[Go-diff] GO update 05/01/2009
Remote CVS for Gene Ontology
gocvs at genome.stanford.edu
Fri May 1 21:30:54 PDT 2009
OBODIFF of gene_ontology_write.obo version 1.582 by 1.586
Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0002138
* Created object of type obo:TERM with id GO:0070623
* Created object of type obo:TERM with id GO:0070624
* Created object of type obo:TERM with id GO:0070625
* Created object of type obo:TERM with id GO:0070626
* Created object of type obo:TERM with id GO:0070627
* Created object of type obo:TERM with id GO:0070628
* Created object of type obo:TERM with id GO:0070629
* Created object of type obo:TERM with id GO:0070630
* Populated new object GO:0002138 (macro)
* Changed name of GO:0002138 from "<new term>" to "retinoic acid biosynthetic process"
* Set definition of GO:0002138 to "The chemical reactions and pathways resulting in the biosynthesis of retinoic acid, one of the three components that makes up vitamin A."
* Added definition dbxref GOC:hjd to GO:0002138
* Added synonym "retinoic acid anabolic process" to GO:0002138
* Changed synonym scope of GO:0002138 from "Related" to "Exact"
* Copied GO:0002138 to GO:0042573 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0002138
* Populated new object GO:0070623 (macro)
* Changed name of GO:0070623 from "<new term>" to "regulation of thiamin biosynthetic process"
* Set definition of GO:0070623 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of thiamin."
* Added definition dbxref GOC:mah to GO:0070623
* Added GO:0070623 to category gosubset_prok
* Added synonym "regulation of thiamin anabolism" to GO:0070623
* Added general dbxref GOC:mah to synonym regulation of thiamin anabolism of GO:0070623
* Changed synonym scope of GO:0070623 from "Related" to "Exact"
* Added synonym "regulation of thiamin biosynthesis" to GO:0070623
* Added general dbxref GOC:mah to synonym regulation of thiamin biosynthesis of GO:0070623
* Changed synonym scope of GO:0070623 from "Related" to "Exact"
* Added synonym "regulation of thiamin formation" to GO:0070623
* Added general dbxref GOC:mah to synonym regulation of thiamin formation of GO:0070623
* Changed synonym scope of GO:0070623 from "Related" to "Exact"
* Added synonym "regulation of thiamin synthesis" to GO:0070623
* Added general dbxref GOC:mah to synonym regulation of thiamin synthesis of GO:0070623
* Changed synonym scope of GO:0070623 from "Related" to "Exact"
* Copied GO:0070623 to GO:0030656 with type OBO_REL:is_a
* Copied GO:0070623 to GO:0009228 with type regulates
* Assigned namespace "biological_process" to GO:0070623
* Populated new object GO:0070624 (macro)
* Changed name of GO:0070624 from "<new term>" to "negative regulation of thiamin biosynthetic process"
* Set definition of GO:0070624 to "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of thiamin."
* Added definition dbxref GOC:mah to GO:0070624
* Added GO:0070624 to category gosubset_prok
* Added synonym "down regulation of thiamin biosynthetic process" to GO:0070624
* Added general dbxref GOC:mah to synonym down regulation of thiamin biosynthetic process of GO:0070624
* Changed synonym scope of GO:0070624 from "Related" to "Exact"
* Added synonym "down-regulation of thiamin biosynthetic process" to GO:0070624
* Added general dbxref GOC:mah to synonym down-regulation of thiamin biosynthetic process of GO:0070624
* Changed synonym scope of GO:0070624 from "Related" to "Exact"
* Added synonym "downregulation of thiamin biosynthetic process" to GO:0070624
* Added general dbxref GOC:mah to synonym downregulation of thiamin biosynthetic process of GO:0070624
* Changed synonym scope of GO:0070624 from "Related" to "Exact"
* Added synonym "inhibition of thiamin biosynthetic process" to GO:0070624
* Added general dbxref GOC:mah to synonym inhibition of thiamin biosynthetic process of GO:0070624
* Changed synonym scope of GO:0070624 from "Related" to "Narrow"
* Added synonym "negative regulation of thiamin anabolism" to GO:0070624
* Added general dbxref GOC:mah to synonym negative regulation of thiamin anabolism of GO:0070624
* Changed synonym scope of GO:0070624 from "Related" to "Exact"
* Added synonym "negative regulation of thiamin biosynthesis" to GO:0070624
* Added general dbxref GOC:mah to synonym negative regulation of thiamin biosynthesis of GO:0070624
* Changed synonym scope of GO:0070624 from "Related" to "Exact"
* Added synonym "negative regulation of thiamin formation" to GO:0070624
* Added general dbxref GOC:mah to synonym negative regulation of thiamin formation of GO:0070624
* Changed synonym scope of GO:0070624 from "Related" to "Exact"
* Added synonym "negative regulation of thiamin synthesis" to GO:0070624
* Added general dbxref GOC:mah to synonym negative regulation of thiamin synthesis of GO:0070624
* Changed synonym scope of GO:0070624 from "Related" to "Exact"
* Copied GO:0070624 to GO:0009228 with type negatively_regulates
* Copied GO:0070624 to GO:0070623 with type OBO_REL:is_a
* Copied GO:0070624 to GO:0046137 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070624
* Populated new object GO:0070625 (macro)
* Changed name of GO:0070625 from "<new term>" to "zymogen granule exocytosis"
* Set definition of GO:0070625 to "The release of intracellular molecules contained within the zymogen granule by fusion of the granule with the plasma membrane of the oocyte, requiring calcium ions."
* Added definition dbxref GOC:vk to GO:0070625
* Added definition dbxref PMID:17442889 to GO:0070625
* Copied GO:0070625 to GO:0017156 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070625
* Populated new object GO:0070626 (macro)
* Changed name of GO:0070626 from "<new term>" to "(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity"
* Set definition of GO:0070626 to "Catalysis of the reaction: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide."
* Added definition dbxref GOC:mah to GO:0070626
* Added definition dbxref GOC:pde to GO:0070626
* Added general dbxref EC:4.3.2.2 to GO:0070626
* Added general dbxref MetaCyc:AMPSYN-RXN to GO:0070626
* Added general dbxref Reactome:7065 to GO:0070626
* Added GO:0070626 to category gosubset_prok
* Added synonym "adenylosuccinase activity" to GO:0070626
* Added general dbxref GOC:mah to synonym adenylosuccinase activity of GO:0070626
* Added general dbxref EC:4.3.2.2 to synonym adenylosuccinase activity of GO:0070626
* Changed synonym scope of GO:0070626 from "Related" to "Broad"
* Added synonym "adenylosuccinate lyase activity" to GO:0070626
* Added general dbxref GOC:mah to synonym adenylosuccinate lyase activity of GO:0070626
* Changed synonym scope of GO:0070626 from "Related" to "Broad"
* Added synonym "succino AMP-lyase activity" to GO:0070626
* Added general dbxref GOC:mah to synonym succino AMP-lyase activity of GO:0070626
* Added general dbxref EC:4.3.2.2 to synonym succino AMP-lyase activity of GO:0070626
* Changed synonym scope of GO:0070626 from "Related" to "Broad"
* Copied GO:0070626 to GO:0016842 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0070626
* Populated new object GO:0070627 (macro)
* Changed name of GO:0070627 from "<new term>" to "ferrous iron import"
* Set definition of GO:0070627 to "The directed movement of ferrous iron (Fe(II) or Fe2+) ions across a membrane into a cell or organelle."
* Added definition dbxref GOC:mah to GO:0070627
* Added synonym "ferrous ion import" to GO:0070627
* Changed synonym scope of GO:0070627 from "Related" to "Exact"
* Added synonym "ferrous iron uptake" to GO:0070627
* Changed synonym scope of GO:0070627 from "Related" to "Exact"
* Copied GO:0070627 to GO:0034755 with type OBO_REL:is_a
* Copied GO:0070627 to GO:0015684 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070627
* Populated new object GO:0070628 (macro)
* Changed name of GO:0070628 from "<new term>" to "proteasome binding"
* Set definition of GO:0070628 to "Interacting selectively with a proteasome, a large multisubunit protein complex that catalyzes protein degradation."
* Added definition dbxref GOC:mah to GO:0070628
* Copied GO:0070628 to GO:0032403 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0070628
* Populated new object GO:0070629 (macro)
* Changed name of GO:0070629 from "<new term>" to "1,4-alpha-glucan metabolic process"
* Set definition of GO:0070629 to "The chemical reactions and pathways involving alpha-1,4 glucans, compounds composed of glucose residues linked by 1,4-alpha-D-glucosidic bonds."
* Added definition dbxref GOC:mah to GO:0070629
* Added GO:0070629 to category gosubset_prok
* Added synonym "1,4-alpha-glucan metabolism" to GO:0070629
* Added general dbxref GOC:mah to synonym 1,4-alpha-glucan metabolism of GO:0070629
* Changed synonym scope of GO:0070629 from "Related" to "Exact"
* Added synonym "alpha-1,4 glucan metabolic process" to GO:0070629
* Added general dbxref GOC:mah to synonym alpha-1,4 glucan metabolic process of GO:0070629
* Changed synonym scope of GO:0070629 from "Related" to "Exact"
* Added synonym "alpha-1,4 glucan metabolism" to GO:0070629
* Added general dbxref GOC:mah to synonym alpha-1,4 glucan metabolism of GO:0070629
* Changed synonym scope of GO:0070629 from "Related" to "Exact"
* Copied GO:0070629 to GO:0030978 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070629
* Populated new object GO:0070630 (macro)
* Changed name of GO:0070630 from "<new term>" to "1,4-alpha-glucan biosynthetic process"
* Set definition of GO:0070630 to "The chemical reactions and pathways resulting in the formation of alpha-1,4 glucans, compounds composed of glucose residues linked by 1,4-alpha-D-glucosidic bonds."
* Added definition dbxref GOC:mah to GO:0070630
* Added synonym "1,4-alpha-glucan anabolism" to GO:0070630
* Added general dbxref GOC:mah to synonym 1,4-alpha-glucan anabolism of GO:0070630
* Changed synonym scope of GO:0070630 from "Related" to "Exact"
* Added synonym "1,4-alpha-glucan biosynthesis" to GO:0070630
* Added general dbxref GOC:mah to synonym 1,4-alpha-glucan biosynthesis of GO:0070630
* Changed synonym scope of GO:0070630 from "Related" to "Exact"
* Added synonym "1,4-alpha-glucan formation" to GO:0070630
* Added general dbxref GOC:mah to synonym 1,4-alpha-glucan formation of GO:0070630
* Changed synonym scope of GO:0070630 from "Related" to "Exact"
* Added synonym "1,4-alpha-glucan synthesis" to GO:0070630
* Added general dbxref GOC:mah to synonym 1,4-alpha-glucan synthesis of GO:0070630
* Changed synonym scope of GO:0070630 from "Related" to "Exact"
* Added synonym "alpha-1,4 glucan anabolism" to GO:0070630
* Added general dbxref GOC:mah to synonym alpha-1,4 glucan anabolism of GO:0070630
* Changed synonym scope of GO:0070630 from "Related" to "Exact"
* Added synonym "alpha-1,4 glucan biosynthesis" to GO:0070630
* Added general dbxref GOC:mah to synonym alpha-1,4 glucan biosynthesis of GO:0070630
* Changed synonym scope of GO:0070630 from "Related" to "Exact"
* Added synonym "alpha-1,4 glucan biosynthetic process" to GO:0070630
* Added general dbxref GOC:mah to synonym alpha-1,4 glucan biosynthetic process of GO:0070630
* Changed synonym scope of GO:0070630 from "Related" to "Exact"
* Added synonym "alpha-1,4 glucan formation" to GO:0070630
* Added general dbxref GOC:mah to synonym alpha-1,4 glucan formation of GO:0070630
* Changed synonym scope of GO:0070630 from "Related" to "Exact"
* Added synonym "alpha-1,4 glucan synthesis" to GO:0070630
* Added general dbxref GOC:mah to synonym alpha-1,4 glucan synthesis of GO:0070630
* Changed synonym scope of GO:0070630 from "Related" to "Exact"
* Copied GO:0070630 to GO:0030979 with type OBO_REL:is_a
* Copied GO:0070630 to GO:0070629 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070630
* Deleted GO:0000266 --OBO_REL:is_a--> GO:0007005
* Copied GO:0000266 to GO:0070584 with type OBO_REL:is_a
* Copied GO:0002085 to GO:0045995 with type OBO_REL:is_a
* Copied GO:0002085 to GO:0022603 with type OBO_REL:is_a
* Changed comment from "Exclusively located at the anticodon wobble position (position 34) of eubacterial and some organellar tRNAIle2. This modification converts the codon specificity from AUG to AUA, and it also converts the aminoacylation specificity of the tRNA from methionine to isoleucine. Requires ATP." to "Exclusively located at the anticodon wobble position (i.e., position 34) of eubacterial and some organellar tRNAIle2. This modification converts the codon specificity from AUG to AUA, and it also converts the aminoacylation specificity of the tRNA from methionine to isoleucine. Requires ATP."
* Changed name of GO:0004018 from "adenylosuccinate lyase activity" to "N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity"
* Added general dbxref GOC:mah to synonym adenylosuccinase activity of GO:0004018
* Changed synonym scope of GO:0004018 from "Exact" to "Broad"
* Added general dbxref GOC:mah to synonym succino AMP-lyase activity of GO:0004018
* Changed synonym scope of GO:0004018 from "Exact" to "Broad"
* Added synonym "adenylosuccinate lyase activity" to GO:0004018
* Added general dbxref GOC:mah to synonym adenylosuccinate lyase activity of GO:0004018
* Changed synonym scope of GO:0004018 from "Related" to "Broad"
* added secondary id GO:0043735 to GO:0004768
* Added synonym "delta-9 acyl-phospholipid desaturase activity" to GO:0004768
* Copied GO:0006109 to GO:0080090 with type OBO_REL:is_a
* Copied GO:0006521 to GO:0080090 with type OBO_REL:is_a
* Changed definition of GO:0006924 from "A type of T cell apoptosis that occurs towards the end of the expansion phase following the initial activation of mature T cells by antigen and is triggered by T cell receptor stimulation and signals transmitted via various surface-expressed members of the TNF receptor family such as Fas, Fas ligand, and TNF and the p55 and p75 TNF receptors." to "A type of T cell apoptosis that occurs towards the end of the expansion phase following the initial activation of mature T cells by antigen and is triggered by T cell receptor stimulation and signals transmitted via various surface-expressed members of the TNF receptor family such as Fas ligand, Fas, and TNF and the p55 and p75 TNF receptors."
* Deleted GO:0008053 --OBO_REL:is_a--> GO:0007005
* Copied GO:0008053 to GO:0070584 with type OBO_REL:is_a
* Added synonym "Barr body formation" to GO:0009048
* Copied GO:0009962 to GO:0080090 with type OBO_REL:is_a
* Copied GO:0010602 to GO:0080090 with type OBO_REL:is_a
* Copied GO:0010717 to GO:0051239 with type OBO_REL:is_a
* Copied GO:0010755 to GO:0070613 with type OBO_REL:is_a
* Changed definition of GO:0019410 from "The metabolic process by which carbon monoxide (CO) is oxidized to carbon dioxide (CO2) to generate energy; energy conservation likely uses sodium ion gradients for ATP synthesis and is coupled to quantitative sulfide methylation." to "The metabolic process by which carbon monoxide (CO) is oxidized to carbon dioxide (CO2) to generate energy. Conservation of energy in this process likely uses sodium ion gradients for ATP synthesis and is coupled to quantitative sulfide methylation."
* Set definition of GO:0042264 to "The posttranslational hydroxylation of peptidyl-aspartic acid to form peptidyl-hydroxyaspartic acid."
* Added definition dbxref GOC:mah to GO:0042264
* Set definition of GO:0042265 to "The posttranslational hydroxylation of peptidyl-asparagine to form peptidyl-hydroxyasparagine."
* Added definition dbxref GOC:mah to GO:0042265
* Deleted GO:0043735 --OBO_REL:is_a--> GO:0016717
* Destroyed object GO:0043735
* Changed definition of GO:0052049 from "An interaction with the host organism mediated by a substance secreted by the other organism by a type III secretion system. The host is defined as the larger of the organisms involved in a symbiotic interaction." to "An interaction with the host organism mediated by a substance secreted by the symbiont organism by a type III secretion system. The host is defined as the larger of the organisms involved in a symbiotic interaction."
* Deleted GO:0070487 --OBO_REL:is_a--> GO:0070527
* Deleted GO:0070488 --OBO_REL:is_a--> GO:0070527
* Deleted GO:0070489 --OBO_REL:is_a--> GO:0070527
* Changed definition of GO:0070603 from "A chromatin remodeling complex that contains an ortholog of the Sacccharomyces ATPase Swi2/Snf2 as one of the core components." to "A chromatin remodeling complex that contains an ortholog of the Saccharomyces ATPase Swi2/Snf2 as one of the core components."
* Changed definition of GO:0070614 from "The directed movement of tungstate (WO4 2-) ions into, out of, within or between cells. Tungstate is a bivalent oxoanion of tungstet." to "The directed movement of tungstate (WO4 2-) ions into, out of, within or between cells. Tungstate is a bivalent oxoanion of tungsten."
* Copied GO:0070616 to GO:0030656 with type OBO_REL:is_a
* Copied GO:0070617 to GO:0046137 with type OBO_REL:is_a
* Changed definition of GO:0080121 from "The directed movement of AMP, adenosine monophosphate, into, out of,
within or between cells." to "The directed movement of AMP, adenosine monophosphate, into, out of, within or between cells."
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