[Go-diff] GO update 04/28/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Mon Apr 28 21:30:45 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.42 by 1.44

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034416
* Created object of type obo:TERM with id GO:0034417
* Created object of type obo:TERM with id GO:0034418
* Created object of type obo:TERM with id GO:0060236
* Created object of type obo:TERM with id GO:0060237
* Created object of type obo:TERM with id GO:0060238
* Created object of type obo:TERM with id GO:0060239
* Created object of type obo:TERM with id GO:0060240
* Populated new object GO:0034416 (macro)
  * Changed name of GO:0034416 from "<new term>" to "bisphosphoglycerate phosphatase activity"
  * Set definition of GO:0034416 to "Catalysis of the reaction: 2,3-diphosphoglycerate + H2O = phosphoglycerate + phosphate."
  * Added definition dbxref EC:3.1.3.13 to GO:0034416
  * Added definition dbxref GOC:mah to GO:0034416
  * Added definition dbxref PMID:18413611 to GO:0034416
  * Added synonym "2,3-bisphosphoglycerate phosphatase activity" to GO:0034416
  * Added general dbxref EC:3.1.3.13 to synonym 2,3-bisphosphoglycerate phosphatase activity of GO:0034416
  * Changed synonym scope of GO:0034416 from "Related" to "Exact"
  * Added synonym "2,3-diphosphoglycerate phosphatase activity" to GO:0034416
  * Added general dbxref EC:3.1.3.13 to synonym 2,3-diphosphoglycerate phosphatase activity of GO:0034416
  * Changed synonym scope of GO:0034416 from "Related" to "Exact"
  * Added synonym "2,3-diphosphoglyceric acid phosphatase activity" to GO:0034416
  * Added general dbxref EC:3.1.3.13 to synonym 2,3-diphosphoglyceric acid phosphatase activity of GO:0034416
  * Changed synonym scope of GO:0034416 from "Related" to "Exact"
  * Added synonym "diphosphoglycerate phosphatase activity" to GO:0034416
  * Added general dbxref EC:3.1.3.13 to synonym diphosphoglycerate phosphatase activity of GO:0034416
  * Changed synonym scope of GO:0034416 from "Related" to "Exact"
  * Added synonym "glycerate-2,3-diphosphate phosphatase activity" to GO:0034416
  * Added general dbxref EC:3.1.3.13 to synonym glycerate-2,3-diphosphate phosphatase activity of GO:0034416
  * Changed synonym scope of GO:0034416 from "Related" to "Exact"
  * Copied GO:0034416 to GO:0016791 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034416
* Populated new object GO:0034417 (macro)
  * Changed name of GO:0034417 from "<new term>" to "bisphosphoglycerate 3-phosphatase activity"
  * Set definition of GO:0034417 to "Catalysis of the reaction: 2,3-diphosphoglycerate + H2O = 2-phosphoglycerate + phosphate."
  * Added definition dbxref EC:3.1.3.13 to GO:0034417
  * Added definition dbxref GOC:mah to GO:0034417
  * Added definition dbxref PMID:18413611 to GO:0034417
  * Added synonym "2,3-bisphospho-D-glycerate 3-phosphohydrolase activity" to GO:0034417
  * Added general dbxref EC:3.1.3.13 to synonym 2,3-bisphospho-D-glycerate 3-phosphohydrolase activity of GO:0034417
  * Changed synonym scope of GO:0034417 from "Related" to "Exact"
  * Copied GO:0034417 to GO:0034416 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034417
* Populated new object GO:0034418 (macro)
  * Changed name of GO:0034418 from "<new term>" to "urate biosynthetic process"
  * Set definition of GO:0034418 to "The chemical reactions and pathways resulting in the formation of urate, the anion of uric acid, 2,6,8-trioxypurine."
  * Added definition dbxref GOC:mah to GO:0034418
  * Added synonym "urate anabolism" to GO:0034418
  * Added synonym "urate biosynthesis" to GO:0034418
  * Changed synonym scope of GO:0034418 from "Related" to "Exact"
  * Added synonym "urate formation" to GO:0034418
  * Changed synonym scope of GO:0034418 from "Related" to "Exact"
  * Added synonym "urate synthesis" to GO:0034418
  * Changed synonym scope of GO:0034418 from "Related" to "Exact"
  * Added synonym "uric acid biosynthetic process" to GO:0034418
  * Changed synonym scope of GO:0034418 from "Related" to "Exact"
  * Copied GO:0034418 to GO:0046415 with type OBO_REL:is_a
  * Copied GO:0034418 to GO:0044271 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034418
* Populated new object GO:0060236 (macro)
  * Changed name of GO:0060236 from "<new term>" to "regulation of mitotic spindle organization and biogenesis"
  * Set definition of GO:0060236 to "Any process that modulates the rate, frequency or extent of the microtubule spindle during a mitotic cell cycle."
  * Added definition dbxref GOC:dph to GO:0060236
  * Added definition dbxref GOC:tb to GO:0060236
  * Copied GO:0060236 to GO:0032886 with type OBO_REL:is_a
  * Copied GO:0060236 to GO:0010564 with type OBO_REL:is_a
  * Copied GO:0060236 to GO:0007052 with type regulates
  * Assigned namespace "biological_process" to GO:0060236
* Populated new object GO:0060237 (macro)
  * Changed name of GO:0060237 from "<new term>" to "regulation of fungal-type cell wall organization and biogenesis"
  * Set definition of GO:0060237 to "Any process that modulates the rate, frequenct or extent of the formation, arrangement of constituent parts, or disassembly of the fungal-type cell wall."
  * Added definition dbxref GOC:dph to GO:0060237
  * Added definition dbxref GOC:tb to GO:0060237
  * Copied GO:0060237 to GO:0051128 with type OBO_REL:is_a
  * Copied GO:0060237 to GO:0031505 with type regulates
  * Assigned namespace "biological_process" to GO:0060237
* Populated new object GO:0060238 (macro)
  * Changed name of GO:0060238 from "<new term>" to "regulation of signal transduction during conjugation with cellular fusion"
  * Set definition of GO:0060238 to "Any process that modulates the rate, frequency or extent of the series of molecular signals that bring about the relay, amplification or dampening of a signal generated in response to a cue, such as starvation or pheromone exposure, in organisms that undergo conjugation with cellular fusion."
  * Added definition dbxref GOC:dph to GO:0060238
  * Added definition dbxref GOC:tb to GO:0060238
  * Copied GO:0060238 to GO:0009966 with type OBO_REL:is_a
  * Copied GO:0060238 to GO:0032005 with type regulates
  * Assigned namespace "biological_process" to GO:0060238
* Populated new object GO:0060239 (macro)
  * Changed name of GO:0060239 from "<new term>" to "positive regulation of signal transduction during conjugation with cellular fusion"
  * Set definition of GO:0060239 to "Any process that increases the rate, frequency or extent of the series of molecular signals that bring about the relay, amplification or dampening of a signal generated in response to a cue, such as starvation or pheromone exposure, in organisms that undergo conjugation with cellular fusion."
  * Added definition dbxref GOC:dph to GO:0060239
  * Added definition dbxref GOC:tb to GO:0060239
  * Copied GO:0060239 to GO:0032005 with type positively_regulates
  * Copied GO:0060239 to GO:0060238 with type OBO_REL:is_a
  * Copied GO:0060239 to GO:0009967 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060239
* Populated new object GO:0060240 (macro)
  * Changed name of GO:0060240 from "<new term>" to "negative regulation of signal transduction during conjugation with cellular fusion"
  * Set definition of GO:0060240 to "Any process that decreases the rate, frequency or extent of the series of molecular signals that bring about the relay, amplification or dampening of a signal generated in response to a cue, such as starvation or pheromone exposure, in organisms that undergo conjugation with cellular fusion."
  * Added definition dbxref GOC:dph to GO:0060240
  * Added definition dbxref GOC:tb to GO:0060240
  * Copied GO:0060240 to GO:0032005 with type negatively_regulates
  * Copied GO:0060240 to GO:0009968 with type OBO_REL:is_a
  * Copied GO:0060240 to GO:0060238 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060240
* Changed name of GO:0000324 from "vacuole, cell cycle-correlated morphology" to "fungal-type vacuole"
* Added synonym "vacuole, cell cycle-correlated morphology" to GO:0000324
* Changed synonym scope of GO:0000324 from "Related" to "Exact"
* Changed name of GO:0000325 from "vacuole, cell cycle independent morphology" to "plant-type vacuole"
* Added synonym "vacuole, cell cycle-independent morphology" to GO:0000325
* Changed synonym scope of GO:0000325 from "Related" to "Exact"
* Changed name of GO:0000328 from "lumen of vacuole with cell cycle-correlated morphology" to "fungal-type vacuole lumen"
* Added synonym "lumen of vacuole with cell cycle-correlated morphology" to GO:0000328
* Changed synonym scope of GO:0000328 from "Related" to "Exact"
* Changed name of GO:0000329 from "membrane of vacuole with cell cycle-correlated morphology" to "fungal-type vacuole membrane"
* Added synonym "fungal-type vacuolar membrane" to GO:0000329
* Added synonym "membrane of vacuole with cell cycle-correlated morphology" to GO:0000329
* Changed synonym scope of GO:0000329 from "Related" to "Exact"
* Changed name of GO:0000330 from "lumen of vacuole with cell cycle-independent morphology" to "plant-type vacuole lumen"
* Added synonym "lumen of vacuole with cell cycle-independent morphology" to GO:0000330
* Changed synonym scope of GO:0000330 from "Related" to "Exact"
* Added synonym "lumazine synthase activity" to GO:0000906
* Added general dbxref MetaCyc:LUMAZINESYN-CPLX to synonym lumazine synthase activity of GO:0000906
* Changed synonym scope of GO:0000906 from "Related" to "Broad"
* Changed name of GO:0004083 from "bisphosphoglycerate phosphatase activity" to "bisphosphoglycerate 2-phosphatase activity"
* Deleted synonym "2,3-bisphosphoglycerate phosphatase activity" from GO:0004083
* Deleted synonym "2,3-diphosphoglycerate phosphatase activity" from GO:0004083
* Deleted synonym "2,3-diphosphoglyceric acid phosphatase activity" from GO:0004083
* Deleted synonym "diphosphoglycerate phosphatase activity" from GO:0004083
* Deleted synonym "glycerate-2,3-diphosphate phosphatase activity" from GO:0004083
* Deleted GO:0004083 --OBO_REL:is_a--> GO:0016791
* Copied GO:0004083 to GO:0034416 with type OBO_REL:is_a
* Added general dbxref BRENDA:2.5.1.9 to synonym lumazine synthase activity of GO:0004746
* Changed synonym scope of GO:0004746 from "Exact" to "Broad"
* Deleted GO:0005084 --OBO_REL:is_a--> GO:0017137
* Deleted GO:0005084 --OBO_REL:is_a--> GO:0005083
* Destroyed object GO:0005084
* Deleted GO:0009020 --OBO_REL:is_a--> GO:0016424
* Copied GO:0009020 to GO:0016423 with type OBO_REL:is_a
* Changed definition of GO:0009272 from "The chemical reactions and pathways resulting in the formation of the fungal-type cell wall." to "The chemical reactions and pathways resulting in the formation of the fungal-type cell wall. The fungal-type cell wall contains beta-glucan and may contain chitin."
* Changed name of GO:0009705 from "membrane of vacuole with cell cycle-independent morphology" to "plant-type vacuole membrane"
* Added synonym "membrane of vacuole with cell cycle-independent morphology" to GO:0009705
* Changed synonym scope of GO:0009705 from "Related" to "Exact"
* Added synonym "uric acid transmembrane transporter activity" to GO:0015143
* Changed synonym scope of GO:0015143 from "Related" to "Exact"
* Added synonym "uric acid transport" to GO:0015747
* Changed synonym scope of GO:0015747 from "Related" to "Exact"
* Added comment "Note that the methyl donor is usually S-adenosyl-L-methionine, but there is at least one exception (see GO:0030698)."
* added secondary id GO:0016431 to GO:0016300
* Added synonym "tRNA (uridine) methyltransferase activity" to GO:0016300
* Changed synonym scope of GO:0016300 from "Related" to "Exact"
* added secondary id GO:0016424 to GO:0016423
* Added synonym "tRNA (guanosine) methyltransferase activity" to GO:0016423
* Changed synonym scope of GO:0016423 from "Related" to "Exact"
* Deleted GO:0016424 --OBO_REL:is_a--> GO:0008757
* Deleted GO:0016424 --OBO_REL:is_a--> GO:0008175
* Deleted GO:0009020 --OBO_REL:is_a--> GO:0016424
* Destroyed object GO:0016424
* Deleted GO:0016431 --OBO_REL:is_a--> GO:0008175
* Deleted GO:0030696 --OBO_REL:is_a--> GO:0016431
* Destroyed object GO:0016431
* added secondary id GO:0005084 to GO:0017137
* Added synonym "Rab escort protein activity" to GO:0017137
* Changed synonym scope of GO:0017137 from "Related" to "Narrow"
* Added synonym "REP" to GO:0017137
* Changed synonym scope of GO:0017137 from "Related" to "Narrow"
* Copied GO:0017137 to GO:0005083 with type OBO_REL:is_a
* Added synonym "uric acid catabolic process" to GO:0019628
* Changed synonym scope of GO:0019628 from "Related" to "Exact"
* Deleted GO:0030696 --OBO_REL:is_a--> GO:0016431
* Copied GO:0030696 to GO:0016300 with type OBO_REL:is_a
* Changed name of GO:0032995 from "regulation of chitin- and beta-glucan-containing cell wall biogenesis" to "regulation of fungal-type cell wall biogenesis"
* Changed definition of GO:0032995 from "Any process that modulates the chemical reactions and pathways resulting in the formation of the chitin- and beta-glucan-containing cell wall." to "Any process that modulates the chemical reactions and pathways resulting in the formation of the fungal-type cell wall. The fungal-type cell wall contains beta-glucan and may contain chitin."
* Added definition dbxref GOC:dph to GO:0032995
* Added definition dbxref GOC:tb to GO:0032995
* Added synonym "regulation of chitin- and beta-glucan-containing cell wall biogenesis" to GO:0032995
* Changed synonym scope of GO:0032995 from "Related" to "Exact"
* Deleted GO:0032995 --part_of--> GO:0009272
* Deleted GO:0032995 --OBO_REL:is_a--> GO:0051128
* Copied GO:0032995 to GO:0060237 with type OBO_REL:is_a
* Copied GO:0032995 to GO:0009272 with type regulates
* Deleted GO:0040003 --OBO_REL:is_a--> GO:0007592
* Copied GO:0040003 to GO:0042335 with type OBO_REL:is_a

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