[Go-diff] GO update 03/18/2009

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Wed Mar 18 21:30:49 PDT 2009 

OBODIFF of gene_ontology_write.obo version 1.481 by 1.482

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0070507
* Created object of type obo:TERM with id GO:0070508
* Created object of type obo:TERM with id GO:0070509
* Created object of type obo:TERM with id GO:0070510
* Created object of type obo:TERM with id GO:0070511
* Created object of type obo:TERM with id GO:0070512
* Created object of type obo:TERM with id GO:0070513
* Populated new object GO:0070507 (macro)
  * Changed name of GO:0070507 from "<new term>" to "regulation of microtubule cytoskeleton organization"
  * Set definition of GO:0070507 to "Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins."
  * Added definition dbxref GOC:mah to GO:0070507
  * Added synonym "regulation of microtubule cytoskeleton organisation" to GO:0070507
  * Added general dbxref GOC:mah to synonym regulation of microtubule cytoskeleton organisation of GO:0070507
  * Changed synonym scope of GO:0070507 from "Related" to "Exact"
  * Copied GO:0070507 to GO:0000226 with type OBO_REL:is_a
  * Copied GO:0070507 to GO:0032886 with type regulates
  * Assigned namespace "biological_process" to GO:0070507
* Populated new object GO:0070508 (macro)
  * Changed name of GO:0070508 from "<new term>" to "cholesterol import"
  * Set definition of GO:0070508 to "The directed movement of cholesterol into a cell or organelle."
  * Added definition dbxref GOC:rl to GO:0070508
  * Added synonym "cholesterol uptake" to GO:0070508
  * Added general dbxref GOC:rl to synonym cholesterol uptake of GO:0070508
  * Changed synonym scope of GO:0070508 from "Related" to "Exact"
  * Copied GO:0070508 to GO:0030301 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070508
* Populated new object GO:0070509 (macro)
  * Changed name of GO:0070509 from "<new term>" to "calcium ion import"
  * Set definition of GO:0070509 to "The directed movement of calcium ions into a cell or organelle."
  * Added definition dbxref GOC:mah to GO:0070509
  * Added synonym "calcium ion uptake" to GO:0070509
  * Added general dbxref GOC:mah to synonym calcium ion uptake of GO:0070509
  * Changed synonym scope of GO:0070509 from "Related" to "Exact"
  * Copied GO:0070509 to GO:0006816 with type OBO_REL:is_a
  * Copied GO:0070509 to GO:0034220 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070509
* Populated new object GO:0070510 (macro)
  * Changed name of GO:0070510 from "<new term>" to "regulation of histone H4-K20 methylation"
  * Set definition of GO:0070510 to "Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 20 of histone H4."
  * Added definition dbxref GOC:mah to GO:0070510
  * Copied GO:0070510 to GO:0031060 with type OBO_REL:is_a
  * Copied GO:0070510 to GO:0034770 with type regulates
  * Assigned namespace "biological_process" to GO:0070510
* Populated new object GO:0070511 (macro)
  * Changed name of GO:0070511 from "<new term>" to "negative regulation of histone H4-K20 methylation"
  * Set definition of GO:0070511 to "Any process that stops, prevents or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 20 of histone H4."
  * Added definition dbxref GOC:mah to GO:0070511
  * Added synonym "down regulation of histone H4-K20 methylation" to GO:0070511
  * Added general dbxref GOC:mah to synonym down regulation of histone H4-K20 methylation of GO:0070511
  * Changed synonym scope of GO:0070511 from "Related" to "Exact"
  * Added synonym "down-regulation of histone H4-K20 methylation" to GO:0070511
  * Added general dbxref GOC:mah to synonym down-regulation of histone H4-K20 methylation of GO:0070511
  * Changed synonym scope of GO:0070511 from "Related" to "Exact"
  * Added synonym "downregulation of histone H4-K20 methylation" to GO:0070511
  * Added general dbxref GOC:mah to synonym downregulation of histone H4-K20 methylation of GO:0070511
  * Changed synonym scope of GO:0070511 from "Related" to "Exact"
  * Added synonym "inhibition of histone H4-K20 methylation" to GO:0070511
  * Added general dbxref GOC:mah to synonym inhibition of histone H4-K20 methylation of GO:0070511
  * Changed synonym scope of GO:0070511 from "Related" to "Narrow"
  * Copied GO:0070511 to GO:0034770 with type negatively_regulates
  * Copied GO:0070511 to GO:0031061 with type OBO_REL:is_a
  * Copied GO:0070511 to GO:0070510 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070511
* Populated new object GO:0070512 (macro)
  * Changed name of GO:0070512 from "<new term>" to "positive regulation of histone H4-K20 methylation"
  * Set definition of GO:0070512 to "Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 20 of histone H4."
  * Added definition dbxref GOC:mah to GO:0070512
  * Added synonym "activation of histone H4-K20 methylation" to GO:0070512
  * Added general dbxref GOC:mah to synonym activation of histone H4-K20 methylation of GO:0070512
  * Changed synonym scope of GO:0070512 from "Related" to "Narrow"
  * Added synonym "stimulation of histone H4-K20 methylation" to GO:0070512
  * Added general dbxref GOC:mah to synonym stimulation of histone H4-K20 methylation of GO:0070512
  * Changed synonym scope of GO:0070512 from "Related" to "Narrow"
  * Added synonym "up regulation of histone H4-K20 methylation" to GO:0070512
  * Added general dbxref GOC:mah to synonym up regulation of histone H4-K20 methylation of GO:0070512
  * Changed synonym scope of GO:0070512 from "Related" to "Exact"
  * Added synonym "up-regulation of histone H4-K20 methylation" to GO:0070512
  * Added general dbxref GOC:mah to synonym up-regulation of histone H4-K20 methylation of GO:0070512
  * Changed synonym scope of GO:0070512 from "Related" to "Exact"
  * Added synonym "upregulation of histone H4-K20 methylation" to GO:0070512
  * Added general dbxref GOC:mah to synonym upregulation of histone H4-K20 methylation of GO:0070512
  * Changed synonym scope of GO:0070512 from "Related" to "Exact"
  * Copied GO:0070512 to GO:0031062 with type OBO_REL:is_a
  * Copied GO:0070512 to GO:0034770 with type positively_regulates
  * Copied GO:0070512 to GO:0070510 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070512
* Populated new object GO:0070513 (macro)
  * Changed name of GO:0070513 from "<new term>" to "death domain binding"
  * Set definition of GO:0070513 to "Interacting selectively with a death domain of a protein. The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD bind each other forming oligomers. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB."
  * Added definition dbxref GOC:rl to GO:0070513
  * Added definition dbxref InterPro:IPR000488 to GO:0070513
  * Added definition dbxref Pfam:PF00531 to GO:0070513
  * Copied GO:0070513 to GO:0019904 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070513
* Changed name of GO:0000027 from "ribosomal large subunit assembly and maintenance" to "ribosomal large subunit assembly"
* Changed definition of GO:0000027 from "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form and maintain the large ribosomal subunit." to "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit."
* Changed name of GO:0000028 from "ribosomal small subunit assembly and maintenance" to "ribosomal small subunit assembly"
* Changed definition of GO:0000028 from "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form and maintain the small ribosomal subunit." to "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit."
* Added synonym "ATP-dependent proteolysis" to GO:0004176
* Added general dbxref GOC:mah to synonym ATP-dependent proteolysis of GO:0004176
* Changed definition of GO:0005123 from "Interacting selectively with a death receptor." to "Interacting selectively with any member of the death receptor (DR) family. The DR family falls within the tumor necrosis factor receptor superfamily and is characterized by a cytoplasmic region of ~80 residues termed the death domain (DD)."
* Added definition dbxref GOC:rl to GO:0005123
* Added definition dbxref PMID:15654015 to GO:0005123
* Added synonym "APO binding" to GO:0005123
* Added general dbxref GOC:rl to synonym APO binding of GO:0005123
* Changed synonym scope of GO:0005123 from "Related" to "Narrow"
* Added synonym "DR binding" to GO:0005123
* Added general dbxref GOC:rl to synonym DR binding of GO:0005123
* Changed synonym scope of GO:0005123 from "Related" to "Narrow"
* Added synonym "EDAR binding" to GO:0005123
* Added general dbxref GOC:rl to synonym EDAR binding of GO:0005123
* Changed synonym scope of GO:0005123 from "Related" to "Narrow"
* Added synonym "FAS binding" to GO:0005123
* Added general dbxref GOC:rl to synonym FAS binding of GO:0005123
* Changed synonym scope of GO:0005123 from "Related" to "Narrow"
* Added synonym "KILLER binding" to GO:0005123
* Added general dbxref GOC:rl to synonym KILLER binding of GO:0005123
* Changed synonym scope of GO:0005123 from "Related" to "Narrow"
* Added synonym "NGFR binding" to GO:0005123
* Added general dbxref GOC:rl to synonym NGFR binding of GO:0005123
* Changed synonym scope of GO:0005123 from "Related" to "Narrow"
* Added synonym "TNFR1 binding" to GO:0005123
* Added general dbxref GOC:rl to synonym TNFR1 binding of GO:0005123
* Changed synonym scope of GO:0005123 from "Related" to "Narrow"
* Added synonym "TRAIL binding" to GO:0005123
* Added general dbxref GOC:rl to synonym TRAIL binding of GO:0005123
* Changed synonym scope of GO:0005123 from "Related" to "Narrow"
* Deleted GO:0005123 --OBO_REL:is_a--> GO:0005102
* Copied GO:0005123 to GO:0032813 with type OBO_REL:is_a
* Added definition dbxref PMID:15654015 to GO:0005163
* Copied GO:0005163 to GO:0005123 with type OBO_REL:is_a
* Deleted synonym "high-density lipoprotein" from GO:0005319
* Deleted synonym "low-density lipoprotein" from GO:0005319
* Deleted synonym "very-low-density lipoprotein" from GO:0005319
* Added synonym "ATP-dependent proteolysis" to GO:0006508
* Added general dbxref GOC:mah to synonym ATP-dependent proteolysis of GO:0006508
* Changed synonym scope of GO:0006508 from "Related" to "Narrow"
* Copied GO:0006606 to GO:0034504 with type part_of
* added secondary id GO:0008632 to GO:0006915
* Changed definition of GO:0006915 from "A form of programmed cell death characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), classically little or no ultrastructural modifications of cytoplasmic organelles, plasma membrane blebbing (but maintenance of its integrity until the final stages of the process) and engulfment by resident phagocytes. Apoptosis is usually induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle the cell and result in cell death." to "A form of programmed cell death that begins when a cell receives internal or external signals that trigger the activity of proteolytic caspases, proceeds through a series of characteristic stages typically including rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), and plasma membrane blebbing (but maintenance of its integrity until the final stages of the process), and ends with the death of the cell."
* Added synonym "apoptotic program" to GO:0006915
* Added general dbxref GOC:add to synonym apoptotic program of GO:0006915
* Changed synonym scope of GO:0006915 from "Related" to "Narrow"
* Deleted GO:0006919 --part_of--> GO:0008632
* Copied GO:0006919 to GO:0006915 with type part_of
* Deleted GO:0006921 --part_of--> GO:0008632
* Copied GO:0006921 to GO:0006915 with type part_of
* Deleted GO:0008632 --OBO_REL:is_a--> GO:0007242
* Deleted GO:0008632 --part_of--> GO:0006915
* Deleted GO:0006919 --part_of--> GO:0008632
* Deleted GO:0008637 --part_of--> GO:0008632
* Deleted GO:0008633 --part_of--> GO:0008632
* Deleted GO:0030262 --part_of--> GO:0008632
* Deleted GO:0006921 --part_of--> GO:0008632
* Deleted GO:0043277 --part_of--> GO:0008632
* Destroyed object GO:0008632
* Deleted GO:0008633 --part_of--> GO:0008632
* Copied GO:0008633 to GO:0006915 with type part_of
* Deleted GO:0008637 --part_of--> GO:0008632
* Copied GO:0008637 to GO:0006915 with type part_of
* Deleted GO:0030262 --part_of--> GO:0008632
* Copied GO:0030262 to GO:0006915 with type part_of
* Deleted GO:0032886 --OBO_REL:is_a--> GO:0051493
* Copied GO:0032886 to GO:0050794 with type OBO_REL:is_a
* Deleted GO:0032970 --OBO_REL:is_a--> GO:0051493
* Copied GO:0032970 to GO:0050794 with type OBO_REL:is_a
* Changed name of GO:0034551 from "mitochondrial cytochrome bc(1) complex assembly" to "mitochondrial respiratory chain complex III assembly"
* Deleted synonym "mitochondrial respiratory chain complex III assembly" from GO:0034551
* Added synonym "mitochondrial cytochrome bc(1) complex assembly" to GO:0034551
* Added general dbxref GOC:mcc to synonym mitochondrial cytochrome bc(1) complex assembly of GO:0034551
* Changed synonym scope of GO:0034551 from "Related" to "Exact"
* Deleted GO:0043277 --part_of--> GO:0008632
* Copied GO:0051434 to GO:0070513 with type OBO_REL:is_a
* Copied GO:0051457 to GO:0034504 with type part_of

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