[Go-diff] GO update 07/28/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Mon Jul 28 21:30:46 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.145 by 1.146

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034619
* Created object of type obo:TERM with id GO:0034620
* Created object of type obo:TERM with id GO:0034621
* Created object of type obo:TERM with id GO:0034622
* Created object of type obo:TERM with id GO:0034623
* Populated new object GO:0034619 (macro)
  * Changed name of GO:0034619 from "<new term>" to "cellular chaperone-mediated protein complex assembly"
  * Set definition of GO:0034619 to "The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell, mediated by chaperone molecules that do not form part of the finished complex."
  * Added definition dbxref GOC:mah to GO:0034619
  * Added GO:0034619 to category gosubset_prok
  * Added synonym "chaperone activity" to GO:0034619
  * Copied GO:0034619 to GO:0043623 with type OBO_REL:is_a
  * Copied GO:0034619 to GO:0051131 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034619
* Populated new object GO:0034620 (macro)
  * Changed name of GO:0034620 from "<new term>" to "cellular response to unfolded protein"
  * Added comment "Note that this term should not be confused with 'unfolded protein response ; GO:0030968', which refers to one specific response to the presence of unfolded proteins in the ER."
  * Set definition of GO:0034620 to "A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus."
  * Added definition dbxref GOC:mah to GO:0034620
  * Added GO:0034620 to category gosubset_prok
  * Added synonym "heat shock protein activity" to GO:0034620
  * Copied GO:0034620 to GO:0006986 with type OBO_REL:is_a
  * Copied GO:0034620 to GO:0051716 with type OBO_REL:is_a
  * Copied GO:0034620 to GO:0051789 with type OBO_REL:is_a
  * Copied GO:0034620 to GO:0006950 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034620
* Populated new object GO:0034621 (macro)
  * Changed name of GO:0034621 from "<new term>" to "cellular macromolecular complex subunit organization"
  * Set definition of GO:0034621 to "Any process carried out at the cellular level by which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex."
  * Added definition dbxref GOC:mah to GO:0034621
  * Added definition dbxref GOC:mtg_mpo to GO:0034621
  * Added GO:0034621 to category gosubset_prok
  * Added synonym "cellular macromolecular complex organization" to GO:0034621
  * Changed synonym scope of GO:0034621 from "Related" to "Exact"
  * Added synonym "cellular macromolecular complex subunit organisation" to GO:0034621
  * Changed synonym scope of GO:0034621 from "Related" to "Exact"
  * Copied GO:0034621 to GO:0009987 with type OBO_REL:is_a
  * Copied GO:0034621 to GO:0043933 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034621
* Populated new object GO:0034622 (macro)
  * Changed name of GO:0034622 from "<new term>" to "cellular macromolecular complex assembly"
  * Set definition of GO:0034622 to "The aggregation, arrangement and bonding together of a set of macromolecules to form a complex, carried out at the cellular level."
  * Added definition dbxref GOC:mah to GO:0034622
  * Added GO:0034622 to category goslim_pir
  * Added GO:0034622 to category gosubset_prok
  * Added synonym "cellular macromolecule complex assembly" to GO:0034622
  * Changed synonym scope of GO:0034622 from "Related" to "Exact"
  * Copied GO:0034622 to GO:0034621 with type OBO_REL:is_a
  * Copied GO:0034622 to GO:0065003 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034622
* Populated new object GO:0034623 (macro)
  * Changed name of GO:0034623 from "<new term>" to "cellular macromolecular complex disassembly"
  * Set definition of GO:0034623 to "The disaggregation of a macromolecular complex into its constituent components, carried out at the cellular level."
  * Added definition dbxref GOC:mah to GO:0034623
  * Added GO:0034623 to category gosubset_prok
  * Added synonym "cellular macromolecule complex disassembly" to GO:0034623
  * Changed synonym scope of GO:0034623 from "Related" to "Exact"
  * Copied GO:0034623 to GO:0034621 with type OBO_REL:is_a
  * Copied GO:0034623 to GO:0032984 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034623
* Changed definition of GO:0000343 from "The plastid-encoded plastid RNA polymerase A (PEP-A) is a plastid-encoded DNA-directed RNA polymerase that resembles eubacterial multisubunit RNA polymerases with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-A is generated from the PEP-B form during chloroplast maturation to generate a complex composed of at least thirteen polypeptides that is not sensitive to the antibiotic rifampicin, like its precursor form the PEP-B complex." to "A plastid-encoded DNA-directed RNA polymerase complex that resembles eubacterial multisubunit RNA polymerases, with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-A is generated from the PEP-B form during chloroplast maturation to generate a complex composed of at least thirteen polypeptides that is not sensitive to the antibiotic rifampicin, like its precursor form the PEP-B complex."
* Changed definition of GO:0000344 from "The plastid-encoded plastid RNA polymerase B (PEP-B) is a plastid-encoded DNA-directed RNA polymerase that resembles eubacterial multisubunit RNA polymerases with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-B is distinguished from PEP-A by its sensitivity to the antibiotic rifampicin. PEP-B is found in both etioplasts and chloroplasts, but is the predominate form in etioplasts. It forms the core of the PEP-A form; the conversion from PEP-B to PEP-A occurs during chloroplast maturation." to "A plastid-encoded DNA-directed RNA polymerase complex that resembles eubacterial multisubunit RNA polymerases with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-B is distinguished from PEP-A by its sensitivity to the antibiotic rifampicin. PEP-B is found in both etioplasts and chloroplasts, but is the predominate form in etioplasts. It forms the core of the PEP-A form; the conversion from PEP-B to PEP-A occurs during chloroplast maturation."
* Changed definition of GO:0000427 from "Plastid-encoded plastid RNA polymerases are plastid-encoded DNA-directed RNA polymerases that resemble eubacterial multisubunit RNA polymerases with a core composed of alpha, beta, and beta-prime subunits. Some forms contain multiple additional subunits. An additional sigma factor subunit is required for promoter recognition." to "An RNA polymerase complex containing polypeptides encoded by the plastid genome. Plastid-encoded DNA-directed RNA polymerases resemble eubacterial multisubunit RNA polymerases, with a core composed of alpha, beta, and beta-prime subunits. Some forms contain multiple additional subunits. An additional sigma factor subunit is required for promoter recognition."
* Added definition dbxref GOC:mah to GO:0000427
* Copied GO:0000747 to GO:0022413 with type OBO_REL:is_a
* Deleted GO:0005652 --part_of--> GO:0005635
* Copied GO:0005652 to GO:0005637 with type part_of
* added secondary id GO:0016022 to GO:0005788
* Added synonym "endoplasmic reticulum cisterna" to GO:0005788
* Changed synonym scope of GO:0005788 from "Related" to "Exact"
* Added synonym "ER cisterna" to GO:0005788
* Changed synonym scope of GO:0005788 from "Related" to "Exact"
* Changed definition of GO:0006887 from "The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell. This is the process whereby most molecules are secreted from eukaryotic cells." to "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell. This is the process whereby most molecules are secreted from eukaryotic cells."
* Added definition dbxref GOC:mah to GO:0006887
* Deleted GO:0006887 --part_of--> GO:0032940
* Copied GO:0006887 to GO:0032940 with type OBO_REL:is_a
* Copied GO:0007051 to GO:0000279 with type part_of
* Changed definition of GO:0007140 from "Meiosis in the male germline." to "Progression through the nuclear division phase of a meiotic cell cycle in the male germline."
* Changed definition of GO:0007143 from "Meiosis in the female germline." to "Progression through the nuclear division phase of a meiotic cell cycle in the female germline."
* Added definition dbxref GOC:mah to GO:0007143
* Deleted GO:0008154 --OBO_REL:is_a--> GO:0044267
* Copied GO:0008154 to GO:0034621 with type OBO_REL:is_a
* Deleted GO:0009379 --OBO_REL:is_a--> GO:0043234
* Copied GO:0009379 to GO:0033202 with type OBO_REL:is_a
* Deleted GO:0009743 --OBO_REL:is_a--> GO:0009719
* Deleted GO:0014801 --OBO_REL:is_a--> GO:0016529
* Copied GO:0014801 to GO:0044432 with type OBO_REL:is_a
* Copied GO:0014801 to GO:0016529 with type part_of
* Deleted GO:0014802 --OBO_REL:is_a--> GO:0016529
* Copied GO:0014802 to GO:0031984 with type OBO_REL:is_a
* Copied GO:0014802 to GO:0044432 with type OBO_REL:is_a
* Copied GO:0014802 to GO:0016529 with type part_of
* Deleted GO:0015869 --OBO_REL:is_a--> GO:0015031
* Copied GO:0015869 to GO:0006886 with type OBO_REL:is_a
* Deleted GO:0016022 --OBO_REL:is_a--> GO:0044432
* Destroyed object GO:0016022
* Changed definition of GO:0016029 from "The internal stores of calcium found at the base of the rhabdomere." to "A membrane-bounded compartment that is found at the base of the rhabdomere and contains stored calcium, InsP3 receptors and smooth endoplasmic reticulum Ca2+-ATPase."
* Added definition dbxref PMID:11707492 to GO:0016029
* Added synonym "SMC" to GO:0016029
* Added synonym "submicrovillar cisterna" to GO:0016029
* Added general dbxref PMID:11707492 to synonym submicrovillar cisterna of GO:0016029
* Changed synonym scope of GO:0016029 from "Related" to "Exact"
* Deleted GO:0016029 --OBO_REL:is_a--> GO:0044459
* Copied GO:0016029 to GO:0005790 with type part_of
* Copied GO:0016029 to GO:0031984 with type OBO_REL:is_a
* Deleted GO:0022618 --OBO_REL:is_a--> GO:0065003
* Copied GO:0022618 to GO:0034622 with type OBO_REL:is_a
* Added synonym "multisubunit RNA polymerase" to GO:0030880
* Changed synonym scope of GO:0030880 from "Related" to "Exact"
* Deleted GO:0030968 --OBO_REL:is_a--> GO:0006986
* Copied GO:0030968 to GO:0034620 with type OBO_REL:is_a
* Deleted GO:0031333 --OBO_REL:is_a--> GO:0051248
* Deleted GO:0031334 --OBO_REL:is_a--> GO:0051247
* Changed definition of GO:0031984 from "A membrane-enclosed compartment that is a part of an organelle." to "A compartment that is completely or partially membrane-enclosed, and is part of an organelle."
* Added definition dbxref GOC:mah to GO:0031984
* Deleted GO:0032594 --OBO_REL:is_a--> GO:0015031
* Copied GO:0032594 to GO:0006886 with type OBO_REL:is_a
* Deleted GO:0032986 --OBO_REL:is_a--> GO:0032984
* Copied GO:0032986 to GO:0034623 with type OBO_REL:is_a
* Deleted GO:0032988 --OBO_REL:is_a--> GO:0032984
* Copied GO:0032988 to GO:0034623 with type OBO_REL:is_a
* Deleted GO:0034514 --OBO_REL:is_a--> GO:0006986
* Copied GO:0034514 to GO:0034620 with type OBO_REL:is_a
* Deleted GO:0043200 --OBO_REL:is_a--> GO:0009719
* Deleted GO:0043254 --OBO_REL:is_a--> GO:0051246
* Deleted GO:0043623 --OBO_REL:is_a--> GO:0044267
* Copied GO:0043623 to GO:0034622 with type OBO_REL:is_a
* Deleted GO:0043624 --OBO_REL:is_a--> GO:0044267
* Copied GO:0043624 to GO:0034623 with type OBO_REL:is_a
* Changed definition of GO:0045054 from "The constitutive pathway required by all cells, along which substances are moved around and out of the cell. Transport vesicles destined for the plasma membrane leave the trans-Golgi network in a steady stream. The membrane proteins and the lipids in these vesicles provide new components for the plasma membrane, while the soluble proteins inside the vesicles are secreted to the extracellular space by exocytosis." to "A process of exocytosis found in all eukaryotic cells, in which transport vesicles destined for the plasma membrane leave the trans-Golgi network in a steady stream. Upon exocytosis, the membrane proteins and lipids in these vesicles provide new components for the plasma membrane, and the soluble proteins inside the vesicles are released into the extracellular space."
* Added definition dbxref GOC:mah to GO:0045054
* Deleted GO:0045054 --OBO_REL:is_a--> GO:0032940
* Copied GO:0045054 to GO:0006887 with type OBO_REL:is_a
* Changed definition of GO:0045055 from "The regulated secretory pathway is a second secretory pathway in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand." to "A process of exocytosis in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand."
* Added definition dbxref GOC:mah to GO:0045055
* Deleted GO:0045105 --OBO_REL:is_a--> GO:0019538
* Copied GO:0045105 to GO:0043933 with type OBO_REL:is_a
* Deleted GO:0048236 --OBO_REL:is_a--> GO:0007126
* Copied GO:0048236 to GO:0051321 with type OBO_REL:is_a
* Deleted GO:0051258 --OBO_REL:is_a--> GO:0044267
* Copied GO:0051258 to GO:0043623 with type OBO_REL:is_a
* Deleted GO:0051261 --OBO_REL:is_a--> GO:0044267
* Copied GO:0051261 to GO:0043624 with type OBO_REL:is_a
* Deleted GO:0065004 --OBO_REL:is_a--> GO:0065003
* Copied GO:0065004 to GO:0034622 with type OBO_REL:is_a

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