formation of the chitin- and beta-glucan-containing cell wall." to "The chemical reactions and pathways resulting in the formation of the fungal-type cell wall."
* Added synonym "chitin- and beta-glucan-containing cell wall biogenesis" to GO:0009272
* Changed synonym scope of GO:0009272 from "Related" to "Narrow"
* Deleted GO:0010504 --OBO_REL:is_a--> GO:0030996
* Copied GO:0010504 to GO:0030996 with type part_of
* Deleted GO:0016202 --OBO_REL:is_a--> GO:0014706
* Copied GO:0016202 to GO:0014706 with type part_of
* Deleted GO:0030150 --OBO_REL:is_a--> GO:0006626
* Added synonym "sorophore development" to GO:0031150
* Changed synonym scope of GO:0031150 from "Related" to "Exact"
* Deleted GO:0031392 --OBO_REL:is_a--> GO:0001516
* Copied GO:0031392 to GO:0001516 with type part_of
* Changed name of GO:0031505 from "chitin- and beta-glucan-containing cell wall organization and biogenesis" to "fungal-type cell wall organization and biogenesis"
* Changed definition of GO:0031505 from "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the cell wall; as in, but not restricted to, the fungi (Fungi, ncbi_taxonomy_id:4751)." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the fungal-type cell wall."
* Changed synonym scope of GO:0031505 from "Broad" to "Related"
* Changed synonym scope of GO:0031505 from "Exact" to "Narrow"
* Changed synonym scope of GO:0031505 from "Broad" to "Related"
* Added synonym "chitin- and beta-glucan-containing cell wall organization and biogenesis" to GO:0031505
* Changed synonym scope of GO:0031505 from "Related" to "Narrow"
* Deleted GO:0032350 --OBO_REL:is_a--> GO:0042445
* Copied GO:0032350 to GO:0042445 with type part_of
* Deleted GO:0032830 --OBO_REL:is_a--> GO:0002361
* Deleted GO:0032831 --OBO_REL:is_a--> GO:0002361
* Added synonym "regulation of chitin metabolism" to GO:0032882
* Changed synonym scope of GO:0032882 from "Related" to "Exact"
* Added synonym "regulation of chitin anabolism" to GO:0032883
* Changed synonym scope of GO:0032883 from "Related" to "Exact"
* Added synonym "regulation of chitin biosynthes" to GO:0032883
* Added synonym "regulation of chitin formation" to GO:0032883
* Changed synonym scope of GO:0032883 from "Related" to "Exact"
* Added synonym "regulation of chitin synthesis" to GO:0032883
* Changed synonym scope of GO:0032883 from "Related" to "Exact"
* Added synonym "regulation of cell wall chitin anabolism" to GO:0032884
* Changed synonym scope of GO:0032884 from "Related" to "Exact"
* Added synonym "regulation of cell wall chitin biosynthesis" to GO:0032884
* Changed synonym scope of GO:0032884 from "Related" to "Exact"
* Added synonym "regulation of cell wall chitin formation" to GO:0032884
* Changed synonym scope of GO:0032884 from "Related" to "Exact"
* Added synonym "regulation of cell wall chitin synthesis" to GO:0032884
* Changed synonym scope of GO:0032884 from "Related" to "Exact"
* Copied GO:0032884 to GO:0006038 with type part_of
* Copied GO:0032884 to GO:0034222 with type OBO_REL:is_a
* Deleted GO:0032886 --OBO_REL:is_a--> GO:0007017
* Copied GO:0032886 to GO:0007017 with type part_of
* Deleted GO:0032928 --OBO_REL:is_a--> GO:0031325
* Deleted GO:0032928 --OBO_REL:is_a--> GO:0042554
* Copied GO:0032928 to GO:0042554 with type part_of
* Copied GO:0032928 to GO:0031323 with type OBO_REL:is_a
* Copied GO:0032930 to GO:0031325 with type OBO_REL:is_a
* Changed definition of GO:0033890 from "Catalysis of the reaction: exonucleolytic cleavage that removes extra residues from the 3'-terminus of tRNA to produce 5'-mononucleotides.." to "Catalysis of the reaction: exonucleolytic cleavage that removes extra residues from the 3'-terminus of tRNA to produce 5'-mononucleotides."
* Changed definition of GO:0033918 from "Catalysis of the reaction: endohydrolysis of 1,4-beta-D-linkages between D-galactose 4-sulfate and 3,6-anhydro-D-galactose in kappa-carrageenans.." to "Catalysis of the reaction: endohydrolysis of 1,4-beta-D-linkages between D-galactose 4-sulfate and 3,6-anhydro-D-galactose in kappa-carrageenans."
* Changed synonym scope of GO:0033920 from "Broad" to "Exact"
* Changed definition of GO:0033945 from "Catalysis of the reaction: hydrolysis of cellobiose from the reducing end of xyloglucans consisting of a beta-1,4-linked glucan carrying alpha-D-xylosyl groups on O-6 of the glucose residues. To be a substrate, the first residue must be unsubstituted, the second residue may bear a xylosyl group, whether further glycosylated or not, and the third residue, which becomes the new terminus by the action of the enzyme, is preferably xylosylated, but this xylose residue must not be further substituted.." to "Catalysis of the reaction: hydrolysis of cellobiose from the reducing end of xyloglucans consisting of a beta-1,4-linked glucan carrying alpha-D-xylosyl groups on O-6 of the glucose residues. To be a substrate, the first residue must be unsubstituted, the second residue may bear a xylosyl group, whether further glycosylated or not, and the third residue, which becomes the new terminus by the action of the enzyme, is preferably xylosylated, but this xylose residue must not be further substituted."
* Changed definition of GO:0033996 from "Catalysis of the reaction: Produces di-beta-D-fructofuranose 2,6':2',6-dianhydride (DFA IV) by successively eliminating the diminishing (2->6)-beta-D-fructan (levan) chain from the terminal D-fructosyl-D-fructosyl disaccharide.." to "Catalysis of the reaction: Produces di-beta-D-fructofuranose 2,6':2',6-dianhydride (DFA IV) by successively eliminating the diminishing (2->6)-beta-D-fructan (levan) chain from the terminal D-fructosyl-D-fructosyl disaccharide."
* Changed definition of GO:0033997 from "Catalysis of the reaction: Produces alpha-D-fructofuranose beta-D-fructofuranose 1,2':2,1'-dianhydride (DFA I) by successively eliminating the diminishing (2->1)-beta-D-fructan (inulin) chain from the terminal D-fructosyl-D-fructosyl disaccharide.." to "Catalysis of the reaction: Produces alpha-D-fructofuranose beta-D-fructofuranose 1,2':2,1'-dianhydride (DFA I) by successively eliminating the diminishing (2->1)-beta-D-fructan (inulin) chain from the terminal D-fructosyl-D-fructosyl disaccharide."
* Changed definition of GO:0033998 from "Catalysis of the reaction: Produces alpha-D-fructofuranose beta-D-fructofuranose 1,2':2,3'-dianhydride (DFA III) by successively eliminating the diminishing (2->1)-beta-D-fructan (inulin) chain from the terminal D-fructosyl-D-fructosyl disaccharide.." to "Catalysis of the reaction: Produces alpha-D-fructofuranose beta-D-fructofuranose 1,2':2,3'-dianhydride (DFA III) by successively eliminating the diminishing (2->1)-beta-D-fructan (inulin) chain from the terminal D-fructosyl-D-fructosyl disaccharide."
* Changed definition of GO:0033999 from "Catalysis of the reaction: Eliminative cleavage of dermatan sulfate containing 1,4-beta-D-hexosaminyl and 1,3-beta-D-glucurosonyl or 1,3-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups to yield a 4,5-unsaturated dermatan-sulfate disaccharide (DeltaUA-GalNAC-4S).." to "Catalysis of the reaction: Eliminative cleavage of dermatan sulfate containing 1,4-beta-D-hexosaminyl and 1,3-beta-D-glucurosonyl or 1,3-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups to yield a 4,5-unsaturated dermatan-sulfate disaccharide (DeltaUA-GalNAC-4S)."
* Changed definition of GO:0034201 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 oleate stimulus." 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 oleate stimulus."
* Deleted synonym "v wall chitin synthesis" from GO:0034217
* Added synonym "spore wall chitin synthesis" to GO:0034217
* Changed synonym scope of GO:0034217 from "Related" to "Exact"
* Copied GO:0034217 to GO:0030476 with type part_of
* Deleted GO:0035155 --OBO_REL:is_a--> GO:0035154
* Copied GO:0035155 to GO:0035154 with type part_of
* Deleted GO:0035157 --OBO_REL:is_a--> GO:0035156
* Copied GO:0035157 to GO:0035156 with type part_of
* Deleted GO:0043380 --OBO_REL:is_a--> GO:0043379
* Copied GO:0043380 to GO:0043379 with type part_of
* Copied GO:0043681 to GO:0006626 with type OBO_REL:is_a
* Deleted GO:0045039 --OBO_REL:is_a--> GO:0006626
* Deleted GO:0045040 --OBO_REL:is_a--> GO:0006626
* Deleted GO:0045041 --OBO_REL:is_a--> GO:0006626
* Deleted GO:0048509 --OBO_REL:is_a--> GO:0048507
* Copied GO:0048509 to GO:0048507 with type part_of
* Deleted GO:0051056 --OBO_REL:is_a--> GO:0007264
* Copied GO:0051056 to GO:0007264 with type part_of
* Deleted GO:0051569 --OBO_REL:is_a--> GO:0051568
* Copied GO:0051569 to GO:0051568 with type part_of
* Deleted GO:0051570 --OBO_REL:is_a--> GO:0051567
* Copied GO:0051570 to GO:0051567 with type part_of
* Changed definition of GO:0060214 from "Formation of the inner endothelial cell layer of the heart, which connects the
heart to the vascular system." to "Formation of the inner endothelial cell layer of the heart, which connects the heart to the vascular system."