From gocvs at genome.Stanford.EDU  Wed Aug  1 21:30:40 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Wed, 1 Aug 2007 21:30:40 -0700 (PDT)
Subject: [go-diff] GO update 08/01/2007
Message-ID: <200708020430.VAA01400@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.435 by 5.437

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033560
* Created object of type obo:TERM with id GO:0033561
* Created object of type obo:TERM with id GO:0043876
* Created object of type obo:TERM with id GO:0043877
* Created object of type obo:TERM with id GO:0043878
* Created object of type obo:TERM with id GO:0043879
* Created object of type obo:TERM with id GO:0043880
* Created object of type obo:TERM with id GO:0043881
* Created object of type obo:TERM with id GO:0043882
* Created object of type obo:TERM with id GO:0043883
* Created object of type obo:TERM with id GO:0043884
* Created object of type obo:TERM with id GO:0043885
* Created object of type obo:TERM with id GO:0043886
* Populated new object GO:0033560 (macro)
  * Changed name of GO:0033560 from "<new term>" to "folate reductase activity"
  * Set definition of GO:0033560 to "Catalysis of the reaction: 7,8-dihydrofolate + NADP+ = folate + NADPH +
H+."
  * Added definition dbxref GOC:pd to GO:0033560
  * Added GO:0033560 to category gosubset_prok
  * Copied GO:0033560 to GO:0016646 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033560
* Populated new object GO:0033561 (macro)
  * Changed name of GO:0033561 from "<new term>" to "regulation of water loss via skin"
  * Set definition of GO:0033561 to "A process that modulates the rate or extent of water loss from an organism via the skin."
  * Added definition dbxref GOC:mah to GO:0033561
  * Added synonym "skin barrier function" to GO:0033561
  * Copied GO:0033561 to GO:0030104 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033561
* Populated new object GO:0043876 (macro)
  * Changed name of GO:0043876 from "<new term>" to "D-threonine aldolase activity"
  * Set definition of GO:0043876 to "Catalysis of the reaction: D-threonine (or D-allo-threonine) = glycine + acetaldehyde."
  * Added definition dbxref PMID:9642221 to GO:0043876
  * Added definition dbxref UniProt:A2SCK2 to GO:0043876
  * Added general dbxref EC:4.1.2.- to GO:0043876
  * Added GO:0043876 to category gosubset_prok
  * Added synonym "D-allo-TA" to GO:0043876
  * Changed synonym scope of GO:0043876 from "Related" to "Exact"
  * Added synonym "D-allo-threonine aldolase activity" to GO:0043876
  * Changed synonym scope of GO:0043876 from "Related" to "Exact"
  * Added synonym "D-TA" to GO:0043876
  * Changed synonym scope of GO:0043876 from "Related" to "Exact"
  * Added synonym "DtaAS" to GO:0043876
  * Added synonym "low-specificity D-threonine aldolase" to GO:0043876
  * Changed synonym scope of GO:0043876 from "Related" to "Narrow"
  * Copied GO:0043876 to GO:0016832 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043876
* Populated new object GO:0043877 (macro)
  * Changed name of GO:0043877 from "<new term>" to "galactosamine-6-phosphate isomerase activity"
  * Added comment "This function is part of the pathway of N-acetyl-galactosamine and galactosamine utilization."
  * Set definition of GO:0043877 to "Catalysis of the reaction: D-galactosamine 6-phosphate + H2O = D-tagatose 6-phosphate + NH3."
  * Added definition dbxref UniProt:P42912 to GO:0043877
  * Added general dbxref EC:5.3.1.- to GO:0043877
  * Added GO:0043877 to category gosubset_prok
  * Added synonym "AgaI" to GO:0043877
  * Added synonym "galactosamine-6-phosphate deaminase" to GO:0043877
  * Changed synonym scope of GO:0043877 from "Related" to "Exact"
  * Copied GO:0043877 to GO:0016861 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043877
* Populated new object GO:0043878 (macro)
  * Changed name of GO:0043878 from "<new term>" to "glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity"
  * Set definition of GO:0043878 to "Catalysis of the reaction: D-glyceraldehyde 3-phosphate + NAD+ + H2O = 3-phospho-D-glycerate + NADH + H+."
  * Added definition dbxref PMID:9497334 to GO:0043878
  * Added general dbxref EC:1.2.1.- to GO:0043878
  * Added GO:0043878 to category gosubset_prok
  * Added synonym "glyceraldehyde-3-phosphate dehydrogenase (NAD) (non-phosphorylating) activity" to GO:0043878
  * Changed synonym scope of GO:0043878 from "Related" to "Exact"
  * Added synonym "glyceraldehyde-3-phosphate dehydrogenase (NAD) activity" to GO:0043878
  * Changed synonym scope of GO:0043878 from "Related" to "Exact"
  * Added synonym "NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase" to GO:0043878
  * Changed synonym scope of GO:0043878 from "Related" to "Exact"
  * Added synonym "non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (NAD)" to GO:0043878
  * Changed synonym scope of GO:0043878 from "Related" to "Exact"
  * Copied GO:0043878 to GO:0008943 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043878
* Populated new object GO:0043879 (macro)
  * Changed name of GO:0043879 from "<new term>" to "glycolate transmembrane transporter activity"
  * Set definition of GO:0043879 to "Catalysis of the transfer of glycolate from one side of a membrane to the other. Glycolate is the smallest alpha-hydroxy acid (AHA)."
  * Added definition dbxref GOC:jl to GO:0043879
  * Added definition dbxref http://en.wikipedia.org/ to GO:0043879
  * Added definition dbxref UniProt:Q46839 to GO:0043879
  * Added GO:0043879 to category gosubset_prok
  * Added synonym "glcA" to GO:0043879
  * Added synonym "glycolate permease" to GO:0043879
  * Added synonym "glycolic acid transmembrane transporter activity" to GO:0043879
  * Changed synonym scope of GO:0043879 from "Related" to "Exact"
  * Added synonym "hydroxyacetic acid transmembrane transporter activity" to GO:0043879
  * Changed synonym scope of GO:0043879 from "Related" to "Exact"
  * Copied GO:0043879 to GO:0008514 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043879
* Populated new object GO:0043880 (macro)
  * Changed name of GO:0043880 from "<new term>" to "crotonyl-CoA reductase activity"
  * Set definition of GO:0043880 to "Catalysis of the reduction of crotonyl-CoA to butyryl-CoA."
  * Added definition dbxref IPR:010085 to GO:0043880
  * Added definition dbxref PMID:11162231 to GO:0043880
  * Added definition dbxref UniProt:A1B8U5 to GO:0043880
  * Added GO:0043880 to category gosubset_prok
  * Added synonym "CCR" to GO:0043880
  * Changed synonym scope of GO:0043880 from "Related" to "Exact"
  * Added synonym "crotonyl-coenzyme A reductase" to GO:0043880
  * Changed synonym scope of GO:0043880 from "Related" to "Exact"
  * Copied GO:0043880 to GO:0016491 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043880
* Populated new object GO:0043881 (macro)
  * Changed name of GO:0043881 from "<new term>" to "mesaconyl-CoA hydratase activity"
  * Added comment "This function is part of an alternate glyoxylate cycle for acetate assimilation."
  * Set definition of GO:0043881 to "Catalysis of the hydration of mesaconyl-CoA to beta-methylmalyl-CoA."
  * Added definition dbxref PMID:16856935 to GO:0043881
  * Added definition dbxref PMID:16856937 to GO:0043881
  * Added GO:0043881 to category gosubset_prok
  * Added synonym "beta-methylmalyl-CoA dehydratase" to GO:0043881
  * Changed synonym scope of GO:0043881 from "Related" to "Exact"
  * Added synonym "mch" to GO:0043881
  * Added synonym "mesaconyl-coenzyme A hydratase activity" to GO:0043881
  * Changed synonym scope of GO:0043881 from "Related" to "Exact"
  * Copied GO:0043881 to GO:0016836 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043881
* Populated new object GO:0043882 (macro)
  * Changed name of GO:0043882 from "<new term>" to "malate:sodium symporter activity"
  * Set definition of GO:0043882 to "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: malate(out) + Na+(out) = malate(in) + Na+(in)."
  * Added definition dbxref GOC:jl to GO:0043882
  * Added definition dbxref UniProt:O05256 to GO:0043882
  * Added GO:0043882 to category gosubset_prok
  * Added synonym "malate Na(+) symporter" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Exact"
  * Added synonym "malate-sodium symporter activity" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Exact"
  * Added synonym "malate/sodium cotransporter activity" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Exact"
  * Added synonym "malate/sodium symporter activity" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Exact"
  * Added synonym "malate:Na+ symporter activity" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Exact"
  * Added synonym "malate:sodium cotransporter activity" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Exact"
  * Added synonym "Na(+)-malate symporter" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Exact"
  * Added synonym "Na+:malate symporter activity" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Exact"
  * Added synonym "sodium-dependent malate transporter" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Broad"
  * Added synonym "sodium/malate symporter activity" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Exact"
  * Added synonym "sodium:malate symporter activity" to GO:0043882
  * Changed synonym scope of GO:0043882 from "Related" to "Exact"
  * Copied GO:0043882 to GO:0015296 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043882
* Populated new object GO:0043883 (macro)
  * Changed name of GO:0043883 from "<new term>" to "malolactic enzyme activity"
  * Added comment "This function is part of the process of degradation of L-malic acid by lactic acid bacteria."
  * Set definition of GO:0043883 to "Catalysis of the reaction: malate + H+ = L-lactate + CO2."
  * Added definition dbxref MetaCyc:RXN8E-5623 to GO:0043883
  * Added definition dbxref PMID:3139053 to GO:0043883
  * Added general dbxref EC:1.-.-.- to GO:0043883
  * Added general dbxref MetaCyc:RXN8E-5623 to GO:0043883
  * Added GO:0043883 to category gosubset_prok
  * Added synonym "MleS" to GO:0043883
  * Copied GO:0043883 to GO:0016491 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043883
* Populated new object GO:0043884 (macro)
  * Changed name of GO:0043884 from "<new term>" to "CO-methylating acetyl-CoA synthase activity"
  * Set definition of GO:0043884 to "Catalysis of the reaction: acetyl-CoA + corrinoid protein = CO + methylcorrinoid protein + CoA."
  * Added definition dbxref EC:2.3.1.169 to GO:0043884
  * Added definition dbxref PMID:1748656 to GO:0043884
  * Added general dbxref EC:2.3.1.169 to GO:0043884
  * Added general dbxref MetaCyc:ACETYLSYNCLTH-RXN to GO:0043884
  * Added GO:0043884 to category gosubset_prok
  * Added synonym "acetyl-CoA synthase activity" to GO:0043884
  * Changed synonym scope of GO:0043884 from "Related" to "Broad"
  * Added synonym "acetyl-CoA:corrinoid protein O-acetyltransferase" to GO:0043884
  * Changed synonym scope of GO:0043884 from "Related" to "Exact"
  * Added synonym "CO-methylating acetyl-coenzyme A synthase activity" to GO:0043884
  * Changed synonym scope of GO:0043884 from "Related" to "Exact"
  * Copied GO:0043884 to GO:0016747 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043884
* Populated new object GO:0043885 (macro)
  * Changed name of GO:0043885 from "<new term>" to "carbon-monoxide dehydrogenase (ferredoxin) activity"
  * Set definition of GO:0043885 to "Catalysis of the reaction: CO + H2O + oxidized ferredoxin = CO2 + reduced ferredoxin."
  * Added definition dbxref EC:1.2.7.4 to GO:0043885
  * Added general dbxref EC:1.2.7.4 to GO:0043885
  * Added general dbxref MetaCyc:CARBON-MONOXIDE-DEHYDROGENASE-RXN to GO:0043885
  * Added GO:0043885 to category gosubset_prok
  * Added synonym "carbon monoxide dehydrogenase (ferredoxin) activity" to GO:0043885
  * Changed synonym scope of GO:0043885 from "Related" to "Exact"
  * Added synonym "carbon monoxide dehydrogenase activity" to GO:0043885
  * Changed synonym scope of GO:0043885 from "Related" to "Exact"
  * Added synonym "carbon-monoxide dehydrogenase activity" to GO:0043885
  * Changed synonym scope of GO:0043885 from "Related" to "Exact"
  * Added synonym "carbon-monoxide,water:ferredoxin oxidoreductase" to GO:0043885
  * Changed synonym scope of GO:0043885 from "Related" to "Exact"
  * Added synonym "carbon-monoxide:(acceptor) oxidoreductase" to GO:0043885
  * Changed synonym scope of GO:0043885 from "Related" to "Exact"
  * Added synonym "CO dehydrogenase activity" to GO:0043885
  * Changed synonym scope of GO:0043885 from "Related" to "Exact"
  * Added synonym "CO-dehydrogenase (ferredoxin) activity" to GO:0043885
  * Changed synonym scope of GO:0043885 from "Related" to "Exact"
  * Added synonym "CO-dehydrogenase activity" to GO:0043885
  * Changed synonym scope of GO:0043885 from "Related" to "Exact"
  * Added synonym "CODH" to GO:0043885
  * Copied GO:0043885 to GO:0016625 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043885
* Populated new object GO:0043886 (macro)
  * Changed name of GO:0043886 from "<new term>" to "structural constituent of carboxysome"
  * Set definition of GO:0043886 to "The action of a molecule that contributes to the structural integrity of a carboxysome, an organelle found in the Cyanobacteria consisting of a proteinaceous coat and enzymes for the fixation of carbon dioxide."
  * Added definition dbxref GOC:jl to GO:0043886
  * Added GO:0043886 to category gosubset_prok
  * Copied GO:0043886 to GO:0005198 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043886
* Deleted definition dbxref ISBN:1555811337 from GO:0000179
* Added definition dbxref Modification and Editing of RNA (ISBN:1555811337) to GO:0000179
* Added synonym "THO complex part of TREX complex" to GO:0000445
* Changed synonym scope of GO:0000445 from "Related" to "Exact"
* Changed definition of GO:0000481 from "Any process involved in the maturation of a precursor 5S ribosomal RNA (rRNA) molecule into a mature 5S rRNA molecule" to "Any process involved in the maturation of a precursor 5S ribosomal RNA (rRNA) molecule into a mature 5S rRNA molecule."
* Changed definition of GO:0000483 from "Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small SubUnit (SSU) rRNA, the 5.8S rRNA, 2S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with four genes, in this order, are produced in the nuclei of D. melanogaster as well as in those of other dipteran  species." to "Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small SubUnit (SSU) rRNA, the 5.8S rRNA, 2S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with four genes, in this order, are produced in the nuclei of D. melanogaster as well as in those of other dipteran species."
* Changed definition of GO:0000487 from "Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 8.8S rRNA, the 2S rRNA, and the Large Subunit (LSU)  in that order from 5' to 3' along the primary transcript." to "Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 8.8S rRNA, the 2S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript."
* Added synonym "L-threonine acetaldehyde-lyase" to GO:0004793
* Changed synonym scope of GO:0004793 from "Related" to "Exact"
* Added synonym "L-threonine aldolase activity" to GO:0004793
* Changed synonym scope of GO:0004793 from "Related" to "Exact"
* Added synonym "4.2.1.16" to GO:0004794
* Added synonym "L-serine dehydratase" to GO:0004794
* Added synonym "serine deaminase" to GO:0004794
* Added synonym "threonine deaminase" to GO:0004794
* Changed synonym scope of GO:0004794 from "Related" to "Exact"
* Copied GO:0007004 to GO:0006278 with type OBO_REL:is_a
* Set definition of GO:0008732 to "Catalysis of the reaction: L-allo-threonine = glycine + acetaldehyde."
* Added definition dbxref MetaCyc:LTAA-RXN to GO:0008732
* Added definition dbxref PMID:9228760 to GO:0008732
* Added general dbxref MetaCyc:LTAA-RXN to GO:0008732
* Added synonym "L-allo-threonine acetaldehyde-lyase" to GO:0008732
* Changed synonym scope of GO:0008732 from "Related" to "Exact"
* Added synonym "LtaA" to GO:0008732
* Added synonym "threonine 3-dehydrogenase activity" to GO:0008743
* Changed synonym scope of GO:0008743 from "Related" to "Broad"
* Added synonym "D-glyceraldehyde-3-phosphate:NADP+ oxidoreductase" to GO:0008886
* Changed synonym scope of GO:0008886 from "Related" to "Exact"
* Added synonym "dehydrogenase, glyceraldehyde phosphate (nicotinamide adenine dinucleotide phosphate)" to GO:0008886
* Changed synonym scope of GO:0008886 from "Related" to "Broad"
* Added synonym "glyceraldehyde 3-phosphate dehydrogenase (NADP)" to GO:0008886
* Changed synonym scope of GO:0008886 from "Related" to "Exact"
* Added synonym "glyceraldehyde phosphate dehydrogenase (NADP)" to GO:0008886
* Changed synonym scope of GO:0008886 from "Related" to "Broad"
* Added synonym "glyceraldehyde-3-phosphate dehydrogenase (NADP)" to GO:0008886
* Changed synonym scope of GO:0008886 from "Related" to "Exact"
* Added synonym "glyceraldehyde-3-phosphate:NADP reductase" to GO:0008886
* Changed synonym scope of GO:0008886 from "Related" to "Exact"
* Added synonym "NADP-glyceraldehyde phosphate dehydrogenase" to GO:0008886
* Changed synonym scope of GO:0008886 from "Related" to "Broad"
* Added synonym "NADP-glyceraldehyde-3-phosphate dehydrogenase" to GO:0008886
* Changed synonym scope of GO:0008886 from "Related" to "Exact"
* Added synonym "nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase" to GO:0008886
* Changed synonym scope of GO:0008886 from "Related" to "Exact"
* Added synonym "triosephosphate dehydrogenase" to GO:0008886
* Changed synonym scope of GO:0008886 from "Related" to "Broad"
* Added synonym "AgaY" to GO:0009025
* Added synonym "AgaZ" to GO:0009025
* Added synonym "D-tagatose-1,6-bisphosphate triosephosphate lyase" to GO:0009025
* Changed synonym scope of GO:0009025 from "Related" to "Exact"
* Added synonym "KbaY" to GO:0009025
* Added synonym "tagatose-1,6-bisphosphate aldolase 1" to GO:0009025
* Changed synonym scope of GO:0009025 from "Related" to "Exact"
* Deleted definition dbxref ISBN:1555811337 from GO:0009451
* Added definition dbxref Modification and Editing of RNA (ISBN:1555811337) to GO:0009451
* Added synonym "threonine export protein" to GO:0015565
* Added synonym "threonine export transporter activity" to GO:0015565
* Changed synonym scope of GO:0015565 from "Related" to "Exact"
* Changed synonym scope of GO:0015572 from "Exact" to "Related"
* Added synonym "D-GlcNAc transmembrane transporter activity" to GO:0015572
* Changed synonym scope of GO:0015572 from "Related" to "Exact"
* Added synonym "N-Acetyl-D-glucosamine permease" to GO:0015572
* Added synonym "N-acetyl-D-glucosamine transmembrane transporter activity" to GO:0015572
* Changed synonym scope of GO:0015572 from "Related" to "Exact"
* Added synonym "N-acetylchitosamine transmembrane transporter activity" to GO:0015572
* Changed synonym scope of GO:0015572 from "Related" to "Exact"
* Added synonym "SIR2" to GO:0017136
* Changed name of GO:0019170 from "D-lactaldehyde dehydrogenase activity" to "methylglyoxal reductase (NADH-dependent) activity"
* Added synonym "D-lactaldehyde dehydrogenase activity" to GO:0019170
* Changed synonym scope of GO:0019170 from "Related" to "Exact"
* Changed name of GO:0022002 from "wnt receptor signaling involved in negative regulation of anterior neural cell fate of the neural plate" to "Wnt receptor signaling involved in negative regulation of anterior neural cell fate of the neural plate"
* Deleted synonym "wnt receptor signaling involved in down regulation of anterior neural cell fate of the neural plate" from GO:0022002
* Deleted synonym "wnt receptor signaling involved in down-regulation of anterior neural cell fate of the neural plate" from GO:0022002
* Deleted synonym "wnt receptor signaling involved in downregulation of anterior neural cell fate of the neural plate" from GO:0022002
* Deleted synonym "wnt receptor signaling involved in inhibition of anterior neural cell fate of the neural plate" from GO:0022002
* Deleted synonym "wnt receptor signalling involved in negative regulation of anterior neural cell fate of the neural plate" from GO:0022002
* Added synonym "Wnt receptor signaling involved in down regulation of anterior neural cell fate of the neural plate" to GO:0022002
* Changed synonym scope of GO:0022002 from "Related" to "Exact"
* Added synonym "Wnt receptor signaling involved in down-regulation of anterior neural cell fate of the neural plate" to GO:0022002
* Changed synonym scope of GO:0022002 from "Related" to "Exact"
* Added synonym "Wnt receptor signaling involved in downregulation of anterior neural cell fate of the neural plate" to GO:0022002
* Changed synonym scope of GO:0022002 from "Related" to "Exact"
* Added synonym "Wnt receptor signaling involved in inhibition of anterior neural cell fate of the neural plate" to GO:0022002
* Changed synonym scope of GO:0022002 from "Related" to "Narrow"
* Added synonym "Wnt receptor signalling involved in negative regulation of anterior neural cell fate of the neural plate" to GO:0022002
* Changed synonym scope of GO:0022002 from "Related" to "Exact"
* Added synonym "ChnAC" to GO:0030341
* Added synonym "chondroitin AC eliminase" to GO:0030341
* Changed synonym scope of GO:0030341 from "Related" to "Exact"
* Added synonym "chondroitin lyase activity" to GO:0030341
* Changed synonym scope of GO:0030341 from "Related" to "Exact"
* Added synonym "chondroitin sulfate lyase" to GO:0030341
* Changed synonym scope of GO:0030341 from "Related" to "Exact"
* Added synonym "chondroitinase AC" to GO:0030341
* Added synonym "chondroitinase activity" to GO:0030341
* Changed synonym scope of GO:0030341 from "Related" to "Broad"
* Deleted definition dbxref ISBN:1555811337 from GO:0030696
* Added definition dbxref Modification and Editing of RNA (ISBN:1555811337) to GO:0030696
* Deleted definition dbxref ISBN:1555811337 from GO:0030697
* Added definition dbxref Modification and Editing of RNA (ISBN:1555811337) to GO:0030697
* Deleted definition dbxref ISBN:1555811337 from GO:0030698
* Added definition dbxref Modification and Editing of RNA (ISBN:1555811337) to GO:0030698
* Changed definition of GO:0033503 from "A ubiquitin-conjugating enzyme complex that contains two RING finger proteins, which have ubiquitin ligase activity, in addition to a protein with ubiquitin-conjugating enzyme activity; catalyzes the ubiquitination of histone H2B at lysine 119 (or the equivalent residue). In Schizosaccharomyces the subunits are Rhp1p, Rfp1p and Rfp2p." to "A ubiquitin-conjugating enzyme complex that contains two RING finger proteins, which have ubiquitin ligase activity, in addition to a protein with ubiquitin-conjugating enzyme activity; catalyzes the ubiquitination of histone H2B at lysine 119 (or the equivalent residue). In Schizosaccharomyces the subunits are Rhp1, Brl2/Rfp1 and Brl1/Rfp2."
* Added definition dbxref PMID:17374714 to GO:0033503
* Changed name of GO:0043365 from "[formate-C-acetyltransferase]-activating enzyme" to "[formate-C-acetyltransferase]-activating enzyme activity"
* Deleted definition dbxref Reactome:MONOMER-4222 from GO:0043798
* Added definition dbxref Reactome:GKI-RXN to GO:0043798
* Added general dbxref EC:2.7.1.- to GO:0043798
* Added general dbxref MetaCyc:GKI-RXN to GO:0043798
* Added synonym "D-glycerate 2-kinase activity" to GO:0043798
* Changed synonym scope of GO:0043798 from "Related" to "Exact"
* Added synonym "AcuC" to GO:0045129


From gocvs at genome.Stanford.EDU  Thu Aug  2 21:30:39 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Thu, 2 Aug 2007 21:30:39 -0700 (PDT)
Subject: [go-diff] GO update 08/02/2007
Message-ID: <200708030430.VAA26652@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.437 by 5.439

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033562
* Created object of type obo:TERM with id GO:0033563
* Created object of type obo:TERM with id GO:0033564
* Created object of type obo:TERM with id GO:0033565
* Created object of type obo:TERM with id GO:0033566
* Created object of type obo:TERM with id GO:0033567
* Created object of type obo:TERM with id GO:0033568
* Created object of type obo:TERM with id GO:0033569
* Created object of type obo:TERM with id GO:0033570
* Created object of type obo:TERM with id GO:0033571
* Created object of type obo:TERM with id GO:0033572
* Created object of type obo:TERM with id GO:0033573
* Created object of type obo:TERM with id GO:0033574
* Created object of type obo:TERM with id GO:0043887
* Created object of type obo:TERM with id GO:0043888
* Created object of type obo:TERM with id GO:0043889
* Populated new object GO:0033562 (macro)
  * Changed name of GO:0033562 from "<new term>" to "small RNA-mediated cotranscriptional gene silencing"
  * Set definition of GO:0033562 to "A process by which the targeting of nascent transcripts by the RITS complex mediates chromatin modifications and promotes the degradation of nascent transcripts synthesized in heterochromatic regions."
  * Added definition dbxref GOC:mah to GO:0033562
  * Added definition dbxref PMID:17512405 to GO:0033562
  * Copied GO:0033562 to GO:0031047 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033562
* Populated new object GO:0033563 (macro)
  * Changed name of GO:0033563 from "<new term>" to "dorsal/ventral axon guidance"
  * Set definition of GO:0033563 to "The process by which the migration of an axon growth cone is directed to a specific target site along the dorsal-ventral body axis in response to a combination of attractive and repulsive cues."
  * Added definition dbxref GOC:kva to GO:0033563
  * Added synonym "dorsal-ventral axon guidance" to GO:0033563
  * Changed synonym scope of GO:0033563 from "Related" to "Exact"
  * Copied GO:0033563 to GO:0007411 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033563
* Populated new object GO:0033564 (macro)
  * Changed name of GO:0033564 from "<new term>" to "anterior/posterior axon guidance"
  * Set definition of GO:0033564 to "The process by which the migration of an axon growth cone is directed to a specific target site along the anterior-posterior body axis in response to a combination of attractive and repulsive cues."
  * Added definition dbxref GOC:kva to GO:0033564
  * Added synonym "anterior-posterior axon guidance" to GO:0033564
  * Changed synonym scope of GO:0033564 from "Related" to "Exact"
  * Copied GO:0033564 to GO:0007411 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033564
* Populated new object GO:0033565 (macro)
  * Changed name of GO:0033565 from "<new term>" to "Vps27p-Hse1p complex"
  * Set definition of GO:0033565 to "A protein complex required for the recycling of Golgi proteins, formation of lumenal membranes and sorting of ubiquitinated proteins into those membranes. This complex includes Vps1p and Hse1p in yeast and the Hrs and STAM proteins in mammals."
  * Added definition dbxref GOC:rb to GO:0033565
  * Added definition dbxref PMID:12055639 to GO:0033565
  * Added definition dbxref PMID:17543868 to GO:0033565
  * Copied GO:0033565 to GO:0044440 with type OBO_REL:is_a
  * Copied GO:0033565 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033565
* Populated new object GO:0033566 (macro)
  * Changed name of GO:0033566 from "<new term>" to "gamma-tubulin complex localization"
  * Set definition of GO:0033566 to "The processes by which a gamma-tubulin complex is transported to, or maintained in, a specific location."
  * Added definition dbxref GOC:mah to GO:0033566
  * Copied GO:0033566 to GO:0031503 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033566
* Populated new object GO:0033567 (macro)
  * Changed name of GO:0033567 from "<new term>" to "DNA replication, Okazaki fragment processing"
  * Set definition of GO:0033567 to "The DNA metabolic process, occurring during lagging strand synthesis, by which RNA primers are removed from Okazaki fragments, the resulting gaps filled by DNA polymerization, and the ends ligated to form a continuous strand."
  * Added definition dbxref GOC:mah to GO:0033567
  * Added definition dbxref ISBN:0716720094 to GO:0033567
  * Copied GO:0033567 to GO:0006259 with type OBO_REL:is_a
  * Copied GO:0033567 to GO:0006273 with type part_of
  * Assigned namespace "biological_process" to GO:0033567
* Populated new object GO:0033568 (macro)
  * Changed name of GO:0033568 from "<new term>" to "lactoferrin receptor activity"
  * Set definition of GO:0033568 to "Combining with lactoferrin to initiate a change in cell activity."
  * Added definition dbxref GOC:mlg to GO:0033568
  * Copied GO:0033568 to GO:0004888 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033568
* Populated new object GO:0033569 (macro)
  * Changed name of GO:0033569 from "<new term>" to "lactoferrin transmembrane transporter activity"
  * Set definition of GO:0033569 to "Catalysis of the transfer of lactoferrin from one side of a membrane to the other."
  * Added definition dbxref GOC:mlg to GO:0033569
  * Copied GO:0033569 to GO:0015450 with type OBO_REL:is_a
  * Copied GO:0033569 to GO:0015091 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033569
* Populated new object GO:0033570 (macro)
  * Changed name of GO:0033570 from "<new term>" to "transferrin transmembrane transporter activity"
  * Set definition of GO:0033570 to "Catalysis of the transfer of transferrin from one side of a membrane to the other."
  * Added definition dbxref GOC:mlg to GO:0033570
  * Copied GO:0033570 to GO:0015450 with type OBO_REL:is_a
  * Copied GO:0033570 to GO:0015091 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033570
* Populated new object GO:0033571 (macro)
  * Changed name of GO:0033571 from "<new term>" to "lactoferrin transport"
  * Set definition of GO:0033571 to "The directed movement of lactoferrin into, out of, within or between cells."
  * Added definition dbxref GOC:mlg to GO:0033571
  * Copied GO:0033571 to GO:0015031 with type OBO_REL:is_a
  * Copied GO:0033571 to GO:0015682 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033571
* Populated new object GO:0033572 (macro)
  * Changed name of GO:0033572 from "<new term>" to "transferrin transport"
  * Set definition of GO:0033572 to "The directed movement of transferrin into, out of, within or between cells."
  * Added definition dbxref GOC:mlg to GO:0033572
  * Copied GO:0033572 to GO:0015031 with type OBO_REL:is_a
  * Copied GO:0033572 to GO:0015682 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033572
* Populated new object GO:0033573 (macro)
  * Changed name of GO:0033573 from "<new term>" to "high affinity iron permease complex"
  * Set definition of GO:0033573 to "A protein complex composed of a multicopper ferroxidase that oxidizes Fe(II) to Fe(III), and a ferric iron permease that transports the produced Fe(III) into the cell."
  * Added definition dbxref GOC:jp to GO:0033573
  * Added definition dbxref PMID:16522632 to GO:0033573
  * Added definition dbxref PMID:8599111 to GO:0033573
  * Copied GO:0033573 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0033573 to GO:0044459 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033573
* Populated new object GO:0033574 (macro)
  * Changed name of GO:0033574 from "<new term>" to "response to testosterone stimulus"
  * Set definition of GO:0033574 to "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus."
  * Added definition dbxref GOC:sl to GO:0033574
  * Copied GO:0033574 to GO:0048545 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033574
* Populated new object GO:0043887 (macro)
  * Changed name of GO:0043887 from "<new term>" to "melibiose:sodium symporter activity"
  * Set definition of GO:0043887 to "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: melibiose(out) + Na+(out) = melibiose(in) + Na+(in)."
  * Added definition dbxref PMID:1970646 to GO:0043887
  * Added definition dbxref UniProt:P02921 to GO:0043887
  * Added GO:0043887 to category gosubset_prok
  * Added synonym "MelB" to GO:0043887
  * Added synonym "melibiose carrier protein" to GO:0043887
  * Added synonym "melibiose permease" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Broad"
  * Added synonym "melibiose-Na+ symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "melibiose-sodium symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "melibiose/Na+ symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "melibiose/sodium symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "melibiose:Na+ symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "Na+ (Li+)/melibiose symporter" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "Na+-melibiose symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "Na+/melibiose symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "Na+:melibiose symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "sodium-melibiose symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "sodium/melibiose symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "sodium:melibiose symporter activity" to GO:0043887
  * Changed synonym scope of GO:0043887 from "Related" to "Exact"
  * Added synonym "thiomethylgalactoside permease II" to GO:0043887
  * Copied GO:0043887 to GO:0015487 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043887
* Populated new object GO:0043888 (macro)
  * Changed name of GO:0043888 from "<new term>" to "(S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase activity"
  * Added comment "This function is involved in archaeal lipid synthesis."
  * Set definition of GO:0043888 to "Catalysis of the transfer of a geranylgeranyl group from geranylgeranyl diphosphate to (S)-3-O-geranylgeranylglyceryl phosphate to form (S)-2,3-di-O-geranylgeranylglyceryl phosphate."
  * Added definition dbxref PMID:15356000 to GO:0043888
  * Added definition dbxref PMID:16494480 to GO:0043888
  * Added general dbxref EC:2.5.1.- to GO:0043888
  * Added GO:0043888 to category gosubset_prok
  * Added synonym "2,3-dGGGPS" to GO:0043888
  * Changed synonym scope of GO:0043888 from "Related" to "Exact"
  * Added synonym "DGGGP synthase" to GO:0043888
  * Changed synonym scope of GO:0043888 from "Related" to "Exact"
  * Added synonym "DGGGPS" to GO:0043888
  * Changed synonym scope of GO:0043888 from "Related" to "Exact"
  * Added synonym "UbiA" to GO:0043888
  * Copied GO:0043888 to GO:0004337 with type OBO_REL:is_a
  * Copied GO:0043888 to GO:0002094 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043888
* Populated new object GO:0043889 (macro)
  * Changed name of GO:0043889 from "<new term>" to "(S)-3-O-geranylgeranylglyceryl phosphate activity"
  * Added comment "This function is involved in archaeal lipid synthesis."
  * Set definition of GO:0043889 to "Catalysis of the alkylation of the primary hydroxyl group in (S)-glyceryl phosphate by geranylgeranyl diphosphate to form (S)-3-O-geranylgeranylglyceryl phosphate."
  * Added definition dbxref PMID:12801917 to GO:0043889
  * Added definition dbxref PMID:17253090 to GO:0043889
  * Added definition dbxref PMID:8408023 to GO:0043889
  * Added GO:0043889 to category gosubset_prok
  * Added synonym "(S)-3-O-geranylgeranylglycerylphosphate activity" to GO:0043889
  * Changed synonym scope of GO:0043889 from "Related" to "Exact"
  * Added synonym "(S)-GGGP synthase" to GO:0043889
  * Changed synonym scope of GO:0043889 from "Related" to "Exact"
  * Added synonym "GGGP synthase" to GO:0043889
  * Changed synonym scope of GO:0043889 from "Related" to "Exact"
  * Added synonym "GGGPS" to GO:0043889
  * Changed synonym scope of GO:0043889 from "Related" to "Exact"
  * Copied GO:0043889 to GO:0004659 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043889
* Changed definition of GO:0003896 from "Catalysis of the synthesis of short RNA primers for the Okazaki fragments on both DNA template strands at the replication fork. A DNA-directed RNA polymerase that forms a complex with alpha DNA polymerase." to "Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases. Catalyzed by a DNA-directed RNA polymerase that forms a complex with alpha DNA polymerase."
* Deleted definition dbxref ISBN:0198547684 from GO:0003896
* Added definition dbxref GOC:mah to GO:0003896
* Added definition dbxref ISBN:0716720094 to GO:0003896
* Added synonym "sucrose permease activity" to GO:0008515
* Changed comment from "Note that this function was formerly EC:1.18.99.1." to "Note that this function was formely EC 1.12.1.1, EC 1.12.7.1, EC 1.98.1.1, EC 1.18.3.1 and EC 1.18.99.1."
* Added synonym "1.18.99.1" to GO:0008901
* Added synonym "[Fe] hydrogenase" to GO:0008901
* Changed synonym scope of GO:0008901 from "Related" to "Exact"
* Added synonym "[Fe] hydrogenase gamma" to GO:0008901
* Added synonym "bidirectional hydrogenase" to GO:0008901
* Changed synonym scope of GO:0008901 from "Related" to "Broad"
* Added synonym "H2 oxidizing hydrogenase" to GO:0008901
* Changed synonym scope of GO:0008901 from "Related" to "Broad"
* Added synonym "H2 producing hydrogenase" to GO:0008901
* Changed synonym scope of GO:0008901 from "Related" to "Broad"
* Added synonym "hydrogen-lyase" to GO:0008901
* Changed synonym scope of GO:0008901 from "Related" to "Broad"
* Added synonym "hydrogen:ferredoxin oxidoreductase" to GO:0008901
* Changed synonym scope of GO:0008901 from "Related" to "Exact"
* Added synonym "hydrogenase (ferredoxin)" to GO:0008901
* Changed synonym scope of GO:0008901 from "Related" to "Exact"
* Added synonym "hydrogenase I" to GO:0008901
* Added synonym "hydrogenase II" to GO:0008901
* Added synonym "hydrogenlyase" to GO:0008901
* Changed synonym scope of GO:0008901 from "Related" to "Broad"
* Added synonym "uptake hydrogenase" to GO:0008901
* Changed synonym scope of GO:0008901 from "Related" to "Broad"
* Deleted GO:0009328 --OBO_REL:is_a--> GO:0005941
* Copied GO:0009328 to GO:0043234 with type OBO_REL:is_a
* Copied GO:0009328 to GO:0044444 with type OBO_REL:is_a
* Added GO:0015158 to category gosubset_prok
* Added synonym "raffinose permease" to GO:0015158
* Added GO:0015487 to category gosubset_prok
* Changed synonym scope of GO:0018492 from "Exact" to "Broad"
* Changed name of GO:0021512 from "spinal cord anterior-posterior patterning" to "spinal cord anterior/posterior patterning"
* Added synonym "spinal cord anterior-posterior patterning" to GO:0021512
* Changed synonym scope of GO:0021512 from "Related" to "Exact"
* Changed name of GO:0021513 from "spinal cord dorsal-ventral patterning" to "spinal cord dorsal/ventral patterning"
* Added synonym "spinal cord dorsal-ventral patterning" to GO:0021513
* Changed synonym scope of GO:0021513 from "Related" to "Exact"
* Changed name of GO:0021797 from "forebrain anterior-posterior pattern formation" to "forebrain anterior/posterior pattern formation"
* Added synonym "forebrain anterior-posterior pattern formation" to GO:0021797
* Changed synonym scope of GO:0021797 from "Related" to "Exact"
* Changed name of GO:0021798 from "forebrain dorsal-ventral pattern formation" to "forebrain dorsal/ventral pattern formation"
* Added synonym "forebrain dorsal-ventral pattern formation" to GO:0021798
* Changed synonym scope of GO:0021798 from "Related" to "Exact"
* Copied GO:0030337 to GO:0030234 with type OBO_REL:is_a
* Deleted GO:0031510 --OBO_REL:is_a--> GO:0005941
* Copied GO:0031510 to GO:0044428 with type OBO_REL:is_a
* Copied GO:0031510 to GO:0043234 with type OBO_REL:is_a
* Added synonym "Mex67-Mtr2 complex" to GO:0042272
* Changed synonym scope of GO:0042272 from "Related" to "Exact"
* Added synonym "NXF1-NXT1 complex" to GO:0042272
* Changed synonym scope of GO:0042272 from "Related" to "Exact"
* Added synonym "TAP-p15 complex" to GO:0042272
* Changed synonym scope of GO:0042272 from "Related" to "Exact"
* Deleted synonym "Okazaki fragment processing" from GO:0043137
* Deleted GO:0043137 --part_of--> GO:0006273
* Copied GO:0043137 to GO:0033567 with type part_of
* Changed synonym scope of GO:0043885 from "Exact" to "Broad"


From gocvs at genome.Stanford.EDU  Fri Aug  3 21:30:39 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Fri, 3 Aug 2007 21:30:39 -0700 (PDT)
Subject: [go-diff] GO update 08/03/2007
Message-ID: <200708040430.VAA11701@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.439 by 5.440

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033575
* Created object of type obo:TERM with id GO:0033576
* Created object of type obo:TERM with id GO:0033577
* Created object of type obo:TERM with id GO:0033578
* Created object of type obo:TERM with id GO:0033579
* Created object of type obo:TERM with id GO:0033580
* Created object of type obo:TERM with id GO:0033581
* Created object of type obo:TERM with id GO:0033582
* Created object of type obo:TERM with id GO:0033583
* Populated new object GO:0033575 (macro)
  * Changed name of GO:0033575 from "<new term>" to "protein amino acid glycosylation at cell surface"
  * Set definition of GO:0033575 to "The addition of a sugar unit to a protein amino acid at the surface of a cell."
  * Added definition dbxref GOC:mah to GO:0033575
  * Added definition dbxref PMID:12042244 to GO:0033575
  * Copied GO:0033575 to GO:0006486 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033575
* Populated new object GO:0033576 (macro)
  * Changed name of GO:0033576 from "<new term>" to "protein amino acid glycosylation in cytosol"
  * Set definition of GO:0033576 to "The addition of a sugar unit to a protein amino acid in the cytosol."
  * Added definition dbxref GOC:mah to GO:0033576
  * Added definition dbxref PMID:12042244 to GO:0033576
  * Copied GO:0033576 to GO:0006486 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033576
* Populated new object GO:0033577 (macro)
  * Changed name of GO:0033577 from "<new term>" to "protein amino acid glycosylation in endoplasmic reticulum"
  * Set definition of GO:0033577 to "The addition of a sugar unit to a protein amino acid in the endoplasmic reticulum."
  * Added definition dbxref GOC:mah to GO:0033577
  * Added definition dbxref PMID:12042244 to GO:0033577
  * Added synonym "protein amino acid glycosylation in ER" to GO:0033577
  * Changed synonym scope of GO:0033577 from "Related" to "Exact"
  * Copied GO:0033577 to GO:0006486 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033577
* Populated new object GO:0033578 (macro)
  * Changed name of GO:0033578 from "<new term>" to "protein amino acid glycosylation in Golgi"
  * Set definition of GO:0033578 to "The addition of a sugar unit to a protein amino acid in any compartment of the Golgi apparatus."
  * Added definition dbxref GOC:mah to GO:0033578
  * Added definition dbxref PMID:12042244 to GO:0033578
  * Copied GO:0033578 to GO:0006486 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033578
* Populated new object GO:0033579 (macro)
  * Changed name of GO:0033579 from "<new term>" to "protein amino acid galactosylation in endoplasmic reticulum"
  * Set definition of GO:0033579 to "The addition of a galactose unit to a protein amino acid in the endoplasmic reticulum."
  * Added definition dbxref GOC:mah to GO:0033579
  * Added synonym "protein amino acid galactosylation in ER" to GO:0033579
  * Changed synonym scope of GO:0033579 from "Related" to "Exact"
  * Copied GO:0033579 to GO:0033577 with type OBO_REL:is_a
  * Copied GO:0033579 to GO:0042125 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033579
* Populated new object GO:0033580 (macro)
  * Changed name of GO:0033580 from "<new term>" to "protein amino acid galactosylation at cell surface"
  * Set definition of GO:0033580 to "The addition of a galactose unit to a protein amino acid at the surface of a cell."
  * Added definition dbxref GOC:mah to GO:0033580
  * Copied GO:0033580 to GO:0042125 with type OBO_REL:is_a
  * Copied GO:0033580 to GO:0033575 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033580
* Populated new object GO:0033581 (macro)
  * Changed name of GO:0033581 from "<new term>" to "protein amino acid galactosylation in Golgi"
  * Set definition of GO:0033581 to "The addition of a galactose unit to a protein amino acid in any compartment of the Golgi apparatus."
  * Added definition dbxref GOC:mah to GO:0033581
  * Copied GO:0033581 to GO:0042125 with type OBO_REL:is_a
  * Copied GO:0033581 to GO:0033578 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033581
* Populated new object GO:0033582 (macro)
  * Changed name of GO:0033582 from "<new term>" to "protein amino acid galactosylation in cytosol"
  * Set definition of GO:0033582 to "The addition of a galactose unit to a protein amino acid in the cytosol."
  * Added definition dbxref GOC:mah to GO:0033582
  * Copied GO:0033582 to GO:0033576 with type OBO_REL:is_a
  * Copied GO:0033582 to GO:0042125 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033582
* Populated new object GO:0033583 (macro)
  * Changed name of GO:0033583 from "<new term>" to "rhabdomere membrane"
  * Set definition of GO:0033583 to "The portion of the plasma membrane surrounding the rhabdomere."
  * Added definition dbxref GOC:mah to GO:0033583
  * Copied GO:0033583 to GO:0031253 with type OBO_REL:is_a
  * Copied GO:0033583 to GO:0016028 with type part_of
  * Assigned namespace "cellular_component" to GO:0033583
* Changed comment from "Note that this term should be used for the annotation of gene products whose molecular function is unknown by annotating to this node with the evidence code ND, no data." to "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this."
* Changed comment from "Note that this term should be used for the annotation of gene products whose cellular component is unknown by annotating to this node with the evidence code ND, no data." to "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this."
* Added synonym "peroxisome membrane" to GO:0005778
* Changed synonym scope of GO:0005778 from "Related" to "Exact"
* Added synonym "metabolic energy generation" to GO:0006091
* Changed comment from "Note that this term should be used for the annotation of gene products whose biological process is unknown by annotating to this node with the evidence code ND, no data." to "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this."
* Added synonym "uridine monophosphate kinase activity" to GO:0009041
* Changed synonym scope of GO:0009041 from "Related" to "Exact"
* Changed name of GO:0009380 from "excinuclease ABC complex" to "excinuclease repair complex"
* Deleted GO:0009380 --OBO_REL:is_a--> GO:0005941
* Copied GO:0009380 to GO:0044424 with type OBO_REL:is_a
* Copied GO:0009380 to GO:0043234 with type OBO_REL:is_a
* Deleted GO:0016028 --OBO_REL:is_a--> GO:0043232
* Deleted GO:0016028 --OBO_REL:is_a--> GO:0044459
* Copied GO:0016028 to GO:0042995 with type OBO_REL:is_a
* Changed definition of GO:0031261 from "A multiprotein complex assembled at eukaryotic DNA replication origins immediately prior to the initiation of DNA replication. The preinitiation complex is formed by the assembly of additional proteins onto an existing prereplicative complex. In budding yeast, the additional proteins include Cdc45p, Sld2p, Sld3p, Dbp11p, DNA polymerases, and others." to "A multiprotein complex assembled at eukaryotic DNA replication origins immediately prior to the initiation of DNA replication. The preinitiation complex is formed by the assembly of additional proteins onto an existing prereplicative complex. In budding yeast, the additional proteins include Cdc45p, Sld2p, Sld3p, Dpb11p, DNA polymerases, and others."
* Changed definition of GO:0033560 from "Catalysis of the reaction: 7,8-dihydrofolate + NADP+ = folate + NADPH +
H+." to "Catalysis of the reaction: 7,8-dihydrofolate + NADP+ = folate + NADPH + H+."
* Added synonym "flagellum axoneme" to GO:0035086
* Changed synonym scope of GO:0035086 from "Related" to "Exact"
* Deleted GO:0042125 --part_of--> GO:0009101
* Deleted GO:0042125 --OBO_REL:is_a--> GO:0006464
* Copied GO:0042125 to GO:0006486 with type OBO_REL:is_a
* Changed definition of GO:0043874 from "Catalysis of the reactions: 5-(methylthio)-2,3-dioxopentyl phosphate + H2O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate
(1a) 5-(methylthio)-2,3-dioxopentyl phosphate = 2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate
(1b) 2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate + H2O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate." to "Catalysis of the reactions: 5-(methylthio)-2,3-dioxopentyl phosphate + H2O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate (1a) 5-(methylthio)-2,3-dioxopentyl phosphate = 2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate (1b) 2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate + H2O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate."
* Changed definition of GO:0060164 from "The process controlling the timing and/or rate at which a relatively
unspecialized cell acquires features of a neuron." to "The process controlling the timing and/or rate at which a relatively unspecialized cell acquires features of a neuron."
* Changed definition of GO:0060165 from "The process controlling the timing and/or rate at which a relatively
unspecialized cell in the subpallium acquires features of a neuron. The
subpallium is the base region of the telencephalon." to "The process controlling the timing and/or rate at which a relatively unspecialized cell in the subpallium acquires features of a neuron. The subpallium is the base region of the telencephalon."
* Changed definition of GO:0060166 from "The biological process whose specific outcome is the progression of
the olfactory pit from an initial condition to its mature state. This
process begins with the formation of the olfactory pit, which is an indentation of the olfactory placode, and ends when the pits hollows out to
form the nasopharynx." to "The biological process whose specific outcome is the progression of the olfactory pit from an initial condition to its mature state. This process begins with the formation of the olfactory pit, which is an indentation of the olfactory placode, and ends when the pits hollows out to form the nasopharynx."
* Changed definition of GO:0060167 from "Any process that modulates the frequency, rate or extent of the
adenosine receptor signaling pathway. The adenosine receptor pathway is
the series of molecular signals generated as a consequence of an adenosine
receptor binding to one of its physiological ligands." to "Any process that modulates the frequency, rate or extent of the adenosine receptor signaling pathway. The adenosine receptor pathway is the series of molecular signals generated as a consequence of an adenosine receptor binding to one of its physiological ligands."
* Changed definition of GO:0060168 from "Any process that activates or increases the frequency, rate or extent
of the adenosine receptor signaling pathway. The adenosine receptor pathway
is the series of molecular signals generated as a consequence of an
adenosine receptor binding to one of its physiological ligands." to "Any process that activates or increases the frequency, rate or extent of the adenosine receptor signaling pathway. The adenosine receptor pathway is the series of molecular signals generated as a consequence of an adenosine receptor binding to one of its physiological ligands."
* Changed definition of GO:0060169 from "Any process that stops, prevents or reduces the frequency, rate or
extent of the adenosine receptor signaling pathway. The adenosine receptor pathway is the series of molecular signals generated as a consequence of an adenosine receptor binding to one of its physiological ligands." to "Any process that stops, prevents or reduces the frequency, rate or extent of the adenosine receptor signaling pathway. The adenosine receptor pathway is the series of molecular signals generated as a consequence of an adenosine receptor binding to one of its physiological ligands."


From gocvs at genome.Stanford.EDU  Sat Aug  4 21:30:38 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Sat, 4 Aug 2007 21:30:38 -0700 (PDT)
Subject: [go-diff] GO update 08/04/2007
Message-ID: <200708050430.VAA28847@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.440 by 5.441

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Deleted GO:0033551 --OBO_REL:is_a--> GO:0010324


From gocvs at genome.Stanford.EDU  Mon Aug  6 21:30:39 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Mon, 6 Aug 2007 21:30:39 -0700 (PDT)
Subject: [go-diff] GO update 08/06/2007
Message-ID: <200708070430.VAA29980@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.441 by 5.442

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033584
* Created object of type obo:TERM with id GO:0033585
* Created object of type obo:TERM with id GO:0033586
* Populated new object GO:0033584 (macro)
  * Changed name of GO:0033584 from "<new term>" to "tyrosine biosynthetic process from chorismate via L-arogenate"
  * Set definition of GO:0033584 to "The chemical reactions and pathways resulting in the formation of tyrosine from other compounds, including chorismate, via the intermediate L-arogenate."
  * Added definition dbxref GOC:mah to GO:0033584
  * Added definition dbxref MetaCyc:PWY-3461 to GO:0033584
  * Added general dbxref MetaCyc:PWY-3461 to GO:0033584
  * Added GO:0033584 to category gosubset_prok
  * Added synonym "tyrosine anabolism from chorismate via L-arogenate" to GO:0033584
  * Changed synonym scope of GO:0033584 from "Related" to "Exact"
  * Added synonym "tyrosine formation from chorismate via L-arogenate" to GO:0033584
  * Changed synonym scope of GO:0033584 from "Related" to "Exact"
  * Added synonym "tyrosine synthesis from chorismate via L-arogenate" to GO:0033584
  * Changed synonym scope of GO:0033584 from "Related" to "Exact"
  * Copied GO:0033584 to GO:0006571 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033584
* Populated new object GO:0033585 (macro)
  * Changed name of GO:0033585 from "<new term>" to "L-phenylalanine biosynthetic process from chorismate via phenylpyruvate"
  * Set definition of GO:0033585 to "The chemical reactions and pathways resulting in the formation of L-phenylalanine from other compounds, including chorismate, via the intermediate phenylpyruvate."
  * Added definition dbxref GOC:go_curators to GO:0033585
  * Added general dbxref MetaCyc:PHESYN to GO:0033585
  * Added GO:0033585 to category gosubset_prok
  * Added synonym "L-phenylalanine anabolism from chorismate via phenylpyruvate" to GO:0033585
  * Changed synonym scope of GO:0033585 from "Related" to "Exact"
  * Added synonym "L-phenylalanine biosynthetic process from chorismate via phenylpyruvate" to GO:0033585
  * Changed synonym scope of GO:0033585 from "Related" to "Exact"
  * Added synonym "L-phenylalanine formation from chorismate via phenylpyruvate" to GO:0033585
  * Changed synonym scope of GO:0033585 from "Related" to "Exact"
  * Added synonym "L-phenylalanine synthesis from chorismate via phenylpyruvate" to GO:0033585
  * Changed synonym scope of GO:0033585 from "Related" to "Exact"
  * Copied GO:0033585 to GO:0009094 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033585
* Populated new object GO:0033586 (macro)
  * Changed name of GO:0033586 from "<new term>" to "L-phenylalanine biosynthetic process from chorismate via L-arogenate"
  * Set definition of GO:0033586 to "The chemical reactions and pathways resulting in the formation of L-phenylalanine from other compounds, including chorismate, via the intermediate L-arogenate."
  * Added definition dbxref GOC:go_curators to GO:0033586
  * Added general dbxref MetaCyc:PWY-3462 to GO:0033586
  * Added GO:0033586 to category gosubset_prok
  * Added synonym "L-phenylalanine anabolism from chorismate via L-arogenate" to GO:0033586
  * Changed synonym scope of GO:0033586 from "Related" to "Exact"
  * Added synonym "L-phenylalanine biosynthesis from chorismate via L-arogenate" to GO:0033586
  * Changed synonym scope of GO:0033586 from "Related" to "Exact"
  * Added synonym "L-phenylalanine formation from chorismate via L-arogenate" to GO:0033586
  * Changed synonym scope of GO:0033586 from "Related" to "Exact"
  * Added synonym "L-phenylalanine synthesis from chorismate via L-arogenate" to GO:0033586
  * Changed synonym scope of GO:0033586 from "Related" to "Exact"
  * Copied GO:0033586 to GO:0009094 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033586
* added secondary id GO:0009096 to GO:0000162
* Changed definition of GO:0000162 from "The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid." to "The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate."
* Deleted definition dbxref ISBN:0198547684 from GO:0000162
* Added definition dbxref GOC:mah to GO:0000162
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0000162
* Added definition dbxref MetaCyc:TRPSYN-PWY to GO:0000162
* Added synonym "aromatic amino acid family biosynthetic process, anthranilate pathway" to GO:0000162
* Changed synonym scope of GO:0000162 from "Related" to "Exact"
* Deleted GO:0000162 --OBO_REL:is_a--> GO:0009096
* Copied GO:0000162 to GO:0009073 with type OBO_REL:is_a
* Deleted GO:0006571 --OBO_REL:is_a--> GO:0009423
* Copied GO:0006571 to GO:0009073 with type OBO_REL:is_a
* added secondary id GO:0016089 to GO:0009073
* Deleted general dbxref MetaCyc:COMPLETE-ARO from GO:0009073
* Added general dbxref MetaCyc:COMPLETE-ARO-PWY to GO:0009073
* Added synonym "aromatic amino acid family biosynthetic process, shikimate pathway" to GO:0009073
* added secondary id GO:0019274 to GO:0009094
* added secondary id GO:0019275 to GO:0009094
* Deleted general dbxref MetaCyc:COMPLETE-ARO from GO:0009094
* Added synonym "phenylalanine biosynthetic process, prephenate pathway" to GO:0009094
* Added synonym "phenylalanine biosynthetic process, shikimate pathway" to GO:0009094
* Changed definition of GO:0009095 from "The pathway of phenylalanine and tyrosine biosynthesis from chorismate, utilizing prephenate as an intermediate." to "The chemical reactions and pathways resulting in the formation of phenylalanine and tyrosine from other compounds, including chorismate, via the intermediate prephenate."
* Deleted definition dbxref ISBN:0198547684 from GO:0009095
* Added definition dbxref GOC:mah to GO:0009095
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0009095
* Deleted GO:0009096 --OBO_REL:is_a--> GO:0009073
* Deleted GO:0000162 --OBO_REL:is_a--> GO:0009096
* Destroyed object GO:0009096
* Deleted GO:0009423 --OBO_REL:is_a--> GO:0009095
* Deleted GO:0009423 --OBO_REL:is_a--> GO:0016089
* Deleted GO:0009423 --OBO_REL:is_a--> GO:0046394
* Copied GO:0009423 to GO:0043650 with type OBO_REL:is_a
* Deleted GO:0016089 --part_of--> GO:0009698
* Deleted GO:0016089 --OBO_REL:is_a--> GO:0009073
* Deleted GO:0009423 --OBO_REL:is_a--> GO:0016089
* Deleted GO:0019540 --OBO_REL:is_a--> GO:0016089
* Destroyed object GO:0016089
* Deleted GO:0019274 --OBO_REL:is_a--> GO:0009094
* Deleted GO:0019274 --OBO_REL:is_a--> GO:0009095
* Destroyed object GO:0019274
* Deleted GO:0019275 --OBO_REL:is_a--> GO:0009094
* Deleted GO:0019275 --OBO_REL:is_a--> GO:0009423
* Destroyed object GO:0019275
* Deleted GO:0019291 --OBO_REL:is_a--> GO:0006558
* Deleted GO:0019291 --OBO_REL:is_a--> GO:0006571
* Destroyed object GO:0019291
* Added synonym "tyrosine biosynthetic process from chorismate via p-hydroxyphenylpyruvate" to GO:0019292
* Changed synonym scope of GO:0019292 from "Related" to "Exact"
* added secondary id GO:0019291 to GO:0019293
* Deleted general dbxref MetaCyc:TYRSYN2 from GO:0019293
* Added synonym "tyrosine anabolism from chorismate via L-phenylalanine" to GO:0019293
* Changed synonym scope of GO:0019293 from "Related" to "Exact"
* Added synonym "tyrosine biosynthetic process from chorismate via L-phenylalanine" to GO:0019293
* Changed synonym scope of GO:0019293 from "Related" to "Exact"
* Added synonym "tyrosine formation from chorismate via L-phenylalanine" to GO:0019293
* Changed synonym scope of GO:0019293 from "Related" to "Exact"
* Added synonym "tyrosine synthesis from chorismate via L-phenylalanine" to GO:0019293
* Changed synonym scope of GO:0019293 from "Related" to "Exact"
* Copied GO:0019293 to GO:0006558 with type OBO_REL:is_a
* Deleted GO:0019540 --OBO_REL:is_a--> GO:0016089
* Deleted GO:0043650 --OBO_REL:is_a--> GO:0016053
* Copied GO:0043650 to GO:0046394 with type OBO_REL:is_a


From gocvs at genome.Stanford.EDU  Tue Aug  7 21:30:39 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Tue, 7 Aug 2007 21:30:39 -0700 (PDT)
Subject: [go-diff] GO update 08/07/2007
Message-ID: <200708080430.VAA06822@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.442 by 5.444

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033587
* Populated new object GO:0033587 (macro)
  * Changed name of GO:0033587 from "<new term>" to "shikimate biosynthetic process"
  * Set definition of GO:0033587 to "The chemical reactions and pathways resulting in the breakdown of shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid."
  * Added definition dbxref ChEBI:36208 to GO:0033587
  * Added definition dbxref GOC:mah to GO:0033587
  * Added synonym "shikimate anabolism" to GO:0033587
  * Changed synonym scope of GO:0033587 from "Related" to "Exact"
  * Added synonym "shikimate biosynthesis" to GO:0033587
  * Changed synonym scope of GO:0033587 from "Related" to "Exact"
  * Added synonym "shikimate formation" to GO:0033587
  * Changed synonym scope of GO:0033587 from "Related" to "Exact"
  * Added synonym "shikimate synthesis" to GO:0033587
  * Changed synonym scope of GO:0033587 from "Related" to "Exact"
  * Copied GO:0033587 to GO:0019632 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033587
* Deleted GO:0006571 --OBO_REL:is_a--> GO:0009073
* Copied GO:0006571 to GO:0009095 with type OBO_REL:is_a
* added secondary id GO:0043361 to GO:0007403
* Changed definition of GO:0007403 from "Process by which a cell becomes capable of differentiating autonomously into a glial cell regardless of its environment; upon determination, the cell fate cannot be reversed." to "MERGED DEFINITION:
TARGET DEFINITION: Process by which a cell becomes capable of differentiating autonomously into a glial cell regardless of its environment; upon determination, the cell fate cannot be reversed.
--------------------
SOURCE DEFINITION: Process by which a cell becomes capable of differentiating autonomously into a glial cell regardless of its environment; upon determination, the cell fate cannot be reversed. As in, but not restricted to, the roundworms (Nematoda, ncbi_taxonomy_id:6231) and the taxon Protostomia (Protostomia, ncbi_taxonomy_id:33317)."
* Added synonym "glial cell fate determination (sensu Nematoda and Protostomia)" to GO:0007403
* Changed synonym scope of GO:0007403 from "Related" to "Exact"
* added secondary id GO:0043349 to GO:0007405
* added secondary id GO:0043350 to GO:0007405
* Added definition dbxref GOC:mtg_sensu to GO:0007405
* Added synonym "neuroblast proliferation (sensu Nematoda and Protostomia)" to GO:0007405
* Changed synonym scope of GO:0007405 from "Related" to "Exact"
* Added synonym "neuroblast proliferation (sensu Vertebrata)" to GO:0007405
* Changed synonym scope of GO:0007405 from "Related" to "Exact"
* added secondary id GO:0043351 to GO:0007407
* added secondary id GO:0043352 to GO:0007407
* Added definition dbxref GOC:mtg_sensu to GO:0007407
* Added synonym "neuroblast activation (sensu Nematoda and Protostomia)" to GO:0007407
* Changed synonym scope of GO:0007407 from "Related" to "Exact"
* Added synonym "neuroblast activation (sensu Vertebrata)" to GO:0007407
* Changed synonym scope of GO:0007407 from "Related" to "Exact"
* added secondary id GO:0043359 to GO:0008347
* Added definition dbxref GOC:mtg_sensu to GO:0008347
* Added synonym "glial cell migration (sensu Nematoda and Protostomia)" to GO:0008347
* Changed synonym scope of GO:0008347 from "Related" to "Exact"
* Copied GO:0009073 to GO:0046417 with type OBO_REL:is_a
* Deleted GO:0009094 --OBO_REL:is_a--> GO:0009073
* Copied GO:0009094 to GO:0009095 with type OBO_REL:is_a
* Added general dbxref MetaCyc:PHETYRSYN-PWY to GO:0009095
* Deleted GO:0009712 --OBO_REL:is_a--> GO:0009698
* Deleted GO:0009713 --OBO_REL:is_a--> GO:0009699
* added secondary id GO:0043360 to GO:0010001
* Added definition dbxref GOC:mtg_sensu to GO:0010001
* Added synonym "glial cell differentiation (sensu Nematoda and Protostomia)" to GO:0010001
* Changed synonym scope of GO:0010001 from "Related" to "Exact"
* Deleted GO:0019614 --OBO_REL:is_a--> GO:0046271
* Changed definition of GO:0019632 from "The chemical reactions and pathways involving shikimate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids." to "The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids."
* Added definition dbxref ChEBI:36208 to GO:0019632
* Changed definition of GO:0019633 from "The chemical reactions and pathways resulting in the breakdown of shikimate, the anion of shikimic acid." to "The chemical reactions and pathways resulting in the breakdown of shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid."
* Added definition dbxref ChEBI:36208 to GO:0019633
* Deleted GO:0043339 --OBO_REL:is_a--> GO:0045196
* Deleted GO:0043340 --OBO_REL:is_a--> GO:0043339
* Deleted GO:0043341 --OBO_REL:is_a--> GO:0043339
* Destroyed object GO:0043339
* Deleted GO:0043340 --OBO_REL:is_a--> GO:0043339
* Deleted GO:0043340 --OBO_REL:is_a--> GO:0045200
* Destroyed object GO:0043340
* Deleted GO:0043341 --OBO_REL:is_a--> GO:0043339
* Deleted GO:0043341 --OBO_REL:is_a--> GO:0045201
* Destroyed object GO:0043341
* Deleted GO:0043342 --OBO_REL:is_a--> GO:0045196
* Deleted GO:0043343 --OBO_REL:is_a--> GO:0043342
* Deleted GO:0043344 --OBO_REL:is_a--> GO:0043342
* Destroyed object GO:0043342
* Deleted GO:0043343 --OBO_REL:is_a--> GO:0043342
* Deleted GO:0043343 --OBO_REL:is_a--> GO:0045200
* Destroyed object GO:0043343
* Deleted GO:0043344 --OBO_REL:is_a--> GO:0043342
* Deleted GO:0043344 --OBO_REL:is_a--> GO:0045201
* Destroyed object GO:0043344
* Deleted GO:0043349 --OBO_REL:is_a--> GO:0007405
* Destroyed object GO:0043349
* Deleted GO:0043350 --OBO_REL:is_a--> GO:0007405
* Destroyed object GO:0043350
* Deleted GO:0043351 --OBO_REL:is_a--> GO:0007407
* Destroyed object GO:0043351
* Deleted GO:0043352 --OBO_REL:is_a--> GO:0007407
* Destroyed object GO:0043352
* Deleted GO:0043359 --OBO_REL:is_a--> GO:0008347
* Destroyed object GO:0043359
* Deleted GO:0043360 --OBO_REL:is_a--> GO:0010001
* Destroyed object GO:0043360
* Deleted GO:0043361 --OBO_REL:is_a--> GO:0007403
* Destroyed object GO:0043361
* added secondary id GO:0043339 to GO:0045196
* added secondary id GO:0043342 to GO:0045196
* Added definition dbxref GOC:mtg_sensu to GO:0045196
* Added synonym "establishment and/or maintenance of neuroblast polarity (sensu Nematoda and Protostomia)" to GO:0045196
* Changed synonym scope of GO:0045196 from "Related" to "Exact"
* Added synonym "establishment and/or maintenance of neuroblast polarity (sensu Vertebrata)" to GO:0045196
* Changed synonym scope of GO:0045196 from "Related" to "Exact"
* added secondary id GO:0043340 to GO:0045200
* added secondary id GO:0043343 to GO:0045200
* Added definition dbxref GOC:mtg_sensu to GO:0045200
* Added synonym "establishment of neuroblast polarity (sensu Nematoda and Protostomia)" to GO:0045200
* Changed synonym scope of GO:0045200 from "Related" to "Exact"
* Added synonym "establishment of neuroblast polarity (sensu Vertebrata)" to GO:0045200
* Changed synonym scope of GO:0045200 from "Related" to "Exact"
* added secondary id GO:0043341 to GO:0045201
* added secondary id GO:0043344 to GO:0045201
* Added definition dbxref GOC:mtg_sensu to GO:0045201
* Added synonym "maintenance of neuroblast polarity (sensu Nematoda and Protostomia)" to GO:0045201
* Changed synonym scope of GO:0045201 from "Related" to "Exact"
* Added synonym "maintenance of neuroblast polarity (sensu Vertebrata)" to GO:0045201
* Changed synonym scope of GO:0045201 from "Related" to "Exact"


From gocvs at genome.Stanford.EDU  Wed Aug  8 21:30:39 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Wed, 8 Aug 2007 21:30:39 -0700 (PDT)
Subject: [go-diff] GO update 08/08/2007
Message-ID: <200708090430.VAA23732@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.444 by 5.448

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033588
* Created object of type obo:TERM with id GO:0033589
* Created object of type obo:TERM with id GO:0033590
* Populated new object GO:0033588 (macro)
  * Changed name of GO:0033588 from "<new term>" to "Elongator holoenzyme complex"
  * Set definition of GO:0033588 to "A heterohexameric protein complex that is involved in tRNA modification, and exerts indirect effects on transcriptional elongation and exocytosis. The complex can associate physically with hyperphosphorylated RNA polymerase II; it contains two discrete heterotrimeric subcomplexes. In Saccharomyces, the core complex consists of Iki3p/Elp1p, Elp2p, and Elp3p, and the other consists of Elp4p, Iki1p/Elp5p, and Elp6p."
  * Added definition dbxref GOC:mah to GO:0033588
  * Added definition dbxref PMID:11689709 to GO:0033588
  * Added definition dbxref PMID:17018299 to GO:0033588
  * Copied GO:0033588 to GO:0044424 with type OBO_REL:is_a
  * Copied GO:0033588 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033588
* Populated new object GO:0033589 (macro)
  * Changed name of GO:0033589 from "<new term>" to "Elongator core complex"
  * Set definition of GO:0033589 to "A heterotrimeric protein complex that forms part of the Elongator holoenzyme complex, which is involved in tRNA modification, and exerts indirect effects on transcriptional elongation and exocytosis. In Saccharomyces, the core complex consists of Iki3p/Elp1p, Elp2p, and Elp3p; the proteins are conserved in human."
  * Added definition dbxref GOC:mah to GO:0033589
  * Added definition dbxref PMID:11689709 to GO:0033589
  * Added definition dbxref PMID:17018299 to GO:0033589
  * Copied GO:0033589 to GO:0033588 with type part_of
  * Copied GO:0033589 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033589
* Populated new object GO:0033590 (macro)
  * Changed name of GO:0033590 from "<new term>" to "response to cobalamin"
  * Set definition of GO:0033590 to "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cobalamin (vitamin B12) stimulus."
  * Added definition dbxref GOC:sl to GO:0033590
  * Added synonym "response to vitamin B12" to GO:0033590
  * Changed synonym scope of GO:0033590 from "Related" to "Exact"
  * Copied GO:0033590 to GO:0033273 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033590
* Changed name of GO:0001542 from "ovulation (sensu Mammalia)" to "ovulation from ovarian follicle"
* Changed definition of GO:0001542 from "The process leading to the rupture of the follicle, releasing the centrally located oocyte. As in, but not restricted to, mammals (Mammalia, ncbi_taxonomy_id:40674)." to "The process leading to the rupture of the follicle, releasing the centrally located oocyte into the oviduct."
* Added definition dbxref GOC:mtg_sensu to GO:0001542
* Added synonym "ovulation (sensu Mammalia)" to GO:0001542
* Changed synonym scope of GO:0001542 from "Related" to "Exact"
* Changed name of GO:0001744 from "optic placode formation (sensu Endopterygota)" to "optic lobe placode formation"
* Changed definition of GO:0001744 from "Establishment of the optic placode, a thickened area of densely packed ectoderm cells directly overlying the optic vesicle in the early embryo. In Drosophila for example, the placode appears in the dorsolateral region of the head in late stage 11 embryos and is the precursor to the larval visual system. As in, but not restricted to, the Holometabola (Endopterygota, ncbi_taxonomy_id:33392)." to "Establishment of the optic placode, a thickened area of densely packed ectoderm cells directly overlying the optic vesicle in the early embryo. In Drosophila for example, the placode appears in the dorsolateral region of the head in late stage 11 embryos and is the precursor to the larval visual system."
* Added definition dbxref GOC:mtg_sensu to GO:0001744
* Deleted synonym "optic lobe placode development (sensu Drosophila)" from GO:0001744
* Added synonym "optic lobe and Bolwig's organ precursor formation" to GO:0001744
* Changed synonym scope of GO:0001744 from "Related" to "Exact"
* Added synonym "optic lobe placode formation (sensu Drosophila)" to GO:0001744
* Changed synonym scope of GO:0001744 from "Related" to "Exact"
* Added synonym "optic placode formation (sensu Endopterygota)" to GO:0001744
* Changed synonym scope of GO:0001744 from "Related" to "Exact"
* Changed name of GO:0001748 from "optic placode development (sensu Endopterygota)" to "optic lobe placode development"
* Changed definition of GO:0001748 from "The process whose specific outcome is the progression of the optic placode over time, from its formation to the mature structure. During embryonic stage 12 the placode starts to invaginate, forming a pouch. Cells that will form Bolwig's organ segregate from the ventral lip of this pouch, remaining in the head epidermis. The remainder of the invagination loses contact with the outer surface and becomes the optic lobe. As in, but not restricted to, the Holometabola (Endopterygota, ncbi_taxonomy_id:33392)." to "The process whose specific outcome is the progression of the optic placode over time, from its formation to the mature structure. During embryonic stage 12 the placode starts to invaginate, forming a pouch. Cells that will form Bolwig's organ segregate from the ventral lip of this pouch, remaining in the head epidermis. The remainder of the invagination loses contact with the outer surface and becomes the optic lobe."
* Added synonym "optic lobe and Bolwig's organ precursor development" to GO:0001748
* Changed synonym scope of GO:0001748 from "Related" to "Exact"
* Added synonym "optic placode development (sensu Endopterygota)" to GO:0001748
* Changed synonym scope of GO:0001748 from "Related" to "Exact"
* Changed comment from "This term was made obsolete because it represents a biological process and not a molecular function. To update annotations, consider the function ontology term 'synaptic vesicle targeting ; GO:GO:0016080'." to "This term was made obsolete because it represents a biological process and not a molecular function."
* Changed comment from "This term was made obsolete because it is a type of cell rather than a cellular component. To update annotations, consider the fungal anatomy ontology term 'ascus ; FAO:0000014'." to "This term was made obsolete because it is a type of cell rather than a cellular component. To update annotations, consider external ontology term 'ascus ; FAO:0000014'."
* Changed comment from "This term was made obsolete because it represents a type of whole cell rather than a cellular component. To update annotations, consider the fungal anatomy ontology term 'shmoo ; FAO:0001023'." to "This term was made obsolete because it represents a type of whole cell rather than a cellular component. To update annotations, consider external ontology term 'shmoo ; FAO:0001023'."
* Deleted GO:0007293 --part_of--> GO:0009993
* Copied GO:0007293 to GO:0048477 with type part_of
* Deleted GO:0007295 --part_of--> GO:0009993
* Copied GO:0007295 to GO:0048477 with type part_of
* Changed name of GO:0007297 from "follicle cell migration (sensu Insecta)" to "ovarian follicle cell migration"
* Changed definition of GO:0007297 from "The directed movement of follicle cells that takes place during oogenesis. During egg chamber formation, follicle cells migrate to envelop the germ-line cysts and move in between cysts. At stage 10B, follicle cells migrate centripetally between the nurse cells and the oocyte, enclosing the anterior of the egg. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." to "The directed movement of follicle cells that takes place during oogenesis. During egg chamber formation, follicle cells migrate to envelop the germ-line cysts and move in between cysts. At stage 10B, follicle cells migrate centripetally between the nurse cells and the oocyte, enclosing the anterior of the egg."
* Added definition dbxref GOC:mtg_sensu to GO:0007297
* Added synonym "follicle cell migration (sensu Insecta)" to GO:0007297
* Changed synonym scope of GO:0007297 from "Related" to "Exact"
* Changed name of GO:0007298 from "border follicle cell migration (sensu Insecta)" to "border follicle cell migration"
* Changed definition of GO:0007298 from "The directed movement of the border cells through the nurse cells to reach the oocyte. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." to "The directed movement of the border cells through the nurse cells to reach the oocyte."
* Added definition dbxref GOC:mtg_sensu to GO:0007298
* Added synonym "border follicle cell migration (sensu Insecta)" to GO:0007298
* Changed synonym scope of GO:0007298 from "Related" to "Exact"
* Changed name of GO:0007299 from "follicle cell adhesion (sensu Insecta)" to "ovarian follicle cell adhesion"
* Changed definition of GO:0007299 from "The attachment of a somatic follicle cell to another somatic follicle cell or to its substratum, the germline cells. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." to "The attachment of a somatic follicle cell to another somatic follicle cell or to its substratum, the germline cells."
* Added definition dbxref GOC:mtg_sensu to GO:0007299
* Added synonym "follicle cell adhesion (sensu Insecta)" to GO:0007299
* Changed synonym scope of GO:0007299 from "Related" to "Exact"
* Deleted GO:0007300 --part_of--> GO:0009993
* Copied GO:0007300 to GO:0048477 with type part_of
* Deleted GO:0007308 --part_of--> GO:0009993
* Copied GO:0007308 to GO:0048477 with type part_of
* Changed definition of GO:0007403 from "MERGED DEFINITION:
TARGET DEFINITION: Process by which a cell becomes capable of differentiating autonomously into a glial cell regardless of its environment; upon determination, the cell fate cannot be reversed.
--------------------
SOURCE DEFINITION: Process by which a cell becomes capable of differentiating autonomously into a glial cell regardless of its environment; upon determination, the cell fate cannot be reversed. As in, but not restricted to, the roundworms (Nematoda, ncbi_taxonomy_id:6231) and the taxon Protostomia (Protostomia, ncbi_taxonomy_id:33317)." to "Process by which a cell becomes capable of differentiating autonomously into a glial cell regardless of its environment; upon determination, the cell fate cannot be reversed."
* Added definition dbxref GOC:mtg_sensu to GO:0007403
* Changed name of GO:0008069 from "dorsal/ventral axis determination, follicular epithelium (sensu Insecta)" to "dorsal/ventral axis determination, ovarian follicular epithelium"
* Changed definition of GO:0008069 from "Polarization of the follicle cells along the dorsal/ventral axis. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." to "Polarization of the ovarian follicle cells along the dorsal/ventral axis."
* Added definition dbxref GOC:mtg_sensu to GO:0008069
* Added synonym "dorsal/ventral axis determination, follicular epithelium (sensu Insecta)" to GO:0008069
* Changed synonym scope of GO:0008069 from "Related" to "Exact"
* Changed name of GO:0008070 from "maternal determination of dorsal/ventral axis, follicular epithelium, germ-line encoded" to "maternal determination of dorsal/ventral axis, ovarian follicular epithelium, germ-line encoded"
* Changed definition of GO:0008070 from "Polarization of the follicle cells along the dorsal-ventral axis by a gene product encoded by cells of the germ line." to "Polarization of the ovarian follicle cells along the dorsal-ventral axis by a gene product encoded by cells of the germ line."
* Added definition dbxref GOC:mtg_sensu to GO:0008070
* Changed name of GO:0008071 from "maternal determination of dorsal/ventral axis, follicular epithelium, soma encoded (sensu Insecta)" to "maternal determination of dorsal/ventral axis, ovarian follicular epithelium, soma encoded"
* Changed definition of GO:0008071 from "Polarization of the follicle cells along the dorsal-ventral axis by a gene product encoded by somatic cells. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." to "Polarization of the ovarian follicle cells along the dorsal-ventral axis by a gene product encoded by somatic cells."
* Added definition dbxref GOC:mtg_sensu to GO:0008071
* Added synonym "maternal determination of dorsal/ventral axis, follicular epithelium, soma encoded (sensu Insecta)" to GO:0008071
* Changed synonym scope of GO:0008071 from "Related" to "Exact"
* Deleted GO:0009993 --OBO_REL:is_a--> GO:0048477
* Deleted GO:0030707 --part_of--> GO:0009993
* Deleted GO:0007300 --part_of--> GO:0009993
* Deleted GO:0048132 --part_of--> GO:0009993
* Deleted GO:0030717 --part_of--> GO:0009993
* Deleted GO:0007293 --part_of--> GO:0009993
* Deleted GO:0007295 --part_of--> GO:0009993
* Deleted GO:0007308 --part_of--> GO:0009993
* Destroyed object GO:0009993
* Changed comment from "This term was made obsolete because it describes a gene product rather than a function. To update annotations, consider molecular_function term 'hydrogen ion channel activity ; GO:0015252'." to "This term was made obsolete because it describes a gene product rather than a function."
* Changed comment from "This term was made obsolete because it wrongly combines voltage-gated anion channel activity and porin activity. To update annotations, consider molecular_function term 'voltage-gated anion channel activity ; GO:0022844' or its children." to "This term was made obsolete because it wrongly combines voltage-gated anion channel activity and porin activity."
* Changed comment from "This term was made obsolete because it arbitrarily groups three substrates. To update annotations, consider biological_process terms 'arbutin transport ; GO:0042949', 'cellobiose transport ; GO:0019533', and 'salicin transport ; GO:0042948'." to "This term was made obsolete because it arbitrarily groups three substrates."
* Changed comment from "This term was made obsolete because it represents a biological process. To update annotations, use the molecular function term 'regulation of sodium:hydrogen antiporter activity ; GO:0022899'." to "This term was made obsolete because it represents a biological process. To update annotations, use external ontology term 'regulation of sodium:hydrogen antiporter activity ; GO:0022899'."
* Changed name of GO:0030707 from "ovarian follicle cell development (sensu Insecta)" to "ovarian follicle cell development"
* Changed definition of GO:0030707 from "The process that occurs during oogenesis involving the ovarian follicle cells, somatic cells which surround the germ cells of an ovary. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." to "The process that occurs during oogenesis involving the ovarian follicle cells, somatic cells which surround the germ cells of an ovary."
* Added definition dbxref GOC:mtg_sensu to GO:0030707
* Added synonym "ovarian follicle cell development (sensu Insecta)" to GO:0030707
* Changed synonym scope of GO:0030707 from "Related" to "Exact"
* Deleted GO:0030707 --part_of--> GO:0009993
* Copied GO:0030707 to GO:0048477 with type part_of
* Changed name of GO:0030713 from "stalk formation (sensu Insecta)" to "ovarian follicle cell stalk formation"
* Changed definition of GO:0030713 from "Differentiation of follicle cells to create the interfollicular stalks that connect the egg chambers of progressive developmental stages. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." to "Development of ovarian follicle cells to create the interfollicular stalks that connect the egg chambers of progressive developmental stages."
* Added definition dbxref GOC:mtg_sensu to GO:0030713
* Added synonym "stalk formation (sensu Insecta)" to GO:0030713
* Changed synonym scope of GO:0030713 from "Related" to "Exact"
* Deleted GO:0030713 --OBO_REL:is_a--> GO:0030154
* Copied GO:0030713 to GO:0000904 with type OBO_REL:is_a
* Deleted GO:0030717 --part_of--> GO:0009993
* Copied GO:0030717 to GO:0048477 with type part_of
* Changed name of GO:0033565 from "Vps27p-Hse1p complex" to "ESCRT-0 complex"
* Added synonym "Hrs/STAM complex" to GO:0033565
* Changed synonym scope of GO:0033565 from "Related" to "Exact"
* Added synonym "Vps27p-Hse1p complex" to GO:0033565
* Changed synonym scope of GO:0033565 from "Related" to "Exact"
* Deleted GO:0048132 --part_of--> GO:0009993
* Copied GO:0048132 to GO:0048477 with type part_of
* added secondary id GO:0009993 to GO:0048477
* Added synonym "oogenesis (sensu Insecta)" to GO:0048477
* Changed synonym scope of GO:0048477 from "Related" to "Exact"


From gocvs at genome.Stanford.EDU  Thu Aug  9 21:30:39 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Thu, 9 Aug 2007 21:30:39 -0700 (PDT)
Subject: [go-diff] GO update 08/09/2007
Message-ID: <200708100430.VAA00470@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.448 by 5.452

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033591
* Created object of type obo:TERM with id GO:0033592
* Created object of type obo:TERM with id GO:0033593
* Created object of type obo:TERM with id GO:0033594
* Created object of type obo:TERM with id GO:0033595
* Created object of type obo:TERM with id GO:0033596
* Created object of type obo:TERM with id GO:0033597
* Created object of type obo:TERM with id GO:0033598
* Created object of type obo:TERM with id GO:0033599
* Created object of type obo:TERM with id GO:0033600
* Created object of type obo:TERM with id GO:0033601
* Created object of type obo:TERM with id GO:0043890
* Created object of type obo:TERM with id GO:0043891
* Created object of type obo:TERM with id GO:0043892
* Created object of type obo:TERM with id GO:0043893
* Created object of type obo:TERM with id GO:0043894
* Created object of type obo:TERM with id GO:0043895
* Created object of type obo:TERM with id GO:0043896
* Created object of type obo:TERM with id GO:0043897
* Populated new object GO:0033591 (macro)
  * Changed name of GO:0033591 from "<new term>" to "response to L-ascorbic acid"
  * Set definition of GO:0033591 to "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an L-ascorbic acid (vitamin C) stimulus."
  * Added definition dbxref GOC:sl to GO:0033591
  * Added synonym "response to ascorbic acid" to GO:0033591
  * Changed synonym scope of GO:0033591 from "Related" to "Broad"
  * Added synonym "response to L-ascorbate" to GO:0033591
  * Changed synonym scope of GO:0033591 from "Related" to "Exact"
  * Added synonym "response to vitamin C" to GO:0033591
  * Changed synonym scope of GO:0033591 from "Related" to "Exact"
  * Copied GO:0033591 to GO:0033273 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033591
* Populated new object GO:0033592 (macro)
  * Changed name of GO:0033592 from "<new term>" to "RNA strand annealing activity"
  * Set definition of GO:0033592 to "Facilitates the base-pairing of complementary single-stranded RNA."
  * Added definition dbxref GOC:mah to GO:0033592
  * Copied GO:0033592 to GO:0003725 with type OBO_REL:is_a
  * Copied GO:0033592 to GO:0003727 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0033592
* Populated new object GO:0033593 (macro)
  * Changed name of GO:0033593 from "<new term>" to "BRCA2-MAGE-D1 complex"
  * Set definition of GO:0033593 to "A heterodimeric protein complex formed of BRCA2 and MAGE-D1; may mediate the synergistic activities of the two proteins in regulating cell growth."
  * Added definition dbxref PMID:15930293 to GO:0033593
  * Copied GO:0033593 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0033593 to GO:0044424 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033593
* Populated new object GO:0033594 (macro)
  * Changed name of GO:0033594 from "<new term>" to "response to hydroxyisoflavone"
  * Set definition of GO:0033594 to "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydroxyisoflavone stimulus."
  * Added definition dbxref ChEBI:38755 to GO:0033594
  * Added definition dbxref GOC:mah to GO:0033594
  * Copied GO:0033594 to GO:0014070 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033594
* Populated new object GO:0033595 (macro)
  * Changed name of GO:0033595 from "<new term>" to "response to genistein"
  * Set definition of GO:0033595 to "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a genistein stimulus."
  * Added definition dbxref ChEBI:28088 to GO:0033595
  * Added definition dbxref GOC:mah to GO:0033595
  * Copied GO:0033595 to GO:0014070 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033595
* Populated new object GO:0033596 (macro)
  * Changed name of GO:0033596 from "<new term>" to "TSC1-TSC2 complex"
  * Set definition of GO:0033596 to "A heterodimeric protein complex consisting of tumerin and hamartin; its formation may regulate hamartin homomultimer formation."
  * Added definition dbxref PMID:10585443 to GO:0033596
  * Added definition dbxref PMID:9580671 to GO:0033596
  * Added synonym "tuberin-hamartin complex " to GO:0033596
  * Changed synonym scope of GO:0033596 from "Related" to "Exact"
  * Copied GO:0033596 to GO:0044445 with type OBO_REL:is_a
  * Copied GO:0033596 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033596
* Populated new object GO:0033597 (macro)
  * Changed name of GO:0033597 from "<new term>" to "mitotic checkpoint complex"
  * Set definition of GO:0033597 to "A multiprotein complex that functions as a mitotic checkpoint inhibitor of the anaphase-promoting complex/cyclosome (APC/C). In budding yeast this complex consists of Mad2p, Mad3p, Bub3p and Cdc20p, and in mammalian cells it consists of MAD2, BUBR1, BUB3, and CDC20."
  * Added definition dbxref PMID:10704439 to GO:0033597
  * Added definition dbxref PMID:11535616 to GO:0033597
  * Added definition dbxref PMID:11726501 to GO:0033597
  * Added definition dbxref PMID:17650307 to GO:0033597
  * Added synonym "MCC" to GO:0033597
  * Changed synonym scope of GO:0033597 from "Related" to "Exact"
  * Copied GO:0033597 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0033597 to GO:0044424 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033597
* Populated new object GO:0033598 (macro)
  * Changed name of GO:0033598 from "<new term>" to "mammary gland epithelial cell proliferation"
  * Set definition of GO:0033598 to "The multiplication or reproduction of mammary gland epithelial cells, resulting in the rapid expansion of a cell population. Mammary gland epithelial cells make up the covering of surfaces of the mammary gland. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk."
  * Added definition dbxref GOC:dph to GO:0033598
  * Added definition dbxref GOC:mah to GO:0033598
  * Copied GO:0033598 to GO:0050673 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033598
* Populated new object GO:0033599 (macro)
  * Changed name of GO:0033599 from "<new term>" to "regulation of mammary gland epithelial cell proliferation"
  * Set definition of GO:0033599 to "Any process that modulates the frequency, rate or extent of mammary gland epithelial cell proliferation."
  * Added definition dbxref GOC:mah to GO:0033599
  * Copied GO:0033599 to GO:0033598 with type part_of
  * Copied GO:0033599 to GO:0050678 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033599
* Populated new object GO:0033600 (macro)
  * Changed name of GO:0033600 from "<new term>" to "negative regulation of mammary gland epithelial cell proliferation"
  * Set definition of GO:0033600 to "Any process that stops, prevents or reduces the rate or extent of mammary gland epithelial cell proliferation."
  * Added definition dbxref GOC:mah to GO:0033600
  * Added synonym "down regulation of mammary gland epithelial cell proliferation" to GO:0033600
  * Changed synonym scope of GO:0033600 from "Related" to "Exact"
  * Added synonym "down-regulation of mammary gland epithelial cell proliferation" to GO:0033600
  * Changed synonym scope of GO:0033600 from "Related" to "Exact"
  * Added synonym "downregulation of mammary gland epithelial cell proliferation" to GO:0033600
  * Changed synonym scope of GO:0033600 from "Related" to "Exact"
  * Added synonym "inhibition of mammary gland epithelial cell proliferation" to GO:0033600
  * Changed synonym scope of GO:0033600 from "Related" to "Narrow"
  * Copied GO:0033600 to GO:0033599 with type OBO_REL:is_a
  * Copied GO:0033600 to GO:0050680 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033600
* Populated new object GO:0033601 (macro)
  * Changed name of GO:0033601 from "<new term>" to "positive regulation of mammary gland epithelial cell proliferation"
  * Set definition of GO:0033601 to "Any process that activates or increases the rate or extent of mammary gland epithelial cell proliferation."
  * Added definition dbxref GOC:mah to GO:0033601
  * Added synonym "activation of mammary gland epithelial cell proliferation" to GO:0033601
  * Changed synonym scope of GO:0033601 from "Related" to "Narrow"
  * Added synonym "stimulation of mammary gland epithelial cell proliferation" to GO:0033601
  * Changed synonym scope of GO:0033601 from "Related" to "Narrow"
  * Added synonym "up regulation of mammary gland epithelial cell proliferation" to GO:0033601
  * Changed synonym scope of GO:0033601 from "Related" to "Exact"
  * Added synonym "up-regulation of mammary gland epithelial cell proliferation" to GO:0033601
  * Changed synonym scope of GO:0033601 from "Related" to "Exact"
  * Added synonym "upregulation of mammary gland epithelial cell proliferation" to GO:0033601
  * Changed synonym scope of GO:0033601 from "Related" to "Exact"
  * Copied GO:0033601 to GO:0050679 with type OBO_REL:is_a
  * Copied GO:0033601 to GO:0033599 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033601
* Populated new object GO:0043890 (macro)
  * Changed name of GO:0043890 from "<new term>" to "N-acetylgalactosamine-6-sulfatase activity"
  * Set definition of GO:0043890 to "Catalysis of the reaction: hydrolysis of the 6-sulfate groups of the N-acetyl-D-galactosamine 6-sulfate units of chondroitin sulfate and of the D-galactose 6-sulfate units of keratan sulfate."
  * Added definition dbxref EC:3.1.6.4 to GO:0043890
  * Added general dbxref EC:3.1.6.4 to GO:0043890
  * Added general dbxref MetaCyc:3.1.6.4-RXN to GO:0043890
  * Added GO:0043890 to category gosubset_prok
  * Added synonym "acetylgalactosamine 6-sulfatase" to GO:0043890
  * Changed synonym scope of GO:0043890 from "Related" to "Exact"
  * Added synonym "chondroitin sulfatase" to GO:0043890
  * Changed synonym scope of GO:0043890 from "Related" to "Broad"
  * Added synonym "chondroitinase" to GO:0043890
  * Changed synonym scope of GO:0043890 from "Related" to "Broad"
  * Added synonym "galactose-6-sulfate sulfatase" to GO:0043890
  * Changed synonym scope of GO:0043890 from "Related" to "Exact"
  * Added synonym "N-acetyl-D-galactosamine-6-sulfate 6-sulfohydrolase" to GO:0043890
  * Changed synonym scope of GO:0043890 from "Related" to "Exact"
  * Added synonym "N-acetylgalactosamine 6-sulfatase" to GO:0043890
  * Changed synonym scope of GO:0043890 from "Related" to "Exact"
  * Added synonym "N-acetylgalactosamine-6-sulfate sulfatase" to GO:0043890
  * Changed synonym scope of GO:0043890 from "Related" to "Exact"
  * Copied GO:0043890 to GO:0008484 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043890
* Populated new object GO:0043891 (macro)
  * Changed name of GO:0043891 from "<new term>" to "glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity"
  * Set definition of GO:0043891 to "Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H + H+."
  * Added definition dbxref EC:1.2.1.59 to GO:0043891
  * Added general dbxref EC:1.2.1.59 to GO:0043891
  * Added general dbxref MetaCyc:GAPDHSYNEC-RXN to GO:0043891
  * Added GO:0043891 to category gosubset_prok
  * Added synonym "D-glyceraldehyde 3-phosphate:NAD(P)+ oxidoreductase (phosphorylating)" to GO:0043891
  * Changed synonym scope of GO:0043891 from "Related" to "Exact"
  * Added synonym "glyceraldehyde-3-phosphate dehydrogenase (NAD(P)) (phosphorylating)" to GO:0043891
  * Changed synonym scope of GO:0043891 from "Related" to "Exact"
  * Added synonym "triosephosphate dehydrogenase (NAD(P))" to GO:0043891
  * Changed synonym scope of GO:0043891 from "Related" to "Exact"
  * Copied GO:0043891 to GO:0008943 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043891
* Populated new object GO:0043892 (macro)
  * Changed name of GO:0043892 from "<new term>" to "methylglyoxal reductase (NADPH-dependent) activity"
  * Set definition of GO:0043892 to "Catalysis of the reaction: lactaldehyde + NADP+ = methylglyoxal + NADPH + H+."
  * Added definition dbxref EC:1.1.1.283 to GO:0043892
  * Added general dbxref EC:1.1.1.283 to GO:0043892
  * Added general dbxref MetaCyc:1.1.1.283-RXN to GO:0043892
  * Added general dbxref MetaCyc:RXN-8636 to GO:0043892
  * Added GO:0043892 to category gosubset_prok
  * Added synonym "Gre2" to GO:0043892
  * Added synonym "lactaldehyde dehydrogenase (NADP+)" to GO:0043892
  * Changed synonym scope of GO:0043892 from "Related" to "Exact"
  * Copied GO:0043892 to GO:0016616 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043892
* Populated new object GO:0043893 (macro)
  * Changed name of GO:0043893 from "<new term>" to "acetate:cation symporter activity"
  * Set definition of GO:0043893 to "Catalysis of the transfer of acetate from one side of a membrane to the other according to the reaction: acetate(out) + cation(out) = acetate(in) + cation(in)."
  * Added definition dbxref GOC:jl to GO:0043893
  * Added GO:0043893 to category gosubset_prok
  * Added synonym "acetate permease" to GO:0043893
  * Changed synonym scope of GO:0043893 from "Related" to "Broad"
  * Added synonym "acetate-cation symporter activity" to GO:0043893
  * Changed synonym scope of GO:0043893 from "Related" to "Exact"
  * Added synonym "acetate/cation symporter activity" to GO:0043893
  * Changed synonym scope of GO:0043893 from "Related" to "Exact"
  * Added synonym "ActP" to GO:0043893
  * Added synonym "cation-acetate symporter activity" to GO:0043893
  * Changed synonym scope of GO:0043893 from "Related" to "Exact"
  * Added synonym "cation/acetate symporter activity" to GO:0043893
  * Changed synonym scope of GO:0043893 from "Related" to "Exact"
  * Added synonym "cation:acetate symporter activity" to GO:0043893
  * Changed synonym scope of GO:0043893 from "Related" to "Exact"
  * Copied GO:0043893 to GO:0015294 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043893
* Populated new object GO:0043894 (macro)
  * Changed name of GO:0043894 from "<new term>" to "protein acetyltransferase activity"
  * Set definition of GO:0043894 to "Catalysis of the acetylation of residue Lys609 of the enzyme acetyl-CoA synthetase, using acetyl-CoA as substrate."
  * Added definition dbxref PMID:15236963 to GO:0043894
  * Added GO:0043894 to category gosubset_prok
  * Added synonym "Pat" to GO:0043894
  * Added synonym "Pat enzyme" to GO:0043894
  * Copied GO:0043894 to GO:0016407 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043894
* Populated new object GO:0043895 (macro)
  * Changed name of GO:0043895 from "<new term>" to "cyclomaltodextrin glucanotransferase activity"
  * Set definition of GO:0043895 to "Catalysis of the cyclization of part of a 1,4-alpha-D-glucan chain by formation of a 1,4-alpha-D-glucosidic bond."
  * Added definition dbxref EC:2.4.1.19 to GO:0043895
  * Added general dbxref EC:2.4.1.19 to GO:0043895
  * Added general dbxref MetaCyc:2.4.1.19-RXN to GO:0043895
  * Added synonym "1,4-alpha-D-glucan 4-alpha-D-(1,4-alpha-D-glucano)-transferase (cyclizing)" to GO:0043895
  * Changed synonym scope of GO:0043895 from "Related" to "Exact"
  * Added synonym "alpha-1,4-glucan 4-glycosyltransferase, cyclizing" to GO:0043895
  * Added synonym "alpha-cyclodextrin glucanotransferase" to GO:0043895
  * Added synonym "alpha-cyclodextrin glycosyltransferase" to GO:0043895
  * Added synonym "Bacillus macerans amylase" to GO:0043895
  * Added synonym "beta-cyclodextrin glucanotransferase" to GO:0043895
  * Added synonym "beta-cyclodextrin glycosyltransferase" to GO:0043895
  * Added synonym "BMA" to GO:0043895
  * Added synonym "CGTase" to GO:0043895
  * Added synonym "cyclodextrin glucanotransferase" to GO:0043895
  * Changed synonym scope of GO:0043895 from "Related" to "Broad"
  * Added synonym "cyclodextrin glycosyltransferase" to GO:0043895
  * Added synonym "cyclomaltodextrin glucotransferase" to GO:0043895
  * Added synonym "cyclomaltodextrin glycosyltransferase" to GO:0043895
  * Added synonym "gamma-cyclodextrin glycosyltransferase" to GO:0043895
  * Added synonym "konchizaimu" to GO:0043895
  * Added synonym "neutral-cyclodextrin glycosyltransferase" to GO:0043895
  * Copied GO:0043895 to GO:0016758 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043895
* Populated new object GO:0043896 (macro)
  * Changed name of GO:0043896 from "<new term>" to "glucan 1,6-alpha-glucosidase activity"
  * Set definition of GO:0043896 to "Catalysis of the hydrolysis of (1->6)-alpha-D-glucosidic linkages in (1->6)-alpha-D-glucans and derived oligosaccharides."
  * Added definition dbxref EC:3.2.1.70 to GO:0043896
  * Added general dbxref EC:3.2.1.70 to GO:0043896
  * Added general dbxref MetaCyc:3.2.1.70-RXN to GO:0043896
  * Added GO:0043896 to category gosubset_prok
  * Added synonym "exo-1,6-beta-glucosidase" to GO:0043896
  * Added synonym "glucan-1,6-alpha-glucosidase activity" to GO:0043896
  * Changed synonym scope of GO:0043896 from "Related" to "Exact"
  * Added synonym "glucodextrinase" to GO:0043896
  * Changed synonym scope of GO:0043896 from "Related" to "Broad"
  * Copied GO:0043896 to GO:0004553 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043896
* Populated new object GO:0043897 (macro)
  * Changed name of GO:0043897 from "<new term>" to "glucan 1,4-alpha-maltohydrolase activity"
  * Set definition of GO:0043897 to "Catalysis of the hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains."
  * Added definition dbxref EC:3.2.1.133 to GO:0043897
  * Added general dbxref EC:3.2.1.133 to GO:0043897
  * Added general dbxref MetaCyc:3.2.1.133-RXN to GO:0043897
  * Added GO:0043897 to category gosubset_prok
  * Added synonym "1,4-alpha-D-glucan alpha-maltohydrolase" to GO:0043897
  * Changed synonym scope of GO:0043897 from "Related" to "Exact"
  * Added synonym "glucan-1,4-alpha-maltohydrolase activity" to GO:0043897
  * Changed synonym scope of GO:0043897 from "Related" to "Exact"
  * Added synonym "maltogenic alpha-amylase" to GO:0043897
  * Changed synonym scope of GO:0043897 from "Related" to "Exact"
  * Copied GO:0043897 to GO:0004553 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0043897
* Deleted GO:0000154 --OBO_REL:is_a--> GO:0016072
* Changed definition of GO:0000472 from "Endonucleolytic cleavage at the 5'-ETS and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA." to "Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA."
* Changed definition of GO:0001744 from "Establishment of the optic placode, a thickened area of densely packed ectoderm cells directly overlying the optic vesicle in the early embryo. In Drosophila for example, the placode appears in the dorsolateral region of the head in late stage 11 embryos and is the precursor to the larval visual system." to "Establishment of the optic placode, a thickened area of densely packed ectoderm cells directly overlying the optic vesicle in the early embryo. In Drosophila, for example, the placode appears in the dorsolateral region of the head in late stage 11 embryos and is the precursor to the larval visual system."
* Changed definition of GO:0001745 from "The process by which the anatomical structures of the compound eye are generated and organized. Morphogenesis pertains to the creation of form. The adult compound eye is a precise assembly of 700-800 ommatidia. Each ommatidia is composed of 20 cells, identified by cell type and position." to "The process by which the anatomical structures of the compound eye are generated and organized. Morphogenesis pertains to the creation of form. The adult compound eye is a precise assembly of 700-800 ommatidia. Each ommatidium is composed of 20 cells, identified by cell type and position."
* Deleted definition dbxref ISBN:0471331309 from GO:0003923
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0003923
* Changed comment from "This term was made obsolete because it is a type of cell rather than a cellular component. To update annotations, consider external ontology term 'ascus ; FAO:0000014'." to "This term was made obsolete because it is a type of cell rather than a cellular component. To update annotations, consider fungal anatomy ontology term 'ascus ; FAO:0000014'."
* Changed comment from "This term was made obsolete because it represents a type of whole cell rather than a cellular component. To update annotations, consider external ontology term 'shmoo ; FAO:0001023'." to "This term was made obsolete because it represents a type of whole cell rather than a cellular component. To update annotations, consider fungal anatomy ontology term 'shmoo ; FAO:0001023'."
* Deleted definition dbxref ISBN:0471331309 from GO:0005967
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0005967
* Deleted definition dbxref ISBN:0471331309 from GO:0006119
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0006119
* Deleted GO:0006400 --OBO_REL:is_a--> GO:0006399
* Deleted definition dbxref ISBN:0471331309 from GO:0006488
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0006488
* Changed definition of GO:0006613 from "The targeting of proteins to a membrane that occurs during translation. The transport of most secretory proteins, particularly those with more than 100 amino acids, into the endoplasmic reticulum lumen occurs in this manner." to "The targeting of proteins to a membrane that occurs during translation. The transport of most secretory proteins, particularly those with more than 100 amino acids, into the endoplasmic reticulum lumen occurs in this manner, as does the import of some proteins into mitochondria."
* Added definition dbxref PMID:10512867 to GO:0006613
* Added definition dbxref PMID:16896215 to GO:0006613
* Deleted GO:0006613 --OBO_REL:is_a--> GO:0045047
* Copied GO:0006613 to GO:0006605 with type OBO_REL:is_a
* Copied GO:0006614 to GO:0045047 with type OBO_REL:is_a
* Deleted definition dbxref ISBN:0471331309 from GO:0006657
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0006657
* Changed definition of GO:0007297 from "The directed movement of follicle cells that takes place during oogenesis. During egg chamber formation, follicle cells migrate to envelop the germ-line cysts and move in between cysts. At stage 10B, follicle cells migrate centripetally between the nurse cells and the oocyte, enclosing the anterior of the egg." to "The directed movement of ovarian follicle cells that takes place during oogenesis. During egg chamber formation, follicle cells migrate to envelop the germ-line cysts and move in between cysts. At stage 10B, follicle cells migrate centripetally between the nurse cells and the oocyte, enclosing the anterior of the egg."
* Deleted definition dbxref ISBN:0471331309 from GO:0008403
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0008403
* Copied GO:0009987 to GO:0051704 with type disjoint_from
* Copied GO:0009987 to GO:0032501 with type disjoint_from
* Changed definition of GO:0015360 from "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: acetate(out) = acetate(in)." to "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: acetate(out) + H+(out) = acetate(in) + H+(in)."
* Added synonym "hydrogen:acetate symporter activity" to GO:0015360
* Changed synonym scope of GO:0015360 from "Related" to "Exact"
* Copied GO:0015360 to GO:0043893 with type OBO_REL:is_a
* Deleted definition dbxref ISBN:0471331309 from GO:0016129
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0016129
* Set definition of GO:0016799 to "Catalysis of the hydrolysis of any N-glycosyl bond."
* Added definition dbxref GOC:jl to GO:0016799
* Changed comment from "This term was made obsolete because it represents a biological process. To update annotations, use external ontology term 'regulation of sodium:hydrogen antiporter activity ; GO:0022899'." to "This term was made obsolete because it represents a biological process."
* Deleted GO:0019578 --OBO_REL:is_a--> GO:0046394
* Deleted definition dbxref ISBN:0471331309 from GO:0030342
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0030342
* Deleted definition dbxref ISBN:0471331309 from GO:0030343
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0030343
* Deleted definition dbxref ISBN:0471331309 from GO:0031374
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0031374
* Deleted definition dbxref ISBN:0471331309 from GO:0031375
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0031375
* Deleted definition dbxref ISBN:0471331309 from GO:0031376
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0031376
* Deleted definition dbxref ISBN:0471331309 from GO:0031377
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0031377
* Deleted definition dbxref ISBN:0471331309 from GO:0031378
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0031378
* Deleted definition dbxref ISBN:0471331309 from GO:0045250
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0045250
* Deleted definition dbxref ISBN:0471331309 from GO:0046407
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0046407
* Deleted definition dbxref ISBN:0471331309 from GO:0046408
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0046408
* Deleted definition dbxref ISBN:0471331309 from GO:0046422
* Added definition dbxref Biochemical Pathways (ISBN:0471331309) to GO:0046422
* Changed definition of GO:0046667 from "Programmed cell death that occurs in the retina to remove excess cells between ommatidia, thus resulting in a hexagonal lattice, precise with respect to cell number and position surrounding each ommatidia." to "Programmed cell death that occurs in the retina to remove excess cells between ommatidia, thus resulting in a hexagonal lattice, precise with respect to cell number and position surrounding each ommatidium."
* Changed synonym scope of GO:0048477 from "Exact" to "Related"
* Copied GO:0051704 to GO:0032501 with type disjoint_from


From gocvs at genome.Stanford.EDU  Fri Aug 10 21:30:39 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Fri, 10 Aug 2007 21:30:39 -0700 (PDT)
Subject: [go-diff] GO update 08/10/2007
Message-ID: <200708110430.VAA12892@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.452 by 5.453

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0033602
* Created object of type obo:TERM with id GO:0033603
* Created object of type obo:TERM with id GO:0033604
* Created object of type obo:TERM with id GO:0033605
* Created object of type obo:TERM with id GO:0033607
* Populated new object GO:0033602 (macro)
  * Changed name of GO:0033602 from "<new term>" to "negative regulation of dopamine secretion"
  * Set definition of GO:0033602 to "Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of dopamine."
  * Added definition dbxref GOC:sl to GO:0033602
  * Added synonym "down regulation of dopamine secretion" to GO:0033602
  * Changed synonym scope of GO:0033602 from "Related" to "Exact"
  * Added synonym "down-regulation of dopamine secretion" to GO:0033602
  * Changed synonym scope of GO:0033602 from "Related" to "Exact"
  * Added synonym "downregulation of dopamine secretion" to GO:0033602
  * Changed synonym scope of GO:0033602 from "Related" to "Exact"
  * Added synonym "inhibition of dopamine secretion" to GO:0033602
  * Changed synonym scope of GO:0033602 from "Related" to "Narrow"
  * Copied GO:0033602 to GO:0033604 with type OBO_REL:is_a
  * Copied GO:0033602 to GO:0014059 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033602
* Populated new object GO:0033603 (macro)
  * Changed name of GO:0033603 from "<new term>" to "positive regulation of dopamine secretion"
  * Set definition of GO:0033603 to "Any process that activates or increases the frequency, rate or extent of the regulated release of dopamine."
  * Added definition dbxref GOC:sl to GO:0033603
  * Added synonym "activation of dopamine secretion" to GO:0033603
  * Changed synonym scope of GO:0033603 from "Related" to "Narrow"
  * Added synonym "stimulation of dopamine secretion" to GO:0033603
  * Changed synonym scope of GO:0033603 from "Related" to "Narrow"
  * Added synonym "up regulation of dopamine secretion" to GO:0033603
  * Changed synonym scope of GO:0033603 from "Related" to "Exact"
  * Added synonym "up-regulation of dopamine secretion" to GO:0033603
  * Changed synonym scope of GO:0033603 from "Related" to "Exact"
  * Added synonym "upregulation of dopamine secretion" to GO:0033603
  * Changed synonym scope of GO:0033603 from "Related" to "Exact"
  * Copied GO:0033603 to GO:0033605 with type OBO_REL:is_a
  * Copied GO:0033603 to GO:0014059 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033603
* Populated new object GO:0033604 (macro)
  * Changed name of GO:0033604 from "<new term>" to "negative regulation of catecholamine secretion"
  * Set definition of GO:0033604 to "Any process that stops, prevents or reduces the frequency, rate or extent of the regulated release of a catecholamine."
  * Added definition dbxref GOC:mah to GO:0033604
  * Added synonym "down regulation of catecholamine secretion" to GO:0033604
  * Changed synonym scope of GO:0033604 from "Related" to "Exact"
  * Added synonym "down-regulation of catecholamine secretion" to GO:0033604
  * Changed synonym scope of GO:0033604 from "Related" to "Exact"
  * Added synonym "downregulation of catecholamine secretion" to GO:0033604
  * Changed synonym scope of GO:0033604 from "Related" to "Exact"
  * Added synonym "inhibition of catecholamine secretion" to GO:0033604
  * Changed synonym scope of GO:0033604 from "Related" to "Narrow"
  * Copied GO:0033604 to GO:0046929 with type OBO_REL:is_a
  * Copied GO:0033604 to GO:0050433 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033604
* Populated new object GO:0033605 (macro)
  * Changed name of GO:0033605 from "<new term>" to "positive regulation of catecholamine secretion"
  * Set definition of GO:0033605 to "Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine."
  * Added definition dbxref GOC:mah to GO:0033605
  * Added synonym "activation of catecholamine secretion" to GO:0033605
  * Changed synonym scope of GO:0033605 from "Related" to "Narrow"
  * Added synonym "stimulation of catecholamine secretion" to GO:0033605
  * Changed synonym scope of GO:0033605 from "Related" to "Narrow"
  * Added synonym "up regulation of catecholamine secretion" to GO:0033605
  * Changed synonym scope of GO:0033605 from "Related" to "Exact"
  * Added synonym "up-regulation of catecholamine secretion" to GO:0033605
  * Changed synonym scope of GO:0033605 from "Related" to "Exact"
  * Added synonym "upregulation of catecholamine secretion" to GO:0033605
  * Changed synonym scope of GO:0033605 from "Related" to "Exact"
  * Copied GO:0033605 to GO:0001956 with type OBO_REL:is_a
  * Copied GO:0033605 to GO:0050433 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0033605
* Populated new object GO:0033607 (macro)
  * Changed name of GO:0033607 from "<new term>" to "SOD1-Bcl-2 complex"
  * Set definition of GO:0033607 to "A heterodimeric protein complex formed of superoxide dismutase 1 and Bcl-2. Complex formation is thought to link superoxide dismutase to an apoptotic pathway."
  * Added definition dbxref PMID:15233914 to GO:0033607
  * Added definition dbxref PMID:16790527 to GO:0033607
  * Copied GO:0033607 to GO:0044424 with type OBO_REL:is_a
  * Copied GO:0033607 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0033607
* Deleted GO:0006613 --OBO_REL:is_a--> GO:0006605
* Deleted GO:0007308 --part_of--> GO:0048477
* Copied GO:0032811 to GO:0033604 with type OBO_REL:is_a
* Copied GO:0032812 to GO:0033605 with type OBO_REL:is_a
* Deleted GO:0033597 --OBO_REL:is_a--> GO:0044424
* Copied GO:0033597 to GO:0044428 with type OBO_REL:is_a
* Changed definition of GO:0051603 from "The hydrolysis of a peptide bond or bonds within a protein during the chemical reactions and pathways resulting in the breakdown of a protein." to "The hydrolysis of a peptide bond or bonds within a protein during the chemical reactions and pathways resulting in the breakdown of a protein by individual cells."


From gocvs at genome.Stanford.EDU  Tue Aug 14 21:30:39 2007
From: gocvs at genome.Stanford.EDU (Remote CVS for Gene Ontology)
Date: Tue, 14 Aug 2007 21:30:39 -0700 (PDT)
Subject: [go-diff] GO update 08/14/2007
Message-ID: <200708150430.VAA28099@bread.Stanford.EDU>

OBODIFF of gene_ontology_edit.obo version 5.453 by 5.454

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0032509
* Created object of type obo:TERM with id GO:0032510
* Created object of type obo:TERM with id GO:0032511
* Created object of type obo:TERM with id GO:0032512
* Created object of type obo:TERM with id GO:0032513
* Created object of type obo:TERM with id GO:0032514
* Created object of type obo:TERM with id GO:0032515
* Created object of type obo:TERM with id GO:0032516
* Populated new object GO:0032509 (macro)
  * Changed name of GO:0032509 from "<new term>" to "endosome transport via multivesicular body sorting pathway"
  * Set definition of GO:0032509 to "The directed movement of substances from endosomes to lysosomes or vacuoles by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the target compartment."
  * Added definition dbxref GOC:mah to GO:0032509
  * Added definition dbxref PMID:12461556 to GO:0032509
  * Added definition dbxref PMID:16689637 to GO:0032509
  * Added synonym "endosome transport via MVB sorting pathway" to GO:0032509
  * Changed synonym scope of GO:0032509 from "Related" to "Exact"
  * Copied GO:0032509 to GO:0016197 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0032509
* Populated new object GO:0032510 (macro)
  * Changed name of GO:0032510 from "<new term>" to "endosome to lysosome transport via multivesicular body sorting pathway"
  * Set definition of GO:0032510 to "The directed movement of substances from endosomes to lysosomes by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the lysosome."
  * Added definition dbxref GOC:mah to GO:0032510
  * Added definition dbxref PMID:12461556 to GO:0032510
  * Added definition dbxref PMID:16689637 to GO:0032510
  * Added synonym "endosome to lysosome transport via MVB sorting pathway" to GO:0032510
  * Changed synonym scope of GO:0032510 from "Related" to "Exact"
  * Copied GO:0032510 to GO:0045022 with type OBO_REL:is_a
  * Copied GO:0032510 to GO:0032509 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0032510
* Populated new object GO:0032511 (macro)
  * Changed name of GO:0032511 from "<new term>" to "late endosome to vacuole transport via multivesicular body sorting pathway"
  * Set definition of GO:0032511 to "The directed movement of substances from endosomes to vacuoles by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the vacuole."
  * Added definition dbxref GOC:mah to GO:0032511
  * Added definition dbxref PMID:12461556 to GO:0032511
  * Added definition dbxref PMID:16689637 to GO:0032511
  * Added synonym "endosome to vacuole transport via MVB sorting pathway" to GO:0032511
  * Changed synonym scope of GO:0032511 from "Related" to "Exact"
  * Copied GO:0032511 to GO:0032509 with type OBO_REL:is_a
  * Copied GO:0032511 to GO:0045324 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0032511
* Populated new object GO:0032512 (macro)
  * Changed name of GO:0032512 from "<new term>" to "regulation of protein phosphatase type 2B activity"
  * Set definition of GO:0032512 to "Any process that modulates the activity of the enzyme protein phosphatase type 2B."
  * Added definition dbxref GOC:mah to GO:0032512
  * Added synonym "regulation of calcineurin activity" to GO:0032512
  * Changed synonym scope of GO:0032512 from "Related" to "Exact"
  * Copied GO:0032512 to GO:0043666 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0032512
* Populated new object GO:0032513 (macro)
  * Changed name of GO:0032513 from "<new term>" to "negative regulation of protein phosphatase type 2B activity"
  * Set definition of GO:0032513 to "Any process that stops or reduces the activity of the enzyme protein phosphatase type 2B."
  * Added definition dbxref GOC:mah to GO:0032513
  * Added GO:0032513 to category gosubset_prok
  * Added synonym "down regulation of protein phosphatase type 2B activity" to GO:0032513
  * Changed synonym scope of GO:0032513 from "Related" to "Exact"
  * Added synonym "down-regulation of protein phosphatase type 2B activity" to GO:0032513
  * Changed synonym scope of GO:0032513 from "Related" to "Exact"
  * Added synonym "downregulation of protein phosphatase type 2B activity" to GO:0032513
  * Changed synonym scope of GO:0032513 from "Related" to "Exact"
  * Added synonym "inhibition of protein phosphatase type 2B activity" to GO:0032513
  * Changed synonym scope of GO:0032513 from "Related" to "Narrow"
  * Added synonym "negative regulation of calcineurin activity" to GO:0032513
  * Changed synonym scope of GO:0032513 from "Related" to "Exact"
  * Copied GO:0032513 to GO:0051004 with type OBO_REL:is_a
  * Copied GO:0032513 to GO:0032515 with type OBO_REL:is_a
  * Copied GO:0032513 to GO:0032512 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0032513
* Populated new object GO:0032514 (macro)
  * Changed name of GO:0032514 from "<new term>" to "positive regulation of protein phosphatase type 2B activity"
  * Set definition of GO:0032514 to "Any process that activates or increases the activity of the enzyme protein phosphatase type 2B."
  * Added definition dbxref GOC:mah to GO:0032514
  * Added GO:0032514 to category gosubset_prok
  * Added synonym "activation of protein phosphatase type 2B activity" to GO:0032514
  * Changed synonym scope of GO:0032514 from "Related" to "Narrow"
  * Added synonym "calcineurin activation" to GO:0032514
  * Changed synonym scope of GO:0032514 from "Related" to "Exact"
  * Added synonym "positive regulation of calcineurin activity" to GO:0032514
  * Changed synonym scope of GO:0032514 from "Related" to "Exact"
  * Added synonym "stimulation of protein phosphatase type 2B activity" to GO:0032514
  * Changed synonym scope of GO:0032514 from "Related" to "Narrow"
  * Added synonym "up regulation of protein phosphatase type 2B activity" to