[Obo-diffs] changes for: biological_process_prerelease

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Starting obodiff at /users/cjm/cvs/geneontology/oboedit/launch_scripts using 1024M of memory
[INFO] Reading [obo-all/biological_process_prerelease/biological_process_prerelease.obo.CURRENT]
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[INFO] Reading [obo-all/biological_process_prerelease/biological_process_prerelease.obo]
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* Created object of type obo:TERM with id GO:0035989
* Created object of type obo:TERM with id GO:0035990
* Created object of type obo:TERM with id GO:0035991
* [Changed name of GO:0035989 from "null" to "tendon development", Set definition of GO:0035989 to "The process whose specific outcome is the progression of a tendon over time, from its formation to the mature structure. A tendon is a fibrous, strong, connective tissue that connects muscle to bone or integument and is capable of withstanding tension. Tendons and muscles work together to exert a pulling force.", Added definition dbxref GOC:yaf to GO:0035989, Added definition dbxref PMID:21412429 to GO:0035989, Added definition dbxref UBERON:0000043 to GO:0035989, Added synonym "sinew development" to GO:0035989, Added general dbxref UBERON:0000043 to synonym sinew development of GO:0035989, Created link GO:0035989 -OBO_REL:is_a-> GO:0009888, Assigned namespace "biological_process" to GO:0035989]
  * Changed name of GO:0035989 from "null" to "tendon development"
  * Set definition of GO:0035989 to "The process whose specific outcome is the progression of a tendon over time, from its formation to the mature structure. A tendon is a fibrous, strong, connective tissue that connects muscle to bone or integument and is capable of withstanding tension. Tendons and muscles work together to exert a pulling force."
  * Added definition dbxref GOC:yaf to GO:0035989
  * Added definition dbxref PMID:21412429 to GO:0035989
  * Added definition dbxref UBERON:0000043 to GO:0035989
  * Added synonym "sinew development" to GO:0035989
  * Added general dbxref UBERON:0000043 to synonym sinew development of GO:0035989
  * Created link GO:0035989 -OBO_REL:is_a-> GO:0009888
  * Assigned namespace "biological_process" to GO:0035989
* [Changed name of GO:0035990 from "null" to "tendon cell differentiation", Set definition of GO:0035990 to "The process in which a relatively unspecialized cell acquires the specialized features of a tendon cell. Tendon cell are elongated fibrocytes in which the cytoplasm is stretched between the collagen fibres of the tendon. Tendon cells have a central cell nucleus with a prominent nucleolus, a well-developed rough endoplasmic reticulum, and are responsible for synthesis and turnover of tendon fibres and ground substance.", Added definition dbxref CL:0000388 to GO:0035990, Added definition dbxref GOC:yaf to GO:0035990, Added definition dbxref PMID:21412429 to GO:0035990, Added synonym "muscle attachment cell differentiation" to GO:0035990, Added general dbxref CL:0000388 to synonym muscle attachment cell differentiation of GO:0035990, Changed synonym scope of GO:0035990 from "Related" to "Exact", Added synonym "tenocyte differentiation" to GO:0035990, Added general dbxref 
 CL:0000388 to synonym tenocyte differentiation of GO:0035990, Created link GO:0035990 -OBO_REL:is_a-> GO:0030154, Created link GO:0035990 -part_of-> GO:0035989, Assigned namespace "biological_process" to GO:0035990]
  * Changed name of GO:0035990 from "null" to "tendon cell differentiation"
  * Set definition of GO:0035990 to "The process in which a relatively unspecialized cell acquires the specialized features of a tendon cell. Tendon cell are elongated fibrocytes in which the cytoplasm is stretched between the collagen fibres of the tendon. Tendon cells have a central cell nucleus with a prominent nucleolus, a well-developed rough endoplasmic reticulum, and are responsible for synthesis and turnover of tendon fibres and ground substance."
  * Added definition dbxref CL:0000388 to GO:0035990
  * Added definition dbxref GOC:yaf to GO:0035990
  * Added definition dbxref PMID:21412429 to GO:0035990
  * Added synonym "muscle attachment cell differentiation" to GO:0035990
  * Added general dbxref CL:0000388 to synonym muscle attachment cell differentiation of GO:0035990
  * Changed synonym scope of GO:0035990 from "Related" to "Exact"
  * Added synonym "tenocyte differentiation" to GO:0035990
  * Added general dbxref CL:0000388 to synonym tenocyte differentiation of GO:0035990
  * Created link GO:0035990 -OBO_REL:is_a-> GO:0030154
  * Created link GO:0035990 -part_of-> GO:0035989
  * Assigned namespace "biological_process" to GO:0035990
* [Changed name of GO:0035991 from "null" to "nitric oxide sensor activity", Set definition of GO:0035991 to "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of nitric oxide (NO).", Added definition dbxref GOC:kmv to GO:0035991, Added definition dbxref PMID:21491957 to GO:0035991, Added synonym "NO sensor activity" to GO:0035991, Added general dbxref CHEBI:16480 to synonym NO sensor activity of GO:0035991, Changed synonym scope of GO:0035991 from "Related" to "Exact", Created link GO:0035991 -OBO_REL:is_a-> GO:0070026, Assigned namespace "molecular_function" to GO:0035991]
  * Changed name of GO:0035991 from "null" to "nitric oxide sensor activity"
  * Set definition of GO:0035991 to "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of nitric oxide (NO)."
  * Added definition dbxref GOC:kmv to GO:0035991
  * Added definition dbxref PMID:21491957 to GO:0035991
  * Added synonym "NO sensor activity" to GO:0035991
  * Added general dbxref CHEBI:16480 to synonym NO sensor activity of GO:0035991
  * Changed synonym scope of GO:0035991 from "Related" to "Exact"
  * Created link GO:0035991 -OBO_REL:is_a-> GO:0070026
  * Assigned namespace "molecular_function" to GO:0035991
* Changed synonym scope of GO:0008471 from "Exact" to "Related"
* Changed synonym scope of GO:0008471 from "Exact" to "Related"
* Changed synonym scope of GO:0008471 from "Exact" to "Related"
* Changed definition of GO:0008811 from "Catalysis of the reaction: acetyl-CoA + chloramphenicol = chloramphenicol 3-acetate + CoA." to "Catalysis of the reaction: chloramphenicol + acetyl-CoA = chloramphenicol 3-acetate + CoA."
* Set definition of GO:0008985 to "Catalysis of the reaction: pyruvate + ferricytochrome b1 + H2O = CO2 + acetate + ferrocytochrome b1."
* Added definition dbxref EC:1.2.2.2 to GO:0008985
* Changed synonym scope of GO:0008985 from "Exact" to "Related"
* Changed synonym scope of GO:0008985 from "Exact" to "Related"
* Changed synonym scope of GO:0008985 from "Exact" to "Related"
* Changed synonym scope of GO:0015020 from "Exact" to "Narrow"
* Changed synonym scope of GO:0015020 from "Exact" to "Narrow"
* Changed synonym scope of GO:0015020 from "Exact" to "Narrow"
* Changed synonym scope of GO:0015020 from "Exact" to "Narrow"
* Changed synonym scope of GO:0015020 from "Exact" to "Narrow"
* Changed synonym scope of GO:0015020 from "Exact" to "Narrow"
* Changed definition of GO:0018117 from "The addition of phospho-adenosine to a protein amino acid." to "The addition of an adenylyl group (adenosine 5'-monophosphate; AMP) to a protein amino acid."
* Added definition dbxref GOC:jsg to GO:0018117
* Added definition dbxref GOC:sart to GO:0018117
* Added definition dbxref PMID:21607083 to GO:0018117
* Added synonym "protein AMPylation" to GO:0018117
* Added general dbxref GOC:jsg to synonym protein AMPylation of GO:0018117
* Added general dbxref PMID:21607083 to synonym protein AMPylation of GO:0018117
* Added general dbxref GOC:sart to synonym protein AMPylation of GO:0018117
* Changed synonym scope of GO:0018117 from "Related" to "Exact"
* Added general dbxref GOC:mah to synonym forebrain dorsal-ventral pattern formation of GO:0021798
* Deleted definition dbxref KEGG_PATHWAY:map00440 from GO:0033051
* Added definition dbxref KEGG:map00440 to GO:0033051
* Changed synonym scope of GO:0033805 from "Exact" to "Narrow"
* Changed synonym scope of GO:0033805 from "Exact" to "Narrow"
* Deleted synonym "sarcosine-dimethylglycine methyltransferase activity" from GO:0033805
* Added synonym "sarcosine dimethylglycine methyltransferase activity" to GO:0033805
* Added general dbxref EC:2.1.1.157 to synonym sarcosine dimethylglycine methyltransferase activity of GO:0033805
* Changed synonym scope of GO:0033805 from "Related" to "Narrow"
* Changed synonym scope of GO:0033884 from "Exact" to "Narrow"
* Changed synonym scope of GO:0034019 from "Exact" to "Broad"
* Changed synonym scope of GO:0034019 from "Exact" to "Narrow"
* Changed definition of GO:0046987 from "Catalysis of the transfer, in a beta 1,3 linkage, of D-glucuronic acid (GlcUA) from UDP-GlcUA to N-acetyllactosamine (galactosyl beta-1,4-N-acetylglucosamine)." to "Catalysis of the transfer, in a beta 1,3 linkage, of D-glucuronic acid (GlcUA) from UDP-D-glucuronic acid to N-acetyllactosamine (galactosyl beta-1,4-N-acetylglucosamine)."
* Deleted synonym "ATP:1D-myo-inositol-1,3,4-trisphosphate 5-phosphotransferase activity" from GO:0047325
* Deleted synonym "ATP:1D-myo-inositol-1,3,4-trisphosphate 6-phosphotransferase activity" from GO:0047325
* Changed synonym scope of GO:0047325 from "Exact" to "Broad"
* Changed definition of GO:0047331 from "Catalysis of the reaction: diphosphate + glycerol = glycerol 1-phosphate + H(+) + phosphate." to "Catalysis of the reaction: glycerol + diphosphate = glycerol 1-phosphate + H(+) + phosphate."
* Deleted general dbxref KEGG:R04002 from synonym ATP:branched-chain-fatty-acid 1-phosphotransferase activity of GO:0047758
* Added general dbxref EC:2.7.2.14 to synonym ATP:branched-chain-fatty-acid 1-phosphotransferase activity of GO:0047758
* Changed synonym scope of GO:0047758 from "Broad" to "Exact"
* Changed synonym scope of GO:0052725 from "Exact" to "Broad"
* Changed synonym scope of GO:0052731 from "Exact" to "Related"
* Changed comment from "Note that the overall reaction representing three successive executions of this activity is N1,N5,N10-tricoumaroyl spermidine + 3 NADPH + 3 O2 = N1,N5,N10-tricaffeoyl spermidine +3 NADP+ + 3 H2O; this corresponds to the MetaCyc reaction RXN-11260 (http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-11260)." to "Note that the overall reaction representing three successive executions of this activity is N1,N5,N10-tricoumaroyl spermidine + 3 NADPH + 3 O2 = N1,N5,N10-tricaffeoyl spermidine + 3 NADP+ + 3 H2O; this corresponds to the MetaCyc reaction RXN-11260 (http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-11260)."
* Changed comment from "This reaction falls within the larger set of reactions associated with EC 2.6.1.28 (See BRENDA: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.6.1.28; note: 3-indole-2-oxopropanoate = indolepyruvate)." to "This reaction falls within the larger set of reactions associated with EC 2.6.1.28 (See BRENDA: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.6.1.28; note: 3-indole-2-oxopropanoate = indolepyruvate = 3-(indol-3-yl)pyruvate)."
* Changed definition of GO:0080097 from "Catalysis of the reaction: L-tryptophan + pyruvate = indolepyruvate + L-alanine." to "Catalysis of the reaction: L-tryptophan + pyruvate = 3-(indol-3-yl)pyruvate + L-alanine."
* Deleted definition dbxref PMID:18394996 from GO:0080097
* Added definition dbxref MetaCyc:RXN-10139 to GO:0080097
* Added general dbxref EC:2.6.1.28 to GO:0080097
* Added general dbxref RHEA:27587 to GO:0080097
* Changed definition of GO:0080098 from "Catalysis of the reaction: L-tyrosine + pyruvate = 4-hydroxyphenylpyruvate + L-alanine." to "Catalysis of the reaction: L-tyrosine + pyruvate = (4-hydroxyphenyl)pyruvate + L-alanine."
* Deleted definition dbxref PMID:18394996 from GO:0080098
* Added definition dbxref MetaCyc:RXN3O-4157 to GO:0080098
* Added general dbxref EC:2.6.1.50 to GO:0080100
* Added general dbxref EC:2.1.1.71 to GO:0080101
* Added general dbxref KEGG:R01320 to GO:0080101
* Added general dbxref MetaCyc:RXN4FS-2 to GO:0080101
* Changed definition of GO:0080102 from "Catalysis of the conversion of 3-methylthiopropyl glucosinolate to 3-methylsulfinylpropyl glucosinolate." to "Catalysis of the reaction: 3-methylthiopropyl-glucosinolate = 3-methylsulfinylpropyl-glucosinolate."
* Added general dbxref MetaCyc:RXN-2221 to GO:0080102
* Changed definition of GO:0080103 from "Catalysis of the conversion of 4-methylthiopropyl glucosinolate to 4-methylsulfinylpropyl glucosinolate." to "Catalysis of the reaction: 4-methylthiopropyl-glucosinolate = 4-methylsulfinylpropyl-glucosinolate."
* Changed definition of GO:0080104 from "Catalysis of the conversion of 5-methylthiopropyl glucosinolate to 5-methylsulfinylpropyl glucosinolate." to "Catalysis of the reaction: 5-methylthiopropyl-glucosinolate = 5-methylsulfinylpropyl-glucosinolate."
* Changed definition of GO:0080105 from "Catalysis of the conversion of 6-methylthiopropyl glucosinolate to 6-methylsulfinylpropyl glucosinolate." to "Catalysis of the reaction: 6-methylthiopropyl-glucosinolate = 6-methylsulfinylpropyl-glucosinolate."
* Changed definition of GO:0080106 from "Catalysis of the conversion of 7-methylthiopropyl glucosinolate to 7-methylsulfinylpropyl glucosinolate." to "Catalysis of the reaction: 7-methylthiopropyl-glucosinolate = 7-methylsulfinylpropyl-glucosinolate."
* Changed definition of GO:0080107 from "Catalysis of the conversion of 8-methylthiopropyl glucosinolate to 8-methylsulfinylpropyl glucosinolate." to "Catalysis of the reaction: 8-methylthiopropyl-glucosinolate = 8-methylsulfinylpropyl-glucosinolate."
* Added general dbxref EC:4.2.1.84 to GO:0080109
* Added general dbxref KEGG:R04020 to GO:0080109
* Added general dbxref MetaCyc:RXN-7567 to GO:0080109
* Changed definition of GO:0080118 from "Catalysis of the transfer of a sulfate group from 3'-phosphoadenosine 5'-phosphosulfate to the hydroxyl group of a brassinosteroid acceptor, producing the sulfated brassinosteroid derivative and 3'-phosphoadenosine 5'-phosphate." to "Catalysis of the reaction: a brassinosteriod + 3'-phosphoadenosine-5'-phosphosulfate = sulfated brassinosteroid + adenosine-3',5'-diphosphate. This reaction is the transfer of a sulfate group to the hydroxyl group of a brassinosteroid acceptor, producing the sulfated brassinosteroid derivative."
* Added general dbxref EC:2.6.1.1 to GO:0080130
* Added general dbxref EC:2.6.1.5 to GO:0080130
* Added general dbxref EC:2.6.1.57 to GO:0080130
* Added general dbxref EC:2.6.1.9 to GO:0080130
* Added general dbxref KEGG:R00694 to GO:0080130
* Added general dbxref MetaCyc:RXN-10814 to GO:0080130
* Changed definition of GO:0080131 from "Catalysis of the reaction: a hydroxyjasmonate + phosphoadenosine-5'-phosphosulfate = a hydroxyjasmonate sulfate + adenosine-3',5'-bisphosphate." to "Catalysis of the reaction: a hydroxyjasmonate + 3'-phosphoadenosine-5'-phosphosulfate = a hydroxyjasmonate sulfate + adenosine-3',5'-diphosphate."