From gocvs at genome.stanford.edu  Wed Jul  2 21:30:46 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Wed, 2 Jul 2008 21:30:46 -0700 (PDT)
Subject: [Go-diff] GO update 07/02/2008
Message-ID: <200807030430.VAA29411@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.123 by 1.124

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034583
* Created object of type obo:TERM with id GO:0034584
* Created object of type obo:TERM with id GO:0034585
* Created object of type obo:TERM with id GO:0034586
* Created object of type obo:TERM with id GO:0034587
* Created object of type obo:TERM with id GO:0034588
* Created object of type obo:TERM with id GO:0034589
* Created object of type obo:TERM with id GO:0034590
* Created object of type obo:TERM with id GO:0034591
* Created object of type obo:TERM with id GO:0034592
* Created object of type obo:TERM with id GO:0034593
* Created object of type obo:TERM with id GO:0034594
* Created object of type obo:TERM with id GO:0034595
* Created object of type obo:TERM with id GO:0034596
* Created object of type obo:TERM with id GO:0034597
* Populated new object GO:0034583 (macro)
  * Changed name of GO:0034583 from "<new term>" to "21U-RNA binding"
  * Set definition of GO:0034583 to "Interacting selectively with a 21U-RNA, a 21-nucleotide RNA characterized by a uridine 5'-monophosphate and a modified 3' end resistant to periodate degradation. 21U-RNAs are derived from distinct, autonomously expressed loci within the genome."
  * Added definition dbxref GOC:kmv to GO:0034583
  * Copied GO:0034583 to GO:0003723 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034583
* Populated new object GO:0034584 (macro)
  * Changed name of GO:0034584 from "<new term>" to "piRNA binding"
  * Set definition of GO:0034584 to "Interacting selectively with a piRNA, a Piwi-associated RNA, a 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism."
  * Added definition dbxref GOC:kmv to GO:0034584
  * Added synonym "Piwi-associated RNA binding" to GO:0034584
  * Changed synonym scope of GO:0034584 from "Related" to "Exact"
  * Copied GO:0034584 to GO:0003723 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034584
* Populated new object GO:0034585 (macro)
  * Changed name of GO:0034585 from "<new term>" to "21U-RNA metabolic process"
  * Set definition of GO:0034585 to "The chemical reactions and pathways involving 21U-RNAs, a class of single-stranded RNA molecules of about 21 nucleotides in length characterized by a uridine 5'-monophosphate and a modified 3' end resistant to periodate degradation. 21U-RNAs are derived from distinct, autonomously expressed loci within the genome."
  * Added definition dbxref GOC:kmv to GO:0034585
  * Added synonym "21U-RNA metabolism" to GO:0034585
  * Changed synonym scope of GO:0034585 from "Related" to "Exact"
  * Copied GO:0034585 to GO:0016070 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034585
* Populated new object GO:0034586 (macro)
  * Changed name of GO:0034586 from "<new term>" to "21U-RNA catabolic process"
  * Set definition of GO:0034586 to "The chemical reactions and pathways resulting in the breakdown of 21U-RNAs, a class of single-stranded RNA molecules of about 21 nucleotides in length characterized by a uridine 5'-monophosphate and a modified 3' end resistant to periodate degradation. 21U-RNAs are derived from distinct, autonomously expressed loci within the genome."
  * Added definition dbxref GOC:kmv to GO:0034586
  * Added synonym "21U-RNA breakdown" to GO:0034586
  * Changed synonym scope of GO:0034586 from "Related" to "Exact"
  * Added synonym "21U-RNA catabolism" to GO:0034586
  * Changed synonym scope of GO:0034586 from "Related" to "Exact"
  * Added synonym "21U-RNA degradation" to GO:0034586
  * Changed synonym scope of GO:0034586 from "Related" to "Exact"
  * Copied GO:0034586 to GO:0034585 with type OBO_REL:is_a
  * Copied GO:0034586 to GO:0006401 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034586
* Populated new object GO:0034587 (macro)
  * Changed name of GO:0034587 from "<new term>" to "piRNA metabolic process"
  * Set definition of GO:0034587 to "The chemical reactions and pathways involving piRNAs, Piwi-associated RNAs, a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism."
  * Added definition dbxref GOC:kmv to GO:0034587
  * Added synonym "piRNA metabolism" to GO:0034587
  * Changed synonym scope of GO:0034587 from "Related" to "Exact"
  * Added synonym "Piwi-associated RNA metabolic process" to GO:0034587
  * Changed synonym scope of GO:0034587 from "Related" to "Exact"
  * Copied GO:0034587 to GO:0016070 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034587
* Populated new object GO:0034588 (macro)
  * Changed name of GO:0034588 from "<new term>" to "piRNA catabolic process"
  * Set definition of GO:0034588 to "The chemical reactions and pathways resulting in the breakdown of piRNAs, Piwi-associated RNAs, a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism."
  * Added definition dbxref GOC:kmv to GO:0034588
  * Added synonym "piRNA breakdown" to GO:0034588
  * Changed synonym scope of GO:0034588 from "Related" to "Exact"
  * Added synonym "piRNA catabolism" to GO:0034588
  * Changed synonym scope of GO:0034588 from "Related" to "Exact"
  * Added synonym "piRNA degradation" to GO:0034588
  * Changed synonym scope of GO:0034588 from "Related" to "Exact"
  * Added synonym "Piwi-associated RNA catabolic process" to GO:0034588
  * Changed synonym scope of GO:0034588 from "Related" to "Exact"
  * Copied GO:0034588 to GO:0034587 with type OBO_REL:is_a
  * Copied GO:0034588 to GO:0006401 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034588
* Populated new object GO:0034589 (macro)
  * Changed name of GO:0034589 from "<new term>" to "hydroxyproline transport"
  * Set definition of GO:0034589 to "The directed movement of hydroxyproline into, out of, within or between cells."
  * Added definition dbxref GOC:mah to GO:0034589
  * Added definition dbxref PMID:14502423 to GO:0034589
  * Added synonym "4-hydroxyproline transport" to GO:0034589
  * Changed synonym scope of GO:0034589 from "Related" to "Exact"
  * Added synonym "L-hydroxyproline transport" to GO:0034589
  * Changed synonym scope of GO:0034589 from "Related" to "Narrow"
  * Copied GO:0034589 to GO:0015804 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034589
* Populated new object GO:0034590 (macro)
  * Changed name of GO:0034590 from "<new term>" to "L-hydroxyproline transmembrane transporter activity"
  * Set definition of GO:0034590 to "Catalysis of the transfer of L-hydroxyproline from one side of a membrane to the other."
  * Added definition dbxref GOC:mah to GO:0034590
  * Added definition dbxref PMID:14502423 to GO:0034590
  * Added synonym "4-hydroxyproline transmembrane transporter activity" to GO:0034590
  * Changed synonym scope of GO:0034590 from "Related" to "Broad"
  * Copied GO:0034590 to GO:0015175 with type OBO_REL:is_a
  * Copied GO:0034590 to GO:0015179 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034590
* Populated new object GO:0034591 (macro)
  * Changed name of GO:0034591 from "<new term>" to "rhoptry lumen"
  * Set definition of GO:0034591 to "The volume enclosed by the rhoptry membrane."
  * Added definition dbxref GOC:rph to GO:0034591
  * Added definition dbxref PMID:17997128 to GO:0034591
  * Copied GO:0034591 to GO:0020008 with type part_of
  * Copied GO:0034591 to GO:0043233 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034591
* Populated new object GO:0034592 (macro)
  * Changed name of GO:0034592 from "<new term>" to "synaptic vesicle lumen"
  * Set definition of GO:0034592 to "The volume enclosed by the synaptic vesicle membrane."
  * Added definition dbxref GOC:rph to GO:0034592
  * Copied GO:0034592 to GO:0060205 with type OBO_REL:is_a
  * Copied GO:0034592 to GO:0008021 with type part_of
  * Assigned namespace "cellular_component" to GO:0034592
* Populated new object GO:0034593 (macro)
  * Changed name of GO:0034593 from "<new term>" to "phosphatidylinositol bisphosphate phosphatase activity"
  * Set definition of GO:0034593 to "Catalysis of the removal of one of the two phosphate groups of a phosphatidylinositol bisphosphate."
  * Added definition dbxref GOC:mah to GO:0034593
  * Added synonym "diphosphoinositide phosphatase activity" to GO:0034593
  * Added synonym "phosphatidyl-inositol-bisphosphate phosphatase activity" to GO:0034593
  * Changed synonym scope of GO:0034593 from "Related" to "Exact"
  * Added synonym "phosphatidylinositol-bisphosphatase activity" to GO:0034593
  * Added synonym "triphosphoinositide phosphatase activity" to GO:0034593
  * Added synonym "triphosphoinositide phosphomonoesterase activity" to GO:0034593
  * Copied GO:0034593 to GO:0004437 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034593
* Populated new object GO:0034594 (macro)
  * Changed name of GO:0034594 from "<new term>" to "phosphatidylinositol trisphosphate phosphatase activity"
  * Set definition of GO:0034594 to "Catalysis of the removal of one of the three phosphate groups of a phosphatidylinositol trisphosphate."
  * Added definition dbxref GOC:mah to GO:0034594
  * Copied GO:0034594 to GO:0004437 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034594
* Populated new object GO:0034595 (macro)
  * Changed name of GO:0034595 from "<new term>" to "phosphoinositide 5-phosphatase activity"
  * Set definition of GO:0034595 to "Catalysis of the removal the of the 5-phosphate group of a phosphatidylinositol phosphate."
  * Added definition dbxref GOC:elh to GO:0034595
  * Added synonym "polyphosphoinositol lipid 5-phosphatase activity" to GO:0034595
  * Changed synonym scope of GO:0034595 from "Related" to "Exact"
  * Copied GO:0034595 to GO:0004437 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034595
* Populated new object GO:0034596 (macro)
  * Changed name of GO:0034596 from "<new term>" to "phosphoinositide 4-phosphatase activity"
  * Set definition of GO:0034596 to "Catalysis of the removal the of the 4-phosphate group of a phosphatidylinositol phosphate."
  * Added definition dbxref GOC:mah to GO:0034596
  * Copied GO:0034596 to GO:0004437 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034596
* Populated new object GO:0034597 (macro)
  * Changed name of GO:0034597 from "<new term>" to "phosphatidyl-inositol-4,5-bisphosphate 4-phosphatase activity"
  * Set definition of GO:0034597 to "Catalysis of the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 3-phosphate + phosphate."
  * Added definition dbxref GOC:mah to GO:0034597
  * Added general dbxref EC:3.1.3.66 to GO:0034597
  * Added general dbxref MetaCyc:3.1.3.66-RXN to GO:0034597
  * Added synonym "1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate 4-phosphohydrolase activity" to GO:0034597
  * Changed synonym scope of GO:0034597 from "Related" to "Exact"
  * Added synonym "D-myo-inositol-4,5-bisphosphate 4-phosphohydrolase activity" to GO:0034597
  * Changed synonym scope of GO:0034597 from "Related" to "Exact"
  * Added synonym "inositol polyphosphate 4-phosphatase type II activity" to GO:0034597
  * Added general dbxref EC:3.1.3.66 to synonym inositol polyphosphate 4-phosphatase type II activity of GO:0034597
  * Added synonym "phosphatidyl-myo-inositol-4,5-bisphosphate 4-phosphohydrolase activity" to GO:0034597
  * Changed synonym scope of GO:0034597 from "Related" to "Exact"
  * Copied GO:0034597 to GO:0042577 with type OBO_REL:is_a
  * Copied GO:0034597 to GO:0034593 with type OBO_REL:is_a
  * Copied GO:0034597 to GO:0034596 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034597
* Deleted GO:0001668 --OBO_REL:is_a--> GO:0004437
* Deleted GO:0001668 --OBO_REL:is_a--> GO:0042577
* Destroyed object GO:0001668
* Changed name of GO:0004439 from "phosphoinositide 5-phosphatase activity" to "phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity"
* added secondary id GO:0001668 to GO:0004439
* Deleted synonym "diphosphoinositide phosphatase activity" from GO:0004439
* Deleted synonym "inositol triphosphate 5-phosphomonoesterase activity" from GO:0004439
* Deleted synonym "IP(3) phosphatase activity" from GO:0004439
* Deleted synonym "IP3 phosphatase activity" from GO:0004439
* Deleted synonym "phosphatidyl-inositol-bisphosphate phosphatase activity" from GO:0004439
* Deleted synonym "phosphatidyl-myo-inositol-4,5-bisphosphate 4-phosphohydrolase activity" from GO:0004439
* Changed synonym scope of GO:0004439 from "Exact" to "Broad"
* Deleted synonym "polyphosphoinositol lipid 5-phosphatase activity" from GO:0004439
* Deleted synonym "type II inositol polyphosphate 5-phosphatase activity" from GO:0004439
* Deleted synonym "type II inositol-1,4,5-trisphosphate 5-phosphatase activity" from GO:0004439
* Deleted GO:0004439 --OBO_REL:is_a--> GO:0004437
* Copied GO:0004439 to GO:0034593 with type OBO_REL:is_a
* Copied GO:0004439 to GO:0034595 with type OBO_REL:is_a
* Added synonym "<new synonym>" to GO:0004445
* Added synonym "inositol triphosphate 5-phosphomonoesterase activity" to GO:0004445
* Changed synonym scope of GO:0004445 from "Related" to "Exact"
* Added synonym "type II inositol polyphosphate 5-phosphatase activity" to GO:0004445
* Added synonym "type II inositol-1,4,5-trisphosphate 5-phosphatase activity" to GO:0004445
* Changed synonym scope of GO:0004445 from "Related" to "Narrow"
* Deleted GO:0005930 --OBO_REL:is_a--> GO:0044446
* Added synonym "PtdIns biosynthesis" to GO:0006661
* Changed synonym scope of GO:0006661 from "Related" to "Exact"
* Added synonym "PtdIns biosynthetic process" to GO:0006661
* Changed synonym scope of GO:0006661 from "Related" to "Exact"
* Changed comment from "MERGED COMMENT:
TARGET COMMENT: Note that this term should not be confused with 'pseudouridylate synthase activity ; GO:0004730', which refers to the formation of free pseudouridine from uracil and ribose-5-phosphate.
--------------------
SOURCE COMMENT: Note that this term should not be confused with 'pseudouridylate synthase activity ; GO:0004730', which refers to the formation of free pseudouridine from uracil and ribose-5-phosphate." to "Note that this term should not be confused with 'pseudouridylate synthase activity ; GO:0004730', which refers to the formation of free pseudouridine from uracil and ribose-5-phosphate."
* Changed comment from "This term was made obsolete because it was defined incorrectly: there are no known peptidases using a
catalytic mechanism involving arginine and lysine, and the Arabidopsis metacaspases that prompted addition of this term are in fact cysteine-type endopeptidases." to "This term was made obsolete because it was defined incorrectly: there are no known peptidases using a catalytic mechanism involving arginine and lysine, and the Arabidopsis metacaspases that prompted addition of this term are in fact cysteine-type endopeptidases."
* Changed definition of GO:0016010 from "A multiprotein complex that forms the critical link between the cytoskeleton and extracellular matrix; typical of, but not confined, to muscle cells. The constituents of the complex are somewhat tissue specific. The rod-like dystrophin forms a link between the actin cytoskeleton and the plasma membrane; links between dystrophin and the extracellular matrix are provided by the sarcoglycan complex." to "A multiprotein complex that forms a strong mechanical link between the cytoskeleton and extracellular matrix; typical of, but not confined to, muscle cells. The complex is composed of transmembrane, cytoplasmic, and extracellular proteins, including dystrophin, sarcoglycans, dystroglycan, dystrobrevins, syntrophins, sarcospan, caveolin-3, and NO synthase."
* Deleted definition dbxref http://www.dmd.nl/dap.html#dg from GO:0016010
* Added definition dbxref PMID:15117830 to GO:0016010
* Added definition dbxref PMID:16710609 to GO:0016010
* Deleted synonym "DGC complex" from GO:0016010
* Added synonym "DGC" to GO:0016010
* Changed synonym scope of GO:0016010 from "Related" to "Exact"
* Added synonym "dystrophin glycoprotein complex" to GO:0016010
* Changed synonym scope of GO:0016010 from "Related" to "Exact"
* Changed definition of GO:0016011 from "Includes alpha- and beta-dystroglycan; alternative products of the same gene; the laminin-binding component of the dystrophin-associated glycoprotein complex, providing a link between the subsarcolemmal cytoskeleton (in muscle cells) and the extracellular matrix. Alpha-dystroglycan is an extracellular protein binding to alpha-laminin and to beta-dystroglycan; beta-dystroglycan is a transmembrane protein which binds alpha-dystroglycan and dystrophin." to "A protein complex that includes alpha- and beta-dystroglycan, which are alternative products of the same gene; the laminin-binding component of the dystrophin-associated glycoprotein complex, providing a link between the subsarcolemmal cytoskeleton (in muscle cells) and the extracellular matrix. Alpha-dystroglycan is an extracellular protein binding to alpha-laminin and to beta-dystroglycan; beta-dystroglycan is a transmembrane protein which binds alpha-dystroglycan and dystrophin."
* Deleted definition dbxref http://www.dmd.nl/dap.html#dg from GO:0016011
* Added definition dbxref PMID:15117830 to GO:0016011
* Added definition dbxref PMID:16710609 to GO:0016011
* Changed definition of GO:0016012 from "Formed of five N-glycosylated sarcoglycans: alpha-, beta-, gamma-, delta-, and epsilon sarcoglycan, single-pass transmembrane proteins that form a complex which is fixed to the dystrophin axis by a lateral association with the dystroglycan complex." to "A protein complex formed of four sarcoglycans plus sarcospan; there are six known sarcoglycans: alpha-, beta-, gamma-, delta-, epsilon- and zeta-sarcoglycan; all are N-glycosylated single-pass transmembrane proteins. The sarcoglycan-sarcospan complex is a subcomplex of the dystrophin glycoprotein complex, and is fixed to the dystrophin axis by a lateral association with the dystroglycan complex."
* Deleted definition dbxref http://www.dmd.nl/dap.html#dg from GO:0016012
* Added definition dbxref PMID:15117830 to GO:0016012
* Added definition dbxref PMID:16710609 to GO:0016012
* Added synonym "sarcoglycan-sarcospan complex" to GO:0016012
* Changed synonym scope of GO:0016012 from "Related" to "Exact"
* Deleted GO:0016012 --OBO_REL:is_a--> GO:0044421
* Changed definition of GO:0016013 from "Includes alpha-, beta1-, beta2-syntrophins and syntrophin-like proteins; the syntrophin complex binds to the second half of the carboxy-terminal domain of dystrophin; also associates with neuronal nitric oxide synthase." to "A protein complex that includes alpha-, beta1-, beta2-syntrophins and syntrophin-like proteins; the syntrophin complex binds to the second half of the carboxy-terminal domain of dystrophin; also associates with neuronal nitric oxide synthase."
* Deleted definition dbxref http://www.dmd.nl/dap.html#dg from GO:0016013
* Added definition dbxref http://www.dmd.nl/DGC.html#syn to GO:0016013
* Deleted GO:0016013 --OBO_REL:is_a--> GO:0044421
* Changed definition of GO:0016014 from "A complex of alpha- and beta-dystrobrevin." to "A protein complex comprising alpha- and beta-dystrobrevin; forms part of the dystrophin glycoprotein complex."
* Deleted definition dbxref http://www.dmd.nl/dap.html#dg from GO:0016014
* Added definition dbxref PMID:15117830 to GO:0016014
* Added definition dbxref PMID:16710609 to GO:0016014
* Deleted GO:0016014 --OBO_REL:is_a--> GO:0044421
* Deleted GO:0016314 --OBO_REL:is_a--> GO:0004437
* Copied GO:0016314 to GO:0034594 with type OBO_REL:is_a
* Deleted synonym "inositol polyphosphate 4-phosphatase activity" from GO:0016316
* Deleted synonym "phosphoinositide 4-phosphatase activity" from GO:0016316
* Deleted GO:0016316 --OBO_REL:is_a--> GO:0004437
* Copied GO:0016316 to GO:0034596 with type OBO_REL:is_a
* Copied GO:0016316 to GO:0034593 with type OBO_REL:is_a
* Added synonym "PtdIns catabolic process" to GO:0031161
* Changed synonym scope of GO:0031161 from "Related" to "Exact"
* Added synonym "PtdIns catabolism" to GO:0031161
* Changed synonym scope of GO:0031161 from "Related" to "Exact"
* Deleted GO:0034485 --OBO_REL:is_a--> GO:0004437
* Copied GO:0034485 to GO:0034594 with type OBO_REL:is_a
* Copied GO:0034485 to GO:0034595 with type OBO_REL:is_a
* Changed definition of GO:0034515 from "A multisubunit proteasome complex that localizes in
the cytoplasm as dot-like structures when cells are in a quiescent state." to "A multisubunit proteasome complex that localizes in the cytoplasm as dot-like structures when cells are in a quiescent state."
* Deleted GO:0043813 --OBO_REL:is_a--> GO:0004437
* Copied GO:0043813 to GO:0034593 with type OBO_REL:is_a
* Copied GO:0043813 to GO:0034595 with type OBO_REL:is_a
* Deleted GO:0044447 --OBO_REL:is_a--> GO:0044446
* Added synonym "IP(3) phosphatase activity" to GO:0046030
* Changed synonym scope of GO:0046030 from "Related" to "Exact"
* Added synonym "IP3 phosphatase activity" to GO:0046030
* Changed synonym scope of GO:0046030 from "Related" to "Exact"
* Added synonym "PtdIns metabolic process" to GO:0046488
* Changed synonym scope of GO:0046488 from "Related" to "Exact"
* Added synonym "PtdIns metabolism" to GO:0046488
* Changed synonym scope of GO:0046488 from "Related" to "Exact"
* Added synonym "phosphatidylinositol phosphate biosynthetic process" to GO:0046854
* Changed synonym scope of GO:0046854 from "Related" to "Narrow"
* Added synonym "phosphatidylinositol phosphate phosphorylation" to GO:0046854
* Changed synonym scope of GO:0046854 from "Related" to "Narrow"
* Added synonym "PtdInsP biosynthesis" to GO:0046854
* Changed synonym scope of GO:0046854 from "Related" to "Narrow"
* Added synonym "phosphatidylinositol phosphate catabolic process" to GO:0046856
* Changed synonym scope of GO:0046856 from "Related" to "Narrow"
* Added synonym "phosphatidylinositol phosphate dephosphorylation" to GO:0046856
* Changed synonym scope of GO:0046856 from "Related" to "Narrow"
* Added synonym "PIP catabolism" to GO:0046856
* Changed synonym scope of GO:0046856 from "Related" to "Narrow"
* Added synonym "PtdInsP catabolism" to GO:0046856
* Changed synonym scope of GO:0046856 from "Related" to "Narrow"
* Added synonym "PtdInsP dephosphorylation" to GO:0046856
* Changed synonym scope of GO:0046856 from "Related" to "Narrow"
* Deleted GO:0051800 --OBO_REL:is_a--> GO:0004437
* Copied GO:0051800 to GO:0034593 with type OBO_REL:is_a
* Copied GO:0065010 to GO:0043227 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Thu Jul  3 21:30:46 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Thu, 3 Jul 2008 21:30:46 -0700 (PDT)
Subject: [Go-diff] GO update 07/03/2008
Message-ID: <200807040430.VAA09687@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.124 by 1.126

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Changed definition of GO:0034560 from "Catalysis of the reaction: bisphenol A  + NADH + H+ + O2 = 2,2-bis(4-hydroxyphenyl)-1-propanol + NAD+ + H2O." to "Catalysis of the reaction: bisphenol A + NADH + H+ + O2 = 2,2-bis(4-hydroxyphenyl)-1-propanol + NAD+ + H2O."
* Changed definition of GO:0034570 from "Catalysis of the reaction: hydroxymonodemethylisoproturon  + H2O = formaldehyde + 4'-(2-hydroxyisopropyl)phenylurea + 2 H+ + 2 e-." to "Catalysis of the reaction: hydroxymonodemethylisoproturon + H2O = formaldehyde + 4'-(2-hydroxyisopropyl)phenylurea + 2 H+ + 2 e-."
* Changed definition of GO:0044456 from "The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell." to "Any constituent part of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell."
* Deleted synonym "activation by organism of host gene-4-gene resistance" from GO:0052101
* Deleted synonym "induction by organism of host gene-4-gene resistance" from GO:0052101
* Added synonym "activation by organism of host gene-for-gene resistance" to GO:0052101
* Changed synonym scope of GO:0052101 from "Related" to "Exact"
* Added synonym "induction by organism of host gene-for-gene resistance" to GO:0052101
* Changed synonym scope of GO:0052101 from "Related" to "Exact"
* Deleted synonym "modulation by organism of host gene-4-gene resistance" from GO:0052158
* Added synonym "modulation by organism of host gene-for-gene resistance" to GO:0052158
* Changed synonym scope of GO:0052158 from "Related" to "Exact"
* Deleted synonym "activation by organism of gene-4-gene resistance in other organism" from GO:0052286
* Deleted synonym "induction by organism of gene-4-gene resistance in other organism" from GO:0052286
* Added synonym "activation by organism of gene-for-gene resistance in other organism" to GO:0052286
* Changed synonym scope of GO:0052286 from "Related" to "Exact"
* Added synonym "induction by organism of gene-for-gene resistance in other organism" to GO:0052286
* Changed synonym scope of GO:0052286 from "Related" to "Exact"
* Deleted synonym "modulation by organism of gene-4-gene resistance in other organism" from GO:0052297
* Added synonym "modulation by organism of gene-for-gene resistance in other organism" to GO:0052297
* Changed synonym scope of GO:0052297 from "Related" to "Exact"
* Deleted synonym "activation by organism of symbiont gene-4-gene resistance" from GO:0052402
* Deleted synonym "induction by organism of symbiont gene-4-gene resistance" from GO:0052402
* Added synonym "activation by organism of symbiont gene-for-gene resistance" to GO:0052402
* Changed synonym scope of GO:0052402 from "Related" to "Exact"
* Added synonym "induction by organism of symbiont gene-for-gene resistance" to GO:0052402
* Changed synonym scope of GO:0052402 from "Related" to "Exact"
* Deleted synonym "positive regulation by organism of gene-4-gene resistance in other organism" from GO:0052423
* Added synonym "positive regulation by organism of gene-for-gene resistance in other organism" to GO:0052423
* Changed synonym scope of GO:0052423 from "Related" to "Exact"
* Deleted synonym "modulation by organism of symbiont gene-4-gene resistance" from GO:0052466
* Added synonym "modulation by organism of symbiont gene-for-gene resistance" to GO:0052466
* Changed synonym scope of GO:0052466 from "Related" to "Exact"
* Deleted synonym "positive regulation by organism of host gene-4-gene resistance" from GO:0052527
* Added synonym "positive regulation by organism of host gene-for-gene resistance" to GO:0052527
* Changed synonym scope of GO:0052527 from "Related" to "Exact"
* Deleted synonym "positive regulation by organism of symbiont gene-4-gene resistance" from GO:0052530
* Added synonym "positive regulation by organism of symbiont gene-for-gene resistance" to GO:0052530
* Changed synonym scope of GO:0052530 from "Related" to "Exact"

From gocvs at genome.stanford.edu  Tue Jul  8 21:30:47 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Tue, 8 Jul 2008 21:30:47 -0700 (PDT)
Subject: [Go-diff] GO update 07/08/2008
Message-ID: <200807090430.VAA25221@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.126 by 1.127

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034598
* Populated new object GO:0034598 (macro)
  * Changed name of GO:0034598 from "<new term>" to "phosphothreonine lyase activity"
  * Set definition of GO:0034598 to "Catalysis of the removal of the phosphate group from phosphothreonine by cleavage of the C-OP bond with the concomitant abstraction of the alpha proton, generating a double bond-containing product."
  * Added definition dbxref PMID:17303758 to GO:0034598
  * Added definition dbxref PMID:18084305 to GO:0034598
  * Copied GO:0034598 to GO:0016838 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034598
* Deleted GO:0005578 --OBO_REL:is_a--> GO:0044421
* Deleted GO:0016010 --OBO_REL:is_a--> GO:0044421
* Deleted GO:0016010 --part_of--> GO:0005605
* Deleted GO:0016010 --OBO_REL:is_a--> GO:0044420
* Deleted GO:0016010 --OBO_REL:is_a--> GO:0044444
* Deleted GO:0016011 --OBO_REL:is_a--> GO:0044444
* Deleted GO:0016011 --OBO_REL:is_a--> GO:0044421
* Deleted GO:0016011 --OBO_REL:is_a--> GO:0044420
* Deleted GO:0016012 --OBO_REL:is_a--> GO:0044420
* Deleted GO:0016012 --OBO_REL:is_a--> GO:0044444
* Deleted GO:0016013 --OBO_REL:is_a--> GO:0044459
* Deleted GO:0016013 --OBO_REL:is_a--> GO:0044420
* Deleted GO:0016013 --OBO_REL:is_a--> GO:0044444
* Deleted GO:0016014 --OBO_REL:is_a--> GO:0044420
* Deleted GO:0016014 --OBO_REL:is_a--> GO:0044444
* Deleted GO:0016014 --OBO_REL:is_a--> GO:0044459
* Changed definition of GO:0020008 from "A specialized secretory organelle, with a tubular or sacular shape, found in the apical complex." to "A large, club-shaped secretory organelle that forms part of the apical complex of an apicomplexan parasite, and consists of a bulbous body and a narrow electron-dense neck that extends through the conoid at the apical tip of the parasite. The rhoptry necks serve as ducts through which the contents of the rhoptries are secreted after attachment to the host has been completed and at the commencement of invasion. Rhoptry proteins function in the biogenesis and host organellar association of the parasitophorous vacuole."
* Deleted definition dbxref PMID:17305424 from GO:0020008
* Added definition dbxref PMID:11801218 to GO:0020008
* Added definition dbxref PMID:16002398 to GO:0020008
* Added synonym "paired organelles" to GO:0020008
* Added synonym "toxoneme" to GO:0020008
* Changed definition of GO:0020009 from "Elongated tubular organelle arranged longitudinally in the apical complex of an apicomplexan parasite." to "A small, elongated secretory organelle that forms part of the apical complex, located along the main axis of an apicomplexan parasite cell within the extreme apical region and at the periphery under the inner membrane complex. Of the three specialized secretory compartments identified in apicomplexans, micronemes discharge their contents first, during initial contact of the parasite's apical pole with the host cell surface. Micronemal proteins function during parasite attachment and penetration into the target cell."
* Added definition dbxref PMID:11801218 to GO:0020009
* Added synonym "sarconeme" to GO:0020009
* Deleted GO:0021748 --OBO_REL:is_a--> GO:0048856
* Deleted GO:0021748 --part_of--> GO:0021747
* Copied GO:0021748 to GO:0021747 with type OBO_REL:is_a
* Deleted GO:0021749 --OBO_REL:is_a--> GO:0048856
* Deleted GO:0021749 --part_of--> GO:0021747
* Copied GO:0021749 to GO:0021747 with type OBO_REL:is_a
* Deleted GO:0021895 --OBO_REL:is_a--> GO:0030154
* Copied GO:0021895 to GO:0030182 with type OBO_REL:is_a
* Deleted GO:0031012 --OBO_REL:is_a--> GO:0005575
* Copied GO:0031012 to GO:0044421 with type OBO_REL:is_a
* Added synonym "homotypic vacuole fusion" to GO:0042144
* Changed synonym scope of GO:0042144 from "Related" to "Exact"
* Changed definition of GO:0045177 from "The apical region of a cell." to "The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue."
* Deleted definition dbxref GOC:bf from GO:0045177
* Added definition dbxref GOC:mah to GO:0045177
* Added definition dbxref ISBN:0815316194 to GO:0045177
* Changed definition of GO:0045178 from "The basal region of a cell." to "The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue."
* Deleted definition dbxref GOC:bf from GO:0045178
* Added definition dbxref GOC:bmah to GO:0045178
* Added definition dbxref ISBN:0185316194 to GO:0045178
* Added synonym "PIP biosynthesis" to GO:0046854
* Changed synonym scope of GO:0046854 from "Related" to "Narrow"
* Copied GO:0060113 to GO:0035315 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Wed Jul  9 21:30:46 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Wed, 9 Jul 2008 21:30:46 -0700 (PDT)
Subject: [Go-diff] GO update 07/09/2008
Message-ID: <200807100430.VAA04128@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.127 by 1.129

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0043925
* Created object of type obo:TERM with id GO:0043926
* Created object of type obo:TERM with id GO:0043927
* Created object of type obo:TERM with id GO:0043928
* Created object of type obo:TERM with id GO:0043929
* Created object of type obo:TERM with id GO:0043930
* Created object of type obo:TERM with id GO:0043931
* Created object of type obo:TERM with id GO:0043932
* Populated new object GO:0043925 (macro)
  * Changed name of GO:0043925 from "<new term>" to "microtubule-associated DASH complex"
  * Added comment "Note that this complex is conserved in fungi but has not been observed in metazoans."
  * Set definition of GO:0043925 to "A large protein complex, containing around 8-10 subunits in yeast, including Duo1p, Dam1p, Dad1p and Ask1p. The complex associates with microtubules and plays a role in spindle attachment, chromosome segregation and spindle stability."
  * Added definition dbxref GOC:jl to GO:0043925
  * Added definition dbxref GOC:mtg_mpo to GO:0043925
  * Added definition dbxref PMID:11782438 to GO:0043925
  * Added definition dbxref PMID:11799062 to GO:0043925
  * Copied GO:0043925 to GO:0005828 with type part_of
  * Copied GO:0043925 to GO:0005875 with type OBO_REL:is_a
  * Copied GO:0043925 to GO:0042729 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0043925
* Populated new object GO:0043926 (macro)
  * Changed name of GO:0043926 from "<new term>" to "kinetochore-associated DASH complex"
  * Added comment "Note that this complex is conserved in fungi but has not been observed in metazoans."
  * Set definition of GO:0043926 to "A large protein complex, containing around 8-10 subunits in yeast, including Duo1p, Dam1p, Dad1p and Ask1p. The complex associates with kinetochores and plays a role in spindle attachment, chromosome segregation and spindle stability."
  * Added definition dbxref GOC:jl to GO:0043926
  * Added definition dbxref GOC:mtg_mpo to GO:0043926
  * Added definition dbxref PMID:11782438 to GO:0043926
  * Added definition dbxref PMID:11799062 to GO:0043926
  * Added synonym "condensed nuclear chromosome kinetochore-associated DASH complex" to GO:0043926
  * Changed synonym scope of GO:0043926 from "Related" to "Exact"
  * Copied GO:0043926 to GO:0042729 with type OBO_REL:is_a
  * Copied GO:0043926 to GO:0000778 with type part_of
  * Assigned namespace "cellular_component" to GO:0043926
* Populated new object GO:0043927 (macro)
  * Changed name of GO:0043927 from "<new term>" to "exonucleolytic nuclear-transcribed mRNA catabolic process involved in endonucleolytic cleavage-dependent decay"
  * Set definition of GO:0043927 to "The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 5'-cap."
  * Added definition dbxref GOC:mtg_mpo to GO:0043927
  * Copied GO:0043927 to GO:0000291 with type OBO_REL:is_a
  * Copied GO:0043927 to GO:0000294 with type part_of
  * Assigned namespace "biological_process" to GO:0043927
* Populated new object GO:0043928 (macro)
  * Changed name of GO:0043928 from "<new term>" to "exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay"
  * Set definition of GO:0043928 to "The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail."
  * Added definition dbxref GOC:mtg_mpo to GO:0043928
  * Copied GO:0043928 to GO:0000290 with type part_of
  * Copied GO:0043928 to GO:0000291 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0043928
* Populated new object GO:0043929 (macro)
  * Changed name of GO:0043929 from "<new term>" to "primary ovarian follicle growth during double layer follicle stage"
  * Set definition of GO:0043929 to "Increase in size of primary follicles including oocyte growth and granulosa and/or theca cell proliferation until more than one layer of granulosa cells is present (preantral follicle), during the double layer follicle stage of oogenesis."
  * Added definition dbxref GOC:mtg_mpo to GO:0043929
  * Copied GO:0043929 to GO:0048161 with type part_of
  * Copied GO:0043929 to GO:0001545 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0043929
* Populated new object GO:0043930 (macro)
  * Changed name of GO:0043930 from "<new term>" to "primary ovarian follicle growth during primary follicle stage"
  * Set definition of GO:0043930 to "Increase in size of primary follicles including oocyte growth and granulosa and/or theca cell proliferation until more than one layer of granulosa cells is present (preantral follicle) during the primary follicle stage of oogenesis."
  * Added definition dbxref GOC:mtg_mpo to GO:0043930
  * Copied GO:0043930 to GO:0001545 with type OBO_REL:is_a
  * Copied GO:0043930 to GO:0048160 with type part_of
  * Assigned namespace "biological_process" to GO:0043930
* Populated new object GO:0043931 (macro)
  * Changed name of GO:0043931 from "<new term>" to "ossification involved in skeletal development"
  * Set definition of GO:0043931 to "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone involved in the progression of the skeleton from its formation to its mature state."
  * Added definition dbxref GOC:mtg_mpo to GO:0043931
  * Copied GO:0043931 to GO:0001501 with type part_of
  * Copied GO:0043931 to GO:0001503 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0043931
* Populated new object GO:0043932 (macro)
  * Changed name of GO:0043932 from "<new term>" to "ossification involved in bone remodeling"
  * Set definition of GO:0043932 to "The formation of bone involved in the continuous turnover of bone matrix and mineral."
  * Added definition dbxref GOC:mtg_mpo to GO:0043932
  * Added synonym "ossification involved in bone remodelling" to GO:0043932
  * Copied GO:0043932 to GO:0046849 with type part_of
  * Copied GO:0043932 to GO:0001503 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0043932
* Deleted GO:0000291 --part_of--> GO:0000288
* Deleted GO:0000291 --part_of--> GO:0000294
* Changed name of GO:0000352 from "trans assembly of SL containing precatalytic spliceosome" to "trans assembly of SL-containing precatalytic spliceosome"
* Added definition dbxref GOC:mtg_mpo to GO:0000352
* Added synonym "trans assembly of spliced leader-containing precatalytic spliceosome" to GO:0000352
* Changed synonym scope of GO:0000352 from "Related" to "Exact"
* Added definition dbxref GOC:mtg_mpo to GO:0000354
* Added definition dbxref GOC:mtg_mpo to GO:0001503
* Deleted GO:0001503 --part_of--> GO:0046849
* Deleted GO:0001503 --part_of--> GO:0001501
* Added definition dbxref GOC:mtg_mpo to GO:0001545
* Deleted GO:0001545 --part_of--> GO:0048161
* Deleted GO:0001545 --part_of--> GO:0048160
* Changed definition of GO:0042729 from "A large protein complex, containing around 8-10 subunits in yeast, including Duo1p, Dam1p, Dad1p and Ask1p. Associating with microtubules and kinetochores, the complex plays a role spindle attachment, chromosome segregation and spindle stability." to "A large protein complex, containing around 8-10 subunits in yeast, including Duo1p, Dam1p, Dad1p and Ask1p. The complexes associate with kinetochores or microtubules and play a role spindle attachment, chromosome segregation and spindle stability."
* Deleted GO:0042729 --part_of--> GO:0000778
* Deleted GO:0042729 --OBO_REL:is_a--> GO:0044454
* Deleted GO:0042729 --OBO_REL:is_a--> GO:0005875
* Deleted GO:0042729 --part_of--> GO:0005828
* Copied GO:0042729 to GO:0043234 with type OBO_REL:is_a
* Changed name of GO:0045291 from "nuclear mRNA trans splicing, splice leader addition" to "nuclear mRNA trans splicing, SL addition"
* Added synonym "nuclear mRNA trans splicing, spliced leader addition" to GO:0045291
* Changed synonym scope of GO:0045291 from "Related" to "Exact"

From gocvs at genome.stanford.edu  Thu Jul 10 21:30:45 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Thu, 10 Jul 2008 21:30:45 -0700 (PDT)
Subject: [Go-diff] GO update 07/10/2008
Message-ID: <200807110430.VAA13810@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.129 by 1.130

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Deleted general dbxref MetaCyc:MANNOSYL-CHITO-DOLICHOL%20BIOSYNTHESIS from GO:0019347
* Added general dbxref MetaCyc:MANNOSYL-CHITO-DOLICHOL-BIOSYNTHESIS to GO:0019347
* Changed definition of GO:0020010 from "A spiral cytoskeletal structure located at the apical end of the apical complex in some apicomplexan parasites. Fibers form a left-handed spiral, and are comprised of tubulin protofilaments organized in a ribbon-like structure that differs from the comventional tubular structure characteristic of mictotubules." to "A spiral cytoskeletal structure located at the apical end of the apical complex in some apicomplexan parasites. Fibers form a left-handed spiral, and are comprised of tubulin protofilaments organized in a ribbon-like structure that differs from the conventional tubular structure characteristic of mictotubules."

From gocvs at genome.stanford.edu  Mon Jul 14 21:30:45 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Mon, 14 Jul 2008 21:30:45 -0700 (PDT)
Subject: [Go-diff] GO update 07/14/2008
Message-ID: <200807150430.VAA26203@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.130 by 1.131

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034599
* Created object of type obo:TERM with id GO:0034600
* Populated new object GO:0034599 (macro)
  * Changed name of GO:0034599 from "<new term>" to "cellular response to oxidative stress"
  * Set definition of GO:0034599 to "A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals."
  * Added definition dbxref GOC:mah to GO:0034599
  * Copied GO:0034599 to GO:0006979 with type OBO_REL:is_a
  * Copied GO:0034599 to GO:0033554 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034599
* Populated new object GO:0034600 (macro)
  * Changed name of GO:0034600 from "<new term>" to "macromolecular complex organization"
  * Set definition of GO:0034600 to "Any process by which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex."
  * Added definition dbxref GOC:mah to GO:0034600
  * Copied GO:0034600 to GO:0008150 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034600
* Changed definition of GO:0000280 from "The partitioning of the nucleus and its genetic information." to "A process by which a cell nucleus is divided into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei."
* Deleted definition dbxref GOC:bf from GO:0000280
* Deleted definition dbxref GOC:jl from GO:0000280
* Deleted definition dbxref http://www.biology-online.org/ from GO:0000280
* Added definition dbxref GOC:mah to GO:0000280
* Deleted GO:0000280 --OBO_REL:is_a--> GO:0009987
* Copied GO:0000280 to GO:0048285 with type OBO_REL:is_a
* Changed definition of GO:0000417 from "A protein complex proposed to be involved in replication-indepdent chromatin assembly. For example, in Saccharomyces, the complex contains Hir1p, Hir2p, Hir3p, and Hpc2p." to "A protein complex proposed to be involved in replication-independent chromatin assembly. For example, in Saccharomyces, the complex contains Hir1p, Hir2p, Hir3p, and Hpc2p."
* Deleted GO:0006267 --OBO_REL:is_a--> GO:0043623
* Copied GO:0006267 to GO:0065004 with type OBO_REL:is_a
* Deleted GO:0006337 --OBO_REL:is_a--> GO:0031498
* Copied GO:0006337 to GO:0032986 with type OBO_REL:is_a
* Copied GO:0006337 to GO:0031498 with type part_of
* Deleted GO:0006461 --OBO_REL:is_a--> GO:0019538
* Copied GO:0006506 to GO:0044249 with type OBO_REL:is_a
* Copied GO:0016051 to GO:0009058 with type OBO_REL:is_a
* Copied GO:0016457 to GO:0065004 with type OBO_REL:is_a
* Copied GO:0032187 to GO:0051641 with type OBO_REL:is_a
* Changed definition of GO:0032594 from "The directed movement of a protein within a lipid bilayer." to "The directed movement of a protein from one location to another within a lipid bilayer."
* Deleted GO:0032984 --OBO_REL:is_a--> GO:0043170
* Copied GO:0032984 to GO:0034600 with type OBO_REL:is_a
* Changed definition of GO:0034367 from "The acquisition, loss, or modification of molecules within a complex. The remodeling process begins with an existing complex, and ends with an altered complex." to "The acquisition, loss, or modification of macromolecules within a complex, resulting in the alteration of an existing complex."
* Added definition dbxref GOC:mtg_mpo to GO:0034367
* Deleted GO:0034367 --OBO_REL:is_a--> GO:0043170
* Copied GO:0034367 to GO:0034600 with type OBO_REL:is_a
* Copied GO:0042715 to GO:0065004 with type OBO_REL:is_a
* Copied GO:0042776 to GO:0006839 with type OBO_REL:is_a
* Deleted GO:0043241 --OBO_REL:is_a--> GO:0019538
* Deleted GO:0051205 --OBO_REL:is_a--> GO:0032594
* Copied GO:0051205 to GO:0008104 with type OBO_REL:is_a
* Copied GO:0051904 to GO:0006810 with type OBO_REL:is_a
* Deleted GO:0065003 --OBO_REL:is_a--> GO:0043170
* Copied GO:0065003 to GO:0034600 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Tue Jul 15 21:30:46 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Tue, 15 Jul 2008 21:30:46 -0700 (PDT)
Subject: [Go-diff] GO update 07/15/2008
Message-ID: <200807160430.VAA04735@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.131 by 1.133

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010628
* Created object of type obo:TERM with id GO:0010629
* Created object of type obo:TERM with id GO:0010630
* Created object of type obo:TERM with id GO:0034601
* Created object of type obo:TERM with id GO:0034602
* Created object of type obo:TERM with id GO:0034603
* Created object of type obo:TERM with id GO:0034604
* Created object of type obo:TERM with id GO:0034605
* Populated new object GO:0010628 (macro)
  * Changed name of GO:0010628 from "<new term>" to "positive regulation of gene expression"
  * Set definition of GO:0010628 to "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form."
  * Added definition dbxref GOC:dph to GO:0010628
  * Added definition dbxref GOC:tb to GO:0010628
  * Copied GO:0010628 to GO:0010468 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010628
* Populated new object GO:0010629 (macro)
  * Changed name of GO:0010629 from "<new term>" to "negative regulation of gene expression"
  * Set definition of GO:0010629 to "Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form."
  * Added definition dbxref GOC:dph to GO:0010629
  * Added definition dbxref GOC:tb to GO:0010629
  * Copied GO:0010629 to GO:0010468 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010629
* Populated new object GO:0010630 (macro)
  * Changed name of GO:0010630 from "<new term>" to "regulation of transcription, start site selection"
  * Set definition of GO:0010630 to "Any process that modulates the frequency, rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA by a mechanism that selects the start site along that template."
  * Added definition dbxref GOC:dph to GO:0010630
  * Added definition dbxref GOC:tb to GO:0010630
  * Copied GO:0010630 to GO:0045449 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010630
* Populated new object GO:0034601 (macro)
  * Changed name of GO:0034601 from "<new term>" to "oxoglutarate dehydrogenase [NAD(P)+] activity"
  * Set definition of GO:0034601 to "Catalysis of the reaction: 2-oxoglutarate + CoA + NAD(P)+ = succinyl-CoA + CO2 + NAD(P)H."
  * Added definition dbxref GOC:mah to GO:0034601
  * Added general dbxref EC:1.2.1.52 to GO:0034601
  * Added general dbxref MetaCyc:OXOGLUTARATE-DEHYDROGENASE-(NADP+)-RXN to GO:0034601
  * Copied GO:0034601 to GO:0016620 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034601
* Populated new object GO:0034602 (macro)
  * Changed name of GO:0034602 from "<new term>" to "oxoglutarate dehydrogenase (NAD+) activity"
  * Set definition of GO:0034602 to "Catalysis of the reaction: 2-oxoglutarate + CoA + NAD+ = succinyl-CoA + CO2 + NADH."
  * Added definition dbxref GOC:mah to GO:0034602
  * Added general dbxref EC:1.2.1.52 to GO:0034602
  * Added general dbxref MetaCyc:OXOGLUTARATE-DEHYDROGENASE-(NADP+)-RXN to GO:0034602
  * Copied GO:0034602 to GO:0034601 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034602
* Populated new object GO:0034603 (macro)
  * Changed name of GO:0034603 from "<new term>" to "pyruvate dehydrogenase [NAD(P)+] activity"
  * Set definition of GO:0034603 to "Catalysis of the reaction: pyruvate + CoA + NAD(P)+ = acetyl-CoA + CO2 + NAD(P)H."
  * Added definition dbxref GOC:mah to GO:0034603
  * Added general dbxref EC:1.2.1.51 to GO:0034603
  * Added general dbxref MetaCyc:PYRUVATE-DEHYDROGENASE-(NADP+)-RXN to GO:0034603
  * Copied GO:0034603 to GO:0016620 with type OBO_REL:is_a
  * Copied GO:0034603 to GO:0004738 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034603
* Populated new object GO:0034604 (macro)
  * Changed name of GO:0034604 from "<new term>" to "pyruvate dehydrogenase (NAD+) activity"
  * Set definition of GO:0034604 to "Catalysis of the reaction: pyruvate + CoA + NAD+ = acetyl-CoA + CO2 + NADH."
  * Added definition dbxref GOC:mah to GO:0034604
  * Added general dbxref EC:1.2.1.51 to GO:0034604
  * Added general dbxref MetaCyc:PYRUVATE-DEHYDROGENASE-(NADP+)-RXN to GO:0034604
  * Copied GO:0034604 to GO:0034603 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034604
* Populated new object GO:0034605 (macro)
  * Changed name of GO:0034605 from "<new term>" to "cellular response to heat"
  * Set definition of GO:0034605 to "A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism."
  * Added definition dbxref GOC:mah to GO:0034605
  * Copied GO:0034605 to GO:0033554 with type OBO_REL:is_a
  * Copied GO:0034605 to GO:0009408 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034605
* Deleted GO:0005176 --OBO_REL:is_a--> GO:0005125
* Copied GO:0005176 to GO:0005102 with type OBO_REL:is_a
* Copied GO:0008634 to GO:0010629 with type OBO_REL:is_a
* Copied GO:0016481 to GO:0010629 with type OBO_REL:is_a
* Deleted GO:0031990 --OBO_REL:is_a--> GO:0009408
* Copied GO:0031990 to GO:0034605 with type OBO_REL:is_a
* Deleted GO:0035080 --OBO_REL:is_a--> GO:0009408
* Copied GO:0035080 to GO:0034605 with type OBO_REL:is_a
* Deleted GO:0043125 --OBO_REL:is_a--> GO:0005125
* Copied GO:0043125 to GO:0005102 with type OBO_REL:is_a
* Copied GO:0045814 to GO:0010629 with type OBO_REL:is_a
* Copied GO:0045815 to GO:0010628 with type OBO_REL:is_a
* Copied GO:0045871 to GO:0010629 with type OBO_REL:is_a
* Copied GO:0045872 to GO:0010628 with type OBO_REL:is_a
* Copied GO:0045885 to GO:0010628 with type OBO_REL:is_a
* Copied GO:0045941 to GO:0010628 with type OBO_REL:is_a
* Deleted GO:0050164 --OBO_REL:is_a--> GO:0016620
* Copied GO:0050164 to GO:0034601 with type OBO_REL:is_a
* Deleted GO:0050243 --OBO_REL:is_a--> GO:0004738
* Deleted GO:0050243 --OBO_REL:is_a--> GO:0016620
* Copied GO:0050243 to GO:0034603 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Thu Jul 17 21:30:45 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Thu, 17 Jul 2008 21:30:45 -0700 (PDT)
Subject: [Go-diff] GO update 07/17/2008
Message-ID: <200807180430.VAA25488@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.133 by 1.134

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Added comment "This term was made obsolete because it implies that every protein that is ubiquitinated is also subsequently deubiquinitated, which is not true. Also, the process ontology does not include analogous terms for other small modifiers."
* Changed definition of GO:0006512 from "The cyclical process by which one or more ubiquitin moieties are added to (ubiquitination) and removed from (deubiquitination) a protein." to "OBSOLETE. The cyclical process by which one or more ubiquitin moieties are added to (ubiquitination) and removed from (deubiquitination) a protein."
* Deleted GO:0006512 --OBO_REL:is_a--> GO:0043687
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 1dd3e6f
* Added synonym "protein sorting along secretory pathway" to GO:0006605
* Changed synonym scope of GO:0006605 from "Related" to "Narrow"
* Added synonym "synaptic vesicle fusion" to GO:0016189
* Changed synonym scope of GO:0016189 from "Related" to "Broad"
* Deleted synonym "synaptic vesicle fission" from GO:0016192
* Deleted synonym "synaptic vesicle fusion" from GO:0016192
* Deleted synonym "synaptic vesicle internalization" from GO:0016192
* Deleted synonym "synaptic vesicle retrieval" from GO:0016192
* Added synonym "protein sorting along secretory pathway" to GO:0016192
* Deleted GO:0016567 --OBO_REL:is_a--> GO:0006512
* Copied GO:0016567 to GO:0043687 with type OBO_REL:is_a
* Deleted GO:0016579 --OBO_REL:is_a--> GO:0006512
* Copied GO:0016579 to GO:0043687 with type OBO_REL:is_a
* Added synonym "synaptic vesicle fusion" to GO:0031629
* Changed synonym scope of GO:0031629 from "Related" to "Broad"
* Added synonym "synaptic vesicle internalization" to GO:0031629
* Added comment "This term was made obsolete because its definition is very similar to that of its parent term, actin cortical patch localization (GO:0051666), but somewhat unclear, and not similar enough to merge the terms."
* Changed definition of GO:0048228 from "Any process that establish the spatial arrangement of actin cortical patches. An actin cortical patch is a discrete actin-containing structure found at the plasma membrane in fungal cells." to "OBSOLETE. Any process that establish the spatial arrangement of actin cortical patches. An actin cortical patch is a discrete actin-containing structure found at the plasma membrane in fungal cells."
* Deleted GO:0048228 --OBO_REL:is_a--> GO:0030866
* Deleted GO:0048228 --OBO_REL:is_a--> GO:0051666
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 1ee3434
* Changed definition of GO:0048488 from "Invagination of the axonal plasma membrane creating a membrane bound vesicle. Without this process the presynaptic terminal would swell up due to fusion of vesicle membranes during neurotransmitter release. The vesicles created may subsequently be used for neurotransmitter storage/release." to "Invagination of the axonal plasma membrane creating a membrane-bounded vesicle. Without this process the presynaptic terminal would swell up due to fusion of vesicle membranes during neurotransmitter release. The vesicles created may subsequently be used for neurotransmitter storage/release."
* Added synonym "synaptic vesicle retrieval" to GO:0048488
* Added synonym "synaptic vesicle fission" to GO:0048489
* Added synonym "synaptic vesicle fusion" to GO:0048489

From gocvs at genome.stanford.edu  Tue Jul 22 21:30:45 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Tue, 22 Jul 2008 21:30:45 -0700 (PDT)
Subject: [Go-diff] GO update 07/22/2008
Message-ID: <200807230430.VAA00226@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.134 by 1.139

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010631
* Created object of type obo:TERM with id GO:0010632
* Created object of type obo:TERM with id GO:0010633
* Created object of type obo:TERM with id GO:0010634
* Created object of type obo:TERM with id GO:0010635
* Created object of type obo:TERM with id GO:0010636
* Created object of type obo:TERM with id GO:0010637
* Created object of type obo:TERM with id GO:0010638
* Created object of type obo:TERM with id GO:0010639
* Created object of type obo:TERM with id GO:0010640
* Created object of type obo:TERM with id GO:0010641
* Created object of type obo:TERM with id GO:0010642
* Created object of type obo:TERM with id GO:0043933
* Created object of type obo:TERM with id GO:0060269
* Created object of type obo:TERM with id GO:0060270
* Created object of type obo:TERM with id GO:0060271
* Created object of type obo:TERM with id GO:0060272
* Created object of type obo:TERM with id GO:0060273
* Populated new object GO:0010631 (macro)
  * Changed name of GO:0010631 from "<new term>" to "epithelial cell migration"
  * Set definition of GO:0010631 to "The orderly movement of epithelial cells from one site to another, often during the development of a multicellular organism."
  * Added definition dbxref GOC:dph to GO:0010631
  * Added definition dbxref GOC:tb to GO:0010631
  * Copied GO:0010631 to GO:0016477 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010631
* Populated new object GO:0010632 (macro)
  * Changed name of GO:0010632 from "<new term>" to "regulation of epithelial cell migration"
  * Set definition of GO:0010632 to "Any process that modulates the frequency, rate or extent of epithelial cell migration."
  * Added definition dbxref GOC:dph to GO:0010632
  * Added definition dbxref GOC:tb to GO:0010632
  * Copied GO:0010632 to GO:0010631 with type regulates
  * Copied GO:0010632 to GO:0030334 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010632
* Populated new object GO:0010633 (macro)
  * Changed name of GO:0010633 from "<new term>" to "negative regulation of epithelial cell migration"
  * Set definition of GO:0010633 to "Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell migration."
  * Added definition dbxref GOC:dph to GO:0010633
  * Added definition dbxref GOC:tb to GO:0010633
  * Copied GO:0010633 to GO:0030336 with type OBO_REL:is_a
  * Copied GO:0010633 to GO:0010631 with type negatively_regulates
  * Copied GO:0010633 to GO:0010632 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010633
* Populated new object GO:0010634 (macro)
  * Changed name of GO:0010634 from "<new term>" to "positive regulation of epithelial cell migration"
  * Set definition of GO:0010634 to "Any process that activates or increases the frequency, rate or extent of epithelial cell migration."
  * Added definition dbxref GOC:dph to GO:0010634
  * Added definition dbxref GOC:tb to GO:0010634
  * Copied GO:0010634 to GO:0030335 with type OBO_REL:is_a
  * Copied GO:0010634 to GO:0010632 with type OBO_REL:is_a
  * Copied GO:0010634 to GO:0010631 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010634
* Populated new object GO:0010635 (macro)
  * Changed name of GO:0010635 from "<new term>" to "regulation of mitochondrial fusion"
  * Set definition of GO:0010635 to "Any process that modulates the frequency, rate or extent of merging of two or more mitochondria within a cell to form a single compartment."
  * Added definition dbxref GOC:dph to GO:0010635
  * Added definition dbxref GOC:tb to GO:0010635
  * Copied GO:0010635 to GO:0008053 with type regulates
  * Copied GO:0010635 to GO:0033043 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010635
* Populated new object GO:0010636 (macro)
  * Changed name of GO:0010636 from "<new term>" to "positive regulation of mitochondrial fusion"
  * Set definition of GO:0010636 to "Any process that increases the frequency, rate or extent of merging of two or more mitochondria within a cell to form a single compartment."
  * Added definition dbxref GOC:dph to GO:0010636
  * Added definition dbxref GOC:tb to GO:0010636
  * Copied GO:0010636 to GO:0010638 with type OBO_REL:is_a
  * Copied GO:0010636 to GO:0010635 with type OBO_REL:is_a
  * Copied GO:0010636 to GO:0008053 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010636
* Populated new object GO:0010637 (macro)
  * Changed name of GO:0010637 from "<new term>" to "negative regulation of mitochondrial fusion"
  * Set definition of GO:0010637 to "Any process that decreases the frequency, rate or extent of merging of two or more mitochondria within a cell to form a single compartment."
  * Added definition dbxref GOC:dph to GO:0010637
  * Added definition dbxref GOC:tb to GO:0010637
  * Copied GO:0010637 to GO:0008053 with type negatively_regulates
  * Copied GO:0010637 to GO:0010639 with type OBO_REL:is_a
  * Copied GO:0010637 to GO:0010635 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010637
* Populated new object GO:0010638 (macro)
  * Changed name of GO:0010638 from "<new term>" to "positive regulation of organelle organization and biogenesis"
  * Set definition of GO:0010638 to "Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle."
  * Added definition dbxref GOC:dph to GO:0010638
  * Added definition dbxref GOC:tb to GO:0010638
  * Copied GO:0010638 to GO:0051130 with type OBO_REL:is_a
  * Copied GO:0010638 to GO:0033043 with type OBO_REL:is_a
  * Copied GO:0010638 to GO:0006996 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010638
* Populated new object GO:0010639 (macro)
  * Changed name of GO:0010639 from "<new term>" to "negative regulation of organelle organization and biogenesis"
  * Set definition of GO:0010639 to "Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle."
  * Added definition dbxref GOC:dph to GO:0010639
  * Added definition dbxref GOC:tb to GO:0010639
  * Copied GO:0010639 to GO:0006996 with type negatively_regulates
  * Copied GO:0010639 to GO:0033043 with type OBO_REL:is_a
  * Copied GO:0010639 to GO:0051129 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010639
* Populated new object GO:0010640 (macro)
  * Changed name of GO:0010640 from "<new term>" to "regulation of platelet-derived growth factor receptor signaling pathway"
  * Set definition of GO:0010640 to "Any process that modulates the frequency, rate or extent of the
platelet-derived growth factor receptor signaling pathway."
  * Added definition dbxref GOC:dph to GO:0010640
  * Added definition dbxref GOC:hjd to GO:0010640
  * Added definition dbxref GOC:tb to GO:0010640
  * Copied GO:0010640 to GO:0009966 with type OBO_REL:is_a
  * Copied GO:0010640 to GO:0048008 with type regulates
  * Assigned namespace "biological_process" to GO:0010640
* Populated new object GO:0010641 (macro)
  * Changed name of GO:0010641 from "<new term>" to "positive regulation of platelet-derived growth factor receptor signaling pathway"
  * Set definition of GO:0010641 to "Any process that increases the frequency, rate or extent of the
platelet-derived growth factor receptor signaling pathway."
  * Added definition dbxref GOC:dph to GO:0010641
  * Added definition dbxref GOC:hjd to GO:0010641
  * Added definition dbxref GOC:tb to GO:0010641
  * Copied GO:0010641 to GO:0048008 with type positively_regulates
  * Copied GO:0010641 to GO:0010640 with type OBO_REL:is_a
  * Copied GO:0010641 to GO:0009967 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010641
* Populated new object GO:0010642 (macro)
  * Changed name of GO:0010642 from "<new term>" to "negative regulation of platelet-derived growth factor receptor signaling pathway"
  * Set definition of GO:0010642 to "Any process that stops, prevents or reduces the frequency, rate or
extent of the platelet-derived growth factor receptor signaling pathway."
  * Added definition dbxref GOC:dph to GO:0010642
  * Added definition dbxref GOC:hjd to GO:0010642
  * Added definition dbxref GOC:tb to GO:0010642
  * Copied GO:0010642 to GO:0010640 with type OBO_REL:is_a
  * Copied GO:0010642 to GO:0048008 with type negatively_regulates
  * Copied GO:0010642 to GO:0009968 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010642
* Populated new object GO:0043933 (macro)
  * Changed name of GO:0043933 from "<new term>" to "macromolecular complex subunit organization"
  * Set definition of GO:0043933 to "The acquisition, loss, or modification of macromolecules resulting in the formation, disassembly or alteration of a macromolecular complex."
  * Added definition dbxref GOC:mtg_mpo to GO:0043933
  * Added synonym "macromolecular complex subunit organisation" to GO:0043933
  * Changed synonym scope of GO:0043933 from "Related" to "Exact"
  * Copied GO:0043933 to GO:0008150 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0043933
* Populated new object GO:0060269 (macro)
  * Changed name of GO:0060269 from "<new term>" to "centripetally migrating follicle cell migration"
  * Set definition of GO:0060269 to "The cell migration process in which a follicle cell migrates as part of an epithelial sheet between the nurse cells and the oocyte. At the end of migration, they cover the anterior of the oocyte."
  * Added definition dbxref GOC:dph to GO:0060269
  * Copied GO:0060269 to GO:0007297 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060269
* Populated new object GO:0060270 (macro)
  * Changed name of GO:0060270 from "<new term>" to "main body follicle cell migration"
  * Set definition of GO:0060270 to "The ovarian follicle cell migration process in which follicle cells migrate posteeriorly to form a columnar epithelium over the oocyte."
  * Added definition dbxref GOC:dph to GO:0060270
  * Copied GO:0060270 to GO:0007297 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060270
* Populated new object GO:0060271 (macro)
  * Changed name of GO:0060271 from "<new term>" to "cilium morphogenesis"
  * Set definition of GO:0060271 to "A process that is carried out at the cellular level and by which the structure of a cilium is organized. Morphogenesis pertains to the creation of form."
  * Added definition dbxref GOC:dph to GO:0060271
  * Added synonym "cilium organization" to GO:0060271
  * Added general dbxref GOC:dph to synonym cilium organization of GO:0060271
  * Copied GO:0060271 to GO:0048858 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060271
* Populated new object GO:0060272 (macro)
  * Changed name of GO:0060272 from "<new term>" to "embryonic skeletal joint morphogenesis"
  * Set definition of GO:0060272 to "The process by which the anatomical structures of skeletal joints are generated and organized during the embryonic phase. A joint is the connecting structure between the bones of the skeleton. Morphogenesis pertains to the creation of form."
  * Added definition dbxref GOC:dph to GO:0060272
  * Copied GO:0060272 to GO:0048704 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060272
* Populated new object GO:0060273 (macro)
  * Changed name of GO:0060273 from "<new term>" to "crying behavior"
  * Set definition of GO:0060273 to "The behavior in which an organism sheds tears, often accompanied by non-verbal vocalizations and in response to external or internal stimuli."
  * Added definition dbxref GOC:dph to GO:0060273
  * Copied GO:0060273 to GO:0007610 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060273
* Deleted GO:0007427 --OBO_REL:is_a--> GO:0016477
* Copied GO:0007427 to GO:0010631 with type OBO_REL:is_a
* Copied GO:0031057 to GO:0010639 with type OBO_REL:is_a
* Deleted GO:0031058 --OBO_REL:is_a--> GO:0051130
* Copied GO:0031058 to GO:0010638 with type OBO_REL:is_a
* Deleted GO:0032205 --OBO_REL:is_a--> GO:0051129
* Copied GO:0032205 to GO:0010639 with type OBO_REL:is_a
* Deleted GO:0032206 --OBO_REL:is_a--> GO:0051130
* Copied GO:0032206 to GO:0010638 with type OBO_REL:is_a
* Copied GO:0032989 to GO:0048869 with type OBO_REL:is_a
* Deleted GO:0033026 --OBO_REL:is_a--> GO:0034351
* Deleted GO:0033027 --OBO_REL:is_a--> GO:0034352
* Deleted GO:0033030 --OBO_REL:is_a--> GO:0034351
* Deleted GO:0033031 --OBO_REL:is_a--> GO:0034352
* Deleted GO:0033046 --OBO_REL:is_a--> GO:0051129
* Copied GO:0033046 to GO:0010639 with type OBO_REL:is_a
* Deleted GO:0034351 --OBO_REL:is_a--> GO:0034391
* Deleted GO:0034352 --OBO_REL:is_a--> GO:0034391
* Changed name of GO:0042254 from "ribosome biogenesis and assembly" to "ribosome biogenesis"
* Deleted synonym "ribosome biogenesis" from GO:0042254
* Added synonym "ribosome biogenesis and assembly" to GO:0042254
* Changed synonym scope of GO:0042254 from "Related" to "Exact"
* Changed name of GO:0042273 from "ribosomal large subunit biogenesis and assembly" to "ribosomal large subunit biogenesis"
* Added synonym "ribosomal large subunit biogenesis and assembly" to GO:0042273
* Changed synonym scope of GO:0042273 from "Related" to "Exact"
* Changed name of GO:0042274 from "ribosomal small subunit biogenesis and assembly" to "ribosomal small subunit biogenesis"
* Added synonym "ribosomal small subunit biogenesis and assembly" to GO:0042274
* Changed synonym scope of GO:0042274 from "Related" to "Exact"
* Deleted GO:0045701 --OBO_REL:is_a--> GO:0051129
* Copied GO:0045701 to GO:0010639 with type OBO_REL:is_a
* Deleted GO:0045702 --OBO_REL:is_a--> GO:0051130
* Copied GO:0045702 to GO:0010638 with type OBO_REL:is_a
* Deleted GO:0045798 --OBO_REL:is_a--> GO:0051129
* Copied GO:0045798 to GO:0010639 with type OBO_REL:is_a
* Deleted GO:0045799 --OBO_REL:is_a--> GO:0051130
* Copied GO:0045799 to GO:0010638 with type OBO_REL:is_a
* Deleted GO:0045875 --OBO_REL:is_a--> GO:0051129
* Copied GO:0045875 to GO:0010639 with type OBO_REL:is_a
* Deleted GO:0045876 --OBO_REL:is_a--> GO:0051130
* Copied GO:0045876 to GO:0010638 with type OBO_REL:is_a
* Deleted GO:0046606 --OBO_REL:is_a--> GO:0051129
* Copied GO:0046606 to GO:0010639 with type OBO_REL:is_a
* Deleted GO:0046607 --OBO_REL:is_a--> GO:0051130
* Copied GO:0046607 to GO:0010638 with type OBO_REL:is_a
* Deleted GO:0048701 --part_of--> GO:0048704
* Copied GO:0048701 to GO:0048704 with type OBO_REL:is_a
* Changed definition of GO:0048704 from "The process by which the anatomical structures of skeleton are generated and organized during the embryonic phase. Morphogenesis pertains to the creation of form." to "The process by which the anatomical structures of the skeleton are generated and organized during the embryonic phase. Morphogenesis pertains to the creation of form."
* Changed definition of GO:0048705 from "The process by which the anatomical structures of skeleton are generated and organized. Morphogenesis pertains to the creation of form." to "The process by which the anatomical structures of the skeleton are generated and organized. Morphogenesis pertains to the creation of form."
* Deleted GO:0051494 --OBO_REL:is_a--> GO:0051129
* Copied GO:0051494 to GO:0010639 with type OBO_REL:is_a
* Deleted GO:0051495 --OBO_REL:is_a--> GO:0051130
* Copied GO:0051495 to GO:0010638 with type OBO_REL:is_a
* Deleted GO:0060211 --OBO_REL:is_a--> GO:0031440
* Copied GO:0060211 to GO:0060255 with type OBO_REL:is_a
* Copied GO:0060211 to GO:0051252 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Wed Jul 23 21:30:47 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Wed, 23 Jul 2008 21:30:47 -0700 (PDT)
Subject: [Go-diff] GO update 07/23/2008
Message-ID: <200807240430.VAA27988@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.139 by 1.140

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034606
* Created object of type obo:TERM with id GO:0034607
* Created object of type obo:TERM with id GO:0034608
* Created object of type obo:TERM with id GO:0034609
* Created object of type obo:TERM with id GO:0034610
* Created object of type obo:TERM with id GO:0034611
* Created object of type obo:TERM with id GO:0034612
* Created object of type obo:TERM with id GO:0034613
* Populated new object GO:0034606 (macro)
  * Changed name of GO:0034606 from "<new term>" to "response to hermaphrodite contact"
  * Set definition of GO:0034606 to "The response by the male to a hermaphrodite after initial contact following mate finding. The male stops forward locomotion, presses the ventral side of his tail against his partner's body, and begins moving backward along the hermaphrodite. Male response behavior is initiated when sensory neurons located in the rays of his tail contact a potential mate."
  * Added definition dbxref PMID:18050467 to GO:0034606
  * Added definition dbxref WB_REF:WBPaper00002109 to GO:0034606
  * Copied GO:0034606 to GO:0060179 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034606
* Populated new object GO:0034607 (macro)
  * Changed name of GO:0034607 from "<new term>" to "turning behavior involved in mating"
  * Set definition of GO:0034607 to "The sharp ventral turn performed by the male as he approaches either the hermaphrodite head or tail, whilst trying to locate his partner's vulva. Turning occurs via a sharp ventral coil of the male's tail."
  * Added definition dbxref PMID:18050467 to GO:0034607
  * Added definition dbxref WB_REF:WBPaper00002109 to GO:0034607
  * Added synonym "turning behavior during mating" to GO:0034607
  * Changed synonym scope of GO:0034607 from "Related" to "Exact"
  * Copied GO:0034607 to GO:0060179 with type OBO_REL:is_a
  * Copied GO:0034607 to GO:0035178 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034607
* Populated new object GO:0034608 (macro)
  * Changed name of GO:0034608 from "<new term>" to "vulval location"
  * Set definition of GO:0034608 to "Location, by the male, of his partner's vulva when backing along the ventral side of the hermaphrodite during mating. The male stops at
the vulva, coordinates his movements to the hermaphrodite's, and
positions his tail precisely over the vulva so that he may insert his spicules and ejaculate."
  * Added definition dbxref PMID:18050467 to GO:0034608
  * Copied GO:0034608 to GO:0060179 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034608
* Populated new object GO:0034609 (macro)
  * Changed name of GO:0034609 from "<new term>" to "spicule insertion"
  * Set definition of GO:0034609 to "Insertion of the male copulatory spicules into the hermaphrodite. Spicule insertion behavior initiates when the male cloaca contacts the vulva. During most mating encounters, the spicule tips will prod the vulva continuously until they partially penetrate, which then causes the protractors to contract completely so that the spicules extend through the vulva."
  * Added definition dbxref PMID:18050467 to GO:0034609
  * Copied GO:0034609 to GO:0060179 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034609
* Populated new object GO:0034610 (macro)
  * Changed name of GO:0034610 from "<new term>" to "oligodeoxyribonucleotidase activity"
  * Set definition of GO:0034610 to "Catalysis of the exonucleolytic cleavage of oligodeoxyribonucleotides to yield deoxyribonucleoside 5'-phosphates."
  * Added definition dbxref GOC:mah to GO:0034610
  * Added synonym "DNA oligonucleotidase activity" to GO:0034610
  * Changed synonym scope of GO:0034610 from "Related" to "Exact"
  * Copied GO:0034610 to GO:0004536 with type OBO_REL:is_a
  * Copied GO:0034610 to GO:0008946 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034610
* Populated new object GO:0034611 (macro)
  * Changed name of GO:0034611 from "<new term>" to "oligoribonucleotidase activity"
  * Set definition of GO:0034611 to "Catalysis of the exonucleolytic cleavage of oligoribonucleotides to yield ribonucleoside 5'-phosphates."
  * Added definition dbxref GOC:mah to GO:0034611
  * Added synonym "RNA oligonucleotidase activity" to GO:0034611
  * Changed synonym scope of GO:0034611 from "Related" to "Exact"
  * Copied GO:0034611 to GO:0008946 with type OBO_REL:is_a
  * Copied GO:0034611 to GO:0004540 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034611
* Populated new object GO:0034612 (macro)
  * Changed name of GO:0034612 from "<new term>" to "response to tumor necrosis factor"
  * Set definition of GO:0034612 to "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus."
  * Added definition dbxref GOC:mah to GO:0034612
  * Added synonym "response to TNF" to GO:0034612
  * Changed synonym scope of GO:0034612 from "Related" to "Exact"
  * Copied GO:0034612 to GO:0034097 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034612
* Populated new object GO:0034613 (macro)
  * Changed name of GO:0034613 from "<new term>" to "cellular protein localization"
  * Set definition of GO:0034613 to "Any process by which a protein is transported to, and/or maintained in, a specific location within or at the surface of a cell."
  * Added definition dbxref GOC:mah to GO:0034613
  * Copied GO:0034613 to GO:0008104 with type OBO_REL:is_a
  * Copied GO:0034613 to GO:0051641 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034613
* Changed definition of GO:0000172 from "A ribonucleoprotein complex that performs the first cleavage in rRNA transcript processing and is also involved in mitochondrial RNA processing." to "A ribonucleoprotein complex that cleaves the rRNA precursor as part of rRNA transcript processing. It also has other roles: In S. cerevisiae it is involved in cell cycle-regulated degradation of daughter cell-specific mRNAs, while in mammalian cells it also enters the mitochondria and processes RNAs to create RNA primers for DNA replication."
* Added definition dbxref GOC:sgd_curators to GO:0000172
* Added definition dbxref PMID:14729943 to GO:0000172
* Added definition dbxref PMID:7510714 to GO:0000172
* Deleted GO:0000172 --OBO_REL:is_a--> GO:0030529
* Copied GO:0000172 to GO:0005732 with type OBO_REL:is_a
* Changed definition of GO:0000957 from "The chemical reactions and pathways resulting in the breakdown of RNA within the mitochondrion." to "The chemical reactions and pathways resulting in the breakdown of RNA transcribed from the mitochondrial genome and occurring in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000957
* Changed definition of GO:0000958 from "The chemical reactions and pathways resulting in the breakdown of mRNA within the mitochondrion." to "The chemical reactions and pathways resulting in the breakdown of mRNA transcribed from the mitochondrial genome and occurring in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000958
* Changed definition of GO:0000959 from "The chemical reactions and pathways involving RNA in the mitochondrion." to "The chemical reactions and pathways involving RNA transcribed from the mitochondrial genome and occurring in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000959
* Changed definition of GO:0000960 from "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catabolism of RNA within the mitochondrion." to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome."
* Added definition dbxref GOC:mah to GO:0000960
* Changed definition of GO:0000961 from "Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways involving catabolism of RNA within the mitochondrion." to "Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome."
* Added definition dbxref GOC:mah to GO:0000961
* Changed definition of GO:0000962 from "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catabolism of RNA within the mitochondrion." to "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome."
* Added definition dbxref GOC:mah to GO:0000962
* Changed definition of GO:0000963 from "The conversion of a primary RNA molecule transcribed from a mitochondrial genome into one or more mature RNA molecules." to "The conversion of a primary RNA molecule transcribed from a mitochondrial genome into one or more mature RNA molecules; occurs in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000963
* Changed definition of GO:0000964 from "Any process involved in forming the mature 5' end of an RNA molecule transcribed from a mitochondrial genome." to "Any process involved in forming the mature 5' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000964
* Changed definition of GO:0000965 from "Any process involved in forming the mature 3' end of an RNA molecule transcribed from a mitochondrial genome." to "Any process involved in forming the mature 3' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion."
* Added definition dbxref GOC:mah to GO:0000965
* Added comment "Note that enzymes with this activity also act on D-glucitol (giving D-fructose) and other closely related sugar alcohols."
* Added synonym " L-iditol:NAD+ 5-oxidoreductase activity" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym  L-iditol:NAD+ 5-oxidoreductase activity of GO:0003939
* Changed synonym scope of GO:0003939 from "Related" to "Exact"
* Added synonym "L-iditol (sorbitol) dehydrogenase activity" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym L-iditol (sorbitol) dehydrogenase activity of GO:0003939
* Added synonym "L-iditol:NAD oxidoreductase activity" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym L-iditol:NAD oxidoreductase activity of GO:0003939
* Changed synonym scope of GO:0003939 from "Related" to "Exact"
* Added synonym "NAD+-dependent sorbitol dehydrogenase activity" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym NAD+-dependent sorbitol dehydrogenase activity of GO:0003939
* Added synonym "NAD-dependent sorbitol dehydrogenase activity" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym NAD-dependent sorbitol dehydrogenase activity of GO:0003939
* Added synonym "NAD-sorbitol dehydrogenase" to GO:0003939
* Added general dbxref EC:1.1.1.14 to synonym NAD-sorbitol dehydrogenase of GO:0003939
* Deleted GO:0005732 --OBO_REL:is_a--> GO:0044452
* Copied GO:0005732 to GO:0044424 with type OBO_REL:is_a
* Deleted GO:0007035 --part_of--> GO:0007033
* Copied GO:0007569 to GO:0009987 with type OBO_REL:is_a
* Added comment "Note that enzymes with this activity usually also hydrolyze NAD+ to NMN and AMP."
* Changed definition of GO:0008946 from "Catalysis of the exonucleolytic cleavage of oligonucleotides to yield nucleoside 5'-phosphates; also hydrolyzes NAD+ to NMN and AMP." to "Catalysis of the exonucleolytic cleavage of oligonucleotides to yield nucleoside 5'-phosphates."
* Deleted synonym "oligoribonuclease activity" from GO:0008946
* Deleted GO:0008946 --OBO_REL:is_a--> GO:0016895
* Deleted GO:0008946 --OBO_REL:is_a--> GO:0004540
* Copied GO:0008946 to GO:0004518 with type OBO_REL:is_a
* Deleted GO:0010621 --OBO_REL:is_a--> GO:0008104
* Copied GO:0010621 to GO:0034613 with type OBO_REL:is_a
* Copied GO:0016192 to GO:0009987 with type OBO_REL:is_a
* Changed definition of GO:0030686 from "A preribosomal complex consisting of the 35S pre-rRNA, the 5S rRNA, early-associating ribosomal proteins, and associated proteins." to "A large ribonucleoprotein complex considered to be the earliest preribosomal complex. In S. cerevisiae, it has a size of 90S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins."
* Deleted definition dbxref PMID:10567516 from GO:0030686
* Added definition dbxref PMID:12150911 to GO:0030686
* Added definition dbxref PMID:12957375 to GO:0030686
* Added definition dbxref PMID:15120992 to GO:0030686
* Copied GO:0031428 to GO:0044452 with type OBO_REL:is_a
* Copied GO:0031429 to GO:0044452 with type OBO_REL:is_a
* Changed definition of GO:0032040 from "A large ribonuclear protein complex containing the U3 snoRNA and associated proteins (28 in S. cerevisiae) that is involved in processing of the pre-18S rRNA to form the small ribosomal subunit." to "A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins."
* Added definition dbxref PMID:12957375 to GO:0032040
* Added definition dbxref PMID:15120992 to GO:0032040
* Added definition dbxref PMID:15590835 to GO:0032040
* Deleted GO:0033365 --OBO_REL:is_a--> GO:0008104
* Copied GO:0033365 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0034394 --OBO_REL:is_a--> GO:0008104
* Copied GO:0034394 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0034497 --OBO_REL:is_a--> GO:0008104
* Copied GO:0034497 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0034501 --OBO_REL:is_a--> GO:0008104
* Copied GO:0034501 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0034502 --OBO_REL:is_a--> GO:0008104
* Copied GO:0034502 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0051205 --OBO_REL:is_a--> GO:0008104
* Copied GO:0051205 to GO:0034613 with type OBO_REL:is_a
* Deleted GO:0051641 --OBO_REL:is_a--> GO:0016043
* Copied GO:0051641 to GO:0009987 with type OBO_REL:is_a
* Copied GO:0055085 to GO:0009987 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Thu Jul 24 21:30:46 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Thu, 24 Jul 2008 21:30:46 -0700 (PDT)
Subject: [Go-diff] GO update 07/24/2008
Message-ID: <200807250430.VAA05953@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.140 by 1.142

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034614
* Created object of type obo:TERM with id GO:0034615
* Created object of type obo:TERM with id GO:0034616
* Populated new object GO:0034614 (macro)
  * Changed name of GO:0034614 from "<new term>" to "cellular response to reactive oxygen species"
  * Set definition of GO:0034614 to "A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals."
  * Added definition dbxref GOC:mah to GO:0034614
  * Added GO:0034614 to category gosubset_prok
  * Added synonym "cellular response to active oxygen species" to GO:0034614
  * Changed synonym scope of GO:0034614 from "Related" to "Exact"
  * Added synonym "cellular response to AOS" to GO:0034614
  * Changed synonym scope of GO:0034614 from "Related" to "Exact"
  * Added synonym "cellular response to reactive oxidative species" to GO:0034614
  * Changed synonym scope of GO:0034614 from "Related" to "Exact"
  * Added synonym "cellular response to reactive oxygen intermediate" to GO:0034614
  * Changed synonym scope of GO:0034614 from "Related" to "Exact"
  * Added synonym "cellular response to ROI" to GO:0034614
  * Changed synonym scope of GO:0034614 from "Related" to "Exact"
  * Added synonym "cellular response to ROS" to GO:0034614
  * Changed synonym scope of GO:0034614 from "Related" to "Exact"
  * Copied GO:0034614 to GO:0000302 with type OBO_REL:is_a
  * Copied GO:0034614 to GO:0034599 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034614
* Populated new object GO:0034615 (macro)
  * Changed name of GO:0034615 from "<new term>" to "GCH1 complex"
  * Set definition of GO:0034615 to "A protein complex that possesses GTP cyclohydrolase I activity. In E. coli and human, the complex is a homodecamer, and monomers are catalytically inactive."
  * Added definition dbxref PMID:16696853 to GO:0034615
  * Added synonym "GTP cyclohydrolase I complex" to GO:0034615
  * Changed synonym scope of GO:0034615 from "Related" to "Exact"
  * Copied GO:0034615 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034615 to GO:0044424 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034615
* Populated new object GO:0034616 (macro)
  * Changed name of GO:0034616 from "<new term>" to "response to laminar fluid shear stress"
  * Set definition of GO:0034616 to "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a laminar fluid shear stress stimulus. Laminar fluid flow is the force acting on an object in a system where the fluid is moving across a solid surface in parallel layers. As an example, laminar shear stress can be seen where blood flows against the luminal side of blood vessel walls."
  * Added definition dbxref GOC:ecd to GO:0034616
  * Copied GO:0034616 to GO:0034405 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034616
* Changed definition of GO:0000053 from "The chemical reactions and pathways involving argininosuccinate, 2-(Nw-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate." to "The chemical reactions and pathways involving argininosuccinate, 2-(N(omega)-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate."
* Changed definition of GO:0000902 from "Any process that modulates the size or shape of a cell." to "The developmental process by which the size or shape of a cell is generated and organized. Morphogenesis pertains to the creation of form."
* Deleted synonym "negative regulation of cell shape and cell size" from GO:0000902
* Deleted synonym "positive regulation of cell shape and cell size" from GO:0000902
* Deleted synonym "regulation of cell shape and cell size" from GO:0000902
* Changed definition of GO:0004055 from "Catalysis of the reaction: ATP + L-citrulline + L-aspartate = AMP + diphosphate + (Nw-L-arginino)succinate." to "Catalysis of the reaction: ATP + L-citrulline + L-aspartate = AMP + diphosphate + (N(omega)-L-arginino)succinate."
* Deleted GO:0005624 --OBO_REL:is_a--> GO:0000267
* Copied GO:0005624 to GO:0005626 with type OBO_REL:is_a
* Changed definition of GO:0007269 from "The regulated release of neurotransmitter into the synaptic cleft. A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, y aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin." to "The regulated release of neurotransmitter into the synaptic cleft. A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma-aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin."
* Changed definition of GO:0010640 from "Any process that modulates the frequency, rate or extent of the
platelet-derived growth factor receptor signaling pathway." to "Any process that modulates the frequency, rate or extent of the platelet-derived growth factor receptor signaling pathway."
* Changed definition of GO:0010641 from "Any process that increases the frequency, rate or extent of the
platelet-derived growth factor receptor signaling pathway." to "Any process that increases the frequency, rate or extent of the platelet-derived growth factor receptor signaling pathway."
* Changed definition of GO:0010642 from "Any process that stops, prevents or reduces the frequency, rate or
extent of the platelet-derived growth factor receptor signaling pathway." to "Any process that stops, prevents or reduces the frequency, rate or extent of the platelet-derived growth factor receptor signaling pathway."
* Copied GO:0016188 to GO:0021700 with type OBO_REL:is_a
* Changed definition of GO:0022604 from "Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is any process that modulates the size or shape of a cell." to "Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process by which the size or shape of a cell is generated and organized."
* Added synonym "negative regulation of cell shape and cell size" to GO:0022604
* Added general dbxref GOC:tb to synonym negative regulation of cell shape and cell size of GO:0022604
* Added general dbxref GOC:dph to synonym negative regulation of cell shape and cell size of GO:0022604
* Added synonym "positive regulation of cell shape and cell size" to GO:0022604
* Added general dbxref GOC:tb to synonym positive regulation of cell shape and cell size of GO:0022604
* Added general dbxref GOC:dph to synonym positive regulation of cell shape and cell size of GO:0022604
* Added synonym "regulation of cell shape and cell size" to GO:0022604
* Added general dbxref GOC:tb to synonym regulation of cell shape and cell size of GO:0022604
* Added general dbxref GOC:dph to synonym regulation of cell shape and cell size of GO:0022604
* Deleted GO:0032984 --OBO_REL:is_a--> GO:0034600
* Copied GO:0032984 to GO:0043933 with type OBO_REL:is_a
* Deleted GO:0034367 --OBO_REL:is_a--> GO:0034600
* Copied GO:0034367 to GO:0043933 with type OBO_REL:is_a
* Deleted GO:0034600 --OBO_REL:is_a--> GO:0008150
* Deleted GO:0034367 --OBO_REL:is_a--> GO:0034600
* Deleted GO:0032984 --OBO_REL:is_a--> GO:0034600
* Deleted GO:0065003 --OBO_REL:is_a--> GO:0034600
* Destroyed object GO:0034600
* Added synonym "cellular response to heat stress" to GO:0034605
* Changed synonym scope of GO:0034605 from "Related" to "Exact"
* Changed definition of GO:0034608 from "Location, by the male, of his partner's vulva when backing along the ventral side of the hermaphrodite during mating. The male stops at
the vulva, coordinates his movements to the hermaphrodite's, and
positions his tail precisely over the vulva so that he may insert his spicules and ejaculate." to "Location, by the male, of his partner's vulva when backing along the ventral side of the hermaphrodite during mating. The male stops at the vulva, coordinates his movements to the hermaphrodite's, and positions his tail precisely over the vulva so that he may insert his spicules and ejaculate."
* added secondary id GO:0034600 to GO:0043933
* Added synonym "macromolecular complex organization" to GO:0043933
* Changed synonym scope of GO:0043933 from "Related" to "Exact"
* Copied GO:0046797 to GO:0021700 with type OBO_REL:is_a
* Copied GO:0051426 to GO:0021700 with type OBO_REL:is_a
* Copied GO:0060074 to GO:0021700 with type OBO_REL:is_a
* Deleted GO:0065003 --OBO_REL:is_a--> GO:0034600
* Copied GO:0065003 to GO:0043933 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Fri Jul 25 21:30:46 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Fri, 25 Jul 2008 21:30:46 -0700 (PDT)
Subject: [Go-diff] GO update 07/25/2008
Message-ID: <200807260430.VAA13829@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.142 by 1.145

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034617
* Created object of type obo:TERM with id GO:0034618
* Populated new object GO:0034617 (macro)
  * Changed name of GO:0034617 from "<new term>" to "tetrahydrobiopterin binding"
  * Set definition of GO:0034617 to "Interacting selectively with a tetrahydrobiopterin, 5,6,7,8-tetrahydrobiopterin or a derivative thereof; tetrahydrobiopterins are enzyme cofactors that carry electrons in redox reactions."
  * Added definition dbxref ChEBI:15372 to GO:0034617
  * Added definition dbxref GOC:mah to GO:0034617
  * Added definition dbxref GOC:rl to GO:0034617
  * Added synonym "BH4 binding" to GO:0034617
  * Changed synonym scope of GO:0034617 from "Related" to "Exact"
  * Added synonym "H4biopterin binding" to GO:0034617
  * Changed synonym scope of GO:0034617 from "Related" to "Exact"
  * Added synonym "sapropterin binding" to GO:0034617
  * Changed synonym scope of GO:0034617 from "Related" to "Exact"
  * Copied GO:0034617 to GO:0050662 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034617
* Populated new object GO:0034618 (macro)
  * Changed name of GO:0034618 from "<new term>" to "arginine binding"
  * Set definition of GO:0034618 to "Interacting selectively with 2-amino-5-(carbamimidamido)pentanoic acid."
  * Added definition dbxref ChEBI:29016 to GO:0034618
  * Added definition dbxref GOC:rl to GO:0034618
  * Added synonym "aminopentanoic acid binding" to GO:0034618
  * Added synonym "Arg binding" to GO:0034618
  * Changed synonym scope of GO:0034618 from "Related" to "Exact"
  * Copied GO:0034618 to GO:0016597 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034618
* Deleted GO:0000262 --OBO_REL:is_a--> GO:0005694
* Copied GO:0000262 to GO:0000229 with type OBO_REL:is_a
* Added GO:0000782 to category gosubset_prok
* Changed definition of GO:0000821 from "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving arginine, 2-amino-5-guanidinopentanoic acid." to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid."
* Added definition dbxref ChEBI:29016 to GO:0000821
* Deleted GO:0000835 --OBO_REL:is_a--> GO:0000151
* Copied GO:0000835 to GO:0000153 with type OBO_REL:is_a
* Deleted synonym "<new synonym>" from GO:0004445
* Changed comment from "Note that this term does not refer to vesicle, but instead to structures in which lipids do not necessarily form bilayers." to "Note that this term does not refer to vesicles, but instead to structures in which lipids do not necessarily form bilayers."
* Deleted GO:0005839 --OBO_REL:is_a--> GO:0044445
* Copied GO:0005839 to GO:0044424 with type OBO_REL:is_a
* Changed definition of GO:0006525 from "The chemical reactions and pathways involving arginine, 2-amino-5-guanidinopentanoic acid." to "The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid."
* Added definition dbxref ChEBI:29016 to GO:0006525
* Changed definition of GO:0006526 from "The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-guanidinopentanoic acid, a chiral alpha-amino acid found in peptide linkage in proteins." to "The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid."
* Added definition dbxref ChEBI:29016 to GO:0006526
* Changed definition of GO:0006527 from "The chemical reactions and pathways resulting in the breakdown of arginine, 2-amino-5-guanidinopentanoic acid, a chiral alpha-amino acid found in peptide linkage in proteins." to "The chemical reactions and pathways resulting in the breakdown of arginine, 2-amino-5-(carbamimidamido)pentanoic acid."
* Added definition dbxref ChEBI:29016 to GO:0006527
* Changed definition of GO:0007126 from "Progression through meiosis, the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiosis occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations." to "Progression through the nuclear division phase of a meiotic cell cycle, the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiotic division occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations."
* Deleted GO:0009508 --OBO_REL:is_a--> GO:0005694
* Copied GO:0009508 to GO:0000229 with type OBO_REL:is_a
* Added GO:0010468 to category gosubset_prok
* Added GO:0010528 to category gosubset_prok
* Added GO:0010556 to category gosubset_prok
* Added GO:0010559 to category gosubset_prok
* Added GO:0015322 to category gosubset_prok
* Added GO:0015844 to category gosubset_prok
* Added GO:0016409 to category gosubset_prok
* Added GO:0016653 to category gosubset_prok
* Set definition of GO:0016890 to "Catalysis of the hydrolysis of ester linkages at specific sites within a deoxyribonucleic acid molecule by creating internal breaks."
* Added definition dbxref GOC:jl to GO:0016890
* Added GO:0016890 to category gosubset_prok
* Copied GO:0020003 to GO:0043230 with type OBO_REL:is_a
* Changed definition of GO:0020017 from "The lipid bilayer surrounding the flagellum; continuous with the plasma membrane." to "The portion of the plasma membrane surrounding the flagellum."
* Added definition dbxref GOC:mah to GO:0020017
* Copied GO:0020017 to GO:0031253 with type OBO_REL:is_a
* Added GO:0022803 to category gosubset_prok
* Added GO:0022804 to category gosubset_prok
* Added GO:0022829 to category gosubset_prok
* Added GO:0022857 to category gosubset_prok
* Added GO:0022884 to category gosubset_prok
* Added GO:0022885 to category gosubset_prok
* Added GO:0022891 to category gosubset_prok
* Added GO:0022892 to category gosubset_prok
* Added GO:0022898 to category gosubset_prok
* Added GO:0022900 to category gosubset_prok
* Copied GO:0030663 to GO:0030660 with type OBO_REL:is_a
* Deleted GO:0030672 --OBO_REL:is_a--> GO:0012506
* Copied GO:0030672 to GO:0030665 with type OBO_REL:is_a
* Changed definition of GO:0030673 from "The plasma membrane of an axon; it is a specialized trilaminar random mosaic of protein molecules floating within a fluid matrix of highly mobile phospholipid molecules, 7-8 nm in thickness." to "The portion of the plasma membrane surrounding an axon; it is a specialized trilaminar random mosaic of protein molecules floating within a fluid matrix of highly mobile phospholipid molecules, 7-8 nm in thickness."
* Copied GO:0030981 to GO:0015630 with type part_of
* Added GO:0031341 to category gosubset_prok
* Changed name of GO:0032053 from "basal body organization and biogenesis" to "microtubule basal body organization and biogenesis"
* Changed definition of GO:0032053 from "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a basal body, a short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium or flagellum." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a microtubule basal body, a short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium or flagellum."
* Changed name of GO:0032054 from "basal body duplication" to "microtubule basal body duplication"
* Changed definition of GO:0032054 from "Construction of a new basal body." to "Construction of a new microtubule basal body."
* Added GO:0032268 to category gosubset_prok
* Added GO:0032409 to category gosubset_prok
* Added GO:0032412 to category gosubset_prok
* Added GO:0032505 to category gosubset_prok
* Added GO:0032768 to category gosubset_prok
* Added GO:0032844 to category gosubset_prok
* Added GO:0032881 to category gosubset_prok
* Added GO:0032885 to category gosubset_prok
* Added GO:0032984 to category gosubset_prok
* Added GO:0033020 to category gosubset_prok
* Added GO:0033059 to category gosubset_prok
* Deleted GO:0033115 --OBO_REL:is_a--> GO:0055035
* Copied GO:0033115 to GO:0055035 with type part_of
* Copied GO:0033115 to GO:0009843 with type OBO_REL:is_a
* Added GO:0033238 to category gosubset_prok
* Added GO:0033500 to category gosubset_prok
* Added GO:0033619 to category gosubset_prok
* Added GO:0033643 to category gosubset_prok
* Added GO:0033644 to category gosubset_prok
* Added GO:0033646 to category gosubset_prok
* Added GO:0033647 to category gosubset_prok
* Added GO:0033648 to category gosubset_prok
* Added GO:0033655 to category gosubset_prok
* Added GO:0034061 to category gosubset_prok
* Added GO:0034062 to category gosubset_prok
* Added GO:0034068 to category gosubset_prok
* Added GO:0034069 to category gosubset_prok
* Added GO:0034212 to category gosubset_prok
* Added GO:0034308 to category gosubset_prok
* Added GO:0034311 to category gosubset_prok
* Added GO:0034338 to category gosubset_prok
* Added GO:0034357 to category gosubset_prok
* Added GO:0034595 to category gosubset_prok
* Removed GO:0035103 from category gosubset_prok
* Removed GO:0035104 from category gosubset_prok
* Deleted GO:0042650 --OBO_REL:is_a--> GO:0042651
* Copied GO:0042650 to GO:0055035 with type OBO_REL:is_a
* Added GO:0043244 to category gosubset_prok
* Added GO:0043470 to category gosubset_prok
* Added GO:0043471 to category gosubset_prok
* Added GO:0043900 to category gosubset_prok
* Changed definition of GO:0043933 from "The acquisition, loss, or modification of macromolecules resulting in the formation, disassembly or alteration of a macromolecular complex." to "Any process by which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex."
* Added GO:0043933 to category gosubset_prok
* Added GO:0048583 to category gosubset_prok
* Deleted GO:0048786 --OBO_REL:is_a--> GO:0043232
* Added GO:0050795 to category gosubset_prok
* Deleted GO:0055028 --OBO_REL:is_a--> GO:0005874
* Copied GO:0055028 to GO:0005881 with type OBO_REL:is_a
* Added GO:0055086 to category gosubset_prok
* Added GO:0055114 to category gosubset_prok
* Added GO:0060191 to category gosubset_prok
* Added GO:0060255 to category gosubset_prok

From gocvs at genome.stanford.edu  Mon Jul 28 21:30:46 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Mon, 28 Jul 2008 21:30:46 -0700 (PDT)
Subject: [Go-diff] GO update 07/28/2008
Message-ID: <200807290430.VAA19525@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.145 by 1.146

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034619
* Created object of type obo:TERM with id GO:0034620
* Created object of type obo:TERM with id GO:0034621
* Created object of type obo:TERM with id GO:0034622
* Created object of type obo:TERM with id GO:0034623
* Populated new object GO:0034619 (macro)
  * Changed name of GO:0034619 from "<new term>" to "cellular chaperone-mediated protein complex assembly"
  * Set definition of GO:0034619 to "The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell, mediated by chaperone molecules that do not form part of the finished complex."
  * Added definition dbxref GOC:mah to GO:0034619
  * Added GO:0034619 to category gosubset_prok
  * Added synonym "chaperone activity" to GO:0034619
  * Copied GO:0034619 to GO:0043623 with type OBO_REL:is_a
  * Copied GO:0034619 to GO:0051131 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034619
* Populated new object GO:0034620 (macro)
  * Changed name of GO:0034620 from "<new term>" to "cellular response to unfolded protein"
  * Added comment "Note that this term should not be confused with 'unfolded protein response ; GO:0030968', which refers to one specific response to the presence of unfolded proteins in the ER."
  * Set definition of GO:0034620 to "A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus."
  * Added definition dbxref GOC:mah to GO:0034620
  * Added GO:0034620 to category gosubset_prok
  * Added synonym "heat shock protein activity" to GO:0034620
  * Copied GO:0034620 to GO:0006986 with type OBO_REL:is_a
  * Copied GO:0034620 to GO:0051716 with type OBO_REL:is_a
  * Copied GO:0034620 to GO:0051789 with type OBO_REL:is_a
  * Copied GO:0034620 to GO:0006950 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034620
* Populated new object GO:0034621 (macro)
  * Changed name of GO:0034621 from "<new term>" to "cellular macromolecular complex subunit organization"
  * Set definition of GO:0034621 to "Any process carried out at the cellular level by which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex."
  * Added definition dbxref GOC:mah to GO:0034621
  * Added definition dbxref GOC:mtg_mpo to GO:0034621
  * Added GO:0034621 to category gosubset_prok
  * Added synonym "cellular macromolecular complex organization" to GO:0034621
  * Changed synonym scope of GO:0034621 from "Related" to "Exact"
  * Added synonym "cellular macromolecular complex subunit organisation" to GO:0034621
  * Changed synonym scope of GO:0034621 from "Related" to "Exact"
  * Copied GO:0034621 to GO:0009987 with type OBO_REL:is_a
  * Copied GO:0034621 to GO:0043933 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034621
* Populated new object GO:0034622 (macro)
  * Changed name of GO:0034622 from "<new term>" to "cellular macromolecular complex assembly"
  * Set definition of GO:0034622 to "The aggregation, arrangement and bonding together of a set of macromolecules to form a complex, carried out at the cellular level."
  * Added definition dbxref GOC:mah to GO:0034622
  * Added GO:0034622 to category goslim_pir
  * Added GO:0034622 to category gosubset_prok
  * Added synonym "cellular macromolecule complex assembly" to GO:0034622
  * Changed synonym scope of GO:0034622 from "Related" to "Exact"
  * Copied GO:0034622 to GO:0034621 with type OBO_REL:is_a
  * Copied GO:0034622 to GO:0065003 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034622
* Populated new object GO:0034623 (macro)
  * Changed name of GO:0034623 from "<new term>" to "cellular macromolecular complex disassembly"
  * Set definition of GO:0034623 to "The disaggregation of a macromolecular complex into its constituent components, carried out at the cellular level."
  * Added definition dbxref GOC:mah to GO:0034623
  * Added GO:0034623 to category gosubset_prok
  * Added synonym "cellular macromolecule complex disassembly" to GO:0034623
  * Changed synonym scope of GO:0034623 from "Related" to "Exact"
  * Copied GO:0034623 to GO:0034621 with type OBO_REL:is_a
  * Copied GO:0034623 to GO:0032984 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034623
* Changed definition of GO:0000343 from "The plastid-encoded plastid RNA polymerase A (PEP-A) is a plastid-encoded DNA-directed RNA polymerase that resembles eubacterial multisubunit RNA polymerases with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-A is generated from the PEP-B form during chloroplast maturation to generate a complex composed of at least thirteen polypeptides that is not sensitive to the antibiotic rifampicin, like its precursor form the PEP-B complex." to "A plastid-encoded DNA-directed RNA polymerase complex that resembles eubacterial multisubunit RNA polymerases, with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-A is generated from the PEP-B form during chloroplast maturation to generate a complex composed of at least thirteen polypeptides that is not sensitive to the antibiotic rifampicin, like its precursor form the PEP-B complex."
* Changed definition of GO:0000344 from "The plastid-encoded plastid RNA polymerase B (PEP-B) is a plastid-encoded DNA-directed RNA polymerase that resembles eubacterial multisubunit RNA polymerases with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-B is distinguished from PEP-A by its sensitivity to the antibiotic rifampicin. PEP-B is found in both etioplasts and chloroplasts, but is the predominate form in etioplasts. It forms the core of the PEP-A form; the conversion from PEP-B to PEP-A occurs during chloroplast maturation." to "A plastid-encoded DNA-directed RNA polymerase complex that resembles eubacterial multisubunit RNA polymerases with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-B is distinguished from PEP-A by its sensitivity to the antibiotic rifampicin. PEP-B is found in both etioplasts and chloroplasts, but is the predominate form in etioplasts. It forms the core of the PEP-A form; the conversion from PEP-B to PEP-A occurs during chloroplast maturation."
* Changed definition of GO:0000427 from "Plastid-encoded plastid RNA polymerases are plastid-encoded DNA-directed RNA polymerases that resemble eubacterial multisubunit RNA polymerases with a core composed of alpha, beta, and beta-prime subunits. Some forms contain multiple additional subunits. An additional sigma factor subunit is required for promoter recognition." to "An RNA polymerase complex containing polypeptides encoded by the plastid genome. Plastid-encoded DNA-directed RNA polymerases resemble eubacterial multisubunit RNA polymerases, with a core composed of alpha, beta, and beta-prime subunits. Some forms contain multiple additional subunits. An additional sigma factor subunit is required for promoter recognition."
* Added definition dbxref GOC:mah to GO:0000427
* Copied GO:0000747 to GO:0022413 with type OBO_REL:is_a
* Deleted GO:0005652 --part_of--> GO:0005635
* Copied GO:0005652 to GO:0005637 with type part_of
* added secondary id GO:0016022 to GO:0005788
* Added synonym "endoplasmic reticulum cisterna" to GO:0005788
* Changed synonym scope of GO:0005788 from "Related" to "Exact"
* Added synonym "ER cisterna" to GO:0005788
* Changed synonym scope of GO:0005788 from "Related" to "Exact"
* Changed definition of GO:0006887 from "The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell. This is the process whereby most molecules are secreted from eukaryotic cells." to "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell. This is the process whereby most molecules are secreted from eukaryotic cells."
* Added definition dbxref GOC:mah to GO:0006887
* Deleted GO:0006887 --part_of--> GO:0032940
* Copied GO:0006887 to GO:0032940 with type OBO_REL:is_a
* Copied GO:0007051 to GO:0000279 with type part_of
* Changed definition of GO:0007140 from "Meiosis in the male germline." to "Progression through the nuclear division phase of a meiotic cell cycle in the male germline."
* Changed definition of GO:0007143 from "Meiosis in the female germline." to "Progression through the nuclear division phase of a meiotic cell cycle in the female germline."
* Added definition dbxref GOC:mah to GO:0007143
* Deleted GO:0008154 --OBO_REL:is_a--> GO:0044267
* Copied GO:0008154 to GO:0034621 with type OBO_REL:is_a
* Deleted GO:0009379 --OBO_REL:is_a--> GO:0043234
* Copied GO:0009379 to GO:0033202 with type OBO_REL:is_a
* Deleted GO:0009743 --OBO_REL:is_a--> GO:0009719
* Deleted GO:0014801 --OBO_REL:is_a--> GO:0016529
* Copied GO:0014801 to GO:0044432 with type OBO_REL:is_a
* Copied GO:0014801 to GO:0016529 with type part_of
* Deleted GO:0014802 --OBO_REL:is_a--> GO:0016529
* Copied GO:0014802 to GO:0031984 with type OBO_REL:is_a
* Copied GO:0014802 to GO:0044432 with type OBO_REL:is_a
* Copied GO:0014802 to GO:0016529 with type part_of
* Deleted GO:0015869 --OBO_REL:is_a--> GO:0015031
* Copied GO:0015869 to GO:0006886 with type OBO_REL:is_a
* Deleted GO:0016022 --OBO_REL:is_a--> GO:0044432
* Destroyed object GO:0016022
* Changed definition of GO:0016029 from "The internal stores of calcium found at the base of the rhabdomere." to "A membrane-bounded compartment that is found at the base of the rhabdomere and contains stored calcium, InsP3 receptors and smooth endoplasmic reticulum Ca2+-ATPase."
* Added definition dbxref PMID:11707492 to GO:0016029
* Added synonym "SMC" to GO:0016029
* Added synonym "submicrovillar cisterna" to GO:0016029
* Added general dbxref PMID:11707492 to synonym submicrovillar cisterna of GO:0016029
* Changed synonym scope of GO:0016029 from "Related" to "Exact"
* Deleted GO:0016029 --OBO_REL:is_a--> GO:0044459
* Copied GO:0016029 to GO:0005790 with type part_of
* Copied GO:0016029 to GO:0031984 with type OBO_REL:is_a
* Deleted GO:0022618 --OBO_REL:is_a--> GO:0065003
* Copied GO:0022618 to GO:0034622 with type OBO_REL:is_a
* Added synonym "multisubunit RNA polymerase" to GO:0030880
* Changed synonym scope of GO:0030880 from "Related" to "Exact"
* Deleted GO:0030968 --OBO_REL:is_a--> GO:0006986
* Copied GO:0030968 to GO:0034620 with type OBO_REL:is_a
* Deleted GO:0031333 --OBO_REL:is_a--> GO:0051248
* Deleted GO:0031334 --OBO_REL:is_a--> GO:0051247
* Changed definition of GO:0031984 from "A membrane-enclosed compartment that is a part of an organelle." to "A compartment that is completely or partially membrane-enclosed, and is part of an organelle."
* Added definition dbxref GOC:mah to GO:0031984
* Deleted GO:0032594 --OBO_REL:is_a--> GO:0015031
* Copied GO:0032594 to GO:0006886 with type OBO_REL:is_a
* Deleted GO:0032986 --OBO_REL:is_a--> GO:0032984
* Copied GO:0032986 to GO:0034623 with type OBO_REL:is_a
* Deleted GO:0032988 --OBO_REL:is_a--> GO:0032984
* Copied GO:0032988 to GO:0034623 with type OBO_REL:is_a
* Deleted GO:0034514 --OBO_REL:is_a--> GO:0006986
* Copied GO:0034514 to GO:0034620 with type OBO_REL:is_a
* Deleted GO:0043200 --OBO_REL:is_a--> GO:0009719
* Deleted GO:0043254 --OBO_REL:is_a--> GO:0051246
* Deleted GO:0043623 --OBO_REL:is_a--> GO:0044267
* Copied GO:0043623 to GO:0034622 with type OBO_REL:is_a
* Deleted GO:0043624 --OBO_REL:is_a--> GO:0044267
* Copied GO:0043624 to GO:0034623 with type OBO_REL:is_a
* Changed definition of GO:0045054 from "The constitutive pathway required by all cells, along which substances are moved around and out of the cell. Transport vesicles destined for the plasma membrane leave the trans-Golgi network in a steady stream. The membrane proteins and the lipids in these vesicles provide new components for the plasma membrane, while the soluble proteins inside the vesicles are secreted to the extracellular space by exocytosis." to "A process of exocytosis found in all eukaryotic cells, in which transport vesicles destined for the plasma membrane leave the trans-Golgi network in a steady stream. Upon exocytosis, the membrane proteins and lipids in these vesicles provide new components for the plasma membrane, and the soluble proteins inside the vesicles are released into the extracellular space."
* Added definition dbxref GOC:mah to GO:0045054
* Deleted GO:0045054 --OBO_REL:is_a--> GO:0032940
* Copied GO:0045054 to GO:0006887 with type OBO_REL:is_a
* Changed definition of GO:0045055 from "The regulated secretory pathway is a second secretory pathway in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand." to "A process of exocytosis in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand."
* Added definition dbxref GOC:mah to GO:0045055
* Deleted GO:0045105 --OBO_REL:is_a--> GO:0019538
* Copied GO:0045105 to GO:0043933 with type OBO_REL:is_a
* Deleted GO:0048236 --OBO_REL:is_a--> GO:0007126
* Copied GO:0048236 to GO:0051321 with type OBO_REL:is_a
* Deleted GO:0051258 --OBO_REL:is_a--> GO:0044267
* Copied GO:0051258 to GO:0043623 with type OBO_REL:is_a
* Deleted GO:0051261 --OBO_REL:is_a--> GO:0044267
* Copied GO:0051261 to GO:0043624 with type OBO_REL:is_a
* Deleted GO:0065004 --OBO_REL:is_a--> GO:0065003
* Copied GO:0065004 to GO:0034622 with type OBO_REL:is_a

From gocvs at genome.stanford.edu  Wed Jul 30 21:30:45 2008
From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology)
Date: Wed, 30 Jul 2008 21:30:45 -0700 (PDT)
Subject: [Go-diff] GO update 07/30/2008
Message-ID: <200807310430.VAA06926@bread.Stanford.EDU>

OBODIFF of gene_ontology_write.obo version 1.146 by 1.147

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034624
* Created object of type obo:TERM with id GO:0034625
* Created object of type obo:TERM with id GO:0034626
* Populated new object GO:0034624 (macro)
  * Changed name of GO:0034624 from "<new term>" to "DNA recombinase assembly involved in gene conversion at mating-type locus"
  * Set definition of GO:0034624 to "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA, involved in the conversion of the mating-type locus from one allele to another."
  * Added definition dbxref GOC:mah to GO:0034624
  * Copied GO:0034624 to GO:0000730 with type OBO_REL:is_a
  * Copied GO:0034624 to GO:0007534 with type part_of
  * Assigned namespace "biological_process" to GO:0034624
* Populated new object GO:0034625 (macro)
  * Changed name of GO:0034625 from "<new term>" to "fatty acid elongation, monounsaturated fatty acid"
  * Set definition of GO:0034625 to "Elongation of a fatty acid chain into which one C-C double bond has been introduced."
  * Added definition dbxref GOC:mah to GO:0034625
  * Added GO:0034625 to category gosubset_prok
  * Copied GO:0034625 to GO:0019368 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034625
* Populated new object GO:0034626 (macro)
  * Changed name of GO:0034626 from "<new term>" to "fatty acid elongation, polyunsaturated fatty acid"
  * Set definition of GO:0034626 to "Elongation of a fatty acid chain into which two or more C-C double bonds have been introduced."
  * Added definition dbxref GOC:mah to GO:0034626
  * Added GO:0034626 to category gosubset_prok
  * Copied GO:0034626 to GO:0019368 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034626
* Deleted GO:0000730 --part_of--> GO:0007534
* Deleted GO:0000730 --OBO_REL:is_a--> GO:0006461
* Copied GO:0007533 to GO:0022413 with type OBO_REL:is_a
* Deleted GO:0020010 --OBO_REL:is_a--> GO:0005874
* Copied GO:0020010 to GO:0044430 with type OBO_REL:is_a
* Copied GO:0031574 to GO:0007093 with type OBO_REL:is_a
* Changed definition of GO:0033289 from "A microtubule located within the conoid." to "A microtubule located such that it threads through the conoid and projects through the polar ring."
* Added definition dbxref PMID:11901169 to GO:0033289
* Changed definition of GO:0043679 from "The nerve ending is the structure in which the distal end of the axon of a nerve fiber terminates. Sensory nerve endings are classified as either free or encapsulated. The free nerve ending are the most common type of nerve ending, and are most frequently found in the skin." to "A cell projection in which the distal end of the axon of a nerve fiber terminates. Sensory nerve endings are classified as either free or encapsulated. The free nerve ending are the most common type of nerve ending, and are most frequently found in the skin."
* Added definition dbxref GOC:mah to GO:0043679
* Deleted GO:0043679 --part_of--> GO:0043005
* Copied GO:0043679 to GO:0033267 with type OBO_REL:is_a