[Go-diff] GO update 12/18/2008

Thu Dec 18 21:30:48 PST 2008

OBODIFF of gene_ontology_write.obo version 1.358 by 1.360

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0060389
* Created object of type obo:TERM with id GO:0070209
* Created object of type obo:TERM with id GO:0070210
* Created object of type obo:TERM with id GO:0070211
* Created object of type obo:TERM with id GO:0070212
* Created object of type obo:TERM with id GO:0070213
* Created object of type obo:TERM with id GO:0070214
* Populated new object GO:0060389 (macro)
  * Changed name of GO:0060389 from "<new term>" to "pathway-restricted SMAD protein phosphorylation"
  * Set definition of GO:0060389 to "The process of introducing a phosphate group on to a pathway restricted SMAD protein. A pathway restricted SMAD protein is an effector protein that acts directly downstream of the transforming growth factor family receptor."
  * Added definition dbxref GOC:dph to GO:0060389
  * Added definition dbxref ISBN:3527303782 to GO:0060389
  * Copied GO:0060389 to GO:0007179 with type part_of
  * Copied GO:0060389 to GO:0006468 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0060389
* Populated new object GO:0070209 (macro)
  * Changed name of GO:0070209 from "<new term>" to "ASTRA complex"
  * Set definition of GO:0070209 to "A protein complex that is part of the chromatin remodeling machinery; the acronym stands for ASsembly of Tel, Rvb and Atm-like kinase. In Saccharomyces cerevisiae this complex includes Rvb1p, Rvb2p, Tra1p, Tel2p, Asa1p, Ttilp and Tti2p."
  * Added definition dbxref GOC:rb to GO:0070209
  * Added definition dbxref PMID:19040720 to GO:0070209
  * Copied GO:0070209 to GO:0016585 with type OBO_REL:is_a
  * Copied GO:0070209 to GO:0000790 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070209
* Populated new object GO:0070210 (macro)
  * Changed name of GO:0070210 from "<new term>" to "Rpd3L-Expanded complex"
  * Set definition of GO:0070210 to "A protein complex that contains a histone deacetyltransferase and is part of the chromatin remodeling machinery. In Saccharomyces cerevisiae this complex contains the Rpd3p, Sin3p, Ume1p, Pho23p, Sap30p, Sds3p, Cti6p, Rxt2p, Rxt3p, Dep1p, Ume6p, Ash1p, Dot6p, Snt1, Sif2p, Set3p, Hos2p, Tos4p and Tod6p proteins."
  * Added definition dbxref GOC:rb to GO:0070210
  * Added definition dbxref PMID:19040720 to GO:0070210
  * Added synonym "Clr6-LE complex" to GO:0070210
  * Added general dbxref GOC:vw to synonym Clr6-LE complex of GO:0070210
  * Changed synonym scope of GO:0070210 from "Related" to "Exact"
  * Copied GO:0070210 to GO:0016585 with type OBO_REL:is_a
  * Copied GO:0070210 to GO:0000790 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070210
* Populated new object GO:0070211 (macro)
  * Changed name of GO:0070211 from "<new term>" to "Snt2C complex"
  * Set definition of GO:0070211 to "A protein complex that is part of the chromatin remodeling machinery. In Saccharomyces cerevisiae this complex contains Snt2p, Ecm5p and Rpd3p."
  * Added definition dbxref GOC:rb to GO:0070211
  * Added definition dbxref PMID:19040720 to GO:0070211
  * Copied GO:0070211 to GO:0000790 with type OBO_REL:is_a
  * Copied GO:0070211 to GO:0016585 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070211
* Populated new object GO:0070212 (macro)
  * Changed name of GO:0070212 from "<new term>" to "protein amino acid poly-ADP-ribosylation"
  * Set definition of GO:0070212 to "The transfer of multiple ADP-ribose residues from NAD to a protein amino acid, forming a poly(ADP-ribose) chain."
  * Added definition dbxref GOC:mah to GO:0070212
  * Added definition dbxref GOC:rl to GO:0070212
  * Added synonym "addition of poly-ADP-ribose to protein" to GO:0070212
  * Added general dbxref GOC:rl to synonym addition of poly-ADP-ribose to protein of GO:0070212
  * Changed synonym scope of GO:0070212 from "Related" to "Exact"
  * Added synonym "poly(ADP-ribose) addition to protein" to GO:0070212
  * Added general dbxref GOC:rl to synonym poly(ADP-ribose) addition to protein of GO:0070212
  * Changed synonym scope of GO:0070212 from "Related" to "Exact"
  * Added synonym "protein poly(ADP-ribose) metabolism" to GO:0070212
  * Added general dbxref GOC:rl to synonym protein poly(ADP-ribose) metabolism of GO:0070212
  * Added synonym "protein poly(ADP-ribose) synthesis" to GO:0070212
  * Added general dbxref GOC:rl to synonym protein poly(ADP-ribose) synthesis of GO:0070212
  * Changed synonym scope of GO:0070212 from "Related" to "Exact"
  * Copied GO:0070212 to GO:0006471 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070212
* Populated new object GO:0070213 (macro)
  * Changed name of GO:0070213 from "<new term>" to "protein amino acid auto-ADP-ribosylation"
  * Set definition of GO:0070213 to "The ADP-ribosylation by a protein of one or more of its own amino acid residues, or residues on an identical protein."
  * Added definition dbxref GOC:rl to GO:0070213
  * Copied GO:0070213 to GO:0006471 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070213
* Populated new object GO:0070214 (macro)
  * Changed name of GO:0070214 from "<new term>" to "CSK-GAP-A.p62 complex"
  * Added comment "Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'."
  * Set definition of GO:0070214 to "A protein complex that contains the protein-tyrosine kinase CSK and the GTPase-activating protein (GAP)-associated p62 (GAP-A.p62); may mediate translocation of proteins, including GAP and CSK, to membrane or cytoskeletal regions upon c-Src activation."
  * Added definition dbxref PMID:7544435 to GO:0070214
  * Copied GO:0070214 to GO:0044444 with type OBO_REL:is_a
  * Copied GO:0070214 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0070214 to GO:0031252 with type part_of
  * Assigned namespace "cellular_component" to GO:0070214
* Changed name of GO:0000812 from "SWR1 complex" to "Swr1 complex"
* Copied GO:0000812 to GO:0000790 with type part_of
* Set definition of GO:0007182 to "The process of introducing a phosphate group on to a common-partner SMAD protein. A common partner SMAD protein binds to pathway-restricted SMAD proteins forming a complex that tranlocates to the nucleus."
* Added definition dbxref GOC:dph to GO:0007182
* Added definition dbxref ISBN:3527303782 to GO:0007182
* Added synonym "common mediator SMAD protein phosphorylation" to GO:0007182
* Changed synonym scope of GO:0007182 from "Related" to "Exact"
* Set definition of GO:0007184 to "The vectorial transfer of a SMAD proteins from the cytoplasm into the nucleus, through the nuclear pore. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways."
* Added definition dbxref GOC:dph to GO:0007184
* Deleted GO:0008696 --OBO_REL:is_a--> GO:0016829
* Copied GO:0008696 to GO:0016833 with type OBO_REL:is_a
* Added synonym "nitric oxide synthase-dystrophin complex, skeletal muscle" to GO:0016013
* Added general dbxref CORUM:416 to synonym nitric oxide synthase-dystrophin complex, skeletal muscle of GO:0016013
* Added comment "Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available."
* Changed definition of GO:0019814 from "A multiprotein complex that functions as an antibody. Immunoglobulins (Igs) are composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. The classes of Ig are IgA, IgD, IgE, IgG and IgM; they may be embedded in the plasma membrane or circulate in the blood or lymph." to "A protein complex that in its canonical form is composed of two
identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph."
* Deleted definition dbxref ISBN:0140512713 from GO:0019814
* Added definition dbxref GOC:add to GO:0019814
* Added definition dbxref ISBN:0781765196 to GO:0019814
* Added synonym "antibody" to GO:0019814
* Added general dbxref GOC:add to synonym antibody of GO:0019814
* Changed synonym scope of GO:0019814 from "Related" to "Narrow"
* Added comment "Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available."
* Changed definition of GO:0019815 from "A membrane-bound antigen receptor complex consisting in its basic form of an antigen-binding subunit (the membrane immunoglobulin or mIg), comprised of two identical heavy chains and two identical light chains held together by disulfide bonds, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." to "An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins."
* Added definition dbxref GOC:add to GO:0019815
* Deleted synonym "BCR" from GO:0019815
* Added synonym "antibody" to GO:0019815
* Added general dbxref GOC:mah to synonym antibody of GO:0019815
* Added synonym "BCR complex" to GO:0019815
* Changed synonym scope of GO:0019815 from "Related" to "Exact"
* Deleted GO:0019815 --part_of--> GO:0001772
* Deleted GO:0030509 --OBO_REL:is_a--> GO:0007178
* Copied GO:0030509 to GO:0007179 with type OBO_REL:is_a
* Changed name of GO:0031011 from "INO80 complex" to "Ino80 complex"
* Copied GO:0031011 to GO:0000790 with type part_of
* Copied GO:0034967 to GO:0000790 with type part_of
* Deleted GO:0042101 --part_of--> GO:0001772
* Added comment "Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available."
* Changed definition of GO:0042571 from "A multi-subunit complex that functions as an antibody and circulates in the blood, lymph, mucosal areas, and other fluids of the body. In its basic form, circulating immunoglobulin is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms are polymers of the basic structure and contain additional components such as J-chain and the secretory component." to "An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph.  In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds.  Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component."
* Added definition dbxref GOC:add to GO:0042571
* Added synonym "antibody" to GO:0042571
* Added general dbxref GOC:add to synonym antibody of GO:0042571
* Changed synonym scope of GO:0042571 from "Related" to "Exact"
* Copied GO:0046482 to GO:0046655 with type part_of