[Go-diff] GO update 05/08/2009

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Fri May 8 21:30:54 PDT 2009 

OBODIFF of gene_ontology_write.obo version 1.598 by 1.603

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created category Fission yeast GO slim (goslim_pombe)
* Created object of type obo:TERM with id GO:0002144
* Created object of type obo:TERM with id GO:0060583
* Created object of type obo:TERM with id GO:0060584
* Created object of type obo:TERM with id GO:0060585
* Created object of type obo:TERM with id GO:0060586
* Created object of type obo:TERM with id GO:0060587
* Created object of type obo:TERM with id GO:0060588
* Created object of type obo:TERM with id GO:0060589
* Created object of type obo:TERM with id GO:0060590
* Created object of type obo:TERM with id GO:0070639
* Created object of type obo:TERM with id GO:0070640
* Created object of type obo:TERM with id GO:0070641
* Created object of type obo:TERM with id GO:0070642
* Created object of type obo:TERM with id GO:0070643
* Created object of type obo:TERM with id GO:0070644
* Populated new object GO:0002144 (macro)
  * Changed name of GO:0002144 from "<new term>" to "cytosolic tRNA wobble base thiouridylase complex"
  * Set definition of GO:0002144 to "A complex of two proteins involved in the thiolation of U34 in glutamate, lysine, and glutamine tRNAs of eukaryotes."
  * Added definition dbxref PMID:18391219 to GO:0002144
  * Added synonym "Cut1-Cut2 complex" to GO:0002144
  * Changed synonym scope of GO:0002144 from "Related" to "Narrow"
  * Added synonym "tRNA thioudridylase" to GO:0002144
  * Changed synonym scope of GO:0002144 from "Related" to "Broad"
  * Copied GO:0002144 to GO:0005829 with type part_of
  * Copied GO:0002144 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0002144
* Populated new object GO:0060583 (macro)
  * Changed name of GO:0060583 from "<new term>" to "regulation of actin cortical patch localization"
  * Set definition of GO:0060583 to "Any process that modulates the localization of an actin cortical patch. An actin cortical patch is a discrete actin-containing structure found just beneath the plasma membrane in fungal cells."
  * Added definition dbxref GOC:dph to GO:0060583
  * Added definition dbxref GOC:tb to GO:0060583
  * Copied GO:0060583 to GO:0051666 with type regulates
  * Copied GO:0060583 to GO:0060341 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060583
* Populated new object GO:0060584 (macro)
  * Changed name of GO:0060584 from "<new term>" to "regulation of prostaglandin-endoperoxide synthase activity"
  * Set definition of GO:0060584 to "Any process that modulates the rate, frequency or extent of prostaglandin-endoperoxidase activity. Prostaglandin-endoperoxidase activity is the catalysis of the reaction: arachidonate + donor-H2 + 2 O2 = prostaglandin H2 + acceptor + H2O."
  * Added definition dbxref GOC:dph to GO:0060584
  * Added definition dbxref GOC:tb to GO:0060584
  * Copied GO:0060584 to GO:0051341 with type OBO_REL:is_a
  * Copied GO:0060584 to GO:0004666 with type regulates
  * Assigned namespace "biological_process" to GO:0060584
* Populated new object GO:0060585 (macro)
  * Changed name of GO:0060585 from "<new term>" to "positive regulation of prostaglandin-endoperoxidase synthase activity"
  * Set definition of GO:0060585 to "Any process that increases the rate, frequency or extent of prostaglandin-endoperoxidase activity. Prostaglandin-endoperoxidase activity is the catalysis of the reaction: arachidonate + donor-H2 + 2 O2 = prostaglandin H2 + acceptor + H2O."
  * Added definition dbxref GOC:dph to GO:0060585
  * Added definition dbxref GOC:tb to GO:0060585
  * Copied GO:0060585 to GO:0051353 with type OBO_REL:is_a
  * Copied GO:0060585 to GO:0004666 with type positively_regulates
  * Copied GO:0060585 to GO:0060584 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060585
* Populated new object GO:0060586 (macro)
  * Changed name of GO:0060586 from "<new term>" to "multicellular organismal iron ion homeostasis"
  * Set definition of GO:0060586 to "Any process involved in the maintenance of the distribution of iron stores within tissues and organs of a multicellular organism."
  * Added definition dbxref GOC:dph to GO:0060586
  * Added definition dbxref GOC:hjd to GO:0060586
  * Added definition dbxref GOC:tb to GO:0060586
  * Copied GO:0060586 to GO:0055072 with type OBO_REL:is_a
  * Copied GO:0060586 to GO:0048871 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060586
* Populated new object GO:0060587 (macro)
  * Changed name of GO:0060587 from "<new term>" to "regulation of lipoprotein lipid oxidation"
  * Set definition of GO:0060587 to "Any process that modulates the rate, frequency or extent of lipoprotein lipid oxidation. Lipoprotein lipid oxidation is the modification of a lipoprotein by oxidation of the lipid moiety."
  * Added definition dbxref GOC:dph to GO:0060587
  * Added definition dbxref GOC:tb to GO:0060587
  * Copied GO:0060587 to GO:0019216 with type OBO_REL:is_a
  * Copied GO:0060587 to GO:0034439 with type regulates
  * Assigned namespace "biological_process" to GO:0060587
* Populated new object GO:0060588 (macro)
  * Changed name of GO:0060588 from "<new term>" to "negative regulation of lipoprotein lipid oxidation"
  * Set definition of GO:0060588 to "Any process that decreases the rate, frequency or extent of lipoprotein lipid oxidation. Lipoprotein lipid oxidation is the modification of a lipoprotein by oxidation of the lipid moiety."
  * Added definition dbxref GOC:dph to GO:0060588
  * Added definition dbxref GOC:tb to GO:0060588
  * Copied GO:0060588 to GO:0060587 with type OBO_REL:is_a
  * Copied GO:0060588 to GO:0045833 with type OBO_REL:is_a
  * Copied GO:0060588 to GO:0034439 with type negatively_regulates
  * Assigned namespace "biological_process" to GO:0060588
* Populated new object GO:0060589 (macro)
  * Changed name of GO:0060589 from "<new term>" to "nucleoside-triphosphatase regulator activity"
  * Set definition of GO:0060589 to "Modulates the rate of NTP hydrolysis by a NTPase."
  * Added definition dbxref GOC:dph to GO:0060589
  * Added definition dbxref GOC:tb to GO:0060589
  * Added synonym "NTPase regulator activity" to GO:0060589
  * Added general dbxref GOC:tb to synonym NTPase regulator activity of GO:0060589
  * Added general dbxref GOC:dph to synonym NTPase regulator activity of GO:0060589
  * Changed synonym scope of GO:0060589 from "Related" to "Exact"
  * Copied GO:0060589 to GO:0017111 with type regulates
  * Copied GO:0060589 to GO:0030234 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0060589
* Populated new object GO:0060590 (macro)
  * Changed name of GO:0060590 from "<new term>" to "ATPase regulator activity"
  * Set definition of GO:0060590 to "Modulates the rate of ATP hydrolysis by an ATPase."
  * Added definition dbxref GOC:dph to GO:0060590
  * Added definition dbxref GOC:tb to GO:0060590
  * Copied GO:0060590 to GO:0016887 with type regulates
  * Copied GO:0060590 to GO:0060589 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0060590
* Populated new object GO:0070639 (macro)
  * Changed name of GO:0070639 from "<new term>" to "vitamin D2 metabolic process"
  * Set definition of GO:0070639 to "The chemical reactions and pathways involving vitamin D2, (3S,5Z,7E,22E)-9,10-secoergosta-5,7,10(19),22-tetraen-3-ol."
  * Added definition dbxref ChEBI:28934 to GO:0070639
  * Added definition dbxref GOC:mah to GO:0070639
  * Added synonym "calciferol metabolic process" to GO:0070639
  * Added general dbxref ChEBI:28934 to synonym calciferol metabolic process of GO:0070639
  * Changed synonym scope of GO:0070639 from "Related" to "Exact"
  * Added synonym "ergocalciferol metabolic process" to GO:0070639
  * Added general dbxref ChEBI:28934 to synonym ergocalciferol metabolic process of GO:0070639
  * Changed synonym scope of GO:0070639 from "Related" to "Exact"
  * Added synonym "vitamin D2 metabolism" to GO:0070639
  * Added general dbxref GOC:mah to synonym vitamin D2 metabolism of GO:0070639
  * Changed synonym scope of GO:0070639 from "Related" to "Exact"
  * Copied GO:0070639 to GO:0042359 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070639
* Populated new object GO:0070640 (macro)
  * Changed name of GO:0070640 from "<new term>" to "vitamin D3 metabolic process"
  * Set definition of GO:0070640 to "The chemical reactions and pathways involving vitamin D3, (3S,5Z,7E)-9,10-secocholesta-5,7,10(19)-trien-3-ol."
  * Added definition dbxref ChEBI:28940 to GO:0070640
  * Added definition dbxref GOC:mah to GO:0070640
  * Added synonym "calciol metabolic process" to GO:0070640
  * Added general dbxref ChEBI:28940 to synonym calciol metabolic process of GO:0070640
  * Changed synonym scope of GO:0070640 from "Related" to "Exact"
  * Added synonym "cholecalciferol metabolic process" to GO:0070640
  * Added general dbxref ChEBI:28940 to synonym cholecalciferol metabolic process of GO:0070640
  * Changed synonym scope of GO:0070640 from "Related" to "Exact"
  * Added synonym "vitamin D3 metabolism" to GO:0070640
  * Added general dbxref GOC:mah to synonym vitamin D3 metabolism of GO:0070640
  * Changed synonym scope of GO:0070640 from "Related" to "Exact"
  * Copied GO:0070640 to GO:0042359 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070640
* Populated new object GO:0070641 (macro)
  * Changed name of GO:0070641 from "<new term>" to "vitamin D4 metabolic process"
  * Set definition of GO:0070641 to "The chemical reactions and pathways involving vitamin D4, (3S,5Z,7E)-9,10-secoergosta-5,7,10(19)-trien-3-ol."
  * Added definition dbxref ChEBI:33237 to GO:0070641
  * Added definition dbxref GOC:mah to GO:0070641
  * Added synonym "vitamin D4 metabolism" to GO:0070641
  * Added general dbxref GOC:mah to synonym vitamin D4 metabolism of GO:0070641
  * Changed synonym scope of GO:0070641 from "Related" to "Exact"
  * Copied GO:0070641 to GO:0042359 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070641
* Populated new object GO:0070642 (macro)
  * Changed name of GO:0070642 from "<new term>" to "vitamin D5 metabolic process"
  * Set definition of GO:0070642 to "The chemical reactions and pathways involving vitamin D5, (1S,3Z)-3-[(2E)-2-[(1R,3aS,7aR)-1-[(1R,4S)-4-ethyl-1,5-dimethylhexyl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylene-1-cyclohexanol."
  * Added definition dbxref GOC:mah to GO:0070642
  * Added definition dbxref PubChem_Compound:9547700 to GO:0070642
  * Added synonym "vitamin D5 metabolism" to GO:0070642
  * Added general dbxref GOC:mah to synonym vitamin D5 metabolism of GO:0070642
  * Changed synonym scope of GO:0070642 from "Related" to "Exact"
  * Copied GO:0070642 to GO:0042359 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070642
* Populated new object GO:0070643 (macro)
  * Changed name of GO:0070643 from "<new term>" to "vitamin D 25-hydroxylase activity"
  * Set definition of GO:0070643 to "Catalysis of the hydroxylation of C-25 of any form of vitamin D."
  * Added definition dbxref GOC:mah to GO:0070643
  * Added synonym "calciferol 25-hydroxylase activity" to GO:0070643
  * Added general dbxref GOC:mah to synonym calciferol 25-hydroxylase activity of GO:0070643
  * Changed synonym scope of GO:0070643 from "Related" to "Narrow"
  * Added synonym "cholecalciferol 25-hydroxylase activity" to GO:0070643
  * Added general dbxref GOC:mah to synonym cholecalciferol 25-hydroxylase activity of GO:0070643
  * Changed synonym scope of GO:0070643 from "Related" to "Narrow"
  * Added synonym "ergocalciferol 25-hydroxylase activity" to GO:0070643
  * Added general dbxref GOC:mah to synonym ergocalciferol 25-hydroxylase activity of GO:0070643
  * Changed synonym scope of GO:0070643 from "Related" to "Narrow"
  * Added synonym "vitamin D2 25-hydroxylase activity" to GO:0070643
  * Added general dbxref GOC:mah to synonym vitamin D2 25-hydroxylase activity of GO:0070643
  * Changed synonym scope of GO:0070643 from "Related" to "Narrow"
  * Copied GO:0070643 to GO:0016491 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070643
* Populated new object GO:0070644 (macro)
  * Changed name of GO:0070644 from "<new term>" to "vitamin D response element binding"
  * Set definition of GO:0070644 to "Interacting selectively with the vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum."
  * Added definition dbxref GOC:vk to GO:0070644
  * Added definition dbxref PMID:17426122 to GO:0070644
  * Added synonym "VDRE binding" to GO:0070644
  * Added general dbxref PMID:17426122 to synonym VDRE binding of GO:0070644
  * Added general dbxref GOC:vk to synonym VDRE binding of GO:0070644
  * Changed synonym scope of GO:0070644 from "Related" to "Exact"
  * Copied GO:0070644 to GO:0010843 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070644
* Added GO:0000723 to category goslim_pombe
* Added GO:0000747 to category goslim_pombe
* Copied GO:0000774 to GO:0060590 with type OBO_REL:is_a
* Added GO:0000910 to category goslim_pombe
* Copied GO:0001671 to GO:0060590 with type OBO_REL:is_a
* Copied GO:0005215 to GO:0006810 with type part_of
* Added GO:0005975 to category goslim_pombe
* Added GO:0006091 to category goslim_pombe
* Added GO:0006260 to category goslim_pombe
* Added GO:0006281 to category goslim_pombe
* Added GO:0006310 to category goslim_pombe
* Added GO:0006338 to category goslim_pombe
* Added GO:0006350 to category goslim_pombe
* Added GO:0006412 to category goslim_pombe
* Added GO:0006457 to category goslim_pombe
* Added GO:0006461 to category goslim_pombe
* Added GO:0006486 to category goslim_pombe
* Added GO:0006520 to category goslim_pombe
* Added GO:0006605 to category goslim_pombe
* Added GO:0006629 to category goslim_pombe
* Added GO:0006766 to category goslim_pombe
* Added GO:0006913 to category goslim_pombe
* Added GO:0006950 to category goslim_pombe
* Added GO:0007005 to category goslim_pombe
* Added GO:0007010 to category goslim_pombe
* Added GO:0007047 to category goslim_pombe
* Added GO:0007059 to category goslim_pombe
* Added GO:0007126 to category goslim_pombe
* Added GO:0007163 to category goslim_pombe
* Added GO:0007165 to category goslim_pombe
* Added GO:0007346 to category goslim_pombe
* Deleted GO:0007377 --OBO_REL:is_a--> GO:0009653
* Copied GO:0007377 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0007390 --OBO_REL:is_a--> GO:0009653
* Copied GO:0007390 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0007392 --OBO_REL:is_a--> GO:0009653
* Copied GO:0007392 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0008258 --OBO_REL:is_a--> GO:0009653
* Copied GO:0008258 to GO:0048598 with type OBO_REL:is_a
* Changed name of GO:0010761 from "fibroblast cell migration" to "fibroblast migration"
* Added synonym "fibroblast cell migration" to GO:0010761
* Added general dbxref GOC:dph to synonym fibroblast cell migration of GO:0010761
* Changed synonym scope of GO:0010761 from "Related" to "Exact"
* Changed name of GO:0010762 from "regulation of fibroblast cell migration" to "regulation of fibroblast migration"
* Added synonym "regulation of fibroblast cell migration" to GO:0010762
* Added general dbxref GOC:dph to synonym regulation of fibroblast cell migration of GO:0010762
* Changed synonym scope of GO:0010762 from "Related" to "Exact"
* Changed name of GO:0010763 from "positive regulation of fibroblast cell migration" to "positive regulation of fibroblast migration"
* Added synonym "positive regulation of fibroblast cell migration" to GO:0010763
* Added general dbxref GOC:dph to synonym positive regulation of fibroblast cell migration of GO:0010763
* Changed synonym scope of GO:0010763 from "Related" to "Exact"
* Changed name of GO:0010764 from "negative regulation of fibroblast cell migration" to "negative regulation of fibroblast migration"
* Added synonym "negative regulation of fibroblast cell migration" to GO:0010764
* Added general dbxref GOC:dph to synonym negative regulation of fibroblast cell migration of GO:0010764
* Changed synonym scope of GO:0010764 from "Related" to "Exact"
* Added synonym "primary neural tube morphogenesis" to GO:0014020
* Added general dbxref GOC:dph to synonym primary neural tube morphogenesis of GO:0014020
* Changed synonym scope of GO:0014020 from "Related" to "Exact"
* Deleted GO:0014020 --OBO_REL:is_a--> GO:0035239
* Copied GO:0014020 to GO:0001838 with type OBO_REL:is_a
* Deleted GO:0014021 --OBO_REL:is_a--> GO:0035239
* Copied GO:0014021 to GO:0001838 with type OBO_REL:is_a
* Added GO:0016071 to category goslim_pombe
* Added GO:0016192 to category goslim_pombe
* Deleted GO:0021506 --OBO_REL:is_a--> GO:0002009
* Copied GO:0021506 to GO:0016331 with type OBO_REL:is_a
* Deleted GO:0021507 --OBO_REL:is_a--> GO:0002009
* Copied GO:0021507 to GO:0016331 with type OBO_REL:is_a
* Deleted GO:0021994 --OBO_REL:is_a--> GO:0002009
* Copied GO:0021994 to GO:0016331 with type OBO_REL:is_a
* Deleted GO:0021995 --OBO_REL:is_a--> GO:0002009
* Copied GO:0021995 to GO:0016331 with type OBO_REL:is_a
* Added GO:0030163 to category goslim_pombe
* Changed definition of GO:0030343 from "Catalysis of the hydroxylation of C-25 of cholecalciferol (vitamin D3) to form 25-hydroxycholecalciferol." to "Catalysis of the reaction: vitamin D3 + NADPH + H+ + O2 = calcidiol + NADP+ + H2O."
* Added definition dbxref MetaCyc:RXN-9829 to GO:0030343
* Added general dbxref MetaCyc:RXN-9829 to GO:0030343
* Deleted GO:0030343 --OBO_REL:is_a--> GO:0016491
* Copied GO:0030343 to GO:0070643 with type OBO_REL:is_a
* Added GO:0030437 to category goslim_pombe
* Deleted GO:0030695 --OBO_REL:is_a--> GO:0030234
* Copied GO:0030695 to GO:0060589 with type OBO_REL:is_a
* Added GO:0032446 to category goslim_pombe
* Added GO:0032569 to category goslim_pombe
* Deleted GO:0033505 --OBO_REL:is_a--> GO:0009653
* Copied GO:0033505 to GO:0048598 with type OBO_REL:is_a
* Copied GO:0042030 to GO:0060590 with type OBO_REL:is_a
* Added GO:0042254 to category goslim_pombe
* Deleted GO:0042733 --OBO_REL:is_a--> GO:0009653
* Copied GO:0042733 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0048314 --OBO_REL:is_a--> GO:0009653
* Copied GO:0048314 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0048558 --OBO_REL:is_a--> GO:0009653
* Copied GO:0048558 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0048611 --OBO_REL:is_a--> GO:0009653
* Copied GO:0048611 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0048613 --OBO_REL:is_a--> GO:0009653
* Copied GO:0048613 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0048615 --OBO_REL:is_a--> GO:0009653
* Copied GO:0048615 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0048617 --OBO_REL:is_a--> GO:0009653
* Copied GO:0048617 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0048619 --OBO_REL:is_a--> GO:0009653
* Copied GO:0048619 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0048702 --OBO_REL:is_a--> GO:0009653
* Copied GO:0048702 to GO:0048598 with type OBO_REL:is_a
* Deleted GO:0048703 --OBO_REL:is_a--> GO:0009653
* Copied GO:0048703 to GO:0048598 with type OBO_REL:is_a
* Added GO:0051186 to category goslim_pombe
* Added GO:0055085 to category goslim_pombe
* Added GO:0055086 to category goslim_pombe
* Copied GO:0060561 to GO:0010623 with type OBO_REL:is_a
* Changed definition of GO:0060562 from "The process by which the anatomical structures of a tube are generated and organized from an epithelium. Morphogenesis pertains to the creation of form. Epithelial transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." to "The process by which the anatomical structures of a tube are generated and organized from an epithelium. Morphogenesis pertains to the creation of form. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system."
* Copied GO:0060562 to GO:0002009 with type OBO_REL:is_a
* Copied GO:0070561 to GO:0033280 with type OBO_REL:is_a

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