[Go-diff] GO update 06/03/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Tue Jun 3 21:30:45 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.88 by 1.92

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034496
* Created object of type obo:TERM with id GO:0034497
* Created object of type obo:TERM with id GO:0034498
* Created object of type obo:TERM with id GO:0034499
* Created object of type obo:TERM with id GO:0034500
* Created object of type obo:TERM with id GO:0034501
* Created object of type obo:TERM with id GO:0034502
* Created object of type obo:TERM with id GO:0034503
* Created object of type obo:TERM with id GO:0043914
* Created object of type obo:TERM with id GO:0043915
* Created object of type obo:TERM with id GO:0043916
* Created object of type obo:TERM with id GO:0060256
* Created object of type obo:TERM with id GO:0060257
* Created object of type obo:TERM with id GO:0060258
* Created object of type obo:TERM with id GO:0060259
* Created object of type obo:TERM with id GO:0060260
* Created object of type obo:TERM with id GO:0060261
* Populated new object GO:0034496 (macro)
  * Changed name of GO:0034496 from "<new term>" to "multivesicular body membrane disassembly"
  * Set definition of GO:0034496 to "The controlled breakdown of the membranes of multivesicular bodies."
  * Added definition dbxref GOC:rb to GO:0034496
  * Added synonym "MVB membrane disassembly" to GO:0034496
  * Changed synonym scope of GO:0034496 from "Related" to "Exact"
  * Copied GO:0034496 to GO:0030397 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034496
* Populated new object GO:0034497 (macro)
  * Changed name of GO:0034497 from "<new term>" to "protein localization to pre-autophagosomal structure"
  * Set definition of GO:0034497 to "Any process by which a protein is transported to, or maintained at, the pre-autophagosomal structure (PAS)."
  * Added definition dbxref GOC:rb to GO:0034497
  * Added synonym "protein localization to PAS" to GO:0034497
  * Changed synonym scope of GO:0034497 from "Related" to "Exact"
  * Copied GO:0034497 to GO:0008104 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034497
* Populated new object GO:0034498 (macro)
  * Changed name of GO:0034498 from "<new term>" to "early endosome to Golgi transport"
  * Set definition of GO:0034498 to "The directed movement of substances from early endosomes to the Golgi."
  * Added definition dbxref GOC:rb to GO:0034498
  * Added synonym "PGE to Golgi transport" to GO:0034498
  * Changed synonym scope of GO:0034498 from "Related" to "Exact"
  * Added synonym "post-Golgi endosome to Golgi transport" to GO:0034498
  * Changed synonym scope of GO:0034498 from "Related" to "Exact"
  * Copied GO:0034498 to GO:0048193 with type OBO_REL:is_a
  * Copied GO:0034498 to GO:0016197 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034498
* Populated new object GO:0034499 (macro)
  * Changed name of GO:0034499 from "<new term>" to "late endosome to Golgi transport"
  * Set definition of GO:0034499 to "The directed movement of substances from late endosomes to the Golgi."
  * Added definition dbxref GOC:rb to GO:0034499
  * Added synonym "prevacuolar endosome to Golgi transport" to GO:0034499
  * Changed synonym scope of GO:0034499 from "Related" to "Exact"
  * Added synonym "PVE to Golgi transport" to GO:0034499
  * Changed synonym scope of GO:0034499 from "Related" to "Exact"
  * Copied GO:0034499 to GO:0048193 with type OBO_REL:is_a
  * Copied GO:0034499 to GO:0016197 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034499
* Populated new object GO:0034500 (macro)
  * Changed name of GO:0034500 from "<new term>" to "rDNA separation"
  * Set definition of GO:0034500 to "The cell cycle process whereby rDNA repeat regions are physically detached from each other during chromosome separation."
  * Added definition dbxref GOC:mah to GO:0034500
  * Copied GO:0034500 to GO:0051304 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034500
* Populated new object GO:0034501 (macro)
  * Changed name of GO:0034501 from "<new term>" to "protein localization to kinetochore"
  * Set definition of GO:0034501 to "Any process by which a protein is transported to, or maintained at, the kinetochore."
  * Added definition dbxref GOC:mah to GO:0034501
  * Added synonym "condensin localization to kinetochore" to GO:0034501
  * Changed synonym scope of GO:0034501 from "Related" to "Narrow"
  * Copied GO:0034501 to GO:0008104 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034501
* Populated new object GO:0034502 (macro)
  * Changed name of GO:0034502 from "<new term>" to "protein localization to chromosome"
  * Set definition of GO:0034502 to "Any process by which a protein is transported to, or maintained at, a specific location on a chromosome."
  * Added definition dbxref GOC:mah to GO:0034502
  * Added synonym "condensin localization to chromosome" to GO:0034502
  * Changed synonym scope of GO:0034502 from "Related" to "Narrow"
  * Copied GO:0034502 to GO:0008104 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034502
* Populated new object GO:0034503 (macro)
  * Changed name of GO:0034503 from "<new term>" to "protein localization to nucleolar rDNA repeats"
  * Set definition of GO:0034503 to "Any process by which a protein is transported to, or maintained at, the rDNA repeats on a chromosome in the nucleolus."
  * Added definition dbxref GOC:mah to GO:0034503
  * Added synonym "condensin localization to nucleolar rDNA repeats" to GO:0034503
  * Changed synonym scope of GO:0034503 from "Related" to "Narrow"
  * Copied GO:0034503 to GO:0034502 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034503
* Populated new object GO:0043914 (macro)
  * Changed name of GO:0043914 from "<new term>" to "NADPH:sulfur oxidoreductase activity"
  * Set definition of GO:0043914 to "Catalysis of the reaction: NADPH + S0 = H2S + NADP."
  * Added definition dbxref GOC:jl to GO:0043914
  * Added definition dbxref PMID:17449625 to GO:0043914
  * Added general dbxref EC:1.-.-.- to GO:0043914
  * Added general dbxref IMG:03008 to GO:0043914
  * Added GO:0043914 to category gosubset_prok
  * Added synonym "CoA-dependent NAD(P)H sulfur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "coenzyme A-dependent NAD(P)H sulfur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NAD(P)H elemental sulfur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NAD(P)H sulfur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NAD(P)H sulphur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NAD(P)H:sulfur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NADPH:sulphur oxidoreductase activity" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Added synonym "NSR" to GO:0043914
  * Changed synonym scope of GO:0043914 from "Related" to "Exact"
  * Copied GO:0043914 to GO:0016491 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043914
* Populated new object GO:0043915 (macro)
  * Changed name of GO:0043915 from "<new term>" to "L-seryl-tRNA(Sec) kinase activity"
  * Set definition of GO:0043915 to "Catalysis of the reaction: ATP + L-seryl-tRNA(Sec) = ADP + O-phospho-L-seryl-tRNA(Sec)."
  * Added definition dbxref GOC:jl to GO:0043915
  * Added definition dbxref IMG:03019 to GO:0043915
  * Added definition dbxref UniProt:Q8IV42 to GO:0043915
  * Added general dbxref EC:2.7.1.- to GO:0043915
  * Added general dbxref IMG:03019 to GO:0043915
  * Added GO:0043915 to category gosubset_prok
  * Added synonym "O-phosphoseryl-tRNA(Sec) kinase activity" to GO:0043915
  * Changed synonym scope of GO:0043915 from "Related" to "Exact"
  * Copied GO:0043915 to GO:0016773 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043915
* Populated new object GO:0043916 (macro)
  * Changed name of GO:0043916 from "<new term>" to "DNA-7-methylguanine glycosylase activity"
  * Set definition of GO:0043916 to "Catalysis of the hydrolysis of alkylated DNA; recognizes and removes the alkylated base 7-methylguanine."
  * Added definition dbxref GOC:jl to GO:0043916
  * Added definition dbxref PMID:16468998 to GO:0043916
  * Added general dbxref EC:3.2.2.- to GO:0043916
  * Added general dbxref IMG:03021 to GO:0043916
  * Added GO:0043916 to category gosubset_prok
  * Copied GO:0043916 to GO:0003905 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043916
* Populated new object GO:0060256 (macro)
  * Changed name of GO:0060256 from "<new term>" to "regulation of flocculation"
  * Set definition of GO:0060256 to "Any process that modulates the rate, frequency or extent of the non-sexual aggregation of single-celled organisms."
  * Added definition dbxref GOC:dph to GO:0060256
  * Added definition dbxref GOC:tb to GO:0060256
  * Copied GO:0060256 to GO:0043900 with type OBO_REL:is_a
  * Copied GO:0060256 to GO:0000128 with type regulates
  * Assigned namespace "biological_process" to GO:0060256
* Populated new object GO:0060257 (macro)
  * Changed name of GO:0060257 from "<new term>" to "negative regulation of flocculation"
  * Set definition of GO:0060257 to "Any process that decreases the rate, frequency or extent of the non-sexual aggregation of single-celled organisms."
  * Added definition dbxref GOC:dph to GO:0060257
  * Added definition dbxref GOC:tb to GO:0060257
  * Copied GO:0060257 to GO:0043901 with type OBO_REL:is_a
  * Copied GO:0060257 to GO:0060256 with type OBO_REL:is_a
  * Copied GO:0060257 to GO:0000128 with type negatively_regulates
  * Assigned namespace "biological_process" to GO:0060257
* Populated new object GO:0060258 (macro)
  * Changed name of GO:0060258 from "<new term>" to "negative regulation of filamentous growth"
  * Set definition of GO:0060258 to "Any process that decreases the frequency, rate or extent of the process by which a multicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape."
  * Added definition dbxref GOC:dph to GO:0060258
  * Added definition dbxref GOC:tb to GO:0060258
  * Copied GO:0060258 to GO:0030447 with type negatively_regulates
  * Copied GO:0060258 to GO:0010570 with type OBO_REL:is_a
  * Copied GO:0060258 to GO:0045926 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060258
* Populated new object GO:0060259 (macro)
  * Changed name of GO:0060259 from "<new term>" to "regulation of feeding behavior"
  * Set definition of GO:0060259 to "Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food."
  * Added definition dbxref GOC:dph to GO:0060259
  * Added definition dbxref GOC:tb to GO:0060259
  * Added synonym "regulation of feeding behaviour" to GO:0060259
  * Added general dbxref GOC:tb to synonym regulation of feeding behaviour of GO:0060259
  * Added general dbxref GOC:dph to synonym regulation of feeding behaviour of GO:0060259
  * Changed synonym scope of GO:0060259 from "Related" to "Exact"
  * Copied GO:0060259 to GO:0050795 with type OBO_REL:is_a
  * Copied GO:0060259 to GO:0007631 with type regulates
  * Assigned namespace "biological_process" to GO:0060259
* Populated new object GO:0060260 (macro)
  * Changed name of GO:0060260 from "<new term>" to "regulation of transcription initiation from RNA polymerase II promoter"
  * Set definition of GO:0060260 to "Any process that modulates the rate, frequency or extent of a process involved in starting transcription from the RNA polymerase II promoter."
  * Added definition dbxref GOC:dph to GO:0060260
  * Added definition dbxref GOC:tb to GO:0060260
  * Copied GO:0060260 to GO:0060255 with type OBO_REL:is_a
  * Copied GO:0060260 to GO:0006367 with type regulates
  * Assigned namespace "biological_process" to GO:0060260
* Populated new object GO:0060261 (macro)
  * Changed name of GO:0060261 from "<new term>" to "positive regulation of transcription initiation from RNA polymerase II promoter"
  * Set definition of GO:0060261 to "Any process that increases the rate, frequency or extent of a process involved in starting transcription from the RNA polymerase II promoter."
  * Added definition dbxref GOC:dph to GO:0060261
  * Added definition dbxref GOC:tb to GO:0060261
  * Copied GO:0060261 to GO:0060260 with type OBO_REL:is_a
  * Copied GO:0060261 to GO:0010604 with type OBO_REL:is_a
  * Copied GO:0060261 to GO:0006367 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0060261
* Added synonym "PAS formation" to GO:0000045
* Changed synonym scope of GO:0000045 from "Related" to "Narrow"
* Deleted GO:0000045 --OBO_REL:is_a--> GO:0006996
* Copied GO:0000045 to GO:0016050 with type OBO_REL:is_a
* Added synonym "perivacuolar space" to GO:0000407
* Changed synonym scope of GO:0000407 from "Related" to "Narrow"
* Deleted general dbxref 2.1.1.73 (EC:<new dbxref>) from synonym site-specific DNA-methyltransferase (cytosine-specific) activity of GO:0003886
* Added general dbxref EC:2.1.1.37 to synonym site-specific DNA-methyltransferase (cytosine-specific) activity of GO:0003886
* Added synonym "vacuolar proteolysis" to GO:0006624
* Changed synonym scope of GO:0006624 from "Related" to "Exact"
* Added synonym "sense organ development" to GO:0007423
* Added general dbxref GOC:dph to synonym sense organ development of GO:0007423
* Changed synonym scope of GO:0007423 from "Related" to "Exact"
* Added synonym "sense organ boundary specification" to GO:0008052
* Added general dbxref GOC:dph to synonym sense organ boundary specification of GO:0008052
* Changed synonym scope of GO:0008052 from "Related" to "Exact"
* added secondary id GO:0034262 to GO:0016236
* Added synonym "autophagy in response to cellular starvation" to GO:0016236
* Changed synonym scope of GO:0016236 from "Related" to "Exact"
* Added synonym "non-specific autophagy" to GO:0016236
* Changed synonym scope of GO:0016236 from "Related" to "Exact"
* Copied GO:0016236 to GO:0009267 with type OBO_REL:is_a
* Added synonym "sense organ precursor cell fate determination" to GO:0016360
* Added general dbxref GOC:dph to synonym sense organ precursor cell fate determination of GO:0016360
* Changed synonym scope of GO:0016360 from "Related" to "Exact"
* Deleted synonym "<new synonym>" from GO:0019988
* Added synonym "cytoplasm-to-vacuole targeting" to GO:0032258
* Changed synonym scope of GO:0032258 from "Related" to "Exact"
* Copied GO:0032258 to GO:0006914 with type part_of
* Deleted GO:0034262 --OBO_REL:is_a--> GO:0009267
* Deleted GO:0034262 --OBO_REL:is_a--> GO:0006914
* Destroyed object GO:0034262
* Changed definition of GO:0034270 from "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." to "A protein complex that is involved in the CVT pathway. In budding yeast, the CVT complex consists of multimers of preApe1p."
* Deleted synonym "preAPE1-Atg11p complex" from GO:0034270
* Changed definition of GO:0034464 from "A protein complex that associates with the primary cilium and is cilium biogenesis; consists of seven conserved proteins: BBS1, BBS2, BBS4, BBS5, BBS7, BBS8
and BBS9." to "A protein complex that associates with the primary cilium and is cilium biogenesis; consists of seven conserved proteins: BBS1, BBS2, BBS4, BBS5, BBS7, BBS8 and BBS9."
* Changed definition of GO:0034485 from "Catalysis of the reaction: phosphatidylinositol 3,4,5-trisphosphate +
H2O = phosphatidylinositol 3,4-bisphosphate + phosphate." to "Catalysis of the reaction: phosphatidylinositol 3,4,5-trisphosphate + H2O = phosphatidylinositol 3,4-bisphosphate + phosphate."
* Changed definition of GO:0043733 from "Catalysis of the hydrolysis of alkylated DNA; recognizes and removes alkylated purines and pyrimidines by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic or apyrimidinic (AP) site. This enzyme is unable to excise N-7-methylpurines or oxidized bases, such as hypoxanthine." to "Catalysis of the hydrolysis of alkylated DNA; recognizes and removes alkylated 3-methylpurines and pyrimidines by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic or apyrimidinic (AP) site."
* Added general dbxref IMG:00576 to GO:0043733
* Changed definition of GO:0043736 from "Catalysis of the hydrolysis of alkylated DNA; recognizes and removes both N-3- and N-7-methyl purines by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic or apyrimidinic (AP) site." to "Catalysis of the hydrolysis of alkylated DNA; recognizes and removes both N-3- and N-7-methyl purines by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic (AP) site."
* Added general dbxref EC:3.2.2.- to GO:0043736
* Added general dbxref IMG:00578 to GO:0043736
* Added synonym "sense organ precursor cell division" to GO:0045035
* Added general dbxref GOC:dph to synonym sense organ precursor cell division of GO:0045035
* Changed synonym scope of GO:0045035 from "Related" to "Exact"
* Copied GO:0051709 to GO:0043900 with type OBO_REL:is_a
* Copied GO:0051711 to GO:0043901 with type OBO_REL:is_a
* Copied GO:0051712 to GO:0043902 with type OBO_REL:is_a
* Deleted GO:0052330 --part_of--> GO:0051883
* Copied GO:0052330 to GO:0051883 with type positively_regulates

More information about the Go-diff mailing list