[Go-diff] GO update 10/03/2008
Remote CVS for Gene Ontology
gocvs at genome.stanford.edu
Fri Oct 3 21:30:46 PDT 2008
OBODIFF of gene_ontology_write.obo version 1.247 by 1.250
Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010765
* Created object of type obo:TERM with id GO:0010766
* Created object of type obo:TERM with id GO:0010767
* Created object of type obo:TERM with id GO:0010768
* Created object of type obo:TERM with id GO:0070058
* Created object of type obo:TERM with id GO:0070059
* Created object of type obo:TERM with id GO:0070060
* Created object of type obo:TERM with id GO:0070061
* Created object of type obo:TERM with id GO:0070062
* Created object of type obo:TERM with id GO:0070063
* Created object of type obo:TERM with id GO:0070064
* Created object of type obo:TERM with id GO:0070065
* Created object of type obo:TERM with id GO:0070066
* Created object of type obo:TERM with id GO:0070067
* Created object of type obo:TERM with id GO:0070068
* Populated new object GO:0010765 (macro)
* Changed name of GO:0010765 from "<new term>" to "positive regulation of sodium ion transport"
* Set definition of GO:0010765 to "Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of, within or between cells."
* Added definition dbxref GOC:dph to GO:0010765
* Added definition dbxref GOC:tb to GO:0010765
* Copied GO:0010765 to GO:0006814 with type positively_regulates
* Copied GO:0010765 to GO:0043270 with type OBO_REL:is_a
* Copied GO:0010765 to GO:0002028 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010765
* Populated new object GO:0010766 (macro)
* Changed name of GO:0010766 from "<new term>" to "negative regulation of sodium ion transport"
* Set definition of GO:0010766 to "Any process that decreases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of, within or between cells."
* Added definition dbxref GOC:dph to GO:0010766
* Added definition dbxref GOC:tb to GO:0010766
* Copied GO:0010766 to GO:0043271 with type OBO_REL:is_a
* Copied GO:0010766 to GO:0002028 with type OBO_REL:is_a
* Copied GO:0010766 to GO:0006814 with type negatively_regulates
* Assigned namespace "biological_process" to GO:0010766
* Populated new object GO:0010767 (macro)
* Changed name of GO:0010767 from "<new term>" to "regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage"
* Set definition of GO:0010767 to "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus."
* Added definition dbxref GOC:dph to GO:0010767
* Added definition dbxref GOC:tb to GO:0010767
* Copied GO:0010767 to GO:0009411 with type OBO_REL:is_a
* Copied GO:0010767 to GO:0043618 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010767
* Populated new object GO:0010768 (macro)
* Changed name of GO:0010768 from "<new term>" to "negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage"
* Set definition of GO:0010768 to "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus."
* Added definition dbxref GOC:dph to GO:0010768
* Added definition dbxref GOC:tb to GO:0010768
* Copied GO:0010768 to GO:0000122 with type OBO_REL:is_a
* Copied GO:0010768 to GO:0010767 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010768
* Populated new object GO:0070058 (macro)
* Changed name of GO:0070058 from "<new term>" to "tRNA gene clustering"
* Set definition of GO:0070058 to "The process by which tRNA genes, which are not linearly connected on the chromosome, are transported in three dimensions to, and maintained together in, the nucleolus. This clustered positioning leads to transcriptional silencing of nearby RNA polymerase II promoters (termed tRNA gene mediated (tgm) silencing) in S. cerevisiae."
* Added definition dbxref GOC:jh to GO:0070058
* Added definition dbxref GOC:mah to GO:0070058
* Added definition dbxref PMID:18708579 to GO:0070058
* Copied GO:0070058 to GO:0051276 with type OBO_REL:is_a
* Copied GO:0070058 to GO:0051641 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070058
* Populated new object GO:0070059 (macro)
* Changed name of GO:0070059 from "<new term>" to "apoptosis in response to endoplasmic reticulum stress"
* Set definition of GO:0070059 to "Apoptosis that occurs in response to a stimulus indicating 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:0070059
* Added definition dbxref PMID:18701708 to GO:0070059
* Added synonym "apoptosis in response to ER stress" to GO:0070059
* Changed synonym scope of GO:0070059 from "Related" to "Exact"
* Added synonym "apoptosis triggered by ER stress" to GO:0070059
* Changed synonym scope of GO:0070059 from "Related" to "Exact"
* Added synonym "endoplasmic reticulum stress-induced apoptosis" to GO:0070059
* Changed synonym scope of GO:0070059 from "Related" to "Exact"
* Added synonym "ER stress-induced apoptosis" to GO:0070059
* Changed synonym scope of GO:0070059 from "Related" to "Exact"
* Copied GO:0070059 to GO:0006915 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070059
* Populated new object GO:0070060 (macro)
* Changed name of GO:0070060 from "<new term>" to "'de novo' actin filament nucleation"
* Set definition of GO:0070060 to "The actin nucleation process by which actin monomers combine in the absence of any existing actin filaments; elongation of the actin oligomer formed by nucleation leads to the formation of an unbranched filament."
* Added definition dbxref GOC:mah to GO:0070060
* Added definition dbxref PMID:17477841 to GO:0070060
* Added synonym "formin-mediated actin filament nucleation" to GO:0070060
* Changed synonym scope of GO:0070060 from "Related" to "Narrow"
* Added synonym "unbranched actin filament nucleation" to GO:0070060
* Copied GO:0070060 to GO:0045010 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070060
* Populated new object GO:0070061 (macro)
* Changed name of GO:0070061 from "<new term>" to "fructose binding"
* Set definition of GO:0070061 to "Interacting selectively with the D- or L-enantiomer of fructose, the ketohexose arabino-hex-2-ulose."
* Added definition dbxref ChEBI:28757 to GO:0070061
* Added definition dbxref GOC:mah to GO:0070061
* Added GO:0070061 to category gosubset_prok
* Copied GO:0070061 to GO:0048029 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0070061
* Populated new object GO:0070062 (macro)
* Changed name of GO:0070062 from "<new term>" to "extracellular vesicular exosome"
* Set definition of GO:0070062 to "A membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane."
* Added definition dbxref GOC:mah to GO:0070062
* Added definition dbxref PMID:15908444 to GO:0070062
* Added definition dbxref PMID:17641064 to GO:0070062
* Copied GO:0070062 to GO:0065010 with type OBO_REL:is_a
* Copied GO:0070062 to GO:0031988 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0070062
* Populated new object GO:0070063 (macro)
* Changed name of GO:0070063 from "<new term>" to "RNA polymerase binding"
* Set definition of GO:0070063 to "Interacting selectively with an RNA polymerase."
* Added definition dbxref GOC:mah to GO:0070063
* Added GO:0070063 to category gosubset_prok
* Copied GO:0070063 to GO:0019899 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0070063
* Populated new object GO:0070064 (macro)
* Changed name of GO:0070064 from "<new term>" to "proline-rich region binding"
* Set definition of GO:0070064 to "Interacting selectively with a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein."
* Added definition dbxref GOC:mah to GO:0070064
* Copied GO:0070064 to GO:0005515 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0070064
* Populated new object GO:0070065 (macro)
* Changed name of GO:0070065 from "<new term>" to "cellubrevin-VAMP4-syntaxin-16 complex"
* Set definition of GO:0070065 to "A SNARE complex that contains cellubrevin (VAMP3), VAMP4, and syntaxin 16 (or orthologs thereof)."
* Added definition dbxref PMID:11839770 to GO:0070065
* Added synonym "SNARE complex (Vamp3, Vamp4, Stx16)" to GO:0070065
* Added general dbxref CORUM:875 to synonym SNARE complex (Vamp3, Vamp4, Stx16) of GO:0070065
* Changed synonym scope of GO:0070065 from "Related" to "Narrow"
* Added synonym "Vamp3-Vamp4-Stx16 complex" to GO:0070065
* Added general dbxref CORUM:875 to synonym Vamp3-Vamp4-Stx16 complex of GO:0070065
* Changed synonym scope of GO:0070065 from "Related" to "Narrow"
* Copied GO:0070065 to GO:0031201 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0070065
* Populated new object GO:0070066 (macro)
* Changed name of GO:0070066 from "<new term>" to "cellubrevin-VAMP4-endobrevin-syntaxin-6 complex"
* Set definition of GO:0070066 to "A SNARE complex that contains cellubrevin (VAMP3), VAMP4, endobrevin (VAMP8), and syntaxin 6 (or orthologs thereof)."
* Added definition dbxref PMID:11839770 to GO:0070066
* Added synonym "SNARE complex (Vamp3, Vamp4, Vam8, Stx6)" to GO:0070066
* Added general dbxref CORUM:874 to synonym SNARE complex (Vamp3, Vamp4, Vam8, Stx6) of GO:0070066
* Changed synonym scope of GO:0070066 from "Related" to "Narrow"
* Added synonym "Vamp3-Vamp4-Vam8-Stx6 complex" to GO:0070066
* Added general dbxref CORUM:874 to synonym Vamp3-Vamp4-Vam8-Stx6 complex of GO:0070066
* Changed synonym scope of GO:0070066 from "Related" to "Narrow"
* Copied GO:0070066 to GO:0031201 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0070066
* Populated new object GO:0070067 (macro)
* Changed name of GO:0070067 from "<new term>" to "syntaxin-6-syntaxin-16-Vti1a complex"
* Set definition of GO:0070067 to "A SNARE complex that contains syntaxin 6, syntaxin 16, and Vti1a (or orthologs thereof)."
* Added definition dbxref PMID:11839770 to GO:0070067
* Copied GO:0070067 to GO:0031201 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0070067
* Populated new object GO:0070068 (macro)
* Changed name of GO:0070068 from "<new term>" to "VAMP4-syntaxin-6-syntaxin-16-Vti1a complex"
* Set definition of GO:0070068 to "A SNARE complex that contains VAMP4, syntaxin 6, syntaxin 16, and Vti1a (or orthologs thereof)."
* Added definition dbxref PMID:11839770 to GO:0070068
* Added synonym "SNARE complex (Vamp4, Stx6, Stx16, Vti1a)" to GO:0070068
* Added general dbxref CORUM:877 to synonym SNARE complex (Vamp4, Stx6, Stx16, Vti1a) of GO:0070068
* Changed synonym scope of GO:0070068 from "Related" to "Narrow"
* Added synonym "Vamp4-Stx6-Stx16-Vti1a complex" to GO:0070068
* Added general dbxref CORUM:877 to synonym Vamp4-Stx6-Stx16-Vti1a complex of GO:0070068
* Copied GO:0070068 to GO:0031201 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0070068
* Changed definition of GO:0005534 from "Interacting selectively with galactose (galacto-hexose), a common constituent of many oligo- and polysaccharides." to "Interacting selectively with the aldohexose galactose (galacto-hexose), a common constituent of many oligo- and polysaccharides."
* Added definition dbxref ChEBI:28260 to GO:0005534
* Changed definition of GO:0005536 from "Interacting selectively with the D- and L-enantiomers of glucose." to "Interacting selectively with the D- or L-enantiomer of glucose."
* Added definition dbxref ChEBI:17234 to GO:0005536
* Added definition dbxref ChEBI:37684 to GO:0005537
* Changed definition of GO:0005885 from "A stable complex of seven subunits, two actin-related proteins, Arp2 and Arp3, and five novel proteins (ARPC1-5). Functions in the nucleation of actin filaments." to "A stable protein complex that contains two actin-related proteins, Arp2 and Arp3, and five novel proteins (ARPC1-5)., and functions in the nucleation of branched actin filaments."
* Added definition dbxref GOC:vw to GO:0005885
* Changed definition of GO:0009925 from "Part of the plasma membrane at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis." to "The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis."
* Changed definition of GO:0010722 from "Any process that modulates the frequency, rate or extent of
ferrochelatase activity; catalysis of the reaction: protoporphyrin + Fe2+ =
protoheme + 2 H+." to "Any process that modulates the frequency, rate or extent of ferrochelatase activity; catalysis of the reaction: protoporphyrin + Fe2+ = protoheme + 2 H+."
* Changed definition of GO:0010736 from "Interacting selectively with the serum response element (SRE), a short
sequence with dyad symmetry found in the promoters of some of the cellular
immediate-early genes, regulated by serum." to "Interacting selectively with the serum response element (SRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum."
* Deleted GO:0014802 --OBO_REL:is_a--> GO:0031984
* Changed definition of GO:0016323 from "Part of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis." to "The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis."
* Changed definition of GO:0016324 from "Part of the plasma membrane at the apical end of the cell." to "The region of the plasma membrane located at the apical end of the cell."
* Added definition dbxref ChEBI:24163 to GO:0016936
* Changed definition of GO:0030056 from "Point of contact between the basal surface of epithelial cells and the basal lamina. Morphologically resembles desmosomes; attached to intermediate filaments." to "A cell-substrate junction that forms a point of contact between the basal surface of epithelial cells and the basal lamina. Morphologically resembles desmosomes; attached to intermediate filaments."
* Changed definition of GO:0030479 from "Discrete actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. As in, but not restricted to, the fungi (Fungi, ncbi_taxonomy_id:4751)." to "A discrete actin-containing structure found at the plasma membrane in cells, at sites of endocytosis; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. As in, but not restricted to, the fungi (Fungi, ncbi_taxonomy_id:4751)."
* Added definition dbxref PMID:16959963 to GO:0030479
* Added comment "Note that this term refers to membrane-bounded compartments that are not considered organelles in their own right, but form parts of larger organelles."
* Changed definition of GO:0031984 from "A compartment that is completely or partially membrane-enclosed, and is part of an organelle." to "A compartment that consists of a lumen and an enclosing membrane, and is part of an organelle."
* Added synonym "intramolecular proline-rich region binding" to GO:0032840
* Changed synonym scope of GO:0032840 from "Related" to "Exact"
* Copied GO:0032840 to GO:0070064 with type OBO_REL:is_a
* Added definition dbxref ChEBI:18222 to GO:0033222
* Added definition dbxref ChEBI:26546 to GO:0033296
* Deleted definition dbxref http://en.wikipedia.org from GO:0033691
* Added definition dbxref ChEBI:26667 to GO:0033691
* Changed definition of GO:0034314 from "The initial step in the formation of an actin filament, in which actin monomers combine to form a new filament, mediated by the Arp2/3 protein complex and its interaction with other proteins." to "The actin nucleation process by which actin monomers combine to form a new branch on the side of an existing actin filament; mediated by the Arp2/3 protein complex and its interaction with other proteins."
* Added definition dbxref PMID:18640983 to GO:0034314
* Added synonym "actin filament branch nucleation" to GO:0034314
* Changed synonym scope of GO:0034314 from "Related" to "Exact"
* Added synonym "branched actin filament nucleation" to GO:0034314
* Changed synonym scope of GO:0034314 from "Related" to "Exact"
* Deleted GO:0034397 --OBO_REL:is_a--> GO:0050000
* Copied GO:0034397 to GO:0051641 with type OBO_REL:is_a
* Copied GO:0034397 to GO:0051276 with type OBO_REL:is_a
* Changed definition of GO:0034976 from "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." 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 endoplasmic reticulum (ER) stress. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen."
* Changed definition of GO:0042806 from "Interacting selectively with fucose, a 5-carbon (pentose) sugar." to "Interacting selectively with fucose, the pentose 6-deoxygalactose."
* Added definition dbxref ChEBI:33984 to GO:0042806
* Deleted GO:0043175 --OBO_REL:is_a--> GO:0019899
* Copied GO:0043175 to GO:0070063 with type OBO_REL:is_a
* Changed definition of GO:0046691 from "A narrow enfolded luminal membrane channel, lined with numerous microvilli, that appears to extend into the cytoplasm of the cell. A specialized network of intracellular canaliculi is a characteristic feature of parietal cells of the gastric mucosa in vertebrates." to "An apical plasma membrane part that forms a narrow enfolded luminal membrane channel, lined with numerous microvilli, that appears to extend into the cytoplasm of the cell. A specialized network of intracellular canaliculi is a characteristic feature of parietal cells of the gastric mucosa in vertebrates."
* Added definition dbxref GOC:mah to GO:0046691
* Added definition dbxref ChEBI:28800 to GO:0046871
* Changed definition of GO:0048029 from "Interacting selectively with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides." to "Interacting selectively with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H?[CHOH]n?C(=O)[CHOH]m?H with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides."
* Added definition dbxref ChEBI:35381 to GO:0048029
* Added definition dbxref ChEBI:33812 to GO:0048032
* Changed definition of GO:0060337 from "A series of molecular events generated as a consequence of a type I
interferon binding to a cell surface receptor. Type I interferons include
the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega
gene families." to "A series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families."
* Changed definition of GO:0060338 from "Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I
interferon binding to a cell surface receptor." to "Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor."
* Changed definition of GO:0060339 from "Any process that decreases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I
interferon binding to a cell surface receptor." to "Any process that decreases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor."
* Changed definition of GO:0060340 from "Any process that increases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I
interferon binding to a cell surface receptor." to "Any process that increases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor."
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