[Go-diff] GO update 03/04/2009

Remote CVS for Gene Ontology gocvs at genome.stanford.edu
Wed Mar 4 21:30:49 PST 2009 

OBODIFF of gene_ontology_write.obo version 1.464 by 1.465

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0070477
* Created object of type obo:TERM with id GO:0070478
* Created object of type obo:TERM with id GO:0070479
* Created object of type obo:TERM with id GO:0070480
* Created object of type obo:TERM with id GO:0070481
* Populated new object GO:0070477 (macro)
  * Changed name of GO:0070477 from "<new term>" to "endospore core"
  * Set definition of GO:0070477 to "An intracellular part that represents the innermost portion of an endospore; the endospore core is dehydrated, enriched in dipicolinic acid and divaletn cations, and metabolically inactive."
  * Added definition dbxref GOC:mah to GO:0070477
  * Added definition dbxref PMID:15035041 to GO:0070477
  * Added definition dbxref PMID:18035610 to GO:0070477
  * Copied GO:0070477 to GO:0044424 with type OBO_REL:is_a
  * Assigned namespace "cellular_component" to GO:0070477
* Populated new object GO:0070478 (macro)
  * Changed name of GO:0070478 from "<new term>" to "nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay"
  * Set definition of GO:0070478 to "The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; 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 PMID:12769863 to GO:0070478
  * Added synonym "3'-5' NMD" to GO:0070478
  * Added general dbxref GOC:jp to synonym 3'-5' NMD of GO:0070478
  * Changed synonym scope of GO:0070478 from "Related" to "Exact"
  * Added synonym "3'-5' nonsense-mediated decay" to GO:0070478
  * Added general dbxref GOC:jp to synonym 3'-5' nonsense-mediated decay of GO:0070478
  * Changed synonym scope of GO:0070478 from "Related" to "Exact"
  * Added synonym "3'-5' nonsense-mediated mRNA decay" to GO:0070478
  * Added general dbxref GOC:jp to synonym 3'-5' nonsense-mediated mRNA decay of GO:0070478
  * Changed synonym scope of GO:0070478 from "Related" to "Exact"
  * Added synonym "nuclear-transcribed mRNA breakdown, 3'-5' exonucleolytic nonsense-mediated decay" to GO:0070478
  * Added general dbxref GOC:mah to synonym nuclear-transcribed mRNA breakdown, 3'-5' exonucleolytic nonsense-mediated decay of GO:0070478
  * Changed synonym scope of GO:0070478 from "Related" to "Exact"
  * Added synonym "nuclear-transcribed mRNA catabolism, 3'-5' exonucleolytic nonsense-mediated decay" to GO:0070478
  * Added general dbxref GOC:mah to synonym nuclear-transcribed mRNA catabolism, 3'-5' exonucleolytic nonsense-mediated decay of GO:0070478
  * Changed synonym scope of GO:0070478 from "Related" to "Exact"
  * Added synonym "nuclear-transcribed mRNA degradation, 3'-5' exonucleolytic nonsense-mediated decay" to GO:0070478
  * Added general dbxref GOC:mah to synonym nuclear-transcribed mRNA degradation, 3'-5' exonucleolytic nonsense-mediated decay of GO:0070478
  * Changed synonym scope of GO:0070478 from "Related" to "Exact"
  * Copied GO:0070478 to GO:0034427 with type OBO_REL:is_a
  * Copied GO:0070478 to GO:0043928 with type OBO_REL:is_a
  * Copied GO:0070478 to GO:0000184 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070478
* Populated new object GO:0070479 (macro)
  * Changed name of GO:0070479 from "<new term>" to "nuclear-transcribed mRNA catabolic process, 5'-3' exonucleolytic nonsense-mediated decay"
  * Set definition of GO:0070479 to "The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; occurs when the 5' end is not protected by a 5'-cap; degradation proceeds in the 5' to 3' direction.'"
  * Added definition dbxref PMID:18554525 to GO:0070479
  * Added synonym "5'-3' NMD" to GO:0070479
  * Added general dbxref GOC:jp to synonym 5'-3' NMD of GO:0070479
  * Changed synonym scope of GO:0070479 from "Related" to "Exact"
  * Added synonym "5'-3' nonsense-mediated decay" to GO:0070479
  * Added general dbxref GOC:jp to synonym 5'-3' nonsense-mediated decay of GO:0070479
  * Changed synonym scope of GO:0070479 from "Related" to "Exact"
  * Added synonym "5'-3' nonsense-mediated mRNA decay" to GO:0070479
  * Added general dbxref GOC:jp to synonym 5'-3' nonsense-mediated mRNA decay of GO:0070479
  * Changed synonym scope of GO:0070479 from "Related" to "Exact"
  * Added synonym "nuclear-transcribed mRNA breakdown, 5'-3' exonucleolytic nonsense-mediated decay" to GO:0070479
  * Added general dbxref GOC:mah to synonym nuclear-transcribed mRNA breakdown, 5'-3' exonucleolytic nonsense-mediated decay of GO:0070479
  * Changed synonym scope of GO:0070479 from "Related" to "Exact"
  * Added synonym "nuclear-transcribed mRNA catabolism, 5'-3' exonucleolytic nonsense-mediated decay" to GO:0070479
  * Added general dbxref GOC:mah to synonym nuclear-transcribed mRNA catabolism, 5'-3' exonucleolytic nonsense-mediated decay of GO:0070479
  * Changed synonym scope of GO:0070479 from "Related" to "Exact"
  * Added synonym "nuclear-transcribed mRNA degradation, 5'-3' exonucleolytic nonsense-mediated decay" to GO:0070479
  * Added general dbxref GOC:mah to synonym nuclear-transcribed mRNA degradation, 5'-3' exonucleolytic nonsense-mediated decay of GO:0070479
  * Changed synonym scope of GO:0070479 from "Related" to "Exact"
  * Copied GO:0070479 to GO:0000184 with type OBO_REL:is_a
  * Copied GO:0070479 to GO:0070480 with type OBO_REL:is_a
  * Copied GO:0070479 to GO:0034428 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070479
* Populated new object GO:0070480 (macro)
  * Changed name of GO:0070480 from "<new term>" to "exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-independent decay"
  * Set definition of GO:0070480 to "The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 5'-cap."
  * Added definition dbxref GOC:jp to GO:0070480
  * Added synonym "exonucleolytic nuclear-transcribed mRNA breakdown involved in deadenylation-independent decay" to GO:0070480
  * Added general dbxref GOC:mah to synonym exonucleolytic nuclear-transcribed mRNA breakdown involved in deadenylation-independent decay of GO:0070480
  * Changed synonym scope of GO:0070480 from "Related" to "Exact"
  * Added synonym "exonucleolytic nuclear-transcribed mRNA catabolism involved in deadenylation-independent decay" to GO:0070480
  * Added general dbxref GOC:mah to synonym exonucleolytic nuclear-transcribed mRNA catabolism involved in deadenylation-independent decay of GO:0070480
  * Changed synonym scope of GO:0070480 from "Related" to "Exact"
  * Added synonym "exonucleolytic nuclear-transcribed mRNA degradation involved in deadenylation-independent decay" to GO:0070480
  * Added general dbxref GOC:mah to synonym exonucleolytic nuclear-transcribed mRNA degradation involved in deadenylation-independent decay of GO:0070480
  * Changed synonym scope of GO:0070480 from "Related" to "Exact"
  * Copied GO:0070480 to GO:0000291 with type OBO_REL:is_a
  * Copied GO:0070480 to GO:0031086 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070480
* Populated new object GO:0070481 (macro)
  * Changed name of GO:0070481 from "<new term>" to "nuclear-transcribed mRNA catabolic process, non-stop decay"
  * Set definition of GO:0070481 to "The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon."
  * Added definition dbxref PMID:11910110 to GO:0070481
  * Added synonym "non-stop decay" to GO:0070481
  * Added general dbxref GOC:jp to synonym non-stop decay of GO:0070481
  * Changed synonym scope of GO:0070481 from "Related" to "Exact"
  * Added synonym "non-stop mRNA decay" to GO:0070481
  * Added general dbxref GOC:jp to synonym non-stop mRNA decay of GO:0070481
  * Changed synonym scope of GO:0070481 from "Related" to "Exact"
  * Added synonym "nonstop mRNA decay" to GO:0070481
  * Added general dbxref GOC:jp to synonym nonstop mRNA decay of GO:0070481
  * Changed synonym scope of GO:0070481 from "Related" to "Exact"
  * Added synonym "nuclear-transcribed mRNA breakdown, non-stop decay" to GO:0070481
  * Added general dbxref GOC:mah to synonym nuclear-transcribed mRNA breakdown, non-stop decay of GO:0070481
  * Changed synonym scope of GO:0070481 from "Related" to "Exact"
  * Added synonym "nuclear-transcribed mRNA catabolism, non-stop decay" to GO:0070481
  * Added general dbxref GOC:mah to synonym nuclear-transcribed mRNA catabolism, non-stop decay of GO:0070481
  * Changed synonym scope of GO:0070481 from "Related" to "Exact"
  * Added synonym "nuclear-transcribed mRNA degradation, non-stop decay" to GO:0070481
  * Added general dbxref GOC:mah to synonym nuclear-transcribed mRNA degradation, non-stop decay of GO:0070481
  * Changed synonym scope of GO:0070481 from "Related" to "Exact"
  * Copied GO:0070481 to GO:0000956 with type OBO_REL:is_a
  * Assigned namespace "biological_process" to GO:0070481
* Changed definition of GO:0000288 from "A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps: poly(A) tail shortening, deadenylylation-dependent decapping, and decay of the transcript body, and that can regulate mRNA stability." to "A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability."
* Added definition dbxref GOC:jp to GO:0000288
* Deleted GO:0042729 --OBO_REL:is_a--> GO:0044428
* added secondary id GO:0055030 to GO:0043591
* Changed definition of GO:0043591 from "The structures that lie outside the inner membrane and surround the entire endospore." to "The structures that lie outside the inner membrane and surround the entire endospore; consists of a peptidoglycan-containing inner layer (the endospore cortex) surrounded by a multilayered proteinaceous coat. An exosporium may be present as an extreme outer layer."
* Added definition dbxref PMID:15035041 to GO:0043591
* Added synonym "endospore wall" to GO:0043591
* Added general dbxref GOC:mah to synonym endospore wall of GO:0043591
* Changed synonym scope of GO:0043591 from "Related" to "Exact"
* Added synonym "peptidoglycan-based spore wall" to GO:0043591
* Added general dbxref GOC:mtg_sensu to synonym peptidoglycan-based spore wall of GO:0043591
* Changed synonym scope of GO:0043591 from "Related" to "Exact"
* Added synonym "spore wall (sensu Bacteria)" to GO:0043591
* Added general dbxref GOC:mtg_sensu to synonym spore wall (sensu Bacteria) of GO:0043591
* Changed synonym scope of GO:0043591 from "Related" to "Exact"
* Deleted GO:0043591 --OBO_REL:is_a--> GO:0030312
* Copied GO:0043591 to GO:0031160 with type OBO_REL:is_a
* Added synonym "perispore" to GO:0043592
* Deleted GO:0043928 --part_of--> GO:0000290
* Copied GO:0043928 to GO:0000288 with type part_of
* Deleted GO:0045821 --OBO_REL:is_a--> GO:0010676
* Deleted GO:0055030 --OBO_REL:is_a--> GO:0031160
* Destroyed object GO:0055030
* Changed definition of GO:0055087 from "A heterotrimeric protein complex that regulates RNA degradation by the exosome complex." to "A protein complex that regulates RNA degradation by the exosome complex. In Saccharomyces the complex has a heterotetrameric stoichiometry consisting of one copy of Ski2p and Ski3. and two copies of Ski8p."
* Added definition dbxref PMID:18042677 to GO:0055087

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