[Go-diff] GO update 01/05/2009

Mon Jan 5 21:30:48 PST 2009

OBODIFF of gene_ontology_write.obo version 1.368 by 1.370

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010843
* Created object of type obo:TERM with id GO:0010844
* Created object of type obo:TERM with id GO:0010845
* Created object of type obo:TERM with id GO:0010846
* Created object of type obo:TERM with id GO:0010847
* Created object of type obo:TERM with id GO:0010848
* Populated new object GO:0010843 (macro)
  * Changed name of GO:0010843 from "<new term>" to "promoter binding"
  * Set definition of GO:0010843 to "Interacting selectively within the regulatory region composed of the transcription start site and binding sites for transcription factor complexes of the basal transcription machinery."
  * Added definition dbxref GOC:dph to GO:0010843
  * Added definition dbxref GOC:tb to GO:0010843
  * Added synonym "DNA binding, transcription promoter" to GO:0010843
  * Added general dbxref GOC:tb to synonym DNA binding, transcription promoter of GO:0010843
  * Added general dbxref GOC:dph to synonym DNA binding, transcription promoter of GO:0010843
  * Changed synonym scope of GO:0010843 from "Related" to "Exact"
  * Copied GO:0010843 to GO:0043565 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0010843
* Populated new object GO:0010844 (macro)
  * Changed name of GO:0010844 from "<new term>" to "recombination hotspot binding"
  * Set definition of GO:0010844 to "Interacting selectively with a region in a genome which promotes recombination."
  * Added definition dbxref GOC:dph to GO:0010844
  * Added definition dbxref GOC:tb to GO:0010844
  * Added synonym "DNA binding, recombination hotspot" to GO:0010844
  * Added general dbxref GOC:tb to synonym DNA binding, recombination hotspot of GO:0010844
  * Added general dbxref GOC:dph to synonym DNA binding, recombination hotspot of GO:0010844
  * Changed synonym scope of GO:0010844 from "Related" to "Exact"
  * Copied GO:0010844 to GO:0003677 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0010844
* Populated new object GO:0010845 (macro)
  * Changed name of GO:0010845 from "<new term>" to "positive regulation of reciprocal meiotic recombination"
  * Set definition of GO:0010845 to "Any process that increases the frequency, rate or extent of recombination during meiosis. Reciprocal meiotic recombination is the cell cycle process whereby double strand breaks are formed and repaired through a double Holliday junction intermediate."
  * Added definition dbxref GOC:dph to GO:0010845
  * Added definition dbxref GOC:tb to GO:0010845
  * Added synonym "positive regulation of meiotic recombination" to GO:0010845
  * Added general dbxref GOC:tb to synonym positive regulation of meiotic recombination of GO:0010845
  * Added general dbxref GOC:dph to synonym positive regulation of meiotic recombination of GO:0010845
  * Copied GO:0010845 to GO:0045911 with type OBO_REL:is_a
  * Copied GO:0010845 to GO:0010520 with type OBO_REL:is_a
  * Copied GO:0010845 to GO:0045836 with type OBO_REL:is_a
  * Copied GO:0010845 to GO:0007131 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010845
* Populated new object GO:0010846 (macro)
  * Changed name of GO:0010846 from "<new term>" to "activation of reciprocal meiotic recombination"
  * Set definition of GO:0010846 to "Any process that starts the inactive process of reciprocal meiotic recombination. Reciprocal meiotic recombination is the cell cycle process whereby double strand breaks are formed and repaired through a double Holliday junction intermediate."
  * Added definition dbxref GOC:dph to GO:0010846
  * Added definition dbxref GOC:tb to GO:0010846
  * Added synonym "activation of meiotic recombination" to GO:0010846
  * Added general dbxref GOC:tb to synonym activation of meiotic recombination of GO:0010846
  * Added general dbxref GOC:dph to synonym activation of meiotic recombination of GO:0010846
  * Copied GO:0010846 to GO:0010845 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010846
* Populated new object GO:0010847 (macro)
  * Changed name of GO:0010847 from "<new term>" to "regulation of chromatin assembly"
  * Set definition of GO:0010847 to "Any process the modulates the frequency, rate or extent of chromatin assembly. Chromatin assembly is the assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus."
  * Added definition dbxref GOC:dph to GO:0010847
  * Added definition dbxref GOC:tb to GO:0010847
  * Copied GO:0010847 to GO:0031497 with type regulates
  * Copied GO:0010847 to GO:0001672 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010847
* Populated new object GO:0010848 (macro)
  * Changed name of GO:0010848 from "<new term>" to "regulation of chromatin disassembly"
  * Set definition of GO:0010848 to "Any process that modulates the frequency, rate or extent of chromatin disassembly. Chromatin disassembly is the controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, and other proteins."
  * Added definition dbxref GOC:dph to GO:0010848
  * Added definition dbxref GOC:tb to GO:0010848
  * Copied GO:0010848 to GO:0001672 with type OBO_REL:is_a
  * Copied GO:0010848 to GO:0031498 with type regulates
  * Assigned namespace "biological_process" to GO:0010848
* Changed definition of GO:0010520 from "Any process that modulates the frequency, rate or extent of recombination during meiosis." to "Any process that modulates the frequency, rate or extent of recombination during meiosis. Reciprocal meiotic recombination is the cell cycle process whereby double strand breaks are formed and repaired through a double Holliday junction intermediate."
* Copied GO:0010523 to GO:0060402 with type negatively_regulates
* Copied GO:0010524 to GO:0060402 with type positively_regulates
* Deleted GO:0010736 --OBO_REL:is_a--> GO:0043565
* Copied GO:0010736 to GO:0010843 with type OBO_REL:is_a
* Changed definition of GO:0010842 from "The process whereby the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and
horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the
ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the
radially oriented M?ller glia." to "The process whereby the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the radially oriented M?ller glia."
* Added definition dbxref ChEBI:30413 to GO:0020037
* Copied GO:0020037 to GO:0005506 with type OBO_REL:is_a
* Deleted GO:0032810 --OBO_REL:is_a--> GO:0043565
* Copied GO:0032810 to GO:0010843 with type OBO_REL:is_a
* Deleted GO:0034056 --OBO_REL:is_a--> GO:0043565
* Copied GO:0034056 to GO:0010843 with type OBO_REL:is_a
* Changed definition of GO:0045128 from "Any process that stops, prevents or reduces the frequency, rate or extent of recombination during meiosis." to "Any process that decreases the frequency, rate or extent of recombination during meiosis. Reciprocal meiotic recombination is the cell cycle process whereby double strand breaks are formed and repaired through a double Holliday junction intermediate."
* Added definition dbxref GOC:dph to GO:0045128
* Added definition dbxref GOC:tb to GO:0045128
* Deleted GO:0045297 --OBO_REL:is_a--> GO:0007617
* Copied GO:0045297 to GO:0019098 with type OBO_REL:is_a
* Added comment "This term was made obsolete because it was derived from an EC entry (2.5.1.64) that has since been split into two entries."
* Changed definition of GO:0046410 from "Catalysis of the reaction: 2-oxoglutarate + isochorismate = 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate + pyruvate + CO2." to "OBSOLETE. Catalysis of the reaction: 2-oxoglutarate + isochorismate = 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate + pyruvate + CO2."
* Deleted general dbxref EC:2.5.1.64 from GO:0046410
* Removed GO:0046410 from category gosubset_prok
* Deleted GO:0046410 --OBO_REL:is_a--> GO:0004659
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 182b279