[Go-diff] GO update 09/17/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Wed Sep 17 21:30:46 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.216 by 1.218

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010704
* Created object of type obo:TERM with id GO:0010705
* Created object of type obo:TERM with id GO:0010706
* Created object of type obo:TERM with id GO:0010707
* Created object of type obo:TERM with id GO:0010708
* Created object of type obo:TERM with id GO:0010709
* Created object of type obo:TERM with id GO:0034986
* Created object of type obo:TERM with id GO:0034987
* Created object of type obo:TERM with id GO:0034988
* Created object of type obo:TERM with id GO:0034989
* Created object of type obo:TERM with id GO:0034990
* Created object of type obo:TERM with id GO:0034991
* Created object of type obo:TERM with id GO:0034992
* Created object of type obo:TERM with id GO:0034993
* Created object of type obo:TERM with id GO:0034994
* Populated new object GO:0010704 (macro)
  * Changed name of GO:0010704 from "<new term>" to "meiotic DNA double-strand break processing involved in meiotic gene conversion"
  * Set definition of GO:0010704 to "The cell cycle process whereby the 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang resulting in the transfer of genetic information from one helix to another."
  * Added definition dbxref GOC:dph to GO:0010704
  * Added definition dbxref GOC:tb to GO:0010704
  * Copied GO:0010704 to GO:0006311 with type part_of
  * Copied GO:0010704 to GO:0000706 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010704
* Populated new object GO:0010705 (macro)
  * Changed name of GO:0010705 from "<new term>" to "meiotic DNA double-strand break processing involved in meiotic recombination"
  * Set definition of GO:0010705 to "The cell cycle process whereby the 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang occurs resulting in double strand break formation and repair through a double Holliday junction intermediate."
  * Added definition dbxref GOC:dph to GO:0010705
  * Added definition dbxref GOC:tb to GO:0010705
  * Copied GO:0010705 to GO:0000706 with type OBO_REL:is_a
  * Copied GO:0010705 to GO:0007131 with type part_of
  * Assigned namespace "biological_process" to GO:0010705
* Populated new object GO:0010706 (macro)
  * Changed name of GO:0010706 from "<new term>" to "biosynthesis of lactosylceramide precursor to ganglioside"
  * Set definition of GO:0010706 to "The chemical reactions and pathways resulting in the formation of lactosylceramides, Gal beta(1,4)Glc beta(1,1') ceramides, any compound formed by the replacement of the glycosidic C1 hydroxyl group of lactose by a ceramide group as a precursor of gangliosides."
  * Added definition dbxref GOC:dph to GO:0010706
  * Added definition dbxref GOC:tb to GO:0010706
  * Added synonym "lactosylceramide biosynthesis leading to ganglioside" to GO:0010706
  * Added general dbxref GOC:tb to synonym lactosylceramide biosynthesis leading to ganglioside of GO:0010706
  * Added general dbxref GOC:dph to synonym lactosylceramide biosynthesis leading to ganglioside of GO:0010706
  * Added synonym "lactosylceramide biosynthetic process leading to ganglioside" to GO:0010706
  * Added general dbxref GOC:tb to synonym lactosylceramide biosynthetic process leading to ganglioside of GO:0010706
  * Added general dbxref GOC:dph to synonym lactosylceramide biosynthetic process leading to ganglioside of GO:0010706
  * Copied GO:0010706 to GO:0001574 with type OBO_REL:is_a
  * Copied GO:0010706 to GO:0001572 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010706
* Populated new object GO:0010707 (macro)
  * Changed name of GO:0010707 from "<new term>" to "biosynthesis of lactosylceramide precursor to globoside"
  * Set definition of GO:0010707 to "The chemical reactions and pathways resulting in the formation of lactosylceramides, Gal beta(1,4)Glc beta(1,1') ceramides, any compound formed by the replacement of the glycosidic C1 hydroxyl group of lactose by a ceramide group as a precursor of globosides."
  * Added definition dbxref GOC:dph to GO:0010707
  * Added definition dbxref GOC:tb to GO:0010707
  * Added synonym "lactosylceramide biosynthesis leading to globoside" to GO:0010707
  * Added general dbxref GOC:tb to synonym lactosylceramide biosynthesis leading to globoside of GO:0010707
  * Added general dbxref GOC:dph to synonym lactosylceramide biosynthesis leading to globoside of GO:0010707
  * Added synonym "lactosylceramide biosynthetic process leading to globoside" to GO:0010707
  * Added general dbxref GOC:tb to synonym lactosylceramide biosynthetic process leading to globoside of GO:0010707
  * Added general dbxref GOC:dph to synonym lactosylceramide biosynthetic process leading to globoside of GO:0010707
  * Copied GO:0010707 to GO:0001572 with type OBO_REL:is_a
  * Copied GO:0010707 to GO:0001576 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010707
* Populated new object GO:0010708 (macro)
  * Changed name of GO:0010708 from "<new term>" to "heteroduplex formation involved in gene conversion at mating-type locus"
  * Set definition of GO:0010708 to "The formation of a stable duplex DNA that contains one strand from each of the two recombining DNA molecules resulting in the conversion of the mating-type locus from one allele to another."
  * Added definition dbxref GOC:dph to GO:0010708
  * Added definition dbxref GOC:tb to GO:0010708
  * Copied GO:0010708 to GO:0007534 with type part_of
  * Copied GO:0010708 to GO:0030491 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010708
* Populated new object GO:0010709 (macro)
  * Changed name of GO:0010709 from "<new term>" to "heteroduplex formation involved in double-strand break repair via synthesis-dependent strand annealing"
  * Set definition of GO:0010709 to "The formation of a stable duplex DNA that contains one strand from each of the two recombining DNA molecules resulting in the error-free repair of a double-strand break without the exchange of adjacent sequences."
  * Added definition dbxref GOC:dph to GO:0010709
  * Added definition dbxref GOC:tb to GO:0010709
  * Copied GO:0010709 to GO:0030491 with type OBO_REL:is_a
  * Copied GO:0010709 to GO:0045003 with type part_of
  * Assigned namespace "biological_process" to GO:0010709
* Populated new object GO:0034986 (macro)
  * Changed name of GO:0034986 from "<new term>" to "iron chaperone activity"
  * Set definition of GO:0034986 to "Assists in the delivery of iron ions to target proteins or compartments."
  * Added definition dbxref GOC:vk to GO:0034986
  * Copied GO:0034986 to GO:0005506 with type OBO_REL:is_a
  * Copied GO:0034986 to GO:0016530 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034986
* Populated new object GO:0034987 (macro)
  * Changed name of GO:0034987 from "<new term>" to "immunoglobulin receptor binding"
  * Set definition of GO:0034987 to "Interacting selectively with one or more specific sites on an immunoglobulin receptor molecule."
  * Added definition dbxref GOC:vk to GO:0034987
  * Added synonym "Fc receptor binding" to GO:0034987
  * Copied GO:0034987 to GO:0005102 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034987
* Populated new object GO:0034988 (macro)
  * Changed name of GO:0034988 from "<new term>" to "Fc-gamma receptor I complex binding"
  * Set definition of GO:0034988 to "Interacting selectively with one or more specific sites on the Fc-gamma receptor I complex. The complex functions primarily as an activating receptor for IgG."
  * Added definition dbxref GOC:vk to GO:0034988
  * Copied GO:0034988 to GO:0034987 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034988
* Populated new object GO:0034989 (macro)
  * Changed name of GO:0034989 from "<new term>" to "GTP-Ral binding"
  * Set definition of GO:0034989 to "Interacting selectively with the GTP-bound form of the Ral protein."
  * Added definition dbxref GOC:vk to GO:0034989
  * Copied GO:0034989 to GO:0017160 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034989
* Populated new object GO:0034990 (macro)
  * Changed name of GO:0034990 from "<new term>" to "nuclear mitotic cohesin complex"
  * Added comment "Note that this term should be used to annotate gene products found in cohesin complexes in organisms that undergo closed mitosis (i. e. where the nuclear envelope does not break down, as in fungi). For organisms in which the nuclear envelope breaks down during mitosis, the parent should be used."
  * Set definition of GO:0034990 to "A cohesin complex that mediates sister chromatid cohesion in the nucleus during mitosis; has a subunit composition distinct from that of the meiotic cohesin complex."
  * Added definition dbxref GOC:mah to GO:0034990
  * Copied GO:0034990 to GO:0000798 with type OBO_REL:is_a
  * Copied GO:0034990 to GO:0030892 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034990
* Populated new object GO:0034991 (macro)
  * Changed name of GO:0034991 from "<new term>" to "nuclear meiotic cohesin complex"
  * Added comment "Note that this term should be used to annotate gene products found in cohesin complexes in organisms that undergo closed mitosis (i. e. where the nuclear envelope does not break down, as in fungi). For organisms in which the nuclear envelope breaks down during mitosis, the parent should be used."
  * Set definition of GO:0034991 to "A cohesin complex that mediates sister chromatid cohesion in the nucleus during meiosis; has a subunit composition distinct from that of the meiotic cohesin complex."
  * Added definition dbxref GOC:mah to GO:0034991
  * Copied GO:0034991 to GO:0000798 with type OBO_REL:is_a
  * Copied GO:0034991 to GO:0030893 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034991
* Populated new object GO:0034992 (macro)
  * Changed name of GO:0034992 from "<new term>" to "microtubule organizing center attachment site"
  * Added comment "Note that this term should not be confused with the cellular component term 'perinuclear region ; GO:0048471'."
  * Set definition of GO:0034992 to "A region of the nuclear envelope to which a microtubule organizing center (MTOC) attaches; protein complexes embedded in the nuclear envelope mediate direct or indirect linkages between the microtubule cytoskeleton and the nuclear envelope."
  * Added definition dbxref GOC:mah to GO:0034992
  * Added definition dbxref PMID:18692466 to GO:0034992
  * Added synonym "MAS" to GO:0034992
  * Changed synonym scope of GO:0034992 from "Related" to "Exact"
  * Added synonym "microtubule organising centre attachment site" to GO:0034992
  * Changed synonym scope of GO:0034992 from "Related" to "Exact"
  * Added synonym "MTOC attachment site" to GO:0034992
  * Changed synonym scope of GO:0034992 from "Related" to "Exact"
  * Copied GO:0034992 to GO:0044428 with type OBO_REL:is_a
  * Copied GO:0034992 to GO:0005635 with type part_of
  * Assigned namespace "cellular_component" to GO:0034992
* Populated new object GO:0034993 (macro)
  * Changed name of GO:0034993 from "<new term>" to "SUN-KASH complex"
  * Set definition of GO:0034993 to "A protein complex that spans the nuclear outer and inner membranes, thereby linking the major cytoplasmic cytoskeleton elements to the nuclear lumen; the complex is conserved in eukaryotes and contains proteins with SUN and KASH domains."
  * Added definition dbxref GOC:mah to GO:0034993
  * Added definition dbxref PMID:18692466 to GO:0034993
  * Copied GO:0034993 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034993 to GO:0034992 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034993
* Populated new object GO:0034994 (macro)
  * Changed name of GO:0034994 from "<new term>" to "microtubule organizing center attachment site organization"
  * Set definition of GO:0034994 to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a microtubule organizing center attachment site. A microtubule organizing center attachment site is a region of the nuclear envelope to which a microtubule organizing center (MTOC) attaches."
  * Added definition dbxref GOC:mah to GO:0034994
  * Added definition dbxref PMID:18692466 to GO:0034994
  * Added synonym "MAS organization" to GO:0034994
  * Changed synonym scope of GO:0034994 from "Related" to "Exact"
  * Added synonym "microtubule organising centre attachment site organisation" to GO:0034994
  * Added synonym "MTOC attachment site organization" to GO:0034994
  * Changed synonym scope of GO:0034994 from "Related" to "Exact"
  * Copied GO:0034994 to GO:0016043 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034994
* Changed definition of GO:0000372 from "The splicing of Group I introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group I introns and involved in determining the locations of the splice sites (there do not appear to be consensu thes splice site sequences) as well as having a role in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions, generally with exogenous guanosine as the initiating nucleophile. The intron is excised as a linear piece (though it may subsequently circularize)." to "The splicing of Group I introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group I introns and involved in determining the locations of the splice sites (there do not appear to be consensus splice site sequences) as well as having a role in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions, generally with exogenous guanosine as the initiating nucleophile. The intron is excised as a linear piece (though it may subsequently circularize)."
* Changed definition of GO:0000373 from "The splicing of Group II introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group II introns and containing splice site consensu thes sequences, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions (mechanistically similar to those for splicing of nuclear mRNAs) initiated by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat." to "The splicing of Group II introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group II introns and containing splice site consensus sequences, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions (mechanistically similar to those for splicing of nuclear mRNAs) initiated by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat."
* Changed definition of GO:0000374 from "The splicing of Group III introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group III introns, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions begun by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat. Though very similar in structure and mechanism to Group II introns, Group III introns are smaller and more streamlined and the splice site consensu thes sequences are not as well conserved." to "The splicing of Group III introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group III introns, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions begun by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat. Though very similar in structure and mechanism to Group II introns, Group III introns are smaller and more streamlined and the splice site consensus sequences are not as well conserved."
* Changed definition of GO:0000419 from "RNA polymerase IVb is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensu thes sequence as well as other sequences. The remainder of the complex is composed of smaller subunits." to "RNA polymerase IVb is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits."
* Deleted GO:0000706 --part_of--> GO:0006311
* Deleted GO:0000706 --part_of--> GO:0007131
* Added comment "Note that this term and its children should be used to annotate gene products found in cohesin complexes in organisms that undergo closed mitosis (i.e. where the nuclear envelope does not break down, as in fungi). For organisms in which the nuclear envelope breaks down during mitosis, the parent should be used."
* Changed definition of GO:0000798 from "A protein complex required for cohesion between sister chromatids that remain in the nucleus." to "A cohesin complex required for cohesion between sister chromatids that remain in the nucleus."
* Deleted GO:0001572 --part_of--> GO:0001574
* Deleted GO:0001572 --part_of--> GO:0001576
* Changed definition of GO:0002030 from "The process that inhibits the signaling function of a G-protein coupled receptor by addition of a phosphate group to its third intracellular loop consensu thes site." to "The process that inhibits the signaling function of a G-protein coupled receptor by addition of a phosphate group to its third intracellular loop consensus site."
* Added synonym "Fc-receptor mediated stimulatory signaling pathway" to GO:0002431
* Changed synonym scope of GO:0002431 from "Related" to "Exact"
* Added synonym "Fc-receptor mediated inhibitory signaling pathway" to GO:0002774
* Changed synonym scope of GO:0002774 from "Related" to "Exact"
* Deleted synonym "Gra-pase activity" from GO:0004309
* Added synonym "Gra-Pase activity" to GO:0004309
* Added general dbxref EC:3.6.1.11 to synonym Gra-Pase activity of GO:0004309
* Changed synonym scope of GO:0004309 from "Related" to "Exact"
* Changed comment from "Consider also annotating to the molecular function term 'nucleic acid binding ; GO:0003676'." to "Consider also annotating to the molecular function term 'nucleic acid binding ; GO:0003676'. Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis."
* Deleted GO:0005637 --OBO_REL:is_a--> GO:0044453
* Copied GO:0005637 to GO:0005635 with type part_of
* Deleted GO:0005638 --OBO_REL:is_a--> GO:0044453
* Copied GO:0005638 to GO:0044428 with type OBO_REL:is_a
* Deleted GO:0005640 --OBO_REL:is_a--> GO:0044453
* Copied GO:0005640 to GO:0005635 with type part_of
* Deleted GO:0005643 --OBO_REL:is_a--> GO:0044453
* Copied GO:0005643 to GO:0005635 with type part_of
* Changed definition of GO:0006990 from "The activation of genes whose promoters contain a specific sequence elements such as the unfolded protein response element (UPRE; consensu thes CAGCGTG) or the ER stress-response element (ERSE; CCAAN(N)9CCACG), as a result of signaling via the unfolded protein response." to "The activation of genes whose promoters contain a specific sequence elements such as the unfolded protein response element (UPRE; consensus CAGCGTG) or the ER stress-response element (ERSE; CCAAN(N)9CCACG), as a result of signaling via the unfolded protein response."
* Added comment "Note that, although the enzyme to which this term refers is also known as 'ribonuclease PH', and degrades tRNA in the 3'-5' direction in vivo, the term does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis."
* Changed definition of GO:0016532 from "A copper chaperone specifically delivering copper to the Cu-Zn superoxide dismutase." to "A copper chaperone activity that specifically delivers copper to the Cu-Zn superoxide dismutase."
* Deleted GO:0030491 --part_of--> GO:0045003
* Deleted GO:0030491 --part_of--> GO:0007534
* Changed definition of GO:0030911 from "Interacting selectively with a tetratricopeptide repeat (TPR) domain of a protein, the consensu thes sequence of which is defined by a pattern of small and large hydrophobic amino acids and a structure composed of helices." to "Interacting selectively with a tetratricopeptide repeat (TPR) domain of a protein, the consensus sequence of which is defined by a pattern of small and large hydrophobic amino acids and a structure composed of helices."
* Deleted GO:0031015 --OBO_REL:is_a--> GO:0044453
* Copied GO:0031015 to GO:0005635 with type part_of
* Deleted GO:0031080 --OBO_REL:is_a--> GO:0044453
* Copied GO:0031080 to GO:0005635 with type part_of
* Added synonym "Fc-receptor complex" to GO:0032997
* Changed synonym scope of GO:0032997 from "Related" to "Exact"
* Deleted GO:0035212 --part_of--> GO:0040008
* Copied GO:0035212 to GO:0040008 with type OBO_REL:is_a
* Added synonym "nuclear positioning" to GO:0040023
* Changed synonym scope of GO:0040023 from "Related" to "Exact"
* Deleted GO:0042217 --part_of--> GO:0006567
* Deleted GO:0042217 --part_of--> GO:0009087
* Changed definition of GO:0047525 from "Catalysis of the reaction: 2'-hydroxydihydrodaidzein + NADP+ = 2'-hydroxydaidzen + NADPH + H+." to "Catalysis of the reaction: 2'-hydroxydihydrodaidzein + NADP+ = 2'-hydroxydaidzein + NADPH + H+."
* Deleted general dbxref MetaCyc:2'-HYDROXYDAIDZEIN-REDUCTASE-RXN from GO:0047525
* Added general dbxref MetaCyc:RXN-4502 to GO:0047525
* Deleted GO:0055047 --part_of--> GO:0009856

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