[Go-diff] GO update 05/01/2008

[Remote CVS for Gene Ontology]

OBODIFF of gene_ontology_write.obo version 1.48 by 1.50

Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Added comment "This term was made obsolete because the activities used in the U2- and U12-type complexes are the same. The cellular component ontology should (and does) represent the two different complexes, but the molecular function ontology should not."
* Changed definition of GO:0000362 from "Catalysis of the first transesterification reaction of U2-type spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, which is still joined to the 3' exon. The catalytic site is thought to be formed by U6 and/or U2 snRNA, and/or associated proteins." to "OBSOLETE. Catalysis of the first transesterification reaction of U2-type spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, which is still joined to the 3' exon. The catalytic site is thought to be formed by U6 and/or U2 snRNA, and/or associated proteins."
* Deleted GO:0000362 --OBO_REL:is_a--> GO:0000384
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 10fbbf2
* Added comment "This term was made obsolete because the activities used in the U2- and U12-type complexes are the same. The cellular component ontology should (and does) represent the two different complexes, but the molecular function ontology should not."
* Changed definition of GO:0000363 from "Catalysis of the first transesterification reaction of U12-type spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, which is still joined to the 3' exon. The catalytic site is thought to be formed by U6atac snRNA and/or U2atac snRNA, and/or associated proteins." to "OBSOLETE. Catalysis of the first transesterification reaction of U12-type spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, which is still joined to the 3' exon. The catalytic site is thought to be formed by U6atac snRNA and/or U2atac snRNA, and/or associated proteins."
* Deleted GO:0000363 --OBO_REL:is_a--> GO:0000384
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 1fc159e
* Added comment "This term was made obsolete because the activities used in the U2- and U12-type complexes are the same. The cellular component ontology should (and does) represent the two different complexes, but the molecular function ontology should not."
* Changed definition of GO:0000364 from "Catalysis of the second transesterification reaction of U2-type spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure. The catalytic site is thought to be formed by U6 and/or U2 snRNAs and/or associated proteins." to "OBSOLETE. Catalysis of the second transesterification reaction of U2-type spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure. The catalytic site is thought to be formed by U6 and/or U2 snRNAs and/or associated proteins."
* Deleted GO:0000364 --OBO_REL:is_a--> GO:0000386
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at ef4879
* Added comment "This term was made obsolete because the activities used in the U2- and U12-type complexes are the same. The cellular component ontology should (and does) represent the two different complexes, but the molecular function ontology should not."
* Changed definition of GO:0000367 from "Catalysis of the second transesterification reaction of U12-type spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure. The catalytic site is thought to be formed by U6 and/or U2 snRNAs and/or associated proteins." to "OBSOLETE. Catalysis of the second transesterification reaction of U12-type spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure. The catalytic site is thought to be formed by U6 and/or U2 snRNAs and/or associated proteins."
* Deleted GO:0000367 --OBO_REL:is_a--> GO:0000386
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 17f30a0
* Deleted general dbxref GOC:tb from GO:0010568
* Changed definition of GO:0031202 from "An activity which binds RNA and functions to assist splicing of substrate RNA(s) by facilitating the formation and stabilization of a catalytic conformation in which the splice junctions of the RNA(s) to be spliced are positioned for a transesterification reaction that occurs between two sites within the RNA(s) to be spliced." to "An activity which assists splicing of substrate RNA(s) by facilitating the formation and stabilization of a series of catalytic conformations in which key RNA sequences are positioned for a series of two transesterification reactions which result in removal of the intron sequence and joining of two exons."
* Added comment "This term was made obsolete because, although it was requested, it is not needed after all; it was not defined clearly, and does not necessarily correspond to a catalytic activity."
* Changed definition of GO:0034335 from "Catalysis of the formation of positive or negative supercoils in a DNA molecule or region thereof; may be associated with a geometric or topological change in the DNA molecule." to "OBSOLETE. Catalysis of the formation of positive or negative supercoils in a DNA molecule or region thereof; may be associated with a geometric or topological change in the DNA molecule."
* Deleted GO:0034335 --OBO_REL:is_a--> GO:0016853
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 15170bc
* Changed name of GO:0051652 from "maintenance of chromosome localization" to "maintenance of chromosome location"
* Added definition dbxref GOC:dph to GO:0051652
* Added definition dbxref GOC:tb to GO:0051652
* Added synonym "maintenance of chromosome localization" to GO:0051652
* Added general dbxref GOC:tb to synonym maintenance of chromosome localization of GO:0051652
* Added general dbxref GOC:dph to synonym maintenance of chromosome localization of GO:0051652
* Deleted GO:0051652 --OBO_REL:is_a--> GO:0051651
* Changed name of GO:0051655 from "maintenance of vesicle localization" to "maintenance of vesicle location"
* Added definition dbxref GOC:dph to GO:0051655
* Added definition dbxref GOC:tb to GO:0051655
* Added synonym "maintenance of vesicle localization" to GO:0051655
* Added general dbxref GOC:tb to synonym maintenance of vesicle localization of GO:0051655
* Added general dbxref GOC:dph to synonym maintenance of vesicle localization of GO:0051655
* Deleted GO:0051655 --OBO_REL:is_a--> GO:0051651
* Changed name of GO:0051657 from "maintenance of organelle localization" to "maintenance of organelle location"
* Added definition dbxref GOC:dph to GO:0051657
* Added definition dbxref GOC:tb to GO:0051657
* Added synonym "maintenance of organelle localization" to GO:0051657
* Added general dbxref GOC:tb to synonym maintenance of organelle localization of GO:0051657
* Added general dbxref GOC:dph to synonym maintenance of organelle localization of GO:0051657
* Deleted GO:0051657 --OBO_REL:is_a--> GO:0051235
* Copied GO:0051657 to GO:0051651 with type OBO_REL:is_a
* Changed name of GO:0051658 from "maintenance of nucleus localization" to "maintenance of nucleus location"
* Added definition dbxref GOC:dph to GO:0051658
* Added definition dbxref GOC:tb to GO:0051658
* Added synonym "maintenance of nucleus localization" to GO:0051658
* Added general dbxref GOC:tb to synonym maintenance of nucleus localization of GO:0051658
* Added general dbxref GOC:dph to synonym maintenance of nucleus localization of GO:0051658
* Deleted GO:0051658 --OBO_REL:is_a--> GO:0051651
* Changed name of GO:0051659 from "maintenance of mitochondrion localization" to "maintenance of mitochondrion location"
* Added definition dbxref GOC:dph to GO:0051659
* Added definition dbxref GOC:tb to GO:0051659
* Added synonym "maintenance of mitochondrion localization" to GO:0051659
* Added general dbxref GOC:tb to synonym maintenance of mitochondrion localization of GO:0051659
* Added general dbxref GOC:dph to synonym maintenance of mitochondrion localization of GO:0051659
* Deleted GO:0051659 --OBO_REL:is_a--> GO:0051651
* Changed name of GO:0051661 from "maintenance of centrosome localization" to "maintenance of centrosome location"
* Added definition dbxref GOC:dph to GO:0051661
* Added definition dbxref GOC:tb to GO:0051661
* Added synonym "maintenance of centrosome localization" to GO:0051661
* Added general dbxref GOC:tb to synonym maintenance of centrosome localization of GO:0051661
* Added general dbxref GOC:dph to synonym maintenance of centrosome localization of GO:0051661
* Deleted GO:0051661 --OBO_REL:is_a--> GO:0051651
* Changed name of GO:0051684 from "maintenance of Golgi localization" to "maintenance of Golgi location"
* Added definition dbxref GOC:dph to GO:0051684
* Added definition dbxref GOC:tb to GO:0051684
* Added synonym "maintenance of Golgi localization" to GO:0051684
* Added general dbxref GOC:tb to synonym maintenance of Golgi localization of GO:0051684
* Added general dbxref GOC:dph to synonym maintenance of Golgi localization of GO:0051684
* Deleted GO:0051684 --OBO_REL:is_a--> GO:0051651
* Changed name of GO:0051685 from "maintenance of ER localization" to "maintenance of ER location"
* Added definition dbxref GOC:dph to GO:0051685
* Added definition dbxref GOC:tb to GO:0051685
* Added synonym "maintenance of ER localization" to GO:0051685
* Added general dbxref GOC:tb to synonym maintenance of ER localization of GO:0051685
* Added general dbxref GOC:dph to synonym maintenance of ER localization of GO:0051685
* Deleted GO:0051685 --OBO_REL:is_a--> GO:0051651
* Changed name of GO:0051687 from "maintenance of spindle localization" to "maintenance of spindle location"
* Added definition dbxref GOC:dph to GO:0051687
* Added definition dbxref GOC:tb to GO:0051687
* Added synonym "maintenance of spindle localization" to GO:0051687
* Added general dbxref GOC:tb to synonym maintenance of spindle localization of GO:0051687
* Added general dbxref GOC:dph to synonym maintenance of spindle localization of GO:0051687
* Deleted GO:0051687 --OBO_REL:is_a--> GO:0051651
* Changed name of GO:0051688 from "maintenance of plastid localization" to "maintenance of plastid location"
* Added definition dbxref GOC:dph to GO:0051688
* Added definition dbxref GOC:tb to GO:0051688
* Added synonym "maintenance of plastid localization" to GO:0051688
* Added general dbxref GOC:tb to synonym maintenance of plastid localization of GO:0051688
* Added general dbxref GOC:dph to synonym maintenance of plastid localization of GO:0051688
* Deleted GO:0051688 --OBO_REL:is_a--> GO:0051651