From gocvs at genome.Stanford.EDU  Tue May  1 21:30:38 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Tue, 1 May 2007 21:30:38 -0700 (PDT)
Subject: [go-diff] GO update 05/01/2007
Message-ID: <200705020430.VAA08644@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.304 by 5.307

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010424
* Created object of type obo:TERM with id GO:0010425
* Created object of type obo:TERM with id GO:0010426
* Created object of type obo:TERM with id GO:0010427
* Created object of type obo:TERM with id GO:0033185
* Created object of type obo:TERM with id GO:0033186
* Created object of type obo:TERM with id GO:0055048
* Created object of type obo:TERM with id GO:0055049
* Created object of type obo:TERM with id GO:0055050
* Populated new object GO:0010424 (macro)
  * Changed name of GO:0010424 from "<new term>" to "cytosine methylation within a CG sequence"
  * Set definition of GO:0010424 to "The covalent transfer of a methyl group to C-5 or N-4 of a cytosine located within a CG sequence in a DNA molecule."
  * Added definition dbxref PMID:17239600 to GO:0010424
  * Added synonym "DNA methylation on cytosine at CG residues" to GO:0010424
  * Copied GO:0010424 to GO:0032776 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010424
* Populated new object GO:0010425 (macro)
  * Changed name of GO:0010425 from "<new term>" to "cytosine methylation within a CNG sequence"
  * Set definition of GO:0010425 to "The covalent transfer of a methyl group to C-5 or N-4 of a cytosine
located within a CNG sequence in a DNA molecule. N stands for any nucleotide"
  * Added definition dbxref PMID:17239600 to GO:0010425
  * Added synonym "DNA methylation on cytosine at CNG residues" to GO:0010425
  * Copied GO:0010425 to GO:0032776 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010425
* Populated new object GO:0010426 (macro)
  * Changed name of GO:0010426 from "<new term>" to "cytosine methylation within a CNN sequence"
  * Set definition of GO:0010426 to "The covalent transfer of a methyl group to C-5 or N-4 of a cytosine located within a CNN sequence in a DNA molecule. N stands for any nucleotide."
  * Added definition dbxref PMID:17239600 to GO:0010426
  * Added synonym "DNA methylation on cytosine at CNN residues" to GO:0010426
  * Copied GO:0010426 to GO:0032776 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010426
* Populated new object GO:0010427 (macro)
  * Changed name of GO:0010427 from "<new term>" to "abscisic acid binding activity"
  * Set definition of GO:0010427 to "Interacting selectively with abscisic acid, plant hormones that regulate aspects of plant growth."
  * Added definition dbxref PMID:17347412 to GO:0010427
  * Added synonym "ABA binding activity" to GO:0010427
  * Added synonym "abscisate binding activity" to GO:0010427
  * Copied GO:0010427 to GO:0042562 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0010427
* Populated new object GO:0033185 (macro)
  * Changed name of GO:0033185 from "<new term>" to "dolichol-phosphate-mannose synthase complex"
  * Set definition of GO:0033185 to "A protein complex that possesses dolichyl-phosphate beta-D-mannosyltransferase activity; contains a catalytic subunit, a regulatory subunit, and a third subunit that stabilizes the complex. In human and several other metazoa, the subunits are named DPM1, DPM2 and DPM3, respectively."
  * Added definition dbxref PMID:10835346 to GO:0033185
  * Added synonym "dolichyl-phosphate beta-D-mannosyltransferase complex" to GO:0033185
  * Changed synonym scope of GO:0033185 from "Related" to "Exact"
  * Added synonym "DPM synthase complex" to GO:0033185
  * Changed synonym scope of GO:0033185 from "Related" to "Exact"
  * Copied GO:0033185 to GO:0031501 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033185
* Populated new object GO:0033186 (macro)
  * Changed name of GO:0033186 from "<new term>" to "CAF-1 complex"
  * Set definition of GO:0033186 to "A conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). In many species the CAF-1 subunits are designated p150, p60, and p48."
  * Added definition dbxref PMID:17065558 to GO:0033186
  * Added definition dbxref PMID:17083276 to GO:0033186
  * Copied GO:0033186 to GO:0005678 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033186
* Populated new object GO:0055048 (macro)
  * Changed name of GO:0055048 from "<new term>" to "anastral spindle assembly"
  * Set definition of GO:0055048 to "The formation of the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart, in the absence of centrosomes. Formation is initiated by the nucleation of microtubules (MTs) in the vicinity of condensed chromatin. MTs then attach to and congress around the chromatin due to activity of microtubule motors. A bipolar spindle is formed by focusing of the terminal ends of the MT array into spindle poles by molecular motors and cross-linking proteins."
  * Added definition dbxref GOC:mtg_sensu to GO:0055048
  * Added definition dbxref GOC:rg to GO:0055048
  * Added definition dbxref GOC:tb to GO:0055048
  * Added definition dbxref PMID:15034926 to GO:0055048
  * Copied GO:0055048 to GO:0051225 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0055048
* Populated new object GO:0055049 (macro)
  * Changed name of GO:0055049 from "<new term>" to "astral spindle assembly"
  * Set definition of GO:0055049 to "The formation of the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart, in the presence of centrosomes."
  * Added definition dbxref GOC:tb to GO:0055049
  * Copied GO:0055049 to GO:0051225 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0055049
* Populated new object GO:0055050 (macro)
  * Changed name of GO:0055050 from "<new term>" to "astral spindle assembly involved in male meiosis"
  * Set definition of GO:0055050 to "The formation of the astral spindle in male meiotic cells."
  * Added definition dbxref GOC:tb to GO:0055050
  * Copied GO:0055050 to GO:0055049 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0055050
* Added synonym "dolichol-phosphate-mannose synthase activity" to GO:0004582
* Changed synonym scope of GO:0004582 from "Related" to "Exact"
* Added synonym "DPM synthase activity" to GO:0004582
* Changed synonym scope of GO:0004582 from "Related" to "Exact"
* Changed name of GO:0007053 from "male meiotic spindle assembly (sensu Metazoa)" to "spindle assembly involved in male meiosis"
* Added synonym "male meiotic spindle assembly (sensu Metazoa)" to GO:0007053
* Deleted GO:0007053 --OBO_REL:is_a--> GO:0051226
* Copied GO:0007053 to GO:0051225 with type OBO_REL:is_a
* Changed name of GO:0007054 from "male meiosis I spindle assembly (sensu Metazoa)" to "spindle assembly involved in male meiosis I"
* Added synonym "male meiosis I spindle assembly (sensu Metazoa)" to GO:0007054
* Changed name of GO:0007055 from "male meiosis II spindle assembly (sensu Metazoa)" to "spindle assembly involved male meiosis II"
* Added synonym "male meiosis II spindle assembly (sensu Metazoa)" to GO:0007055
* Changed name of GO:0007056 from "female meiotic spindle assembly (sensu Metazoa)" to "spindle assembly involved in female meiosis"
* Added synonym "female meiotic spindle assembly (sensu Metazoa)" to GO:0007056
* Deleted GO:0007056 --OBO_REL:is_a--> GO:0051226
* Copied GO:0007056 to GO:0051225 with type OBO_REL:is_a
* Changed name of GO:0007057 from "female meiosis I spindle assembly (sensu Metazoa)" to "spindle assembly involved in female meiosis I"
* Added synonym "female meiosis I spindle assembly (sensu Metazoa)" to GO:0007057
* Changed name of GO:0007058 from "female meiosis II spindle assembly (sensu Metazoa)" to "spindle assembly involved in female meiosis II"
* Added synonym "female meiosis II spindle assembly (sensu Metazoa)" to GO:0007058
* Changed name of GO:0009971 from "male meiotic spindle assembly (sensu Viridiplantae)" to "anastral spindle assembly involved in male meiosis"
* Changed definition of GO:0009971 from "The formation of the spindle in male meiotic cells. As in, but not restricted to, green plants and algae (Viridiplantae, ncbi_taxonomy_id:33090)." to "The formation of the anastral spindle in male meiotic cells."
* Added definition dbxref GOC:tb to GO:0009971
* Added synonym "male meiotic spindle assembly (sensu Viridiplantae)" to GO:0009971
* Changed synonym scope of GO:0009971 from "Related" to "Exact"
* Deleted GO:0009971 --OBO_REL:is_a--> GO:0051226
* Copied GO:0009971 to GO:0055048 with type OBO_REL:is_a
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"
* Changed definition of GO:0060113 from "The process whereby relatively unspecialized cells,  acquire specialized structural and/or functional features of inner ear receptor cells. Inner ear receptor cells are mechanorecptors found in the inner ear responsible for transducing signals involved in balance and sensory perception of sound." to "The process whereby relatively unspecialized cells, acquire specialized structural and/or functional features of inner ear receptor cells. Inner ear receptor cells are mechanorecptors found in the inner ear responsible for transducing signals involved in balance and sensory perception of sound."


From gocvs at genome.Stanford.EDU  Wed May  2 21:30:39 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Wed, 2 May 2007 21:30:39 -0700 (PDT)
Subject: [go-diff] GO update 05/02/2007
Message-ID: <200705030430.VAA08495@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.307 by 5.308

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033187
* Created object of type obo:TERM with id GO:0033188
* Populated new object GO:0033187 (macro)
  * Changed name of GO:0033187 from "<new term>" to "inositol pyrophosphate synthase activity"
  * Set definition of GO:0033187 to "Catalysis of the reaction: ATP + 1D-myo-inositol
hexakisphosphate = ADP + 4-diphospho-1D-myo-inositol (1,2,3,5,6)pentakisphosphate or ATP + 1D-myo-inositol hexakisphosphate = ADP + 6-diphospho-1D-myo-inositol (1,2,3,4,5)pentakisphosphate."
  * Added definition dbxref PMID:17412958 to GO:0033187
  * Added definition dbxref PMID:17412959 to GO:0033187
  * Added synonym "inositol diphosphate synthase activity" to GO:0033187
  * Changed synonym scope of GO:0033187 from "Related" to "Exact"
  * Copied GO:0033187 to GO:0004428 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033187
* Populated new object GO:0033188 (macro)
  * Changed name of GO:0033188 from "<new term>" to "sphingomyelin synthase activity"
  * Set definition of GO:0033188 to "Catalysis of the reaction: a ceramide + a phosphatidylcholine = a sphingomyelin + a 1,2-diacyl-sn-glycerol."
  * Added definition dbxref EC:2.7.8.27 to GO:0033188
  * Added general dbxref EC:2.7.8.27 to GO:0033188
  * Copied GO:0033188 to GO:0016780 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033188
* Changed definition of GO:0001739 from "A condensed mass of chromatin that represents an inactivated X chromosome." to "A condensed mass of compacted chromatin that represents an inactivated X chromosome."
* Changed definition of GO:0005721 from "Chromatin located near the centromere of a chromosome." to "A region of heterochromatin located near the centromere of a chromosome."
* Set definition of GO:0005943 to "A heterodimeric protein complex that possesses 1-phosphatidylinositol-4-phosphate 3-kinase activity; comprises a catalytic subunit of 110-120 kDa and an associated regulatory subunit that is a member of a family of related proteins often called p85 proteins."
* Added definition dbxref PMID:9759495 to GO:0005943
* Deleted GO:0005943 --OBO_REL:is_a--> GO:0005941
* Copied GO:0005943 to GO:0043234 with type OBO_REL:is_a
* Copied GO:0005943 to GO:0044464 with type OBO_REL:is_a
* Set definition of GO:0005944 to "A heterodimeric protein complex that possesses 1-phosphatidylinositol-4-phosphate 3-kinase activity; comprises a catalytic subunit of 110-120 kDa and an associated regulatory subunit that is larger than, and unrelated to, the p85 proteins present in class IA complexes."
* Added definition dbxref PMID:9759495 to GO:0005944
* Deleted GO:0005944 --OBO_REL:is_a--> GO:0005941
* Copied GO:0005944 to GO:0044464 with type OBO_REL:is_a
* Copied GO:0005944 to GO:0043234 with type OBO_REL:is_a
* Changed definition of GO:0005946 from "An enzyme complex that in yeast is composed of three or four polypeptides: TPS1, TPS2, TPS3 and TSL1. Catalyzes the formation of alpha,alpha-trehalose 6-phosphate and UDP from UDP-glucose and D-glucose 6-phosphate." to "A protein complex that possesses alpha,alpha-trehalose-phosphate synthase (UDP-forming) and trehalose-phosphatase activities, and thus catalyzes two reactions in trehalose biosynthesis. In the complex identified in Saccharomyces, Tps1p has alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity, Tps2p has trehalose 6-phosphate phosphatase activity; Tps3p is a regulatory subunit, and an additional subunit, Tsl1p, may be present."
* Deleted definition dbxref GOC:jl from GO:0005946
* Deleted definition dbxref UniProtKB:P38426 from GO:0005946
* Added definition dbxref PMID:9837904 to GO:0005946
* Added synonym "trehalose-6-phosphate synthase/phosphatase" to GO:0005946
* Changed synonym scope of GO:0005946 from "Related" to "Exact"
* Changed comment from "Note that in eukaryotes, carbamoyl-phosphate synthase is usually a single polypeptide, not a complex, and should therefore not be annotated to this component term." to "Note that in higher eukaryotes, carbamoyl-phosphate synthase is usually a single polypeptide, not a complex, and should therefore not be annotated to this component term."
* Changed definition of GO:0005951 from "An enzyme complex that exists in monomer, dimer, and higher oligomeric forms. Catalysis of the reaction: 2 ATP + L-glutamine + carbon dioxide (CO2) + H2O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate." to "A protein complex that catalyzes the formation of carbamoyl phosphate; comprises a small subunit that binds and cleaves glutamine, and a large subunit that accepts the ammonia moiety cleaved from glutamine, binds all of the remaining substrates and effectors, and carries out all of the other catalytic events."
* Deleted definition dbxref PMID:2868386 from GO:0005951
* Added definition dbxref PMID:8626695 to GO:0005951
* Added synonym "arginine-specific carbamoyl phosphate synthetase complex" to GO:0005951
* Changed synonym scope of GO:0005951 from "Related" to "Narrow"
* Added synonym "carbamoyl phosphate synthase complex" to GO:0005951
* Changed synonym scope of GO:0005951 from "Related" to "Exact"
* Added synonym "carbamoyl-phosphate synthase arginine-specific complex" to GO:0005951
* Changed synonym scope of GO:0005951 from "Related" to "Narrow"
* Changed definition of GO:0016581 from "An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in both vertebrates and invertebrates. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins." to "An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins."
* Added definition dbxref PMID:17289569 to GO:0016581
* Added synonym "SHREC complex" to GO:0016581
* Changed synonym scope of GO:0016581 from "Related" to "Exact"
* Changed definition of GO:0031618 from "Chromatin located near the centromere of a chromosome in the nucleus." to "A region of heterochromatin located near the centromere of a chromosome in the nucleus."
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"


From gocvs at genome.Stanford.EDU  Thu May  3 21:30:38 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Thu, 3 May 2007 21:30:38 -0700 (PDT)
Subject: [go-diff] GO update 05/03/2007
Message-ID: <200705040430.VAA06410@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.308 by 5.310

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010428
* Created object of type obo:TERM with id GO:0010429
* Created object of type obo:TERM with id GO:0010430
* Created object of type obo:TERM with id GO:0033189
* Created object of type obo:TERM with id GO:0033190
* Populated new object GO:0010428 (macro)
  * Changed name of GO:0010428 from "<new term>" to "methyl-CpNpG binding"
  * Set definition of GO:0010428 to "Interacting selectively with a methylated cytosine/unspecified/guanine trinucleotide."
  * Added definition dbxref PMID:17239600 to GO:0010428
  * Copied GO:0010428 to GO:0000166 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0010428
* Populated new object GO:0010429 (macro)
  * Changed name of GO:0010429 from "<new term>" to "methyl-CpNpN binding"
  * Set definition of GO:0010429 to "Interacting selectively with a methylated
cytosine/unspecified/unspecified trinucleotide."
  * Added definition dbxref PMID:17239600 to GO:0010429
  * Copied GO:0010429 to GO:0000166 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0010429
* Populated new object GO:0010430 (macro)
  * Changed name of GO:0010430 from "<new term>" to "fatty acid omega-oxidation"
  * Set definition of GO:0010430 to "The metabolic oxidation of a long-chain fatty acid by successive cycles of reactions during each of which the omega-carbon in a fatty acid (the carbon furthest in the alkyl chain from the carboxylic acid) is progressively oxidized first to an alcohol and then to a carboxylic acid, creating a molecule with a carboxylic acid on both ends."
  * Added definition dbxref PMID:16404574 to GO:0010430
  * Copied GO:0010430 to GO:0019395 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010430
* Populated new object GO:0033189 (macro)
  * Changed name of GO:0033189 from "<new term>" to "response to vitamin A"
  * Set definition of GO:0033189 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 vitamin A stimulus."
  * Added definition dbxref GOC:sl to GO:0033189
  * Added synonym "response to retinol" to GO:0033189
  * Changed synonym scope of GO:0033189 from "Related" to "Narrow"
  * Copied GO:0033189 to GO:0007584 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033189
* Populated new object GO:0033190 (macro)
  * Changed name of GO:0033190 from "<new term>" to "solanapyrone synthase activity"
  * Set definition of GO:0033190 to "Catalysis of the cyclization of double bonds in prosolanapyrone II to form (-)-solanapyrone A."
  * Added definition dbxref GOC:cb to GO:0033190
  * Added definition dbxref PMID:9659400 to GO:0033190
  * Copied GO:0033190 to GO:0009975 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033190
* Added synonym "carbamoyl phosphate synthase activity" to GO:0004086
* Changed synonym scope of GO:0004086 from "Related" to "Exact"
* Added synonym "carbamoyl phosphate synthase (ammonia) activity" to GO:0004087
* Changed synonym scope of GO:0004087 from "Related" to "Exact"
* Added synonym "carbamoyl phosphate synthase (glutamine-hydrolyzing) activity" to GO:0004088
* Changed synonym scope of GO:0004088 from "Related" to "Exact"
* Added synonym "ecdysone receptor holocomplex" to GO:0008230
* Changed name of GO:0008231 from "repressor ecdysone receptor holocomplex" to "repressor ecdysone receptor complex"
* Set definition of GO:0008231 to "A protein complex consisting of a heterodimer of Ecdysone receptor (EcR) and ultraspiracle (usp) plus an associated corepressor such as SMRTER, which represses transcription of target genes."
* Added definition dbxref PMID:10488333 to GO:0008231
* Added synonym "repressor ecdysone receptor holocomplex" to GO:0008231
* Changed name of GO:0008232 from "activator ecdysone receptor holocomplex" to "activator ecdysone receptor complex"
* Set definition of GO:0008232 to "A protein complex consisting of a heterodimer of Ecdysone receptor (EcR) and ultraspiracle (usp) bound to the ligand ecdysone, which activates transcription of target genes."
* Added definition dbxref PMID:10488333 to GO:0008232
* Added synonym "activator ecdysone receptor holocomplex" to GO:0008232
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"


From gocvs at genome.Stanford.EDU  Fri May  4 21:30:40 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Fri, 4 May 2007 21:30:40 -0700 (PDT)
Subject: [go-diff] GO update 05/04/2007
Message-ID: <200705050430.VAA03185@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.310 by 5.312

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033191
* Created object of type obo:TERM with id GO:0033192
* Populated new object GO:0033191 (macro)
  * Changed name of GO:0033191 from "<new term>" to "macrophomate synthase activity"
  * Set definition of GO:0033191 to "Catalysis of the reaction: a
2-pyrone + oxalacetate = macrophomate."
  * Added definition dbxref ChEBI:38228 to GO:0033191
  * Added definition dbxref GOC:cb to GO:0033191
  * Added definition dbxref PMID:10984474 to GO:0033191
  * Copied GO:0033191 to GO:0016744 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033191
* Populated new object GO:0033192 (macro)
  * Changed name of GO:0033192 from "<new term>" to "calmodulin-dependent protein phosphatase activity"
  * Set definition of GO:0033192 to "Catalysis of the reaction: protein serine/threonine phosphate + H2O = protein serine/threonine + phosphate, dependent on the presence of calcium-bound calmodulin."
  * Added definition dbxref GOC:mah to GO:0033192
  * Added definition dbxref PMID:15359118 to GO:0033192
  * Added synonym "Ca2+/CaM-dependent protein phosphatase activity" to GO:0033192
  * Added synonym "calcineurin activity" to GO:0033192
  * Changed synonym scope of GO:0033192 from "Related" to "Narrow"
  * Added synonym "calcium- and calmodulin-dependent protein phosphatase activity" to GO:0033192
  * Changed synonym scope of GO:0033192 from "Related" to "Exact"
  * Added synonym "calcium/calmodulin-dependent protein phosphatase activity" to GO:0033192
  * Changed synonym scope of GO:0033192 from "Related" to "Exact"
  * Copied GO:0033192 to GO:0004723 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033192
* Changed name of GO:0004683 from "calmodulin regulated protein kinase activity" to "calmodulin-dependent protein kinase activity"
* added secondary id GO:0004684 to GO:0004683
* added secondary id GO:0004685 to GO:0004683
* added secondary id GO:0004688 to GO:0004683
* Set definition of GO:0004683 to "Catalysis of the reaction: ATP + a protein serine/threonine = ADP + protein serine/threonine phosphate, dependent on the presence of calcium-bound calmodulin."
* Added definition dbxref GOC:mah to GO:0004683
* Added definition dbxref PMID:11264466 to GO:0004683
* Added general dbxref EC:2.7.1.123 to GO:0004683
* Added general dbxref MetaCyc:2.7.1.123-RXN to GO:0004683
* Added synonym "Ca2+/CaM-dependent kinase activity" to GO:0004683
* Changed synonym scope of GO:0004683 from "Related" to "Exact"
* Added synonym "calcium- and calmodulin-dependent protein kinase activity" to GO:0004683
* Changed synonym scope of GO:0004683 from "Related" to "Exact"
* Added synonym "calcium/calmodulin-dependent protein kinase activity" to GO:0004683
* Changed synonym scope of GO:0004683 from "Related" to "Exact"
* Added synonym "calmodulin regulated protein kinase activity" to GO:0004683
* Changed synonym scope of GO:0004683 from "Related" to "Exact"
* Added synonym "calmodulin-dependent protein kinase I activity" to GO:0004683
* Changed synonym scope of GO:0004683 from "Related" to "Narrow"
* Added synonym "CaM kinase activity" to GO:0004683
* Changed synonym scope of GO:0004683 from "Related" to "Exact"
* Added synonym "CaMKI" to GO:0004683
* Changed synonym scope of GO:0004683 from "Related" to "Narrow"
* Added synonym "CaMKII" to GO:0004683
* Changed synonym scope of GO:0004683 from "Related" to "Narrow"
* Added synonym "CaMKIV" to GO:0004683
* Changed synonym scope of GO:0004683 from "Related" to "Narrow"
* Added synonym "multifunctional calcium- and calmodulin-regulated protein kinase activity" to GO:0004683
* Added synonym "multifunctional calcium/calmodulin regulated protein kinase activity" to GO:0004683
* Changed synonym scope of GO:0004683 from "Related" to "Exact"
* Deleted GO:0004684 --OBO_REL:is_a--> GO:0004683
* Destroyed object GO:0004684
* Deleted GO:0004685 --OBO_REL:is_a--> GO:0004683
* Destroyed object GO:0004685
* Deleted GO:0004688 --OBO_REL:is_a--> GO:0004683
* Destroyed object GO:0004688
* Changed definition of GO:0004723 from "Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate." to "Catalysis of the reaction: protein serine/threonine phosphate + H2O = protein serine/threonine + phosphate, dependent on the presence of calcium ions."
* Added definition dbxref GOC:mah to GO:0004723
* Changed definition of GO:0005891 from "A protein complex that forms a transmembrane channel through which calcium ions may cross a cell membrane in response to changes in membrane potential." to "A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential."
* Changed definition of GO:0005892 from "A protein complex that acts as an acetylcholine receptor, and forms a transmembrane channel through which ions may cross a cell membrane in response to ligand binding. The complex is a homo- or heteropentamer of subunits that are members of a neurotransmitter receptor superfamily." to "A protein complex that acts as an acetylcholine receptor, and forms a transmembrane channel through which ions may pass in response to ligand binding. The complex is a homo- or heteropentamer of subunits that are members of a neurotransmitter receptor superfamily."
* Set definition of GO:0008282 to "A protein complex that comprises four pore-forming (Kir6.x) and four regulatory sulphonylurea receptor (SURx) subunits and forms a transmembrane channel through which ions may pass. The opening and closing of the channel is regulated by ATP: binding of ATP to the Kir6.2 subunit inhibits channel activity, whereas binding of Mg2+-complexed ATP or ADP to the SUR1 subunit stimulates channel activity."
* Added definition dbxref PMID:16308567 to GO:0008282
* Added definition dbxref PMID:16956886 to GO:0008282
* Changed name of GO:0008913 from "lauroyl transferase activity" to "lauroyltransferase activity"
* Added synonym "lauroyl transferase activity" to GO:0008913
* Changed synonym scope of GO:0008913 from "Related" to "Exact"
* Deleted GO:0008913 --OBO_REL:is_a--> GO:0016740
* Copied GO:0008913 to GO:0008415 with type OBO_REL:is_a
* Set definition of GO:0009931 to "Catalysis of the reaction: ATP + a protein serine/threonine = ADP + protein serine/threonine phosphate, dependent on the presence of calcium ions."
* Added definition dbxref GOC:mah to GO:0009931
* Changed definition of GO:0010425 from "The covalent transfer of a methyl group to C-5 or N-4 of a cytosine
located within a CNG sequence in a DNA molecule. N stands for any nucleotide" to "The covalent transfer of a methyl group, to C-5 or N-4, of a cytosine located within a CNG sequence in a DNA molecule. N stands for any nucleotide."
* Changed definition of GO:0010426 from "The covalent transfer of a methyl group to C-5 or N-4 of a cytosine located within a CNN sequence in a DNA molecule. N stands for any nucleotide." to "The covalent transfer of a methyl group, to C-5 or N-4, of a cytosine located within a CNN sequence in a DNA molecule. N stands for any nucleotide."
* Changed definition of GO:0010429 from "Interacting selectively with a methylated
cytosine/unspecified/unspecified trinucleotide." to "Interacting selectively with a methylated cytosine/unspecified/unspecified trinucleotide."
* Changed definition of GO:0016409 from "Catalysis of the transfer of an palmitoyl (CH3-[CH2]6-CO-) group to an acceptor molecule." to "Catalysis of the transfer of a palmitoyl (CH3-[CH2]14-CO-) group to an acceptor molecule."
* Deleted GO:0017118 --OBO_REL:is_a--> GO:0016740
* Copied GO:0017118 to GO:0008415 with type OBO_REL:is_a
* Changed definition of GO:0033167 from "A ribonucleoprotein complex that contains members of the Argonaute family of proteins, additional protein subunits, and duplex
siRNA; required for heterochromatin assembly and siRNA generation. Possibly involved in the conversion of ds siRNA to ss siRNA." to "A ribonucleoprotein complex that contains members of the Argonaute family of proteins, additional protein subunits, and duplex siRNA; required for heterochromatin assembly and siRNA generation. Possibly involved in the conversion of ds siRNA to ss siRNA."
* Added synonym "chromatin assembly factor 1 complex" to GO:0033186
* Changed synonym scope of GO:0033186 from "Related" to "Exact"
* Changed definition of GO:0033187 from "Catalysis of the reaction: ATP + 1D-myo-inositol
hexakisphosphate = ADP + 4-diphospho-1D-myo-inositol (1,2,3,5,6)pentakisphosphate or ATP + 1D-myo-inositol hexakisphosphate = ADP + 6-diphospho-1D-myo-inositol (1,2,3,4,5)pentakisphosphate." to "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + 4-diphospho-1D-myo-inositol (1,2,3,5,6)pentakisphosphate or ATP + 1D-myo-inositol hexakisphosphate = ADP + 6-diphospho-1D-myo-inositol (1,2,3,4,5)pentakisphosphate."
* Deleted GO:0046919 --OBO_REL:is_a--> GO:0016740
* Copied GO:0046919 to GO:0008415 with type OBO_REL:is_a
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"
* Changed name of GO:0051256 from "mitotic spindle midzone assembly" to "spindle midzone assembly involved in mitosis"
* Changed definition of GO:0051256 from "The formation of the mitotic spindle midzone, the area in the center of the mitotic spindle where the spindle microtubules from opposite poles overlap." to "The formation of the spindle midzone, the area in the center of the spindle where the spindle microtubules from opposite poles overlap, during the process of mitosis."
* Added definition dbxref GOC:rg to GO:0051256
* Added definition dbxref GOC:tb to GO:0051256
* Deleted synonym "spindle midzone assembly during mitosis" from GO:0051256
* Deleted synonym "spindle midzone biogenesis during mitosis" from GO:0051256
* Deleted synonym "spindle midzone formation during mitosis" from GO:0051256
* Added synonym "mitotic spindle midzone assembly" to GO:0051256
* Added synonym "spindle midzone assembly involved in mitosis" to GO:0051256
* Changed synonym scope of GO:0051256 from "Related" to "Exact"
* Added synonym "spindle midzone biogenesis involved in mitosis" to GO:0051256
* Changed synonym scope of GO:0051256 from "Related" to "Exact"
* Added synonym "spindle midzone formation involved in mitosis" to GO:0051256
* Changed synonym scope of GO:0051256 from "Related" to "Exact"
* Changed name of GO:0051257 from "meiotic spindle midzone assembly" to "spindle midzone assembly involved in meiosis"
* Changed definition of GO:0051257 from "The formation of the meiotic spindle midzone, the area in the center of the meiotic spindle where the spindle microtubules from opposite poles overlap." to "The formation of the spindle midzone, the area in the center of the spindle where the spindle microtubules from opposite poles overlap, during the process of meiosis."
* Added definition dbxref GOC:rg to GO:0051257
* Added definition dbxref GOC:tb to GO:0051257
* Deleted synonym "spindle midzone assembly during meiosis" from GO:0051257
* Deleted synonym "spindle midzone biogenesis during meiosis" from GO:0051257
* Deleted synonym "spindle midzone formation during meiosis" from GO:0051257
* Added synonym "meiotic spindle midzone assembly" to GO:0051257
* Added synonym "spindle midzone assembly involved in meiosis" to GO:0051257
* Changed synonym scope of GO:0051257 from "Related" to "Exact"
* Added synonym "spindle midzone biogenesis involved in meiosis" to GO:0051257
* Changed synonym scope of GO:0051257 from "Related" to "Exact"
* Added synonym "spindle midzone formation involved in meiosis" to GO:0051257
* Changed synonym scope of GO:0051257 from "Related" to "Exact"
* Changed definition of GO:0060104 from "An electron dense, amorphous envelope that comprises the outermost layer of the cuticle. The surface coat is loosely apposed to the epicuticle, has distinct biochemical properties, is synthesized by cells other than the underlying hypodermis, and is labile. In addition to
serving as a lubricant to protect against abrasion and dehydration, the surface coat may also play important roles in infection and immune evasion." to "An electron dense, amorphous envelope that comprises the outermost layer of the cuticle. The surface coat is loosely apposed to the epicuticle, has distinct biochemical properties, is synthesized by cells other than the underlying hypodermis, and is labile. In addition to serving as a lubricant to protect against abrasion and dehydration, the surface coat may also play important roles in infection and immune evasion."


From gocvs at genome.Stanford.EDU  Tue May  8 21:30:37 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Tue, 8 May 2007 21:30:37 -0700 (PDT)
Subject: [go-diff] GO update 05/08/2007
Message-ID: <200705090430.VAA24868@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.312 by 5.315

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033193
* Created object of type obo:TERM with id GO:0033194
* Created object of type obo:TERM with id GO:0033195
* Created object of type obo:TERM with id GO:0055051
* Created object of type obo:TERM with id GO:0055052
* Populated new object GO:0033193 (macro)
  * Changed name of GO:0033193 from "<new term>" to "Lsd1/2 complex"
  * Set definition of GO:0033193 to "A nucleosome-binding protein complex that comprises two SWIRM domain histone demethylases and two PHD finger proteins. The complex is involved in transcriptional regulation via heterochromatic silencing and the regulation of chromatin boundary formation, and was first identified in fission yeast."
  * Added definition dbxref GOC:vw to GO:0033193
  * Added definition dbxref PMID:17371846 to GO:0033193
  * Added definition dbxref PMID:17434129 to GO:0033193
  * Added definition dbxref PMID:17440621 to GO:0033193
  * Added synonym "SAPHIRE complex" to GO:0033193
  * Added general dbxref PMID:17371846 to synonym SAPHIRE complex of GO:0033193
  * Changed synonym scope of GO:0033193 from "Related" to "Exact"
  * Added synonym "Swm complex" to GO:0033193
  * Added general dbxref PMID:17440621 to synonym Swm complex of GO:0033193
  * Changed synonym scope of GO:0033193 from "Related" to "Exact"
  * Added synonym "Swm1/2 complex" to GO:0033193
  * Added general dbxref PMID:17440621 to synonym Swm1/2 complex of GO:0033193
  * Copied GO:0033193 to GO:0044427 with type OBO_REL:is_a
  * Copied GO:0033193 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033193
* Populated new object GO:0033194 (macro)
  * Changed name of GO:0033194 from "<new term>" to "response to hydroperoxide"
  * Set definition of GO:0033194 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 hydroperoxide stimulus. Hydroperoxides are monosubstitution products of hydrogen peroxide, HOOH."
  * Added definition dbxref ChEBI:35923 to GO:0033194
  * Added definition dbxref GOC:mah to GO:0033194
  * Copied GO:0033194 to GO:0006979 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033194
* Populated new object GO:0033195 (macro)
  * Changed name of GO:0033195 from "<new term>" to "response to alkyl hydroperoxide"
  * Set definition of GO:0033195 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 an alkyl hydroperoxide stimulus. Alkyl hydroperoxides are monosubstitution products of hydrogen peroxide, HOOH, where the substituent is an alkyl group."
  * Added definition dbxref ChEBI:35923 to GO:0033195
  * Added definition dbxref GOC:mah to GO:0033195
  * Copied GO:0033195 to GO:0033194 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033195
* Populated new object GO:0055051 (macro)
  * Changed name of GO:0055051 from "<new term>" to "ATP-binding cassette (ABC) transporter complex, integrated substrate binding"
  * Set definition of GO:0055051 to "A complex for the transport of metabolites out of the cell, consisting of 4 domains: two ATP-binding domains and two membrane spanning domains. In some cases, all 4 domains are contained on 1 polypeptide, while in others one ATP-binding domain and one membrane spanning domain are together on one polypeptide in what is called a "half transporter". Two "half-transporters" come together to form a functional transporter. Transport of the substrate across the membrane is driven by the hydrolysis of ATP."
  * Added definition dbxref GOC:mlg to GO:0055051
  * Added definition dbxref GOC:mtg_sensu to GO:0055051
  * Copied GO:0055051 to GO:0043190 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0055051
* Populated new object GO:0055052 (macro)
  * Changed name of GO:0055052 from "<new term>" to "ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing"
  * Set definition of GO:0055052 to "A complex for the transport of metabolites into the cell, consisting of 5 subunits: two ATP-binding subunits, two membrane spanning subunits, and one substrate-binding subunit. In organisms with two membranes, the substrate-binding protein moves freely in the periplasmic space and joins the other subunits only when bound with substrate. In organisms with only one membrane the substrate-binding protein is tethered to the cytoplasmic membrane and associated with the other subunits. Transport of the substrate across the membrane is driven by the hydrolysis of ATP."
  * Added definition dbxref GOC:mlg to GO:0055052
  * Added definition dbxref GOC:mtg_sensu to GO:0055052
  * Copied GO:0055052 to GO:0043190 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0055052
* Added synonym "heterochromatic silencing at rDNA" to GO:0000183
* Changed synonym scope of GO:0000183 from "Related" to "Exact"
* Added synonym "3' to 5' mRNA deadenylation" to GO:0000289
* Added synonym "mRNA deadenylation" to GO:0000289
* Changed definition of GO:0006096 from "The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) in other compounds, including pyruvate." to "The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle."
* Deleted definition dbxref http://cancerweb.ncl.ac.uk/ from GO:0006096
* Added definition dbxref ISBN:0716720094 to GO:0006096
* Added synonym "heterochromatic silencing" to GO:0006342
* Changed synonym scope of GO:0006342 from "Related" to "Exact"
* Added synonym "establishment of heterochromatic silencing" to GO:0006343
* Changed synonym scope of GO:0006343 from "Related" to "Exact"
* Added synonym "maintenance of heterochromatic silencing" to GO:0006344
* Changed synonym scope of GO:0006344 from "Related" to "Exact"
* Added synonym "methylation-dependent heterochromatic silencing" to GO:0006346
* Changed synonym scope of GO:0006346 from "Related" to "Exact"
* Added synonym "heterochromatic silencing at telomere" to GO:0006348
* Changed synonym scope of GO:0006348 from "Related" to "Exact"
* Deleted GO:0006982 --OBO_REL:is_a--> GO:0006979
* Copied GO:0006982 to GO:0033194 with type OBO_REL:is_a
* Set definition of GO:0009355 to "A DNA polymerase complex that contains two UmuD' and one UmuC subunits, and acts in translesion DNA synthesis."
* Added definition dbxref PMID:10430871 to GO:0009355
* Added definition dbxref PMID:10542196 to GO:0009355
* Set definition of GO:0009360 to "A DNA polymerase complex that contains two complexes of the catalytic alpha, beta, delta and epsilon polymerase/exonuclease subunits, plus the DnaX complex, a heptamer that includes the tau and gamma products of the dnaX gene and confers structural asymmetry that allows the polymerase to replicate both leading and lagging strands."
* Added definition dbxref PMID:11525729 to GO:0009360
* Added definition dbxref PMID:12940977 to GO:0009360
* Changed definition of GO:0016615 from "Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate using NAD+ or NADPH." to "Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate."
* Added definition dbxref GOC:mah to GO:0016615
* Added synonym "heterochromatic silencing at silent mating-type cassette" to GO:0030466
* Changed synonym scope of GO:0030466 from "Related" to "Exact"
* Added synonym "heterochromatic silencing at centromere" to GO:0030702
* Changed synonym scope of GO:0030702 from "Related" to "Exact"
* Added synonym "small RNA-mediated heterochromatic silencing" to GO:0031048
* Changed synonym scope of GO:0031048 from "Related" to "Exact"
* Added synonym "regulation of heterochromatic silencing" to GO:0031935
* Added synonym "negative regulation of heterochromatic silencing" to GO:0031936
* Changed synonym scope of GO:0031936 from "Related" to "Exact"
* Added synonym "positive regulation of heterochromatic silencing" to GO:0031937
* Changed synonym scope of GO:0031937 from "Related" to "Exact"
* Added synonym "regulation of heterochromatic silencing at telomere" to GO:0031938
* Changed synonym scope of GO:0031938 from "Related" to "Exact"
* Added synonym "negative regulation of heterochromatic silencing at telomere" to GO:0031939
* Changed synonym scope of GO:0031939 from "Related" to "Exact"
* Added synonym "positive regulation of heterochromatic silencing at telomere" to GO:0031940
* Changed synonym scope of GO:0031940 from "Related" to "Exact"
* Changed definition of GO:0043190 from "A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In bacteria and archaebacteria, ABC transporters also recruit substrate binding proteins to bind substrate external to the cell and deliver it to the transporter." to "A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter."
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"
* added secondary id GO:0051226 to GO:0051225
* added secondary id GO:0051227 to GO:0051225
* Added definition dbxref GOC:mtg_sensu to GO:0051225
* Added definition dbxref GOC:rg to GO:0051225
* Added definition dbxref GOC:tb to GO:0051225
* Added synonym "meiotic spindle assembly" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "meiotic spindle biogenesis" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "meiotic spindle biosynthesis" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "meiotic spindle formation" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "mitotic spindle assembly" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "mitotic spindle biogenesis" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "mitotic spindle biosynthesis" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "mitotic spindle formation" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "spindle assembly involved in meiosis" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "spindle assembly involved in mitosis" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "spindle biogenesis involved in meiosis" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "spindle biogenesis involved in mitosis" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "spindle formation involved in meiosis" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Added synonym "spindle formation involved in mitosis" to GO:0051225
* Changed synonym scope of GO:0051225 from "Related" to "Narrow"
* Deleted GO:0051226 --OBO_REL:is_a--> GO:0051225
* Deleted GO:0051226 --OBO_REL:is_a--> GO:0000212
* Deleted GO:0051257 --part_of--> GO:0051226
* Destroyed object GO:0051226
* Deleted GO:0051227 --OBO_REL:is_a--> GO:0051225
* Deleted GO:0051227 --OBO_REL:is_a--> GO:0007052
* Deleted GO:0051256 --part_of--> GO:0051227
* Destroyed object GO:0051227
* Deleted GO:0051256 --part_of--> GO:0051227
* Copied GO:0051256 to GO:0051225 with type part_of
* Deleted GO:0051257 --part_of--> GO:0051226
* Copied GO:0051257 to GO:0051225 with type part_of


From gocvs at genome.Stanford.EDU  Wed May  9 21:30:40 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Wed, 9 May 2007 21:30:40 -0700 (PDT)
Subject: [go-diff] GO update 05/09/2007
Message-ID: <200705100430.VAA24776@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.315 by 5.317

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033196
* Created object of type obo:TERM with id GO:0033197
* Created object of type obo:TERM with id GO:0033198
* Created object of type obo:TERM with id GO:0033199
* Created object of type obo:TERM with id GO:0033200
* Created object of type obo:TERM with id GO:0033201
* Populated new object GO:0033196 (macro)
  * Changed name of GO:0033196 from "<new term>" to "tryparedoxin peroxidase activity"
  * Set definition of GO:0033196 to "Catalysis of the reaction: tryparedoxin + H2O2 = tryparedoxin disulfide + H2O."
  * Added definition dbxref GOC:mah to GO:0033196
  * Added synonym "TXNPx activity" to GO:0033196
  * Changed synonym scope of GO:0033196 from "Related" to "Exact"
  * Copied GO:0033196 to GO:0051920 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033196
* Populated new object GO:0033197 (macro)
  * Changed name of GO:0033197 from "<new term>" to "response to vitamin E"
  * Set definition of GO:0033197 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 vitamin E stimulus."
  * Added definition dbxref GOC:sl to GO:0033197
  * Added synonym "response to DL-alpha-tocopherol acetate" to GO:0033197
  * Changed synonym scope of GO:0033197 from "Related" to "Narrow"
  * Added synonym "response to DL-alpha-tocopheryl acetate" to GO:0033197
  * Changed synonym scope of GO:0033197 from "Related" to "Narrow"
  * Added synonym "response to O-Acetyl-alpha-tocopherol" to GO:0033197
  * Changed synonym scope of GO:0033197 from "Related" to "Narrow"
  * Copied GO:0033197 to GO:0007584 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033197
* Populated new object GO:0033198 (macro)
  * Changed name of GO:0033198 from "<new term>" to "response to ATP"
  * Set definition of GO:0033198 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 an ATP (adenosine 5'-triphosphate) stimulus."
  * Added definition dbxref GOC:sl to GO:0033198
  * Added synonym "response to adenosine 5'-triphosphate" to GO:0033198
  * Changed synonym scope of GO:0033198 from "Related" to "Exact"
  * Added synonym "response to adenosine triphosphate" to GO:0033198
  * Changed synonym scope of GO:0033198 from "Related" to "Exact"
  * Copied GO:0033198 to GO:0010033 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033198
* Populated new object GO:0033199 (macro)
  * Changed name of GO:0033199 from "<new term>" to "inositol heptakisphosphate 4-kinase activity"
  * Set definition of GO:0033199 to "Catalysis of the reaction: ATP + 4-diphospho-1D-myo-inositol (1,2,3,5,6)pentakisphosphate = 4,5-bisdiphosphoinositol-1D-myoinositol (1,2,3,6)tetrakisphosphate, or ATP + 6-diphospho-1D-myo-inositol (1,2,3,4,5)pentakisphosphate = 5,6-bisdiphosphoinositol-1D-myoinositol (1,2,3,4)tetrakisphosphate."
  * Added definition dbxref PMID:17412958 to GO:0033199
  * Added synonym "IP7 4-kinase activity" to GO:0033199
  * Changed synonym scope of GO:0033199 from "Related" to "Exact"
  * Copied GO:0033199 to GO:0004428 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033199
* Populated new object GO:0033200 (macro)
  * Changed name of GO:0033200 from "<new term>" to "inositol heptakisphosphate 5-kinase activity"
  * Set definition of GO:0033200 to "Catalysis of the reaction: ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = 4,5-bisdiphosphoinositol-1D-myoinositol (1,2,3,6)tetrakisphosphate, or ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = 5,6-bisdiphosphoinositol-1D-myoinositol
(1,2,3,4)tetrakisphosphate."
  * Added definition dbxref PMID:17412958 to GO:0033200
  * Added synonym "IP7 5-kinase activity" to GO:0033200
  * Changed synonym scope of GO:0033200 from "Related" to "Exact"
  * Copied GO:0033200 to GO:0004428 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033200
* Populated new object GO:0033201 (macro)
  * Changed name of GO:0033201 from "<new term>" to "alpha-1,4-glucan synthase activity"
  * Set definition of GO:0033201 to "Catalysis of the reaction: RDP-glucose + [alpha-D-glucosyl-(1,4)]n = RDP + [alpha-D-glucosyl-(1,4)]n+1, where RDP is ADP or UDP."
  * Added definition dbxref PMID:17472966 to GO:0033201
  * Added synonym "1,4-alpha-glucan synthase activity" to GO:0033201
  * Changed synonym scope of GO:0033201 from "Related" to "Exact"
  * Copied GO:0033201 to GO:0016758 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033201
* Copied GO:0000776 to GO:0043234 with type OBO_REL:is_a
* Added synonym "beta-1,3-glucan synthase activity" to GO:0003843
* Changed synonym scope of GO:0003843 from "Related" to "Exact"
* Changed definition of GO:0003844 from "Catalysis of the transfer of a segment of a 1,4-a-D-glucan chain to a primary hydroxyl group in a similar glucan chain." to "Catalysis of the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxyl group in a similar glucan chain."
* Copied GO:0005819 to GO:0043234 with type OBO_REL:is_a
* Added synonym "TPx activity" to GO:0008379
* Changed synonym scope of GO:0008379 from "Related" to "Exact"
* Added synonym "TrxPx activity" to GO:0008379
* Changed synonym scope of GO:0008379 from "Related" to "Exact"
* Deleted GO:0008379 --OBO_REL:is_a--> GO:0004601
* Copied GO:0008379 to GO:0051920 with type OBO_REL:is_a
* Changed definition of GO:0008622 from "A nuclear DNA polymerase with proofreading exonuclease activity. High processivity in the absence of PCNA. Also involved in nucleotide-excision repair and mismatch repair." to "A heterotetrameric DNA polymerase complex that catalyzes processive DNA synthesis in the absence of PCNA, but is further stimulated in the presence of PCNA. The complex contains a large catalytic subunit and three small subunits, and is best characterized in Saccharomyces, in which the subunits are named Pol2p, Dpb2p, Dpb3p, and Dpb4p. Some evidence suggests that DNA polymerase epsilon is the leading strand polymerase; it is also involved in nucleotide-excision repair and mismatch repair."
* Added definition dbxref PMID:15814431 to GO:0008622
* Changed name of GO:0008932 from "murein lytic endotransglycosylase E activity" to "lytic endotransglycosylase activity"
* Set definition of GO:0008932 to "Catalysis of the specific cleavage of the beta-1,4 glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues in peptidoglycan, with the concomitant formation of 1,6-anhydro-N-acetylmuramyl residues. Acts on linkages within peptidoglycan chains (i.e. not at the ends) to produce shorter strands with 1,6-anhydromuramic acid ends."
* Added definition dbxref PMID:10964424 to GO:0008932
* Added definition dbxref PMID:9642199 to GO:0008932
* Added synonym "murein lytic endotransglycosylase E activity" to GO:0008932
* Changed synonym scope of GO:0008932 from "Related" to "Narrow"
* Deleted GO:0008932 --OBO_REL:is_a--> GO:0016757
* Copied GO:0008932 to GO:0008933 with type OBO_REL:is_a
* Changed name of GO:0008933 from "murein transglycosylase B activity" to "lytic transglycosylase activity"
* Set definition of GO:0008933 to "Catalysis of the specific cleavage of the beta-1,4 glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues in peptidoglycan, with the concomitant formation of 1,6-anhydro-N-acetylmuramyl residues."
* Added definition dbxref PMID:10964424 to GO:0008933
* Added synonym "murein transglycosylase B activity" to GO:0008933
* Changed synonym scope of GO:0008933 from "Related" to "Narrow"
* Deleted GO:0008933 --OBO_REL:is_a--> GO:0004553
* Copied GO:0008933 to GO:0016757 with type OBO_REL:is_a
* Changed definition of GO:0016035 from "A low fidelity DNA-directed DNA polymerase that functions during replication, to promote the extension of forks whose progression is stopped for any reason; a non-processive enzyme with no 3'-5' exonuclease activity; possesses deoxycytidyl transferase activity, incorporating deoxycytidyl opposite abasic sites. Functions during DNA repair and mutagenesis. Composed of two subunits." to "A heterodimeric DNA polymerase complex that catalyzes error-prone DNA synthesis in contexts such as translesion synthesis and double-stranded break repair. First characterized in Saccharomyces, in which the subunits are Rev3p and Rev7p; a third protein, Rev1p, is often associated with the polymerase dimer."
* Deleted definition dbxref PMID:11205328 from GO:0016035
* Added definition dbxref PMID:16631579 to GO:0016035
* Added definition dbxref PMID:16971464 to GO:0016035
* Deleted GO:0016035 --OBO_REL:is_a--> GO:0044451
* Copied GO:0016035 to GO:0044446 with type OBO_REL:is_a
* Added synonym "transglycosylase" to GO:0016757
* Changed synonym scope of GO:0016757 from "Related" to "Exact"
* Set definition of GO:0020036 to "A disk-like structure that appears at the periphery of a red blood cell infected by an apicomplexan parasite, characterized by a translucent lumen and an electron-dense coat of variable thickness; often appears to be tethered to the host cell membrane by fibrous connections with the erythrocyte cytoskeleton."
* Added definition dbxref PMID:16705161 to GO:0020036
* Deleted GO:0021886 --part_of--> GO:0021854
* Deleted GO:0021886 --OBO_REL:is_a--> GO:0030154
* Copied GO:0021886 to GO:0021979 with type OBO_REL:is_a
* Copied GO:0021979 to GO:0021854 with type part_of
* Deleted GO:0021985 --OBO_REL:is_a--> GO:0016337
* Copied GO:0021985 to GO:0048856 with type OBO_REL:is_a
* Added synonym "1,4alpha-glucan-protein synthase (UDP-forming) activity" to GO:0047210
* Changed synonym scope of GO:0047210 from "Related" to "Exact"
* Added synonym "1,4alpha-glucan-protein synthase (ADP-forming) activity" to GO:0047211
* Changed synonym scope of GO:0047211 from "Related" to "Exact"
* Added synonym "1,3-alpha-glucan synthase activity" to GO:0047657
* Changed synonym scope of GO:0047657 from "Related" to "Exact"
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"
* Deleted synonym "thioredoxin peroxidase activity" from GO:0051920
* Deleted synonym "TrxPx activity" from GO:0051920
* Deleted synonym "tryparedoxin peroxidase activity" from GO:0051920
* Deleted synonym "TXNPx activity" from GO:0051920


From gocvs at genome.Stanford.EDU  Thu May 10 21:30:38 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Thu, 10 May 2007 21:30:38 -0700 (PDT)
Subject: [go-diff] GO update 05/10/2007
Message-ID: <200705110430.VAA23129@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.317 by 5.320

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010431
* Created object of type obo:TERM with id GO:0010432
* Created object of type obo:TERM with id GO:0010433
* Created object of type obo:TERM with id GO:0010434
* Created object of type obo:TERM with id GO:0060115
* Created object of type obo:TERM with id GO:0060116
* Created object of type obo:TERM with id GO:0060117
* Created object of type obo:TERM with id GO:0060118
* Created object of type obo:TERM with id GO:0060119
* Created object of type obo:TERM with id GO:0060120
* Created object of type obo:TERM with id GO:0060121
* Created object of type obo:TERM with id GO:0060122
* Populated new object GO:0010431 (macro)
  * Changed name of GO:0010431 from "<new term>" to "seed maturation"
  * Set definition of GO:0010431 to "A process in seed development that occurs after embryogenesis by which a quiescent state is established in a seed. Seed maturation is characterized by storage compound accumulation, acquisition of desiccation tolerance, growth arrest and the entry into a dormancy period of variable length that is broken upon germination."
  * Added definition dbxref PMID:16096971 to GO:0010431
  * Copied GO:0010431 to GO:0048316 with type part_of
  * Copied GO:0010431 to GO:0048609 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010431
* Populated new object GO:0010432 (macro)
  * Changed name of GO:0010432 from "<new term>" to "bract development"
  * Set definition of GO:0010432 to "The process whose specific outcome is the progression of the bract over time, from its formation to the mature structure. A bract is a leaf, usually different in form from the foliage leaves, subtending a flower or inflorescence."
  * Added definition dbxref GOC:tb to GO:0010432
  * Added definition dbxref PMID:16554366 to GO:0010432
  * Added definition dbxref PO:0009055 to GO:0010432
  * Copied GO:0010432 to GO:0048856 with type OBO_REL:is_a
  * Copied GO:0010432 to GO:0048827 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010432
* Populated new object GO:0010433 (macro)
  * Changed name of GO:0010433 from "<new term>" to "bract morphogenesis"
  * Set definition of GO:0010433 to "The process by which the anatomical structure of bract are generated and organized. A bract is a leaf, usually different in form from the foliage leaves, subtending a flower or inflorescence. Morphogenesis pertains to the creation of form."
  * Added definition dbxref GOC:tb to GO:0010433
  * Added definition dbxref PMID:16554366 to GO:0010433
  * Added definition dbxref PO:0009055 to GO:0010433
  * Copied GO:0010433 to GO:0009887 with type OBO_REL:is_a
  * Copied GO:0010433 to GO:0010432 with type part_of
  * Assigned namespace "biological_process" to GO:0010433
* Populated new object GO:0010434 (macro)
  * Changed name of GO:0010434 from "<new term>" to "bract formation"
  * Set definition of GO:0010434 to "The process that gives rise to a bract. This process pertains to the initial formation of a structure from unspecified parts. A bract is a leaf, usually different in form from the foliage leaves, subtending a flower or inflorescence."
  * Added definition dbxref GOC:tb to GO:0010434
  * Added definition dbxref PMID:16554366 to GO:0010434
  * Added definition dbxref PO:0009055 to GO:0010434
  * Copied GO:0010434 to GO:0048646 with type OBO_REL:is_a
  * Copied GO:0010434 to GO:0010433 with type part_of
  * Assigned namespace "biological_process" to GO:0010434
* Populated new object GO:0060115 (macro)
  * Changed name of GO:0060115 from "<new term>" to "vestibular receptor cell fate commitment"
  * Set definition of GO:0060115 to "xx"
  * Added definition dbxref GOC:dph to GO:0060115
  * Copied GO:0060115 to GO:0060120 with type OBO_REL:is_a
  * Copied GO:0060115 to GO:0060114 with type part_of
  * Assigned namespace "biological_process" to GO:0060115
* Populated new object GO:0060116 (macro)
  * Changed name of GO:0060116 from "<new term>" to "vestibular receptor cell morphogenesis"
  * Set definition of GO:0060116 to "xx"
  * Added definition dbxref GOC:dph to GO:0060116
  * Copied GO:0060116 to GO:0042472 with type part_of
  * Copied GO:0060116 to GO:0000902 with type OBO_REL:is_a
  * Copied GO:0060116 to GO:0060118 with type part_of
  * Assigned namespace "biological_process" to GO:0060116
* Populated new object GO:0060117 (macro)
  * Changed name of GO:0060117 from "<new term>" to "auditory receptor cell development"
  * Set definition of GO:0060117 to "The process whose specific outcome is the progression of an auditory receptor cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate."
  * Added definition dbxref GOC:dph to GO:0060117
  * Copied GO:0060117 to GO:0042491 with type part_of
  * Copied GO:0060117 to GO:0060119 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060117
* Populated new object GO:0060118 (macro)
  * Changed name of GO:0060118 from "<new term>" to "vestibular receptor cell development"
  * Set definition of GO:0060118 to "The process whose specific outcome is the progression of a vestibular receptor cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate."
  * Added definition dbxref GOC:dph to GO:0060118
  * Copied GO:0060118 to GO:0060114 with type part_of
  * Copied GO:0060118 to GO:0060119 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060118
* Populated new object GO:0060119 (macro)
  * Changed name of GO:0060119 from "<new term>" to "inner ear receptor cell development"
  * Set definition of GO:0060119 to "The process whose specific outcome is the progression of an inner ear receptor cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate."
  * Added definition dbxref GOC:dph to GO:0060119
  * Copied GO:0060119 to GO:0060113 with type part_of
  * Copied GO:0060119 to GO:0048468 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060119
* Populated new object GO:0060120 (macro)
  * Changed name of GO:0060120 from "<new term>" to "inner ear receptor cell fate commitment"
  * Set definition of GO:0060120 to "The process by which a cell becomes committed to become an inner ear receptor cell."
  * Added definition dbxref GOC:dph to GO:0060120
  * Copied GO:0060120 to GO:0045165 with type OBO_REL:is_a
  * Copied GO:0060120 to GO:0060113 with type part_of
  * Assigned namespace "biological_process" to GO:0060120
* Populated new object GO:0060121 (macro)
  * Changed name of GO:0060121 from "<new term>" to "vestibular receptor cell stereocilium organization and biogenesis"
  * Set definition of GO:0060121 to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of vestibular hair cells."
  * Added definition dbxref GOC:dph to GO:0060121
  * Copied GO:0060121 to GO:0060122 with type OBO_REL:is_a
  * Copied GO:0060121 to GO:0060116 with type part_of
  * Assigned namespace "biological_process" to GO:0060121
* Populated new object GO:0060122 (macro)
  * Changed name of GO:0060122 from "<new term>" to "inner ear receptor stereocilium organization and biogenesis"
  * Set definition of GO:0060122 to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of inner ear receptor cells."
  * Added definition dbxref GOC:dph to GO:0060122
  * Copied GO:0060122 to GO:0030030 with type OBO_REL:is_a
  * Copied GO:0060122 to GO:0060119 with type part_of
  * Assigned namespace "biological_process" to GO:0060122
* Added synonym "generation of a signal involved in cell-cell signalling" to GO:0001820
* Changed synonym scope of GO:0001820 from "Related" to "Exact"
* Added synonym "adenosine receptor signalling pathway" to GO:0001973
* Changed synonym scope of GO:0001973 from "Related" to "Exact"
* Added synonym "excitation of vasomotor center by baroreceptor signalling" to GO:0002010
* Changed synonym scope of GO:0002010 from "Related" to "Exact"
* Deleted synonym "desensitization of G-protein coupled receptor protein signaling pathway" from GO:0002029
* Added synonym "desensitisation of G-protein coupled receptor protein signalling pathway" to GO:0002029
* Changed synonym scope of GO:0002029 from "Related" to "Exact"
* Deleted synonym "arrestin-mediated desensitization of G-protein coupled receptor protein signaling pathway" from GO:0002032
* Added synonym "arrestin mediated desensitisation of G-protein coupled receptor protein signalling pathway" to GO:0002032
* Changed synonym scope of GO:0002032 from "Related" to "Exact"
* Deleted GO:0002093 --part_of--> GO:0042491
* Copied GO:0002093 to GO:0060117 with type part_of
* Added synonym "caveolar macromolecular signalling complex" to GO:0002095
* Changed synonym scope of GO:0002095 from "Related" to "Exact"
* Added synonym "innate immune response activating cell surface receptor signalling pathway" to GO:0002220
* Changed synonym scope of GO:0002220 from "Related" to "Exact"
* Added synonym "stimulatory killer cell immunoglobulin-like receptor signalling pathway" to GO:0002222
* Changed synonym scope of GO:0002222 from "Related" to "Exact"
* Added synonym "stimulatory C-type lectin receptor signalling pathway" to GO:0002223
* Changed synonym scope of GO:0002223 from "Related" to "Exact"
* Added synonym "toll-like receptor signalling pathway" to GO:0002224
* Changed synonym scope of GO:0002224 from "Related" to "Exact"
* Added synonym "immune response-activating cell surface receptor signalling pathway" to GO:0002429
* Changed synonym scope of GO:0002429 from "Related" to "Exact"
* Added synonym "complement receptor mediated signalling pathway" to GO:0002430
* Changed synonym scope of GO:0002430 from "Related" to "Exact"
* Added synonym "immune response-regulating cell surface receptor signalling pathway" to GO:0002430
* Changed synonym scope of GO:0002430 from "Related" to "Exact"
* Added synonym "Fc receptor mediated stimulatory signalling pathway" to GO:0002431
* Changed synonym scope of GO:0002431 from "Related" to "Exact"
* Added synonym "cell surface pattern recognition receptor signalling pathway" to GO:0002752
* Changed synonym scope of GO:0002752 from "Related" to "Exact"
* Added synonym "cytoplasmic pattern recognition receptor signalling pathway" to GO:0002753
* Changed synonym scope of GO:0002753 from "Related" to "Exact"
* Added synonym "intracellular vesicle pattern recognition receptor signalling pathway" to GO:0002754
* Changed synonym scope of GO:0002754 from "Related" to "Exact"
* Added synonym "MyD88-dependent toll-like receptor signalling pathway" to GO:0002755
* Changed synonym scope of GO:0002755 from "Related" to "Exact"
* Added synonym "MyD88-independent toll-like receptor signalling pathway" to GO:0002756
* Changed synonym scope of GO:0002756 from "Related" to "Exact"
* Added synonym "immune response-inhibiting cell surface receptor signalling pathway" to GO:0002767
* Changed synonym scope of GO:0002767 from "Related" to "Exact"
* Added synonym "immune response-regulating cell surface receptor signalling pathway" to GO:0002768
* Changed synonym scope of GO:0002768 from "Related" to "Exact"
* Added synonym "natural killer cell inhibitory signalling pathway" to GO:0002769
* Changed synonym scope of GO:0002769 from "Related" to "Exact"
* Added synonym "T cell inhibitory signalling pathway" to GO:0002770
* Changed synonym scope of GO:0002770 from "Related" to "Exact"
* Added synonym "inhibitory killer cell immunoglobulin-like receptor signalling pathway" to GO:0002771
* Changed synonym scope of GO:0002771 from "Related" to "Exact"
* Added synonym "inhibitory C-type lectin receptor signalling pathway" to GO:0002772
* Changed synonym scope of GO:0002772 from "Related" to "Exact"
* Added synonym "B cell inhibitory signalling pathway" to GO:0002773
* Changed synonym scope of GO:0002773 from "Related" to "Exact"
* Added synonym "Fc receptor mediated inhibitory signalling pathway" to GO:0002774
* Changed synonym scope of GO:0002774 from "Related" to "Exact"
* Added synonym "generation of a signal involved in cell-cell signalling" to GO:0003001
* Changed synonym scope of GO:0003001 from "Related" to "Exact"
* Changed definition of GO:0003957 from "Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+." to "Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+. The reaction is B-specific (i.e. the pro-S hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to both NAD+ and NADP+."
* Added definition dbxref http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/1991/113/i07/f-pdf/f_ja00007a002.pdf?sessid=6006l3 to GO:0003957
* Added comment "This term was made obsolete because, according to PUMA2, this "pathway" is a single reaction, corresponding to carbamate kinase activity (GO:0008804; EC:2.7.2.2)."
* Set definition of GO:0006755 to "OBSOLETE (was not defined before being made obsolete)."
* Added definition dbxref GOC:mah to GO:0006755
* Deleted GO:0006755 --OBO_REL:is_a--> GO:0006754
* Deleted GO:0006755 --OBO_REL:is_a--> GO:0016310
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 17b2bef
* Added synonym "daf-2 receptor signaling pathway" to GO:0008286
* Changed synonym scope of GO:0008286 from "Related" to "Narrow"
* Changed definition of GO:0008750 from "Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+." to "Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+. The reaction is A-specific (i.e. the pro-R hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NAD+ and B-specific (i.e. the pro-S hydrogen is transferred) with respect to NADP+."
* Added definition dbxref http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/1991/113/i07/f-pdf/f_ja00007a002.pdf?sessid=6006l3 to GO:0008750
* Set definition of GO:0009327 to "A protein complex that possesses NAD(P)+ transhydrogenase (AB-specific) activity. Homodimeric, trimeric, and heterotetrameric complexes have been identified."
* Added definition dbxref BRENDA:1.6.1.2 to GO:0009327
* Added definition dbxref GOC:mah to GO:0009327
* Deleted GO:0009327 --OBO_REL:is_a--> GO:0005941
* Copied GO:0009327 to GO:0044424 with type OBO_REL:is_a
* Copied GO:0009327 to GO:0043234 with type OBO_REL:is_a
* Deleted GO:0009376 --OBO_REL:is_a--> GO:0005941
* Copied GO:0009376 to GO:0043234 with type OBO_REL:is_a
* Copied GO:0009376 to GO:0044444 with type OBO_REL:is_a
* Set definition of GO:0009377 to "A protein complex that possesses ATP-dependent protease activity; as characterized in E. coli, the complex contains six identical subunits of both ClpY and ClpQ that self-assemble into an oligomeric ring, and two rings of each subunit, two ClpQ rings surrounded by single ClpY rings, to form a dumbbell shape complex."
* Added definition dbxref GOC:mah to GO:0009377
* Added definition dbxref PMID:12670962 to GO:0009377
* Copied GO:0009912 to GO:0060120 with type OBO_REL:is_a
* Deleted GO:0010162 --part_of--> GO:0048316
* Copied GO:0010162 to GO:0010431 with type part_of
* Added synonym "glucose mediated signalling" to GO:0010255
* Changed synonym scope of GO:0010255 from "Related" to "Exact"
* Added synonym "retinoic acid receptor signalling pathway involved in ventral spinal cord interneuron specification" to GO:0021774
* Changed synonym scope of GO:0021774 from "Related" to "Exact"
* Added synonym "smoothened signalling pathway involved in ventral spinal cord interneuron specification" to GO:0021775
* Changed synonym scope of GO:0021775 from "Related" to "Exact"
* Added synonym "smoothened signalling pathway in ventral spinal cord patterning" to GO:0021776
* Changed synonym scope of GO:0021776 from "Related" to "Exact"
* Added synonym "smoothened signalling pathway involved in spinal cord motor neuron cell fate specification" to GO:0021776
* Changed synonym scope of GO:0021776 from "Related" to "Exact"
* Added synonym "motogenic signalling initiating cell movement in the cerebral cortex" to GO:0021807
* Changed synonym scope of GO:0021807 from "Related" to "Exact"
* Added synonym "cytosolic calcium signalling involved in the initiation of cell movement in glial-mediated radial cell migration" to GO:0021808
* Changed synonym scope of GO:0021808 from "Related" to "Exact"
* Added synonym "neurotrophic factor signalling initiating cell movement, involved in cerebral cortex glial-mediated radial migration" to GO:0021809
* Changed synonym scope of GO:0021809 from "Related" to "Exact"
* Added synonym "neurotransmitter signalling initiating cell movement, involved in cerebral cortex glial-mediated radial migration" to GO:0021810
* Changed synonym scope of GO:0021810 from "Related" to "Exact"
* Added synonym "growth factor signalling initiating cell movement involved in cerebral cortex glial-mediated radial migration" to GO:0021811
* Changed synonym scope of GO:0021811 from "Related" to "Exact"
* Added synonym "motogenic signalling involved in postnatal olfactory bulb interneuron migration" to GO:0021837
* Changed synonym scope of GO:0021837 from "Related" to "Exact"
* Added synonym "motogenic signalling involved in interneuron migration from the subpallium to the cortex" to GO:0021838
* Changed synonym scope of GO:0021838 from "Related" to "Exact"
* Added synonym "Wnt receptor signalling pathway in forebrain neuroblast division" to GO:0021874
* Changed synonym scope of GO:0021874 from "Related" to "Exact"
* Added synonym "fibroblast growth factor receptor signalling pathway in forebrain neuroblast division" to GO:0021875
* Changed synonym scope of GO:0021875 from "Related" to "Exact"
* Added synonym "Notch signalling pathway in forebrain neuroblast division" to GO:0021876
* Changed synonym scope of GO:0021876 from "Related" to "Exact"
* Added synonym "Notch signalling pathway involved in forebrain neuron fate commitment" to GO:0021880
* Changed synonym scope of GO:0021880 from "Related" to "Exact"
* Added synonym "Wnt receptor signalling pathway involved in forebrain neuron fate commitment" to GO:0021881
* Changed synonym scope of GO:0021881 from "Related" to "Exact"
* Added synonym "fibroblast growth factor receptor signalling pathway involved in forebrain neuron fate commitment" to GO:0021899
* Changed synonym scope of GO:0021899 from "Related" to "Exact"
* Added synonym "fibroblast growth factor receptor signalling pathway in spinal cord anterior-posterior patterning" to GO:0021907
* Changed synonym scope of GO:0021907 from "Related" to "Exact"
* Added synonym "retinoic acid receptor signalling pathway in spinal cord anterior-posterior patterning" to GO:0021908
* Changed synonym scope of GO:0021908 from "Related" to "Exact"
* Added synonym "smoothened signalling pathway in ventral spinal cord patterning" to GO:0021910
* Changed synonym scope of GO:0021910 from "Related" to "Exact"
* Added synonym "negative regulation of smoothened signalling pathway in ventral spinal cord patterning" to GO:0021914
* Changed synonym scope of GO:0021914 from "Related" to "Exact"
* Added synonym "inductive cell-cell signalling between paraxial mesoderm and motor neuron precursors" to GO:0021916
* Changed synonym scope of GO:0021916 from "Related" to "Exact"
* Added synonym "Wnt receptor signalling pathway involved in regulation of cell proliferation in dorsal spinal cord" to GO:0021922
* Changed synonym scope of GO:0021922 from "Related" to "Exact"
* Added synonym "Purkinje cell-granule cell precursor cell signalling involved in regulation of granule cell precursor cell proliferation" to GO:0021937
* Changed synonym scope of GO:0021937 from "Related" to "Exact"
* Added synonym "smoothened signalling pathway in regulation of granule cell precursor cell proliferation" to GO:0021938
* Changed synonym scope of GO:0021938 from "Related" to "Exact"
* Added synonym "extracellular matrix-granule cell signalling involved in regulation of granule cell precursor proliferation" to GO:0021939
* Changed synonym scope of GO:0021939 from "Related" to "Exact"
* Added synonym "wnt receptor signalling involved in negative regulation of anterior neural cell fate of the neural plate" to GO:0022002
* Changed synonym scope of GO:0022002 from "Related" to "Exact"
* Added synonym "fgf receptor signalling involved in negative regulation of anterior neural cell fate of the neural plate" to GO:0022003
* Changed synonym scope of GO:0022003 from "Related" to "Exact"
* Added synonym "leukemia inhibitory factor signalling pathway involved in forebrain neuron fate commitment" to GO:0022025
* Changed synonym scope of GO:0022025 from "Related" to "Exact"
* Added synonym "epidermal growth factor signalling pathway involved in forebrain neuron fate commitment" to GO:0022026
* Changed synonym scope of GO:0022026 from "Related" to "Exact"
* Added synonym "regulation of rhodopsin mediated signalling" to GO:0022400
* Changed synonym scope of GO:0022400 from "Related" to "Exact"
* Changed synonym scope of GO:0030509 from "Exact" to "Related"
* Changed synonym scope of GO:0030510 from "Exact" to "Related"
* Changed synonym scope of GO:0030513 from "Exact" to "Related"
* Changed synonym scope of GO:0030514 from "Exact" to "Related"
* Added synonym "SREBP-mediated signalling pathway" to GO:0030968
* Changed synonym scope of GO:0030968 from "Related" to "Exact"
* Added synonym "inductive cell-cell signalling" to GO:0031129
* Changed synonym scope of GO:0031129 from "Related" to "Exact"
* Added synonym "mitochondrial signalling pathway" to GO:0031930
* Changed synonym scope of GO:0031930 from "Related" to "Exact"
* Deleted definition dbxref PMID:0 from GO:0032933
* Added definition dbxref PMID:12923525 to GO:0032933
* Added synonym "SREBP-mediated signalling pathway" to GO:0032933
* Changed synonym scope of GO:0032933 from "Related" to "Exact"
* Added synonym "Hedgehog signalling complex" to GO:0035301
* Changed synonym scope of GO:0035301 from "Related" to "Exact"
* Deleted GO:0042491 --OBO_REL:is_a--> GO:0035315
* Added synonym "positive regulation of calcium-mediated signalling" to GO:0050850
* Changed synonym scope of GO:0050850 from "Related" to "Exact"
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"
* Added synonym "Wnt receptor signalling pathway, regulating spindle positioning" to GO:0060069
* Changed synonym scope of GO:0060069 from "Related" to "Exact"
* Added synonym "Wnt receptor signalling pathway through beta-catenin" to GO:0060070
* Changed synonym scope of GO:0060070 from "Related" to "Exact"
* Added synonym "Wnt receptor signalling pathway, planar cell polarity pathway" to GO:0060071
* Changed synonym scope of GO:0060071 from "Related" to "Exact"
* Changed name of GO:0060088 from "stereocilium organization and biogenesis" to "auditory receptor cell stereocilium organization and biogenesis"
* Changed definition of GO:0060088 from "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of auditory and vestibular hair cells." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of auditory hair cells."
* Deleted GO:0060088 --OBO_REL:is_a--> GO:0030030
* Copied GO:0060088 to GO:0060122 with type OBO_REL:is_a
* Changed name of GO:0060113 from "inner ear receptor cell differenatioan" to "inner ear receptor cell differenation"


From gocvs at genome.Stanford.EDU  Fri May 11 21:30:38 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Fri, 11 May 2007 21:30:38 -0700 (PDT)
Subject: [go-diff] GO update 05/11/2007
Message-ID: <200705120430.VAA22529@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.320 by 5.321

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Changed definition of GO:0002719 from "Any process that stops, prevents, or reduces the frequency, rate, or extent of cytokine production during immune response." to "Any process that stops, prevents, or reduces the frequency, rate, or extent of cytokine production during an immune response."
* Set definition of GO:0031668 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 extracellular stimulus."
* Added definition dbxref GOC:mah to GO:0031668
* Set definition of GO:0032107 to "Any process that modulates the frequency, rate or extent of a response to nutrient levels."
* Added definition dbxref GOC:mah to GO:0032107
* Set definition of GO:0032108 to "Any process that stops, prevents or reduces the frequency, rate or extent of a response to nutrient levels."
* Added definition dbxref GOC:mah to GO:0032108
* Set definition of GO:0032109 to "Any process that activates or increases the frequency, rate or extent of a response to nutrient levels."
* Added definition dbxref GOC:mah to GO:0032109
* Set definition of GO:0032684 to "Any process that stops, prevents, or reduces the frequency, rate, or extent of fractalkine production."
* Added definition dbxref GOC:mah to GO:0032684
* Set definition of GO:0032835 to "The progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney."
* Added definition dbxref GOC:mah to GO:0032835
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"


From gocvs at genome.Stanford.EDU  Mon May 14 21:30:38 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Mon, 14 May 2007 21:30:38 -0700 (PDT)
Subject: [go-diff] GO update 05/14/2007
Message-ID: <200705150430.VAA24472@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.321 by 5.324

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0000444
* Created object of type obo:TERM with id GO:0000445
* Created object of type obo:TERM with id GO:0000446
* Created object of type obo:TERM with id GO:0033202
* Created object of type obo:TERM with id GO:0033203
* Created object of type obo:TERM with id GO:0060123
* Created object of type obo:TERM with id GO:0060124
* Created object of type obo:TERM with id GO:0060125
* Populated new object GO:0000444 (macro)
  * Changed name of GO:0000444 from "<new term>" to "MIS12/MIND type complex"
  * Set definition of GO:0000444 to "A multiprotein kinetochore subcomplex that binds to centromeric chromatin and forms part of the inner kinetochore. It helps to recruit outer kinetochore subunits that will bind to microtubules. In humans, it consists of MIS12, DSN1, NSL1 and PMF1. In S. cerevisiae, this complex consists of Mtw1p, Nnf1p, Nsl1p, and Dsn1."
  * Added definition dbxref GOC:krc to GO:0000444
  * Added definition dbxref PMID:14633972 to GO:0000444
  * Added definition dbxref PMID:16585270 to GO:0000444
  * Copied GO:0000444 to GO:0000777 with type part_of
  * Assigned namespace "cellular_component" to GO:0000444
* Populated new object GO:0000445 (macro)
  * Changed name of GO:0000445 from "<new term>" to "THO complex part of transcription export complex"
  * Set definition of GO:0000445 to "The THO complex when it is part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1, Tho2, Thp1, and Mft1, while the human complex is composed of 7 subunits."
  * Added definition dbxref GO:krc to GO:0000445
  * Added definition dbxref PMID:11060033 to GO:0000445
  * Added definition dbxref PMID:11979277 to GO:0000445
  * Added definition dbxref PMID:16983072 to GO:0000445
  * Copied GO:0000445 to GO:0000346 with type part_of
  * Copied GO:0000445 to GO:0000347 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0000445
* Populated new object GO:0000446 (macro)
  * Changed name of GO:0000446 from "<new term>" to "nucleoplasmic THO complex"
  * Set definition of GO:0000446 to "The THO complex when it is acting as a nuclear complex that is required for
transcription elongation through genes containing tandemly repeated DNA sequences. In S. cerevisiae, it is composed of four subunits: Hpr1, Tho2, Thp1, and Mft1, while the human complex is composed of 7 subunits."
  * Added definition dbxref GO:krc to GO:0000446
  * Added definition dbxref PMID:11060033 to GO:0000446
  * Added definition dbxref PMID:11979277 to GO:0000446
  * Added definition dbxref PMID:16983072 to GO:0000446
  * Copied GO:0000446 to GO:0000347 with type OBO_REL:is_a
  * Copied GO:0000446 to GO:0008023 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0000446
* Populated new object GO:0033202 (macro)
  * Changed name of GO:0033202 from "<new term>" to "DNA helicase complex"
  * Set definition of GO:0033202 to "A protein complex that possesses DNA helicase activity."
  * Added definition dbxref GOC:mah to GO:0033202
  * Copied GO:0033202 to GO:0044424 with type OBO_REL:is_a
  * Copied GO:0033202 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033202
* Populated new object GO:0033203 (macro)
  * Changed name of GO:0033203 from "<new term>" to "DNA helicase A complex"
  * Set definition of GO:0033203 to "A homohexameric protein complex that possesses DNA helicase activity; associates with DNA polymerase alpha-primase and translocates in the 5' to 3' direction."
  * Added definition dbxref PMID:9341218 to GO:0033203
  * Copied GO:0033203 to GO:0044428 with type OBO_REL:is_a
  * Copied GO:0033203 to GO:0033202 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033203
* Populated new object GO:0060123 (macro)
  * Changed name of GO:0060123 from "<new term>" to "regulation of growth hormone secretion"
  * Set definition of GO:0060123 to "Any process that modulates the frequency, rate or extent of the regulated release of growth hormone from a cell or group of cells."
  * Added definition dbxref GOC:dph to GO:0060123
  * Copied GO:0060123 to GO:0030252 with type part_of
  * Copied GO:0060123 to GO:0046883 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060123
* Populated new object GO:0060124 (macro)
  * Changed name of GO:0060124 from "<new term>" to "positive regulation of growth hormone secretion"
  * Set definition of GO:0060124 to "Any process that increases the frequency, rate or extent of the
regulated release of growth hormone from a cell or group of cells."
  * Added definition dbxref GOC:dph to GO:0060124
  * Copied GO:0060124 to GO:0060123 with type OBO_REL:is_a
  * Copied GO:0060124 to GO:0046887 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060124
* Populated new object GO:0060125 (macro)
  * Changed name of GO:0060125 from "<new term>" to "negative regulation of growth hormone secretion"
  * Set definition of GO:0060125 to "Any process that decreases or stops the frequency, rate or extent of the
regulated release of growth hormone from a cell or group of cells."
  * Added definition dbxref GOC:dph to GO:0060125
  * Copied GO:0060125 to GO:0046888 with type OBO_REL:is_a
  * Copied GO:0060125 to GO:0060123 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060125
* Changed definition of GO:0000347 from "The THO complex is an oligomeric complex, primarily located in the nucleus, that is involved in transcription elongation by RNA polymerase II and is crucial for transcription of certain coding regions. The complex, though not each of the individual subunits, is found in a range of eukaryotic organisms, from S. cerevisiae to metazoans." to "The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1, Tho2, Thp1, and Mft1, while the human complex is composed of 7 subunits."
* Added definition dbxref PMID:11979277 to GO:0000347
* Added definition dbxref PMID:16983072 to GO:0000347
* Deleted GO:0000347 --part_of--> GO:0000346
* Deleted GO:0000817 --OBO_REL:is_a--> GO:0005875
* Changed definition of GO:0000818 from "A multiprotein complex in yeast consisting of Mtw1p, Nnf1p, Nsl1p, and Dsn1. This complex bridges the subunits that are in contact with centromeric DNA and the subunits bound to microtubules during kinetochore assembly." to "A multiprotein kinetochore subcomplex that binds to centromeric chromatin and forms part of the inner kinetochore. It helps to recruit outer kinetochore subunits that will bind to microtubules. The MIND complex is nuclear localized as the nuclear envelope is not broken down during mitosis. In S. cerevisiae, it consists of at least four proteins: Mtw1p, Nnf1p, Nsl1p, and Dsn1."
* Added definition dbxref GOC:krc to GO:0000818
* Deleted GO:0000818 --OBO_REL:is_a--> GO:0005875
* Copied GO:0000818 to GO:0000444 with type OBO_REL:is_a
* Copied GO:0001839 to GO:0001840 with type part_of
* Deleted GO:0001840 --part_of--> GO:0001839
* Changed definition of GO:0003678 from "Catalysis of the hydrolysis of ATP to unwind the DNA helix at the replication fork, allowing the resulting single strands to be copied." to "Catalysis of the hydrolysis of an NTP or dNTP to unwind the DNA helix."
* Added definition dbxref GOC:mah to GO:0003678
* Changed definition of GO:0006269 from "The generation, by DNA polymerase alpha, of an RNA primer followed by a short segment of DNA on the lagging strand of the replicating DNA." to "The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis."
* Deleted definition dbxref GOC:jl from GO:0006269
* Deleted definition dbxref PMID:12424238 from GO:0006269
* Added definition dbxref PMID:11395402 to GO:0006269
* Deleted GO:0006269 --part_of--> GO:0006273
* Copied GO:0006269 to GO:0006261 with type part_of
* Set definition of GO:0017117 to "A protein complex that possesses single-stranded DNA-dependent DNA helicase activity."
* Added definition dbxref GOC:mah to GO:0017117
* Deleted GO:0017117 --OBO_REL:is_a--> GO:0044428
* Copied GO:0017117 to GO:0033202 with type OBO_REL:is_a
* Copied GO:0031011 to GO:0033202 with type OBO_REL:is_a
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"


From gocvs at genome.Stanford.EDU  Tue May 15 21:30:41 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Tue, 15 May 2007 21:30:41 -0700 (PDT)
Subject: [go-diff] GO update 05/15/2007
Message-ID: <200705160430.VAA23795@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.324 by 5.325

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033204
* Created object of type obo:TERM with id GO:0033205
* Created object of type obo:TERM with id GO:0033206
* Created object of type obo:TERM with id GO:0033207
* Created object of type obo:TERM with id GO:0033208
* Created object of type obo:TERM with id GO:0033209
* Created object of type obo:TERM with id GO:0033210
* Created object of type obo:TERM with id GO:0033211
* Populated new object GO:0033204 (macro)
  * Changed name of GO:0033204 from "<new term>" to "ribonuclease P RNA binding"
  * Set definition of GO:0033204 to "Interacting selectively with the RNA subunit of ribonuclease P."
  * Added definition dbxref GOC:pg to GO:0033204
  * Added definition dbxref PMID:11455963 to GO:0033204
  * Added synonym "RNase P RNA binidng" to GO:0033204
  * Changed synonym scope of GO:0033204 from "Related" to "Exact"
  * Copied GO:0033204 to GO:0003723 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033204
* Populated new object GO:0033205 (macro)
  * Changed name of GO:0033205 from "<new term>" to "cytokinesis during cell cycle"
  * Set definition of GO:0033205 to "The set of processes that occur in the context of cell cycle progression and result in the division of the cytoplasm of a cell and its separation into two daughter cells."
  * Added definition dbxref GOC:mah to GO:0033205
  * Copied GO:0033205 to GO:0000910 with type OBO_REL:is_a
  * Copied GO:0033205 to GO:0000279 with type part_of
  * Assigned namespace "biological_process" to GO:0033205
* Populated new object GO:0033206 (macro)
  * Changed name of GO:0033206 from "<new term>" to "cytokinesis after meiosis"
  * Set definition of GO:0033206 to "The processes resulting in the division of the cytoplasm of a cell after meiosis, resulting in the separation of the original cell into two daughter cells."
  * Added definition dbxref GOC:mah to GO:0033206
  * Copied GO:0033206 to GO:0033205 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033206
* Populated new object GO:0033207 (macro)
  * Changed name of GO:0033207 from "<new term>" to "beta-1,4-N-acetylgalactosaminyltransferase activity"
  * Set definition of GO:0033207 to "Catalysis of the transfer of an N-acetylgalactosaminyl residue from UDP-N-acetyl-galactosamine to an acceptor molecule, forming a beta-1,4 linkage."
  * Added definition dbxref GOC:mah to GO:0033207
  * Added synonym "beta-1,4-GalNAc transferase activity" to GO:0033207
  * Changed synonym scope of GO:0033207 from "Related" to "Exact"
  * Copied GO:0033207 to GO:0008376 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033207
* Populated new object GO:0033208 (macro)
  * Changed name of GO:0033208 from "<new term>" to "UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity"
  * Set definition of GO:0033208 to "Catalysis of the reaction: UDP-N-acetylgalactosamine + N-acetylneuraminyl-alpha-2,3-galactosyl-beta-oligosaccharide = UDP + N-acetylgalactosaminyl-N-acetylneuraminyl-alpha-2,3-galactosyl-beta-oligosaccharide."
  * Added definition dbxref GOC:mah to GO:0033208
  * Added definition dbxref PMID:12678917 to GO:0033208
  * Added definition dbxref PMID:16024623 to GO:0033208
  * Added synonym "Sda beta 1,4GalNAc transferase" to GO:0033208
  * Added synonym "UDP-GalNAc:Neu5Ac-alpha-2-Gal-beta-1-R beta-1,4-N-acetylgalactosaminyltransferase activity" to GO:0033208
  * Changed synonym scope of GO:0033208 from "Related" to "Exact"
  * Copied GO:0033208 to GO:0033207 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033208
* Populated new object GO:0033209 (macro)
  * Changed name of GO:0033209 from "<new term>" to "tumor necrosis factor-mediated signaling pathway"
  * Set definition of GO:0033209 to "A series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor."
  * Added definition dbxref GOC:mah to GO:0033209
  * Added synonym "adipocytokine signaling pathway" to GO:0033209
  * Added synonym "TNF-alpha-mediated signaling pathway" to GO:0033209
  * Changed synonym scope of GO:0033209 from "Related" to "Exact"
  * Added synonym "tumor necrosis factor alpha-mediated signaling pathway" to GO:0033209
  * Changed synonym scope of GO:0033209 from "Related" to "Exact"
  * Copied GO:0033209 to GO:0019221 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033209
* Populated new object GO:0033210 (macro)
  * Changed name of GO:0033210 from "<new term>" to "leptin-mediated signaling pathway"
  * Set definition of GO:0033210 to "A series of molecular signals generated as a consequence of leptin binding to a cell surface receptor."
  * Added definition dbxref GOC:mah to GO:0033210
  * Added synonym "adipocytokine signaling pathway" to GO:0033210
  * Copied GO:0033210 to GO:0019221 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033210
* Populated new object GO:0033211 (macro)
  * Changed name of GO:0033211 from "<new term>" to "adiponectin-mediated signaling pathway"
  * Set definition of GO:0033211 to "A series of molecular signals generated as a consequence of adiponectin binding to a cell surface receptor."
  * Added definition dbxref GOC:mah to GO:0033211
  * Added synonym "adipocytokine signaling pathway" to GO:0033211
  * Copied GO:0033211 to GO:0019221 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033211
* Deleted GO:0000281 --OBO_REL:is_a--> GO:0000910
* Copied GO:0000281 to GO:0033205 with type OBO_REL:is_a
* Copied GO:0000444 to GO:0043234 with type OBO_REL:is_a
* Deleted GO:0000911 --OBO_REL:is_a--> GO:0000910
* Copied GO:0000911 to GO:0033205 with type OBO_REL:is_a
* Copied GO:0000912 to GO:0033205 with type part_of
* Copied GO:0000916 to GO:0033205 with type part_of
* Changed definition of GO:0005856 from "Any of the various filamentous elements that form the internal framework of eukaryotic cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." to "Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles."
* Added definition dbxref PMID:16959967 to GO:0005856
* Deleted GO:0007110 --OBO_REL:is_a--> GO:0040038
* Copied GO:0007110 to GO:0033206 with type OBO_REL:is_a
* Deleted GO:0007111 --OBO_REL:is_a--> GO:0040038
* Copied GO:0007111 to GO:0033206 with type OBO_REL:is_a
* Deleted GO:0007112 --OBO_REL:is_a--> GO:0000910
* Copied GO:0007112 to GO:0033206 with type OBO_REL:is_a
* Changed definition of GO:0007202 from "The series of molecular signals that results in the upregulation of phospholipase C activity in response to the signal." to "The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand."
* Set definition of GO:0008262 to "Interacting selectively with importin-alpha to mediate its transfer across the nuclear membrane to the cytoplasm."
* Added definition dbxref GOC:mah to GO:0008262
* Added definition dbxref PMID:12486120 to GO:0008262
* Added synonym "importin-alpha binding" to GO:0008262
* Added synonym "GlcNAc transferase activity" to GO:0008375
* Changed synonym scope of GO:0008375 from "Related" to "Exact"
* Added synonym "GalNAc transferase activity" to GO:0008376
* Changed synonym scope of GO:0008376 from "Related" to "Exact"
* Changed name of GO:0009356 from "p-aminobenzoate synthetase complex" to "aminodeoxychorismate synthase complex"
* Set definition of GO:0009356 to "A heterodimeric protein complex that possesses 4-amino-4-deoxychorismate synthase activity."
* Added definition dbxref PMID:2251281 to GO:0009356
* Added definition dbxref PMID:7592344 to GO:0009356
* Added synonym "4-amino-4-deoxychorismate synthase complex" to GO:0009356
* Added synonym "ADC synthase complex" to GO:0009356
* Changed synonym scope of GO:0009356 from "Related" to "Exact"
* Added synonym "p-aminobenzoate synthetase complex" to GO:0009356
* Deleted GO:0009356 --OBO_REL:is_a--> GO:0005941
* Copied GO:0009356 to GO:0043234 with type OBO_REL:is_a
* Copied GO:0009356 to GO:0044424 with type OBO_REL:is_a
* Set definition of GO:0009376 to "A protein complex that possesses ATP-dependent protease activity; consists of an ATPase large subunit with homology to other Clp family ATPases and a peptidase small subunit related to the proteasomal beta-subunits of eukaryotes. In the E. coli complex, six identical subunits of both the ATPase, ClpY, and the protease, ClpQ, self-assemble into an oligomeric ring, and two rings of each subunit, two ClpQ rings surrounded by single ClpY rings, form a dumbbell-shaped complex."
* Added definition dbxref PMID:12670962 to GO:0009376
* Added synonym "ClpYQ protease complex" to GO:0009376
* Changed synonym scope of GO:0009376 from "Related" to "Exact"
* Set definition of GO:0009379 to "A DNA helicase complex that forms part of a Holliday junction resolvase complex, where the helicase activity is involved in the migration of the junction branch point. The best-characterized example is the E. coli RuvAB complex, in which a hexamer of RuvB subunits possesses helicase activity that is modulated by association with RuvA ."
* Added definition dbxref PMID:16935884 to GO:0009379
* Added definition dbxref PMID:9442895 to GO:0009379
* Deleted GO:0009379 --OBO_REL:is_a--> GO:0005941
* Copied GO:0009379 to GO:0043234 with type OBO_REL:is_a
* Copied GO:0009379 to GO:0048476 with type part_of
* Deleted GO:0010069 --OBO_REL:is_a--> GO:0000910
* Copied GO:0010069 to GO:0033205 with type OBO_REL:is_a
* Copied GO:0031566 to GO:0033205 with type part_of
* Copied GO:0032186 to GO:0033205 with type part_of
* Added synonym "alpha-1,4-GalNAc transferase activity" to GO:0035248
* Changed synonym scope of GO:0035248 from "Related" to "Exact"
* Deleted GO:0040038 --OBO_REL:is_a--> GO:0000910
* Copied GO:0040038 to GO:0033206 with type OBO_REL:is_a
* Changed definition of GO:0048476 from "An endonuclease complex that resolves Holliday junctions by a nick and counternick mechanism." to "A protein complex that mediates the conversion of a Holliday junction into two separate duplex DNA molecules; the complex includes a single- or multisubunit helicase that catalyzes the extension of heteroduplex DNA by branch migration and a nuclease that resolves the junction by nucleolytic cleavage."
* Deleted definition dbxref GOC:vw from GO:0048476
* Deleted definition dbxref PMID:14527419 from GO:0048476
* Added definition dbxref PMID:11207366 to GO:0048476
* Added definition dbxref PMID:12374758 to GO:0048476
* Added synonym "resolvasome" to GO:0048476
* Added general dbxref PMID:11207366 to synonym resolvasome of GO:0048476
* Changed synonym scope of GO:0048476 from "Related" to "Exact"
* Deleted GO:0048476 --OBO_REL:is_a--> GO:0005941
* Copied GO:0048476 to GO:0043234 with type OBO_REL:is_a
* Copied GO:0048476 to GO:0044424 with type OBO_REL:is_a
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"


From gocvs at genome.Stanford.EDU  Wed May 16 21:30:39 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Wed, 16 May 2007 21:30:39 -0700 (PDT)
Subject: [go-diff] GO update 05/16/2007
Message-ID: <200705170430.VAA23896@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.325 by 5.326

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033212
* Created object of type obo:TERM with id GO:0033213
* Created object of type obo:TERM with id GO:0033214
* Created object of type obo:TERM with id GO:0033215
* Created object of type obo:TERM with id GO:0033216
* Created object of type obo:TERM with id GO:0033217
* Created object of type obo:TERM with id GO:0033218
* Created object of type obo:TERM with id GO:0033219
* Created object of type obo:TERM with id GO:0033220
* Created object of type obo:TERM with id GO:0033221
* Created object of type obo:TERM with id GO:0033222
* Populated new object GO:0033212 (macro)
  * Changed name of GO:0033212 from "<new term>" to "iron assimilation"
  * Set definition of GO:0033212 to "A process by which iron is solubilized and transported into a cell."
  * Added definition dbxref GOC:mah to GO:0033212
  * Copied GO:0033212 to GO:0006879 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033212
* Populated new object GO:0033213 (macro)
  * Changed name of GO:0033213 from "<new term>" to "iron assimilation by capture and transport"
  * Set definition of GO:0033213 to "A process by which iron (Fe3+) is solubilized by binding to a receptor or transport protein and transported into a cell."
  * Added definition dbxref GOC:mah to GO:0033213
  * Copied GO:0033213 to GO:0033212 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033213
* Populated new object GO:0033214 (macro)
  * Changed name of GO:0033214 from "<new term>" to "iron assimilation by chelation and transport"
  * Set definition of GO:0033214 to "A process by which iron (Fe3+) is solubilized by ferric iron-specific chelators, known as siderophores, excreted by a cell; the iron-siderophore complex is then transported into the cell by specific cell surface receptors."
  * Added definition dbxref GOC:mah to GO:0033214
  * Added definition dbxref PMID:16963626 to GO:0033214
  * Copied GO:0033214 to GO:0033212 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033214
* Populated new object GO:0033215 (macro)
  * Changed name of GO:0033215 from "<new term>" to "iron assimilation by reduction and transport"
  * Set definition of GO:0033215 to "A process by which iron is solubilized by reduction from Fe3+ to Fe2+ via a cell surface reductase and subsequent transport of the iron across the membrane by iron uptake proteins."
  * Added definition dbxref GOC:mah to GO:0033215
  * Added definition dbxref PMID:16963626 to GO:0033215
  * Copied GO:0033215 to GO:0033212 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033215
* Populated new object GO:0033216 (macro)
  * Changed name of GO:0033216 from "<new term>" to "ferric iron import"
  * Set definition of GO:0033216 to "The directed movement of ferric iron (Fe(III) or Fe3+) ions into a cell or organelle."
  * Added definition dbxref GOC:mah to GO:0033216
  * Added synonym "ferric ion import" to GO:0033216
  * Changed synonym scope of GO:0033216 from "Related" to "Exact"
  * Added synonym "ferric iron uptake" to GO:0033216
  * Changed synonym scope of GO:0033216 from "Related" to "Exact"
  * Copied GO:0033216 to GO:0015682 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033216
* Populated new object GO:0033217 (macro)
  * Changed name of GO:0033217 from "<new term>" to "regulation of transcription from RNA polymerase II promoter in response to iron ion starvation"
  * Set definition of GO:0033217 to "Modulation of the frequency, rate or extent of transcription from an from RNA polymerase II promoter as a result of a stimulus indicating the organism is deprived of iron ions."
  * Added definition dbxref GOC:mah to GO:0033217
  * Added synonym "regulation of transcription from RNA polymerase II promoter in response to iron deficiency" to GO:0033217
  * Changed synonym scope of GO:0033217 from "Related" to "Exact"
  * Copied GO:0033217 to GO:0006979 with type OBO_REL:is_a
  * Copied GO:0033217 to GO:0043618 with type OBO_REL:is_a
  * Copied GO:0033217 to GO:0010106 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033217
* Populated new object GO:0033218 (macro)
  * Changed name of GO:0033218 from "<new term>" to "amide binding"
  * Set definition of GO:0033218 to "Interacting selectively with an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group."
  * Added definition dbxref ChEBI:32988 to GO:0033218
  * Added definition dbxref GOC:mah to GO:0033218
  * Copied GO:0033218 to GO:0005488 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033218
* Populated new object GO:0033219 (macro)
  * Changed name of GO:0033219 from "<new term>" to "urea binding"
  * Set definition of GO:0033219 to "Interacting selectively with urea, a water-soluble carboxamide with the structure H2N-CO-NH2."
  * Added definition dbxref ChEBI:16199 to GO:0033219
  * Added definition dbxref GOC:mah to GO:0033219
  * Added definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) to GO:0033219
  * Copied GO:0033219 to GO:0033218 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033219
* Populated new object GO:0033220 (macro)
  * Changed name of GO:0033220 from "<new term>" to "amide-transporting ATPase activity"
  * Set definition of GO:0033220 to "Catalysis of the reaction: ATP + H2O + amide(out) = ADP + phosphate + amide(in)."
  * Added definition dbxref GOC:mah to GO:0033220
  * Added GO:0033220 to category gosubset_prok
  * Copied GO:0033220 to GO:0042626 with type OBO_REL:is_a
  * Copied GO:0033220 to GO:0042887 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033220
* Populated new object GO:0033221 (macro)
  * Changed name of GO:0033221 from "<new term>" to "urea-transporting ATPase activity"
  * Set definition of GO:0033221 to "Catalysis of the reaction: ATP + H2O + urea(out) = ADP + phosphate + urea(in)."
  * Added definition dbxref GOC:mlg to GO:0033221
  * Added GO:0033221 to category gosubset_prok
  * Added synonym "carbamide-transporting ATPase activity" to GO:0033221
  * Changed synonym scope of GO:0033221 from "Related" to "Exact"
  * Copied GO:0033221 to GO:0015204 with type OBO_REL:is_a
  * Copied GO:0033221 to GO:0033220 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033221
* Populated new object GO:0033222 (macro)
  * Changed name of GO:0033222 from "<new term>" to "xylose binding"
  * Set definition of GO:0033222 to "Interacting selectively with the D- or L-enantiomer of xylose."
  * Added definition dbxref GOC:mah to GO:0033222
  * Added GO:0033222 to category gosubset_prok
  * Copied GO:0033222 to GO:0048029 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033222
* Added synonym "Mis12 complex" to GO:0000444
* Changed synonym scope of GO:0000444 from "Related" to "Narrow"
* Changed definition of GO:0000446 from "The THO complex when it is acting as a nuclear complex that is required for
transcription elongation through genes containing tandemly repeated DNA sequences. In S. cerevisiae, it is composed of four subunits: Hpr1, Tho2, Thp1, and Mft1, while the human complex is composed of 7 subunits." to "The THO complex when it is acting as a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. In S. cerevisiae, it is composed of four subunits: Hpr1, Tho2, Thp1, and Mft1, while the human complex is composed of 7 subunits."
* Deleted GO:0006881 --part_of--> GO:0006879
* Copied GO:0006881 to GO:0033212 with type part_of
* added secondary id GO:0009572 to GO:0009510
* Changed definition of GO:0009510 from "A narrow cylindrical tubule that runs through the center of a plasmodesma connecting two cells. The latter appears to be continuous with elements of the endoplasmic reticulum membrane of the interconnected cells." to "A tightly wound cylinder of membrane that is located within the plasmodesmal pore and runs the length of the plasmodesma. The desmotubule likely provides a rigid stability to plasmodesmata and confers a fixed diameter and pore size to the plasmodesmal canal, and is linked to the endoplasmic reticulum in each of the adjacent cell."
* Deleted definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) from GO:0009510
* Added definition dbxref http://biology.kenyon.edu/edwards/project/greg/pd.htm to GO:0009510
* Added synonym "desmotubule central rod" to GO:0009510
* Copied GO:0009510 to GO:0044459 with type OBO_REL:is_a
* Set definition of GO:0009546 to "The space between the plasma membrane and the desmotubule of a plasmodesma."
* Added definition dbxref http://biology.kenyon.edu/edwards/project/greg/pd.htm to GO:0009546
* Set definition of GO:0009548 to "The portion of the plasma membrane surrounding a plasmodesma."
* Added definition dbxref GOC:mah to GO:0009548
* Set definition of GO:0009550 to "A plasmodesma that consists of a simple, single channel; found predominantly in young tissue and formed as a function of cell plate formation during cytokinesis."
* Added definition dbxref PMID:15012255 to GO:0009550
* Added synonym "simple plasmodesma" to GO:0009550
* Changed synonym scope of GO:0009550 from "Related" to "Exact"
* Set definition of GO:0009551 to "A plasmodesma with a branched structure, often with many channels leading into a larger central cavity; found in older tissues and usually derived from preexisting primary plasmodesmata."
* Added definition dbxref PMID:15012255 to GO:0009551
* Deleted GO:0009572 --OBO_REL:is_a--> GO:0044459
* Deleted GO:0009572 --part_of--> GO:0009510
* Destroyed object GO:0009572
* Set definition of GO:0009654 to "A complex, composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins, that catalyzes the splitting of water to O2 and 4 H+. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ)."
* Added definition dbxref InterPro:IPR002683 to GO:0009654
* Deleted GO:0015204 --OBO_REL:is_a--> GO:0005275
* Copied GO:0015204 to GO:0042887 with type OBO_REL:is_a
* Added synonym "ferric ion transport" to GO:0015682
* Changed synonym scope of GO:0015682 from "Related" to "Exact"
* Added synonym "ferrous ion transport" to GO:0015684
* Changed synonym scope of GO:0015684 from "Related" to "Exact"
* Deleted GO:0015840 --OBO_REL:is_a--> GO:0015837
* Copied GO:0015840 to GO:0042886 with type OBO_REL:is_a
* Copied GO:0015892 to GO:0033214 with type part_of
* Changed definition of GO:0016533 from "Activates cyclin-dependent kinase 5; composed of regulatory and catalytic subunits." to "A protein complex that activates cyclin-dependent kinase 5; composed of regulatory and catalytic subunits."
* Deleted GO:0019627 --OBO_REL:is_a--> GO:0006807
* Copied GO:0019627 to GO:0043603 with type OBO_REL:is_a
* Set definition of GO:0019907 to "A protein complex that phosphorylates cyclin-dependent kinases such as Cdc2 on Thr161 (or an equivalent residue); contains a catalytic subunit and a regulatory subunit, and some examples also include an assembly factor."
* Added definition dbxref GOC:mah to GO:0019907
* Added definition dbxref PMID:8752210 to GO:0019907
* Added synonym "CAK complex" to GO:0019907
* Changed synonym scope of GO:0019907 from "Related" to "Exact"
* Added synonym "CDK-activating kinase complex" to GO:0019907
* Changed synonym scope of GO:0019907 from "Related" to "Exact"
* Changed definition of GO:0033191 from "Catalysis of the reaction: a
2-pyrone + oxalacetate = macrophomate." to "Catalysis of the reaction: a 2-pyrone + oxalacetate = macrophomate."
* Changed definition of GO:0033200 from "Catalysis of the reaction: ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = 4,5-bisdiphosphoinositol-1D-myoinositol (1,2,3,6)tetrakisphosphate, or ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = 5,6-bisdiphosphoinositol-1D-myoinositol
(1,2,3,4)tetrakisphosphate." to "Catalysis of the reaction: ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = 4,5-bisdiphosphoinositol-1D-myoinositol (1,2,3,6)tetrakisphosphate, or ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = 5,6-bisdiphosphoinositol-1D-myoinositol (1,2,3,4)tetrakisphosphate."
* Deleted definition dbxref ISBN:0781735149 from GO:0042101
* Added definition dbxref Fundamental Immunology (ISBN:0781735149) to GO:0042101
* Deleted definition dbxref ISBN:0781735149 from GO:0042105
* Added definition dbxref Fundamental Immunology (ISBN:0781735149) to GO:0042105
* Deleted definition dbxref ISBN:0781735149 from GO:0042106
* Added definition dbxref Fundamental Immunology (ISBN:0781735149) to GO:0042106
* Changed comment from "Note that although this complex has so far only been described in Saccharomyces, it is likely to be conserved in other eukaryotes." to "Note that this complex is conserved in fungi but has not been observed in metazoans."
* 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 chromosome segregation and spindle stability." to "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."
* Copied GO:0043419 to GO:0043605 with type OBO_REL:is_a
* Copied GO:0043603 to GO:0006807 with type OBO_REL:is_a
* Changed synonym scope of GO:0051091 from "Narrow" to "Exact"
* Changed definition of GO:0060113 from "The process whereby relatively unspecialized cells, acquire specialized structural and/or functional features of inner ear receptor cells. Inner ear receptor cells are mechanorecptors found in the inner ear responsible for transducing signals involved in balance and sensory perception of sound." to "The process whereby relatively unspecialized cells acquire specialized structural and/or functional features of inner ear receptor cells. Inner ear receptor cells are mechanorecptors found in the inner ear responsible for transducing signals involved in balance and sensory perception of sound."
* Deleted synonym "<new synonym>" from GO:0060113
* Deleted synonym "<new synonym>" from GO:0060114
* Changed definition of GO:0060115 from "xx" to "The process by which a cell becomes committed to become a vestibular receptor cell."
* Changed definition of GO:0060116 from "xx" to "Any process that alters the mass volume or shape of a vestibular receptor cell."
* Changed definition of GO:0060124 from "Any process that increases the frequency, rate or extent of the
regulated release of growth hormone from a cell or group of cells." to "Any process that increases the frequency, rate or extent of the regulated release of growth hormone from a cell or group of cells."
* Changed definition of GO:0060125 from "Any process that decreases or stops the frequency, rate or extent of the
regulated release of growth hormone from a cell or group of cells." to "Any process that decreases or stops the frequency, rate or extent of the regulated release of growth hormone from a cell or group of cells."


From gocvs at genome.Stanford.EDU  Thu May 17 21:30:38 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Thu, 17 May 2007 21:30:38 -0700 (PDT)
Subject: [go-diff] GO update 05/17/2007
Message-ID: <200705180430.VAA05395@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.326 by 5.327

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0060126
* Created object of type obo:TERM with id GO:0060127
* Created object of type obo:TERM with id GO:0060128
* Created object of type obo:TERM with id GO:0060129
* Created object of type obo:TERM with id GO:0060130
* Created object of type obo:TERM with id GO:0060131
* Created object of type obo:TERM with id GO:0060132
* Created object of type obo:TERM with id GO:0060133
* Populated new object GO:0060126 (macro)
  * Changed name of GO:0060126 from "<new term>" to "somatotropin secreting cell differentiation"
  * Set definition of GO:0060126 to "The process whereby a relatively unspecialized cell, acquires specialized structural and/or functional features of a somatotropin secreting cell. A somatotropin secreting cell is an acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin."
  * Added definition dbxref GOC:dph to GO:0060126
  * Added synonym "growth hormone secreting cell differentiation" to GO:0060126
  * Added synonym "somatotrope differentiation" to GO:0060126
  * Added synonym "somatotroph differentiation" to GO:0060126
  * Added synonym "somatotrophin secreting cell differentiation" to GO:0060126
  * Added synonym "somatotropic cell differentiation" to GO:0060126
  * Added synonym "somatrophic cell differentiation" to GO:0060126
  * Copied GO:0060126 to GO:0021984 with type part_of
  * Copied GO:0060126 to GO:0030154 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060126
* Populated new object GO:0060127 (macro)
  * Changed name of GO:0060127 from "<new term>" to "prolactin secreting cell differentiation"
  * Set definition of GO:0060127 to "The process whereby a relatively unspecialized cell, acquires specialized structural and/or functional features of a prolactin secreting cell. A prolactin secreting cell is an acidophilic cell of the anterior pituitary that produces prolactin."
  * Added definition dbxref GOC:dph to GO:0060127
  * Added synonym "epsilon-acidophil differentiation" to GO:0060127
  * Changed synonym scope of GO:0060127 from "Related" to "Exact"
  * Added synonym "lactotrope differentiation" to GO:0060127
  * Changed synonym scope of GO:0060127 from "Related" to "Exact"
  * Added synonym "lactotroph differentiation" to GO:0060127
  * Changed synonym scope of GO:0060127 from "Related" to "Exact"
  * Added synonym "lactotropic cell differentiation" to GO:0060127
  * Changed synonym scope of GO:0060127 from "Related" to "Exact"
  * Added synonym "mammotrope differentiation" to GO:0060127
  * Changed synonym scope of GO:0060127 from "Related" to "Exact"
  * Added synonym "mammotroph differentiation" to GO:0060127
  * Changed synonym scope of GO:0060127 from "Related" to "Exact"
  * Added synonym "mammotrophic cell differentiation" to GO:0060127
  * Changed synonym scope of GO:0060127 from "Related" to "Exact"
  * Added synonym "mammotropic cell differentiation" to GO:0060127
  * Changed synonym scope of GO:0060127 from "Related" to "Exact"
  * Copied GO:0060127 to GO:0030154 with type OBO_REL:is_a
  * Copied GO:0060127 to GO:0021984 with type part_of
  * Assigned namespace "biological_process" to GO:0060127
* Populated new object GO:0060128 (macro)
  * Changed name of GO:0060128 from "<new term>" to "adrenocorticotropic hormone secreting cell differentiation"
  * Set definition of GO:0060128 to "The process whereby a relatively unspecialized cell, acquires specialized structural and/or functional features of a adrenocorticotropic hormone secreting cell. An adrenocorticotropic hormone secreting cell is a basophil cell of the anterior pituitary that produces adrenocorticotropic hormone, or corticotropin."
  * Added definition dbxref GOC:dph to GO:0060128
  * Added synonym "adrenocorticotrophic hormone secreting cell differentiation" to GO:0060128
  * Changed synonym scope of GO:0060128 from "Related" to "Exact"
  * Added synonym "corticotrope differentiation" to GO:0060128
  * Changed synonym scope of GO:0060128 from "Related" to "Exact"
  * Added synonym "corticotroph differentiation" to GO:0060128
  * Changed synonym scope of GO:0060128 from "Related" to "Exact"
  * Added synonym "corticotrophin hormone secreting cell differentiation" to GO:0060128
  * Added synonym "corticotropin hormone secreting cell differentiation" to GO:0060128
  * Copied GO:0060128 to GO:0021984 with type part_of
  * Copied GO:0060128 to GO:0030154 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060128
* Populated new object GO:0060129 (macro)
  * Changed name of GO:0060129 from "<new term>" to "thyroid stimulating hormone secreting cell differentiation"
  * Set definition of GO:0060129 to "The process whereby a relatively unspecialized cell, acquires specialized structural and/or functional features of a adrenocorticotropi hormone secreting cell. A thyroid stimulating hormone secreting cell is a basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin."
  * Added definition dbxref GOC:dph to GO:0060129
  * Added synonym "beta-basophil differentiation" to GO:0060129
  * Changed synonym scope of GO:0060129 from "Related" to "Exact"
  * Added synonym "thyrotrope differentiation" to GO:0060129
  * Changed synonym scope of GO:0060129 from "Related" to "Exact"
  * Added synonym "thyrotroph differentiation" to GO:0060129
  * Changed synonym scope of GO:0060129 from "Related" to "Exact"
  * Copied GO:0060129 to GO:0030154 with type OBO_REL:is_a
  * Copied GO:0060129 to GO:0021984 with type part_of
  * Assigned namespace "biological_process" to GO:0060129
* Populated new object GO:0060130 (macro)
  * Changed name of GO:0060130 from "<new term>" to "thyroid stimulating hormone secreting cell development"
  * Set definition of GO:0060130 to "The process whose specific outcome is the progression of a thyroid stimulating hormone secreting cell over time, from its formation to the mature structure. A thyroid stimulating hormone secreting cell is a basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin."
  * Added definition dbxref GOC:dph to GO:0060130
  * Added synonym "beta-basophil development" to GO:0060130
  * Changed synonym scope of GO:0060130 from "Related" to "Exact"
  * Added synonym "thyrotrope development" to GO:0060130
  * Changed synonym scope of GO:0060130 from "Related" to "Exact"
  * Added synonym "thyrotroph development" to GO:0060130
  * Changed synonym scope of GO:0060130 from "Related" to "Exact"
  * Copied GO:0060130 to GO:0048468 with type OBO_REL:is_a
  * Copied GO:0060130 to GO:0060129 with type part_of
  * Assigned namespace "biological_process" to GO:0060130
* Populated new object GO:0060131 (macro)
  * Changed name of GO:0060131 from "<new term>" to "adrenocorticotropic hormone secreting cell development"
  * Set definition of GO:0060131 to "The process whose specific outcome is the progression of a adrenocorticotropic hormone secreting cell over time, from its formation to the mature structure. An adrenocorticotropic hormone secreting cell is a basophil cell of the anterior pituitary that produces adrenocorticotropic hormone, or corticotropin."
  * Added definition dbxref GOC:dph to GO:0060131
  * Added synonym "adrenocorticotrophic hormone secreting cell development" to GO:0060131
  * Changed synonym scope of GO:0060131 from "Related" to "Exact"
  * Added synonym "corticotrope development" to GO:0060131
  * Changed synonym scope of GO:0060131 from "Related" to "Exact"
  * Added synonym "corticotroph development" to GO:0060131
  * Added synonym "corticotrophin hormone secreting cell development" to GO:0060131
  * Added synonym "corticotropin hormone secreting cell development" to GO:0060131
  * Copied GO:0060131 to GO:0060128 with type part_of
  * Copied GO:0060131 to GO:0048468 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060131
* Populated new object GO:0060132 (macro)
  * Changed name of GO:0060132 from "<new term>" to "prolactin secreting cell development"
  * Set definition of GO:0060132 to "The process whose specific outcome is the progression of a prolactin secreting cell over time, from its formation to the mature structure. A prolactin se