[Go-diff] GO update 05/06/2008

Tue May 6 21:30:45 PDT 2008

OBODIFF of gene_ontology_write.obo version 1.54 by 1.55

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0034427
* Created object of type obo:TERM with id GO:0034428
* Created object of type obo:TERM with id GO:0034429
* Populated new object GO:0034427 (macro)
  * Changed name of GO:0034427 from "<new term>" to "nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'"
  * Set definition of GO:0034427 to "The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction."
  * Added definition dbxref GOC:krc to GO:0034427
  * Added definition dbxref GOC:mah to GO:0034427
  * Added synonym "3'-5' exonucleolytic nuclear-transcribed mRNA catabolic process" to GO:0034427
  * Changed synonym scope of GO:0034427 from "Related" to "Exact"
  * Copied GO:0034427 to GO:0000291 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034427
* Populated new object GO:0034428 (macro)
  * Changed name of GO:0034428 from "<new term>" to "nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3'"
  * Set definition of GO:0034428 to "The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 5' end is not protected by a 5'-cap; degradation proceeds in the 5' to 3' direction."
  * Added definition dbxref GOC:krc to GO:0034428
  * Added definition dbxref GOC:mah to GO:0034428
  * Added synonym "5'-3' exonucleolytic nuclear-transcribed mRNA catabolic process" to GO:0034428
  * Changed synonym scope of GO:0034428 from "Related" to "Exact"
  * Copied GO:0034428 to GO:0000291 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034428
* Populated new object GO:0034429 (macro)
  * Changed name of GO:0034429 from "<new term>" to "tectobulbar tract morphogenesis"
  * Set definition of GO:0034429 to "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the optic tectum towards target cells in the premotor reticulospinal system in the hindbrain."
  * Added definition dbxref GOC:dsf to GO:0034429
  * Added definition dbxref PMID:15065115 to GO:0034429
  * Added definition dbxref PMID:17507550 to GO:0034429
  * Added definition dbxref PMID:8038988 to GO:0034429
  * Copied GO:0034429 to GO:0021952 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0034429
* Added comment "Note that this step represents the formation of the B complex (yeast) or the A complex (mammalian)."
* added secondary id GO:0000370 to GO:0000348
* added secondary id GO:0000371 to GO:0000348
* Added synonym "spliceosomal A complex biosynthesis" to GO:0000348
* Changed synonym scope of GO:0000348 from "Related" to "Narrow"
* Added synonym "spliceosomal A complex formation" to GO:0000348
* Changed synonym scope of GO:0000348 from "Related" to "Narrow"
* Added synonym "spliceosomal B complex biosynthesis" to GO:0000348
* Changed synonym scope of GO:0000348 from "Related" to "Narrow"
* Added synonym "spliceosomal B complex formation" to GO:0000348
* Changed synonym scope of GO:0000348 from "Related" to "Narrow"
* Added synonym "U12-type nuclear mRNA branch site recognition" to GO:0000348
* Changed synonym scope of GO:0000348 from "Related" to "Narrow"
* Added synonym "U2-type nuclear mRNA branch site recognition" to GO:0000348
* Changed synonym scope of GO:0000348 from "Related" to "Narrow"
* Copied GO:0000348 to GO:0000398 with type part_of
* Added comment "Note that this step represents the formation of the A2-2 complex (yeast) or the C1 complex (mammalian)."
* added secondary id GO:0000356 to GO:0000349
* added secondary id GO:0000357 to GO:0000349
* Added synonym "spliceosomal A2-2 complex biosynthesis" to GO:0000349
* Changed synonym scope of GO:0000349 from "Related" to "Narrow"
* Added synonym "spliceosomal A2-2 complex formation" to GO:0000349
* Changed synonym scope of GO:0000349 from "Related" to "Narrow"
* Added synonym "spliceosomal C1 complex biosynthesis" to GO:0000349
* Changed synonym scope of GO:0000349 from "Related" to "Narrow"
* Added synonym "spliceosomal C1 complex formation" to GO:0000349
* Changed synonym scope of GO:0000349 from "Related" to "Narrow"
* Added synonym "U12-type catalytic spliceosome formation for first transesterification step" to GO:0000349
* Changed synonym scope of GO:0000349 from "Related" to "Narrow"
* Added synonym "U2-type catalytic spliceosome formation for first transesterification step" to GO:0000349
* Changed synonym scope of GO:0000349 from "Related" to "Narrow"
* Copied GO:0000349 to GO:0000398 with type part_of
* Added comment "Note that this step represents formation of the A2-3 complex (yeast) or the C2 complex (mammalian)."
* added secondary id GO:0000358 to GO:0000350
* added secondary id GO:0000359 to GO:0000350
* Added synonym "formation of catalytic U12-type spliceosome for second transesterification step" to GO:0000350
* Changed synonym scope of GO:0000350 from "Related" to "Narrow"
* Added synonym "formation of catalytic U2-type spliceosome for second transesterification step" to GO:0000350
* Changed synonym scope of GO:0000350 from "Related" to "Narrow"
* Added synonym "spliceosomal A2-3 complex biosynthesis" to GO:0000350
* Changed synonym scope of GO:0000350 from "Related" to "Narrow"
* Added synonym "spliceosomal A2-3 complex formation" to GO:0000350
* Changed synonym scope of GO:0000350 from "Related" to "Narrow"
* Added synonym "spliceosomal C2 complex biosynthesis" to GO:0000350
* Changed synonym scope of GO:0000350 from "Related" to "Narrow"
* Added synonym "spliceosomal C2 complex formation" to GO:0000350
* Changed synonym scope of GO:0000350 from "Related" to "Narrow"
* Copied GO:0000350 to GO:0000398 with type part_of
* Deleted GO:0000351 --part_of--> GO:0006374
* Copied GO:0000351 to GO:0000398 with type part_of
* Added comment "Note that this step represents formation of the A2-1 complex (yeast) or the B1 complex (mammals)."
* added secondary id GO:0000360 to GO:0000354
* added secondary id GO:0000361 to GO:0000354
* Added synonym "cis assembly of U12-type pre-catalytic spliceosome" to GO:0000354
* Changed synonym scope of GO:0000354 from "Related" to "Narrow"
* Added synonym "cis assembly of U2-type pre-catalytic spliceosome" to GO:0000354
* Changed synonym scope of GO:0000354 from "Related" to "Narrow"
* Added synonym "spliceosomal A2-1 complex biosynthesis" to GO:0000354
* Changed synonym scope of GO:0000354 from "Related" to "Narrow"
* Added synonym "spliceosomal A2-1 complex formation" to GO:0000354
* Changed synonym scope of GO:0000354 from "Related" to "Narrow"
* Added synonym "spliceosomal B1 complex biosynthesis" to GO:0000354
* Changed synonym scope of GO:0000354 from "Related" to "Narrow"
* Added synonym "spliceosomal B1 complex formation" to GO:0000354
* Changed synonym scope of GO:0000354 from "Related" to "Narrow"
* Copied GO:0000354 to GO:0000398 with type part_of
* Copied GO:0000354 to GO:0045292 with type part_of
* Deleted GO:0000355 --part_of--> GO:0006375
* Copied GO:0000355 to GO:0000398 with type part_of
* Deleted GO:0000356 --OBO_REL:is_a--> GO:0000349
* Deleted GO:0000356 --part_of--> GO:0006374
* Destroyed object GO:0000356
* Deleted GO:0000357 --part_of--> GO:0006375
* Deleted GO:0000357 --OBO_REL:is_a--> GO:0000349
* Destroyed object GO:0000357
* Deleted GO:0000358 --OBO_REL:is_a--> GO:0000350
* Deleted GO:0000358 --part_of--> GO:0006374
* Destroyed object GO:0000358
* Deleted GO:0000359 --part_of--> GO:0006375
* Deleted GO:0000359 --OBO_REL:is_a--> GO:0000350
* Destroyed object GO:0000359
* Deleted GO:0000360 --OBO_REL:is_a--> GO:0000354
* Deleted GO:0000360 --part_of--> GO:0045292
* Destroyed object GO:0000360
* Deleted GO:0000361 --OBO_REL:is_a--> GO:0000354
* Deleted GO:0000361 --part_of--> GO:0006375
* Destroyed object GO:0000361
* Changed name of GO:0000365 from "nuclear mRNA trans splicing, via U2-type spliceosome" to "nuclear mRNA trans splicing, via spliceosome"
* Added synonym "nuclear mRNA trans splicing, via U2-type spliceosome" to GO:0000365
* Changed synonym scope of GO:0000365 from "Related" to "Narrow"
* Deleted GO:0000365 --OBO_REL:is_a--> GO:0006374
* Copied GO:0000365 to GO:0000398 with type OBO_REL:is_a
* Deleted GO:0000368 --part_of--> GO:0045292
* Deleted GO:0000368 --OBO_REL:is_a--> GO:0000395
* Destroyed object GO:0000368
* Deleted GO:0000369 --part_of--> GO:0006375
* Deleted GO:0000369 --OBO_REL:is_a--> GO:0000395
* Destroyed object GO:0000369
* Deleted GO:0000370 --OBO_REL:is_a--> GO:0000348
* Deleted GO:0000370 --part_of--> GO:0006374
* Destroyed object GO:0000370
* Deleted GO:0000371 --OBO_REL:is_a--> GO:0000348
* Deleted GO:0000371 --part_of--> GO:0006375
* Destroyed object GO:0000371
* Deleted GO:0000382 --OBO_REL:is_a--> GO:0000389
* Deleted GO:0000382 --part_of--> GO:0006375
* Destroyed object GO:0000382
* Deleted GO:0000383 --OBO_REL:is_a--> GO:0000389
* Deleted GO:0000383 --part_of--> GO:0006374
* Destroyed object GO:0000383
* Added comment "Note that this step represents formation of the A1 complex (yeast) or the B2 complex (mammalian)."
* added secondary id GO:0000396 to GO:0000388
* added secondary id GO:0000397 to GO:0000388
* Added synonym "spliceosomal A1 complex biosynthesis" to GO:0000388
* Changed synonym scope of GO:0000388 from "Related" to "Narrow"
* Added synonym "spliceosomal A1 complex formation" to GO:0000388
* Changed synonym scope of GO:0000388 from "Related" to "Narrow"
* Added synonym "spliceosomal B2 complex biosynthesis" to GO:0000388
* Changed synonym scope of GO:0000388 from "Related" to "Narrow"
* Added synonym "spliceosomal B2 complex formation" to GO:0000388
* Changed synonym scope of GO:0000388 from "Related" to "Narrow"
* Added synonym "U12-type spliceosome conformational change to release U4atac and U11" to GO:0000388
* Changed synonym scope of GO:0000388 from "Related" to "Narrow"
* Added synonym "U2-type spliceosome conformational change to release U4 and U1" to GO:0000388
* Changed synonym scope of GO:0000388 from "Related" to "Narrow"
* added secondary id GO:0000382 to GO:0000389
* added secondary id GO:0000383 to GO:0000389
* Added synonym "U12-type nuclear mRNA 3'-splice site recognition" to GO:0000389
* Changed synonym scope of GO:0000389 from "Related" to "Narrow"
* Added synonym "U2-type nuclear mRNA 3'-splice site recognition" to GO:0000389
* Changed synonym scope of GO:0000389 from "Related" to "Narrow"
* Copied GO:0000389 to GO:0000398 with type part_of
* added secondary id GO:0000391 to GO:0000390
* added secondary id GO:0000392 to GO:0000390
* Added synonym "U12-type spliceosome disassembly" to GO:0000390
* Changed synonym scope of GO:0000390 from "Related" to "Narrow"
* Added synonym "U2-type spliceosome disassembly" to GO:0000390
* Changed synonym scope of GO:0000390 from "Related" to "Narrow"
* Deleted GO:0000391 --part_of--> GO:0006374
* Deleted GO:0000391 --OBO_REL:is_a--> GO:0000390
* Destroyed object GO:0000391
* Deleted GO:0000392 --part_of--> GO:0006375
* Deleted GO:0000392 --OBO_REL:is_a--> GO:0000390
* Destroyed object GO:0000392
* Added comment "Note that this step represents formation of the Commitment Complex (CC, in yeast) or the E complex (mammalian)."
* added secondary id GO:0000368 to GO:0000395
* added secondary id GO:0000369 to GO:0000395
* Added synonym "spliceosomal CC complex biosynthesis" to GO:0000395
* Changed synonym scope of GO:0000395 from "Related" to "Narrow"
* Added synonym "spliceosomal CC complex formation" to GO:0000395
* Changed synonym scope of GO:0000395 from "Related" to "Narrow"
* Added synonym "spliceosomal commitment complex biosynthesis" to GO:0000395
* Changed synonym scope of GO:0000395 from "Related" to "Narrow"
* Added synonym "spliceosomal commitment complex formation" to GO:0000395
* Changed synonym scope of GO:0000395 from "Related" to "Narrow"
* Added synonym "spliceosomal E complex biosynthesis" to GO:0000395
* Changed synonym scope of GO:0000395 from "Related" to "Narrow"
* Added synonym "spliceosomal E complex formation" to GO:0000395
* Changed synonym scope of GO:0000395 from "Related" to "Narrow"
* Added synonym "U12-type nuclear mRNA 5' splice site recognition" to GO:0000395
* Changed synonym scope of GO:0000395 from "Related" to "Narrow"
* Added synonym "U12-type nuclear mRNA 5'-splice site recognition" to GO:0000395
* Changed synonym scope of GO:0000395 from "Related" to "Narrow"
* Added synonym "U2-type nuclear mRNA 5' splice site recognition" to GO:0000395
* Changed synonym scope of GO:0000395 from "Related" to "Narrow"
* Added synonym "U2-type nuclear mRNA 5'-splice site recognition" to GO:0000395
* Changed synonym scope of GO:0000395 from "Related" to "Narrow"
* Copied GO:0000395 to GO:0000398 with type part_of
* Copied GO:0000395 to GO:0045292 with type part_of
* Deleted GO:0000396 --part_of--> GO:0006374
* Deleted GO:0000396 --OBO_REL:is_a--> GO:0000388
* Destroyed object GO:0000396
* Deleted GO:0000397 --part_of--> GO:0006375
* Deleted GO:0000397 --OBO_REL:is_a--> GO:0000388
* Destroyed object GO:0000397
* Added comment "Note that although the many U12-type introns have the sequence AT-AC at the intron termini, some introns with these terminal sequences are spliced by the U2-type spliceosome. The distinguishing characteristics are sequences near the 5' splice site and the branch point sequences of the intron. Note that although the majority of U2-type introns have the sequence GU-AG at the intron termini, some introns with these terminal sequences are spliced by the U12-type spliceosome. The distinguishing characteristics are sequences near the 5' splice site and the branch point sequences of the intron."
* added secondary id GO:0006374 to GO:0000398
* added secondary id GO:0006375 to GO:0000398
* Added synonym "nuclear mRNA splicing via U12-type spliceosome" to GO:0000398
* Changed synonym scope of GO:0000398 from "Related" to "Narrow"
* Added synonym "nuclear mRNA splicing via U2-type spliceosome" to GO:0000398
* Changed synonym scope of GO:0000398 from "Related" to "Narrow"
* Added synonym "splicing AT-AC intron" to GO:0000398
* Added synonym "splicing GT-AG intron" to GO:0000398
* Deleted GO:0003721 --OBO_REL:is_a--> GO:0003720
* Copied GO:0003721 to GO:0003964 with type OBO_REL:is_a
* Copied GO:0003721 to GO:0003720 with type part_of
* Deleted GO:0006374 --OBO_REL:is_a--> GO:0000398
* Deleted GO:0000351 --part_of--> GO:0006374
* Deleted GO:0035056 --negatively_regulates--> GO:0006374
* Deleted GO:0000383 --part_of--> GO:0006374
* Deleted GO:0000365 --OBO_REL:is_a--> GO:0006374
* Deleted GO:0000391 --part_of--> GO:0006374
* Deleted GO:0035055 --regulates--> GO:0006374
* Deleted GO:0000396 --part_of--> GO:0006374
* Deleted GO:0000356 --part_of--> GO:0006374
* Deleted GO:0045292 --OBO_REL:is_a--> GO:0006374
* Deleted GO:0000358 --part_of--> GO:0006374
* Deleted GO:0000370 --part_of--> GO:0006374
* Deleted GO:0035057 --positively_regulates--> GO:0006374
* Destroyed object GO:0006374
* Deleted GO:0006375 --OBO_REL:is_a--> GO:0000398
* Deleted GO:0000369 --part_of--> GO:0006375
* Deleted GO:0000359 --part_of--> GO:0006375
* Deleted GO:0000355 --part_of--> GO:0006375
* Deleted GO:0000357 --part_of--> GO:0006375
* Deleted GO:0000392 --part_of--> GO:0006375
* Deleted GO:0000397 --part_of--> GO:0006375
* Deleted GO:0000361 --part_of--> GO:0006375
* Deleted GO:0000382 --part_of--> GO:0006375
* Deleted GO:0000371 --part_of--> GO:0006375
* Destroyed object GO:0006375
* Deleted GO:0006621 --OBO_REL:is_a--> GO:0045185
* Deleted synonym "T3SS complex" from GO:0031522
* Deleted synonym "TTSS complex" from GO:0031522
* Deleted GO:0034424 --part_of--> GO:0005789
* Copied GO:0034424 to GO:0010008 with type part_of
* Deleted GO:0035055 --regulates--> GO:0006374
* Deleted GO:0035055 --OBO_REL:is_a--> GO:0048024
* Deleted GO:0035056 --OBO_REL:is_a--> GO:0035055
* Deleted GO:0035057 --OBO_REL:is_a--> GO:0035055
* Destroyed object GO:0035055
* Deleted GO:0035056 --OBO_REL:is_a--> GO:0048025
* Deleted GO:0035056 --negatively_regulates--> GO:0006374
* Deleted GO:0035056 --OBO_REL:is_a--> GO:0035055
* Destroyed object GO:0035056
* Deleted GO:0035057 --OBO_REL:is_a--> GO:0035055
* Deleted GO:0035057 --OBO_REL:is_a--> GO:0048026
* Deleted GO:0035057 --positively_regulates--> GO:0006374
* Destroyed object GO:0035057
* Set definition of GO:0042150 to "A process of DNA recombination occuring within a plasmid or between plasmids and other plasmids or DNA molecules."
* Added definition dbxref GOC:mlg to GO:0042150
* Deleted GO:0045053 --OBO_REL:is_a--> GO:0045185
* Changed name of GO:0045292 from "nuclear mRNA cis splicing, via U2-type spliceosome" to "nuclear mRNA cis splicing, via spliceosome"
* Changed definition of GO:0045292 from "The joining together, after removal of an intervening sequence composed of one or more introns, of two segments of the same RNA molecule via U2-type spliceosomal catalysis to produce an mRNA composed only of exon sequences that all came from the same primary transcript." to "The joining together, after removal of an intervening sequence composed of one or more introns, of two segments of the same RNA molecule via spliceosomal catalysis to produce an mRNA composed only of exon sequences that all came from the same primary transcript."
* Added synonym "nuclear mRNA cis splicing, via U2-type spliceosome" to GO:0045292
* Changed synonym scope of GO:0045292 from "Related" to "Narrow"
* Deleted GO:0045292 --OBO_REL:is_a--> GO:0006374
* Copied GO:0045292 to GO:0000398 with type OBO_REL:is_a
* added secondary id GO:0035055 to GO:0048024
* Added synonym "regulation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048024
* Changed synonym scope of GO:0048024 from "Related" to "Narrow"
* added secondary id GO:0035056 to GO:0048025
* Added synonym "down regulation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048025
* Changed synonym scope of GO:0048025 from "Related" to "Narrow"
* Added synonym "down-regulation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048025
* Changed synonym scope of GO:0048025 from "Related" to "Narrow"
* Added synonym "downregulation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048025
* Changed synonym scope of GO:0048025 from "Related" to "Narrow"
* Added synonym "inhibition of nuclear mRNA splicing via U2-type spliceosome" to GO:0048025
* Changed synonym scope of GO:0048025 from "Related" to "Narrow"
* Added synonym "negative regulation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048025
* Changed synonym scope of GO:0048025 from "Related" to "Narrow"
* added secondary id GO:0035057 to GO:0048026
* Added synonym "activation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048026
* Changed synonym scope of GO:0048026 from "Related" to "Narrow"
* Added synonym "positive regulation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048026
* Changed synonym scope of GO:0048026 from "Related" to "Narrow"
* Added synonym "stimulation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048026
* Changed synonym scope of GO:0048026 from "Related" to "Narrow"
* Added synonym "up regulation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048026
* Changed synonym scope of GO:0048026 from "Related" to "Narrow"
* Added synonym "up-regulation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048026
* Changed synonym scope of GO:0048026 from "Related" to "Narrow"
* Added synonym "upregulation of nuclear mRNA splicing via U2-type spliceosome" to GO:0048026
* Changed synonym scope of GO:0048026 from "Related" to "Narrow"