[Go-diff] GO update 06/17/2009

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Wed Jun 17 21:30:54 PDT 2009 

OBODIFF of gene_ontology_write.obo version 1.666 by 1.668

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0070726
* Created object of type obo:TERM with id GO:0070727
* Created object of type obo:TERM with id GO:0070728
* Created object of type obo:TERM with id GO:0070729
* Created object of type obo:TERM with id GO:0070730
* Created object of type obo:TERM with id GO:0070731
* Populated new object GO:0070726 (macro)
  * Changed name of GO:0070726 from "<new term>" to "cell wall assembly"
  * Set definition of GO:0070726 to "The aggregation, arrangement and bonding together of a cell wall. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells."
  * Added definition dbxref GOC:mah to GO:0070726
  * Copied GO:0070726 to GO:0042546 with type part_of
  * Copied GO:0070726 to GO:0022607 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070726
* Populated new object GO:0070727 (macro)
  * Changed name of GO:0070727 from "<new term>" to "cellular macromolecule localization"
  * Set definition of GO:0070727 to "Any process by which a macromolecule is transported to, and/or maintained in, a specific location within or at the surface of a cell."
  * Added definition dbxref GOC:mah to GO:0070727
  * Copied GO:0070727 to GO:0033036 with type OBO_REL:is_a
  * Copied GO:0070727 to GO:0051641 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070727
* Populated new object GO:0070728 (macro)
  * Changed name of GO:0070728 from "<new term>" to "leucine binding"
  * Set definition of GO:0070728 to "Interacting selectively with 2-amino-4-methylpentanoic acid."
  * Added definition dbxref ChEBI:25017 to GO:0070728
  * Added definition dbxref GOC:mah to GO:0070728
  * Added synonym "Leu binding" to GO:0070728
  * Added general dbxref GOC:mah to synonym Leu binding of GO:0070728
  * Changed synonym scope of GO:0070728 from "Related" to "Exact"
  * Copied GO:0070728 to GO:0016597 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070728
* Populated new object GO:0070729 (macro)
  * Changed name of GO:0070729 from "<new term>" to "cyclic nucleotide transport"
  * Set definition of GO:0070729 to "The directed movement of a cyclic nucleotide, any nucleotide in which phosphate group is in diester linkage to two positions on the sugar residue, into, out of or within a cell."
  * Added definition dbxref GOC:mah to GO:0070729
  * Added definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) to GO:0070729
  * Copied GO:0070729 to GO:0006862 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070729
* Populated new object GO:0070730 (macro)
  * Changed name of GO:0070730 from "<new term>" to "cAMP transport"
  * Set definition of GO:0070730 to "The directed movement of cyclic AMP (cAMP), into, out of or within a cell."
  * Added definition dbxref GOC:mah to GO:0070730
  * Added definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) to GO:0070730
  * Added synonym "cyclic AMP transport" to GO:0070730
  * Added general dbxref GOC:mah to synonym cyclic AMP transport of GO:0070730
  * Changed synonym scope of GO:0070730 from "Related" to "Exact"
  * Copied GO:0070730 to GO:0070729 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070730
* Populated new object GO:0070731 (macro)
  * Changed name of GO:0070731 from "<new term>" to "cGMP transport"
  * Set definition of GO:0070731 to "The directed movement of cyclic GMP (cGMP), into, out of or within a cell."
  * Added definition dbxref GOC:mah to GO:0070731
  * Added definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) to GO:0070731
  * Added synonym "cyclic GMP transport" to GO:0070731
  * Added general dbxref GOC:mah to synonym cyclic GMP transport of GO:0070731
  * Changed synonym scope of GO:0070731 from "Related" to "Exact"
  * Copied GO:0070731 to GO:0070729 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070731
* Copied GO:0000321 to GO:0051716 with type OBO_REL:is_a
* Removed GO:0000723 from category goslim_pombe
* Copied GO:0000756 to GO:0051716 with type OBO_REL:is_a
* Copied GO:0002007 to GO:0051716 with type OBO_REL:is_a
* Deleted synonym "negative regulation of neural plate biosynthesis" from GO:0002085
* Added synonym "negative regulation of neural plate formation" to GO:0002085
* Added general dbxref GOC:tb to synonym negative regulation of neural plate formation of GO:0002085
* Added general dbxref GOC:dph to synonym negative regulation of neural plate formation of GO:0002085
* Changed synonym scope of GO:0002085 from "Related" to "Exact"
* Deleted GO:0002086 --part_of--> GO:0010802
* Changed name of GO:0002087 from "regulation of respiratory gaseous exchange by neurological process" to "regulation of respiratory gaseous exchange by neurological system process"
* Deleted GO:0002087 --regulates--> GO:0010802
* Changed comment from "In E. coli, the first step of the reaction is reductive elimination of sulphur from L-cysteine by IscS cysteine desulphurase to form an enzyme-bound cysteine-persulphide intermediate. Then, five essential gene products, TusA, TusB, TusC, TusD and TusE, mediate a sulphur relay that delivers the terminal sulphur of persulphide from IscS to MnmA12. The last protein, MnmA catalyzes the transfer of the sulfur from IscS to an ATP activated U34 of the tRNA." to "In E. coli, the first step of the reaction is reductive elimination of sulfur from L-cysteine by IscS cysteine desulfurase to form an enzyme-bound cysteine-persulfide intermediate. Then, five essential gene products, TusA, TusB, TusC, TusD and TusE, mediate a sulfur relay that delivers the terminal sulfur of persulfide from IscS to MnmA12. The last protein, MnmA catalyzes the transfer of the sulfur from IscS to an ATP activated U34 of the tRNA."
* Copied GO:0002818 to GO:0033554 with type OBO_REL:is_a
* added secondary id GO:0010802 to GO:0003016
* Changed definition of GO:0003016 from "A organ system process carried out by any of the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange." to "A system process carried out by the organs and tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange."
* Added definition dbxref GOC:dph to GO:0003016
* Added definition dbxref GOC:tb to GO:0003016
* Added synonym "respiratory gaseous exchange by respiratory system" to GO:0003016
* Changed synonym scope of GO:0003016 from "Related" to "Exact"
* Copied GO:0003016 to GO:0007585 with type OBO_REL:is_a
* Copied GO:0005980 to GO:0044247 with type OBO_REL:is_a
* Copied GO:0005983 to GO:0044247 with type OBO_REL:is_a
* Copied GO:0006047 to GO:0044262 with type OBO_REL:is_a
* Copied GO:0006049 to GO:0044275 with type OBO_REL:is_a
* Copied GO:0006054 to GO:0044262 with type OBO_REL:is_a
* Added GO:0006259 to category goslim_pombe
* Copied GO:0006308 to GO:0034962 with type OBO_REL:is_a
* Removed GO:0006338 from category goslim_pombe
* Added GO:0006399 to category goslim_pombe
* Copied GO:0006401 to GO:0034962 with type OBO_REL:is_a
* Copied GO:0006465 to GO:0044267 with type OBO_REL:is_a
* Copied GO:0006486 to GO:0044262 with type OBO_REL:is_a
* Changed name of GO:0006521 from "regulation of amino acid metabolic process" to "regulation of cellular amino acid metabolic process"
* Copied GO:0006583 to GO:0044249 with type OBO_REL:is_a
* Copied GO:0006716 to GO:0034754 with type OBO_REL:is_a
* Added GO:0006810 to category goslim_pombe
* Deleted GO:0006837 --OBO_REL:is_a--> GO:0015837
* Added synonym "sterol depletion response" to GO:0006991
* Added general dbxref GOC:tb to synonym sterol depletion response of GO:0006991
* Added general dbxref GOC:dph to synonym sterol depletion response of GO:0006991
* Changed synonym scope of GO:0006991 from "Related" to "Exact"
* Changed name of GO:0006992 from "sterol depletion response, sterol regulatory element binding protein cleavage" to "sterol regulatory element binding protein cleavage involved in ER-nuclear sterol response pathway"
* Changed name of GO:0006993 from "sterol depletion response, sterol regulatory element binding protein nuclear translocation" to "sterol regulatory element binding protein nuclear translocation involved in sterol depletion response"
* Added synonym "sterol depletion response, sterol regulatory element binding protein nuclear translocation" to GO:0006993
* Added general dbxref GOC:tb to synonym sterol depletion response, sterol regulatory element binding protein nuclear translocation of GO:0006993
* Added general dbxref GOC:dph to synonym sterol depletion response, sterol regulatory element binding protein nuclear translocation of GO:0006993
* Changed synonym scope of GO:0006993 from "Related" to "Exact"
* Changed name of GO:0006994 from "positive regulation of sterol regulatory element binding protein target gene transcription involved in sterol depletion response" to "positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway"
* Added synonym "positive regulation of sterol regulatory element binding protein target gene transcription involved in sterol depletion response" to GO:0006994
* Added general dbxref GOC:tb to synonym positive regulation of sterol regulatory element binding protein target gene transcription involved in sterol depletion response of GO:0006994
* Added general dbxref GOC:dph to synonym positive regulation of sterol regulatory element binding protein target gene transcription involved in sterol depletion response of GO:0006994
* Changed synonym scope of GO:0006994 from "Related" to "Exact"
* Added GO:0006996 to category goslim_pombe
* Copied GO:0006999 to GO:0034621 with type OBO_REL:is_a
* Deleted GO:0007043 --OBO_REL:is_a--> GO:0006461
* Changed synonym scope of GO:0009273 from "Broad" to "Related"
* Changed synonym scope of GO:0009273 from "Broad" to "Related"
* Changed synonym scope of GO:0009273 from "Related" to "Narrow"
* Changed synonym scope of GO:0009273 from "Related" to "Narrow"
* Changed synonym scope of GO:0009832 from "Exact" to "Narrow"
* Changed synonym scope of GO:0009832 from "Exact" to "Narrow"
* Changed synonym scope of GO:0009832 from "Exact" to "Narrow"
* Changed synonym scope of GO:0009832 from "Exact" to "Related"
* Changed synonym scope of GO:0009832 from "Exact" to "Related"
* Changed synonym scope of GO:0009833 from "Exact" to "Narrow"
* Changed synonym scope of GO:0009833 from "Exact" to "Narrow"
* Changed synonym scope of GO:0009833 from "Exact" to "Related"
* Changed synonym scope of GO:0009833 from "Exact" to "Related"
* Changed synonym scope of GO:0009834 from "Exact" to "Narrow"
* Changed synonym scope of GO:0009834 from "Exact" to "Narrow"
* Changed synonym scope of GO:0009834 from "Exact" to "Related"
* Changed synonym scope of GO:0009834 from "Exact" to "Related"
* Deleted GO:0010802 --OBO_REL:is_a--> GO:0003016
* Deleted GO:0010802 --OBO_REL:is_a--> GO:0007585
* Deleted GO:0002086 --part_of--> GO:0010802
* Deleted GO:0002087 --regulates--> GO:0010802
* Destroyed object GO:0010802
* Deleted GO:0010899 --OBO_REL:is_a--> GO:0050994
* Deleted GO:0010899 --OBO_REL:is_a--> GO:0031329
* Copied GO:0014062 to GO:0051952 with type OBO_REL:is_a
* Copied GO:0014063 to GO:0051953 with type OBO_REL:is_a
* Copied GO:0014064 to GO:0051954 with type OBO_REL:is_a
* Deleted synonym "cellular component biogenesis" from GO:0016043
* Added GO:0016070 to category goslim_pombe
* Added GO:0016568 to category goslim_pombe
* Deleted GO:0019226 --part_of--> GO:0050877
* Copied GO:0019226 to GO:0050877 with type OBO_REL:is_a
* Added GO:0019725 to category goslim_pombe
* Copied GO:0022898 to GO:0034762 with type OBO_REL:is_a
* Changed definition of GO:0030302 from "Transport of deoxynucleotides: a deoxyribonucleoside in ester linkage to phosphate, commonly at the 5' position of its deoxyribose moiety." to "The directed movement of a deoxynucleotide, a deoxyribonucleoside in ester linkage to phosphate, commonly at the 5' position of its deoxyribose moiety, into, out of or within a cell."
* Changed name of GO:0031024 from "interphase microtubule organizing center formation" to "interphase microtubule organizing center assembly"
* Changed definition of GO:0031024 from "The assembly of gamma-tubulin and other proteins into an interphase microtubule organizing center." to "The aggregation, arrangement and bonding together of a set of components, including gamma-tubulin and other proteins, to form an interphase microtubule organizing center."
* Added definition dbxref GOC:mah to GO:0031024
* Added general dbxref GOC:mah to synonym interphase microtubule organizing center biogenesis of GO:0031024
* Changed synonym scope of GO:0031024 from "Exact" to "Related"
* Copied GO:0031024 to GO:0022607 with type OBO_REL:is_a
* Copied GO:0031034 to GO:0043623 with type OBO_REL:is_a
* Changed definition of GO:0031382 from "Formation of a projection by unicellular fungi in response to mating pheromone." to "The aggregation, arrangement and bonding together of a set of components to form a cell projection in response to mating pheromone. This process is observed in unicellular fungi."
* Added definition dbxref GOC:mah to GO:0031382
* Changed name of GO:0034219 from "transmembrane carbohydrate transport" to "carbohydrate transmembrane transport"
* Added synonym "transmembrane carbohydrate transport" to GO:0034219
* Added general dbxref GOC:tb to synonym transmembrane carbohydrate transport of GO:0034219
* Added general dbxref GOC:dph to synonym transmembrane carbohydrate transport of GO:0034219
* Changed synonym scope of GO:0034219 from "Related" to "Exact"
* Changed name of GO:0034220 from "transmembrane ion transport" to "ion transmembrane transport"
* Added synonym "transmembrane ion transport" to GO:0034220
* Added general dbxref GOC:tb to synonym transmembrane ion transport of GO:0034220
* Added general dbxref GOC:dph to synonym transmembrane ion transport of GO:0034220
* Changed synonym scope of GO:0034220 from "Related" to "Exact"
* Deleted GO:0034613 --OBO_REL:is_a--> GO:0051641
* Copied GO:0034613 to GO:0070727 with type OBO_REL:is_a
* Copied GO:0034728 to GO:0034621 with type OBO_REL:is_a
* Changed name of GO:0034755 from "transmembrane iron ion transport" to "iron ion transmembrane transport"
* Changed name of GO:0034759 from "regulation of transmembrane iron ion transport" to "regulation of iron ion transmembrane transport"
* Added synonym "regulation of transmembrane iron ion transport" to GO:0034759
* Added general dbxref GOC:tb to synonym regulation of transmembrane iron ion transport of GO:0034759
* Added general dbxref GOC:dph to synonym regulation of transmembrane iron ion transport of GO:0034759
* Changed synonym scope of GO:0034759 from "Related" to "Exact"
* Changed name of GO:0034760 from "negative regulation of transmembrane iron ion transport" to "negative regulation of iron ion transmembrane transport"
* Added synonym "negative regulation of transmembrane iron ion transport" to GO:0034760
* Added general dbxref GOC:tb to synonym negative regulation of transmembrane iron ion transport of GO:0034760
* Added general dbxref GOC:dph to synonym negative regulation of transmembrane iron ion transport of GO:0034760
* Changed synonym scope of GO:0034760 from "Related" to "Exact"
* Changed name of GO:0034761 from "positive regulation of transmembrane iron ion transport" to "positive regulation of iron ion transmembrane transport"
* Added synonym "positive regulation of transmembrane iron ion transport" to GO:0034761
* Added general dbxref GOC:tb to synonym positive regulation of transmembrane iron ion transport of GO:0034761
* Added general dbxref GOC:dph to synonym positive regulation of transmembrane iron ion transport of GO:0034761
* Changed synonym scope of GO:0034761 from "Related" to "Exact"
* Changed name of GO:0034765 from "regulation of transmembrane ion transport" to "regulation of ion transmembrane transport"
* Added synonym "regulation of transmembrane ion transport" to GO:0034765
* Added general dbxref GOC:tb to synonym regulation of transmembrane ion transport of GO:0034765
* Added general dbxref GOC:dph to synonym regulation of transmembrane ion transport of GO:0034765
* Changed synonym scope of GO:0034765 from "Related" to "Exact"
* Changed name of GO:0034766 from "negative regulation of transmembrane ion transport" to "negative regulation of ion transmembrane transport"
* Added synonym "negative regulation of transmembrane ion transport" to GO:0034766
* Added general dbxref GOC:tb to synonym negative regulation of transmembrane ion transport of GO:0034766
* Added general dbxref GOC:dph to synonym negative regulation of transmembrane ion transport of GO:0034766
* Changed synonym scope of GO:0034766 from "Related" to "Exact"
* Changed name of GO:0034767 from "positive regulation of transmembrane ion transport" to "positive regulation of ion transmembrane transport"
* Changed name of GO:0034775 from "transmembrane glutathione transport" to "glutathione transmembrane transport"
* Added synonym "transmembrane glutathione transport" to GO:0034775
* Added general dbxref GOC:tb to synonym transmembrane glutathione transport of GO:0034775
* Added general dbxref GOC:dph to synonym transmembrane glutathione transport of GO:0034775
* Changed synonym scope of GO:0034775 from "Related" to "Exact"
* Deleted GO:0042244 --OBO_REL:is_a--> GO:0022607
* Copied GO:0042244 to GO:0070726 with type OBO_REL:is_a
* Added GO:0042546 to category goslim_pombe
* Changed synonym scope of GO:0043164 from "Exact" to "Narrow"
* Changed synonym scope of GO:0043164 from "Exact" to "Narrow"
* Changed synonym scope of GO:0043164 from "Exact" to "Narrow"
* Changed synonym scope of GO:0043164 from "Exact" to "Narrow"
* Changed synonym scope of GO:0043164 from "Exact" to "Narrow"
* Changed synonym scope of GO:0043164 from "Exact" to "Narrow"
* Changed synonym scope of GO:0043164 from "Exact" to "Narrow"
* Changed synonym scope of GO:0043164 from "Exact" to "Related"
* Changed synonym scope of GO:0043164 from "Exact" to "Related"
* Changed synonym scope of GO:0043164 from "Exact" to "Related"
* Changed synonym scope of GO:0043164 from "Exact" to "Related"
* Copied GO:0044092 to GO:0003674 with type negatively_regulates
* Copied GO:0044093 to GO:0003674 with type positively_regulates
* Copied GO:0045038 to GO:0006612 with type OBO_REL:is_a
* Copied GO:0045039 to GO:0006612 with type OBO_REL:is_a
* Copied GO:0045040 to GO:0006612 with type OBO_REL:is_a
* Copied GO:0045046 to GO:0006612 with type OBO_REL:is_a
* Changed name of GO:0045763 from "negative regulation of amino acid metabolic process" to "negative regulation of cellular amino acid metabolic process"
* Changed name of GO:0045764 from "positive regulation of amino acid metabolic process" to "positive regulation of cellular amino acid metabolic process"
* Copied GO:0051383 to GO:0034621 with type OBO_REL:is_a
* Copied GO:0051611 to GO:0051952 with type OBO_REL:is_a
* Copied GO:0051612 to GO:0051953 with type OBO_REL:is_a
* Copied GO:0051613 to GO:0051954 with type OBO_REL:is_a
* Deleted synonym "formation by organism of syncitium involving giant cell for nutrient acquisition from host" from GO:0052096
* Copied GO:0052543 to GO:0070727 with type OBO_REL:is_a
* Deleted synonym "heart muscle morphogensis" from GO:0055008
* Added synonym "heart muscle morphogenesis" to GO:0055008
* Changed synonym scope of GO:0055008 from "Related" to "Exact"
* Changed name of GO:0060540 from "diaphragm morphogensis" to "diaphragm morphogenesis"
* Changed definition of GO:0060671 from "The process whereby a trophoblast cell acquires specialized features of an epithelial cell of the placental layrinthine layer." to "The process whereby a trophoblast cell acquires specialized features of an epithelial cell of the placental labyrinthine layer."
* Deleted GO:0060674 --OBO_REL:is_a--> GO:0001944
* Deleted GO:0060685 --OBO_REL:is_a--> GO:0050793
* Copied GO:0060685 to GO:0060688 with type OBO_REL:is_a
* Deleted synonym "DNAse inhibitor activity" from GO:0060703
* Added synonym "DNase inhibitor activity" to GO:0060703
* Added general dbxref GOC:tb to synonym DNase inhibitor activity of GO:0060703
* Added general dbxref GOC:dph to synonym DNase inhibitor activity of GO:0060703
* Changed name of GO:0060715 from "syncitiotrophoblast cell differentiation involved in labyrinthine layer development" to "syncytiotrophoblast cell differentiation involved in labyrinthine layer development"
* Changed definition of GO:0060715 from "The process whereby a chorionic trophoblast cell acquires specialized features of a syncitiotrophoblast of the labyrinthine layer of the placenta." to "The process whereby a chorionic trophoblast cell acquires specialized features of a syncytiotrophoblast of the labyrinthine layer of the placenta."
* Deleted GO:0060721 --OBO_REL:is_a--> GO:0042127
* Deleted GO:0060725 --OBO_REL:is_a--> GO:0065009
* Changed name of GO:0060741 from "prostate gland stromal morphogensis" to "prostate gland stromal morphogenesis"
* Changed name of GO:0070574 from "transmembrane cadmium ion transport" to "cadmium ion transmembrane transport"
* Changed name of GO:0070588 from "transmembrane calcium ion transport" to "calcium ion transmembrane transport"
* Changed definition of GO:0070683 from "A cell cycle checkpoint that blocks cell cycle progression from G2 to M phase until until sister chromatids are sufficiently separated." to "A cell cycle checkpoint that blocks cell cycle progression from G2 to M phase until sister chromatids are sufficiently separated."
* Changed name of GO:0070714 from "RNA guanosine-uridine insertion insertion" to "RNA guanosine-uridine insertion"

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