[Go-diff] GO update 06/09/2009

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Tue Jun 9 21:30:54 PDT 2009 

OBODIFF of gene_ontology_write.obo version 1.645 by 1.651

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0044097
* Created object of type obo:TERM with id GO:0044098
* Created object of type obo:TERM with id GO:0044099
* Created object of type obo:TERM with id GO:0044100
* Created object of type obo:TERM with id GO:0060704
* Created object of type obo:TERM with id GO:0060705
* Created object of type obo:TERM with id GO:0060706
* Created object of type obo:TERM with id GO:0060707
* Created object of type obo:TERM with id GO:0060708
* Created object of type obo:TERM with id GO:0060709
* Created object of type obo:TERM with id GO:0060710
* Created object of type obo:TERM with id GO:0060711
* Created object of type obo:TERM with id GO:0060712
* Created object of type obo:TERM with id GO:0070715
* Created object of type obo:TERM with id GO:0070716
* Populated new object GO:0044097 (macro)
  * Changed name of GO:0044097 from "<new term>" to "secretion by the type IV secretion system"
  * Set definition of GO:0044097 to "The controlled release of proteins or DNA by a cell, via the type IV secretion system."
  * Added definition dbxref GOC:pamgo_curators to GO:0044097
  * Added synonym "secretion via the type IV secretion system" to GO:0044097
  * Changed synonym scope of GO:0044097 from "Related" to "Exact"
  * Copied GO:0044097 to GO:0032940 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0044097
* Populated new object GO:0044098 (macro)
  * Changed name of GO:0044098 from "<new term>" to "DNA secretion by the type IV secretion system"
  * Set definition of GO:0044098 to "The controlled release of DNA by a cell, via the type IV secretion system."
  * Added definition dbxref GOC:pamgo_curators to GO:0044098
  * Added synonym "DNA secretion via the type IV secretion system" to GO:0044098
  * Changed synonym scope of GO:0044098 from "Related" to "Exact"
  * Copied GO:0044098 to GO:0044097 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0044098
* Populated new object GO:0044099 (macro)
  * Changed name of GO:0044099 from "<new term>" to "polar tube"
  * Set definition of GO:0044099 to "A highly specialized structure unique to microsporidia that is required for host cell invasion. In the spore, the polar tube is connected at the anterior end, and then coils around the sporoplasm. Upon appropriate environmental stimulation, the polar tube rapidly discharges out of the spore, pierces a cell membrane and serves as a conduit for sporoplasm passage into the new host cell."
  * Added definition dbxref PMID:12076771 to GO:0044099
  * Added definition dbxref PMID:9723921 to GO:0044099
  * Added definition dbxref UniProtKB:mf to GO:0044099
  * Copied GO:0044099 to GO:0044464 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0044099
* Populated new object GO:0044100 (macro)
  * Changed name of GO:0044100 from "<new term>" to "sporoplasm"
  * Set definition of GO:0044100 to "The complex infective apparatus corresponding to the central mass of cytoplasm within a spore that is injected into a host cell by various parasitic microorganisms."
  * Added definition dbxref PMID:12076771 to GO:0044100
  * Added definition dbxref PMID:16004371 to GO:0044100
  * Added definition dbxref PMID:9723921 to GO:0044100
  * Added definition dbxref UniProtKB:mf to GO:0044100
  * Copied GO:0044100 to GO:0044424 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0044100
* Populated new object GO:0060704 (macro)
  * Changed name of GO:0060704 from "<new term>" to "acinar cell differentiation involved in salivary gland development"
  * Set definition of GO:0060704 to "The process whereby a relatively unspecialized cell acquires specialized structural and/or functional features that characterize an acinar cell of the salivary gland. Acinar cells are protein-secreting cells in the gland."
  * Added definition dbxref GOC:dph to GO:0060704
  * Copied GO:0060704 to GO:0060689 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060704
* Populated new object GO:0060705 (macro)
  * Changed name of GO:0060705 from "<new term>" to "neuron differentiation involved in salivary gland development"
  * Set definition of GO:0060705 to "The process whereby a relatively unspecialized cell acquires specialized structural and/or functional features that characterize the neurons of the salivary gland."
  * Added definition dbxref GOC:dph to GO:0060705
  * Copied GO:0060705 to GO:0060689 with type OBO_REL:is_a
  * Copied GO:0060705 to GO:0030182 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060705
* Populated new object GO:0060706 (macro)
  * Changed name of GO:0060706 from "<new term>" to "cell differentiation involved in embryonic placenta development"
  * Set definition of GO:0060706 to "The process whereby a relatively unspecialized cell acquires specialized features of an epithelial cell of the placenta."
  * Added definition dbxref GOC:dph to GO:0060706
  * Copied GO:0060706 to GO:0001892 with type part_of
  * Copied GO:0060706 to GO:0030154 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060706
* Populated new object GO:0060707 (macro)
  * Changed name of GO:0060707 from "<new term>" to "trophoblast giant cell differentiation"
  * Set definition of GO:0060707 to "The process whereby a relatively unspecialized cell acquires specialized features of a trophoblast giant cell of the placenta. Trophoblast giant cells are the cell of the placenta that line the maternal decidua."
  * Added definition dbxref GOC:dph to GO:0060707
  * Added definition dbxref PMID:16269175 to GO:0060707
  * Copied GO:0060707 to GO:0060706 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060707
* Populated new object GO:0060708 (macro)
  * Changed name of GO:0060708 from "<new term>" to "spongiotrophoblast differentiation"
  * Set definition of GO:0060708 to "The process whereby a relatively unspecialized cell of the ectoplacental cone acquires specialized features of a spongiotrophoblast of the placenta. A spongiotrophoblast cell is a basophilic cell."
  * Added definition dbxref GOC:dph to GO:0060708
  * Added definition dbxref PMID:16269175 to GO:0060708
  * Copied GO:0060708 to GO:0060706 with type OBO_REL:is_a
  * Copied GO:0060708 to GO:0060712 with type part_of
  * Assigned namespace "biological_process" to GO:0060708
* Populated new object GO:0060709 (macro)
  * Changed name of GO:0060709 from "<new term>" to "glycogen cell development involved in embryonic placenta development"
  * Set definition of GO:0060709 to "The process whereby a relatively unspecialized cell acquires specialized features of a glycogen cell of the placenta. A glycogen cell is a vacuolated glycogen-rich cell that appears in compact cell islets of the spongiotrophoblast layer."
  * Added definition dbxref GOC:dph to GO:0060709
  * Added definition dbxref PMID:16269175 to GO:0060709
  * Copied GO:0060709 to GO:0060706 with type OBO_REL:is_a
  * Copied GO:0060709 to GO:0060712 with type part_of
  * Assigned namespace "biological_process" to GO:0060709
* Populated new object GO:0060710 (macro)
  * Changed name of GO:0060710 from "<new term>" to "chorio-allantoic fusion"
  * Set definition of GO:0060710 to "The cell-cell adhesion process by which the cells of the chorion fuse to the cells of the allantois."
  * Added definition dbxref GOC:dph to GO:0060710
  * Copied GO:0060710 to GO:0001890 with type part_of
  * Copied GO:0060710 to GO:0016337 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060710
* Populated new object GO:0060711 (macro)
  * Changed name of GO:0060711 from "<new term>" to "labyrinthine layer development"
  * Set definition of GO:0060711 to "The process by which the labyrinthine layer of the placenta progresses, from its formation to its mature state."
  * Added definition dbxref GOC:dph to GO:0060711
  * Copied GO:0060711 to GO:0048856 with type OBO_REL:is_a
  * Copied GO:0060711 to GO:0001892 with type part_of
  * Assigned namespace "biological_process" to GO:0060711
* Populated new object GO:0060712 (macro)
  * Changed name of GO:0060712 from "<new term>" to "spongiotrophoblast layer development"
  * Set definition of GO:0060712 to "The process by which the spongiotrophoblast layer of the placenta progresses from its formation to its mature state."
  * Added definition dbxref GOC:dph to GO:0060712
  * Copied GO:0060712 to GO:0001892 with type part_of
  * Copied GO:0060712 to GO:0048856 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060712
* Populated new object GO:0070715 (macro)
  * Changed name of GO:0070715 from "<new term>" to "sodium-dependent organic cation transport"
  * Set definition of GO:0070715 to "The directed, sodium-dependent, movement of organic cations into, out of, within or between cells."
  * Added definition dbxref GOC:mah to GO:0070715
  * Copied GO:0070715 to GO:0015695 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070715
* Populated new object GO:0070716 (macro)
  * Changed name of GO:0070716 from "<new term>" to "mismatch repair involved in maintenance of fidelity during DNA-dependent DNA replication"
  * Set definition of GO:0070716 to "A mismatch repair process that corrects errors introduced during DNA replication."
  * Added definition dbxref GOC:mah to GO:0070716
  * Added GO:0070716 to category gosubset_prok
  * Copied GO:0070716 to GO:0045005 with type OBO_REL:is_a
  * Copied GO:0070716 to GO:0006298 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070716
* Copied GO:0002110 to GO:0070705 with type OBO_REL:is_a
* Changed definition of GO:0006298 from "A system for the correction of errors introduced during DNA replication when an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination." to "A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination."
* Deleted GO:0006298 --OBO_REL:is_a--> GO:0045005
* Changed definition of GO:0008274 from "A multiprotein complex composed of gamma-tubulin other non-tubulin proteins that forms a flexible open ring structure thought to be the unit of nucleation at the minus end of a microtubule." to "A multiprotein complex composed of gamma-tubulin and other non-tubulin proteins that forms a flexible open ring structure thought to be the unit of nucleation at the minus end of a microtubule."
* Deleted GO:0008608 --OBO_REL:is_a--> GO:0034453
* Copied GO:0008608 to GO:0051313 with type OBO_REL:is_a
* Copied GO:0015226 to GO:0015651 with type OBO_REL:is_a
* Copied GO:0015879 to GO:0015697 with type OBO_REL:is_a
* Changed definition of GO:0030255 from "The process by which nucleoprotein DNA conjugation intermediates or proteins are transferred into the extracellular milieu or directly into host cells, via the type IV protein secretion system." to "The process by which proteins are transferred into the extracellular milieu or directly into host cells, via the type IV protein secretion system."
* Changed synonym scope of GO:0030255 from "Exact" to "Narrow"
* Copied GO:0030255 to GO:0044097 with type OBO_REL:is_a
* Copied GO:0031297 to GO:0045005 with type OBO_REL:is_a
* Copied GO:0043111 to GO:0045005 with type OBO_REL:is_a
* Changed name of GO:0043684 from "type IV protein secretion system complex" to "type IV secretion system complex"
* Changed definition of GO:0043684 from "A complex of proteins related to those involved in bacterial DNA conjugative transfer, that permits the transfer of nucleoprotein DNA conjugation intermediates or proteins into the extracellular milieu or directly into host cells. In general the type IV complex forms a multisubunit cell-envelope-spanning structure composed of a secretion channel and often a pilus or other surface filament or protein(s)." to "A complex of proteins related to those involved in bacterial DNA conjugative transfer, that permits the transfer of DNA or proteins into the extracellular milieu or directly into host cells. In general the type IV complex forms a multisubunit cell-envelope-spanning structure composed of a secretion channel and often a pilus or other surface filament or protein(s)."
* Added synonym "type IV protein secretion system complex" to GO:0043684
* Changed synonym scope of GO:0043684 from "Related" to "Narrow"
* Changed definition of GO:0045005 from "The correction of errors made during DNA replication by either intrinsic DNA polymerase proofreading activity or via mismatch repair." to "A DNA metabolic process that prevents or corrects errors during DNA replication. Errors can be corrected either by intrinsic DNA polymerase proofreading activity or via mismatch repair."
* Deleted definition dbxref GOC:ai from GO:0045005
* Added definition dbxref GOC:mah to GO:0045005
* Added definition dbxref GOC:vw to GO:0045005
* Changed definition of GO:0048085 from "Establishment of the adult pattern of pigmentation in the chitin-containing cuticle of an organism. An example of this is the adult cuticle pigmentation process in Drosophila malanogaster." to "Establishment of the adult pattern of pigmentation in the chitin-containing cuticle of an organism. An example of this is the adult cuticle pigmentation process in Drosophila melanogaster."
* Copied GO:0048478 to GO:0045005 with type OBO_REL:is_a
* Deleted GO:0051313 --OBO_REL:is_a--> GO:0007017
* Copied GO:0051313 to GO:0034453 with type OBO_REL:is_a
* Copied GO:0060670 to GO:0060711 with type part_of
* Deleted GO:0060671 --part_of--> GO:0001892
* Copied GO:0060671 to GO:0060706 with type OBO_REL:is_a
* Changed definition of GO:0070705 from "The modification of an RNA molecule by insertion of a single nucleotide." to "The modification of an RNA molecule by insertion of one or more nucleotides."
* Deleted GO:0070707 --OBO_REL:is_a--> GO:0009451
* Copied GO:0070707 to GO:0070705 with type OBO_REL:is_a

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