[Go-diff] GO update 06/10/2009

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Wed Jun 10 21:30:53 PDT 2009 

OBODIFF of gene_ontology_write.obo version 1.651 by 1.654

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0002145
* Created object of type obo:TERM with id GO:0060713
* Created object of type obo:TERM with id GO:0060714
* Created object of type obo:TERM with id GO:0070717
* Created object of type obo:TERM with id GO:0070718
* Created object of type obo:TERM with id GO:0070719
* Created object of type obo:TERM with id GO:0070720
* Created object of type obo:TERM with id GO:0070721
* Created object of type obo:TERM with id GO:0070722
* Populated new object GO:0002145 (macro)
  * Changed name of GO:0002145 from "<new term>" to "4-amino-5-hydroxymethyl-2-methylpyrimidine diphosphatase activity"
  * Set definition of GO:0002145 to "4-amino-5-hydroxymethyl-2-methylpyrimidine diphosphate + water = 2-methyl-4-amino-5-hydroxymethyl pyrimidine monophosphate + phosphate."
  * Added definition dbxref GOC:hjd to GO:0002145
  * Added synonym "HMP-PP diphosphatase" to GO:0002145
  * Changed synonym scope of GO:0002145 from "Related" to "Exact"
  * Added synonym "HMP-PP pyrophosphatase" to GO:0002145
  * Changed synonym scope of GO:0002145 from "Related" to "Exact"
  * Copied GO:0002145 to GO:0016462 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0002145
* Populated new object GO:0060713 (macro)
  * Changed name of GO:0060713 from "<new term>" to "labyrinthine layer morphogenesis"
  * Set definition of GO:0060713 to "The process by which the labyrinthine layer of the placenta is generated and organized."
  * Added definition dbxref GOC:dph to GO:0060713
  * Copied GO:0060713 to GO:0009653 with type OBO_REL:is_a
  * Copied GO:0060713 to GO:0060711 with type part_of
  * Assigned namespace "biological_process" to GO:0060713
* Populated new object GO:0060714 (macro)
  * Changed name of GO:0060714 from "<new term>" to "labyrinthine layer formation"
  * Set definition of GO:0060714 to "The developmental process pertaining to the initial formation of the labyrinthine layer of the placenta."
  * Added definition dbxref GOC:dph to GO:0060714
  * Copied GO:0060714 to GO:0060713 with type part_of
  * Copied GO:0060714 to GO:0048646 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060714
* Populated new object GO:0070717 (macro)
  * Changed name of GO:0070717 from "<new term>" to "poly-purine tract binding"
  * Set definition of GO:0070717 to "Interacting selectively with any stretch of purines (adenine or guanine) in an RNA molecule."
  * Added definition dbxref GOC:mah to GO:0070717
  * Copied GO:0070717 to GO:0003727 with type OBO_REL:is_a
  * Assigned namespace "molecular_function" to GO:0070717
* Populated new object GO:0070718 (macro)
  * Changed name of GO:0070718 from "<new term>" to "alphaPDGFR-SHP-2 complex"
  * Set definition of GO:0070718 to "A protein complex that contains the platelet-derived growth factor alpha receptor (alphaPDGFR; PDGFRA) and the adaptor protein SHP-2, and is involved signaling via the PDGFR signaling pathway."
  * Added definition dbxref GOC:mah to GO:0070718
  * Added definition dbxref PMID:8943348 to GO:0070718
  * Added synonym "PDGFRA-SHP-2 complex, PDGF stimulated" to GO:0070718
  * Added general dbxref CORUM:3183 to synonym PDGFRA-SHP-2 complex, PDGF stimulated of GO:0070718
  * Changed synonym scope of GO:0070718 from "Related" to "Narrow"
  * Copied GO:0070718 to GO:0044459 with type OBO_REL:is_a
  * Copied GO:0070718 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070718
* Populated new object GO:0070719 (macro)
  * Changed name of GO:0070719 from "<new term>" to "alphaPDGFR-PLC-gamma-1-PI3K-SHP-2 complex"
  * Set definition of GO:0070719 to "A protein complex that contains the platelet-derived growth factor alpha receptor (alphaPDGFR; PDGFRA), phospholipase C-gamma-1 (PLC-gamma-1), phosphatidylinositol 3-kinase (PI3K) and the adaptor protein SHP-2, and is involved signaling via the PDGFR signaling pathway."
  * Added definition dbxref GOC:mah to GO:0070719
  * Added definition dbxref PMID:8943348 to GO:0070719
  * Added synonym "PDGFRA-PLC-gamma-1-PI3K-SHP-2 complex, PDGF stimulated" to GO:0070719
  * Added general dbxref CORUM:2551 to synonym PDGFRA-PLC-gamma-1-PI3K-SHP-2 complex, PDGF stimulated of GO:0070719
  * Changed synonym scope of GO:0070719 from "Related" to "Narrow"
  * Copied GO:0070719 to GO:0044459 with type OBO_REL:is_a
  * Copied GO:0070719 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070719
* Populated new object GO:0070720 (macro)
  * Changed name of GO:0070720 from "<new term>" to "Grb2-SHP-2 complex"
  * Set definition of GO:0070720 to "A protein complex that contains the receptor adaptor proteins Grb2 and SHP-2, and is involved signaling via the PDGFR signaling pathway."
  * Added definition dbxref GOC:mah to GO:0070720
  * Added definition dbxref PMID:8943348 to GO:0070720
  * Added synonym "GRB2-SHP-2 complex, PDGF stimulated" to GO:0070720
  * Added general dbxref CORUM:3186 to synonym GRB2-SHP-2 complex, PDGF stimulated of GO:0070720
  * Changed synonym scope of GO:0070720 from "Related" to "Narrow"
  * Copied GO:0070720 to GO:0044459 with type OBO_REL:is_a
  * Copied GO:0070720 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070720
* Populated new object GO:0070721 (macro)
  * Changed name of GO:0070721 from "<new term>" to "ISGF3 complex"
  * Set definition of GO:0070721 to "A transcription factor complex that consists of a Stat1-Stat2 heterodimer and the IRF9 protein."
  * Added definition dbxref GOC:mah to GO:0070721
  * Added definition dbxref PMID:8943351 to GO:0070721
  * Added synonym "interferon-stimulated gene factor 3 transcription complex" to GO:0070721
  * Added general dbxref CORUM:60 to synonym interferon-stimulated gene factor 3 transcription complex of GO:0070721
  * Changed synonym scope of GO:0070721 from "Related" to "Exact"
  * Copied GO:0070721 to GO:0005667 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070721
* Populated new object GO:0070722 (macro)
  * Changed name of GO:0070722 from "<new term>" to "Tle3-Aes complex"
  * Set definition of GO:0070722 to "A transcriptional repressor complex that consists of a heterodimer of the proteins Tle3 (also known as Grg3b) and Aes (Grg5), which are homologs of the Drosophila groucho gene product."
  * Added definition dbxref GOC:mah to GO:0070722
  * Added definition dbxref PMID:8955148 to GO:0070722
  * Added synonym "Grg3b-Grg5 complex" to GO:0070722
  * Added general dbxref CORUM:3130 to synonym Grg3b-Grg5 complex of GO:0070722
  * Added general dbxref PMID:8955148 to synonym Grg3b-Grg5 complex of GO:0070722
  * Changed synonym scope of GO:0070722 from "Related" to "Exact"
  * Copied GO:0070722 to GO:0017053 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070722
* Changed name of GO:0008143 from "poly(A) binding" to "poly(A) RNA binding"
* Changed definition of GO:0008143 from "Interacting selectively with the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA." to "Interacting selectively with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA."
* Added definition dbxref GOC:krc to GO:0008143
* Added general dbxref GOC:mah to synonym poly-A binding of GO:0008143
* Changed synonym scope of GO:0008143 from "Exact" to "Broad"
* Added general dbxref GOC:mah to synonym polyadenylate binding of GO:0008143
* Changed synonym scope of GO:0008143 from "Exact" to "Broad"
* Added synonym "poly(A) binding" to GO:0008143
* Added general dbxref GOC:mah to synonym poly(A) binding of GO:0008143
* Changed synonym scope of GO:0008143 from "Related" to "Exact"
* Added synonym "poly(rA) binding" to GO:0008143
* Added general dbxref GOC:mah to synonym poly(rA) binding of GO:0008143
* Changed synonym scope of GO:0008143 from "Related" to "Exact"
* Deleted GO:0008143 --OBO_REL:is_a--> GO:0003727
* Copied GO:0008143 to GO:0070717 with type OBO_REL:is_a
* Deleted GO:0008187 --OBO_REL:is_a--> GO:0003723
* Copied GO:0008187 to GO:0003727 with type OBO_REL:is_a
* Changed name of GO:0008266 from "poly(U) binding" to "poly(U) RNA binding"
* Added synonym "poly(U) binding" to GO:0008266
* Added general dbxref GOC:mah to synonym poly(U) binding of GO:0008266
* Changed synonym scope of GO:0008266 from "Related" to "Exact"
* Deleted GO:0008266 --OBO_REL:is_a--> GO:0003727
* Copied GO:0008266 to GO:0008187 with type OBO_REL:is_a
* Deleted GO:0008608 --part_of--> GO:0007059
* Changed definition of GO:0010467 from "The process by which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." to "The process by which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form."
* Changed name of GO:0017130 from "poly(rC) binding" to "poly(C) RNA binding"
* Added synonym "poly(C) binding" to GO:0017130
* Added general dbxref GOC:mah to synonym poly(C) binding of GO:0017130
* Changed synonym scope of GO:0017130 from "Related" to "Broad"
* Added synonym "poly(rC) binding" to GO:0017130
* Added general dbxref GOC:mah to synonym poly(rC) binding of GO:0017130
* Changed synonym scope of GO:0017130 from "Related" to "Exact"
* Deleted GO:0017130 --OBO_REL:is_a--> GO:0003727
* Copied GO:0017130 to GO:0008187 with type OBO_REL:is_a
* Changed definition of GO:0017131 from "Interacting selectively with U-rich sequence in the 3'-end of mRNAs; required for cytoplasmic polyadenylylation." to "Interacting selectively with U-rich sequence in the 3'-end of nuclear-transcribed mRNAs; required for cytoplasmic polyadenylylation."
* Added definition dbxref GOC:krc to GO:0017131
* Added synonym "U-rich CPE binding" to GO:0017131
* Added general dbxref PMID:7954828 to synonym U-rich CPE binding of GO:0017131
* Changed synonym scope of GO:0017131 from "Related" to "Exact"
* Deleted GO:0031297 --OBO_REL:is_a--> GO:0006259
* Deleted GO:0032300 --OBO_REL:is_a--> GO:0044428
* Copied GO:0032300 to GO:0044424 with type OBO_REL:is_a
* Copied GO:0032301 to GO:0044428 with type OBO_REL:is_a
* Copied GO:0032302 to GO:0044428 with type OBO_REL:is_a
* Copied GO:0032389 to GO:0044428 with type OBO_REL:is_a
* Copied GO:0032390 to GO:0044428 with type OBO_REL:is_a
* Changed name of GO:0034046 from "poly(rG) binding" to "poly(G) RNA binding"
* Added synonym "poly(rG) binding" to GO:0034046
* Added general dbxref GOC:mah to synonym poly(rG) binding of GO:0034046
* Changed synonym scope of GO:0034046 from "Related" to "Exact"
* Deleted GO:0034046 --OBO_REL:is_a--> GO:0003727
* Copied GO:0034046 to GO:0070717 with type OBO_REL:is_a
* Deleted GO:0034994 --OBO_REL:is_a--> GO:0022607
* Added synonym "IL12RB1-IL12RB2 complex" to GO:0042022
* Added general dbxref CORUM:2026 to synonym IL12RB1-IL12RB2 complex of GO:0042022
* Changed synonym scope of GO:0042022 from "Related" to "Narrow"
* Changed definition of GO:0045210 from "The chemical reactions and pathways resulting in the formation of FasL (CD95), an antigen originally found to be expressed on the cell surface of activated human T-lymphocytes and B-lymphocytes and a variety of malignant human lymphoid cell lines." to "The chemical reactions and pathways resulting in the formation of fas ligand (FasL or CD95L), an antigen originally found to be expressed on the cell surface of activated human T-lymphocytes and B-lymphocytes and a variety of malignant human lymphoid cell lines."
* Deleted synonym "Apo-1 biosynthesis" from GO:0045210
* Deleted synonym "Apo-1 biosynthetic process" from GO:0045210
* Deleted synonym "CD95 biosynthesis" from GO:0045210
* Deleted synonym "CD95 biosynthetic process" from GO:0045210
* Deleted synonym "tumor necrosis factor receptor superfamily member 6 biosynthetic process" from GO:0045210
* Added synonym "APT1LG1 biosynthetic process" to GO:0045210
* Added general dbxref GOC:add to synonym APT1LG1 biosynthetic process of GO:0045210
* Changed synonym scope of GO:0045210 from "Related" to "Exact"
* Added synonym "CD178 biosynthetic process" to GO:0045210
* Added general dbxref GOC:add to synonym CD178 biosynthetic process of GO:0045210
* Changed synonym scope of GO:0045210 from "Related" to "Exact"
* Added synonym "CD95L biosynthesis" to GO:0045210
* Added general dbxref GOC:add to synonym CD95L biosynthesis of GO:0045210
* Changed synonym scope of GO:0045210 from "Related" to "Exact"
* Added synonym "CD95L biosynthetic process" to GO:0045210
* Added general dbxref GOC:add to synonym CD95L biosynthetic process of GO:0045210
* Changed synonym scope of GO:0045210 from "Related" to "Exact"
* Added synonym "fas ligand biosynthetic process" to GO:0045210
* Added general dbxref GOC:add to synonym fas ligand biosynthetic process of GO:0045210
* Added general dbxref PRO:000000095 to synonym fas ligand biosynthetic process of GO:0045210
* Changed synonym scope of GO:0045210 from "Related" to "Exact"
* Added synonym "Fas-L biosynthetic process" to GO:0045210
* Added general dbxref GOC:add to synonym Fas-L biosynthetic process of GO:0045210
* Changed synonym scope of GO:0045210 from "Related" to "Exact"
* Added synonym "FASLG biosynthetic process" to GO:0045210
* Added general dbxref GOC:add to synonym FASLG biosynthetic process of GO:0045210
* Changed synonym scope of GO:0045210 from "Related" to "Exact"
* Deleted GO:0060670 --part_of--> GO:0060711
* Copied GO:0060670 to GO:0060713 with type part_of
* Deleted GO:0060710 --part_of--> GO:0001890
* Copied GO:0060710 to GO:0060713 with type part_of

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