From gocvs at genome.stanford.edu Thu May 1 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Thu, 1 May 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 05/01/2008 Message-ID: <200805020430.VAA19507@bread.Stanford.EDU> 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 From gocvs at genome.stanford.edu Fri May 2 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Fri, 2 May 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 05/02/2008 Message-ID: <200805030430.VAA10515@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.50 by 1.53 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034424 * Created object of type obo:TERM with id GO:0034425 * Created object of type obo:TERM with id GO:0034426 * Populated new object GO:0034424 (macro) * Changed name of GO:0034424 from "" to "Vps55/Vps68 complex" * Set definition of GO:0034424 to "A membrane-associated protein complex that is required for a late stage of endosomal transport. In budding yeast, this complex consists of Vps55p and Vps68p proteins." * Added definition dbxref PMID:18216282 to GO:0034424 * Copied GO:0034424 to GO:0005789 with type part_of * Copied GO:0034424 to GO:0043234 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034424 * Populated new object GO:0034425 (macro) * Changed name of GO:0034425 from "" to "etioplast envelope" * Set definition of GO:0034425 to "The double lipid bilayer enclosing the etioplast and separating its contents from the rest of the cytoplasm; includes the intermembrane space." * Added definition dbxref GOC:mah to GO:0034425 * Copied GO:0034425 to GO:0009513 with type part_of * Copied GO:0034425 to GO:0009526 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034425 * Populated new object GO:0034426 (macro) * Changed name of GO:0034426 from "" to "etioplast membrane" * Set definition of GO:0034426 to "Either of the lipid bilayers that surround a etioplast and form the etioplast envelope." * Added definition dbxref GOC:rph to GO:0034426 * Copied GO:0034426 to GO:0034425 with type part_of * Copied GO:0034426 to GO:0042170 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0034426 * Changed definition of GO:0003012 from "The biological processes, occurring at the level of a muscle. Muscle tissue is composed of contractile cells or fibers." to "A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers." * Changed name of GO:0006985 from "EOR-mediated activation of NF-kappaB" to "positive regulation of NF-kappaB transcription factor activity by ER overload response" * Added definition dbxref GOC:dph to GO:0006985 * Added definition dbxref GOC:tb to GO:0006985 * Added synonym "EOR-mediated activation of NF-kappaB " to GO:0006985 * Added general dbxref GOC:tb to synonym EOR-mediated activation of NF-kappaB of GO:0006985 * Added general dbxref GOC:dph to synonym EOR-mediated activation of NF-kappaB of GO:0006985 * Changed synonym scope of GO:0006985 from "Related" to "Exact" * Added synonym "positive regulation of NF-kappaB transcription factor activity by EOR" to GO:0006985 * Added general dbxref GOC:tb to synonym positive regulation of NF-kappaB transcription factor activity by EOR of GO:0006985 * Added general dbxref GOC:dph to synonym positive regulation of NF-kappaB transcription factor activity by EOR of GO:0006985 * Changed synonym scope of GO:0006985 from "Related" to "Exact" * Added definition dbxref GOC:dph to GO:0007559 * Deleted GO:0007559 --part_of--> GO:0002165 * Copied GO:0007559 to GO:0009888 with type part_of * Copied GO:0008240 to GO:0016806 with type OBO_REL:is_a * Set definition of GO:0016271 to "A permanent cessation of all vital functions of a tissue." * Added definition dbxref GOC:dph to GO:0016271 * Changed name of GO:0019988 from "charged-tRNA modification" to "charged-tRNA amino acid modification" * Added synonym "" to GO:0019988 * Changed synonym scope of GO:0019988 from "Related" to "Exact" * Added synonym "charged tRNA amino acid modification" to GO:0019988 * Changed synonym scope of GO:0019988 from "Related" to "Exact" * Added synonym "charged-tRNA modification" to GO:0019988 * Changed name of GO:0030722 from "establishment of oocyte nucleus localization during oocyte axis determination" to "establishment of oocyte nucleus localization involved in oocyte dorsal/ventral axis determination" * Changed definition of GO:0030722 from "The directed movement of the nucleus to a specific location within the cell during the establishment and maintenance of the axes of the oocyte. In the insect oocyte, for example, the nucleus is repositioned to a dorso-anterior position." to "The directed movement of the nucleus to a specific location within the cell during the establishment and maintenance of the dorsal/ventral axis of the oocyte. In the insect oocyte, for example, the nucleus is repositioned to a dorso-anterior position." * Added definition dbxref GOC:dph to GO:0030722 * Added definition dbxref GOC:tb to GO:0030722 * Added synonym "establishment of oocyte nucleus localization during oocyte axis determination" to GO:0030722 * Added general dbxref GOC:tb to synonym establishment of oocyte nucleus localization during oocyte axis determination of GO:0030722 * Added general dbxref GOC:dph to synonym establishment of oocyte nucleus localization during oocyte axis determination of GO:0030722 * Changed name of GO:0031522 from "plasma membrane Sec complex" to "cell envelope Sec complex" * Added synonym "plasma membrane Sec complex" to GO:0031522 * Added synonym "T3SS complex" to GO:0031522 * Changed synonym scope of GO:0031522 from "Related" to "Exact" * Added synonym "TTSS complex" to GO:0031522 * Changed synonym scope of GO:0031522 from "Related" to "Exact" * Deleted GO:0031522 --OBO_REL:is_a--> GO:0044459 * Copied GO:0031522 to GO:0044464 with type OBO_REL:is_a * Changed name of GO:0032088 from "inhibition of NF-kappaB transcription factor" to "negative regulation of NF-kappaB transcription factor activity" * Added definition dbxref GOC:dph to GO:0032088 * Added definition dbxref GOC:tb to GO:0032088 * Added synonym "inhibition of NF-kappaB transcription factor" to GO:0032088 * Added general dbxref GOC:tb to synonym inhibition of NF-kappaB transcription factor of GO:0032088 * Added general dbxref GOC:dph to synonym inhibition of NF-kappaB transcription factor of GO:0032088 * Changed synonym scope of GO:0032088 from "Related" to "Exact" * Changed name of GO:0032792 from "inhibition of CREB transcription factor" to "negative regulation of CREB transcription factor activity" * Added definition dbxref GOC:dph to GO:0032792 * Added definition dbxref GOC:tb to GO:0032792 * Added synonym "inhibition of CREB transcription factor" to GO:0032792 * Added general dbxref GOC:tb to synonym inhibition of CREB transcription factor of GO:0032792 * Added general dbxref GOC:dph to synonym inhibition of CREB transcription factor of GO:0032792 * Changed synonym scope of GO:0032792 from "Related" to "Exact" * Changed name of GO:0032793 from "activation of CREB transcription factor" to "positive regulation of CREB transcription factor activity" * Added definition dbxref GOC:dph to GO:0032793 * Added definition dbxref GOC:tb to GO:0032793 * Added synonym "activation of CREB transcription factor" to GO:0032793 * Added general dbxref GOC:tb to synonym activation of CREB transcription factor of GO:0032793 * Added general dbxref GOC:dph to synonym activation of CREB transcription factor of GO:0032793 * Changed synonym scope of GO:0032793 from "Related" to "Exact" * Deleted GO:0034397 --OBO_REL:is_a--> GO:0032200 * Added definition dbxref GOC:dph to GO:0035069 * Copied GO:0035069 to GO:0007552 with type part_of * Added definition dbxref GOC:dph to GO:0035070 * Copied GO:0035070 to GO:0007552 with type part_of * Added synonym "sense-PTGS" to GO:0035194 * Changed name of GO:0042070 from "maintenance of oocyte nucleus localization during oocyte axis determination" to "maintenance of oocyte nucleus location involved in oocyte dorsal/ventral axis determination" * Added definition dbxref GOC:dph to GO:0042070 * Added definition dbxref GOC:tb to GO:0042070 * Added synonym "maintenance of oocyte nucleus localization during oocyte axis determination" to GO:0042070 * Added general dbxref GOC:tb to synonym maintenance of oocyte nucleus localization during oocyte axis determination of GO:0042070 * Added general dbxref GOC:dph to synonym maintenance of oocyte nucleus localization during oocyte axis determination of GO:0042070 * Changed name of GO:0051092 from "activation of NF-kappaB transcription factor" to "positive regulation of NF-kappaB transcription factor activity" * Added definition dbxref GOC:dph to GO:0051092 * Added definition dbxref GOC:tb to GO:0051092 * Added synonym "activation of NF-kappaB transcription factor" to GO:0051092 * Added general dbxref GOC:tb to synonym activation of NF-kappaB transcription factor of GO:0051092 * Added general dbxref GOC:dph to synonym activation of NF-kappaB transcription factor of GO:0051092 * Changed synonym scope of GO:0051092 from "Related" to "Exact" * Changed name of GO:0051663 from "oocyte nucleus localization during oocyte axis determination" to "oocyte nucleus localization involved in oocyte dorsal/ventral axis determination" * Changed definition of GO:0051663 from "The directed movement of the nucleus to a specific location within a cell during the establishment and maintenance of the axes of the oocyte." to "The directed movement of the nucleus to a specific location within a cell during the establishment and maintenance of the dorsal/ventral axis of the oocyte." * Added definition dbxref GOC:dph to GO:0051663 * Added definition dbxref GOC:tb to GO:0051663 * Added synonym "oocyte nucleus localization during oocyte axis determination" to GO:0051663 * Added general dbxref GOC:tb to synonym oocyte nucleus localization during oocyte axis determination of GO:0051663 * Added general dbxref GOC:dph to synonym oocyte nucleus localization during oocyte axis determination of GO:0051663 From gocvs at genome.stanford.edu Mon May 5 21:30:46 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Mon, 5 May 2008 21:30:46 -0700 (PDT) Subject: [Go-diff] GO update 05/05/2008 Message-ID: <200805060430.VAA26242@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.53 by 1.54 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Changed name of GO:0032255 from "maintenance of secretory granule localization" to "maintenance of secretory granule location" * Added definition dbxref GOC:dph to GO:0032255 * Added definition dbxref GOC:tb to GO:0032255 * Added synonym "maintenance of secretory granule localization" to GO:0032255 * Added general dbxref GOC:tb to synonym maintenance of secretory granule localization of GO:0032255 * Added general dbxref GOC:dph to synonym maintenance of secretory granule localization of GO:0032255 * Changed name of GO:0032257 from "maintenance of dense core granule localization" to "maintenance of dense core granule location" * Added definition dbxref GOC:dph to GO:0032257 * Added definition dbxref GOC:tb to GO:0032257 * Added synonym "maintenance of dense core granule localization" to GO:0032257 * Added general dbxref GOC:tb to synonym maintenance of dense core granule localization of GO:0032257 * Added general dbxref GOC:dph to synonym maintenance of dense core granule localization of GO:0032257 * Changed name of GO:0033370 from "maintenance of protein localization in mast cell secretory granule" to "maintenance of protein location in mast cell secretory granule" * Added definition dbxref GOC:dph to GO:0033370 * Added definition dbxref GOC:tb to GO:0033370 * Added synonym "maintenance of protein localization in mast cell secretory granule" to GO:0033370 * Added general dbxref GOC:tb to synonym maintenance of protein localization in mast cell secretory granule of GO:0033370 * Added general dbxref GOC:dph to synonym maintenance of protein localization in mast cell secretory granule of GO:0033370 * Changed name of GO:0033373 from "maintenance of protease localization in mast cell secretory granule" to "maintenance of protease location in mast cell secretory granule" * Added definition dbxref GOC:dph to GO:0033373 * Added definition dbxref GOC:tb to GO:0033373 * Added synonym "maintenance of protease localization in mast cell secretory granule" to GO:0033373 * Added general dbxref GOC:tb to synonym maintenance of protease localization in mast cell secretory granule of GO:0033373 * Added general dbxref GOC:dph to synonym maintenance of protease localization in mast cell secretory granule of GO:0033373 * Changed name of GO:0033377 from "maintenance of protein localization in T cell secretory granule" to "maintenance of protein location in T cell secretory granule" * Added definition dbxref GOC:dph to GO:0033377 * Added definition dbxref GOC:tb to GO:0033377 * Added synonym "maintenance of protein localization in T cell secretory granule" to GO:0033377 * Added general dbxref GOC:tb to synonym maintenance of protein localization in T cell secretory granule of GO:0033377 * Added general dbxref GOC:dph to synonym maintenance of protein localization in T cell secretory granule of GO:0033377 * Changed name of GO:0033379 from "maintenance of protease localization in T cell secretory granule" to "maintenance of protease location in T cell secretory granule" * Added definition dbxref GOC:dph to GO:0033379 * Added definition dbxref GOC:tb to GO:0033379 * Added synonym "maintenance of protease localization in T cell secretory granule" to GO:0033379 * Added general dbxref GOC:tb to synonym maintenance of protease localization in T cell secretory granule of GO:0033379 * Added general dbxref GOC:dph to synonym maintenance of protease localization in T cell secretory granule of GO:0033379 * Changed name of GO:0033382 from "maintenance of granzyme B localization in T cell secretory granule" to "maintenance of granzyme B location in T cell secretory granule" * Added synonym "maintenance of granzyme B localization in T cell secretory granule" to GO:0033382 * Added general dbxref GOC:tb to synonym maintenance of granzyme B localization in T cell secretory granule of GO:0033382 * Added general dbxref GOC:dph to synonym maintenance of granzyme B localization in T cell secretory granule of GO:0033382 * Changed name of GO:0046594 from "maintenance of pole plasm mRNA localization" to "maintenance of pole plasm mRNA location" * Added definition dbxref GOC:dph to GO:0046594 * Added definition dbxref GOC:tb to GO:0046594 * Added synonym "maintenance of pole plasm mRNA localization" to GO:0046594 * Added general dbxref GOC:tb to synonym maintenance of pole plasm mRNA localization of GO:0046594 * Added general dbxref GOC:dph to synonym maintenance of pole plasm mRNA localization of GO:0046594 * Changed name of GO:0051237 from "maintenance of RNA localization" to "maintenance of RNA location" * Added synonym "maintenance of RNA localization" to GO:0051237 * Added general dbxref GOC:tb to synonym maintenance of RNA localization of GO:0051237 * Added general dbxref GOC:dph to synonym maintenance of RNA localization of GO:0051237 * Changed name of GO:0051649 from "establishment of cellular localization" to "establishment of localization in cell" * Added definition dbxref GOC:dph to GO:0051649 * Added definition dbxref GOC:tb to GO:0051649 * Added synonym "establishment of cellular localization" to GO:0051649 * Added general dbxref GOC:tb to synonym establishment of cellular localization of GO:0051649 * Added general dbxref GOC:dph to synonym establishment of cellular localization of GO:0051649 * Changed name of GO:0051906 from "maintenance of pigment granule localization" to "maintenance of pigment granule location" * Added definition dbxref GOC:dph to GO:0051906 * Added definition dbxref GOC:tb to GO:0051906 * Added synonym "maintenance of pigment granule localization" to GO:0051906 * Added general dbxref GOC:tb to synonym maintenance of pigment granule localization of GO:0051906 * Added general dbxref GOC:dph to synonym maintenance of pigment granule localization of GO:0051906 From gocvs at genome.stanford.edu Tue May 6 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Tue, 6 May 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 05/06/2008 Message-ID: <200805070430.VAA07379@bread.Stanford.EDU> 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 "" 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 "" 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 "" 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" From gocvs at genome.stanford.edu Wed May 7 21:30:46 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Wed, 7 May 2008 21:30:46 -0700 (PDT) Subject: [Go-diff] GO update 05/07/2008 Message-ID: <200805080430.VAA18549@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.55 by 1.58 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0010576 * Created object of type obo:TERM with id GO:0010577 * Created object of type obo:TERM with id GO:0010578 * Created object of type obo:TERM with id GO:0010579 * Created object of type obo:TERM with id GO:0010580 * Created object of type obo:TERM with id GO:0034430 * Created object of type obo:TERM with id GO:0034431 * Created object of type obo:TERM with id GO:0034432 * Created object of type obo:TERM with id GO:0055120 * Populated new object GO:0010576 (macro) * Changed name of GO:0010576 from "" to "metalloenzyme regulator activity" * Set definition of GO:0010576 to "Modulates the activity of a metalloenzyme. A metalloenzyme is any enzyme that contains metal." * Added definition dbxref GOC:dph to GO:0010576 * Added definition dbxref GOC:tb to GO:0010576 * Copied GO:0010576 to GO:0030234 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0010576 * Populated new object GO:0010577 (macro) * Changed name of GO:0010577 from "" to "metalloenzyme activitor activity" * Set definition of GO:0010577 to "Increases the activity of a metalloenzyme. A metalloenzyme is any enzyme that contains metal." * Added definition dbxref GOC:dph to GO:0010577 * Added definition dbxref GOC:tb to GO:0010577 * Copied GO:0010577 to GO:0010576 with type OBO_REL:is_a * Copied GO:0010577 to GO:0008047 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0010577 * Populated new object GO:0010578 (macro) * Changed name of GO:0010578 from "" to "regulation of adenylate cyclase activity involved in G-protein signaling" * Set definition of GO:0010578 to "Any process that modulates the frequency, rate or extent of adenylate cyclase activity that is an integral part of the series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, resulting in a subsequent change in the concentration of cyclic AMP." * Added definition dbxref GOC:dph to GO:0010578 * Added definition dbxref GOC:tb to GO:0010578 * Copied GO:0010578 to GO:0007188 with type part_of * Copied GO:0010578 to GO:0045761 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010578 * Populated new object GO:0010579 (macro) * Changed name of GO:0010579 from "" to "positive regulation of adenylate cyclase activity involved in G-protein signaling" * Set definition of GO:0010579 to "Any process that increases the frequency, rate or extent of adenylate cyclase activity that is an integral part of the series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, resulting in a subsequent change in the concentration of cyclic AMP." * Added definition dbxref GOC:dph to GO:0010579 * Added definition dbxref GOC:tb to GO:0010579 * Copied GO:0010579 to GO:0010578 with type OBO_REL:is_a * Copied GO:0010579 to GO:0045762 with type OBO_REL:is_a * Copied GO:0010579 to GO:0007189 with type part_of * Assigned namespace "biological_process" to GO:0010579 * Populated new object GO:0010580 (macro) * Changed name of GO:0010580 from "" to "activation of adenylate cyclase activity involved in G-protein signaling" * Set definition of GO:0010580 to "Any process that initiates the activity of an inactive adenylate cyclase that is an integral part of the series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, resulting in a subsequent change in the concentration of cyclic AMP." * Added definition dbxref GOC:dph to GO:0010580 * Added definition dbxref GOC:tb to GO:0010580 * Copied GO:0010580 to GO:0010579 with type OBO_REL:is_a * Copied GO:0010580 to GO:0007190 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0010580 * Populated new object GO:0034430 (macro) * Changed name of GO:0034430 from "" to "monolayer-surrounded lipid storage body outer lipid monolayer" * Set definition of GO:0034430 to "The single layer of phopholipids surrounding a lipid storage body." * Added definition dbxref GOC:rph to GO:0034430 * Added synonym "lipid droplet outer lipid monolayer" to GO:0034430 * Added synonym "lipid storage body surface lipid monolayer" to GO:0034430 * Changed synonym scope of GO:0034430 from "Related" to "Exact" * Added synonym "oil body outer lipid monolayer" to GO:0034430 * Changed synonym scope of GO:0034430 from "Related" to "Exact" * Added synonym "oleosome outer lipid monolayer" to GO:0034430 * Changed synonym scope of GO:0034430 from "Related" to "Exact" * Added synonym "spherosome outer lipid monolayer" to GO:0034430 * Changed synonym scope of GO:0034430 from "Related" to "Exact" * Copied GO:0034430 to GO:0044446 with type OBO_REL:is_a * Copied GO:0034430 to GO:0012511 with type part_of * Assigned namespace "cellular_component" to GO:0034430 * Populated new object GO:0034431 (macro) * Changed name of GO:0034431 from "" to "bis(5'-adenosyl)-hexaphosphatase activity" * Set definition of GO:0034431 to "Catalysis of the reaction: P1-P6-bis(5'-adenosyl) hexaphosphate + H2O = AMP + adenosine 5'-pentaphosphate." * Added definition dbxref PMID:10085096 to GO:0034431 * Added definition dbxref PMID:9450008 to GO:0034431 * Added synonym "AP(6)A hydrolase activity" to GO:0034431 * Changed synonym scope of GO:0034431 from "Related" to "Exact" * Added synonym "AP-6-A hydrolase activity" to GO:0034431 * Changed synonym scope of GO:0034431 from "Related" to "Exact" * Added synonym "AP6A hydrolase activity" to GO:0034431 * Changed synonym scope of GO:0034431 from "Related" to "Exact" * Added synonym "diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase activity" to GO:0034431 * Changed synonym scope of GO:0034431 from "Related" to "Exact" * Copied GO:0034431 to GO:0004551 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034431 * Populated new object GO:0034432 (macro) * Changed name of GO:0034432 from "" to "bis(5'-adenosyl)-pentaphosphatase activity" * Set definition of GO:0034432 to "Catalysis of the reaction: P1-P6-bis(5'-adenosyl) pentaphosphate + H2O = AMP + adenosine 5'-tetraphosphate." * Added definition dbxref PMID:10085096 to GO:0034432 * Added definition dbxref PMID:9450008 to GO:0034432 * Added synonym "AP(5)A hydrolase activity" to GO:0034432 * Changed synonym scope of GO:0034432 from "Related" to "Exact" * Added synonym "AP-5-A hydrolase activity" to GO:0034432 * Changed synonym scope of GO:0034432 from "Related" to "Exact" * Added synonym "AP5A hydrolase activity" to GO:0034432 * Changed synonym scope of GO:0034432 from "Related" to "Exact" * Added synonym "diadenosine 5',5'''-P1,P6-pentaphosphate hydrolase activity" to GO:0034432 * Changed synonym scope of GO:0034432 from "Related" to "Exact" * Copied GO:0034432 to GO:0004551 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034432 * Populated new object GO:0055120 (macro) * Changed name of GO:0055120 from "" to "striated muscle dense body" * Set definition of GO:0055120 to "A vinculin-containing myofibril attachment structure of striated muscle that connects sarcomeres to the extracellular matrix. In nematode body wall muscle, the dense body performs the dual role of Z-disk and costamere." * Added definition dbxref GOC:kmva to GO:0055120 * Added definition dbxref PMID:17492481 to GO:0055120 * Copied GO:0055120 to GO:0044449 with type OBO_REL:is_a * Assigned namespace "cellular_component" to GO:0055120 * Deleted GO:0000348 --part_of--> GO:0000398 * Deleted GO:0000349 --part_of--> GO:0000398 * Deleted GO:0000350 --part_of--> GO:0000398 * Deleted GO:0000351 --part_of--> GO:0000398 * Deleted GO:0000354 --part_of--> GO:0000398 * Deleted GO:0000355 --part_of--> GO:0000398 * Deleted GO:0000389 --part_of--> GO:0000398 * Deleted GO:0000395 --part_of--> GO:0000398 * Deleted GO:0007088 --OBO_REL:is_a--> GO:0051726 * Copied GO:0007088 to GO:0007346 with type OBO_REL:is_a * Deleted GO:0007190 --part_of--> GO:0007189 * Deleted synonym "diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase" from GO:0008486 * Changed name of GO:0009275 from "20-80nm peptidoglycan-based cell wall" to "Gram-positive-bacterium-type cell wall" * Added synonym "20-80nm peptidoglycan-based cell wall" to GO:0009275 * Changed synonym scope of GO:0009275 from "Related" to "Exact" * Changed name of GO:0009276 from "1-2nm peptidoglycan-based cell wall" to "Gram-negative-bacterium-type cell wall" * Added synonym "1-2nm peptidoglycan-based cell wall" to GO:0009276 * Changed synonym scope of GO:0009276 from "Related" to "Exact" * Changed name of GO:0009505 from "cellulose and pectin-containing cell wall" to "plant-type cell wall" * Added synonym "cellulose and pectin-containing cell wall" to GO:0009505 * Changed synonym scope of GO:0009505 from "Related" to "Exact" * Changed name of GO:0009664 from "cellulose and pectin-containing cell wall organization and biogenesis" to "plant-type cell wall organization and biogenesis" * Added synonym "cellulose and pectin-containing cell wall organization and biogenesis" to GO:0009664 * Changed synonym scope of GO:0009664 from "Related" to "Exact" * Changed name of GO:0009827 from "cellulose and pectin-containing cell wall modification" to "plant-type cell wall modification" * Added synonym "cellulose and pectin-containing cell wall modification" to GO:0009827 * Changed synonym scope of GO:0009827 from "Related" to "Exact" * Changed name of GO:0009828 from "cellulose and pectin-containing cell wall loosening" to "plant-type cell wall loosening" * Added synonym "cellulose and pectin-containing cell wall loosening" to GO:0009828 * Changed synonym scope of GO:0009828 from "Related" to "Exact" * Changed name of GO:0009831 from "cellulose and pectin-containing cell wall modification during multidimensional cell growth" to "plant-type cell wall modification during multidimensional cell growth" * Added synonym "cellulose and pectin-containing cell wall modification during multidimensional cell growth" to GO:0009831 * Changed synonym scope of GO:0009831 from "Related" to "Exact" * Changed name of GO:0009832 from "cellulose and pectin-containing cell wall biogenesis" to "plant-type cell wall biogenesis" * Added synonym "cellulose and pectin-containing cell wall biogenesis" to GO:0009832 * Changed synonym scope of GO:0009832 from "Related" to "Exact" * Changed name of GO:0009833 from "cellulose and pectin-containing primary cell wall biogenesis" to "plant-type primary cell wall biogenesis" * Added synonym "cellulose and pectin-containing primary cell wall biogenesis" to GO:0009833 * Changed synonym scope of GO:0009833 from "Related" to "Exact" * Changed name of GO:0009834 from "cellulose and pectin-containing secondary cell wall biogenesis" to "plant-type secondary cell wall biogenesis" * Added synonym "cellulose and pectin-containing secondary cell wall biogenesis" to GO:0009834 * Changed synonym scope of GO:0009834 from "Related" to "Exact" * Changed name of GO:0009920 from "cell plate formation involved in cellulose and pectin-containing cell wall biogenesis" to "cell plate formation involved in plant-type cell wall biogenesis" * Added synonym "cell plate formation involved in cellulose and pectin-containing cell wall biogenesis" to GO:0009920 * Changed synonym scope of GO:0009920 from "Related" to "Exact" * Deleted GO:0012511 --OBO_REL:is_a--> GO:0043231 * Copied GO:0012511 to GO:0043229 with type OBO_REL:is_a * Added comment "Note that this term should be used for annotating gene products with caution: it should be used only to annotate gene products demonstrated to reside and function normally in the autophagic vacuole lumen, not for molecules that are temporarily found in the lumen prior to degradation." * Deleted GO:0040020 --OBO_REL:is_a--> GO:0051726 * Copied GO:0040020 to GO:0051445 with type OBO_REL:is_a * Changed name of GO:0043164 from "1-2nm peptidoglycan-based cell wall biogenesis" to "Gram-negative-bacterium-type cell wall biogenesis" * Added synonym "1-2nm peptidoglycan-based cell wall biogenesis" to GO:0043164 * Changed synonym scope of GO:0043164 from "Related" to "Exact" * Deleted GO:0045761 --part_of--> GO:0007188 * Copied GO:0048551 to GO:0010576 with type OBO_REL:is_a * Deleted GO:0051457 --OBO_REL:is_a--> GO:0045185 * Changed name of GO:0052541 from "cellulose and pectin-containing cell wall cellulose metabolic process" to "plant-type cell wall cellulose metabolic process" * Added synonym "cellulose and pectin-containing cell wall cellulose metabolic process" to GO:0052541 * Changed synonym scope of GO:0052541 from "Related" to "Exact" * Changed name of GO:0052546 from "cellulose and pectin-containing cell wall pectin metabolic process" to "plant-type cell wall pectin metabolic process" * Added synonym "cellulose and pectin-containing cell wall pectin metabolic process" to GO:0052546 * Changed synonym scope of GO:0052546 from "Related" to "Exact" From gocvs at genome.stanford.edu Thu May 8 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Thu, 8 May 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 05/08/2008 Message-ID: <200805090430.VAA28943@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.58 by 1.59 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Changed definition of GO:0006950 from "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." to "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." * Added synonym "response to abiotic stress" to GO:0006950 * Added synonym "response to biotic stress" to GO:0006950 * Deleted GO:0006952 --OBO_REL:is_a--> GO:0050896 * Copied GO:0006952 to GO:0006950 with type OBO_REL:is_a * Added synonym "response to biotic stress" to GO:0009607 * Changed synonym scope of GO:0009607 from "Related" to "Narrow" * Added synonym "response to abiotic stress" to GO:0009628 * Changed synonym scope of GO:0009628 from "Related" to "Narrow" * Changed definition of GO:0034430 from "The single layer of phopholipids surrounding a lipid storage body." to "The single layer of phopholipids surrounding a lipid storage body." * Changed definition of GO:0043043 from "The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." to "The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide." * Added definition dbxref GOC:dph to GO:0043043 From gocvs at genome.stanford.edu Fri May 9 21:30:45 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Fri, 9 May 2008 21:30:45 -0700 (PDT) Subject: [Go-diff] GO update 05/09/2008 Message-ID: <200805100430.VAA05471@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.59 by 1.61 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034433 * Created object of type obo:TERM with id GO:0034434 * Created object of type obo:TERM with id GO:0034435 * Created object of type obo:TERM with id GO:0043899 * Populated new object GO:0034433 (macro) * Changed name of GO:0034433 from "" to "steroid esterification" * Set definition of GO:0034433 to "A lipid modification process in which a steroid ester is formed by the combination of a carboxylic acid (often a fatty acid) and a steroid molecule (e.g. cholesterol)." * Added definition dbxref GOC:mah to GO:0034433 * Added definition dbxref GOC:pde to GO:0034433 * Added definition dbxref GOC:rl to GO:0034433 * Copied GO:0034433 to GO:0008202 with type OBO_REL:is_a * Copied GO:0034433 to GO:0030258 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034433 * Populated new object GO:0034434 (macro) * Changed name of GO:0034434 from "" to "sterol esterification" * Set definition of GO:0034434 to "A lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and a sterol molecule (e.g. cholesterol)." * Added definition dbxref GOC:mah to GO:0034434 * Added definition dbxref GOC:pde to GO:0034434 * Added definition dbxref GOC:rl to GO:0034434 * Copied GO:0034434 to GO:0034433 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034434 * Populated new object GO:0034435 (macro) * Changed name of GO:0034435 from "" to "cholesterol esterification" * Set definition of GO:0034435 to "A lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and cholesterol. In the blood this process is associated with the conversion of free cholesterol into cholesteryl ester, which is then sequestered into the core of a lipoprotein particle." * Added definition dbxref GOC:mah to GO:0034435 * Added definition dbxref GOC:pde to GO:0034435 * Added definition dbxref GOC:rl to GO:0034435 * Copied GO:0034435 to GO:0034434 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034435 * Populated new object GO:0043899 (macro) * Changed name of GO:0043899 from "" to "phosphoserine:homoserine phosphotransferase activity" * Set definition of GO:0043899 to "Catalysis of the transfer of a phosphoryl group from phosphoserine to homoserine to form phosphohomoserine." * Added definition dbxref GOC:jl to GO:0043899 * Added definition dbxref PMID:14699121 to GO:0043899 * Added general dbxref EC:2.7.1 to GO:0043899 * Added general dbxref IMG:02616 to GO:0043899 * Added GO:0043899 to category gosubset_prok * Added synonym "thrH" to GO:0043899 * Copied GO:0043899 to GO:0016773 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0043899 * Copied GO:0000046 to GO:0006944 with type OBO_REL:is_a * Changed comment from "Note that the enzyme DNA (cytosine-5-)-methyltransferase also has the activity represented by the molecular function term 'site-specific DNA-methyltransferase (cytosine-specific) activity ; GO:0008326'." to "Note that EC:2.1.1.73 was deleted from EC as the reaction is performed by DNA (cytosine-5-)-methyltransferase (EC:2.1.1.37)." * added secondary id GO:0008326 to GO:0003886 * Added general dbxref MetaCyc:2.1.1.73-RXN to GO:0003886 * Added synonym "site-specific DNA-methyltransferase (cytosine-specific) activity" to GO:0003886 * Added general dbxref 2.1.1.73 (EC:) to synonym site-specific DNA-methyltransferase (cytosine-specific) activity of GO:0003886 * Changed synonym scope of GO:0003886 from "Related" to "Narrow" * Deleted definition dbxref EC:4.3.1.8 from GO:0004418 * Added definition dbxref EC:2.5.1.61 to GO:0004418 * Deleted definition dbxref EC:4.2.1.16 from GO:0004794 * Added definition dbxref EC:4.3.1.19 to GO:0004794 * Deleted synonym "4.2.1.16" from GO:0004794 * Deleted definition dbxref EC:2.7.1.123 from GO:0005954 * Added definition dbxref EC:2.7.11.17 to GO:0005954 * Copied GO:0006906 to GO:0048284 with type OBO_REL:is_a * Copied GO:0008053 to GO:0006944 with type OBO_REL:is_a * Deleted GO:0008326 --OBO_REL:is_a--> GO:0003886 * Destroyed object GO:0008326 * Deleted general dbxref UM-BBD_enzymeID:e0029 from GO:0008959 * Copied GO:0016189 to GO:0048284 with type OBO_REL:is_a * Copied GO:0016320 to GO:0048284 with type OBO_REL:is_a * Deleted general dbxref UM-BBD_enzymeID:e04 from GO:0018459 * Added general dbxref UM-BBD_enzymeID:e0446 to GO:0018459 * Changed definition of GO:0018467 from "Catalysis of the reaction: formaldehyde + NAD+ + H2O = formate + NADH + H+. Unlike EC:1.2.1.1 formaldehyde dehydrogenase (glutathione), this enzyme does not need reduced glutathione." to "Catalysis of the reaction: formaldehyde + NAD+ + H2O = formate + NADH + H+. This enzyme does not need reduced glutathione." * Deleted general dbxref UM-BBD_enzymeID:e0027 from GO:0018478 * Set definition of GO:0018538 to "Catalysis of the reaction: ring opening and carboxylation of an epoxide; the reaction requires CO2 as a cosubstrate and forms a beta-keto acid as a products. An example of such a reaction is: epoxypropane + CO2 + NAD+ + NADPH = acetoacetate + NADH + NADP+." * Added definition dbxref PMID:9555888 to GO:0018538 * Deleted general dbxref UM-BBD_enzymeID:e0040 from GO:0018538 * Deleted definition dbxref UM-BBD_enzymeID:e0405 from GO:0018591 * Added definition dbxref UM-BBD_reactionID:r1023 to GO:0018591 * Deleted general dbxref UM-BBD_enzymeID:e0405 from GO:0018591 * Deleted definition dbxref UM-BBD_enzymeID:e0406 from GO:0018594 * Added definition dbxref UM-BBD_reactionID:r0615 to GO:0018594 * Deleted general dbxref UM-BBD_enzymeID:e0406 from GO:0018594 * Deleted general dbxref UM-BBD_enzymeID:e0193 from GO:0018671 * Deleted definition dbxref UM-BBD_enzymeID:e0386 from GO:0018710 * Added definition dbxref EC:6.4.1.6 to GO:0018710 * Deleted general dbxref UM-BBD_enzymeID:e0386 from GO:0018710 * Set definition of GO:0018755 to "2-chloro-4-hydroxy-6-amino-1,3,5-triazine + OH- = 2,4-dihydroxy-6-amino-1,3,5-triazine + Cl-." * Added definition dbxref UM-BBD_reactionID:r1414 to GO:0018755 * Deleted general dbxref UM-BBD_enzymeID:e0099 from GO:0018755 * Deleted general dbxref UM-BBD_enzymeID:e0096 from GO:0018756 * Deleted definition dbxref UM-BBD_enzymeID:e0361 from GO:0018777 * Added definition dbxref PMID:10464214 to GO:0018777 * Deleted general dbxref UM-BBD_enzymeID:e0361 from GO:0018777 * Set definition of GO:0018781 to "Catalysis of the reaction: 1-halo or 1-pseudohalo-S-triazine -> 1-hydroxy-S-triazine." * Added definition dbxref UM-BBD_ruleID:bt0330 to GO:0018781 * Set definition of GO:0018783 to "Catalysis of the reaction: deisopropyldeethylatrazine + H2O = 2-chloro-4-hydroxy-6-amino-1,3,5-triazine + NH3." * Added definition dbxref UM-BBD_reactionID:0129 to GO:0018783 * Deleted general dbxref UM-BBD_enzymeID:e0095 from GO:0018783 * Deleted definition dbxref UM-BBD_enzymeID:e0183 from GO:0018812 * Added definition dbxref UM-BBD_ruleID:bt0291 to GO:0018812 * Deleted general dbxref UM-BBD_enzymeID:e0183 from GO:0018812 * Deleted GO:0030259 --OBO_REL:is_a--> GO:0043413 * Added general dbxref UM-BBD_enzymeID:e0709 to GO:0051903 From gocvs at genome.stanford.edu Mon May 12 21:30:46 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Mon, 12 May 2008 21:30:46 -0700 (PDT) Subject: [Go-diff] GO update 05/12/2008 Message-ID: <200805130430.VAA26858@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.61 by 1.63 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034436 * Created object of type obo:TERM with id GO:0034437 * Created object of type obo:TERM with id GO:0034438 * Created object of type obo:TERM with id GO:0034439 * Created object of type obo:TERM with id GO:0034440 * Created object of type obo:TERM with id GO:0034441 * Created object of type obo:TERM with id GO:0034442 * Created object of type obo:TERM with id GO:0034443 * Created object of type obo:TERM with id GO:0034444 * Created object of type obo:TERM with id GO:0034445 * Populated new object GO:0034436 (macro) * Changed name of GO:0034436 from "" to "glycoprotein transport" * Set definition of GO:0034436 to "The directed movement of a glycoprotein, any protein that contains covalently bound glycose (i.e. monosaccharide) residues other than as a moiety of nucleic acid, into, out of, within or between cells." * Added definition dbxref GOC:mah to GO:0034436 * Added definition dbxref GOC:rl to GO:0034436 * Copied GO:0034436 to GO:0015031 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034436 * Populated new object GO:0034437 (macro) * Changed name of GO:0034437 from "" to "glycoprotein transporter activity" * Set definition of GO:0034437 to "Enables the directed movement of a glycoprotein, any protein that contains covalently bound glycose (i.e. monosaccharide) residues other than as a moiety of nucleic acid, into, out of, within or between cells." * Added definition dbxref GOC:mah to GO:0034437 * Added definition dbxref GOC:rl to GO:0034437 * Copied GO:0034437 to GO:0008565 with type OBO_REL:is_a * Assigned namespace "molecular_function" to GO:0034437 * Populated new object GO:0034438 (macro) * Changed name of GO:0034438 from "" to "lipoprotein amino acid oxidation" * Set definition of GO:0034438 to "The modification of a lipoprotein by oxidation of one or more amino acids in the protein." * Added definition dbxref GOC:mah to GO:0034438 * Added GO:0034438 to category gosubset_prok * Copied GO:0034438 to GO:0018158 with type OBO_REL:is_a * Copied GO:0034438 to GO:0042161 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034438 * Populated new object GO:0034439 (macro) * Changed name of GO:0034439 from "" to "lipoprotein lipid oxidation" * Set definition of GO:0034439 to "The modification of a lipoprotein by oxidation of the lipid moiety." * Added definition dbxref GOC:mah to GO:0034439 * Added GO:0034439 to category gosubset_prok * Copied GO:0034439 to GO:0042161 with type OBO_REL:is_a * Copied GO:0034439 to GO:0034440 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034439 * Populated new object GO:0034440 (macro) * Changed name of GO:0034440 from "" to "lipid oxidation" * Set definition of GO:0034440 to "The removal of one or more electrons from a lipid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydrogen." * Added definition dbxref GOC:mah to GO:0034440 * Copied GO:0034440 to GO:0030258 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034440 * Populated new object GO:0034441 (macro) * Changed name of GO:0034441 from "" to "plasma lipoprotein oxidation" * Set definition of GO:0034441 to "The modification of a lipoprotein by oxidation of one or more amino acids or the lipid moiety, occurring in the blood plasma." * Added definition dbxref GOC:mah to GO:0034441 * Copied GO:0034441 to GO:0042161 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034441 * Populated new object GO:0034442 (macro) * Changed name of GO:0034442 from "" to "regulation of lipoprotein oxidation" * Set definition of GO:0034442 to "Any process that modulates the frequency, rate or extent of lipoprotein oxidation." * Added definition dbxref GOC:mah to GO:0034442 * Copied GO:0034442 to GO:0042161 with type regulates * Copied GO:0034442 to GO:0050746 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034442 * Populated new object GO:0034443 (macro) * Changed name of GO:0034443 from "" to "negative regulation of lipoprotein oxidation" * Set definition of GO:0034443 to "Any process that stops, prevents, or reduces the frequency, rate or extent of lipoprotein oxidation." * Added definition dbxref GOC:mah to GO:0034443 * Added synonym "inhibition of lipoprotein oxidation" to GO:0034443 * Changed synonym scope of GO:0034443 from "Related" to "Narrow" * Copied GO:0034443 to GO:0050748 with type OBO_REL:is_a * Copied GO:0034443 to GO:0034442 with type OBO_REL:is_a * Copied GO:0034443 to GO:0042161 with type negatively_regulates * Assigned namespace "biological_process" to GO:0034443 * Populated new object GO:0034444 (macro) * Changed name of GO:0034444 from "" to "regulation of plasma lipoprotein oxidation" * Set definition of GO:0034444 to "Any process that modulates the frequency, rate or extent of lipoprotein oxidation, occurring in the blood plasma." * Added definition dbxref GOC:mah to GO:0034444 * Copied GO:0034444 to GO:0034441 with type regulates * Copied GO:0034444 to GO:0034442 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034444 * Populated new object GO:0034445 (macro) * Changed name of GO:0034445 from "" to "negative regulation of plasma lipoprotein oxidation" * Set definition of GO:0034445 to "Any process that stops, prevents, or reduces the frequency, rate or extent of lipoprotein oxidation, occurring in the blood plasma." * Added definition dbxref GOC:mah to GO:0034445 * Added synonym "inhibition of plasma lipoprotein oxidation" to GO:0034445 * Changed synonym scope of GO:0034445 from "Related" to "Narrow" * Copied GO:0034445 to GO:0034444 with type OBO_REL:is_a * Copied GO:0034445 to GO:0034443 with type OBO_REL:is_a * Copied GO:0034445 to GO:0034441 with type negatively_regulates * Assigned namespace "biological_process" to GO:0034445 * Deleted GO:0000139 --OBO_REL:is_a--> GO:0044425 * Copied GO:0002084 to GO:0006464 with type OBO_REL:is_a * Changed name of GO:0006621 from "protein retention in ER" to "protein retention in ER lumen" * Copied GO:0007269 to GO:0006836 with type OBO_REL:is_a * Copied GO:0009306 to GO:0015031 with type OBO_REL:is_a * Deleted GO:0012505 --OBO_REL:is_a--> GO:0016020 * Copied GO:0012505 to GO:0044464 with type OBO_REL:is_a * Deleted GO:0012506 --OBO_REL:is_a--> GO:0044425 * Set definition of GO:0015035 to "Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds." * Added definition dbxref MetaCyc:DISULFOXRED-RXN- to GO:0015035 * Added general dbxref MetaCyc:DISULFOXRED-RXN to GO:0015035 * Set definition of GO:0015036 to "Catalysis of an oxidation-reduction (redox) reaction that interconverts reduced sulfide groups and oxidized disulfide bonds in a substrate." * Added definition dbxref GOC:mah to GO:0015036 * Added definition dbxref MetaCyc:DISULFOXRED-RXN to GO:0015036 * Deleted GO:0015036 --OBO_REL:is_a--> GO:0016491 * Copied GO:0015036 to GO:0016667 with type OBO_REL:is_a * Set definition of GO:0015037 to "Catalysis of the reaction: a peptide with reduced sulfide groups = a peptide with oxidized disulfide bonds." * Added definition dbxref GOC:mah to GO:0015037 * Added definition dbxref MetaCyc:DISULFOXRED-RXN- to GO:0015037 * Set definition of GO:0015038 to "Catalysis of the reaction: 2 glutathione + electron acceptor = glutathione disulfide + electron donor." * Added definition dbxref GOC:mah to GO:0015038 * Copied GO:0019395 to GO:0034440 with type OBO_REL:is_a * Deleted GO:0019867 --OBO_REL:is_a--> GO:0044425 * Copied GO:0019867 to GO:0016020 with type OBO_REL:is_a * Copied GO:0032940 to GO:0006810 with type OBO_REL:is_a * Deleted GO:0042157 --OBO_REL:is_a--> GO:0044267 * Copied GO:0042157 to GO:0044260 with type OBO_REL:is_a * Set definition of GO:0042161 to "The modification of a lipoprotein by oxidation of one or more amino acids or the lipid moiety." * Added definition dbxref GOC:mah to GO:0042161 * Deleted GO:0042161 --OBO_REL:is_a--> GO:0018158 * Copied GO:0042175 to GO:0016020 with type OBO_REL:is_a * Changed name of GO:0045053 from "protein retention in Golgi" to "protein retention in Golgi apparatus" * Copied GO:0045053 to GO:0034067 with type part_of From gocvs at genome.stanford.edu Tue May 13 21:30:47 2008 From: gocvs at genome.stanford.edu (Remote CVS for Gene Ontology) Date: Tue, 13 May 2008 21:30:47 -0700 (PDT) Subject: [Go-diff] GO update 05/13/2008 Message-ID: <200805140430.VAA11014@bread.Stanford.EDU> OBODIFF of gene_ontology_write.obo version 1.63 by 1.64 Starting obodiff at /share/go/bin/oboedit/current using 256M of memory * Created object of type obo:TERM with id GO:0034446 * Created object of type obo:TERM with id GO:0034447 * Populated new object GO:0034446 (macro) * Changed name of GO:0034446 from "" to "substrate adhesion-dependent cell spreading" * Set definition of GO:0034446 to "The morphogenetic process by which flattening of a cell takes place as a consequence of its adhesion to a substrate." * Added definition dbxref GOC:mah to GO:0034446 * Added definition dbxref GOC:pf to GO:0034446 * Added definition dbxref PMID:17050732 to GO:0034446 * Added synonym "cell spreading during cell substrate adhesion" to GO:0034446 * Changed synonym scope of GO:0034446 from "Related" to "Exact" * Added synonym "substrate adhesion dependent cell spreading" to GO:0034446 * Changed synonym scope of GO:0034446 from "Related" to "Exact" * Copied GO:0034446 to GO:0000904 with type OBO_REL:is_a * Copied GO:0034446 to GO:0031589 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034446 * Populated new object GO:0034447 (macro) * Changed name of GO:0034447 from "" to "very-low-density lipoprotein particle clearance" * Set definition of GO:0034447 to "The process by which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." * Added definition dbxref GOC:rl to GO:0034447 * Added synonym "VLDL clearance" to GO:0034447 * Changed synonym scope of GO:0034447 from "Related" to "Exact" * Copied GO:0034447 to GO:0034381 with type OBO_REL:is_a * Assigned namespace "biological_process" to GO:0034447 * Changed definition of GO:0000722 from "The maintenance of proper telomeric length by recombinational processes." to "Any recombinational process that contributes to the maintenance of proper telomeric length." * Changed definition of GO:0000723 from "The maintenance of proper telomeric length and structure by processes that affect and monitor the activity of telomeric proteins and the length of telomeric DNA. These processes includes those that shorten and lengthen the telomeric DNA sequences." to "Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins and the length of telomeric DNA. These processes includes those that shorten and lengthen the telomeric DNA sequences." * Changed definition of GO:0001553 from "Differentiation of theca and granulosa cells into luteal cells. Also other processes involved in the formation of a corpus luteum after ovulation." to "The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation." * Changed definition of GO:0001867 from "Processes involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes." to "Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes." * Changed definition of GO:0002230 from "Host processes that result in the promotion of antiviral immune response mechanisms, thereby limiting viral replication." to "Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication." * Changed definition of GO:0002340 from "Processes of B cell selection that occur in the bone marrow." to "Any B cell selection process that occurs in the bone marrow." * Changed definition of GO:0002341 from "Processes of anergy that occur in the bone marrow." to "Any process contributing to anergy, a state of functional inactivation that occurs as part of tolerance induction, in B cells in the bone marrow." * Changed definition of GO:0002343 from "Processes of B cell selection that occur in the periphery." to "Any B cell selection process that occurs in the periphery." * Changed definition of GO:0002453 from "Any process contributing to anergy in peripheral B cells. Anergy is a state of functional inactivation and occurs as part of tolerance induction." to "Any process contributing to anergy, a state of functional inactivation that occurs as part of tolerance induction, in peripheral B cells." * Changed definition of GO:0006091 from "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances." to "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." * Changed definition of GO:0006310 from "The processes by which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." to "Any process by which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." * Changed definition of GO:0006352 from "Processes involved in the assembly of the RNA polymerase complex at the promoter region of a DNA template resulting in the subsequent synthesis of RNA from that promoter." to "Any process involved in the assembly of the RNA polymerase complex at the promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter." * Changed definition of GO:0006367 from "Processes involved in starting transcription from the RNA polymerase II promoter." to "Any process involved in starting transcription from the RNA polymerase II promoter." * Changed definition of GO:0006884 from "The processes involved in maintaining the equilibrium of a cell's volume. The cell's volume refers to the three-dimensional space occupied by a cell." to "Any process involved in maintaining the equilibrium of a cell's volume. The cell's volume refers to the three-dimensional space occupied by a cell." * Changed definition of GO:0006956 from "Processes involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway." to "Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway." * Changed definition of GO:0006957 from "Processes involved in the activation of any of the steps of the alternative pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes." to "Any process involved in the activation of any of the steps of the alternative pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes." * Changed definition of GO:0006958 from "Processes involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes." to "Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes." * Changed definition of GO:0007107 from "The processes involved in the net addition of membrane at the site of cytokinesis; includes vesicle recruitment and fusion, local lipid synthesis and insertion." to "Any process involved in the net addition of membrane at the site of cytokinesis; includes vesicle recruitment and fusion, local lipid synthesis and insertion." * Changed definition of GO:0007259 from "The processes by which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of cytokines to their cognate receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes." to "Any process by which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of cytokines to their cognate receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes." * Changed definition of GO:0007316 from "The processes by which RNA is transported to, or maintained in, the oocyte pole plasm." to "Any process by which RNA is transported to, or maintained in, the oocyte pole plasm." * Changed definition of GO:0007318 from "The processes by which a protein is transported to, or maintained in, the oocyte pole plasm." to "Any process by which a protein is transported to, or maintained in, the oocyte pole plasm." * Changed definition of GO:0007389 from "The developmental processes that result in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate." to "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate." * Changed definition of GO:0007565 from "The physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth." to "The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth." * Changed definition of GO:0007623 from "The biological processes in an organism that recur with a regularity of approximately 24 hours." to "Any biological process in an organism that recur with a regularity of approximately 24 hours." * Changed definition of GO:0007639 from "The biological processes involved in the maintenance of the equilibrium of cell number within a population of cells in the meristem." to "Any biological process involved in the maintenance of the equilibrium of cell number within a population of cells in the meristem." * Changed definition of GO:0008104 from "The processes by which a protein is transported to, or maintained in, a specific location." to "Any process by which a protein is transported to, or maintained in, a specific location." * Changed definition of GO:0008105 from "The processes by which a protein is transported to, or maintained in, a specific asymmetric distribution." to "Any process by which a protein is transported to, or maintained in, a specific asymmetric distribution." * Changed definition of GO:0008150 from "Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." to "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." * Changed definition of GO:0008152 from "Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." to "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." * Changed definition of GO:0008298 from "The processes by which RNA is transported to, or maintained in, a specific location within the cell." to "Any process by which RNA is transported to, or maintained in, a specific location within the cell." * Changed definition of GO:0008366 from "The processes by which the axon of a neuron is insulated, and that insulation maintained, thereby preventing dispersion of the electrical signal." to "Any process by which the axon of a neuron is insulated, and that insulation maintained, thereby preventing dispersion of the electrical signal." * Changed definition of GO:0009058 from "The energy-requiring part of metabolism in which simpler substances are transformed into more complex ones, as in growth and other biosynthetic processes." to "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." * Added definition dbxref GOC:curators to GO:0009058 * Changed definition of GO:0009307 from "The processes that protect an organism from invading foreign DNA by methylation of self DNA at specific sequences and nucleolytic cleavage of unmethylated foreign DNA." to "Any process that protect an organism from invading foreign DNA by methylation of self DNA at specific sequences and nucleolytic cleavage of unmethylated foreign DNA." * Changed definition of GO:0009405 from "The specific processes that generate the ability of an organism to cause disease in another." to "The set of specific processes that generate the ability of an organism to cause disease in another." * Changed definition of GO:0009631 from "Processes that increase freezing tolerance of an organism in response to low, nonfreezing temperatures." to "Any process that increases freezing tolerance of an organism in response to low, nonfreezing temperatures." * Changed definition of GO:0009650 from "The processes by which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." to "Any process by which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV." * Changed definition of GO:0009777 from "The metabolic processes by which photosynthetic organisms use light energy to convert ADP to ATP without the concomitant reduction of dioxygen (O2) to water that occurs in phosphorylation." to "Any metabolic process by which photosynthetic organisms use light energy to convert ADP to ATP without the concomitant reduction of dioxygen (O2) to water that occurs in phosphorylation." * Changed definition of GO:0009780 from "Processes by which NADP+ is reduced to NADPH. The light reactions of photosynthesis use energy from photons to generate high-energy electrons. These electrons are used directly to reduce NADP+ to NADPH. NADPH is a relatively stable molecule and can pass on its hydrogen atom to other molecules in chemical reactions." to "The process by which NADP+ is reduced to NADPH. The light reactions of photosynthesis use energy from photons to generate high-energy electrons. These electrons are used directly to reduce NADP+ to NADPH. NADPH is a relatively stable molecule and can pass on its hydrogen atom to other molecules in chemical reactions." * Changed definition of GO:0009856 from "Biological processes occurring in plants beginning when the pollen lands on the stigma and continuing up to, but not including, fertilization, as defined by sperm-central cell fusion." to "The cascade of biological processes occurring in plants beginning when the pollen lands on the stigma and continuing up to, but not including, fertilization, as defined by sperm-central cell fusion." * Changed definition of GO:0009949 from "The processes resulting in the establishment of polarity along the anterior/posterior axis." to "Any process resulting in the establishment of polarity along the anterior/posterior axis." * Changed definition of GO:0009951 from "The processes resulting in the establishment of polarity along the dorsal/ventral axis." to "Any process resulting in the establishment of polarity along the dorsal/ventral axis." * Changed definition of GO:0009987 from "Processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." to "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." * Changed definition of GO:0009992 from "Any of the processes involved in the maintenance of an internal equilibrium of water within a cell." to "Any process involved in the maintenance of an internal equilibrium of water within a cell." * Changed definition of GO:0010050 from "The processes involved in the transition of a plant from a juvenile phase of vegetative development to an adult phase of vegetative development." to "Any process involved in the transition of a plant from a juvenile phase of vegetative development to an adult phase of vegetative development." * Changed definition of GO:0010073 from "The processes involved in maintaining the identity, size and shape of a meristem." to "Any process involved in maintaining the identity, size and shape of a meristem." * Changed definition of GO:0010075 from "The processes involved in maintaining the size and shape of a meristem." to "Any process involved in maintaining the size and shape of a meristem." * Changed definition of GO:0010076 from "The processes involved in maintaining the identity of a floral meristem. Identity is considered to be the aggregate of characteristics by which a structure is recognized." to "Any process involved in maintaining the identity of a floral meristem. Identity is considered to be the aggregate of characteristics by which a structure is recognized." * Changed definition of GO:0010077 from "The processes involved in maintaining the identity of an inflorescence meristem. Identity is considered to be the aggregate of characteristics by which a structure is recognized." to "Any process involved in maintaining the identity of an inflorescence meristem. Identity is considered to be the aggregate of characteristics by which a structure is recognized." * Changed definition of GO:0010078 from "The processes involved in maintaining the identity of a root meristem. Identity is considered to be the aggregate of characteristics by which a structure is recognized." to "Any process involved in maintaining the identity of a root meristem. Identity is considered to be the aggregate of characteristics by which a structure is recognized." * Changed definition of GO:0010079 from "The processes involved in maintaining the identity of a vegetative meristem. Identity is considered to be the aggregate of characteristics by which a structure is recognized." to "Any process involved in maintaining the identity of a vegetative meristem. Identity is considered to be the aggregate of characteristics by which a structure is recognized." * Changed definition of GO:0010080 from "The processes involved in maintaining the size and shape of a floral meristem." to "Any process involved in maintaining the size and shape of a floral meristem." * Changed definition of GO:0010081 from "The processes involved in maintaining the size and shape of an inflorescence meristem." to "Any process involved in maintaining the size and shape of an inflorescence meristem." * Changed definition of GO:0010082 from "The processes involved in maintaining the size and shape of a root meristem." to "Any process involved in maintaining the size and shape of a root meristem." * Changed definition of GO:0010083 from "The processes involved in maintaining the size and shape of a vegetative meristem." to "Any process involved in maintaining the size and shape of a vegetative meristem." * Changed definition of GO:0010085 from "The processes resulting in the establishment of polarity along the proximal/distal axis." to "Any process resulting in the establishment of polarity along the proximal/distal axis." * Changed definition of GO:0010091 from "The processes involved in the formation of branches in plant hair cells." to "Any process involved in the formation of branches in plant hair cells." * Changed definition of GO:0010216 from "The processes involved in maintaining the methylation state of a nucleotide sequence." to "Any process involved in maintaining the methylation state of a nucleotide sequence." * Changed definition of GO:0010231 from "The processes by which a dormant state is maintained in a seed." to "Any process by which a dormant state is maintained in a seed." * Changed definition of GO:0010268 from "Any of the processes involved in the maintenance of an internal equilibrium of brassinosteroids within an organism or cell." to "Any process involved in the maintenance of an internal equilibrium of brassinosteroids within an organism or cell." * Changed definition of GO:0010273 from "The processes that reduce or remove the toxicity of copper ion. These include transport of copper away from sensitive areas and to compartments or complexes whose purpose is sequestration of copper ion." to "Any process that reduce or remove the toxicity of copper ion. These include transport of copper away from sensitive areas and to compartments or complexes whose purpose is sequestration of copper ion." * Changed definition of GO:0010286 from "Processes that increase heat tolerance of an organism in response to high temperatures." to "Any process that increases heat tolerance of an organism in response to high temperatures." * Changed definition of GO:0010299 from "The processes that reduce or remove the toxicity of cobalt ion. These include transport of cobalt away from sensitive areas and to compartments or complexes whose purpose is sequestration of cobalt ion." to "Any process that reduce or remove the toxicity of cobalt ion. These include transport of cobalt away from sensitive areas and to compartments or complexes whose purpose is sequestration of cobalt ion." * Changed definition of GO:0010312 from "The processes that reduce or remove the toxicity of zinc ion. These include transport of zinc away from sensitive areas and to compartments or complexes whose purpose is sequestration of zinc ion." to "Any process that reduce or remove the toxicity of zinc ion. These include transport of zinc away from sensitive areas and to compartments or complexes whose purpose is sequestration of zinc ion." * Changed definition of GO:0010336 from "Maintenance of endogenous concentration of primary gibberellic acid equilibrium, or constant level of gibberellic acid in a biological system by a number of biochemical processes including transport, biosynthesis, catabolism and conjugation." to "Any biological process involved in the maintenance of an internal equilibrium of gibberellic acid; may involve transport, biosynthesis, catabolism or conjugation." * Changed definition of GO:0010481 from "The processes resulting in the physical partitioning and separation of an epidermal cell, any of the cells making up the epidermis, into daughter cells." to "Any process resulting in the physical partitioning and separation of an epidermal cell, any of the cells making up the epidermis, into daughter cells." * Changed definition of GO:0010492 from "The processes involved in maintaining the identity of the shoot apical meristem. Identity is considered to be the aggregate of characteristics by which a structure is recognized." to "Any process involved in maintaining the identity of the shoot apical meristem. Identity is considered to be the aggregate of characteristics by which a structure is recognized." * Changed definition of GO:0010509 from "The biological processes involved in the maintenance of an internal equilibrium of a polyamine." to "Any biological process involved in the maintenance of an internal equilibrium of a polyamine." * Changed definition of GO:0014733 from "Processes by which skeletal muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." to "Any process by which skeletal muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." * Changed definition of GO:0014805 from "Processes by which smooth muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." to "Any process by which smooth muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." * Changed definition of GO:0014888 from "Processes by which striated muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." to "Any process by which striated muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." * Changed definition of GO:0015977 from "The processes by which inorganic carbon (usually carbon dioxide) is incorporated into organic compounds (usually carbohydrates)." to "Any process by which inorganic carbon (usually carbon dioxide) is incorporated into organic compounds (usually carbohydrates)." * Changed definition of GO:0017126 from "Processes involved with the formation and assembly of the nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells." to "The process by which the nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells, is formed and assembled." * Changed definition of GO:0019044 from "The processes required for maintaining the latent form of the viral genome within a cell." to "Any process required for maintaining the latent form of the viral genome within a cell." * Changed definition of GO:0019045 from "The processes required for latent viral replication in a cell." to "Any process required for latent viral replication in a cell." * Changed definition of GO:0019050 from "Viral processes and gene products that result in the inhibition of apoptosis, facilitating prolonged cell survival during viral replication." to "Any viral process that results in the inhibition of apoptosis, facilitating prolonged cell survival during viral replication." * Changed definition of GO:0019051 from "Viral processes that result in the induction of apoptosis of infected cells, facilitating release and spread of progeny virions." to "The set of viral processes that result in the induction of apoptosis of infected cells, facilitating release and spread of progeny virions." * Changed definition of GO:0019052 from "Viral processes that result in the inhibition of intracellular (innate immune response) antiviral mechanisms, thereby facilitating viral replication." to "Any viral process that results in the inhibition of intracellular (innate immune response) antiviral mechanisms, thereby facilitating viral replication." * Changed definition of GO:0019053 from "Viral processes that result in the inhibition of extracellular (adaptive immune response) antiviral mechanisms, thereby facilitating viral replication." to "Any viral process that results in the inhibition of extracellular (adaptive immune response) antiviral mechanisms, thereby facilitating viral replication." * Changed definition of GO:0019059 from "Processes involved in the start of virus infection of cells." to "The set of processes involved in the start of virus infection of cells." * Changed definition of GO:0019062 from "The processes involved in the specific binding of a viral antireceptor to a cell surface receptor." to "Any process involved in the specific binding of a viral antireceptor to a cell surface receptor." * Changed definition of GO:0019063 from "The processes required for the introduction of virus particles into the cell." to "Any process required for the introduction of virus particles into the cell." * Changed definition of GO:0019067 from "The processes involved in the assembly, maturation, egress, and release of progeny virions." to "Any process involved in the assembly, maturation, egress, and release of progeny virions." * Changed definition of GO:0019070 from "Viral processes that occur on newly synthesized viral genomes." to "Any viral process that occurs on newly synthesized viral genomes." * Changed definition of GO:0019093 from "The processes by which mitochondrial RNA is transported to, or maintained in, a specific location." to "Any process by which mitochondrial RNA is transported to, or maintained in, a specific location." * Changed definition of GO:0019094 from "The processes by which mRNA is transported to, or maintained in, the oocyte pole plasm." to "Any process by which mRNA is transported to, or maintained in, the oocyte pole plasm." * Changed definition of GO:0019095 from "The processes by which mitochondrial ribosomal RNA is transported to, or maintained in, the oocyte pole plasm." to "Any process by which mitochondrial ribosomal RNA is transported to, or maintained in, the oocyte pole plasm." * Changed definition of GO:0019096 from "The processes by which mitochondrial large ribosomal RNA is transported to, or maintained in, the oocyte pole plasm." to "Any process by which mitochondrial large ribosomal RNA is transported to, or maintained in, the oocyte pole plasm." * Changed definition of GO:0019097 from "The processes by which mitochondrial small ribosomal RNA is transported to, or maintained in, the oocyte pole plasm." to "Any process by which mitochondrial small ribosomal RNA is transported to, or maintained in, the oocyte pole plasm." * Changed definition of GO:0019430 from "The processes involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2)." to "Any process involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2)." * Changed definition of GO:0019725 from "The processes involved in the maintenance of an internal equilibrium at the level of the cell." to "Any process involved in the maintenance of an internal equilibrium at the level of the cell." * Changed definition of GO:0021957 from "Generation of a long process of a pyramidal cell, that carries efferent (outgoing) action potentials from the cell body in cerebral cortex layer V towards target cells in the gray matter of the spinal cord. This axonal processes is a member of those that make up the corticospinal tract." to "Generation of a long process of a pyramidal cell, that carries efferent (outgoing) action potentials from the cell body in cerebral cortex layer V towards target cells in the gray matter of the spinal cord. This axonal process is a member of those that make up the corticospinal tract." * Changed definition of GO:0021958 from "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the dorsal root ganglion towards target cells in the medulla. This axonal processes is a member of those that make up the gracilis tract, a group of axons that are from neurons involved in proprioception from the lower trunk and lower limb." to "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the dorsal root ganglion towards target cells in the medulla. This axonal process is a member of those that make up the gracilis tract, a group of axons that are from neurons involved in proprioception from the lower trunk and lower limb." * Changed definition of GO:0021959 from "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the dorsal root ganglion towards target cells in the medulla. This axonal processes is a member of those that make up the cuneatus tract, a group of axons that are from neurons involved in proprioception from the upper trunk and upper limb." to "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the dorsal root ganglion towards target cells in the medulla. This axonal process is a member of those that make up the cuneatus tract, a group of axons that are from neurons involved in proprioception from the upper trunk and upper limb." * Changed definition of GO:0021960 from "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in one half of the cerebral cortex towards target cells in the contralateral half. This axonal processes is a member of those that make up the anterior commissure, a small midline fiber tract that lies at the anterior end of the corpus callosum." to "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in one half of the cerebral cortex towards target cells in the contralateral half. This axonal process is a member of those that make up the anterior commissure, a small midline fiber tract that lies at the anterior end of the corpus callosum." * Changed definition of GO:0021963 from "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the spinal cord towards target cells in the thalamus. This axonal processes is a member of those that make up the spinothalamic tract, one of the major routes of nociceptive signaling." to "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the spinal cord towards target cells in the thalamus. This axonal process is a member of those that make up the spinothalamic tract, one of the major routes of nociceptive signaling." * Changed definition of GO:0021974 from "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in spinal cord towards target cells in the thalamus. This axonal processes is a member of those that make up the trigeminothalamic tract, one of the major routes of nociceptive and temperature signaling from the face." to "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in spinal cord towards target cells in the thalamus. This axonal process is a member of those that make up the trigeminothalamic tract, one of the major routes of nociceptive and temperature signaling from the face." * Changed definition of GO:0030104 from "Any of the processes involved in the maintenance of an internal equilibrium of water within an organism or cell." to "Any process involved in the maintenance of an internal equilibrium of water within an organism or cell." * Changed definition of GO:0030431 from "The processes by which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain." to "Any process by which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain." * Changed definition of GO:0030718 from "The processes involved in preventing uncommitted germ-line stem cells from differentiating as another cell type." to "Any process involved in preventing uncommitted germ-line stem cells from differentiating as another cell type." * Changed definition of GO:0031081 from "The processes that establish the spatial arrangement of nuclear pores within the nuclear envelope." to "Any process that establish the spatial arrangement of nuclear pores within the nuclear envelope." * Changed definition of GO:0031144 from "The processes by which the proteasome is transported to, or maintained in, a specific location." to "Any process by which the proteasome is transported to, or maintained in, a specific location." * Changed definition of GO:0031345 from "Any process that stops, prevents or reduces the frequency, rate or extent of the processes involved in the formation, arrangement of constituent parts, or disassembly of cell projections." to "Any process that stops, prevents or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections." * Changed definition of GO:0031503 from "The processes by which a protein complex is transported to, or maintained in, a specific location." to "Any process by which a protein complex is transported to, or maintained in, a specific location." * Changed definition of GO:0032189 from "The processes by which a contractile ring is maintained in a location and prevented from moving elsewhere." to "Any process by which a contractile ring is maintained in a location and prevented from moving elsewhere." * Changed definition of GO:0032204 from "Any process that modulates the frequency, rate or extent of processes that affect and monitor the activity of telomeric proteins and the length of telomeric DNA." to "Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA." * Changed definition of GO:0032205 from "Any process that stops, prevents or reduces the frequency, rate or extent of the processes that affect and monitor the activity of telomeric proteins and the length of telomeric DNA." to "Any process that stops, prevents or reduces the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA." * Changed definition of GO:0032206 from "Any process that activates or increases the frequency, rate or extent of the processes that affect and monitor the activity of telomeric proteins and the length of telomeric DNA." to "Any process that activates or increases the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA." * Changed definition of GO:0032207 from "Any process that modulates the frequency, rate or extent of recombinational processes involved in the maintenance of proper telomeric length." to "Any process that modulates the frequency, rate or extent of a recombinational process involved in the maintenance of proper telomeric length." * Changed definition of GO:0032208 from "Any process that stops, prevents or reduces the frequency, rate or extent of recombinational processes involved in the maintenance of proper telomeric length." to "Any process that stops, prevents or reduces the frequency, rate or extent of a recombinational process involved in the maintenance of proper telomeric length." * Changed definition of GO:0032209 from "Any process that activates or increases the frequency, rate or extent of recombinational processes involved in the maintenance of proper telomeric length." to "Any process that activates or increases the frequency, rate or extent of a recombinational process involved in the maintenance of proper telomeric length." * Changed definition of GO:0032252 from "The processes by which a secretory granule is transported to, and/or maintained in, a specific location within the cell." to "Any process by which a secretory granule is transported to, and/or maintained in, a specific location within the cell." * Changed definition of GO:0032253 from "The processes by which a dense core granule is transported to, and/or maintained in, a specific location within the cell." to "Any process by which a dense core granule is transported to, and/or maintained in, a specific location within the cell." * Changed definition of GO:0032255 from "The processes by which a secretory granule is maintained in a specific location within a cell and prevented from moving elsewhere." to "Any process by which a secretory granule is maintained in a specific location within a cell and prevented from moving elsewhere." * Changed definition of GO:0032257 from "The processes by which a dense core granule is maintained in a specific location within a cell and prevented from moving elsewhere." to "Any process by which a dense core granule is maintained in a specific location within a cell and prevented from moving elsewhere." * Changed definition of GO:0032400 from "The processes by which a melanosome is transported to, and/or maintained in, a specific location within the cell." to "Any process by which a melanosome is transported to, and/or maintained in, a specific location within the cell." * Changed definition of GO:0032418 from "The processes by which a lysosome is transported to, and/or maintained in, a specific location." to "Any process by which a lysosome is transported to, and/or maintained in, a specific location." * Changed definition of GO:0032439 from "The processes by which endosomes are transported to, and/or maintained in, a specific location within the cell." to "Any process by which endosomes are transported to, and/or maintained in, a specific location within the cell." * Changed definition of GO:0032501 from "The biological processes, occurring at the level of a multicellular organism, pertinent to its function." to "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." * Changed definition of GO:0032507 from "The processes by which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere." to "Any process by which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere." * Changed definition of GO:0033036 from "The processes by which a macromolecule is transported to, or maintained in, a specific location." to "Any process by which a macromolecule is transported to, or maintained in, a specific location." * Changed definition of GO:0033037 from "The processes by which a polysaccharide is transported to, or maintained in, a specific location." to "Any process by which a polysaccharide is transported to, or maintained in, a specific location." * Changed definition of GO:0033043 from "Any process that modulates the frequency, rate or extent of the processes involved in the formation, arrangement of constituent parts, or disassembly of an organelle." to "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." * Changed definition of GO:0033044 from "Any process that modulates the frequency, rate or extent of the processes involved in the formation, arrangement of constituent parts, or disassembly of a chromosome." to "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome." * Changed definition of GO:0033368 from "The processes by which a protease is transported to, or maintained in, a location within a secretory granule in a mast cell." to "Any process by which a protease is transported to, or maintained in, a location within a secretory granule in a mast cell." * Changed definition of GO:0033375 from "The processes by which a protease is transported to, or maintained in, a location within a secretory granule in a T cell." to "Any process by which a protease is transported to, or maintained in, a location within a secretory granule in a T cell." * Changed definition of GO:0033380 from "The processes by which the protease granzyme B is transported to, or maintained in, a location within a secretory granule in a T cell." to "Any process by which the protease granzyme B is transported to, or maintained in, a location within a secretory granule in a T cell." * Changed definition of GO:0033566 from "The processes by which a gamma-tubulin complex is transported to, or maintained in, a specific location." to "Any process by which a gamma-tubulin complex is transported to, or maintained in, a specific location." * Changed synonym scope of GO:0033903 from "Exact" to "Broad" * Changed synonym scope of GO:0033903 from "Exact" to "Broad" * Changed definition of GO:0034101 from "The processes of regulating the production and elimination of erythrocytes within an organism." to "Any process of regulating the production and elimination of erythrocytes within an organism." * Changed definition of GO:0034397 from "The processes by which a telomere is transported to, and/or maintained in, a specific location." to "Any process by which a telomere is transported to, and/or maintained in, a specific location." * Changed definition of GO:0034433 from "A lipid modification process in which a steroid ester is formed by the combination of a carboxylic acid (often a fatty acid) and a steroid molecule (e.g. cholesterol)." to "A lipid modification process in which a steroid ester is formed by the combination of a carboxylic acid (often a fatty acid) and a steroid molecule (e.g. cholesterol)." * Changed definition of GO:0034434 from "A lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and a sterol molecule (e.g. cholesterol)." to "A lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and a sterol molecule (e.g. cholesterol)." * Changed definition of GO:0042049 from "Any of the processes involved in the maintenance of an internal equilibrium of acyl-CoA within a cell or between a cell and its external environment." to "Any process involved in the maintenance of an internal equilibrium of acyl-CoA within a cell or between a cell and its external environment." * Changed definition of GO:0042245 from "Th