[Go-diff] GO update 08/21/2008

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

OBODIFF of gene_ontology_write.obo version 1.177 by 1.179

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034694
* Created object of type obo:TERM with id GO:0034695
* Created object of type obo:TERM with id GO:0034696
* Created object of type obo:TERM with id GO:0034697
* Created object of type obo:TERM with id GO:0034698
* Created object of type obo:TERM with id GO:0034699
* Created object of type obo:TERM with id GO:0034700
* Created object of type obo:TERM with id GO:0034701
* Created object of type obo:TERM with id GO:0034702
* Created object of type obo:TERM with id GO:0034703
* Created object of type obo:TERM with id GO:0034704
* Created object of type obo:TERM with id GO:0034705
* Created object of type obo:TERM with id GO:0034706
* Created object of type obo:TERM with id GO:0034707
* Created object of type obo:TERM with id GO:0034708
* Created object of type obo:TERM with id GO:0034709
* Populated new object GO:0034694 (macro)
  * Changed name of GO:0034694 from "<new term>" to "response to prostaglandin stimulus"
  * Set definition of GO:0034694 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 prostagladin stimulus."
  * Added definition dbxref GOC:vk to GO:0034694
  * Copied GO:0034694 to GO:0033993 with type OBO_REL:is_a
  * Copied GO:0034694 to GO:0009725 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034694
* Populated new object GO:0034695 (macro)
  * Changed name of GO:0034695 from "<new term>" to "response to prostaglandin E stimulus"
  * Set definition of GO:0034695 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 prostagladin E stimulus."
  * Added definition dbxref GOC:vk to GO:0034695
  * Copied GO:0034695 to GO:0034694 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034695
* Populated new object GO:0034696 (macro)
  * Changed name of GO:0034696 from "<new term>" to "response to prostaglandin F stimulus"
  * Set definition of GO:0034696 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 prostagladin F stimulus."
  * Added definition dbxref GOC:vk to GO:0034696
  * Copied GO:0034696 to GO:0034694 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034696
* Populated new object GO:0034697 (macro)
  * Changed name of GO:0034697 from "<new term>" to "response to prostaglandin I stimulus"
  * Set definition of GO:0034697 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 prostagladin I stimulus."
  * Added definition dbxref GOC:vk to GO:0034697
  * Copied GO:0034697 to GO:0034694 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034697
* Populated new object GO:0034698 (macro)
  * Changed name of GO:0034698 from "<new term>" to "response to gonadotropin stimulus"
  * Set definition of GO:0034698 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 gonadotropin stimulus."
  * Added definition dbxref GOC:vk to GO:0034698
  * Copied GO:0034698 to GO:0009725 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034698
* Populated new object GO:0034699 (macro)
  * Changed name of GO:0034699 from "<new term>" to "response to luteinizing hormone stimulus"
  * Set definition of GO:0034699 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 luteinizing hormone stimulus."
  * Added definition dbxref GOC:vk to GO:0034699
  * Copied GO:0034699 to GO:0034698 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034699
* Populated new object GO:0034700 (macro)
  * Changed name of GO:0034700 from "<new term>" to "allulose 6-phosphate 3-epimerase activity"
  * Set definition of GO:0034700 to "Catalysis of the reaction: D-allulose 6-phosphate = D-fructose 6-phosphate."
  * Added definition dbxref GOC:imk to GO:0034700
  * Copied GO:0034700 to GO:0016857 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034700
* Populated new object GO:0034701 (macro)
  * Changed name of GO:0034701 from "<new term>" to "tripeptidase activity"
  * Set definition of GO:0034701 to "Catalysis of the hydrolysis of a tripeptide."
  * Added definition dbxref GOC:mah to GO:0034701
  * Added general dbxref EC:3.4.13 to GO:0034701
  * Copied GO:0034701 to GO:0008238 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0034701
* Populated new object GO:0034702 (macro)
  * Changed name of GO:0034702 from "<new term>" to "ion channel complex"
  * Set definition of GO:0034702 to "A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient."
  * Added definition dbxref GOC:mah to GO:0034702
  * Added definition dbxref ISBN:071673706X to GO:0034702
  * Copied GO:0034702 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0034702 to GO:0016021 with type part_of
  * Assigned namespace "cellular_component" to GO:0034702
* Populated new object GO:0034703 (macro)
  * Changed name of GO:0034703 from "<new term>" to "cation channel complex"
  * Set definition of GO:0034703 to "An ion channel complex through which cations pass."
  * Added definition dbxref GOC:mah to GO:0034703
  * Copied GO:0034703 to GO:0034702 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034703
* Populated new object GO:0034704 (macro)
  * Changed name of GO:0034704 from "<new term>" to "calcium channel complex"
  * Set definition of GO:0034704 to "An ion channel complex through which calcium ions pass."
  * Added definition dbxref GOC:mah to GO:0034704
  * Copied GO:0034704 to GO:0034703 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034704
* Populated new object GO:0034705 (macro)
  * Changed name of GO:0034705 from "<new term>" to "potassium channel complex"
  * Set definition of GO:0034705 to "An ion channel complex through which potassium ions pass."
  * Added definition dbxref GOC:mah to GO:0034705
  * Copied GO:0034705 to GO:0034703 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034705
* Populated new object GO:0034706 (macro)
  * Changed name of GO:0034706 from "<new term>" to "sodium channel complex"
  * Set definition of GO:0034706 to "An ion channel complex through which sodium ions pass."
  * Added definition dbxref GOC:mah to GO:0034706
  * Copied GO:0034706 to GO:0034703 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034706
* Populated new object GO:0034707 (macro)
  * Changed name of GO:0034707 from "<new term>" to "chloride channel complex"
  * Set definition of GO:0034707 to "An ion channel complex through which chloride ions pass."
  * Added definition dbxref GOC:mah to GO:0034707
  * Copied GO:0034707 to GO:0034702 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034707
* Populated new object GO:0034708 (macro)
  * Changed name of GO:0034708 from "<new term>" to "methyltransferase complex"
  * Set definition of GO:0034708 to "A protein complex that possesses methyltransferase activity."
  * Added definition dbxref GOC:mah to GO:0034708
  * Copied GO:0034708 to GO:0044424 with type OBO_REL:is_a
  * Copied GO:0034708 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034708
* Populated new object GO:0034709 (macro)
  * Changed name of GO:0034709 from "<new term>" to "methylosome"
  * Set definition of GO:0034709 to "A large (20 S) protein complex that possesses protein arginine methyltransferase activity and modifies specific arginines to dimethylarginines in the arginine- and glycine-rich domains of several spliceosomal Sm proteins, thereby targeting these proteins to the survival of motor neurons (SMN) complex for assembly into small nuclear ribonucleoprotein (snRNP) core particles. Proteins found in the methylosome include the methyltransferase JBP1 (PRMT5), pICln (CLNS1A), MEP50 (WDR77), and SM proteins that have RG domains."
  * Added definition dbxref PMID:11713266 to GO:0034709
  * Added definition dbxref PMID:11756452 to GO:0034709
  * Added synonym "20S methylosome" to GO:0034709
  * Changed synonym scope of GO:0034709 from "Related" to "Exact"
  * Added synonym "20S methyltransferase complex" to GO:0034709
  * Changed synonym scope of GO:0034709 from "Related" to "Exact"
  * Copied GO:0034709 to GO:0034708 with type OBO_REL:is_a
  * Copied GO:0034709 to GO:0044444 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0034709
* Changed definition of GO:0000125 from "A large multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. The composition is similar to that of the SAGA complex, but includes fewer Spt and Ada proteins, and more TAFs." to "A large multiprotein complex that possesses histone acetyltransferase activity and is involved in regulation of transcription. The composition is similar to that of the SAGA complex, but includes fewer Spt and Ada proteins, and more TAFs."
* Added synonym "PCAF histone acetylase-associated complex" to GO:0000125
* Changed synonym scope of GO:0000125 from "Related" to "Exact"
* Changed definition of GO:0000145 from "Protein complex peripherally associated with the plasma membrane that determines where secretory vesicles dock and fuse. At least eight complex components are conserved between yeast and mammals." to "A protein complex peripherally associated with the plasma membrane that determines where secretory vesicles dock and fuse. At least eight complex components are conserved between yeast and mammals."
* Added synonym "Sec6/8 complex" to GO:0000145
* Changed synonym scope of GO:0000145 from "Related" to "Exact"
* Deleted GO:0001518 --OBO_REL:is_a--> GO:0043234
* Copied GO:0001518 to GO:0034706 with type OBO_REL:is_a
* Added synonym "RNA polymerase II complex" to GO:0005665
* Changed synonym scope of GO:0005665 from "Related" to "Broad"
* Added synonym "RNAP II complex" to GO:0005665
* Changed synonym scope of GO:0005665 from "Related" to "Broad"
* Added synonym "fatty acid synthetase complex" to GO:0005835
* Changed synonym scope of GO:0005835 from "Related" to "Exact"
* Deleted GO:0005891 --OBO_REL:is_a--> GO:0043234
* Copied GO:0005891 to GO:0034704 with type OBO_REL:is_a
* Copied GO:0005892 to GO:0034702 with type OBO_REL:is_a
* Deleted GO:0008076 --OBO_REL:is_a--> GO:0043234
* Copied GO:0008076 to GO:0034705 with type OBO_REL:is_a
* Changed definition of GO:0008242 from "Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of a-carboxyl to a-amino groups)." to "Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of alpha-carboxyl to alpha-amino groups)."
* Deleted GO:0008282 --OBO_REL:is_a--> GO:0043234
* Copied GO:0008282 to GO:0034702 with type OBO_REL:is_a
* Added synonym "PRMT activity" to GO:0016274
* Changed synonym scope of GO:0016274 from "Related" to "Exact"
* Copied GO:0016274 to GO:0008276 with type OBO_REL:is_a
* Deleted GO:0016472 --OBO_REL:is_a--> GO:0016021
* Copied GO:0016472 to GO:0016021 with type part_of
* Set definition of GO:0016920 to "Catalysis of the release of the N-terminal pyroglutamyl group from a peptide or protein."
* Added definition dbxref EC:3.4.19.3 to GO:0016920
* Added definition dbxref EC:3.4.19.6 to GO:0016920
* Added definition dbxref GOC:mah to GO:0016920
* Deleted GO:0016935 --OBO_REL:is_a--> GO:0043234
* Copied GO:0016935 to GO:0034707 with type OBO_REL:is_a
* Deleted GO:0017071 --OBO_REL:is_a--> GO:0016021
* Deleted GO:0017071 --OBO_REL:is_a--> GO:0043234
* Copied GO:0017071 to GO:0034703 with type OBO_REL:is_a
* Added synonym "PABA peptide hydrolase complex" to GO:0017090
* Changed synonym scope of GO:0017090 from "Related" to "Exact"
* Deleted GO:0017090 --OBO_REL:is_a--> GO:0016021
* Copied GO:0017090 to GO:0016021 with type part_of
* Deleted GO:0019183 --OBO_REL:is_a--> GO:0043234
* Copied GO:0019183 to GO:0034707 with type OBO_REL:is_a
* Deleted general dbxref MetaCyc:UNSAT-FA-ELONG-PWY from GO:0019368
* Added general dbxref MetaCyc:PWY0-862 to GO:0019368
* Added synonym "protein-arginine delta-N-methyltransferase activity" to GO:0019702
* Changed synonym scope of GO:0019702 from "Related" to "Exact"
* Added synonym "type IV PRMT activity" to GO:0019702
* Changed synonym scope of GO:0019702 from "Related" to "Exact"
* Added synonym "type IV protein arginine methyltransferase activity" to GO:0019702
* Changed synonym scope of GO:0019702 from "Related" to "Exact"
* Deleted GO:0019702 --OBO_REL:is_a--> GO:0016273
* Copied GO:0019702 to GO:0016274 with type OBO_REL:is_a
* Added synonym "STAGA coactivator complex" to GO:0030914
* Changed synonym scope of GO:0030914 from "Related" to "Exact"
* Added synonym "INO80 chromatin remodeling complex" to GO:0031011
* Changed synonym scope of GO:0031011 from "Related" to "Exact"
* Deleted GO:0031515 --part_of--> GO:0043527
* Deleted GO:0031515 --OBO_REL:is_a--> GO:0043234
* Deleted GO:0031515 --OBO_REL:is_a--> GO:0044444
* Copied GO:0031515 to GO:0043527 with type OBO_REL:is_a
* Deleted GO:0031533 --OBO_REL:is_a--> GO:0043234
* Copied GO:0031533 to GO:0034708 with type OBO_REL:is_a
* Deleted GO:0032354 --OBO_REL:is_a--> GO:0009725
* Copied GO:0032354 to GO:0034698 with type OBO_REL:is_a
* Deleted GO:0035097 --OBO_REL:is_a--> GO:0043234
* Copied GO:0035097 to GO:0034708 with type OBO_REL:is_a
* Added synonym "type I PRMT activity" to GO:0035242
* Added synonym "type I protein arginine methyltransferase activity" to GO:0035242
* Added synonym "type II PRMT activity" to GO:0035243
* Added synonym "type II protein arginine methyltransferase activity" to GO:0035243
* Deleted GO:0043527 --OBO_REL:is_a--> GO:0043234
* Copied GO:0043527 to GO:0034708 with type OBO_REL:is_a
* Deleted GO:0043528 --part_of--> GO:0043527
* Deleted GO:0043528 --OBO_REL:is_a--> GO:0043234
* Deleted GO:0043528 --OBO_REL:is_a--> GO:0044444
* Copied GO:0043528 to GO:0043527 with type OBO_REL:is_a
* Added synonym "PCNA homotrimer" to GO:0043626
* Changed synonym scope of GO:0043626 from "Related" to "Exact"
* Deleted GO:0043853 --OBO_REL:is_a--> GO:0044424
* Copied GO:0043853 to GO:0034708 with type OBO_REL:is_a
* Deleted synonym "tripeptidase activity" from GO:0045148
* Copied GO:0045148 to GO:0034701 with type OBO_REL:is_a
* Deleted GO:0046696 --OBO_REL:is_a--> GO:0016021
* Copied GO:0046696 to GO:0016021 with type part_of
* Deleted GO:0046930 --OBO_REL:is_a--> GO:0016021
* Copied GO:0046930 to GO:0016021 with type part_of
* Copied GO:0046930 to GO:0044425 with type OBO_REL:is_a
* Deleted GO:0060277 --negatively_regulates--> GO:0006366

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