[Go-diff] GO update 09/22/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Mon Sep 22 21:30:47 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.222 by 1.226

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010710
* Created object of type obo:TERM with id GO:0010711
* Created object of type obo:TERM with id GO:0010712
* Created object of type obo:TERM with id GO:0010713
* Created object of type obo:TERM with id GO:0010714
* Created object of type obo:TERM with id GO:0010715
* Created object of type obo:TERM with id GO:0010716
* Created object of type obo:TERM with id GO:0010717
* Created object of type obo:TERM with id GO:0010718
* Created object of type obo:TERM with id GO:0010719
* Created object of type obo:TERM with id GO:0010720
* Created object of type obo:TERM with id GO:0010721
* Created object of type obo:TERM with id GO:0010722
* Created object of type obo:TERM with id GO:0010723
* Created object of type obo:TERM with id GO:0070016
* Created object of type obo:TERM with id GO:0070017
* Populated new object GO:0010710 (macro)
  * Changed name of GO:0010710 from "<new term>" to "regulation of collagen catabolic process"
  * Set definition of GO:0010710 to "Any process that modulates the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix."
  * Added definition dbxref GOC:dph to GO:0010710
  * Added definition dbxref GOC:tb to GO:0010710
  * Added synonym "regulation of collagen breakdown" to GO:0010710
  * Added general dbxref GOC:tb to synonym regulation of collagen breakdown of GO:0010710
  * Added general dbxref GOC:dph to synonym regulation of collagen breakdown of GO:0010710
  * Changed synonym scope of GO:0010710 from "Related" to "Exact"
  * Added synonym "regulation of collagen catabolism" to GO:0010710
  * Added general dbxref GOC:tb to synonym regulation of collagen catabolism of GO:0010710
  * Added general dbxref GOC:dph to synonym regulation of collagen catabolism of GO:0010710
  * Changed synonym scope of GO:0010710 from "Related" to "Exact"
  * Added synonym "regulation of collagen degradation" to GO:0010710
  * Added general dbxref GOC:tb to synonym regulation of collagen degradation of GO:0010710
  * Added general dbxref GOC:dph to synonym regulation of collagen degradation of GO:0010710
  * Changed synonym scope of GO:0010710 from "Related" to "Exact"
  * Copied GO:0010710 to GO:0030574 with type regulates
  * Copied GO:0010710 to GO:0010712 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010710
* Populated new object GO:0010711 (macro)
  * Changed name of GO:0010711 from "<new term>" to "negative regulation of collagen catabolic process"
  * Set definition of GO:0010711 to "Any process that decreases the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix."
  * Added definition dbxref GOC:dph to GO:0010711
  * Added definition dbxref GOC:tb to GO:0010711
  * Added synonym "down regulation of collagen catabolic process" to GO:0010711
  * Added general dbxref GOC:tb to synonym down regulation of collagen catabolic process of GO:0010711
  * Added general dbxref GOC:dph to synonym down regulation of collagen catabolic process of GO:0010711
  * Changed synonym scope of GO:0010711 from "Related" to "Exact"
  * Added synonym "down-regulation of collagen catabolic process" to GO:0010711
  * Added general dbxref GOC:tb to synonym down-regulation of collagen catabolic process of GO:0010711
  * Added general dbxref GOC:dph to synonym down-regulation of collagen catabolic process of GO:0010711
  * Changed synonym scope of GO:0010711 from "Related" to "Exact"
  * Added synonym "downregulation of collagen catabolic process" to GO:0010711
  * Added general dbxref GOC:tb to synonym downregulation of collagen catabolic process of GO:0010711
  * Added general dbxref GOC:dph to synonym downregulation of collagen catabolic process of GO:0010711
  * Changed synonym scope of GO:0010711 from "Related" to "Exact"
  * Added synonym "inhibition of collagen catabolic process" to GO:0010711
  * Added general dbxref GOC:tb to synonym inhibition of collagen catabolic process of GO:0010711
  * Added general dbxref GOC:dph to synonym inhibition of collagen catabolic process of GO:0010711
  * Changed synonym scope of GO:0010711 from "Related" to "Narrow"
  * Added synonym "negative regulation of collagen breakdown" to GO:0010711
  * Added general dbxref GOC:tb to synonym negative regulation of collagen breakdown of GO:0010711
  * Added general dbxref GOC:dph to synonym negative regulation of collagen breakdown of GO:0010711
  * Changed synonym scope of GO:0010711 from "Related" to "Exact"
  * Added synonym "negative regulation of collagen catabolism" to GO:0010711
  * Added general dbxref GOC:tb to synonym negative regulation of collagen catabolism of GO:0010711
  * Added general dbxref GOC:dph to synonym negative regulation of collagen catabolism of GO:0010711
  * Changed synonym scope of GO:0010711 from "Related" to "Exact"
  * Added synonym "negative regulation of collagen degradation" to GO:0010711
  * Added general dbxref GOC:tb to synonym negative regulation of collagen degradation of GO:0010711
  * Added general dbxref GOC:dph to synonym negative regulation of collagen degradation of GO:0010711
  * Changed synonym scope of GO:0010711 from "Related" to "Exact"
  * Copied GO:0010711 to GO:0010710 with type OBO_REL:is_a
  * Copied GO:0010711 to GO:0010713 with type OBO_REL:is_a
  * Copied GO:0010711 to GO:0030574 with type negatively_regulates
  * Assigned namespace "biological_process" to GO:0010711
* Populated new object GO:0010712 (macro)
  * Changed name of GO:0010712 from "<new term>" to "regulation of collagen metabolic process"
  * Set definition of GO:0010712 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals."
  * Added definition dbxref GOC:dph to GO:0010712
  * Added definition dbxref GOC:tb to GO:0010712
  * Added synonym "regulation of collagen metabolism" to GO:0010712
  * Added general dbxref GOC:tb to synonym regulation of collagen metabolism of GO:0010712
  * Added general dbxref GOC:dph to synonym regulation of collagen metabolism of GO:0010712
  * Changed synonym scope of GO:0010712 from "Related" to "Exact"
  * Copied GO:0010712 to GO:0032963 with type regulates
  * Copied GO:0010712 to GO:0051246 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010712
* Populated new object GO:0010713 (macro)
  * Changed name of GO:0010713 from "<new term>" to "negative regulation of collagen metabolic process"
  * Set definition of GO:0010713 to "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals."
  * Added definition dbxref GOC:dph to GO:0010713
  * Added definition dbxref GOC:tb to GO:0010713
  * Copied GO:0010713 to GO:0010712 with type negatively_regulates
  * Copied GO:0010713 to GO:0051248 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010713
* Populated new object GO:0010714 (macro)
  * Changed name of GO:0010714 from "<new term>" to "positive regulation of collagen metabolic process"
  * Set definition of GO:0010714 to "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals."
  * Added definition dbxref GOC:dph to GO:0010714
  * Added definition dbxref GOC:tb to GO:0010714
  * Added synonym "positive regulation of collagen metabolism" to GO:0010714
  * Added general dbxref GOC:tb to synonym positive regulation of collagen metabolism of GO:0010714
  * Added general dbxref GOC:dph to synonym positive regulation of collagen metabolism of GO:0010714
  * Changed synonym scope of GO:0010714 from "Related" to "Exact"
  * Copied GO:0010714 to GO:0051247 with type OBO_REL:is_a
  * Copied GO:0010714 to GO:0010712 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010714
* Populated new object GO:0010715 (macro)
  * Changed name of GO:0010715 from "<new term>" to "regulation of extracellular matrix disassembly"
  * Set definition of GO:0010715 to "Any process that modulates the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix."
  * Added definition dbxref GOC:dph to GO:0010715
  * Added definition dbxref GOC:tb to GO:0010715
  * Added synonym "regulation of extracellular matrix breakdown" to GO:0010715
  * Added general dbxref GOC:tb to synonym regulation of extracellular matrix breakdown of GO:0010715
  * Added general dbxref GOC:dph to synonym regulation of extracellular matrix breakdown of GO:0010715
  * Changed synonym scope of GO:0010715 from "Related" to "Exact"
  * Added synonym "regulation of extracellular matrix degradation" to GO:0010715
  * Added general dbxref GOC:tb to synonym regulation of extracellular matrix degradation of GO:0010715
  * Added general dbxref GOC:dph to synonym regulation of extracellular matrix degradation of GO:0010715
  * Changed synonym scope of GO:0010715 from "Related" to "Exact"
  * Copied GO:0010715 to GO:0051128 with type OBO_REL:is_a
  * Copied GO:0010715 to GO:0022617 with type regulates
  * Assigned namespace "biological_process" to GO:0010715
* Populated new object GO:0010716 (macro)
  * Changed name of GO:0010716 from "<new term>" to "negative regulation of extracellular matrix disassembly"
  * Set definition of GO:0010716 to "Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix."
  * Added definition dbxref GOC:dph to GO:0010716
  * Added definition dbxref GOC:tb to GO:0010716
  * Added synonym "down regulation of extracellular matrix disassembly" to GO:0010716
  * Added general dbxref GOC:tb to synonym down regulation of extracellular matrix disassembly of GO:0010716
  * Added general dbxref GOC:dph to synonym down regulation of extracellular matrix disassembly of GO:0010716
  * Changed synonym scope of GO:0010716 from "Related" to "Exact"
  * Added synonym "down-regulation of extracellular matrix disassembly" to GO:0010716
  * Added general dbxref GOC:tb to synonym down-regulation of extracellular matrix disassembly of GO:0010716
  * Added general dbxref GOC:dph to synonym down-regulation of extracellular matrix disassembly of GO:0010716
  * Changed synonym scope of GO:0010716 from "Related" to "Exact"
  * Added synonym "downregulation of extracellular matrix disassembly" to GO:0010716
  * Added general dbxref GOC:tb to synonym downregulation of extracellular matrix disassembly of GO:0010716
  * Added general dbxref GOC:dph to synonym downregulation of extracellular matrix disassembly of GO:0010716
  * Changed synonym scope of GO:0010716 from "Related" to "Exact"
  * Added synonym "inhibition of extracellular matrix disassembly" to GO:0010716
  * Added general dbxref GOC:tb to synonym inhibition of extracellular matrix disassembly of GO:0010716
  * Added general dbxref GOC:dph to synonym inhibition of extracellular matrix disassembly of GO:0010716
  * Changed synonym scope of GO:0010716 from "Related" to "Narrow"
  * Added synonym "negative regulation of extracellular matrix breakdown" to GO:0010716
  * Added general dbxref GOC:tb to synonym negative regulation of extracellular matrix breakdown of GO:0010716
  * Added general dbxref GOC:dph to synonym negative regulation of extracellular matrix breakdown of GO:0010716
  * Changed synonym scope of GO:0010716 from "Related" to "Exact"
  * Added synonym "negative regulation of extracellular matrix degradation" to GO:0010716
  * Added general dbxref GOC:tb to synonym negative regulation of extracellular matrix degradation of GO:0010716
  * Added general dbxref GOC:dph to synonym negative regulation of extracellular matrix degradation of GO:0010716
  * Changed synonym scope of GO:0010716 from "Related" to "Exact"
  * Copied GO:0010716 to GO:0051129 with type OBO_REL:is_a
  * Copied GO:0010716 to GO:0010715 with type OBO_REL:is_a
  * Copied GO:0010716 to GO:0022617 with type negatively_regulates
  * Assigned namespace "biological_process" to GO:0010716
* Populated new object GO:0010717 (macro)
  * Changed name of GO:0010717 from "<new term>" to "regulation of epithelial to mesenchymal transition"
  * Set definition of GO:0010717 to "Any process that modulates the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell."
  * Added definition dbxref GOC:dph to GO:0010717
  * Added definition dbxref GOC:tb to GO:0010717
  * Copied GO:0010717 to GO:0001837 with type regulates
  * Copied GO:0010717 to GO:0060284 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010717
* Populated new object GO:0010718 (macro)
  * Changed name of GO:0010718 from "<new term>" to "positive regulation of epithelial to mesenchymal transition"
  * Set definition of GO:0010718 to "Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell."
  * Added definition dbxref GOC:dph to GO:0010718
  * Added definition dbxref GOC:tb to GO:0010718
  * Copied GO:0010718 to GO:0001837 with type positively_regulates
  * Copied GO:0010718 to GO:0010720 with type OBO_REL:is_a
  * Copied GO:0010718 to GO:0010717 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010718
* Populated new object GO:0010719 (macro)
  * Changed name of GO:0010719 from "<new term>" to "negative regulation of epithelial to mesenchymal transition"
  * Set definition of GO:0010719 to "Any process that decreases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell."
  * Added definition dbxref GOC:dph to GO:0010719
  * Added definition dbxref GOC:tb to GO:0010719
  * Copied GO:0010719 to GO:0010721 with type OBO_REL:is_a
  * Copied GO:0010719 to GO:0001837 with type negatively_regulates
  * Copied GO:0010719 to GO:0010717 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010719
* Populated new object GO:0010720 (macro)
  * Changed name of GO:0010720 from "<new term>" to "positive regulation of cell development"
  * Set definition of GO:0010720 to "Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate."
  * Added definition dbxref GOC:dph to GO:0010720
  * Added definition dbxref GOC:tb to GO:0010720
  * Copied GO:0010720 to GO:0048522 with type OBO_REL:is_a
  * Copied GO:0010720 to GO:0060284 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010720
* Populated new object GO:0010721 (macro)
  * Changed name of GO:0010721 from "<new term>" to "negative regulation of cell development"
  * Set definition of GO:0010721 to "Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate."
  * Added definition dbxref GOC:dph to GO:0010721
  * Added definition dbxref GOC:tb to GO:0010721
  * Copied GO:0010721 to GO:0060284 with type negatively_regulates
  * Copied GO:0010721 to GO:0048523 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010721
* Populated new object GO:0010722 (macro)
  * Changed name of GO:0010722 from "<new term>" to "regulation of ferrochelatase activity"
  * Set definition of GO:0010722 to "Any process that modulates the frequency, rate or extent of
ferrochelatase activity; catalysis of the reaction: protoporphyrin + Fe2+ =
protoheme + 2 H+."
  * Added definition dbxref GOC:dph to GO:0010722
  * Added definition dbxref GOC:tb to GO:0010722
  * Copied GO:0010722 to GO:0051339 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010722
* Populated new object GO:0010723 (macro)
  * Changed name of GO:0010723 from "<new term>" to "positive regulation of transcription from RNA polymerase II promoter in response to iron"
  * Set definition of GO:0010723 to "Any process that increases the rate of transcription from an RNA polymerase II promoter in response to an iron stimulus."
  * Added definition dbxref GOC:dph to GO:0010723
  * Added definition dbxref GOC:tb to GO:0010723
  * Copied GO:0010723 to GO:0034395 with type OBO_REL:is_a
  * Copied GO:0010723 to GO:0010552 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010723
* Populated new object GO:0070016 (macro)
  * Changed name of GO:0070016 from "<new term>" to "armadillo repeat domain binding"
  * Set definition of GO:0070016 to "Interacting selectively with the armadillo repeat domain of a protein, an approximately 40 amino acid long tandemly repeated sequence motif  first identified in the Drosophila segment polarity protein armadillo.  Arm-repeat proteins are involved in various processes, including intracellular signalling and cytoskeletal regulation."
  * Added definition dbxref GOC:mah to GO:0070016
  * Added definition dbxref GOC:vk to GO:0070016
  * Added definition dbxref InterPro:IPR000225 to GO:0070016
  * Added synonym "Arm repeat domain binding" to GO:0070016
  * Changed synonym scope of GO:0070016 from "Related" to "Exact"
  * Added synonym "armadillo domain binding" to GO:0070016
  * Changed synonym scope of GO:0070016 from "Related" to "Exact"
  * Added synonym "armadillo repeat binding" to GO:0070016
  * Changed synonym scope of GO:0070016 from "Related" to "Exact"
  * Copied GO:0070016 to GO:0019904 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070016
* Populated new object GO:0070017 (macro)
  * Changed name of GO:0070017 from "<new term>" to "alphav-beta3 integrin-thrombospondin complex"
  * Set definition of GO:0070017 to "A protein complex that consistis of an alphav-beta3 integrin complex bound to thrombospondin."
  * Added definition dbxref PMID:2478219 to GO:0070017
  * Added synonym "ITGAV-ITGB3-THBS1 complex" to GO:0070017
  * Changed synonym scope of GO:0070017 from "Related" to "Narrow"
  * Copied GO:0070017 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0070017 to GO:0044459 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070017
* Copied GO:0001820 to GO:0006837 with type OBO_REL:is_a
* Copied GO:0001821 to GO:0051608 with type OBO_REL:is_a
* Added synonym "NCBP-NIP1 complex" to GO:0005846
* Changed synonym scope of GO:0005846 from "Related" to "Narrow"
* Changed definition of GO:0006810 from "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells." to "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells, or within a multicellular organism."
* Copied GO:0010585 to GO:0006868 with type OBO_REL:is_a
* Copied GO:0014046 to GO:0015872 with type OBO_REL:is_a
* Copied GO:0014051 to GO:0015812 with type OBO_REL:is_a
* Copied GO:0014055 to GO:0015870 with type OBO_REL:is_a
* Deleted GO:0015872 --OBO_REL:is_a--> GO:0006836
* Copied GO:0015872 to GO:0051937 with type OBO_REL:is_a
* Deleted GO:0015874 --OBO_REL:is_a--> GO:0006836
* Copied GO:0015874 to GO:0051937 with type OBO_REL:is_a
* Copied GO:0030150 to GO:0065002 with type OBO_REL:is_a
* Added synonym "microtubule cytoskeleton-dependent nuclear positioning" to GO:0030473
* Changed synonym scope of GO:0030473 from "Related" to "Exact"
* Added synonym "microtubule cytoskeleton-dependent nucleus positioning" to GO:0030473
* Changed synonym scope of GO:0030473 from "Related" to "Exact"
* Added synonym "microtubule-dependent nuclear positioning" to GO:0030473
* Changed synonym scope of GO:0030473 from "Related" to "Exact"
* Added synonym "microtubule-dependent nucleus positioning" to GO:0030473
* Changed synonym scope of GO:0030473 from "Related" to "Exact"
* Added comment "Consider also annotating to the cellular component term 'mitochondrial matrix ; GO:0005759'."
* Copied GO:0032310 to GO:0015732 with type OBO_REL:is_a
* Deleted GO:0032940 --OBO_REL:is_a--> GO:0006810
* Copied GO:0032965 to GO:0010712 with type OBO_REL:is_a
* Copied GO:0032966 to GO:0010713 with type OBO_REL:is_a
* Copied GO:0032967 to GO:0010714 with type OBO_REL:is_a
* Copied GO:0045041 to GO:0065002 with type OBO_REL:is_a
* Copied GO:0046879 to GO:0009914 with type OBO_REL:is_a
* Deleted GO:0046903 --OBO_REL:is_a--> GO:0051234
* Copied GO:0046903 to GO:0006810 with type OBO_REL:is_a
* Deleted GO:0048241 --OBO_REL:is_a--> GO:0006836
* Copied GO:0048241 to GO:0051937 with type OBO_REL:is_a
* Copied GO:0048242 to GO:0048241 with type OBO_REL:is_a
* Copied GO:0048243 to GO:0015874 with type OBO_REL:is_a
* Copied GO:0050432 to GO:0051937 with type OBO_REL:is_a
* Changed name of GO:0065002 from "intracellular protein transport across a membrane" to "intracellular protein transmembrane transport"
* Added synonym "intracellular protein transport across a membrane" to GO:0065002
* Changed synonym scope of GO:0065002 from "Related" to "Exact"

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