[Go-diff] GO update 03/20/2009

Fri Mar 20 21:30:50 PDT 2009

OBODIFF of gene_ontology_write.obo version 1.482 by 1.483

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0070514
* Created object of type obo:TERM with id GO:0070515
* Created object of type obo:TERM with id GO:0070516
* Created object of type obo:TERM with id GO:0070517
* Created object of type obo:TERM with id GO:0070518
* Created object of type obo:TERM with id GO:0070519
* Created object of type obo:TERM with id GO:0070520
* Created object of type obo:TERM with id GO:0070521
* Created object of type obo:TERM with id GO:0070522
* Populated new object GO:0070514 (macro)
  * Changed name of GO:0070514 from "<new term>" to "SRF-myogenin-E12 complex"
  * Set definition of GO:0070514 to "A transcription factor complex that contains the serum response factor (SRF) and the basic helix-loop-helix proteins myogenin and E12, and is involved in activating transcription of muscle-specific genes."
  * Added definition dbxref PMID:8617811 to GO:0070514
  * Copied GO:0070514 to GO:0044428 with type OBO_REL:is_a
  * Copied GO:0070514 to GO:0005667 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070514
* Populated new object GO:0070515 (macro)
  * Changed name of GO:0070515 from "<new term>" to "alphaIIb-beta3 integrin-talin complex"
  * Set definition of GO:0070515 to "A protein complex that consists of an alphaIIb-beta3 integrin complex bound to talin."
  * Added definition dbxref PMID:8663236 to GO:0070515
  * Added synonym "ITGA2b-ITGB3-TLN1 complex" to GO:0070515
  * Added general dbxref CORUM:2378 to synonym ITGA2b-ITGB3-TLN1 complex of GO:0070515
  * Changed synonym scope of GO:0070515 from "Related" to "Narrow"
  * Copied GO:0070515 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0070515 to GO:0044459 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070515
* Populated new object GO:0070516 (macro)
  * Changed name of GO:0070516 from "<new term>" to "CAK-ERCC2 complex"
  * Set definition of GO:0070516 to "A protein complex formed by the association of the cyclin-dependent protein kinase activating kinase (CAK) holoenzyme complex with ERCC2."
  * Added definition dbxref PMID:8692841 to GO:0070516
  * Added definition dbxref PMID:8692842 to GO:0070516
  * Added synonym "cyclin-dependent protein kinase activating kinase holoenzyme-ERCC2 complex" to GO:0070516
  * Added general dbxref GOC:mah to synonym cyclin-dependent protein kinase activating kinase holoenzyme-ERCC2 complex of GO:0070516
  * Changed synonym scope of GO:0070516 from "Related" to "Exact"
  * Copied GO:0070516 to GO:0044428 with type OBO_REL:is_a
  * Copied GO:0070516 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070516
* Populated new object GO:0070517 (macro)
  * Changed name of GO:0070517 from "<new term>" to "DNA replication factor C core complex"
  * Set definition of GO:0070517 to "A protein complex containing three of the five subunits of eukaryotic replication factor C, those corresponding to human p40, p38, and p37."
  * Added definition dbxref PMID:8692848 to GO:0070517
  * Added definition dbxref PMID:9228079 to GO:0070517
  * Added definition dbxref PMID:9582326 to GO:0070517
  * Added GO:0070517 to category goslim_pir
  * Added GO:0070517 to category gosubset_prok
  * Added synonym "RFC core complex" to GO:0070517
  * Added general dbxref CORUM:278 to synonym RFC core complex of GO:0070517
  * Changed synonym scope of GO:0070517 from "Related" to "Exact"
  * Copied GO:0070517 to GO:0043599 with type part_of
  * Copied GO:0070517 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0070517 to GO:0044427 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070517
* Populated new object GO:0070518 (macro)
  * Changed name of GO:0070518 from "<new term>" to "alpha4-beta1 integrin-CD53 complex"
  * Set definition of GO:0070518 to "A protein complex that consists of an alpha4-beta1 integrin complex bound to membrane protein CD53, a member of the tetraspan family."
  * Added definition dbxref PMID:8757325 to GO:0070518
  * Added synonym "ITGA4-ITGB1-CD53 complex" to GO:0070518
  * Added general dbxref CORUM:2420 to synonym ITGA4-ITGB1-CD53 complex of GO:0070518
  * Changed synonym scope of GO:0070518 from "Related" to "Narrow"
  * Copied GO:0070518 to GO:0043234 with type OBO_REL:is_a
  * Copied GO:0070518 to GO:0044459 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070518
* Populated new object GO:0070519 (macro)
  * Changed name of GO:0070519 from "<new term>" to "alpha4-beta1 integrin-CD63 complex"
  * Set definition of GO:0070519 to "A protein complex that consists of an alpha4-beta1 integrin complex bound to membrane protein CD63, a member of the tetraspan family."
  * Added definition dbxref PMID:8757325 to GO:0070519
  * Added synonym "ITGA4-ITGB1-CD63 complex" to GO:0070519
  * Added general dbxref CORUM:2424 to synonym ITGA4-ITGB1-CD63 complex of GO:0070519
  * Changed synonym scope of GO:0070519 from "Related" to "Narrow"
  * Copied GO:0070519 to GO:0044459 with type OBO_REL:is_a
  * Copied GO:0070519 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070519
* Populated new object GO:0070520 (macro)
  * Changed name of GO:0070520 from "<new term>" to "alpha4-beta1 integrin-CD81 complex"
  * Set definition of GO:0070520 to "A protein complex that consists of an alpha4-beta1 integrin complex bound to membrane protein CD81, a member of the tetraspan family."
  * Added definition dbxref PMID:10229664 to GO:0070520
  * Added definition dbxref PMID:8757325 to GO:0070520
  * Added synonym "ITGA4-ITGB1-CD81 complex" to GO:0070520
  * Added general dbxref CORUM:2419 to synonym ITGA4-ITGB1-CD81 complex of GO:0070520
  * Changed synonym scope of GO:0070520 from "Related" to "Narrow"
  * Copied GO:0070520 to GO:0044459 with type OBO_REL:is_a
  * Copied GO:0070520 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070520
* Populated new object GO:0070521 (macro)
  * Changed name of GO:0070521 from "<new term>" to "alpha4-beta1 integrin-CD82 complex"
  * Set definition of GO:0070521 to "A protein complex that consists of an alpha4-beta1 integrin complex bound to membrane protein CD82, a member of the tetraspan family."
  * Added definition dbxref PMID:8757325 to GO:0070521
  * Copied GO:0070521 to GO:0044459 with type OBO_REL:is_a
  * Copied GO:0070521 to GO:0043234 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070521
* Populated new object GO:0070522 (macro)
  * Changed name of GO:0070522 from "<new term>" to "ERCC4-ERCC1 complex"
  * Added comment "Note that process and function information are included in the term and definition for the purpose of describing and distinguishing the complex."
  * Set definition of GO:0070522 to "A heterodimeric protein complex that has endonuclease activity specific for bubble structures characteristic of certain DNA lesions. The subunits are konw as XPF/ERCC4 and ERCC1 in mammals, and Rad1p and Rad10p in S. cerevisiae."
  * Added definition dbxref PMID:14734547 to GO:0070522
  * Added synonym "Rad1-Rad10 complex" to GO:0070522
  * Added general dbxref GOC:mah to synonym Rad1-Rad10 complex of GO:0070522
  * Changed synonym scope of GO:0070522 from "Related" to "Exact"
  * Added synonym "XPF-ERCC1 complex" to GO:0070522
  * Added general dbxref PMID:14734547 to synonym XPF-ERCC1 complex of GO:0070522
  * Changed synonym scope of GO:0070522 from "Related" to "Exact"
  * Copied GO:0070522 to GO:0000109 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070522
* Changed definition of GO:0000214 from "A complex that catalyzes the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron." to "A protein complex that catalyzes the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron."
* Changed definition of GO:0000438 from "The core TFIIH complex when it is part of the general transcription factor TFIIH. In S. cerevisiae, it is composed of Rad3p, Tfb1p, Tfb2p, Ssl1p and Tfb4p. In humans, it is composed of XPD, p62, p55, p44, p34." to "The core TFIIH complex when it is part of the general transcription factor TFIIH. In S. cerevisiae, it is composed of Rad3p, Tfb1p, Tfb2p, Ssl1p and Tfb4p. In humans, it is composed of ERCC2, p62, p55, p44, p34."
* Changed definition of GO:0000439 from "A complex that contains kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. In S. cerevisiae, it is composed of the 5-subunit core (Rad3p, Tfb1p, Tfb2p, Ssl1p and Tfb4p), Ssl2p, and TFIIK (Kin28p, Ccl1p, and Tfb3p). All of the subunits have equivalents in humans: the 5 subunit core is composed of XPD, p62, p55, p44, p34; the equivalent of the TFIIK subcomplex is composed of MO15, Mat1, and a cyclin; the human equivalent of Ssl2p is XPB." to "A complex that contains kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. In S. cerevisiae, it is composed of the 5-subunit core (Rad3p, Tfb1p, Tfb2p, Ssl1p and Tfb4p), Ssl2p, and TFIIK (Kin28p, Ccl1p, and Tfb3p). All of the subunits have equivalents in humans: the 5 subunit core is composed of ERCC2, p62, p55, p44, p34; the equivalent of the TFIIK subcomplex is composed of MO15, Mat1, and a cyclin; the human equivalent of Ssl2p is XPB."
* Changed definition of GO:0000440 from "The core TFIIH complex when it is part of the nucleotide-excision repair factor 3 (NEF3). In S. cerevisiae, it is composed of Rad3p, Tfb1p, Tfb2p, Ssl1p, and Tfb4p. In humans, it is composed of XPD, p62, p55, p44, p34." to "The core TFIIH complex when it is part of the nucleotide-excision repair factor 3 (NEF3). In S. cerevisiae, it is composed of Rad3p, Tfb1p, Tfb2p, Ssl1p, and Tfb4p. In humans, it is composed of ERCC2, p62, p55, p44, p34."
* Changed definition of GO:0000441 from "A complex which is part of both the general transcription factor TFIIH and the nucleotide-excision repair factor 3 complex. It is composed of the tightly associated 5 subunit core TFIIH subcomplex plus one additional, more loosely associated subunit. The subunits are well conserved from yeast to humans. In S. cerevisiae, the 5-subunit core is composed of Rad3, Tfb1, Tfb2, Ssl1, Tfb4 and the loosely associated subunit is Ssl2p (also called Rad25). In humans, the 5 subunit core is composed of XPD, p62, p55, p44, p34 and the loosely associated subunit is XPB." to "A complex which is part of both the general transcription factor TFIIH and the nucleotide-excision repair factor 3 complex. It is composed of the tightly associated 5 subunit core TFIIH subcomplex plus one additional, more loosely associated subunit. The subunits are well conserved from yeast to humans. In S. cerevisiae, the 5-subunit core is composed of Rad3, Tfb1, Tfb2, Ssl1, Tfb4 and the loosely associated subunit is Ssl2p (also called Rad25). In humans, the 5 subunit core is composed of ERCC2, p62, p55, p44, p34 and the loosely associated subunit is XPB."
* Changed definition of GO:0000442 from "The SSL2-core TFIIH complex when it is part of the nucleotide-excision repair factor 3 (NEF3). It is composed of the tightly associated 5 subunit core TFIIH subcomplex plus one additional, less tighly associated subunit. The subunits are well conserved from yeast to humans. In S. cerevisiae, the 5-subunit core is composed of Rad3, Tfb1, Tfb2, Ssl1, Tfb4 and the loosely associated subunit is Ssl2p (also called Rad25). In humans, the 5 subunit core is composed of XPD, p62, p55, p44, p34 and the loosely associated subunit is XPB." to "The SSL2-core TFIIH complex when it is part of the nucleotide-excision repair factor 3 (NEF3). It is composed of the tightly associated 5 subunit core TFIIH subcomplex plus one additional, less tighly associated subunit. The subunits are well conserved from yeast to humans. In S. cerevisiae, the 5-subunit core is composed of Rad3, Tfb1, Tfb2, Ssl1, Tfb4 and the loosely associated subunit is Ssl2p (also called Rad25). In humans, the 5 subunit core is composed of ERCC2, p62, p55, p44, p34 and the loosely associated subunit is XPB."
* Changed definition of GO:0000443 from "The SSL2-core TFIIH complex when it is part of the general transcription factor TFIIH. It is composed of the tightly associated five subunit core TFIIH subcomplex plus one additional, less tighly associated subunit. The subunits are well conserved from yeast to humans. In S. cerevisiae, the 5-subunit core is composed of Rad3, Tfb1, Tfb2, Ssl1, Tfb4 and the loosely associated subunit is Ssl2p (also called Rad25). In humans, the 5 subunit core is composed of XPD, p62, p55, p44, p34 and the loosely associated subunit is XPB." to "The SSL2-core TFIIH complex when it is part of the general transcription factor TFIIH. It is composed of the tightly associated five subunit core TFIIH subcomplex plus one additional, less tighly associated subunit. The subunits are well conserved from yeast to humans. In S. cerevisiae, the 5-subunit core is composed of Rad3, Tfb1, Tfb2, Ssl1, Tfb4 and the loosely associated subunit is Ssl2p (also called Rad25). In humans, the 5 subunit core is composed of ERCC2, p62, p55, p44, p34 and the loosely associated subunit is XPB."
* Changed name of GO:0005668 from "selectivity factor SL1 complex" to "RNA polymerase transcription factor SL1 complex"
* Changed definition of GO:0005668 from "A RNA polymerase I-specific protein complex which in humans has two subunits, tata-binding protein (TBP) and TBP-associated factor 1 (TAF1)." to "A RNA polymerase I-specific transcription factor complex that contains the TATA-box-binding protein (TBP) and at least three TBP-associated factors including proteins known in mammals as TAFI110, TAFI63 and TAFI48."
* Deleted definition dbxref GOC:jl from GO:0005668
* Deleted definition dbxref PMID:9857193 from GO:0005668
* Added definition dbxref PMID:15691654 to GO:0005668
* Added synonym "selectivity factor SL1 complex" to GO:0005668
* Added general dbxref GOC:mah to synonym selectivity factor SL1 complex of GO:0005668
* Changed synonym scope of GO:0005668 from "Related" to "Exact"
* Added synonym "TIF-IB" to GO:0005668
* Added general dbxref CORUM:480 to synonym TIF-IB of GO:0005668
* Added general dbxref PMID:15691654 to synonym TIF-IB of GO:0005668
* Changed synonym scope of GO:0005668 from "Related" to "Exact"
* Deleted GO:0005668 --OBO_REL:is_a--> GO:0005667
* Copied GO:0005668 to GO:0000120 with type OBO_REL:is_a
* Changed definition of GO:0005675 from "A complex that contains kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. In S. cerevisiae, it is composed of the 5-subunit core (Rad3p, Tfb1p, Tfb2p, Ssl1p and Tfb4p), Ssl2p, and TFIIK (Kin28p, Ccl1p, and Tfb3p). All of the subunits have equivalents in humans: the 5 subunit core is composed of XPD, p62, p55, p44, p34; the equivalent of the TFIIK subcomplex is composed of MO15, Mat1, and a cyclin; the human equivalent of Ssl2p is XPB." to "A complex that contains kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. In S. cerevisiae, it is composed of the 5-subunit core (Rad3p, Tfb1p, Tfb2p, Ssl1p and Tfb4p), Ssl2p, and TFIIK (Kin28p, Ccl1p, and Tfb3p). All of the subunits have equivalents in humans: the 5 subunit core is composed of ERCC2, p62, p55, p44, p34; the equivalent of the TFIIK subcomplex is composed of MO15, Mat1, and a cyclin; the human equivalent of Ssl2p is XPB."
* Added synonym "modulator complex" to GO:0005838
* Added general dbxref CORUM:28 to synonym modulator complex of GO:0005838
* Added synonym "PA700-dependent proteasome activator" to GO:0005838
* Added general dbxref CORUM:28 to synonym PA700-dependent proteasome activator of GO:0005838
* Changed synonym scope of GO:0005838 from "Related" to "Exact"
* Added synonym "RAD50-MRE11-NBN complex" to GO:0030870
* Added general dbxref CORUM:2767 to synonym RAD50-MRE11-NBN complex of GO:0030870
* Changed synonym scope of GO:0030870 from "Related" to "Exact"
* Added synonym "RC complex" to GO:0030894
* Added general dbxref PMID:12006500 to synonym RC complex of GO:0030894
* Added general dbxref CORUM:309 to synonym RC complex of GO:0030894
* Added synonym "replication-competent complex" to GO:0030894
* Added general dbxref PMID:12006500 to synonym replication-competent complex of GO:0030894
* Added general dbxref CORUM:309 to synonym replication-competent complex of GO:0030894