[Go-diff] GO update 06/02/2009

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Tue Jun 2 21:30:54 PDT 2009 

OBODIFF of gene_ontology_write.obo version 1.629 by 1.633

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0060669
* Created object of type obo:TERM with id GO:0060670
* Created object of type obo:TERM with id GO:0060671
* Created object of type obo:TERM with id GO:0060672
* Created object of type obo:TERM with id GO:0060673
* Created object of type obo:TERM with id GO:0060674
* Created object of type obo:TERM with id GO:0060675
* Created object of type obo:TERM with id GO:0060676
* Created object of type obo:TERM with id GO:0060677
* Created object of type obo:TERM with id GO:0060678
* Created object of type obo:TERM with id GO:0060679
* Created object of type obo:TERM with id GO:0060680
* Created object of type obo:TERM with id GO:0060681
* Created object of type obo:TERM with id GO:0060682
* Created object of type obo:TERM with id GO:0070680
* Created object of type obo:TERM with id GO:0070681
* Created object of type obo:TERM with id GO:0070682
* Created object of type obo:TERM with id GO:0070683
* Created object of type obo:TERM with id GO:0070684
* Populated new object GO:0060669 (macro)
  * Changed name of GO:0060669 from "<new term>" to "embryonic placental morphogenesis"
  * Set definition of GO:0060669 to "The process by which the embryonic placenta is generated and organized. Morphogenesis pertains to the creation of form."
  * Added definition dbxref GOC:dph to GO:0060669
  * Copied GO:0060669 to GO:0001892 with type part_of
  * Copied GO:0060669 to GO:0048598 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060669
* Populated new object GO:0060670 (macro)
  * Changed name of GO:0060670 from "<new term>" to "branching involved in embryonic placental morphogenesis"
  * Set definition of GO:0060670 to "The process by which the branches of the fetal placental villi are generated and organized. Morphogenesis pertains to the creation of form. The villous part of the placenta is called the labyrinth layer."
  * Added definition dbxref GOC:dph to GO:0060670
  * Added definition dbxref PMID:16916377 to GO:0060670
  * Copied GO:0060670 to GO:0001763 with type OBO_REL:is_a
  * Copied GO:0060670 to GO:0060669 with type part_of
  * Assigned namespace "biological_process" to GO:0060670
* Populated new object GO:0060671 (macro)
  * Changed name of GO:0060671 from "<new term>" to "epithelial cell differentiation involved in embryonic placenta development"
  * Set definition of GO:0060671 to "The process whereby a trophoblast cell acquires specialized features of an epithelial cell of the placenta."
  * Added definition dbxref GOC:dph to GO:0060671
  * Added definition dbxref PMID:16916377 to GO:0060671
  * Copied GO:0060671 to GO:0001892 with type part_of
  * Copied GO:0060671 to GO:0030855 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060671
* Populated new object GO:0060672 (macro)
  * Changed name of GO:0060672 from "<new term>" to "epithelial cell morphogenesis involved in placental branching"
  * Set definition of GO:0060672 to "The change in form (cell shape and size) that occurs when a trophoblast cell elongates to contribute to the branching of the placenta."
  * Added definition dbxref GOC:dph to GO:0060672
  * Added definition dbxref PMID:16916377 to GO:0060672
  * Copied GO:0060672 to GO:0000904 with type OBO_REL:is_a
  * Copied GO:0060672 to GO:0060671 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060672
* Populated new object GO:0060673 (macro)
  * Changed name of GO:0060673 from "<new term>" to "cell-cell signaling involved in placenta development"
  * Set definition of GO:0060673 to "Any process that mediates the transfer of information from one cell to another."
  * Added definition dbxref GOC:dph to GO:0060673
  * Added definition dbxref PMID:16916377 to GO:0060673
  * Copied GO:0060673 to GO:0001892 with type part_of
  * Copied GO:0060673 to GO:0007267 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060673
* Populated new object GO:0060674 (macro)
  * Changed name of GO:0060674 from "<new term>" to "placenta vasculature development"
  * Set definition of GO:0060674 to "The process whose specific outcome is the progression of the vasculature of the placenta over time, from its formation to the mature structure."
  * Added definition dbxref GOC:dph to GO:0060674
  * Added definition dbxref PMID:16916377 to GO:0060674
  * Copied GO:0060674 to GO:0001944 with type OBO_REL:is_a
  * Copied GO:0060674 to GO:0001890 with type part_of
  * Assigned namespace "biological_process" to GO:0060674
* Populated new object GO:0060675 (macro)
  * Changed name of GO:0060675 from "<new term>" to "ureteric bud morphogenesis"
  * Set definition of GO:0060675 to "The process by which the ureteric bud is generated and organized. Morphogenesis pertains to the creation of form."
  * Added definition dbxref GOC:dph to GO:0060675
  * Copied GO:0060675 to GO:0001657 with type part_of
  * Copied GO:0060675 to GO:0009653 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060675
* Populated new object GO:0060676 (macro)
  * Changed name of GO:0060676 from "<new term>" to "ureteric bud formation"
  * Set definition of GO:0060676 to "The developmental process pertaining to the initial formation of the ureteric bud from The Wolffian Duct. This process begins when the bud protrudes from the duct and ends when it is a recognizable bud."
  * Added definition dbxref GOC:dph to GO:0060676
  * Added definition dbxref PMID:16916378 to GO:0060676
  * Copied GO:0060676 to GO:0048646 with type OBO_REL:is_a
  * Copied GO:0060676 to GO:0060675 with type part_of
  * Assigned namespace "biological_process" to GO:0060676
* Populated new object GO:0060677 (macro)
  * Changed name of GO:0060677 from "<new term>" to "ureteric bud elongation"
  * Set definition of GO:0060677 to "The process by which the ureteric bud grows along its axis."
  * Added definition dbxref GOC:dph to GO:0060677
  * Added definition dbxref PMID:16916378 to GO:0060677
  * Copied GO:0060677 to GO:0060560 with type OBO_REL:is_a
  * Copied GO:0060677 to GO:0060675 with type part_of
  * Assigned namespace "biological_process" to GO:0060677
* Populated new object GO:0060678 (macro)
  * Changed name of GO:0060678 from "<new term>" to "dichotomous subdivision of terminal units involved in ureteric bud branching"
  * Set definition of GO:0060678 to "The process whereby a ureteric bud bifurcates at its end."
  * Added definition dbxref GOC:dph to GO:0060678
  * Added definition dbxref PMID:16916378 to GO:0060678
  * Added synonym "bifid subdivision of terminal units involved in ureteric bud branching" to GO:0060678
  * Added general dbxref PMID:16916378 to synonym bifid subdivision of terminal units involved in ureteric bud branching of GO:0060678
  * Added general dbxref GOC:dph to synonym bifid subdivision of terminal units involved in ureteric bud branching of GO:0060678
  * Changed synonym scope of GO:0060678 from "Related" to "Exact"
  * Copied GO:0060678 to GO:0001658 with type part_of
  * Copied GO:0060678 to GO:0060600 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060678
* Populated new object GO:0060679 (macro)
  * Changed name of GO:0060679 from "<new term>" to "trifid subdivision of terminal units involved in ureteric bud branching"
  * Set definition of GO:0060679 to "The process whereby a ureteric bud splits into three units at its end."
  * Added definition dbxref GOC:dph to GO:0060679
  * Added definition dbxref PMID:16916378 to GO:0060679
  * Copied GO:0060679 to GO:0002009 with type OBO_REL:is_a
  * Copied GO:0060679 to GO:0001658 with type part_of
  * Assigned namespace "biological_process" to GO:0060679
* Populated new object GO:0060680 (macro)
  * Changed name of GO:0060680 from "<new term>" to "lateral sprouting involved in ureteric bud morphogenesis"
  * Set definition of GO:0060680 to "The process whereby a branch forms along the side of a ureteric bud."
  * Added definition dbxref GOC:dph to GO:0060680
  * Added definition dbxref PMID:16916378 to GO:0060680
  * Copied GO:0060680 to GO:0001658 with type part_of
  * Copied GO:0060680 to GO:0060601 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060680
* Populated new object GO:0060681 (macro)
  * Changed name of GO:0060681 from "<new term>" to "branch elongation involved in ureteric bud branching"
  * Set definition of GO:0060681 to "The growth of a branch of the ureteric bud along its axis."
  * Added definition dbxref GOC:dph to GO:0060681
  * Added definition dbxref PMID:16916378 to GO:0060681
  * Copied GO:0060681 to GO:0001658 with type part_of
  * Copied GO:0060681 to GO:0060677 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060681
* Populated new object GO:0060682 (macro)
  * Changed name of GO:0060682 from "<new term>" to "primary ureteric bud growth"
  * Set definition of GO:0060682 to "The process by which the primary ureteric bud grows along its axis dorsally toward the metanephric blastema."
  * Added definition dbxref GOC:dph to GO:0060682
  * Added definition dbxref PMID:16916378 to GO:0060682
  * Copied GO:0060682 to GO:0060677 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060682
* Populated new object GO:0070680 (macro)
  * Changed name of GO:0070680 from "<new term>" to "asparaginyl-tRNAasn biosynthesis via transamidation"
  * Set definition of GO:0070680 to "A tRNA aminoacylation process in which asparaginyl-tRNAasn is formed by a tRNA-dependent two-step pathway. In the first step a non-discriminating aspartyl-tRNA synthetase generates the misacylated L-aspartyl-tRNAasn species, and in the second step it is amidated to the correctly charged L-asparaginyl-tRNAasn by the heterotrimeric aspartyl-tRNAAsn amidotransferase."
  * Added definition dbxref GOC:mah to GO:0070680
  * Added definition dbxref MetaCyc:PWY490-4 to GO:0070680
  * Added general dbxref MetaCyc:PWY490-4 to GO:0070680
  * Copied GO:0070680 to GO:0043039 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070680
* Populated new object GO:0070681 (macro)
  * Changed name of GO:0070681 from "<new term>" to "glutaminyl-tRNAgln biosynthesis via transamidation"
  * Set definition of GO:0070681 to "A tRNA aminoacylation process in which glutaminyl-tRNAgln is formed by a tRNA-dependent two-step pathway. In the first step a non-discriminating glutamyl-tRNAGlx synthetase generates the misacylated L-glutamyl-tRNAgln species, and in the second step it is amidated to the correctly charged L-glutaminyl-tRNAgln by a glutamyl-tRNAGln amidotransferase."
  * Added definition dbxref GOC:mah to GO:0070681
  * Added definition dbxref MetaCyc:PWY-5921 to GO:0070681
  * Added general dbxref MetaCyc:PWY-5921 to GO:0070681
  * Copied GO:0070681 to GO:0043039 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070681
* Populated new object GO:0070682 (macro)
  * Changed name of GO:0070682 from "<new term>" to "proteasome regulatory particle assembly"
  * Set definition of GO:0070682 to "The aggregation, arrangement and bonding together of a mature, active proteasome regulatory particle complex."
  * Added definition dbxref GOC:mah to GO:0070682
  * Added definition dbxref GOC:rb to GO:0070682
  * Added definition dbxref PMID:19412159 to GO:0070682
  * Added synonym "proteasome regulatory complex assembly" to GO:0070682
  * Added general dbxref GOC:mah to synonym proteasome regulatory complex assembly of GO:0070682
  * Changed synonym scope of GO:0070682 from "Related" to "Exact"
  * Copied GO:0070682 to GO:0043248 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070682
* Populated new object GO:0070683 (macro)
  * Changed name of GO:0070683 from "<new term>" to "decatenation checkpoint"
  * Set definition of GO:0070683 to "A cell cycle checkpoint that blocks cell cycle progression from G2 to M phase until until sister chromatids are sufficiently separated."
  * Added definition dbxref GOC:jp to GO:0070683
  * Added synonym "topo II checkpoint" to GO:0070683
  * Added general dbxref GOC:jp to synonym topo II checkpoint of GO:0070683
  * Changed synonym scope of GO:0070683 from "Related" to "Exact"
  * Added synonym "topoisomerase II checkpoint" to GO:0070683
  * Added general dbxref GOC:jp to synonym topoisomerase II checkpoint of GO:0070683
  * Changed synonym scope of GO:0070683 from "Related" to "Exact"
  * Copied GO:0070683 to GO:0031576 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070683
* Populated new object GO:0070684 (macro)
  * Changed name of GO:0070684 from "<new term>" to "seminal clot liquefaction"
  * Set definition of GO:0070684 to "The reproductive process by which coagulated semen becomes liquid following ejaculation, allowing the progressive release of motile spermatozoa."
  * Added definition dbxref GOC:mah to GO:0070684
  * Added definition dbxref PMID:18482984 to GO:0070684
  * Added synonym "semen liquefaction" to GO:0070684
  * Added general dbxref PMID:18482984 to synonym semen liquefaction of GO:0070684
  * Changed synonym scope of GO:0070684 from "Related" to "Exact"
  * Copied GO:0070684 to GO:0048609 with type OBO_REL:is_a
  * Copied GO:0070684 to GO:0007320 with type part_of
  * Assigned namespace "biological_process" to GO:0070684
* Changed definition of GO:0001658 from "The process by which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the mesonephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules." to "The process by which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules."
* Added definition dbxref PMID:16916378 to GO:0001658
* Deleted GO:0001658 --part_of--> GO:0001657
* Copied GO:0001658 to GO:0060675 with type part_of
* Added synonym "fetal placenta development" to GO:0001892
* Added general dbxref GOC:dph to synonym fetal placenta development of GO:0001892
* Changed synonym scope of GO:0001892 from "Related" to "Exact"
* Deleted general dbxref MetaCyc:0 from GO:0004663
* Copied GO:0005220 to GO:0008095 with type OBO_REL:is_a
* Changed definition of GO:0030414 from "Stops, prevents or reduces the activity of a peptidase, any enzyme catalyzes the hydrolysis peptide bonds." to "Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds."
* Changed definition of GO:0030956 from "Complex that possesses glutamyl-tRNA(Gln) amidotransferase activity, and therefore creates Gln-tRNA by amidating Glu-tRNA; usually composed of 3 subunits: A, B, and C. Note that the C subunit may not be required in all organisms." to "A protein complex that possesses glutamyl-tRNA(Gln) amidotransferase activity, and therefore creates Gln-tRNA by amidating Glu-tRNA; usually composed of 3 subunits: A, B, and C. Note that the C subunit may not be required in all organisms."
* Added synonym "AdT" to GO:0030956
* Added general dbxref GOC:rb to synonym AdT of GO:0030956
* Added synonym "GatCAB" to GO:0030956
* Added general dbxref GOC:rb to synonym GatCAB of GO:0030956
* Changed synonym scope of GO:0030956 from "Related" to "Narrow"
* Added synonym "GatFAB" to GO:0030956
* Added general dbxref GOC:rb to synonym GatFAB of GO:0030956
* Changed synonym scope of GO:0030956 from "Related" to "Narrow"
* Added synonym "DH4 binding" to GO:0034617
* Added general dbxref GOC:pf to synonym DH4 binding of GO:0034617
* Changed synonym scope of GO:0034617 from "Related" to "Exact"
* Deleted definition dbxref PMID:016926444 from GO:0034662
* Added definition dbxref PMID:16926444 to GO:0034662
* Changed name of GO:0042554 from "superoxide release" to "superoxide anion generation"
* Added synonym "superoxide release" to GO:0042554
* Added general dbxref GOC:mah to synonym superoxide release of GO:0042554
* Added general dbxref GOC:hjd to synonym superoxide release of GO:0042554
* Changed synonym scope of GO:0042554 from "Related" to "Exact"
* Changed definition of GO:0043039 from "The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules." to "The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules."
* Added definition dbxref GOC:mah to GO:0043039
* Added definition dbxref MetaCyc:Aminoacyl-tRNAs to GO:0043039
* Added synonym "aminoacyl-tRNA biosynthesis" to GO:0043039
* Added general dbxref GOC:mah to synonym aminoacyl-tRNA biosynthesis of GO:0043039
* Changed synonym scope of GO:0043039 from "Related" to "Exact"
* Added synonym "aminoacyl-tRNA biosynthetic process" to GO:0043039
* Added general dbxref GOC:mah to synonym aminoacyl-tRNA biosynthetic process of GO:0043039
* Changed synonym scope of GO:0043039 from "Related" to "Exact"
* Deleted definition dbxref PMID:0 from GO:0070603
* Added definition dbxref PMID:16155938 to GO:0070603

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