[go-diff] GO update 02/21/2008

Thu Feb 21 21:30:44 PST 2008

OBODIFF of gene_ontology_edit.obo version 5.700 by 5.702

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034270
* Created object of type obo:TERM with id GO:0034271
* Created object of type obo:TERM with id GO:0034272
* Created object of type obo:TERM with id GO:0034273
* Created object of type obo:TERM with id GO:0034274
* Created object of type obo:TERM with id GO:0034275
* Created object of type obo:TERM with id GO:0034276
* Populated new object GO:0034270 (macro)
  * Changed name of GO:0034270 from "<new term>" to "CVT complex"
  * Set definition of GO:0034270 to "A receptor-cargo protein complex that is involved in the CVT pathway. In budding yeast, the CVT complex consists of the preApe1p and Atg19p proteins."
  * Added definition dbxref GOC:rb to GO:0034270
  * Added definition dbxref PMID:15659643 to GO:0034270
  * Added synonym "preAPE1-Atg11p complex" to GO:0034270
  * Copied GO:0034270 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034270 to GO:0044444 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034270
* Populated new object GO:0034271 (macro)
  * Changed name of GO:0034271 from "<new term>" to "phosphatidylinositol 3-kinase complex I"
  * Added comment "Note that this term should not be confused with '1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex; GO:0005943' or '1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex ; GO:0005944'."
  * Set definition of GO:0034271 to "A protein complex that posseses phosphatidylinositol 3-kinase activity and is involved in autophagy. In budding yeast, this complex consists of Vps30p, Vps34p, Atg14p and Vps15p."
  * Added definition dbxref GOC:rb to GO:0034271
  * Added definition dbxref PMID:11157979 to GO:0034271
  * Added definition dbxref PMID:16421251 to GO:0034271
  * Added synonym "PtdIns-3-kinase complex I" to GO:0034271
  * Changed synonym scope of GO:0034271 from "Related" to "Exact"
  * Copied GO:0034271 to GO:0005942 with type OBO_REL:is_a
  * Copied GO:0034271 to GO:0044444 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034271
* Populated new object GO:0034272 (macro)
  * Changed name of GO:0034272 from "<new term>" to "phosphatidylinositol 3-kinase complex II"
  * Added comment "Note that this term should not be confused with '1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex; GO:0005943' or '1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex ; GO:0005944'."
  * Set definition of GO:0034272 to "A protein complex that posseses phosphatidylinositol 3-kinase activity and is involved in vacuolar protein sorting (VPS) via endosomes. In budding yeast, this complex consists of Vps30p, Vps34p, VPS38 and Vps15p."
  * Added definition dbxref GOC:rb to GO:0034272
  * Added definition dbxref PMID:11157979 to GO:0034272
  * Added definition dbxref PMID:16421251 to GO:0034272
  * Added synonym "PtdIns-3-kinase complex II" to GO:0034272
  * Changed synonym scope of GO:0034272 from "Related" to "Exact"
  * Copied GO:0034272 to GO:0005942 with type OBO_REL:is_a
  * Copied GO:0034272 to GO:0044444 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034272
* Populated new object GO:0034273 (macro)
  * Changed name of GO:0034273 from "<new term>" to "Atg1p signaling complex"
  * Set definition of GO:0034273 to "A protein complex that contains a protein kinase and is required for the autophagosome formation. In budding yeast this complex consists of the kinase Atg1p, Atg13p and Atg17p."
  * Added definition dbxref GOC:rb to GO:0034273
  * Added definition dbxref PMID:15743910 to GO:0034273
  * Added synonym "Atg1p signalling complex" to GO:0034273
  * Changed synonym scope of GO:0034273 from "Related" to "Exact"
  * Copied GO:0034273 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034273 to GO:0044444 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034273
* Populated new object GO:0034274 (macro)
  * Changed name of GO:0034274 from "<new term>" to "Atg12-Atg5-Atg16 complex"
  * Set definition of GO:0034274 to "A protein complex required for the expansion of the autophagosomal membrane. In budding yeast, this complex consists of Atg12p, Atg5p and Atg16p."
  * Added definition dbxref GOC:rb to GO:0034274
  * Added definition dbxref PMID:17986448 to GO:0034274
  * Copied GO:0034274 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034274 to GO:0044444 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034274
* Populated new object GO:0034275 (macro)
  * Changed name of GO:0034275 from "<new term>" to "kynurenic acid metabolic process"
  * Set definition of GO:0034275 to "The chemical reactions and pathways involving kynurenic acid, 4-hydroxyquinoline-2-carboxylic acid."
  * Added definition dbxref ChEBI:18344 to GO:0034275
  * Added definition dbxref GOC:mah to GO:0034275
  * Added synonym "4-hydroxyquinoline-2-carboxylic acid metabolic process" to GO:0034275
  * Changed synonym scope of GO:0034275 from "Related" to "Exact"
  * Added synonym "kynurenic acid metabolism" to GO:0034275
  * Changed synonym scope of GO:0034275 from "Related" to "Exact"
  * Copied GO:0034275 to GO:0046483 with type OBO_REL:is_a
  * Copied GO:0034275 to GO:0032787 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034275
* Populated new object GO:0034276 (macro)
  * Changed name of GO:0034276 from "<new term>" to "kynurenic acid biosynthetic process"
  * Set definition of GO:0034276 to "The chemical reactions and pathways resulting in the formation of kynurenic acid, 4-hydroxyquinoline-2-carboxylic acid."
  * Added definition dbxref ChEBI:18344 to GO:0034276
  * Added definition dbxref GOC:mah to GO:0034276
  * Added synonym "4-hydroxyquinoline-2-carboxylic acid biosynthetic process" to GO:0034276
  * Changed synonym scope of GO:0034276 from "Related" to "Exact"
  * Added synonym "kynurenic acid anabolism" to GO:0034276
  * Changed synonym scope of GO:0034276 from "Related" to "Exact"
  * Added synonym "kynurenic acid biosynthesis" to GO:0034276
  * Changed synonym scope of GO:0034276 from "Related" to "Exact"
  * Added synonym "kynurenic acid formation" to GO:0034276
  * Added synonym "kynurenic acid synthesis" to GO:0034276
  * Changed synonym scope of GO:0034276 from "Related" to "Exact"
  * Copied GO:0034276 to GO:0034275 with type OBO_REL:is_a
  * Copied GO:0034276 to GO:0018130 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034276
* Changed name of GO:0000083 from "G1/S-specific transcription in mitotic cell cycle" to "regulation of G1/S-specific transcription in mitotic cell cycle"
* Added definition dbxref GOC:dph to GO:0000083
* Added definition dbxref GOC:tb to GO:0000083
* Added synonym "G1/S-specific transcription in mitotic cell cycle" to GO:0000083
* Added general dbxref GOC:tb to synonym G1/S-specific transcription in mitotic cell cycle of GO:0000083
* Added general dbxref GOC:dph to synonym G1/S-specific transcription in mitotic cell cycle of GO:0000083
* Changed synonym scope of GO:0000083 from "Related" to "Exact"
* Changed name of GO:0000114 from "G1-specific transcription in mitotic cell cycle" to "regulation of G1-specific transcription in mitotic cell cycle"
* Added definition dbxref GOC:dph to GO:0000114
* Added definition dbxref GOC:tb to GO:0000114
* Added synonym "G1-specific transcription in mitotic cell cycle" to GO:0000114
* Added general dbxref GOC:tb to synonym G1-specific transcription in mitotic cell cycle of GO:0000114
* Added general dbxref GOC:dph to synonym G1-specific transcription in mitotic cell cycle of GO:0000114
* Changed synonym scope of GO:0000114 from "Related" to "Exact"
* Changed name of GO:0000116 from "G2-specific transcription in mitotic cell cycle" to "regulation of G2-specific transcription in mitotic cell cycle"
* Added definition dbxref GOC:dph to GO:0000116
* Added definition dbxref GOC:tb to GO:0000116
* Added synonym "G2-specific transcription in mitotic cell cycle" to GO:0000116
* Added general dbxref GOC:tb to synonym G2-specific transcription in mitotic cell cycle of GO:0000116
* Added general dbxref GOC:dph to synonym G2-specific transcription in mitotic cell cycle of GO:0000116
* Changed synonym scope of GO:0000116 from "Related" to "Exact"
* Changed name of GO:0000117 from "G2/M-specific transcription in mitotic cell cycle" to "regulation of G2/M-specific transcription in mitotic cell cycle"
* Added definition dbxref GOC:dph to GO:0000117
* Added definition dbxref GOC:tb to GO:0000117
* Added synonym "G2/M-specific transcription in mitotic cell cycle" to GO:0000117
* Added general dbxref GOC:tb to synonym G2/M-specific transcription in mitotic cell cycle of GO:0000117
* Added general dbxref GOC:dph to synonym G2/M-specific transcription in mitotic cell cycle of GO:0000117
* Changed synonym scope of GO:0000117 from "Related" to "Exact"
* Deleted GO:0000271 --OBO_REL:is_a--> GO:0009059
* Changed definition of GO:0000497 from "Interacting selectively with nucleic acid via hydrogen bonds between the bases of a gene product molecule and the bases of a target nucleic acid molecule" to "Interacting selectively with nucleic acid via hydrogen bonds between the bases of a gene product molecule and the bases of a target DNA molecule."
* Deleted GO:0001672 --OBO_REL:is_a--> GO:0051052
* Deleted GO:0001821 --OBO_REL:is_a--> GO:0007269
* Changed name of GO:0002220 from "innate immune response activating cell surface receptor signaling pathway" to "innate immune response-activating cell surface receptor signaling pathway"
* Changed name of GO:0003058 from "hormonal regulation of the force of heart contraction" to "regulation of the force of heart contraction by hormone"
* Changed definition of GO:0003058 from "The process by which the hormones modulates the force of heart muscle contraction. A hormone is one of a group of substances formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells, in the same organism, upon which they have a specific regulatory action." to "The process by which hormones modulate the force of heart muscle contraction. A hormone is one of a group of substances formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells, in the same organism, upon which they have a specific regulatory action."
* Added definition dbxref GOC:dph to GO:0003058
* Added definition dbxref GOC:tb to GO:0003058
* Added synonym "hormonal regulation of the force of heart contraction" to GO:0003058
* Added general dbxref GOC:tb to synonym hormonal regulation of the force of heart contraction of GO:0003058
* Added general dbxref GOC:dph to synonym hormonal regulation of the force of heart contraction of GO:0003058
* Changed synonym scope of GO:0003058 from "Related" to "Exact"
* Added comment "Note that most helicases catalyze processive duplex unwinding."
* Deleted GO:0005294 --OBO_REL:is_a--> GO:0005275
* Deleted GO:0005314 --OBO_REL:is_a--> GO:0005275
* Changed name of GO:0005943 from "1-phosphatidylinositol-4-phosphate kinase, class IA complex" to "1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex"
* added secondary id GO:0035030 to GO:0005943
* Changed definition of GO:0005943 from "A heterodimeric protein complex that possesses 1-phosphatidylinositol-4-phosphate 3-kinase activity; comprises a catalytic subunit of 110-120 kDa and an associated regulatory subunit that is a member of a family of related proteins often called p85 proteins." to "A heterodimeric protein complex that possesses 1-phosphatidylinositol-4-phosphate 3-kinase activity; comprises a catalytic Class IA phosphoinositide 3-kinase (PI3K) subunit of 110-120 kDa and an associated SH2 domain-containing regulatory subunit that is a member of a family of related proteins often called p85 proteins. Class I PI3Ks phosphorylate phosphatidylinositol [PI], phosphatidylinositol-4-phosphate [PI(4)P] and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2], and are divided into subclasses A and B according to the type of adaptor subunit with which they associate. Through the interaction with the SH2-containing adaptor subunits, Class IA PI3K catalytic subunits are linked to tyrosine kinase signaling pathways."
* Added definition dbxref PMID:9255069 to GO:0005943
* Added synonym "1-phosphatidylinositol-4-phosphate kinase, class IA complex" to GO:0005943
* Changed synonym scope of GO:0005943 from "Related" to "Exact"
* Added synonym "class IA PI3K complex" to GO:0005943
* Changed synonym scope of GO:0005943 from "Related" to "Exact"
* Added synonym "phosphoinositide 3-kinase complex, class IA" to GO:0005943
* Changed synonym scope of GO:0005943 from "Related" to "Exact"
* Deleted GO:0005943 --OBO_REL:is_a--> GO:0043234
* Copied GO:0005943 to GO:0005942 with type OBO_REL:is_a
* Changed name of GO:0005944 from "1-phosphatidylinositol-4-phosphate kinase, class IB complex" to "1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex"
* added secondary id GO:0035031 to GO:0005944
* Changed definition of GO:0005944 from "A heterodimeric protein complex that possesses 1-phosphatidylinositol-4-phosphate 3-kinase activity; comprises a catalytic subunit of 110-120 kDa and an associated regulatory subunit that is larger than, and unrelated to, the p85 proteins present in class IA complexes." to "A heterodimeric protein complex that possesses 1-phosphatidylinositol-4-phosphate 3-kinase activity; comprises a catalytic Class IB phosphoinositide 3-kinase (PI3K) subunit of 110-120 kDa and an associated regulatory subunit that is larger than, and unrelated to, the p85 proteins present in class IA complexes. Class I PI3Ks phosphorylate phosphatidylinositol [PI], phosphatidylinositol-4-phosphate [PI(4)P] and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] and are divided into subclasses A and B according to the type of adaptor subunit with which they associate. Class IB PI3Ks are stimulated by G-proteins and do not interact with the SH2-domain containing adaptors that bind to Class IA PI3Ks."
* Added definition dbxref PMID:9255069 to GO:0005944
* Added synonym "1-phosphatidylinositol-4-phosphate kinase, class IB complex" to GO:0005944
* Added synonym "class IB PI3K complex" to GO:0005944
* Changed synonym scope of GO:0005944 from "Related" to "Exact"
* Added synonym "phosphoinositide 3-kinase complex, class IB" to GO:0005944
* Changed synonym scope of GO:0005944 from "Related" to "Exact"
* Deleted GO:0005944 --OBO_REL:is_a--> GO:0043234
* Copied GO:0005944 to GO:0005942 with type OBO_REL:is_a
* Deleted GO:0005976 --OBO_REL:is_a--> GO:0043170
* Deleted GO:0006040 --OBO_REL:is_a--> GO:0009308
* Deleted GO:0006286 --OBO_REL:is_a--> GO:0009262
* Copied GO:0006286 to GO:0006308 with type OBO_REL:is_a
* Deleted GO:0006754 --OBO_REL:is_a--> GO:0006753
* Changed definition of GO:0006914 from "The process by which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of nutrient limitation and remodeling the intracellular structure for cell differentiation." to "The process by which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation."
* Changed name of GO:0006985 from "EOR-mediated activation of NF-kappaB" to "activation of NF-kappaB by ER overload"
* Changed synonym scope of GO:0006985 from "Exact" to "Related"
* Added synonym "EOR-mediated activation of NF-kappaB" to GO:0006985
* Deleted GO:0007093 --OBO_REL:is_a--> GO:0007088
* Copied GO:0007093 to GO:0007346 with type OBO_REL:is_a
* Deleted general dbxref EC::2.1.1.37 from synonym EcoRI methylase of GO:0009007
* Added general dbxref EC:2.1.1.37 to synonym EcoRI methylase of GO:0009007
* Changed name of GO:0014843 from "growth factor dependent regulation of satellite cell proliferation" to "regulation of satellite cell proliferation by growth factor"
* Added definition dbxref GOC:dph to GO:0014843
* Added definition dbxref GOC:tb to GO:0014843
* Added synonym "growth factor dependent regulation of satellite cell proliferation" to GO:0014843
* Added general dbxref GOC:tb to synonym growth factor dependent regulation of satellite cell proliferation of GO:0014843
* Added general dbxref GOC:dph to synonym growth factor dependent regulation of satellite cell proliferation of GO:0014843
* Changed synonym scope of GO:0014843 from "Related" to "Exact"
* Deleted GO:0015193 --OBO_REL:is_a--> GO:0005275
* Deleted GO:0015558 --OBO_REL:is_a--> GO:0005275
* Deleted GO:0016245 --OBO_REL:is_a--> GO:0006357
* Copied GO:0016245 to GO:0045944 with type OBO_REL:is_a
* Added definition dbxref GOC:tb to GO:0021875
* Added general dbxref GOC:tb to synonym fibroblast growth factor receptor signalling pathway in forebrain neuroblast division of GO:0021875
* Added general dbxref GOC:dph to synonym fibroblast growth factor receptor signalling pathway in forebrain neuroblast division of GO:0021875
* Changed name of GO:0022003 from "fgf receptor signaling involved in negative regulation of anterior neural cell fate commitment of the neural plate" to "fibroblast growth factor receptor signaling pathway involved in negative regulation of anterior neural cell fate commitment of the neural plate"
* Copied GO:0022003 to GO:0008543 with type OBO_REL:is_a
* Deleted GO:0030834 --OBO_REL:is_a--> GO:0032268
* Copied GO:0031023 to GO:0000226 with type part_of
* Deleted GO:0031057 --OBO_REL:is_a--> GO:0051053
* Deleted GO:0031058 --OBO_REL:is_a--> GO:0051054
* Deleted GO:0032196 --OBO_REL:is_a--> GO:0009987
* Deleted GO:0033666 --OBO_REL:is_a--> GO:0065007
* Deleted GO:0033667 --OBO_REL:is_a--> GO:0065007
* Changed synonym scope of GO:0033920 from "Broad" to "Exact"
* Deleted GO:0034194 --OBO_REL:is_a--> GO:0046395
* Deleted GO:0034195 --OBO_REL:is_a--> GO:0046395
* Deleted GO:0034216 --OBO_REL:is_a--> GO:0015403
* Deleted GO:0034223 --part_of--> GO:0006038
* Deleted GO:0034223 --OBO_REL:is_a--> GO:0051128
* Deleted GO:0034252 --OBO_REL:is_a--> GO:0051172
* Deleted GO:0035030 --OBO_REL:is_a--> GO:0005942
* Destroyed object GO:0035030
* Deleted GO:0035031 --OBO_REL:is_a--> GO:0005942
* Destroyed object GO:0035031
* Deleted GO:0042049 --OBO_REL:is_a--> GO:0019725
* Copied GO:0044262 to GO:0044237 with type OBO_REL:is_a
* Deleted GO:0051205 --OBO_REL:is_a--> GO:0045184