[Go-diff] GO update 09/25/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Thu Sep 25 21:30:47 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.231 by 1.234

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0070034
* Created object of type obo:TERM with id GO:0070035
* Created object of type obo:TERM with id GO:0070036
* Created object of type obo:TERM with id GO:0070037
* Created object of type obo:TERM with id GO:0070038
* Created object of type obo:TERM with id GO:0070039
* Created object of type obo:TERM with id GO:0070040
* Created object of type obo:TERM with id GO:0070041
* Created object of type obo:TERM with id GO:0070042
* Created object of type obo:TERM with id GO:0070043
* Created object of type obo:TERM with id GO:0070044
* Created object of type obo:TERM with id GO:0070045
* Created object of type obo:TERM with id GO:0070046
* Created object of type obo:TERM with id GO:0070047
* Created object of type obo:TERM with id GO:0070048
* Created object of type obo:TERM with id GO:0070049
* Populated new object GO:0070034 (macro)
  * Changed name of GO:0070034 from "<new term>" to "telomeric RNA binding"
  * Set definition of GO:0070034 to "Interacting selectively with the telomerase RNA template or to RNA complementary to it."
  * Added definition dbxref GOC:krc to GO:0070034
  * Added definition dbxref PMID:16884717 to GO:0070034
  * Added synonym "telomeric RNA repeat binding" to GO:0070034
  * Changed synonym scope of GO:0070034 from "Related" to "Narrow"
  * Copied GO:0070034 to GO:0003723 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070034
* Populated new object GO:0070035 (macro)
  * Changed name of GO:0070035 from "<new term>" to "purine NTP-dependent helicase activity"
  * Added comment "Consider also annotating to the molecular function term 'ATP binding ; GO:0005524'."
  * Set definition of GO:0070035 to "Catalysis of the reaction: purine NTP + H2O = purine NTP + phosphate to drive the unwinding of a DNA or RNA helix."
  * Added definition dbxref GOC:mah to GO:0070035
  * Added GO:0070035 to category gosubset_prok
  * Copied GO:0070035 to GO:0004386 with type OBO_REL:is_a
  * Copied GO:0070035 to GO:0042623 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070035
* Populated new object GO:0070036 (macro)
  * Changed name of GO:0070036 from "<new term>" to "GTP-dependent helicase activity"
  * Added comment "Consider also annotating to the molecular function term 'ATP binding ; GO:0005524'."
  * Set definition of GO:0070036 to "Catalysis of the reaction: GTP + H2O = GDP + phosphate to drive the unwinding of a DNA or RNA helix."
  * Added definition dbxref GOC:mah to GO:0070036
  * Added GO:0070036 to category gosubset_prok
  * Copied GO:0070036 to GO:0070035 with type OBO_REL:is_a
  * Copied GO:0070036 to GO:0042623 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070036
* Populated new object GO:0070037 (macro)
  * Changed name of GO:0070037 from "<new term>" to "rRNA (pseudouridine) methyltransferase activity"
  * Set definition of GO:0070037 to "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a pseudouridine residue in an rRNA molecule."
  * Added definition dbxref GOC:imk to GO:0070037
  * Added definition dbxref GOC:mah to GO:0070037
  * Added GO:0070037 to category gosubset_prok
  * Copied GO:0070037 to GO:0008649 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070037
* Populated new object GO:0070038 (macro)
  * Changed name of GO:0070038 from "<new term>" to "rRNA (pseudouridine-N3-)-methyltransferase activity"
  * Set definition of GO:0070038 to "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methylpseudouridine."
  * Added definition dbxref GOC:imk to GO:0070038
  * Added definition dbxref GOC:mah to GO:0070038
  * Added GO:0070038 to category gosubset_prok
  * Copied GO:0070038 to GO:0070037 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070038
* Populated new object GO:0070039 (macro)
  * Changed name of GO:0070039 from "<new term>" to "rRNA (guanosine-2'-O-)-methyltransferase activity"
  * Set definition of GO:0070039 to "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methylguanosine."
  * Added definition dbxref GOC:imk to GO:0070039
  * Added definition dbxref GOC:mah to GO:0070039
  * Added GO:0070039 to category gosubset_prok
  * Copied GO:0070039 to GO:0016435 with type OBO_REL:is_a
  * Copied GO:0070039 to GO:0008171 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070039
* Populated new object GO:0070040 (macro)
  * Changed name of GO:0070040 from "<new term>" to "rRNA (adenine-C2-)-methyltransferase activity"
  * Set definition of GO:0070040 to "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing C2-methyladenine."
  * Added definition dbxref GOC:imk to GO:0070040
  * Added definition dbxref GOC:mah to GO:0070040
  * Added GO:0070040 to category gosubset_prok
  * Copied GO:0070040 to GO:0008169 with type OBO_REL:is_a
  * Copied GO:0070040 to GO:0016433 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070040
* Populated new object GO:0070041 (macro)
  * Changed name of GO:0070041 from "<new term>" to "rRNA (uridine-C5-)-methyltransferase activity"
  * Set definition of GO:0070041 to "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing C5-methyluridine."
  * Added definition dbxref GOC:imk to GO:0070041
  * Added definition dbxref GOC:mah to GO:0070041
  * Added GO:0070041 to category gosubset_prok
  * Copied GO:0070041 to GO:0016436 with type OBO_REL:is_a
  * Copied GO:0070041 to GO:0008169 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070041
* Populated new object GO:0070042 (macro)
  * Changed name of GO:0070042 from "<new term>" to "rRNA (uridine-N3-)-methyltransferase activity"
  * Set definition of GO:0070042 to "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methyluridine."
  * Added definition dbxref GOC:imk to GO:0070042
  * Added definition dbxref GOC:mah to GO:0070042
  * Added GO:0070042 to category gosubset_prok
  * Copied GO:0070042 to GO:0008170 with type OBO_REL:is_a
  * Copied GO:0070042 to GO:0016436 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070042
* Populated new object GO:0070043 (macro)
  * Changed name of GO:0070043 from "<new term>" to "rRNA (guanine-N7-)-methyltransferase activity"
  * Set definition of GO:0070043 to "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N7-methylguanine."
  * Added definition dbxref GOC:imk to GO:0070043
  * Added definition dbxref GOC:mah to GO:0070043
  * Added GO:0070043 to category gosubset_prok
  * Copied GO:0070043 to GO:0008170 with type OBO_REL:is_a
  * Copied GO:0070043 to GO:0016435 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070043
* Populated new object GO:0070044 (macro)
  * Changed name of GO:0070044 from "<new term>" to "synaptobrevin 2-SNAP-25-syntaxin-1a complex"
  * Set definition of GO:0070044 to "A SNARE complex that contains synaptobrevin 2 (VAMP2), SNAP-25, and syntaxin 1a (or orthologs thereof)."
  * Added definition dbxref PMID:10336434 to GO:0070044
  * Added synonym "Snap25-Stx1a-Vamp2 complex" to GO:0070044
  * Changed synonym scope of GO:0070044 from "Related" to "Narrow"
  * Added synonym "SNARE complex (Snap25, Stx1a, Vamp2)" to GO:0070044
  * Added general dbxref CORUM:998 to synonym SNARE complex (Snap25, Stx1a, Vamp2) of GO:0070044
  * Changed synonym scope of GO:0070044 from "Related" to "Narrow"
  * Copied GO:0070044 to GO:0031201 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070044
* Populated new object GO:0070045 (macro)
  * Changed name of GO:0070045 from "<new term>" to "synaptobrevin 2-SNAP-25-syntaxin-2 complex"
  * Set definition of GO:0070045 to "A SNARE complex that contains synaptobrevin 2 (VAMP2), SNAP-25, and syntaxin 2 (or orthologs thereof)."
  * Added definition dbxref PMID:10336434 to GO:0070045
  * Added synonym "SNARE complex (Stx2, Snap25, Vamp2)" to GO:0070045
  * Added general dbxref CORUM:851 to synonym SNARE complex (Stx2, Snap25, Vamp2) of GO:0070045
  * Changed synonym scope of GO:0070045 from "Related" to "Narrow"
  * Added synonym "Stx2-Snap25-Vamp2 complex" to GO:0070045
  * Added general dbxref CORUM:851 to synonym Stx2-Snap25-Vamp2 complex of GO:0070045
  * Changed synonym scope of GO:0070045 from "Related" to "Narrow"
  * Copied GO:0070045 to GO:0031201 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070045
* Populated new object GO:0070046 (macro)
  * Changed name of GO:0070046 from "<new term>" to "synaptobrevin 2-SNAP-25-syntaxin-3 complex"
  * Set definition of GO:0070046 to "A SNARE complex that contains synaptobrevin 2 (VAMP2), SNAP-25, and syntaxin 3 (or orthologs thereof)."
  * Added definition dbxref PMID:10336434 to GO:0070046
  * Added synonym "SNARE complex (Stx3, Snap25, Vamp2)" to GO:0070046
  * Added general dbxref CORUM:852 to synonym SNARE complex (Stx3, Snap25, Vamp2) of GO:0070046
  * Changed synonym scope of GO:0070046 from "Related" to "Narrow"
  * Added synonym "Stx3-Snap25-Vamp2 complex" to GO:0070046
  * Added general dbxref CORUM:852 to synonym Stx3-Snap25-Vamp2 complex of GO:0070046
  * Changed synonym scope of GO:0070046 from "Related" to "Narrow"
  * Copied GO:0070046 to GO:0031201 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070046
* Populated new object GO:0070047 (macro)
  * Changed name of GO:0070047 from "<new term>" to "synaptobrevin 2-SNAP-25-syntaxin-4 complex"
  * Set definition of GO:0070047 to "A SNARE complex that contains synaptobrevin 2 (VAMP2), SNAP-25, and syntaxin 4 (or orthologs thereof)."
  * Added definition dbxref PMID:10336434 to GO:0070047
  * Added synonym "SNARE complex (Stx4, Snap25, Vamp2)" to GO:0070047
  * Added general dbxref CORUM:853 to synonym SNARE complex (Stx4, Snap25, Vamp2) of GO:0070047
  * Changed synonym scope of GO:0070047 from "Related" to "Narrow"
  * Added synonym "Stx4-Snap25-Vamp2 complex" to GO:0070047
  * Added general dbxref CORUM:853 to synonym Stx4-Snap25-Vamp2 complex of GO:0070047
  * Changed synonym scope of GO:0070047 from "Related" to "Narrow"
  * Copied GO:0070047 to GO:0031201 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070047
* Populated new object GO:0070048 (macro)
  * Changed name of GO:0070048 from "<new term>" to "endobrevin-SNAP-25-syntaxin-1a complex"
  * Set definition of GO:0070048 to "A SNARE complex that contains endobrevin (VAMP8), SNAP-25, and syntaxin 1a (or orthologs thereof)."
  * Added definition dbxref PMID:10336434 to GO:0070048
  * Added synonym "SNARE complex (Stx1a, Snap25, Vamp8)" to GO:0070048
  * Added general dbxref CORUM:854 to synonym SNARE complex (Stx1a, Snap25, Vamp8) of GO:0070048
  * Changed synonym scope of GO:0070048 from "Related" to "Narrow"
  * Added synonym "Stx1a-Snap25-Vamp8 complex" to GO:0070048
  * Added general dbxref CORUM:854 to synonym Stx1a-Snap25-Vamp8 complex of GO:0070048
  * Changed synonym scope of GO:0070048 from "Related" to "Narrow"
  * Copied GO:0070048 to GO:0031201 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070048
* Populated new object GO:0070049 (macro)
  * Changed name of GO:0070049 from "<new term>" to "endobrevin-SNAP-25-syntaxin-2 complex"
  * Set definition of GO:0070049 to "A SNARE complex that contains endobrevin (VAMP8), SNAP-25, and syntaxin 2 (or orthologs thereof)."
  * Added definition dbxref PMID:10336434 to GO:0070049
  * Added synonym "SNARE complex (Stx2, Snap25, Vamp8)" to GO:0070049
  * Added general dbxref CORUM:855 to synonym SNARE complex (Stx2, Snap25, Vamp8) of GO:0070049
  * Changed synonym scope of GO:0070049 from "Related" to "Narrow"
  * Added synonym "Stx2-Snap25-Vamp8 complex" to GO:0070049
  * Added general dbxref CORUM:855 to synonym Stx2-Snap25-Vamp8 complex of GO:0070049
  * Changed synonym scope of GO:0070049 from "Related" to "Narrow"
  * Copied GO:0070049 to GO:0031201 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070049
* Added comment "This term was made obsolete because it represents a gene product."
* Set definition of GO:0005061 to "OBSOLETE (was not defined before being made obsolete)."
* Added definition dbxref GOC:mah to GO:0005061
* Deleted GO:0005061 --OBO_REL:is_a--> GO:0005057
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 1645d10
* Deleted GO:0008026 --OBO_REL:is_a--> GO:0004386
* Copied GO:0008026 to GO:0070035 with type OBO_REL:is_a
* Changed definition of GO:0008650 from "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the 2'-O atom of a uridine residue in an rRNA molecule." to "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methyluridine."
* Copied GO:0008650 to GO:0008171 with type OBO_REL:is_a
* Added synonym "telomeric repeat binding" to GO:0042162
* Changed synonym scope of GO:0042162 from "Related" to "Narrow"
* Added comment "This term was made obsolete because it represents two activities."
* Changed definition of GO:0042408 from "Catalysis of the conversion of geranyl diphosphate (GPP) into the acyclic monoterpenes beta-myrcene, (E)-beta-ocimene, and other minor cyclic monoterpenes." to "OBSOLETE. Catalysis of the conversion of geranyl diphosphate (GPP) into the acyclic monoterpenes beta-myrcene, (E)-beta-ocimene, and other minor cyclic monoterpenes."
* Deleted GO:0042408 --OBO_REL:is_a--> GO:0009975
* Deleted GO:0042408 --OBO_REL:is_a--> GO:0016849
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 19d89d
* Added synonym "Vamp2-Snap25-Stx1a-Cplx1 complex" to GO:0070032
* Added general dbxref CORUM:795 to synonym Vamp2-Snap25-Stx1a-Cplx1 complex of GO:0070032
* Changed synonym scope of GO:0070032 from "Related" to "Narrow"
* Added synonym "Vamp2-Snap25-Stx1a-Cplx2 complex" to GO:0070033
* Added general dbxref CORUM:796 to synonym Vamp2-Snap25-Stx1a-Cplx2 complex of GO:0070033
* Changed synonym scope of GO:0070033 from "Related" to "Narrow"

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