[Go-diff] GO update 01/21/2009

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Wed Jan 21 21:30:48 PST 2009 

OBODIFF of gene_ontology_write.obo version 1.400 by 1.406

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0044026
* Created object of type obo:TERM with id GO:0044027
* Created object of type obo:TERM with id GO:0044028
* Created object of type obo:TERM with id GO:0044029
* Created object of type obo:TERM with id GO:0044030
* Created object of type obo:TERM with id GO:0060405
* Created object of type obo:TERM with id GO:0060406
* Created object of type obo:TERM with id GO:0060407
* Created object of type obo:TERM with id GO:0070263
* Created object of type obo:TERM with id GO:0070264
* Created object of type obo:TERM with id GO:0070265
* Created object of type obo:TERM with id GO:0070266
* Created object of type obo:TERM with id GO:0070267
* Created object of type obo:TERM with id GO:0070268
* Created object of type obo:TERM with id GO:0070269
* Created object of type obo:TERM with id GO:0070270
* Created object of type obo:TERM with id GO:0080029
* Populated new object GO:0044026 (macro)
  * Changed name of GO:0044026 from "<new term>" to "DNA hypermethylation"
  * Set definition of GO:0044026 to "An increase in the epigenetic methylation of cytosine and adenosine residues in DNA."
  * Added definition dbxref GOC:jl to GO:0044026
  * Added definition dbxref http://en.wiktionary.org/ to GO:0044026
  * Copied GO:0044026 to GO:0044030 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0044026
* Populated new object GO:0044027 (macro)
  * Changed name of GO:0044027 from "<new term>" to "hypermethylation of CpG island"
  * Set definition of GO:0044027 to "An increase in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes."
  * Added definition dbxref GOC:jl to GO:0044027
  * Added definition dbxref http://en.wikipedia.org/ to GO:0044027
  * Added synonym "DNA hypermethylation of CpG island" to GO:0044027
  * Changed synonym scope of GO:0044027 from "Related" to "Exact"
  * Copied GO:0044027 to GO:0044026 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0044027
* Populated new object GO:0044028 (macro)
  * Changed name of GO:0044028 from "<new term>" to "DNA hypomethylation"
  * Set definition of GO:0044028 to "An decrease in the epigenetic methylation of cytosine and adenosine residues in DNA."
  * Added definition dbxref GOC:jl to GO:0044028
  * Added definition dbxref http://en.wiktionary.org/ to GO:0044028
  * Copied GO:0044028 to GO:0044030 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0044028
* Populated new object GO:0044029 (macro)
  * Changed name of GO:0044029 from "<new term>" to "hypomethylation of CpG island"
  * Set definition of GO:0044029 to "An decrease in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes."
  * Added definition dbxref GOC:jl to GO:0044029
  * Added definition dbxref http://en.wikipedia.org/ to GO:0044029
  * Added synonym "DNA hypomethylation of CpG island" to GO:0044029
  * Changed synonym scope of GO:0044029 from "Related" to "Exact"
  * Copied GO:0044029 to GO:0044028 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0044029
* Populated new object GO:0044030 (macro)
  * Changed name of GO:0044030 from "<new term>" to "regulation of DNA methylation"
  * Set definition of GO:0044030 to "Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine."
  * Added definition dbxref GOC:jl to GO:0044030
  * Copied GO:0044030 to GO:0060255 with type OBO_REL:is_a
  * Copied GO:0044030 to GO:0006306 with type regulates
  * Assigned namespace "biological_process" to GO:0044030
* Populated new object GO:0060405 (macro)
  * Changed name of GO:0060405 from "<new term>" to "regulation of penile erection"
  * Set definition of GO:0060405 to "Any process that modulates the rate, frequency or extent of penile erection. Penile erection is the hardening, enlarging and rising of the penis which often occurs in the sexually aroused male and enables sexual intercourse. Achieved by increased inflow of blood into the vessels of erectile tissue, and decreased outflow."
  * Added definition dbxref GOC:add to GO:0060405
  * Added definition dbxref GOC:dph to GO:0060405
  * Added definition dbxref GOC:tb to GO:0060405
  * Copied GO:0060405 to GO:0043900 with type OBO_REL:is_a
  * Copied GO:0060405 to GO:0043084 with type regulates
  * Copied GO:0060405 to GO:0051239 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060405
* Populated new object GO:0060406 (macro)
  * Changed name of GO:0060406 from "<new term>" to "positive regulation of penile erection"
  * Set definition of GO:0060406 to "Any process that increases the rate, frequency or extent of penile erection. Penile erection is the hardening, enlarging and rising of the penis which often occurs in the sexually aroused male and enables sexual intercourse. Achieved by increased inflow of blood into the vessels of erectile tissue, and decreased outflow."
  * Added definition dbxref GOC:dph to GO:0060406
  * Added definition dbxref GOC:tb to GO:0060406
  * Copied GO:0060406 to GO:0060405 with type OBO_REL:is_a
  * Copied GO:0060406 to GO:0043084 with type positively_regulates
  * Copied GO:0060406 to GO:0051240 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060406
* Populated new object GO:0060407 (macro)
  * Changed name of GO:0060407 from "<new term>" to "negative regulation of penile erection"
  * Set definition of GO:0060407 to "Any process that increases the rate, frequency or extent of penile erection. Penile erection is the hardening, enlarging and rising of the penis which often occurs in the sexually aroused male and enables sexual intercourse. Achieved by increased inflow of blood into the vessels of erectile tissue, and decreased outflow."
  * Added definition dbxref GOC:dph to GO:0060407
  * Added definition dbxref GOC:tb to GO:0060407
  * Copied GO:0060407 to GO:0051241 with type OBO_REL:is_a
  * Copied GO:0060407 to GO:0043084 with type negatively_regulates
  * Copied GO:0060407 to GO:0060405 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060407
* Populated new object GO:0070263 (macro)
  * Changed name of GO:0070263 from "<new term>" to "external side of fungal-type cell wall"
  * Set definition of GO:0070263 to "The side of the fungal-type cell wall that is opposite to the side that faces the cell and its contents."
  * Added definition dbxref GOC:mah to GO:0070263
  * Copied GO:0070263 to GO:0010339 with type OBO_REL:is_a
  * Copied GO:0070263 to GO:0009277 with type part_of
  * Assigned namespace "cellular_component" to GO:0070263
* Populated new object GO:0070264 (macro)
  * Changed name of GO:0070264 from "<new term>" to "transcription factor TFIIIE complex"
  * Set definition of GO:0070264 to "A transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIE contains a specific subset of ribosomal proteins."
  * Added definition dbxref GOC:jp to GO:0070264
  * Added definition dbxref PMID:19116144 to GO:0070264
  * Copied GO:0070264 to GO:0005667 with type OBO_REL:is_a
  * Copied GO:0070264 to GO:0016591 with type part_of
  * Assigned namespace "cellular_component" to GO:0070264
* Populated new object GO:0070265 (macro)
  * Changed name of GO:0070265 from "<new term>" to "necrotic cell death"
  * Added comment "Note that the word necrosis has been widely used in earlier literature to describe forms of cell death which are now known by more precise terms, such as apoptosis. Necrosis can occur in a regulated fashion, involving a precise sequence of signals."
  * Set definition of GO:0070265 to "A cell death process that is morphologically characterized by a gain in cell volume (oncosis), swelling of organelles, plasma membrane rupture and subsequent loss of intracellular contents."
  * Added definition dbxref PMID:18846107 to GO:0070265
  * Added synonym "cellular necrosis" to GO:0070265
  * Added general dbxref GOC:add to synonym cellular necrosis of GO:0070265
  * Changed synonym scope of GO:0070265 from "Related" to "Exact"
  * Added synonym "necrosis" to GO:0070265
  * Added general dbxref GOC:mah to synonym necrosis of GO:0070265
  * Changed synonym scope of GO:0070265 from "Related" to "Broad"
  * Copied GO:0070265 to GO:0008219 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070265
* Populated new object GO:0070266 (macro)
  * Changed name of GO:0070266 from "<new term>" to "necroptosis"
  * Set definition of GO:0070266 to "A necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors and Toll-like receptors."
  * Added definition dbxref GOC:mah to GO:0070266
  * Added definition dbxref PMID:18846107 to GO:0070266
  * Added synonym "programmed necrotic cell death" to GO:0070266
  * Added general dbxref GOC:mah to synonym programmed necrotic cell death of GO:0070266
  * Changed synonym scope of GO:0070266 from "Related" to "Exact"
  * Copied GO:0070266 to GO:0070265 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070266
* Populated new object GO:0070267 (macro)
  * Changed name of GO:0070267 from "<new term>" to "oncosis"
  * Added comment "Note that oncosis is sometimes described as a type of cell death, but recent nomenclature recommendations define it as a feature of necrotic cell death rather than a distinct mode of cell death."
  * Set definition of GO:0070267 to "A cellular process that results in swelling of the cell body, and that is morphologically characteristic of necrotic cell death."
  * Added definition dbxref PMID:17873035 to GO:0070267
  * Added definition dbxref PMID:18846107 to GO:0070267
  * Copied GO:0070267 to GO:0045793 with type OBO_REL:is_a
  * Copied GO:0070267 to GO:0070265 with type part_of
  * Assigned namespace "biological_process" to GO:0070267
* Populated new object GO:0070268 (macro)
  * Changed name of GO:0070268 from "<new term>" to "cornification"
  * Set definition of GO:0070268 to "A type of programmed cell death that occurs in the epidermis, morphologically and biochemically distinct from apoptosis. It leads to the formation of corneocytes, i.e. dead keratinocytes containing an amalgam of specific proteins (e.g., keratin, loricrin, SPR and involucrin) and lipids (e.g., fatty acids and ceramides), which are necessary for the function of the cornified skin layer (mechanical resistance, elasticity, water repellence and structural stability)."
  * Added definition dbxref PMID:18846107 to GO:0070268
  * Copied GO:0070268 to GO:0031424 with type part_of
  * Copied GO:0070268 to GO:0012501 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070268
* Populated new object GO:0070269 (macro)
  * Changed name of GO:0070269 from "<new term>" to "pyroptosis"
  * Set definition of GO:0070269 to "A type of programmed cell death that results from the apical activation of caspase-1."
  * Added definition dbxref PMID:18846107 to GO:0070269
  * Copied GO:0070269 to GO:0012501 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070269
* Populated new object GO:0070270 (macro)
  * Changed name of GO:0070270 from "<new term>" to "mitotic catastrophe"
  * Set definition of GO:0070270 to "A type of programmed cell death that occurs during or shortly after a dysregulated or failed mitosis and can be accompanied by morphological alterations including micronucleation and multinucleation."
  * Added definition dbxref PMID:18846107 to GO:0070270
  * Added synonym "cell death occurring during metaphase" to GO:0070270
  * Added general dbxref PMID:18846107 to synonym cell death occurring during metaphase of GO:0070270
  * Added synonym "cell death preceded by multinucleation" to GO:0070270
  * Added general dbxref PMID:18846107 to synonym cell death preceded by multinucleation of GO:0070270
  * Copied GO:0070270 to GO:0012501 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070270
* Populated new object GO:0080029 (macro)
  * Changed name of GO:0080029 from "<new term>" to "cellular response to boron levels"
  * Set definition of GO:0080029 to "A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of boron."
  * Added definition dbxref PMID:18952773 to GO:0080029
  * Copied GO:0080029 to GO:0010036 with type OBO_REL:is_a
  * Copied GO:0080029 to GO:0031669 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0080029
* Changed synonym scope of GO:0000724 from "Narrow" to "Exact"
* Added synonym "Rad51-dependent recombinational repair" to GO:0000724
* Added general dbxref GOC:mah to synonym Rad51-dependent recombinational repair of GO:0000724
* Changed synonym scope of GO:0000724 from "Related" to "Exact"
* Added synonym "Rad51 nucleoprotein filament formation" to GO:0000730
* Added general dbxref GOC:elh to synonym Rad51 nucleoprotein filament formation of GO:0000730
* Added general dbxref GOC:vw to synonym Rad51 nucleoprotein filament formation of GO:0000730
* Changed synonym scope of GO:0000730 from "Related" to "Exact"
* Changed definition of GO:0005667 from "Any complex, distinct from RNA polymerase, including one or more polypeptides capable of binding DNA at promoters or at cis-acting regulatory sequences, and regulating transcription." to "A protein complex, distinct from RNA polymerase, that associates with DNA at promoters or at cis-acting regulatory sequences, by direct binding or by interaction with other DNA-binding polypeptides or complexes, and regulates transcription."
* Deleted GO:0006886 --OBO_REL:is_a--> GO:0034613
* Copied GO:0006886 to GO:0034613 with type part_of
* Changed definition of GO:0006915 from "A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle the cell and result in cell death. Apoptosis begins internally with condensation and subsequent fragmentation of the cell nucleus (blebbing) while the plasma membrane remains intact. Other characteristics of apoptosis include DNA fragmentation and the exposure of phosphatidyl serine on the cell surface." to "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."
* Added definition dbxref PMID:18846107 to GO:0006915
* Deleted GO:0010216 --part_of--> GO:0006306
* Copied GO:0010216 to GO:0044030 with type OBO_REL:is_a
* added secondary id GO:0016244 to GO:0012501
* Deleted synonym "necrosis" from GO:0012501
* Added synonym "non-apoptotic programmed cell death" to GO:0012501
* Changed synonym scope of GO:0012501 from "Related" to "Narrow"
* Added synonym "nonapoptotic programmed cell death" to GO:0012501
* Changed synonym scope of GO:0012501 from "Related" to "Narrow"
* Added synonym "type II programmed cell death" to GO:0012501
* Deleted GO:0012503 --OBO_REL:is_a--> GO:0043071
* Copied GO:0012503 to GO:0043068 with type OBO_REL:is_a
* Deleted GO:0016244 --OBO_REL:is_a--> GO:0012501
* Deleted GO:0043070 --regulates--> GO:0016244
* Deleted GO:0043071 --positively_regulates--> GO:0016244
* Deleted GO:0043072 --negatively_regulates--> GO:0016244
* Destroyed object GO:0016244
* Changed definition of GO:0032798 from "A conserved eukaryotic protein complex involved in DNA recombinational repair; in Schizosaccharomyces the complex contains two Swi5 monomers and one Sfr1 monomer." to "A conserved DNA recombinase mediator complex that contains two Swi5 monomers and one Sfr1 monomer in Schizosaccharomyces, or orthologs thereof (e.g. Sae3p and Mei5p in Saccharomyces)."
* Added definition dbxref PMID:15620352 to GO:0032798
* Added synonym "Sae3-Mei5 complex" to GO:0032798
* Added general dbxref GOC:elh to synonym Sae3-Mei5 complex of GO:0032798
* Added general dbxref GOC:vw to synonym Sae3-Mei5 complex of GO:0032798
* Changed synonym scope of GO:0032798 from "Related" to "Exact"
* Deleted GO:0032798 --OBO_REL:is_a--> GO:0043234
* Copied GO:0032798 to GO:0033061 with type OBO_REL:is_a
* Changed definition of GO:0033061 from "A protein complex containing two or more Rad51 paralogs and promotes nucleoprotein filament formation during homologous recombination." to "A protein complex that promotes nucleoprotein filament formation during homologous recombination; most known examples contain two or more RecA family proteins (often Rad51 paralogs)."
* Added synonym "Rad51-mediated strand invasion" to GO:0042148
* Added general dbxref GOC:elh to synonym Rad51-mediated strand invasion of GO:0042148
* Changed synonym scope of GO:0042148 from "Related" to "Exact"
* added secondary id GO:0043070 to GO:0043067
* Added synonym "regulation of non-apoptotic programmed cell death" to GO:0043067
* Changed synonym scope of GO:0043067 from "Related" to "Narrow"
* added secondary id GO:0043071 to GO:0043068
* Added synonym "positive regulation of non-apoptotic programmed cell death" to GO:0043068
* Changed synonym scope of GO:0043068 from "Related" to "Narrow"
* added secondary id GO:0043072 to GO:0043069
* Added synonym "negative regulation of non-apoptotic programmed cell death" to GO:0043069
* Changed synonym scope of GO:0043069 from "Related" to "Narrow"
* Deleted GO:0043070 --OBO_REL:is_a--> GO:0043067
* Deleted GO:0043070 --regulates--> GO:0016244
* Deleted GO:0043072 --OBO_REL:is_a--> GO:0043070
* Deleted GO:0052459 --OBO_REL:is_a--> GO:0043070
* Deleted GO:0043071 --OBO_REL:is_a--> GO:0043070
* Destroyed object GO:0043070
* Deleted GO:0043071 --positively_regulates--> GO:0016244
* Deleted GO:0043071 --OBO_REL:is_a--> GO:0043070
* Deleted GO:0043071 --OBO_REL:is_a--> GO:0043068
* Deleted GO:0012503 --OBO_REL:is_a--> GO:0043071
* Deleted GO:0052518 --OBO_REL:is_a--> GO:0043071
* Destroyed object GO:0043071
* Deleted GO:0043072 --OBO_REL:is_a--> GO:0043070
* Deleted GO:0043072 --negatively_regulates--> GO:0016244
* Deleted GO:0043072 --OBO_REL:is_a--> GO:0043069
* Destroyed object GO:0043072
* Changed name of GO:0046863 from "ribulose-1,5-bisphosphate carboxylase/oxygenase activase activity" to "ribulose-1,5-bisphosphate carboxylase/oxygenase activator activity"
* Added synonym "ribulose-1,5-bisphosphate carboxylase/oxygenase activase activity" to GO:0046863
* Added general dbxref GOC:tb to synonym ribulose-1,5-bisphosphate carboxylase/oxygenase activase activity of GO:0046863
* Added general dbxref GOC:dph to synonym ribulose-1,5-bisphosphate carboxylase/oxygenase activase activity of GO:0046863
* Changed synonym scope of GO:0046863 from "Related" to "Exact"
* Changed definition of GO:0048102 from "Destruction of a cell by its own lysosomal contents. This type of programmed cell death is seen when entire tissues, or parts thereof, are committed to destruction, and occurs by the formation of multiple acidic autophagic vacuoles within the doomed cells." to "A form of programmed cell death that is accompanied by macroautophagy, which is characterized by the sequestration of cytoplasmic material within autophagosomes for bulk degradation by lysosomes. Autophagic cell death is characterized by lack of chromatin condensation, massive vacuolization of the cytoplasm, and accumulation of (double-membraned) autophagic vacuoles, with little or no uptake by phagocytic cells"
* Deleted definition dbxref GOC:jic from GO:0048102
* Deleted definition dbxref PMID:11494315 from GO:0048102
* Added definition dbxref GOC:mah to GO:0048102
* Added definition dbxref PMID:18846107 to GO:0048102
* Deleted GO:0052459 --OBO_REL:is_a--> GO:0043070
* Copied GO:0052459 to GO:0043067 with type OBO_REL:is_a
* Deleted GO:0052518 --OBO_REL:is_a--> GO:0043071
* Copied GO:0052518 to GO:0043068 with type OBO_REL:is_a

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