[Go-diff] GO update 02/09/2009

Mon Feb 9 21:30:48 PST 2009

OBODIFF of gene_ontology_write.obo version 1.437 by 1.439

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010899
* Created object of type obo:TERM with id GO:0010900
* Created object of type obo:TERM with id GO:0070306
* Created object of type obo:TERM with id GO:0070307
* Created object of type obo:TERM with id GO:0070308
* Created object of type obo:TERM with id GO:0070309
* Created object of type obo:TERM with id GO:0070310
* Created object of type obo:TERM with id GO:0070311
* Created object of type obo:TERM with id GO:0070312
* Created object of type obo:TERM with id GO:0070313
* Populated new object GO:0010899 (macro)
  * Changed name of GO:0010899 from "<new term>" to "regulation of phosphatidylcholine catabolic process"
  * Set definition of GO:0010899 to "Any process that modulates the rate, frequency or extent of phosphatidylcholine catabolism. Phosphatidylcholine catabolic processes are the chemical reactions and pathways resulting in the breakdown of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline."
  * Added definition dbxref GOC:tb to GO:0010899
  * Copied GO:0010899 to GO:0050994 with type OBO_REL:is_a
  * Copied GO:0010899 to GO:0034638 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010899
* Populated new object GO:0010900 (macro)
  * Changed name of GO:0010900 from "<new term>" to "negative regulation of phosphatidylcholine catabolic process"
  * Set definition of GO:0010900 to "Any process that decreases the rate, frequency or extent of phosphatidylcholine catabolism. Phosphatidylcholine catabolic processes are the chemical reactions and pathways resulting in the breakdown of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline."
  * Added definition dbxref GOC:tb to GO:0010900
  * Copied GO:0010900 to GO:0050995 with type OBO_REL:is_a
  * Copied GO:0010900 to GO:0010899 with type OBO_REL:is_a
  * Copied GO:0010900 to GO:0034638 with type negatively_regulates
  * Assigned namespace "biological_process" to GO:0010900
* Populated new object GO:0070306 (macro)
  * Changed name of GO:0070306 from "<new term>" to "lens fiber cell differentiation"
  * Set definition of GO:0070306 to "The process whereby a relatively unspecialized cell acquires specialized features of a lens fiber cell, any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye. The cytoplasm of a lens ?ber cell is devoid of most intracellular organelles including the cell nucleus, and contains primarily crystallins, a group of water-soluble proteins expressed in very large quantities."
  * Added definition dbxref GOC:mah to GO:0070306
  * Added definition dbxref PMID:7693735 to GO:0070306
  * Added synonym "lens fibre cell differentiation" to GO:0070306
  * Added general dbxref GOC:mah to synonym lens fibre cell differentiation of GO:0070306
  * Changed synonym scope of GO:0070306 from "Related" to "Exact"
  * Copied GO:0070306 to GO:0002088 with type part_of
  * Copied GO:0070306 to GO:0030154 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070306
* Populated new object GO:0070307 (macro)
  * Changed name of GO:0070307 from "<new term>" to "lens fiber cell development"
  * Set definition of GO:0070307 to "The process whose specific outcome is the progression of a lens fiber cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a lens fiber cell fate. A lens fiber cell is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye."
  * Added definition dbxref GOC:mah to GO:0070307
  * Added definition dbxref PMID:7693735 to GO:0070307
  * Added synonym "lens fibre cell development" to GO:0070307
  * Added general dbxref GOC:mah to synonym lens fibre cell development of GO:0070307
  * Changed synonym scope of GO:0070307 from "Related" to "Exact"
  * Copied GO:0070307 to GO:0070306 with type part_of
  * Copied GO:0070307 to GO:0048468 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070307
* Populated new object GO:0070308 (macro)
  * Changed name of GO:0070308 from "<new term>" to "lens fiber cell fate commitment"
  * Set definition of GO:0070308 to "The process whereby the developmental fate of a cell becomes restricted such that it will develop into a lens fiber cell. A lens fiber cell is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye."
  * Added definition dbxref GOC:mah to GO:0070308
  * Added definition dbxref PMID:7693735 to GO:0070308
  * Added synonym "lens fibre cell fate commitment" to GO:0070308
  * Added general dbxref GOC:mah to synonym lens fibre cell fate commitment of GO:0070308
  * Changed synonym scope of GO:0070308 from "Related" to "Exact"
  * Copied GO:0070308 to GO:0045165 with type OBO_REL:is_a
  * Copied GO:0070308 to GO:0070306 with type part_of
  * Assigned namespace "biological_process" to GO:0070308
* Populated new object GO:0070309 (macro)
  * Changed name of GO:0070309 from "<new term>" to "lens fiber cell morphogenesis"
  * Set definition of GO:0070309 to "The process by which the structures of a lens fiber cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a lens fiber cell. A lens fiber cell is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye."
  * Added definition dbxref GOC:mah to GO:0070309
  * Added definition dbxref PMID:7693735 to GO:0070309
  * Added synonym "elongation of lens fiber cell" to GO:0070309
  * Added general dbxref GOC:mah to synonym elongation of lens fiber cell of GO:0070309
  * Added general dbxref GOC:vk to synonym elongation of lens fiber cell of GO:0070309
  * Changed synonym scope of GO:0070309 from "Related" to "Narrow"
  * Added synonym "lens fiber cell morphogenesis during differentiation" to GO:0070309
  * Added general dbxref GOC:mah to synonym lens fiber cell morphogenesis during differentiation of GO:0070309
  * org.geneontology.oboedit.datamodel.history.ChangeSynCategoryHistoryItem at e767ca
  * Changed synonym scope of GO:0070309 from "Related" to "Exact"
  * Added synonym "lens fibre cell morphogenesis" to GO:0070309
  * Added general dbxref GOC:mah to synonym lens fibre cell morphogenesis of GO:0070309
  * Changed synonym scope of GO:0070309 from "Related" to "Exact"
  * Copied GO:0070309 to GO:0002089 with type part_of
  * Copied GO:0070309 to GO:0000904 with type OBO_REL:is_a
  * Copied GO:0070309 to GO:0070307 with type part_of
  * Assigned namespace "biological_process" to GO:0070309
* Populated new object GO:0070310 (macro)
  * Changed name of GO:0070310 from "<new term>" to "ATR-ATRIP complex"
  * Set definition of GO:0070310 to "A protein complex that contains the protein kinase ATR and ATR-interacting protein (ATRIP) and binds single-stranded DNA; ssDNA binding affinity is increased in the presence of replication protein A."
  * Added definition dbxref GOC:mah to GO:0070310
  * Added definition dbxref PMID:14724280 to GO:0070310
  * Added synonym "Mec1-Lcd1 complex" to GO:0070310
  * Added general dbxref PMID:17339343 to synonym Mec1-Lcd1 complex of GO:0070310
  * Changed synonym scope of GO:0070310 from "Related" to "Narrow"
  * Added synonym "Rad3-Rad26 complex" to GO:0070310
  * Added general dbxref PMID:17339343 to synonym Rad3-Rad26 complex of GO:0070310
  * Changed synonym scope of GO:0070310 from "Related" to "Narrow"
  * Copied GO:0070310 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0070310 to GO:0044428 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070310
* Populated new object GO:0070311 (macro)
  * Changed name of GO:0070311 from "<new term>" to "nucleosomal methylation activator complex"
  * Set definition of GO:0070311 to "A protein complex that contains eight subunits in common with the SWI/SNF complex, plus the ATPase BRG1 (SMARCA4) and the histone methyltransferase CARM1; the complex is involved in regulating nuclear receptor-dependent transcription."
  * Added definition dbxref GOC:mah to GO:0070311
  * Added definition dbxref PMID:14729568 to GO:0070311
  * Added synonym "NUMAC" to GO:0070311
  * Added general dbxref PMID:14729568 to synonym NUMAC of GO:0070311
  * Changed synonym scope of GO:0070311 from "Related" to "Exact"
  * Copied GO:0070311 to GO:0016585 with type OBO_REL:is_a
  * Copied GO:0070311 to GO:0035097 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070311
* Populated new object GO:0070312 (macro)
  * Changed name of GO:0070312 from "<new term>" to "RAD52-ERCC4-ERCC1 complex"
  * Added comment "Note that process and function information are included in the term and definition for the purpose of describing and distinguishing the complex."
  * Set definition of GO:0070312 to "A nucleotide-excision repair complex formed by the association of the heterodimeric endonuclease XPF/ERCC4-ERCC1 (Rad1p and Rad10p in S. cerevisiae) with the RAD52 protein."
  * Added definition dbxref PMID:14734547 to GO:0070312
  * Copied GO:0070312 to GO:0000109 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070312
* Populated new object GO:0070313 (macro)
  * Changed name of GO:0070313 from "<new term>" to "RGS6-DNMT1-DMAP1 complex"
  * Set definition of GO:0070313 to "A protein complex formed by the association of RGS6, a negative regulator of heterotrimeric G protein signaling, with the DMAP1-Dnmt1 transcriptional repressor complex; in the complex, RGS6 inhibits the transcriptional repressor activity of DMAP1."
  * Added definition dbxref GOC:mah to GO:0070313
  * Added definition dbxref PMID:14734556 to GO:0070313
  * Copied GO:0070313 to GO:0044428 with type OBO_REL:is_a
  * Copied GO:0070313 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070313
* Changed definition of GO:0000110 from "One of several protein complexes involved in nucleotide-excision repair; possesses DNA damage recognition and endodeoxynuclease activities. In S. cerevisiae, it is composed of Rad1p, Rad10p, and Rad14p." to "One of several protein complexes involved in nucleotide-excision repair; possesses DNA damage recognition and endodeoxynuclease activities. In S. cerevisiae, it is composed of Rad1p, Rad10p, and Rad14p; in human the subunits are ERCC4/XPF, ERCC1 and XPA, respectively."
* Added synonym "XPA-ERCC1-ERCC4 complex" to GO:0000110
* Added general dbxref PMID:8197175 to synonym XPA-ERCC1-ERCC4 complex of GO:0000110
* Changed synonym scope of GO:0000110 from "Related" to "Exact"
* Deleted GO:0010423 --OBO_REL:is_a--> GO:0045939
* Changed definition of GO:0016458 from "Any mechanism, at the level of transcription or post-transcription, causing long-term gene inactivation." to "Any transcriptional or post-transcriptional process carried out at the
cellular level that results in long-term gene inactivation."
* Added definition dbxref GOC:dph to GO:0016458
* Added definition dbxref GOC:tb to GO:0016458
* Copied GO:0016458 to GO:0009987 with type OBO_REL:is_a
* Deleted GO:0045541 --OBO_REL:is_a--> GO:0045939
* Deleted GO:0045542 --OBO_REL:is_a--> GO:0045940
* Deleted GO:0048359 --part_of--> GO:0048316
* Copied GO:0048359 to GO:0010214 with type part_of
* Deleted GO:0051209 --OBO_REL:is_a--> GO:0007204
* Copied GO:0060402 to GO:0007204 with type OBO_REL:is_a