[Go-diff] GO update 09/10/2008

[Remote CVS for Gene Ontology]

OBODIFF of gene_ontology_write.obo version 1.201 by 1.206

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010699
* Created object of type obo:TERM with id GO:0034974
* Created object of type obo:TERM with id GO:0034975
* Created object of type obo:TERM with id GO:0034976
* Created object of type obo:TERM with id GO:0034977
* Created object of type obo:TERM with id GO:0034978
* Created object of type obo:TERM with id GO:0043934
* Created object of type obo:TERM with id GO:0043935
* Populated new object GO:0010699 (macro)
  * Changed name of GO:0010699 from "<new term>" to "cell-cell signaling involved in quorum sensing"
  * Set definition of GO:0010699 to "The cell-cell signaling process in which single-celled organisms monitor population density by detecting the concentration of small diffusible signal molecules."
  * Added definition dbxref GOC:dph to GO:0010699
  * Added definition dbxref GOC:tb to GO:0010699
  * Copied GO:0010699 to GO:0007267 with type OBO_REL:is_a
  * Copied GO:0010699 to GO:0009372 with type part_of
  * Assigned namespace "biological_process" to GO:0010699
* Populated new object GO:0034974 (macro)
  * Changed name of GO:0034974 from "<new term>" to "Swi5-Swi2 complex"
  * Added comment "Note that this term refers to Schizosaccharomyces pombe Swi5 and Swi2, which should not be confused with the unrelated Saccharomyces Swi5p and Swi2p."
  * Set definition of GO:0034974 to "A protein complex involved that contains proteins known in  Schizosaccharomyces as Swi5 monomers and Swi2, and is involved in mating type switching."
  * Added definition dbxref PMID:14663140 to GO:0034974
  * Added synonym "Swi5 complex" to GO:0034974
  * Changed synonym scope of GO:0034974 from "Related" to "Broad"
  * Copied GO:0034974 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034974 to GO:0000790 with type part_of
  * Copied GO:0034974 to GO:0044454 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034974
* Populated new object GO:0034975 (macro)
  * Changed name of GO:0034975 from "<new term>" to "protein folding in endoplasmic reticulum"
  * Set definition of GO:0034975 to "A protein folding process that takes place in the endoplasmic reticulum (ER). Secreted, plasma membrane and organelle proteins are folded in the ER, assisted by chaperones and foldases (protein disulphide isomerases), and additional factors required for optimal folding (ATP, Ca2+ and an oxidizing environment to allow disulfide bond formation)."
  * Added definition dbxref GOC:mah to GO:0034975
  * Added definition dbxref GOC:vw to GO:0034975
  * Added synonym "protein folding in ER" to GO:0034975
  * Changed synonym scope of GO:0034975 from "Related" to "Exact"
  * Copied GO:0034975 to GO:0006457 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034975
* Populated new object GO:0034976 (macro)
  * Changed name of GO:0034976 from "<new term>" to "response to endoplasmic reticulum stress"
  * Set definition of GO:0034976 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 indicating stress endoplasmic reticulum (ER) stress. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen."
  * Added definition dbxref GOC:mah to GO:0034976
  * Added synonym "ER stress response" to GO:0034976
  * Changed synonym scope of GO:0034976 from "Related" to "Exact"
  * Added synonym "response to ER stress" to GO:0034976
  * Changed synonym scope of GO:0034976 from "Related" to "Exact"
  * Copied GO:0034976 to GO:0033554 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034976
* Populated new object GO:0034977 (macro)
  * Changed name of GO:0034977 from "<new term>" to "ABIN2-NFKB1-MAP3K8 complex"
  * Set definition of GO:0034977 to "A protein complex that contains the precursor form of NF-kappaB (p105), the NF-kappaB inhibitor ABIN-2, and the kinase TPL-2 (MAP3K8); the complex stabilizes TPL-2 and is involved in signaling in lipopolysaccharide (LPS)-stimulated macrophages."
  * Added definition dbxref PMID:15169888 to GO:0034977
  * Added synonym "ABIN2-NFKB1-TPL-1 complex" to GO:0034977
  * Changed synonym scope of GO:0034977 from "Related" to "Exact"
  * Copied GO:0034977 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034977 to GO:0044424 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034977
* Populated new object GO:0034978 (macro)
  * Changed name of GO:0034978 from "<new term>" to "PDX1-PBX1b-MRG1 complex"
  * Set definition of GO:0034978 to "A protein complex that contains the homeodomain proteins PDX1, PBX1b and MRG1 (MEIS2) and is involved in the transcriptional regulation of pancreatic acinar cell-specific genes."
  * Added definition dbxref PMID:11279116 to GO:0034978
  * Added definition dbxref PMID:9710595 to GO:0034978
  * Added synonym "acinar cell-specific C complex" to GO:0034978
  * Changed synonym scope of GO:0034978 from "Related" to "Exact"
  * Copied GO:0034978 to GO:0044428 with type OBO_REL:is_a
  * Copied GO:0034978 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034978
* Populated new object GO:0043934 (macro)
  * Changed name of GO:0043934 from "<new term>" to "protein transport by the Sec complex"
  * Added comment "Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular structure term 'cell envelope Sec protein transport complex ; GO:0031522'. For proteins involved in bacterial Type II secretion across the outer membrane, consider annotating to 'protein secretion by the Type II secretion system ; GO:0015628'. For proteins involved in Sec-complex dependent translocation into the eukaryotic endoplasmic reticulum, consider annotating to 'SRP-dependent cotranslational protein targeting to membrane, translocation ; GO:0006616'. Note that this term is used for annotation of proteins that compose the transport complex but not the proteins being transported."
  * Set definition of GO:0043934 to "The process by which unfolded proteins are transported across the cytoplasmic membrane in Gram-positive and Gram-negative bacteria by the Sec complex, in a process involving proteolytic cleavage of an N-terminal signal peptide."
  * Added definition dbxref GOC:pamgo_curators to GO:0043934
  * Added synonym "protein secretion by the Sec complex" to GO:0043934
  * Changed synonym scope of GO:0043934 from "Related" to "Narrow"
  * Added synonym "protein translocation by the Sec complex" to GO:0043934
  * Changed synonym scope of GO:0043934 from "Related" to "Narrow"
  * Copied GO:0043934 to GO:0015031 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0043934
* Populated new object GO:0043935 (macro)
  * Changed name of GO:0043935 from "<new term>" to "protein transport by the Tat complex"
  * Added comment "Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular structure term 'TAT protein translocation system complex ; GO:0033281'. Note that this term is used for annotation of proteins that compose the transport complex but not the proteins being transported."
  * Set definition of GO:0043935 to "The process by which folded proteins are transported across cytoplasmic membranes of bacteria and membranes of organelles derived from bacteria (chloroplasts and mitochondria) by the TAT complex."
  * Added definition dbxref GOC:pamgo_curators to GO:0043935
  * Added GO:0043935 to category gosubset_prok
  * Added synonym "protein secretion by the TAT complex" to GO:0043935
  * Changed synonym scope of GO:0043935 from "Related" to "Narrow"
  * Added synonym "protein translocation by the TAT complex" to GO:0043935
  * Changed synonym scope of GO:0043935 from "Related" to "Narrow"
  * Added synonym "protein translocation by the Twin-arginine translocation complex" to GO:0043935
  * Changed synonym scope of GO:0043935 from "Related" to "Narrow"
  * Copied GO:0043935 to GO:0015031 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0043935
* Changed definition of GO:0000421 from "The lipid bilayer surrounding an autophagic vacuole, a double-membrane bound vesicle in which endogenous cellular material is sequestered." to "The lipid bilayer surrounding an autophagic vacuole, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered."
* Changed definition of GO:0005764 from "Any of a group of related cytoplasmic, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." to "Any of a group of related cytoplasmic, membrane-bounded organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions."
* Changed definition of GO:0005776 from "A double-membrane bound vesicle in which endogenous cellular material is sequestered; known as autophagosome in yeast." to "A double-membrane-bounded vesicle in which endogenous cellular material is sequestered; known as autophagosome in yeast."
* Deleted synonym "ER stress response" from GO:0006983
* Deleted GO:0006983 --OBO_REL:is_a--> GO:0033554
* Copied GO:0006983 to GO:0034976 with type OBO_REL:is_a
* Changed definition of GO:0009372 from "The cell-cell signaling process in which single-celled organisms, usually bacteria, monitor population density by detecting the concentration of small diffusible signal molecules." to "The process by which single-celled organisms, monitor their population density by detecting
the concentration of small, diffusible signal molecules produced by the cells themselves."
* Deleted GO:0009372 --OBO_REL:is_a--> GO:0007267
* Deleted GO:0009372 --part_of--> GO:0048874
* Copied GO:0009372 to GO:0048874 with type OBO_REL:is_a
* Added comment "The type II protein secretion system complex does not include components of the Sec or Tat pathways. For components of these pathways, consider annotating to 'cell envelope Sec complex ; GO:0031522' or 'TAT protein translocation system complex ; GO:0033281'."
* Changed definition of GO:0015627 from "A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of secreted proteins from the cytoplasm into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane." to "A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of proteins into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane. Proteins using the Type II pathway are transported across the cytoplasmic membrane by the Sec or Tat complex."
* Deleted synonym "type II protein (Sec) secretion system complex" from GO:0015627
* Changed comment from "Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular component term 'type II protein secretion system complex ; GO:0015627'." to "Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular component term 'type II protein secretion system complex ; GO:0015627'. This process refers specifically to secretion across the outer membrane. For components of the Sec and Tat pathways, consider annotating to 'protein transport by the Sec complex ; GO:0043934' and 'protein transport by the Tat complex ; GO:0043935'. Note that this term is used for annotation of proteins that compose the secretion complex but not the proteins being secreted."
* Changed definition of GO:0015628 from "The process by which proteins are secreted across the outer membrane by the type II secretion system. Proteins using this pathway are first translocated across the plasma membrane via the Sec (general secretory) or Tat pathways." to "The process by which proteins are secreted across the outer membrane of Gram-negative bacteria by the type II secretion system. Proteins using this pathway are first translocated across the cytoplasmic membrane via the Sec or Tat pathways."
* Deleted synonym "protein secretion by the Sec-dependent system [sensu Bacteria]" from GO:0015628
* Changed definition of GO:0016236 from "The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane bound autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane bound structure, which then fuse with the lysosome (or vacuole) releasing a single-membrane bound autophagic bodies which are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded." to "The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure, which then fuse with the lysosome (or vacuole) releasing a single-membrane-bounded autophagic bodies which are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded."
* Changed comment from "Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular component term 'type III protein secretion system complex ; GO:0030257'." to "Note that this term represents an activity and not a cellular structure. Consider also annotating to the cellular component term 'type III protein secretion system complex ; GO:0030257'. Note that this term is used for annotation of proteins that compose the secretion complex but not the proteins being secreted."
* Changed definition of GO:0030254 from "The process by which proteins are transferred into the extracellular milieu or directly into host cells by the type III secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins." to "The process by which proteins are transferred into the extracellular milieu or directly into host cells by the bacterial type III secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins."
* Changed definition of GO:0030257 from "A complex of approximately 20 proteins, most of which are located in the inner membrane that carries out protein secretion in the type III secretion system; type III secretion also requires a cytoplasmic, probably membrane-associated ATPase." to "A complex of approximately 20 proteins, most of which are located in the cytoplasmic membrane that carries out protein secretion in the bacterial type III secretion system; type III secretion also requires a cytoplasmic, probably membrane-associated ATPase."
* Deleted synonym "ER stress response" from GO:0030968
* Copied GO:0030968 to GO:0034976 with type OBO_REL:is_a
* Changed name of GO:0031522 from "cell envelope Sec complex" to "cell envelope Sec protein transport complex"
* Added comment "Note that this term represents the protein complex involved in transport of proteins across the cytoplasmic membrane. For proteins involved in bacterial Type II secretion across the outer membrane, consider annotating to 'type II protein secretion complex ; GO:0015628'. For proteins involved in Sec-complex dependent translocation into the eukaryotic endoplasmic reticulum, consider annotating to 'Sec-complex associated translocon complex ; GO:0031206'."
* Added synonym "Sec secretion complex" to GO:0031522
* Changed synonym scope of GO:0031522 from "Related" to "Narrow"
* Added synonym "Sec translocation complex" to GO:0031522
* Changed synonym scope of GO:0031522 from "Related" to "Narrow"
* Added comment "Note that this term refers to Schizosaccharomyces pombe Swi5, which should not be confused with the unrelated Saccharomyces Swi5p."
* Changed definition of GO:0032798 from "A conserved eukaryotic protein complex involved in DNA recombination repair; in Schizosaccharomyces the complex contains two Swi5 monomers and one Sfr1 monomer." to "A conserved eukaryotic protein complex involved in DNA recombinational repair; in Schizosaccharomyces the complex contains two Swi5 monomers and one Sfr1 monomer."
* Deleted GO:0032798 --OBO_REL:is_a--> GO:0044428
* Copied GO:0032798 to GO:0000790 with type part_of
* Copied GO:0032798 to GO:0044454 with type OBO_REL:is_a
* Changed name of GO:0033281 from "TAT protein translocation system complex" to "TAT protein transport complex"
* Changed definition of GO:0033281 from "A complex of three proteins integral to the bacterial cytoplasmic membrane involved in translocation of folded proteins across the bacterial cytoplasmic membrane." to "A complex of three proteins integral to the cytoplasmic membrane of bacteria and membranes of organelles derived from bacteria (chloroplasts and mitochondria) involved in membrane transport of folded proteins."
* Added GO:0033281 to category gosubset_prok
* Added synonym "TAT protein secretion complex" to GO:0033281
* Changed synonym scope of GO:0033281 from "Related" to "Narrow"
* Added synonym "TAT protein translocation system complex" to GO:0033281
* Changed synonym scope of GO:0033281 from "Related" to "Narrow"
* Added synonym "Twin-arginine translocation complex " to GO:0033281
* Changed synonym scope of GO:0033281 from "Related" to "Narrow"
* Deleted GO:0034498 --OBO_REL:is_a--> GO:0016197
* Copied GO:0034498 to GO:0042147 with type OBO_REL:is_a
* Deleted GO:0034499 --OBO_REL:is_a--> GO:0016197
* Copied GO:0034499 to GO:0042147 with type OBO_REL:is_a
* Deleted GO:0035052 --part_of--> GO:0010002
* Copied GO:0035052 to GO:0035051 with type part_of
* Deleted GO:0035053 --part_of--> GO:0010002
* Copied GO:0035053 to GO:0035051 with type part_of
* Changed definition of GO:0042147 from "The directed movement of membrane bound vesicles from recycling endosomes back to the trans-Golgi network where they are recycled for further rounds of transport." to "The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport."
* Added definition dbxref PMID:16936697 to GO:0042147
* Changed definition of GO:0042470 from "A tissue-specific, membrane bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells." to "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells."
* Changed definition of GO:0042599 from "A membrane bounded organelle, specialized for the storage and secretion various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome." to "A membrane-bounded organelle, specialized for the storage and secretion various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome."
* Copied GO:0042729 to GO:0044428 with type OBO_REL:is_a
* Changed comment from "Note that this process has been observed in some archeal and bacterial species." to "Note that this process has been observed in some archaeal and bacterial species."
* Changed definition of GO:0043698 from "A tissue-specific, membrane bounded cytoplasmic organelle within which purines crystalize in reflective stacks. Iridosomes are synthesized in iridophore cells and are silver, gold or iridescent in appearance." to "A tissue-specific, membrane-bounded cytoplasmic organelle within which purines crystalize in reflective stacks. Iridosomes are synthesized in iridophore cells and are silver, gold or iridescent in appearance."
* Changed definition of GO:0043699 from "A tissue-specific, membrane bounded cytoplasmic organelle within which uric acid and/or purines crystalize in reflective stacks. Leucosomes are synthesized in leucophore cells and have a whitish cast." to "A tissue-specific, membrane-bounded cytoplasmic organelle within which uric acid and/or purines crystalize in reflective stacks. Leucosomes are synthesized in leucophore cells and have a whitish cast."
* Changed definition of GO:0043700 from "A tissue-specific, membrane bounded cytoplasmic organelle within which pteridine pigments are synthesized and stored. Pterinosomes are synthesized in xanthophores and erythrophore cells and are yellow, orange or red in appearance." to "A tissue-specific, membrane-bounded cytoplasmic organelle within which pteridine pigments are synthesized and stored. Pterinosomes are synthesized in xanthophores and erythrophore cells and are yellow, orange or red in appearance."
* Changed definition of GO:0043701 from "A tissue-specific, membrane bounded cytoplasmic organelle within which an unknown blue pigment is localized. Cyanosomes are synthesized in cyanophores and are blue in appearance." to "A tissue-specific, membrane-bounded cytoplasmic organelle within which an unknown blue pigment is localized. Cyanosomes are synthesized in cyanophores and are blue in appearance."
* Changed definition of GO:0045022 from "The directed movement of substances, in membrane bound vesicles, from the early sorting endosomes to the late sorting endosomes; transport occurs along microtubules and can be experimentally blocked with microtubule-depolymerizing drugs." to "The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the late sorting endosomes; transport occurs along microtubules and can be experimentally blocked with microtubule-depolymerizing drugs."
* Changed name of GO:0045168 from "cell-cell signaling during cell fate commitment" to "cell-cell signaling involved in cell fate commitment"
* Added definition dbxref GOC:dph to GO:0045168
* Added definition dbxref GOC:tb to GO:0045168
* Added general dbxref UM-BBD_enzymeID: e0741 to GO:0047504
* Added general dbxref UM-BBD_enzymeID: e0916 to GO:0047556
* Added general dbxref UM-BBD_enzymeID: e0712 to GO:0047571
* Changed definition of GO:0048757 from "Steps required to form a membrane bound organelle into a pigment granule containing pigment. Maturation is a developmental process, independent of morphogenetic (shape) change, that is required for a cell or structure to attain its fully functional state." to "Steps required to form a membrane-bounded organelle into a pigment granule containing pigment. Maturation is a developmental process, independent of morphogenetic (shape) change, that is required for a cell or structure to attain its fully functional state."
* Changed definition of GO:0048784 from "The chemical reactions and pathways resulting in the formation of a pigment, during the process by which a membrane bound organelle develops into a pigment granule. Maturation is a developmental process, independent of morphogenetic (shape) change, that is required for a cell or structure to attain its fully functional state." to "The chemical reactions and pathways resulting in the formation of a pigment, during the process by which a membrane-bounded organelle develops into a pigment granule. Maturation is a developmental process, independent of morphogenetic (shape) change, that is required for a cell or structure to attain its fully functional state."