[Go-diff] GO update 08/27/2008

Wed Aug 27 21:30:47 PDT 2008

OBODIFF of gene_ontology_write.obo version 1.183 by 1.184

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034720
* Created object of type obo:TERM with id GO:0034721
* Created object of type obo:TERM with id GO:0034722
* Created object of type obo:TERM with id GO:0034723
* Created object of type obo:TERM with id GO:0034724
* Created object of type obo:TERM with id GO:0034725
* Created object of type obo:TERM with id GO:0034726
* Created object of type obo:TERM with id GO:0034727
* Created object of type obo:TERM with id GO:0034728
* Created object of type obo:TERM with id GO:0034729
* Created object of type obo:TERM with id GO:0034730
* Created object of type obo:TERM with id GO:0034731
* Populated new object GO:0034720 (macro)
  * Changed name of GO:0034720 from "<new term>" to "histone H3-K4 demethylation"
  * Set definition of GO:0034720 to "The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone."
  * Added definition dbxref GOC:mah to GO:0034720
  * Added synonym "H3K4 demethylation (me1 me2 and me3)" to GO:0034720
  * Copied GO:0034720 to GO:0016577 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034720
* Populated new object GO:0034721 (macro)
  * Changed name of GO:0034721 from "<new term>" to "histone H3-K4 demethylation, trimethyl-H3-K4-specific"
  * Set definition of GO:0034721 to "The modification of histone H3 by the removal of a methyl group from a trimetylated lysine at position 4 of the histone."
  * Added definition dbxref GOC:mah to GO:0034721
  * Added synonym "H3K4 demethylation (me3)" to GO:0034721
  * Changed synonym scope of GO:0034721 from "Related" to "Exact"
  * Added synonym "histone H3-K4 tridemethylation" to GO:0034721
  * Copied GO:0034721 to GO:0016577 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034721
* Populated new object GO:0034722 (macro)
  * Changed name of GO:0034722 from "<new term>" to "gamma-glutamyl-peptidase activity"
  * Set definition of GO:0034722 to "Catalysis of the cleavage of a gamma-linked glutamate bond."
  * Added definition dbxref EC:3.4.19.9 to GO:0034722
  * Added definition dbxref MEROPS_fam:C26 to GO:0034722
  * Added general dbxref EC:3.4.19.9 to GO:0034722
  * Added GO:0034722 to category gosubset_prok
  * Added synonym "gamma-glutamyl hydrolase activity" to GO:0034722
  * Added general dbxref EC:3.4.19.9 to synonym gamma-glutamyl hydrolase activity of GO:0034722
  * Changed synonym scope of GO:0034722 from "Related" to "Exact"
  * Copied GO:0034722 to GO:0008242 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034722
* Populated new object GO:0034723 (macro)
  * Changed name of GO:0034723 from "<new term>" to "DNA replication-dependent nucleosome organization"
  * Set definition of GO:0034723 to "The formation or destruction of chromatin structures on newly replicated DNA, coupled to strand elongation."
  * Added definition dbxref GOC:mah to GO:0034723
  * Added definition dbxref PMID:17510629 to GO:0034723
  * Added synonym "DNA replication-dependent nucleosome organisation" to GO:0034723
  * Changed synonym scope of GO:0034723 from "Related" to "Exact"
  * Copied GO:0034723 to GO:0006333 with type OBO_REL:is_a
  * Copied GO:0034723 to GO:0034728 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034723
* Populated new object GO:0034724 (macro)
  * Changed name of GO:0034724 from "<new term>" to "DNA replication-independent nucleosome organization"
  * Set definition of GO:0034724 to "The formation or destruction of chromatin structures, occurring outside the context of DNA replication."
  * Added definition dbxref GOC:mah to GO:0034724
  * Added definition dbxref PMID:17510629 to GO:0034724
  * Added synonym "DNA replication-independent nucleosome organisation" to GO:0034724
  * Changed synonym scope of GO:0034724 from "Related" to "Exact"
  * Copied GO:0034724 to GO:0006333 with type OBO_REL:is_a
  * Copied GO:0034724 to GO:0034728 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034724
* Populated new object GO:0034725 (macro)
  * Changed name of GO:0034725 from "<new term>" to "DNA replication-dependent nucleosome disassembly"
  * Set definition of GO:0034725 to "The controlled breakdown of nucleosomes on newly replicated DNA, coupled to strand elongation."
  * Added definition dbxref GOC:mah to GO:0034725
  * Added definition dbxref PMID:17510629 to GO:0034725
  * Copied GO:0034725 to GO:0034723 with type OBO_REL:is_a
  * Copied GO:0034725 to GO:0006337 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034725
* Populated new object GO:0034726 (macro)
  * Changed name of GO:0034726 from "<new term>" to "DNA replication-independent nucleosome disassembly"
  * Set definition of GO:0034726 to "The controlled breakdown of nucleosomes outside the context of DNA replication."
  * Added definition dbxref GOC:mah to GO:0034726
  * Added definition dbxref PMID:17510629 to GO:0034726
  * Copied GO:0034726 to GO:0034724 with type OBO_REL:is_a
  * Copied GO:0034726 to GO:0006337 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034726
* Populated new object GO:0034727 (macro)
  * Changed name of GO:0034727 from "<new term>" to "piecemeal microautophagy of nucleus"
  * Set definition of GO:0034727 to "Degradation of a cell nucleus by microautophagy."
  * Added definition dbxref GOC:jp to GO:0034727
  * Added definition dbxref PMID:18701704 to GO:0034727
  * Added synonym "PMN" to GO:0034727
  * Changed synonym scope of GO:0034727 from "Related" to "Exact"
  * Copied GO:0034727 to GO:0000422 with type OBO_REL:is_a
  * Copied GO:0034727 to GO:0016237 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034727
* Populated new object GO:0034728 (macro)
  * Changed name of GO:0034728 from "<new term>" to "nucleosome organization"
  * Set definition of GO:0034728 to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of one or more nucleosomes."
  * Added definition dbxref GOC:mah to GO:0034728
  * Added synonym "nucleosome organisation" to GO:0034728
  * Changed synonym scope of GO:0034728 from "Related" to "Exact"
  * Copied GO:0034728 to GO:0006325 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034728
* Populated new object GO:0034729 (macro)
  * Changed name of GO:0034729 from "<new term>" to "histone H3-K79 methylation"
  * Set definition of GO:0034729 to "The modification of histone H3 by addition of a methyl group to lysine at position 79 of the histone."
  * Added definition dbxref GOC:se to GO:0034729
  * Added synonym "histone H3 K79 methylation" to GO:0034729
  * Changed synonym scope of GO:0034729 from "Related" to "Exact"
  * Added synonym "histone H3K79me" to GO:0034729
  * Changed synonym scope of GO:0034729 from "Related" to "Exact"
  * Added synonym "histone lysine H3 K79 methylation" to GO:0034729
  * Changed synonym scope of GO:0034729 from "Related" to "Exact"
  * Copied GO:0034729 to GO:0016571 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034729
* Populated new object GO:0034730 (macro)
  * Changed name of GO:0034730 from "<new term>" to "SmD-containing SMN-Sm protein complex"
  * Set definition of GO:0034730 to "An SMN-Sm protein complex formed by the association of the methylated Sm proteins B/B', D1, D2, D3, E, F, and G with the SMN complex."
  * Added definition dbxref PMID:12975319 to GO:0034730
  * Added definition dbxref PMID:17401408 to GO:0034730
  * Added synonym "SMN-containing protein complex" to GO:0034730
  * Changed synonym scope of GO:0034730 from "Related" to "Broad"
  * Copied GO:0034730 to GO:0034719 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034730
* Populated new object GO:0034731 (macro)
  * Changed name of GO:0034731 from "<new term>" to "Lsm-containing SMN-Sm protein complex"
  * Set definition of GO:0034731 to "An SMN-Sm protein complex formed by the association of the methylated Sm proteins B/B', D3, E, F, and G, and Lsm10 and Lsm11, with the SMN complex. This complex forms Sm cores on U7 snRNA."
  * Added definition dbxref PMID:12975319 to GO:0034731
  * Added definition dbxref PMID:17401408 to GO:0034731
  * Added synonym "SMN-containing protein complex" to GO:0034731
  * Changed synonym scope of GO:0034731 from "Related" to "Broad"
  * Copied GO:0034731 to GO:0034719 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034731
* Added comment "This term was made obsolete because it represents a gene product."
* Set definition of GO:0004680 to "OBSOLETE (was not defined before being made obsolete)."
* Added definition dbxref GOC:mah to GO:0004680
* Deleted GO:0004680 --OBO_REL:is_a--> GO:0004674
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at a3b3ce
* Added comment "This term was made obsolete because it represents a gene product."
* Set definition of GO:0004681 to "OBSOLETE (was not defined before being made obsolete)."
* Added definition dbxref GOC:mah to GO:0004681
* Deleted GO:0004681 --OBO_REL:is_a--> GO:0004680
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 171c7df
* Added comment "This term was made obsolete because it represents a gene product."
* Changed definition of GO:0004682 from "Catalysis of the reaction: casein + ATP = phosphocasein + ADP." to "OBSOLETE. Catalysis of the reaction: casein + ATP = phosphocasein + ADP."
* Deleted GO:0004682 --OBO_REL:is_a--> GO:0004680
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at f91ad5
* Added synonym "55S ribosome, mitochondrial" to GO:0005761
* Changed synonym scope of GO:0005761 from "Related" to "Narrow"
* Added synonym "39S ribosomal subunit, mitochondrial" to GO:0005762
* Changed synonym scope of GO:0005762 from "Related" to "Narrow"
* Added synonym "28S ribosomal subunit, mitochondrial" to GO:0005763
* Changed synonym scope of GO:0005763 from "Related" to "Narrow"
* Changed name of GO:0006325 from "establishment and/or maintenance of chromatin architecture" to "establishment or maintenance of chromatin architecture"
* Changed definition of GO:0006325 from "The specification, formation and maintenance of the physical structure of eukaryotic chromatin." to "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin."
* Deleted GO:0006334 --OBO_REL:is_a--> GO:0031497
* Copied GO:0006334 to GO:0031497 with type part_of
* Copied GO:0006334 to GO:0034728 with type OBO_REL:is_a
* Copied GO:0006335 to GO:0034723 with type OBO_REL:is_a
* Copied GO:0006336 to GO:0034724 with type OBO_REL:is_a
* Changed definition of GO:0006337 from "The disassembly of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA." to "The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA."
* Copied GO:0006337 to GO:0034728 with type OBO_REL:is_a
* Added synonym "peptidase activity, acting on peptides containing modified amino acids" to GO:0008242
* Copied GO:0016584 to GO:0034728 with type OBO_REL:is_a
* Changed definition of GO:0031498 from "The disassembly of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, and other proteins." to "The controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, and other proteins."
* Deleted GO:0031914 --OBO_REL:is_a--> GO:0050804
* Deleted GO:0031915 --OBO_REL:is_a--> GO:0050804
* Added comment "Note that a larger complex containing Sm proteins and other subunits is also sometimes referred to as the 'SMN complex'. The larger complex is represented by 'SMN-Sm protein complex ; GO:0034719'."
* Added synonym "SMN core complex" to GO:0032797
* Changed synonym scope of GO:0032797 from "Related" to "Exact"
* Added comment "Note that this complex is sometimes referred to as the 'SMN complex', but it should not be confused with GO:0032797."
* Changed definition of GO:0034719 from "A protein complex formed by the association of several methylated Sm proteins with the SMN complex; the latter contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and unrip proteins. The SMN-Sm complex is involved in spliceosomal snRNP assembly in the cytoplasm." to "A protein complex formed by the association of several methylated Sm proteins with the SMN complex; the latter contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and unrip proteins; additional proteins, including galectin-1 and galectin-3, are also found in the SMN-SM complex. The SMN-Sm complex is involved in spliceosomal snRNP assembly in the cytoplasm."
* Added definition dbxref PMID:11522829 to GO:0034719
* Added synonym "SMN-containing protein complex" to GO:0034719
* Changed synonym scope of GO:0034719 from "Related" to "Broad"
* Copied GO:0042766 to GO:0034728 with type OBO_REL:is_a
* Copied GO:0043486 to GO:0034728 with type OBO_REL:is_a