[Go-diff] GO update 08/18/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Mon Aug 18 21:30:46 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.168 by 

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010669
* Created object of type obo:TERM with id GO:0010670
* Created object of type obo:TERM with id GO:0010671
* Created object of type obo:TERM with id GO:0010672
* Created object of type obo:TERM with id GO:0010673
* Created object of type obo:TERM with id GO:0010674
* Created object of type obo:TERM with id GO:0010675
* Created object of type obo:TERM with id GO:0010676
* Created object of type obo:TERM with id GO:0010677
* Created object of type obo:TERM with id GO:0010678
* Created object of type obo:TERM with id GO:0034660
* Created object of type obo:TERM with id GO:0034661
* Created object of type obo:TERM with id GO:0034662
* Created object of type obo:TERM with id GO:0034663
* Created object of type obo:TERM with id GO:0034664
* Created object of type obo:TERM with id GO:0034665
* Created object of type obo:TERM with id GO:0034666
* Created object of type obo:TERM with id GO:0034667
* Created object of type obo:TERM with id GO:0034668
* Created object of type obo:TERM with id GO:0034669
* Created object of type obo:TERM with id GO:0080011
* Created object of type obo:TERM with id GO:0080012
* Populated new object GO:0010669 (macro)
  * Changed name of GO:0010669 from "<new term>" to "epithelial structure maintenance"
  * Set definition of GO:0010669 to "A tissue homeostatic process required for the maintenance of epithelial structure."
  * Added definition dbxref GOC:dph to GO:0010669
  * Added definition dbxref GOC:tb to GO:0010669
  * Copied GO:0010669 to GO:0001894 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010669
* Populated new object GO:0010670 (macro)
  * Changed name of GO:0010670 from "<new term>" to "positive regulation of oxygen and reactive oxygen species metabolic process"
  * Set definition of GO:0010670 to "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving dioxygen (O2), or any of the reactive oxygen species, e.g. superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (-OH)."
  * Added definition dbxref GOC:dph to GO:0010670
  * Added definition dbxref GOC:tb to GO:0010670
  * Copied GO:0010670 to GO:0006800 with type positively_regulates
  * Copied GO:0010670 to GO:0080010 with type OBO_REL:is_a
  * Copied GO:0010670 to GO:0048522 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010670
* Populated new object GO:0010671 (macro)
  * Changed name of GO:0010671 from "<new term>" to "negative regulation of oxygen and reactive oxygen species metabolic process"
  * Set definition of GO:0010671 to "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving dioxygen (O2), or any of the reactive oxygen species, e.g. superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (-OH)."
  * Added definition dbxref GOC:dph to GO:0010671
  * Added definition dbxref GOC:tb to GO:0010671
  * Copied GO:0010671 to GO:0006800 with type negatively_regulates
  * Copied GO:0010671 to GO:0080010 with type OBO_REL:is_a
  * Copied GO:0010671 to GO:0048523 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010671
* Populated new object GO:0010672 (macro)
  * Changed name of GO:0010672 from "<new term>" to "regulation of transcription from RNA polymerase II promoter, meiotic"
  * Set definition of GO:0010672 to "A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter during meiosis."
  * Added definition dbxref GOC:dph to GO:0010672
  * Added definition dbxref GOC:tb to GO:0010672
  * Copied GO:0010672 to GO:0006357 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010672
* Populated new object GO:0010673 (macro)
  * Changed name of GO:0010673 from "<new term>" to "positive regulation of transcription from RNA polymerase II promoter, meiotic"
  * Set definition of GO:0010673 to "A cell cycle process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter during meiosis."
  * Added definition dbxref GOC:dph to GO:0010673
  * Added definition dbxref GOC:tb to GO:0010673
  * Copied GO:0010673 to GO:0045944 with type OBO_REL:is_a
  * Copied GO:0010673 to GO:0010672 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010673
* Populated new object GO:0010674 (macro)
  * Changed name of GO:0010674 from "<new term>" to "negative regulation of transcription from RNA polymerase II promoter, meiotic"
  * Set definition of GO:0010674 to "A cell cycle process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter during meiosis."
  * Added definition dbxref GOC:dph to GO:0010674
  * Added definition dbxref GOC:tb to GO:0010674
  * Copied GO:0010674 to GO:0000122 with type OBO_REL:is_a
  * Copied GO:0010674 to GO:0010672 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010674
* Populated new object GO:0010675 (macro)
  * Changed name of GO:0010675 from "<new term>" to "regulation of cellular carbohydrate metabolic process"
  * Set definition of GO:0010675 to "Any process that modulates the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells."
  * Added definition dbxref GOC:dph to GO:0010675
  * Added definition dbxref GOC:tb to GO:0010675
  * Copied GO:0010675 to GO:0044262 with type regulates
  * Copied GO:0010675 to GO:0006109 with type OBO_REL:is_a
  * Copied GO:0010675 to GO:0050794 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010675
* Populated new object GO:0010676 (macro)
  * Changed name of GO:0010676 from "<new term>" to "positive regulation of cellular carbohydrate metabolic process"
  * Set definition of GO:0010676 to "Any process that increases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells."
  * Added definition dbxref GOC:dph to GO:0010676
  * Added definition dbxref GOC:tb to GO:0010676
  * Copied GO:0010676 to GO:0045913 with type OBO_REL:is_a
  * Copied GO:0010676 to GO:0010675 with type OBO_REL:is_a
  * Copied GO:0010676 to GO:0031325 with type OBO_REL:is_a
  * Copied GO:0010676 to GO:0044262 with type positively_regulates
  * Assigned namespace "biological_process" to GO:0010676
* Populated new object GO:0010677 (macro)
  * Changed name of GO:0010677 from "<new term>" to "negative regulation of cellular carbohydrate metabolic process"
  * Set definition of GO:0010677 to "Any process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells."
  * Added definition dbxref GOC:dph to GO:0010677
  * Added definition dbxref GOC:tb to GO:0010677
  * Copied GO:0010677 to GO:0031324 with type OBO_REL:is_a
  * Copied GO:0010677 to GO:0044262 with type negatively_regulates
  * Copied GO:0010677 to GO:0010675 with type OBO_REL:is_a
  * Copied GO:0010677 to GO:0045912 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010677
* Populated new object GO:0010678 (macro)
  * Changed name of GO:0010678 from "<new term>" to "negative regulation of cellular carbohydrate metabolic process by repression of transcription"
  * Set definition of GO:0010678 to "Any cellular process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates carried out by repression of transcription."
  * Added definition dbxref GOC:dph to GO:0010678
  * Added definition dbxref GOC:tb to GO:0010678
  * Added synonym "negative regulation of cellular carbohydrate metabolic process by transcriptional repression" to GO:0010678
  * Added general dbxref GOC:tb to synonym negative regulation of cellular carbohydrate metabolic process by transcriptional repression of GO:0010678
  * Added general dbxref GOC:dph to synonym negative regulation of cellular carbohydrate metabolic process by transcriptional repression of GO:0010678
  * Changed synonym scope of GO:0010678 from "Related" to "Exact"
  * Copied GO:0010678 to GO:0010677 with type OBO_REL:is_a
  * Copied GO:0010678 to GO:0016481 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010678
* Populated new object GO:0034660 (macro)
  * Changed name of GO:0034660 from "<new term>" to "ncRNA metabolic process"
  * Set definition of GO:0034660 to "The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs)."
  * Added definition dbxref GOC:mah to GO:0034660
  * Added synonym "ncRNA metabolism" to GO:0034660
  * Changed synonym scope of GO:0034660 from "Related" to "Exact"
  * Copied GO:0034660 to GO:0016070 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034660
* Populated new object GO:0034661 (macro)
  * Changed name of GO:0034661 from "<new term>" to "ncRNA catabolic process"
  * Set definition of GO:0034661 to "The chemical reactions and pathways resulting in the breakdown of non-coding RNA transcripts (ncRNAs). Includes the breakdown of cryptic unstable trascripts (CUTs)."
  * Added definition dbxref GOC:rb to GO:0034661
  * Added definition dbxref PMID:18591258 to GO:0034661
  * Added synonym "ncRNA breakdown" to GO:0034661
  * Changed synonym scope of GO:0034661 from "Related" to "Exact"
  * Added synonym "ncRNA catabolism" to GO:0034661
  * Changed synonym scope of GO:0034661 from "Related" to "Exact"
  * Added synonym "ncRNA degradation" to GO:0034661
  * Changed synonym scope of GO:0034661 from "Related" to "Exact"
  * Copied GO:0034661 to GO:0006401 with type OBO_REL:is_a
  * Copied GO:0034661 to GO:0034660 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034661
* Populated new object GO:0034662 (macro)
  * Changed name of GO:0034662 from "<new term>" to "CFTR-NHERF-ezrin complex"
  * Set definition of GO:0034662 to "A protein complex that contains ezrin, Na+/H+ exchanger regulatory factor (NHERF, also called EBP50), and two copies of the cystic fibrosis transmembrane conductance regulator (CFTR). The CFTR molecules interact with NHERF via their cytoplasmic tail domains; the complex is thought to link the CFTR channel to the actin cytoskeleton and contribute to the regulation of channel activity."
  * Added definition dbxref PMID:016926444 to GO:0034662
  * Added definition dbxref PMID:16129695 to GO:0034662
  * Added definition dbxref PMID:16798722 to GO:0034662
  * Copied GO:0034662 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034662 to GO:0044459 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034662
* Populated new object GO:0034663 (macro)
  * Changed name of GO:0034663 from "<new term>" to "endoplasmic reticulum chaperone complex"
  * Set definition of GO:0034663 to "A protein complex that is located in the endoplasmic reticulum and is composed of chaperone proteins, including BiP, GRP94; CaBP1, protein disulfide isomerase (PDI), ERdj3, cyclophilin B, ERp72, GRP170, UDP-glucosyltransferase, and SDF2-L1."
  * Added definition dbxref PMID:12475965 to GO:0034663
  * Added synonym "endoplasmic reticulum network complex" to GO:0034663
  * Added synonym "ER chaperone complex" to GO:0034663
  * Changed synonym scope of GO:0034663 from "Related" to "Exact"
  * Added synonym "ER network complex" to GO:0034663
  * Copied GO:0034663 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034663 to GO:0044432 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034663
* Populated new object GO:0034664 (macro)
  * Changed name of GO:0034664 from "<new term>" to "Ig heavy chain-bound endoplasmic reticulum chaperone complex"
  * Set definition of GO:0034664 to "A protein complex that is located in the endoplasmic reticulum (ER) and is formed by the association of an immunoglobulin heavy chain with the proteins of the ER chaperone complex; the latter include BiP, GRP94; CaBP1, protein disulfide isomerase (PDI), ERdj3, cyclophilin B, ERp72, GRP170, UDP-glucosyltransferase, and SDF2-L1."
  * Added definition dbxref PMID:12475965 to GO:0034664
  * Added synonym "Ig heavy chain-bound ER chaperone complex" to GO:0034664
  * Changed synonym scope of GO:0034664 from "Related" to "Exact"
  * Added synonym "immunoglobulin heavy chain-bound endoplasmic reticulum chaperone complex" to GO:0034664
  * Changed synonym scope of GO:0034664 from "Related" to "Exact"
  * Copied GO:0034664 to GO:0044432 with type OBO_REL:is_a
  * Copied GO:0034664 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034664
* Populated new object GO:0034665 (macro)
  * Changed name of GO:0034665 from "<new term>" to "alpha1-beta1 integrin complex"
  * Set definition of GO:0034665 to "An integrin complex that comprises one alpha1 subunit and one beta1 subunit."
  * Added definition dbxref PMID:12297042 to GO:0034665
  * Added synonym "ITGA1-ITGB1 complex" to GO:0034665
  * Changed synonym scope of GO:0034665 from "Related" to "Narrow"
  * Added synonym "VLA-1 complex" to GO:0034665
  * Changed synonym scope of GO:0034665 from "Related" to "Exact"
  * Copied GO:0034665 to GO:0008305 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034665
* Populated new object GO:0034666 (macro)
  * Changed name of GO:0034666 from "<new term>" to "alpha2-beta1 integrin complex"
  * Set definition of GO:0034666 to "An integrin complex that comprises one alpha2 subunit and one beta1 subunit."
  * Added definition dbxref PMID:12297042 to GO:0034666
  * Added synonym "ITGA2-ITGB1 complex" to GO:0034666
  * Changed synonym scope of GO:0034666 from "Related" to "Narrow"
  * Added synonym "VLA-2 complex" to GO:0034666
  * Changed synonym scope of GO:0034666 from "Related" to "Exact"
  * Copied GO:0034666 to GO:0008305 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034666
* Populated new object GO:0034667 (macro)
  * Changed name of GO:0034667 from "<new term>" to "alpha3-beta1 integrin complex"
  * Set definition of GO:0034667 to "An integrin complex that comprises one alpha3 subunit and one beta1 subunit."
  * Added definition dbxref PMID:12297042 to GO:0034667
  * Added synonym "ITGA3-ITGB1 complex" to GO:0034667
  * Changed synonym scope of GO:0034667 from "Related" to "Narrow"
  * Added synonym "VLA-3 complex" to GO:0034667
  * Changed synonym scope of GO:0034667 from "Related" to "Exact"
  * Copied GO:0034667 to GO:0008305 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034667
* Populated new object GO:0034668 (macro)
  * Changed name of GO:0034668 from "<new term>" to "alpha4-beta1 integrin complex"
  * Set definition of GO:0034668 to "An integrin complex that comprises one alpha4 subunit and one beta1 subunit."
  * Added definition dbxref PMID:12297042 to GO:0034668
  * Added synonym "ITGA4-ITGB1 complex" to GO:0034668
  * Changed synonym scope of GO:0034668 from "Related" to "Narrow"
  * Added synonym "VLA-4 complex" to GO:0034668
  * Changed synonym scope of GO:0034668 from "Related" to "Exact"
  * Copied GO:0034668 to GO:0008305 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034668
* Populated new object GO:0034669 (macro)
  * Changed name of GO:0034669 from "<new term>" to "alpha4-beta7 integrin complex"
  * Set definition of GO:0034669 to "An integrin complex that comprises one alpha4 subunit and one beta7 subunit."
  * Added definition dbxref PMID:12297042 to GO:0034669
  * Added synonym "ITGA4-ITGB7 complex" to GO:0034669
  * Changed synonym scope of GO:0034669 from "Related" to "Narrow"
  * Copied GO:0034669 to GO:0008305 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034669
* Populated new object GO:0080011 (macro)
  * Changed name of GO:0080011 from "<new term>" to "baruol synthase activity"
  * Set definition of GO:0080011 to "Catalysis of the reaction: (S)-2,3-epoxysqualene = baruol (D:B-Friedo-Baccharan-5,21-dien-3-ol)."
  * Added definition dbxref PMID:17705488 to GO:0080011
  * Copied GO:0080011 to GO:0031559 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0080011
* Populated new object GO:0080012 (macro)
  * Changed name of GO:0080012 from "<new term>" to "N1,N5,N10-tris-(5-hydroxyferuloyl)spermidine O-methyltransferase activity"
  * Set definition of GO:0080012 to "Catalysis of the reaction: N1,N5,N10-tris-(5-hydroxyferuloyl)spermidine + S-adenosylmethionine = N',N''-bis(5-hydroxyferuloyl)-N'''-sinapoylspermidine."
  * Added definition dbxref PMID:18557837 to GO:0080012
  * Copied GO:0080012 to GO:0008171 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0080012
* Deleted synonym "regulation of transcription from RNA polymerase II promoter during G1 phase of cell cycle>" from GO:0000114
* Added synonym "regulation of transcription from RNA polymerase II promoter during G1 phase of cell cycle" to GO:0000114
* Changed synonym scope of GO:0000114 from "Related" to "Exact"
* Deleted synonym "<new synonym>" from GO:0002115
* Added synonym "store-operated calcium import" to GO:0002115
* Changed synonym scope of GO:0002115 from "Related" to "Exact"
* Deleted GO:0006399 --OBO_REL:is_a--> GO:0016070
* Copied GO:0006399 to GO:0034660 with type OBO_REL:is_a
* Deleted GO:0006497 --OBO_REL:is_a--> GO:0042158
* Copied GO:0006497 to GO:0042158 with type part_of
* Changed definition of GO:0008305 from "Any member of a family of heterodimeric transmembrane receptors for cell-adhesion molecules. The alpha and beta subunits are noncovalently bonded." to "A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands."
* Deleted definition dbxref Oxford Dictionary of Biochemistry and Molecular Biology (ISBN:0198506732) from GO:0008305
* Deleted definition dbxref Dorland's Illustrated Medical Dictionary (ISBN:0721662544) from GO:0008305
* Added definition dbxref PMID:17543136 to GO:0008305
* Deleted GO:0010586 --OBO_REL:is_a--> GO:0016070
* Copied GO:0010586 to GO:0034660 with type OBO_REL:is_a
* Deleted GO:0010587 --OBO_REL:is_a--> GO:0006401
* Copied GO:0010587 to GO:0034661 with type OBO_REL:is_a
* Deleted GO:0016072 --OBO_REL:is_a--> GO:0016070
* Copied GO:0016072 to GO:0034660 with type OBO_REL:is_a
* Deleted GO:0016073 --OBO_REL:is_a--> GO:0016070
* Copied GO:0016073 to GO:0034660 with type OBO_REL:is_a
* Deleted GO:0016074 --OBO_REL:is_a--> GO:0016070
* Copied GO:0016074 to GO:0034660 with type OBO_REL:is_a
* Deleted GO:0016075 --OBO_REL:is_a--> GO:0006401
* Copied GO:0016075 to GO:0034661 with type OBO_REL:is_a
* Deleted GO:0016076 --OBO_REL:is_a--> GO:0006401
* Copied GO:0016076 to GO:0034661 with type OBO_REL:is_a
* Deleted GO:0016077 --OBO_REL:is_a--> GO:0006401
* Copied GO:0016077 to GO:0034661 with type OBO_REL:is_a
* Deleted GO:0016078 --OBO_REL:is_a--> GO:0006401
* Copied GO:0016078 to GO:0034661 with type OBO_REL:is_a
* Copied GO:0030277 to GO:0001894 with type OBO_REL:is_a
* Deleted GO:0030503 --regulates--> GO:0045454
* Deleted GO:0030503 --OBO_REL:is_a--> GO:0032844
* Deleted GO:0030503 --OBO_REL:is_a--> GO:0050794
* Destroyed object GO:0030503
* Deleted GO:0034585 --OBO_REL:is_a--> GO:0016070
* Copied GO:0034585 to GO:0034660 with type OBO_REL:is_a
* Deleted GO:0034586 --OBO_REL:is_a--> GO:0006401
* Copied GO:0034586 to GO:0034661 with type OBO_REL:is_a
* Deleted GO:0034587 --OBO_REL:is_a--> GO:0016070
* Copied GO:0034587 to GO:0034660 with type OBO_REL:is_a
* Deleted GO:0034588 --OBO_REL:is_a--> GO:0006401
* Copied GO:0034588 to GO:0034661 with type OBO_REL:is_a
* Copied GO:0035160 to GO:0010669 with type OBO_REL:is_a
* Deleted GO:0042868 --OBO_REL:is_a--> GO:0016070
* Copied GO:0042868 to GO:0034660 with type OBO_REL:is_a
* added secondary id GO:0030503 to GO:0045454
* added secondary id GO:0045867 to GO:0045454
* added secondary id GO:0045868 to GO:0045454
* Changed definition of GO:0045454 from "Any process that maintain the redox environment of a cell or compartment within a cell." to "Any process that maintains the redox environment of a cell or compartment within a cell."
* Added definition dbxref GOC:dph to GO:0045454
* Added definition dbxref GOC:tb to GO:0045454
* Added synonym "regulation of cell redox homeostasis" to GO:0045454
* Changed synonym scope of GO:0045454 from "Related" to "Exact"
* Added synonym "regulation of redox homeostasis" to GO:0045454
* Changed synonym scope of GO:0045454 from "Related" to "Broad"
* Copied GO:0045454 to GO:0050794 with type OBO_REL:is_a

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