[Go-diff] GO update 03/02/2009

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Mon Mar 2 21:30:48 PST 2009 

OBODIFF of gene_ontology_write.obo version 1.461 by 1.463

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010904
* Created object of type obo:TERM with id GO:0010905
* Created object of type obo:TERM with id GO:0010906
* Created object of type obo:TERM with id GO:0010907
* Created object of type obo:TERM with id GO:0070461
* Created object of type obo:TERM with id GO:0070462
* Created object of type obo:TERM with id GO:0070463
* Created object of type obo:TERM with id GO:0070464
* Created object of type obo:TERM with id GO:0070465
* Created object of type obo:TERM with id GO:0070466
* Created object of type obo:TERM with id GO:0070467
* Populated new object GO:0010904 (macro)
  * Changed name of GO:0010904 from "<new term>" to "regulation of UDP-glucose catabolic process"
  * Set definition of GO:0010904 to "Any process that modulates the rate, frequency or extent of UDP-glucose catabolism. UDP-glucose catabolic processes are the chemical reactions and pathways resulting in the breakdown of UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate."
  * Added definition dbxref GOC:tb to GO:0010904
  * Added synonym "regulation of UDP-glucose catabolism" to GO:0010904
  * Added general dbxref GOC:tb to synonym regulation of UDP-glucose catabolism of GO:0010904
  * Changed synonym scope of GO:0010904 from "Related" to "Exact"
  * Copied GO:0010904 to GO:0010906 with type OBO_REL:is_a
  * Copied GO:0010904 to GO:0006258 with type regulates
  * Copied GO:0010904 to GO:0031329 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010904
* Populated new object GO:0010905 (macro)
  * Changed name of GO:0010905 from "<new term>" to "negative regulation of UDP-glucose catabolic process"
  * Set definition of GO:0010905 to "Any process that decreases the rate, frequency or extent of UDP-glucose catabolism. UDP-glucose catabolic processes are the chemical reactions and pathways resulting in the breakdown of UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate."
  * Added definition dbxref GOC:tb to GO:0010905
  * Added synonym "negative regulation of UDP-glucose catabolism" to GO:0010905
  * Added general dbxref GOC:tb to synonym negative regulation of UDP-glucose catabolism of GO:0010905
  * Changed synonym scope of GO:0010905 from "Related" to "Exact"
  * Copied GO:0010905 to GO:0031330 with type OBO_REL:is_a
  * Copied GO:0010905 to GO:0006258 with type negatively_regulates
  * Copied GO:0010905 to GO:0010904 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010905
* Populated new object GO:0010906 (macro)
  * Changed name of GO:0010906 from "<new term>" to "regulation of glucose metabolic process"
  * Set definition of GO:0010906 to "Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose."
  * Added definition dbxref GOC:tb to GO:0010906
  * Added synonym "regulation of glucose metabolism" to GO:0010906
  * Added general dbxref GOC:tb to synonym regulation of glucose metabolism of GO:0010906
  * Changed synonym scope of GO:0010906 from "Related" to "Exact"
  * Copied GO:0010906 to GO:0006006 with type regulates
  * Copied GO:0010906 to GO:0010675 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010906
* Populated new object GO:0010907 (macro)
  * Changed name of GO:0010907 from "<new term>" to "positive regulation of glucose metabolic process"
  * Set definition of GO:0010907 to "Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose."
  * Added definition dbxref GOC:tb to GO:0010907
  * Added synonym "positive regulation of glucose metabolism" to GO:0010907
  * Added general dbxref GOC:tb to synonym positive regulation of glucose metabolism of GO:0010907
  * Changed synonym scope of GO:0010907 from "Related" to "Exact"
  * Copied GO:0010907 to GO:0010676 with type OBO_REL:is_a
  * Copied GO:0010907 to GO:0006006 with type positively_regulates
  * Copied GO:0010907 to GO:0010906 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010907
* Populated new object GO:0070461 (macro)
  * Changed name of GO:0070461 from "<new term>" to "SAGA-type complex"
  * Set definition of GO:0070461 to "A histone acetyltransferase complex that acetylates nucleosomal H3 and H2B and is required for the expression of a subset of Pol II-transcribed genes. The budding yeast complex includes the acetyltransferase Gcn5p, several proteins of the Spt and Ada families, and several TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins."
  * Added definition dbxref GOC:mah to GO:0070461
  * Added definition dbxref PMID:10637607 to GO:0070461
  * Added definition dbxref PMID:17337012 to GO:0070461
  * Added synonym "SAGA family complex" to GO:0070461
  * Added general dbxref PMID:17337012 to synonym SAGA family complex of GO:0070461
  * Changed synonym scope of GO:0070461 from "Related" to "Exact"
  * Copied GO:0070461 to GO:0000123 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070461
* Populated new object GO:0070462 (macro)
  * Changed name of GO:0070462 from "<new term>" to "plus-end specific microtubule depolymerization"
  * Set definition of GO:0070462 to "The removal of tubulin heterodimers from the plus end of a microtubule."
  * Added definition dbxref GOC:krc to GO:0070462
  * Added definition dbxref PMID:16906145 to GO:0070462
  * Added definition dbxref PMID:16906148 to GO:0070462
  * Copied GO:0070462 to GO:0007019 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070462
* Populated new object GO:0070463 (macro)
  * Changed name of GO:0070463 from "<new term>" to "tubulin-dependent ATPase activity"
  * Added comment "Consider also annotating to the molecular function term 'ATP binding ; GO:0005524'."
  * Set definition of GO:0070463 to "Catalysis of the reaction: ATP + H2O = ADP + phosphate, requiring the presence of a tubulin dimer to accelerate release of ADP and phosphate."
  * Added definition dbxref GOC:mah to GO:0070463
  * Added definition dbxref PMID:16906148 to GO:0070463
  * Added synonym "tubulin-activated ATPase activity" to GO:0070463
  * Changed synonym scope of GO:0070463 from "Related" to "Exact"
  * Copied GO:0070463 to GO:0042623 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070463
* Populated new object GO:0070464 (macro)
  * Changed name of GO:0070464 from "<new term>" to "alphav-beta3 integrin-collagen alpha3(VI) complex"
  * Set definition of GO:0070464 to "A protein complex that consists of an alphav-beta3 integrin complex bound to the alpha3 chain of type VI collagen; the integrin binds most strongly to unfolded collagen."
  * Added definition dbxref PMID:8387021 to GO:0070464
  * Copied GO:0070464 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0070464 to GO:0044459 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070464
* Populated new object GO:0070465 (macro)
  * Changed name of GO:0070465 from "<new term>" to "alpha1-beta1 integrin-alpha3(VI) complex"
  * Set definition of GO:0070465 to "A protein complex that consists of an alpha1-beta1 integrin complex bound to a type VI collagen triple helix containing an alpha3(VI) chain."
  * Added definition dbxref PMID:8387021 to GO:0070465
  * Added synonym "ITGA1-ITGB1-COL6A3 complex" to GO:0070465
  * Added general dbxref CORUM:2434 to synonym ITGA1-ITGB1-COL6A3 complex of GO:0070465
  * Changed synonym scope of GO:0070465 from "Related" to "Narrow"
  * Copied GO:0070465 to GO:0044459 with type OBO_REL:is_a
  * Copied GO:0070465 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070465
* Populated new object GO:0070466 (macro)
  * Changed name of GO:0070466 from "<new term>" to "alpha2-beta1 integrin-alpha3(VI) complex"
  * Set definition of GO:0070466 to "A protein complex that consists of an alpha2-beta1 integrin complex bound to a type VI collagen triple helix containing an alpha3(VI) chain."
  * Added definition dbxref PMID:8387021 to GO:0070466
  * Added synonym "ITGA2-ITGB1-COL6A3 complex" to GO:0070466
  * Added general dbxref CORUM:2431 to synonym ITGA2-ITGB1-COL6A3 complex of GO:0070466
  * Changed synonym scope of GO:0070466 from "Related" to "Narrow"
  * Copied GO:0070466 to GO:0044459 with type OBO_REL:is_a
  * Copied GO:0070466 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070466
* Populated new object GO:0070467 (macro)
  * Changed name of GO:0070467 from "<new term>" to "RC-1 DNA recombination complex"
  * Set definition of GO:0070467 to "A protein complex that contains DNA ligase III, DNA polymerase epsilon, a 5'-3' exonuclease, and the SMC1 and SMC2 proteins, and is involved in recombinational repair of deletions and gaps in DNA."
  * Added definition dbxref PMID:8392064 to GO:0070467
  * Added definition dbxref PMID:8670910 to GO:0070467
  * Added synonym "DNA recombination complex RC-1" to GO:0070467
  * Added general dbxref GOC:mah to synonym DNA recombination complex RC-1 of GO:0070467
  * Changed synonym scope of GO:0070467 from "Related" to "Exact"
  * Added synonym "RC-1 complex (recombination complex 1)" to GO:0070467
  * Added general dbxref CORUM:364 to synonym RC-1 complex (recombination complex 1) of GO:0070467
  * Changed synonym scope of GO:0070467 from "Related" to "Exact"
  * Copied GO:0070467 to GO:0044428 with type OBO_REL:is_a
  * Copied GO:0070467 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070467
* Changed definition of GO:0000124 from "A large multiprotein complex that possesses histone acetyltransferase activity and is involved in regulation of transcription. The budding yeast complex includes Gcn5p, several proteins of the Spt and Ada families, and several TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins." to "A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery."
* Added definition dbxref PMID:17337012 to GO:0000124
* Deleted GO:0000124 --OBO_REL:is_a--> GO:0000123
* Copied GO:0000124 to GO:0070461 with type OBO_REL:is_a
* Deleted GO:0000125 --OBO_REL:is_a--> GO:0000123
* Copied GO:0000125 to GO:0070461 with type OBO_REL:is_a
* Added general dbxref Wikipedia:Signal_recognition_particle to GO:0005786
* Copied GO:0006110 to GO:0010906 with type OBO_REL:is_a
* Deleted GO:0006111 --OBO_REL:is_a--> GO:0010675
* Copied GO:0006111 to GO:0010906 with type OBO_REL:is_a
* Added synonym "succinyl-CoA synthetase, ADP-forming" to GO:0009361
* Added general dbxref CORUM:394 to synonym succinyl-CoA synthetase, ADP-forming of GO:0009361
* Changed synonym scope of GO:0009361 from "Related" to "Exact"
* Deleted GO:0030914 --OBO_REL:is_a--> GO:0000123
* Copied GO:0030914 to GO:0070461 with type OBO_REL:is_a
* Added synonym "expulsion of gland contents" to GO:0032941
* Added general dbxref GOC:mah to synonym expulsion of gland contents of GO:0032941
* Copied GO:0033276 to GO:0070461 with type OBO_REL:is_a
* Changed definition of GO:0034505 from "The process by which calcium salts are deposited into calcareous tooth structures such as dental enamel, dentin and cementum." to "The process by which calcium salts are deposited into calcareous tooth structures such as dental enamel, dentine and cementum."
* Added general dbxref Wikipedia:T_cell_receptor to GO:0042101
* Copied GO:0043456 to GO:0010906 with type OBO_REL:is_a
* Added synonym "succinyl-CoA synthetase, GDP-forming" to GO:0045244
* Added general dbxref CORUM:392 to synonym succinyl-CoA synthetase, GDP-forming of GO:0045244
* Changed synonym scope of GO:0045244 from "Related" to "Exact"
* Deleted GO:0045722 --OBO_REL:is_a--> GO:0010676
* Copied GO:0045722 to GO:0010907 with type OBO_REL:is_a
* Copied GO:0045821 to GO:0010907 with type OBO_REL:is_a
* Changed definition of GO:0046695 from "A protein complex similar to the SAGA complex but with a smaller form of Spt7 and no Spt8. Although little is known about the SLIK complex, evidence suggests involvement of the general amino acid control pathway." to "A SAGA-type histone acetyltransferase complex that contains Rtg2 and a smaller form of Spt7 than the fungal SAGA complex, and lacks Spt8. The complex is involved in the yeast retrograde response pathway, which is important for gene expression changes during mitochondrial dysfunction."
* Added definition dbxref PMID:17337012 to GO:0046695
* Deleted GO:0046695 --OBO_REL:is_a--> GO:0000123
* Copied GO:0046695 to GO:0070461 with type OBO_REL:is_a

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