[Go-diff] GO update 10/06/2008

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Mon Oct 6 21:30:48 PDT 2008 

OBODIFF of gene_ontology_write.obo version 1.250 by 1.255

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010769
* Created object of type obo:TERM with id GO:0010770
* Created object of type obo:TERM with id GO:0010771
* Created object of type obo:TERM with id GO:0070069
* Created object of type obo:TERM with id GO:0080014
* Created object of type obo:TERM with id GO:0080015
* Created object of type obo:TERM with id GO:0080016
* Created object of type obo:TERM with id GO:0080017
* Created object of type obo:TERM with id GO:0080018
* Created object of type obo:TERM with id GO:0080019
* Created object of type obo:TERM with id GO:0080020
* Populated new object GO:0010769 (macro)
  * Changed name of GO:0010769 from "<new term>" to "regulation of cell morphogenesis involved in differentiation"
  * Set definition of GO:0010769 to "Any process that modulates the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history."
  * Added definition dbxref GOC:dph to GO:0010769
  * Added definition dbxref GOC:tb to GO:0010769
  * Copied GO:0010769 to GO:0000904 with type regulates
  * Copied GO:0010769 to GO:0022604 with type OBO_REL:is_a
  * Copied GO:0010769 to GO:0060284 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010769
* Populated new object GO:0010770 (macro)
  * Changed name of GO:0010770 from "<new term>" to "positive regulation of cell morphogenesis involved in differentiation"
  * Set definition of GO:0010770 to "Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history."
  * Added definition dbxref GOC:dph to GO:0010770
  * Added definition dbxref GOC:tb to GO:0010770
  * Copied GO:0010770 to GO:0010769 with type OBO_REL:is_a
  * Copied GO:0010770 to GO:0000904 with type positively_regulates
  * Copied GO:0010770 to GO:0010720 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0010770
* Populated new object GO:0010771 (macro)
  * Changed name of GO:0010771 from "<new term>" to "negative regulation of cell morphogenesis involved in differentiation"
  * Set definition of GO:0010771 to "Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history."
  * Added definition dbxref GOC:dph to GO:0010771
  * Added definition dbxref GOC:tb to GO:0010771
  * Copied GO:0010771 to GO:0010769 with type OBO_REL:is_a
  * Copied GO:0010771 to GO:0010721 with type OBO_REL:is_a
  * Copied GO:0010771 to GO:0000904 with type negatively_regulates
  * Assigned namespace "biological_process" to GO:0010771
* Populated new object GO:0070069 (macro)
  * Changed name of GO:0070069 from "<new term>" to "cytochrome complex"
  * Set definition of GO:0070069 to "A protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions."
  * Added definition dbxref GOC:mah to GO:0070069
  * Copied GO:0070069 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070069
* Populated new object GO:0080014 (macro)
  * Changed name of GO:0080014 from "<new term>" to "thalianol hydroxylase activity"
  * Added comment "In Field and Osbourn 2008 (PMID: 18356490), thalianol is referred to as (3S,13S, 3R)-malabarica-8,17,21-trien-3-ol and thalian-diol is referred to as (3S, 13S, 14R)-malabarica-8,17,21-trien-3,?-diol, but the error in this naming system was pointed out in Kolesnikova 2007 (PMID: 17474751). The new names used in the definition have been approved by the authors (Field and Osbourn 2008)."
  * Set definition of GO:0080014 to "Catalysis of the addition of a hydroxyl group to thalianol ((13R,14R,17E)-podioda-8,17,21-trien-3beta-ol) to create thalian-diol((13R,14R,17E)-podioda-8,17,21-trien-3beta,?-diol). Several thalian-diol isomers may be created by the same enzyme because the hydroxyl group may be attached at one of several different available carbons in ring B or C of thalianol (as indicated by the ''?'')."
  * Added definition dbxref PMID:17474751 to GO:0080014
  * Added definition dbxref PMID:18356490 to GO:0080014
  * Copied GO:0080014 to GO:0004497 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0080014
* Populated new object GO:0080015 (macro)
  * Changed name of GO:0080015 from "<new term>" to "sabinene synthase activity"
  * Set definition of GO:0080015 to "Catalysis of the conversion of geranyl diphosphate (GPP) into the cyclic monoterpene sabinene."
  * Added definition dbxref MetaCyc:RXN-5103 to GO:0080015
  * Added definition dbxref PMID:12566586 to GO:0080015
  * Added definition dbxref PMID:9747540 to GO:0080015
  * Copied GO:0080015 to GO:0016838 with type OBO_REL:is_a
  * Copied GO:0080015 to GO:0009975 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0080015
* Populated new object GO:0080016 (macro)
  * Changed name of GO:0080016 from "<new term>" to "(-)-E-beta-caryophyllene synthase activity"
  * Set definition of GO:0080016 to "Catalysis of the reaction: farnesyl diphosphate = (-)-E-beta-caryophyllene + diphosphate."
  * Added definition dbxref MetaCyc:RXN-8414 to GO:0080016
  * Added definition dbxref PMID:12566586 to GO:0080016
  * Added definition dbxref PMID:9442047 to GO:0080016
  * Copied GO:0080016 to GO:0016838 with type OBO_REL:is_a
  * Copied GO:0080016 to GO:0009975 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0080016
* Populated new object GO:0080017 (macro)
  * Changed name of GO:0080017 from "<new term>" to "alpha-humulene synthase activity"
  * Set definition of GO:0080017 to "Catalysis of the reaction: farnesyl diphosphate = alpha-humulene + diphosphate."
  * Added definition dbxref PMID:12566586 to GO:0080017
  * Added definition dbxref PMID:9442047 to GO:0080017
  * Copied GO:0080017 to GO:0016838 with type OBO_REL:is_a
  * Copied GO:0080017 to GO:0009975 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0080017
* Populated new object GO:0080018 (macro)
  * Changed name of GO:0080018 from "<new term>" to "anthocyanin 5-O-glucosyltransferase"
  * Set definition of GO:0080018 to "Catalysis of the reaction:anthocyanin + UDP-D-glucose = anthocyanin-5-O-glucoside + UDP."
  * Added definition dbxref PMID:15807784 to GO:0080018
  * Copied GO:0080018 to GO:0035251 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0080018
* Populated new object GO:0080019 (macro)
  * Changed name of GO:0080019 from "<new term>" to "fatty acyl-CoA reductase (alcohol-forming) activity"
  * Set definition of GO:0080019 to "Catalysis of the reaction: a very long chain fatty acyl-CoA + NADPH = a very long chain primary alcohol + NADP + CoA."
  * Added definition dbxref PMID:16980563 to GO:0080019
  * Copied GO:0080019 to GO:0016620 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0080019
* Populated new object GO:0080020 (macro)
  * Changed name of GO:0080020 from "<new term>" to "regulation of coenzyme A biosynthetic process"
  * Set definition of GO:0080020 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving coenzyme A."
  * Added definition dbxref PMID:18621975 to GO:0080020
  * Copied GO:0080020 to GO:0051196 with type OBO_REL:is_a
  * Copied GO:0080020 to GO:0015937 with type regulates
  * Assigned namespace "biological_process" to GO:0080020
* Changed name of GO:0000904 from "cell morphogenesis during differentiation" to "cell morphogenesis involved in differentiation"
* Added synonym "outer mitochondrial membrane" to GO:0005741
* Changed synonym scope of GO:0005741 from "Related" to "Exact"
* Added synonym "inner mitochondrial membrane" to GO:0005743
* Changed synonym scope of GO:0005743 from "Related" to "Exact"
* Changed definition of GO:0006342 from "Repression of transcription by conversion of large regions of DNA into an inaccessible state often called heterochromatin." to "Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin."
* Added definition dbxref GOC:mah to GO:0006342
* Changed synonym scope of GO:0006342 from "Exact" to "Related"
* Deleted GO:0006342 --OBO_REL:is_a--> GO:0031507
* Added synonym "mitochondrial inner membrane organization" to GO:0007007
* Changed synonym scope of GO:0007007 from "Related" to "Exact"
* Changed name of GO:0009833 from "plant-type primary cell wall biogenesis" to "primary cell wall biogenesis"
* Added synonym "plant-type primary cell wall biogenesis" to GO:0009833
* Changed synonym scope of GO:0009833 from "Related" to "Exact"
* Changed name of GO:0009834 from "plant-type secondary cell wall biogenesis" to "secondary cell wall biogenesis"
* Added synonym "plant-type secondary cell wall biogenesis" to GO:0009834
* Changed synonym scope of GO:0009834 from "Related" to "Exact"
* Added synonym "endomembrane system organization" to GO:0010256
* Changed synonym scope of GO:0010256 from "Related" to "Exact"
* Added synonym "seed oil body organization" to GO:0010344
* Changed synonym scope of GO:0010344 from "Related" to "Exact"
* Copied GO:0010703 to GO:0051241 with type OBO_REL:is_a
* Deleted GO:0010717 --OBO_REL:is_a--> GO:0060284
* Copied GO:0010717 to GO:0010769 with type OBO_REL:is_a
* Deleted GO:0010718 --OBO_REL:is_a--> GO:0010720
* Copied GO:0010718 to GO:0010770 with type OBO_REL:is_a
* Deleted GO:0010719 --OBO_REL:is_a--> GO:0010721
* Copied GO:0010719 to GO:0010771 with type OBO_REL:is_a
* Deleted GO:0010720 --positively_regulates--> GO:0060284
* Deleted GO:0010720 --OBO_REL:is_a--> GO:0048522
* Copied GO:0010720 to GO:0048468 with type positively_regulates
* Copied GO:0010720 to GO:0045597 with type OBO_REL:is_a
* Copied GO:0010720 to GO:0060284 with type OBO_REL:is_a
* Deleted GO:0010721 --negatively_regulates--> GO:0060284
* Deleted GO:0010721 --OBO_REL:is_a--> GO:0048523
* Copied GO:0010721 to GO:0060284 with type OBO_REL:is_a
* Copied GO:0010721 to GO:0045596 with type OBO_REL:is_a
* Copied GO:0010721 to GO:0048468 with type negatively_regulates
* Copied GO:0010725 to GO:0045995 with type OBO_REL:is_a
* Copied GO:0010728 to GO:0031326 with type OBO_REL:is_a
* Copied GO:0010729 to GO:0031328 with type OBO_REL:is_a
* Copied GO:0010730 to GO:0031327 with type OBO_REL:is_a
* Added synonym "oilbody" to GO:0012511
* Changed synonym scope of GO:0012511 from "Related" to "Exact"
* Deleted GO:0015844 --OBO_REL:is_a--> GO:0006836
* Changed definition of GO:0017004 from "The aggregation, arrangement and bonding together of a cytochrome." to "The aggregation, arrangement and bonding together of a cytochrome complex. A  cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions."
* Added definition dbxref GOC:mah to GO:0017004
* Added synonym "actomyosin organization" to GO:0031032
* Changed synonym scope of GO:0031032 from "Related" to "Exact"
* Added synonym "horsetail-astral microtubule array organization and biogenesis" to GO:0032118
* Changed synonym scope of GO:0032118 from "Related" to "Exact"
* Changed definition of GO:0032122 from "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the oral apparatus." to "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the oral apparatus. The oral apparatus is a funnel-like structure used by the cell to collect food and channel it to the cytostome, characteristic of ciliate protozoans."
* Added definition dbxref PMID:10503189 to GO:0032122
* Added synonym "chromosome organization, telomeric" to GO:0032200
* Changed synonym scope of GO:0032200 from "Related" to "Exact"
* Added synonym "organization of chromosome, telomeric region" to GO:0032200
* Changed synonym scope of GO:0032200 from "Related" to "Exact"
* Copied GO:0033604 to GO:0051953 with type OBO_REL:is_a
* Copied GO:0033605 to GO:0051954 with type OBO_REL:is_a
* Added synonym "microRNA biogenesis" to GO:0035196
* Added general dbxref GOC:tb to synonym microRNA biogenesis of GO:0035196
* Added synonym "miRNA biogenesis" to GO:0035196
* Added general dbxref GOC:tb to synonym miRNA biogenesis of GO:0035196
* Added synonym "actomyosin complex" to GO:0042641
* Changed synonym scope of GO:0042641 from "Related" to "Exact"
* Added synonym "actomyosin structure" to GO:0042641
* Changed synonym scope of GO:0042641 from "Related" to "Exact"
* Changed name of GO:0048667 from "neuron morphogenesis during differentiation" to "cell morphogenesis involved in neuron differentiation"
* Added definition dbxref GOC:tb to GO:0048667
* Added synonym "neuron morphogenesis involved in differentiation" to GO:0048667
* Added general dbxref GOC:tb to synonym neuron morphogenesis involved in differentiation of GO:0048667
* Added general dbxref GOC:dph to synonym neuron morphogenesis involved in differentiation of GO:0048667
* Changed synonym scope of GO:0048667 from "Related" to "Exact"
* Changed name of GO:0048938 from "lateral line nerve glial cell morphogenesis during differentiation" to "lateral line nerve glial cell morphogenesis involved in differentiation"
* Changed name of GO:0048940 from "anterior lateral line nerve glial cell morphogenesis during differentiation" to "anterior lateral line nerve glial cell morphogenesis involved in differentiation"
* Changed name of GO:0048942 from "posterior lateral line nerve glial cell morphogenesis during differentiation" to "posterior lateral line nerve glial cell morphogenesis involved in differentiation"
* Deleted GO:0060284 --OBO_REL:is_a--> GO:0050794
* Copied GO:0060284 to GO:0045595 with type OBO_REL:is_a

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