[Go-diff] GO update 09/09/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Tue Sep 9 21:30:47 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.198 by 1.201

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034968
* Created object of type obo:TERM with id GO:0034969
* Created object of type obo:TERM with id GO:0034970
* Created object of type obo:TERM with id GO:0034971
* Created object of type obo:TERM with id GO:0034972
* Created object of type obo:TERM with id GO:0034973
* Populated new object GO:0034968 (macro)
  * Changed name of GO:0034968 from "<new term>" to "histone lysine methylation"
  * Set definition of GO:0034968 to "The modification of a histone by addition of a methyl group to a lysine residue."
  * Added definition dbxref GOC:mah to GO:0034968
  * Copied GO:0034968 to GO:0016571 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034968
* Populated new object GO:0034969 (macro)
  * Changed name of GO:0034969 from "<new term>" to "histone arginine methylation"
  * Set definition of GO:0034969 to "The modification of a histone by addition of a methyl group to an arginine residue."
  * Added definition dbxref GOC:mah to GO:0034969
  * Copied GO:0034969 to GO:0016571 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034969
* Populated new object GO:0034970 (macro)
  * Changed name of GO:0034970 from "<new term>" to "histone H3-R2 methylation"
  * Set definition of GO:0034970 to "The modification of histone H3 by addition of a methyl group to arginine at position 2 of the histone."
  * Added definition dbxref GOC:mah to GO:0034970
  * Added synonym "histone H3 R2 methylation" to GO:0034970
  * Changed synonym scope of GO:0034970 from "Related" to "Exact"
  * Added synonym "histone H3R2me" to GO:0034970
  * Changed synonym scope of GO:0034970 from "Related" to "Exact"
  * Added synonym "histone lysine H3 R2 methylation" to GO:0034970
  * Changed synonym scope of GO:0034970 from "Related" to "Exact"
  * Copied GO:0034970 to GO:0034969 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034970
* Populated new object GO:0034971 (macro)
  * Changed name of GO:0034971 from "<new term>" to "histone H3-R17 methylation"
  * Set definition of GO:0034971 to "The modification of histone H3 by addition of a methyl group to arginine at position 17 of the histone."
  * Added definition dbxref GOC:mah to GO:0034971
  * Added synonym "histone H3 R17 methylation" to GO:0034971
  * Changed synonym scope of GO:0034971 from "Related" to "Exact"
  * Added synonym "histone H3R17me" to GO:0034971
  * Changed synonym scope of GO:0034971 from "Related" to "Exact"
  * Added synonym "histone lysine H3 R17 methylation" to GO:0034971
  * Changed synonym scope of GO:0034971 from "Related" to "Exact"
  * Copied GO:0034971 to GO:0034969 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034971
* Populated new object GO:0034972 (macro)
  * Changed name of GO:0034972 from "<new term>" to "histone H3-R26 methylation"
  * Set definition of GO:0034972 to "The modification of histone H3 by addition of a methyl group to arginine at position 26 of the histone."
  * Added definition dbxref GOC:mah to GO:0034972
  * Added synonym "histone H3 R26 methylation" to GO:0034972
  * Changed synonym scope of GO:0034972 from "Related" to "Exact"
  * Added synonym "histone H3R26me" to GO:0034972
  * Changed synonym scope of GO:0034972 from "Related" to "Exact"
  * Added synonym "histone lysine H3 R26 methylation" to GO:0034972
  * Changed synonym scope of GO:0034972 from "Related" to "Exact"
  * Copied GO:0034972 to GO:0034969 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034972
* Populated new object GO:0034973 (macro)
  * Changed name of GO:0034973 from "<new term>" to "Sid2-Mob1 complex"
  * Set definition of GO:0034973 to "A protein complex that contains a protein kinase (Sid2 in S. pombe) and its regulatory subunit (Mob1). The Sid2p-Mob1p kinase complex is a component of the septation initiation network in fission yeast (called the mitotic exit network in S. cerevisiae) and is required for cytokinesis. The analogous complex in S. cerevisiae is called Dbf2p-Mob1p complex"
  * Added definition dbxref GOC:vw to GO:0034973
  * Added definition dbxref PMID:10837231 to GO:0034973
  * Added definition dbxref PMID:15060149 to GO:0034973
  * Added synonym "Dbf2p-Mob1p complex" to GO:0034973
  * Changed synonym scope of GO:0034973 from "Related" to "Exact"
  * Added synonym "Sid2-Mob1 kinase complex" to GO:0034973
  * Changed synonym scope of GO:0034973 from "Related" to "Exact"
  * Added synonym "Sid2p-Mob1p complex" to GO:0034973
  * Changed synonym scope of GO:0034973 from "Related" to "Exact"
  * Copied GO:0034973 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034973 to GO:0044444 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034973
* Deleted GO:0000494 --OBO_REL:is_a--> GO:0033967
* Deleted GO:0000495 --OBO_REL:is_a--> GO:0033979
* Deleted synonym "Cu-Zn superoxide dismutase activity activity" from GO:0004784
* Added synonym "Cu-Zn superoxide dismutase activity" to GO:0004784
* Added general dbxref EC:1.15.1.1 to synonym Cu-Zn superoxide dismutase activity of GO:0004784
* Changed synonym scope of GO:0004784 from "Related" to "Narrow"
* Deleted synonym "GAP binding" from GO:0005096
* Added synonym "GAP activity" to GO:0005096
* Changed synonym scope of GO:0005096 from "Related" to "Exact"
* Deleted GO:0005652 --part_of--> GO:0005637
* Copied GO:0005652 to GO:0034399 with type part_of
* Changed name of GO:0005911 from "intercellular junction" to "cell-cell junction"
* Deleted synonym "cell-cell junction" from GO:0005911
* Added synonym "intercellular junction" to GO:0005911
* Changed synonym scope of GO:0005911 from "Related" to "Exact"
* Deleted GO:0006412 --OBO_REL:is_a--> GO:0034645
* Copied GO:0006582 to GO:0019748 with type OBO_REL:is_a
* Changed name of GO:0006996 from "organelle organization and biogenesis" to "organelle organization"
* Changed definition of GO:0006996 from "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of any organelle within a cell." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane."
* Added synonym "organelle organization and biogenesis" to GO:0006996
* Added general dbxref GOC:mah to synonym organelle organization and biogenesis of GO:0006996
* Added general dbxref GOC:jl to synonym organelle organization and biogenesis of GO:0006996
* Added general dbxref GOC:dph to synonym organelle organization and biogenesis of GO:0006996
* Changed synonym scope of GO:0006996 from "Related" to "Exact"
* Changed name of GO:0007028 from "cytoplasm organization and biogenesis" to "cytoplasm organization"
* Changed definition of GO:0007028 from "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the cytoplasm and its components." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures."
* Added definition dbxref GOC:dph to GO:0007028
* Added definition dbxref GOC:jl to GO:0007028
* Added definition dbxref GOC:mah to GO:0007028
* Added synonym "cytoplasm organization and biogenesis" to GO:0007028
* Changed synonym scope of GO:0007028 from "Related" to "Exact"
* Changed definition of GO:0007163 from "Any cellular process that results in the  specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns." to "Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns."
* Deleted GO:0009579 --OBO_REL:is_a--> GO:0044464
* Copied GO:0009579 to GO:0044424 with type OBO_REL:is_a
* Deleted GO:0010452 --OBO_REL:is_a--> GO:0016571
* Copied GO:0010452 to GO:0034968 with type OBO_REL:is_a
* Changed definition of GO:0010698 from "Increases the activity of an aceyltransferase, an enzyme which
catalyzes the transfer of an acetyl group to an acceptor molecule." to "Increases the activity of an aceyltransferase, an enzyme which catalyzes the transfer of an acetyl group to an acceptor molecule."
* Changed name of GO:0016043 from "cellular component organization and biogenesis" to "cellular component organization"
* Changed definition of GO:0016043 from "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a cellular component; includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a cellular component."
* Added definition dbxref GOC:jl to GO:0016043
* Added definition dbxref GOC:mah to GO:0016043
* Added synonym "cellular component biogenesis" to GO:0016043
* Changed name of GO:0016044 from "membrane organization and biogenesis" to "membrane organization"
* Changed definition of GO:0016044 from "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of membranes inside and surrounding the cell." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins."
* Added definition dbxref GOC:dph to GO:0016044
* Added definition dbxref GOC:jl to GO:0016044
* Added definition dbxref GOC:mah to GO:0016044
* Added synonym "membrane organization and biogenesis" to GO:0016044
* Changed synonym scope of GO:0016044 from "Related" to "Exact"
* Deleted GO:0016363 --part_of--> GO:0031981
* Copied GO:0016363 to GO:0034399 with type part_of
* Set definition of GO:0016863 to "Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor are the same molecule, one or more carbon-carbon double bonds in the molecule are rearranged, and no oxidized product appears."
* Added definition dbxref EC:5.3.3 to GO:0016863
* Added definition dbxref GOC:mah to GO:0016863
* Set definition of GO:0016864 to "Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor are the same molecule, one or more sulfur-sulfur bonds in the molecule are rearranged, and no oxidized product appears."
* Added definition dbxref EC:5.3.4 to GO:0016864
* Added definition dbxref GOC:mah to GO:0016864
* Deleted GO:0030285 --OBO_REL:is_a--> GO:0016021
* Copied GO:0030285 to GO:0031301 with type OBO_REL:is_a
* Changed definition of GO:0030951 from "Any cellular process that results in the  specification, formation or maintenance of polarized microtubule-based cytoskeletal structures." to "Any cellular process that results in the specification, formation or maintenance of polarized microtubule-based cytoskeletal structures."
* Deleted GO:0032592 --OBO_REL:is_a--> GO:0031228
* Changed name of GO:0034330 from "cell junction assembly and maintenance" to "cell junction organization"
* Changed definition of GO:0034330 from "The assembly and maintenance of junctions between cells or between a cell and its substrate." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix."
* Added definition dbxref GOC:dph to GO:0034330
* Added definition dbxref GOC:jl to GO:0034330
* Added synonym "cell junction assembly and maintenance" to GO:0034330
* Changed synonym scope of GO:0034330 from "Related" to "Exact"
* Added synonym "cell junction biogenesis" to GO:0034330
* Added definition dbxref GOC:dph to GO:0034331
* Added definition dbxref GOC:jl to GO:0034331
* Changed definition of GO:0034399 from "The region of the nucleus adjacent to the nuclear envelope." to "The portion of the nuclear lumen proximal to the inner nuclear membrane."
* Added definition dbxref GOC:mah to GO:0034399
* Copied GO:0034399 to GO:0031981 with type part_of
* Changed definition of GO:0034401 from "Any cellular process that results in the  specification, formation or maintenance of of the physical structure of eukaryotic chromatin during transcription." to "Any cellular process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin during transcription."
* Deleted GO:0034729 --OBO_REL:is_a--> GO:0016571
* Copied GO:0034729 to GO:0034968 with type OBO_REL:is_a
* Deleted GO:0034770 --OBO_REL:is_a--> GO:0016571
* Copied GO:0034770 to GO:0034968 with type OBO_REL:is_a
* Changed definition of GO:0034825 from "Catalysis of the reaction: tetralin + O2 + NADH  + H+ = cis-1,2-dihydroxy-1,2,5,6,7,8-hexahydronaphthalene + NAD+." to "Catalysis of the reaction: tetralin + O2 + NADH + H+ = cis-1,2-dihydroxy-1,2,5,6,7,8-hexahydronaphthalene + NAD+."
* Changed definition of GO:0034910 from "Catalysis of the reaction: 6-hydroxy-3-succinoylpyridine + H2O  = succinic semialdehyde + 2,5-dihydroxypyridine." to "Catalysis of the reaction: 6-hydroxy-3-succinoylpyridine + H2O = succinic semialdehyde + 2,5-dihydroxypyridine."
* Changed definition of GO:0034911 from "Catalysis of the reaction: phthalate +  O2 + NADH + H+ = phthalate 3,4-cis-dihydrodiol+ NAD+." to "Catalysis of the reaction: phthalate + O2 + NADH + H+ = phthalate 3,4-cis-dihydrodiol+ NAD+."
* Changed definition of GO:0034916 from "Catalysis of the reaction: 2-methylhexanoyl-CoA = 2-methylhex-2-enoyl-CoA + 2 H+ +  e-." to "Catalysis of the reaction: 2-methylhexanoyl-CoA = 2-methylhex-2-enoyl-CoA + 2 H+ + e-."
* Deleted GO:0042440 --OBO_REL:is_a--> GO:0019748
* Changed synonym scope of GO:0042716 from "Exact" to "Related"
* Deleted GO:0042717 --OBO_REL:is_a--> GO:0042716
* Copied GO:0042717 to GO:0042716 with type part_of
* Copied GO:0042717 to GO:0034357 with type OBO_REL:is_a
* Changed name of GO:0043062 from "extracellular structure organization and biogenesis" to "extracellular structure organization"
* Added definition dbxref GOC:dph to GO:0043062
* Added definition dbxref GOC:jl to GO:0043062
* Added definition dbxref GOC:mah to GO:0043062
* Added synonym "extracellular structure organization and biogenesis" to GO:0043062
* Added general dbxref GOC:mah to synonym extracellular structure organization and biogenesis of GO:0043062
* Added general dbxref GOC:jl to synonym extracellular structure organization and biogenesis of GO:0043062
* Added general dbxref GOC:dph to synonym extracellular structure organization and biogenesis of GO:0043062
* Changed synonym scope of GO:0043062 from "Related" to "Exact"
* Changed name of GO:0043580 from "periplasmic space organization and biogenesis" to "periplasmic space organization"
* Added definition dbxref GOC:dph to GO:0043580
* Added definition dbxref GOC:mah to GO:0043580
* Added synonym "periplasmic space organization and biogenesis" to GO:0043580
* Added general dbxref GOC:mah to synonym periplasmic space organization and biogenesis of GO:0043580
* Added general dbxref GOC:jl to synonym periplasmic space organization and biogenesis of GO:0043580
* Added general dbxref GOC:dph to synonym periplasmic space organization and biogenesis of GO:0043580
* Changed synonym scope of GO:0043580 from "Related" to "Exact"
* Changed name of GO:0043894 from "protein acetyltransferase activity" to "acetyl-CoA synthetase acetyltransferase activity"
* Changed synonym scope of GO:0043894 from "Related" to "Exact"
* Changed synonym scope of GO:0043894 from "Related" to "Exact"
* Added synonym "protein acetyltransferase activity" to GO:0043894
* Changed synonym scope of GO:0043894 from "Related" to "Broad"
* Deleted GO:0044264 --OBO_REL:is_a--> GO:0044260
* Changed definition of GO:0045197 from "Any cellular process that results in the  specification, formation or maintenance of the apicobasal polarity of an epithelial cell." to "Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of an epithelial cell."
* Changed name of GO:0045216 from "cell-cell junction assembly and maintenance" to "cell-cell junction organization"
* Changed definition of GO:0045216 from "The assembly and maintenance of junctions between cells." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells."
* Added definition dbxref GOC:dph to GO:0045216
* Added definition dbxref GOC:jl to GO:0045216
* Added definition dbxref GOC:mah to GO:0045216
* Added synonym "cell-cell junction assembly and maintenance" to GO:0045216
* Changed synonym scope of GO:0045216 from "Related" to "Exact"
* Added synonym "cell-cell junction biogenesis" to GO:0045216
* Changed name of GO:0045229 from "external encapsulating structure organization and biogenesis" to "external encapsulating structure organization"
* Added definition dbxref GOC:dph to GO:0045229
* Added definition dbxref GOC:jl to GO:0045229
* Added definition dbxref GOC:mah to GO:0045229
* Added synonym "external encapsulating structure organization and biogenesis" to GO:0045229
* Added general dbxref GOC:mah to synonym external encapsulating structure organization and biogenesis of GO:0045229
* Added general dbxref GOC:jl to synonym external encapsulating structure organization and biogenesis of GO:0045229
* Added general dbxref GOC:dph to synonym external encapsulating structure organization and biogenesis of GO:0045229
* Changed synonym scope of GO:0045229 from "Related" to "Exact"
* Copied GO:0046158 to GO:0019748 with type OBO_REL:is_a
* Deleted GO:0048494 --OBO_REL:is_a--> GO:0042716
* Copied GO:0048494 to GO:0042716 with type part_of
* Deleted GO:0051567 --OBO_REL:is_a--> GO:0016571
* Copied GO:0051567 to GO:0034968 with type OBO_REL:is_a
* Deleted GO:0051568 --OBO_REL:is_a--> GO:0016571
* Copied GO:0051568 to GO:0034968 with type OBO_REL:is_a

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