[go-diff] GO update 02/01/2008
Remote CVS for Gene Ontology
gocvs at genome.Stanford.EDU
Fri Feb 1 21:30:44 PST 2008
OBODIFF of gene_ontology_edit.obo version 5.676 by 5.678
Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010521
* Created object of type obo:TERM with id GO:0010522
* Created object of type obo:TERM with id GO:0010523
* Created object of type obo:TERM with id GO:0010524
* Created object of type obo:TERM with id GO:0010525
* Created object of type obo:TERM with id GO:0010526
* Created object of type obo:TERM with id GO:0010527
* Created object of type obo:TERM with id GO:0010528
* Created object of type obo:TERM with id GO:0010529
* Created object of type obo:TERM with id GO:0010530
* Created object of type obo:TERM with id GO:0034230
* Created object of type obo:TERM with id GO:0034231
* Created object of type obo:TERM with id GO:0034232
* Created object of type obo:TERM with id GO:0034233
* Created object of type obo:TERM with id GO:0034234
* Created object of type obo:TERM with id GO:0034235
* Populated new object GO:0010521 (macro)
* Changed name of GO:0010521 from "<new term>" to "telomerase inhibitor activity"
* Set definition of GO:0010521 to "Stops, prevents or reduces the activity of a telomerase. Telomerase catalyzes the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence."
* Added definition dbxref GOC:dph to GO:0010521
* Added definition dbxref GOC:krc to GO:0010521
* Added definition dbxref GOC:tb to GO:0010521
* Copied GO:0010521 to GO:0004857 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0010521
* Populated new object GO:0010522 (macro)
* Changed name of GO:0010522 from "<new term>" to "regulation of calcium ion transport into cytosol"
* Set definition of GO:0010522 to "Any process that modulates the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components."
* Added definition dbxref GOC:dph to GO:0010522
* Added definition dbxref GOC:tb to GO:0010522
* Copied GO:0010522 to GO:0051924 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010522
* Populated new object GO:0010523 (macro)
* Changed name of GO:0010523 from "<new term>" to "negative regulation of calcium ion transport into cytosol"
* Set definition of GO:0010523 to "Any process that decreases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components."
* Added definition dbxref GOC:dph to GO:0010523
* Added definition dbxref GOC:tb to GO:0010523
* Copied GO:0010523 to GO:0010522 with type OBO_REL:is_a
* Copied GO:0010523 to GO:0051926 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010523
* Populated new object GO:0010524 (macro)
* Changed name of GO:0010524 from "<new term>" to "positive regulation of calcium ion transport into cytosol"
* Set definition of GO:0010524 to "Any process that decreases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components."
* Added definition dbxref GOC:dph to GO:0010524
* Added definition dbxref GOC:tb to GO:0010524
* Copied GO:0010524 to GO:0051928 with type OBO_REL:is_a
* Copied GO:0010524 to GO:0010522 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010524
* Populated new object GO:0010525 (macro)
* Changed name of GO:0010525 from "<new term>" to "regulation of transposition, RNA-mediated"
* Set definition of GO:0010525 to "Any process that modulates the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate."
* Added definition dbxref GOC:dph to GO:0010525
* Added definition dbxref GOC:tb to GO:0010525
* Copied GO:0010525 to GO:0032197 with type part_of
* Copied GO:0010525 to GO:0010528 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010525
* Populated new object GO:0010526 (macro)
* Changed name of GO:0010526 from "<new term>" to "negative regulation of transposition, RNA-mediated"
* Set definition of GO:0010526 to "Any process that decreases the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate."
* Added definition dbxref GOC:dph to GO:0010526
* Added definition dbxref GOC:tb to GO:0010526
* Copied GO:0010526 to GO:0010525 with type OBO_REL:is_a
* Copied GO:0010526 to GO:0010529 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010526
* Populated new object GO:0010527 (macro)
* Changed name of GO:0010527 from "<new term>" to "positive regulation of transposition, RNA-mediated"
* Set definition of GO:0010527 to "Any process that increases the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate."
* Added definition dbxref GOC:dph to GO:0010527
* Added definition dbxref GOC:tb to GO:0010527
* Copied GO:0010527 to GO:0010525 with type OBO_REL:is_a
* Copied GO:0010527 to GO:0010530 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010527
* Populated new object GO:0010528 (macro)
* Changed name of GO:0010528 from "<new term>" to "regulation of transposition"
* Set definition of GO:0010528 to "Any process that modulates the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites."
* Added definition dbxref GOC:dph to GO:0010528
* Added definition dbxref GOC:tb to GO:0010528
* Copied GO:0010528 to GO:0000018 with type OBO_REL:is_a
* Copied GO:0010528 to GO:0032196 with type part_of
* Assigned namespace "biological_process" to GO:0010528
* Populated new object GO:0010529 (macro)
* Changed name of GO:0010529 from "<new term>" to "negative regulation of transposition"
* Set definition of GO:0010529 to "Any process that decreases the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites."
* Added definition dbxref GOC:dph to GO:0010529
* Added definition dbxref GOC:tb to GO:0010529
* Copied GO:0010529 to GO:0010528 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010529
* Populated new object GO:0010530 (macro)
* Changed name of GO:0010530 from "<new term>" to "positive regulation of transposition"
* Set definition of GO:0010530 to "Any process that decreases the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites."
* Added definition dbxref GOC:dph to GO:0010530
* Added definition dbxref GOC:tb to GO:0010530
* Copied GO:0010530 to GO:0010528 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010530
* Populated new object GO:0034230 (macro)
* Changed name of GO:0034230 from "<new term>" to "enkephalin processing"
* Set definition of GO:0034230 to "The formation of mature enkephalin, a pentapeptide hormone involved in regulating pain and nociception in the body by proteolytic processing of enkephalin propeptide."
* Added definition dbxref GOC:mah to GO:0034230
* Added definition dbxref GOC:rl to GO:0034230
* Added definition dbxref PMID:8262946 to GO:0034230
* Added synonym "enkephalin formation" to GO:0034230
* Changed synonym scope of GO:0034230 from "Related" to "Exact"
* Added synonym "peptide enkephalin formation" to GO:0034230
* Changed synonym scope of GO:0034230 from "Related" to "Exact"
* Added synonym "peptide enkephalin processing" to GO:0034230
* Changed synonym scope of GO:0034230 from "Related" to "Exact"
* Copied GO:0034230 to GO:0016486 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0034230
* Populated new object GO:0034231 (macro)
* Changed name of GO:0034231 from "<new term>" to "islet amyloid polypeptide processing"
* Set definition of GO:0034231 to "The formation of mature islet amyloid polypeptide (IAPP) by posttranslational processing of pro-islet amyloid polypeptide (pro-IAPP)."
* Added definition dbxref GOC:rl to GO:0034231
* Added definition dbxref PMID:15983213 to GO:0034231
* Added definition dbxref PMID:8262946 to GO:0034231
* Added synonym "IAPP formation" to GO:0034231
* Changed synonym scope of GO:0034231 from "Related" to "Exact"
* Added synonym "IAPP processing" to GO:0034231
* Changed synonym scope of GO:0034231 from "Related" to "Exact"
* Added synonym "islet amyloid peptide formation" to GO:0034231
* Changed synonym scope of GO:0034231 from "Related" to "Exact"
* Added synonym "islet amyloid peptide processing" to GO:0034231
* Changed synonym scope of GO:0034231 from "Related" to "Exact"
* Added synonym "islet amyloid polypeptide formation" to GO:0034231
* Copied GO:0034231 to GO:0016486 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0034231
* Populated new object GO:0034232 (macro)
* Changed name of GO:0034232 from "<new term>" to "spore wall chitin catabolic process"
* Set definition of GO:0034232 to "The chemical reactions and pathways resulting in the breakdown of spore wall chitin, a linear polysaccharide consisting of P-1,4-linked N-acetyl-D-glucosamine residues, found in the walls of fungal-type spores."
* Added definition dbxref GOC:mah to GO:0034232
* Added synonym "spore wall chitin breakdown" to GO:0034232
* Changed synonym scope of GO:0034232 from "Related" to "Exact"
* Added synonym "spore wall chitin catabolism" to GO:0034232
* Changed synonym scope of GO:0034232 from "Related" to "Exact"
* Added synonym "spore wall chitin degradation" to GO:0034232
* Changed synonym scope of GO:0034232 from "Related" to "Exact"
* Copied GO:0034232 to GO:0034218 with type OBO_REL:is_a
* Copied GO:0034232 to GO:0006039 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0034232
* Populated new object GO:0034233 (macro)
* Changed name of GO:0034233 from "<new term>" to "regulation of cell wall chitin catabolic process"
* Set definition of GO:0034233 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of cell wall chitin."
* Added definition dbxref GOC:mah to GO:0034233
* Added synonym "regulation of cell wall chitin breakdown" to GO:0034233
* Changed synonym scope of GO:0034233 from "Related" to "Exact"
* Added synonym "regulation of cell wall chitin catabolism" to GO:0034233
* Changed synonym scope of GO:0034233 from "Related" to "Exact"
* Added synonym "regulation of cell wall chitin formation" to GO:0034233
* Changed synonym scope of GO:0034233 from "Related" to "Exact"
* Copied GO:0034233 to GO:0034222 with type OBO_REL:is_a
* Copied GO:0034233 to GO:0006039 with type part_of
* Assigned namespace "biological_process" to GO:0034233
* Populated new object GO:0034234 (macro)
* Changed name of GO:0034234 from "<new term>" to "regulation of spore wall chitin catabolic process"
* Set definition of GO:0034234 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of spore wall chitin."
* Added definition dbxref GOC:mah to GO:0034234
* Added synonym "regulation of spore wall chitin breakdown" to GO:0034234
* Changed synonym scope of GO:0034234 from "Related" to "Exact"
* Added synonym "regulation of spore wall chitin catabolism" to GO:0034234
* Changed synonym scope of GO:0034234 from "Related" to "Exact"
* Added synonym "regulation of spore wall chitin formation" to GO:0034234
* Changed synonym scope of GO:0034234 from "Related" to "Exact"
* Copied GO:0034234 to GO:0034233 with type OBO_REL:is_a
* Copied GO:0034234 to GO:0034232 with type part_of
* Assigned namespace "biological_process" to GO:0034234
* Populated new object GO:0034235 (macro)
* Changed name of GO:0034235 from "<new term>" to "GPI anchor binding"
* Added comment "Note that this term should be used to annotate gene products that interact non-covalently with GPI anchors, and not proteins that have GPI anchors covalently attached."
* Set definition of GO:0034235 to "Interacting selectively with any glycosylphosphatidylinositol anchor. GPI anchors serve to attach membrane proteins to the lipid bilayer of cell membranes."
* Added definition dbxref GOC:vw to GO:0034235
* Added synonym "glycosylphosphatidylinositol binding" to GO:0034235
* Changed synonym scope of GO:0034235 from "Related" to "Exact"
* Copied GO:0034235 to GO:0035091 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0034235
* Copied GO:0000335 to GO:0010529 with type OBO_REL:is_a
* Copied GO:0000336 to GO:0010530 with type OBO_REL:is_a
* Deleted GO:0000337 --OBO_REL:is_a--> GO:0000018
* Copied GO:0000337 to GO:0010528 with type OBO_REL:is_a
* Changed comment from "See also the cellular component term 'cellular component ; GO:0005575'." to "This term was made obsolete because it was originally intended only as a temporary parent for protein complex terms for which no more specific parents had been found. This term no longer has any children: All protein complex terms are is_a 'protein complex ; GO:0043234' and nearly all have been placed under parents to yield more specific paths traversing a part_of relationship. In other words, the term has been superseded by other terms and relationships in the cellular component ontology, and is no longer needed."
* Changed definition of GO:0005941 from "Used as a holding place for cellular components whose precise localization is, as yet, unknown, or has not been determined by GO (the latter is the major reason for nodes to have this parent); this term should not be used for annotation of gene products." to "OBSOLETE. Used as a holding place for cellular components whose precise localization is, as yet, unknown, or has not been determined by GO (the latter is the major reason for nodes to have this parent); this term should not be used for annotation of gene products."
* Deleted GO:0005941 --OBO_REL:is_a--> GO:0043234
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 13cdabc
* Deleted GO:0006313 --OBO_REL:is_a--> GO:0006310
* Changed definition of GO:0032196 from "Any process involved in mediating the movement of discrete segments of DNA between nonhomolgous sites." to "Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites."
* Copied GO:0032196 to GO:0006310 with type OBO_REL:is_a
* Added comment "This term was made obsolete because nucleoprotein filament formation does not require ATP hydrolysis, so the term is misleading."
* Changed definition of GO:0033171 from "Catalysis of the reaction: ATP + H2O = ADP + phosphate to drive the assembly of proteins such as Rad51p onto single-stranded (ss) DNA to form a helical nucleoprotein filament." to "OBSOLETE. Catalysis of the reaction: ATP + H2O = ADP + phosphate to drive the assembly of proteins such as Rad51p onto single-stranded (ss) DNA to form a helical nucleoprotein filament."
* Deleted GO:0033171 --OBO_REL:is_a--> GO:0033170
* Deleted GO:0033171 --OBO_REL:is_a--> GO:0003677
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 3ca3a4
* Changed synonym scope of GO:0033920 from "Broad" to "Exact"
* Added synonym "regulation of cell wall chitin metabolism" to GO:0034222
* Changed synonym scope of GO:0034222 from "Related" to "Exact"
* Added comment "This term was made obsolete because low-density lipoprotein is a macromolecular complex, not a single class of molecule; its degradation involves the dissociation of non-covalently attached constituents as well as some breaking and reforming of covalent bonds."
* Changed definition of GO:0045192 from "The chemical reactions and pathways resulting in the breakdown of low-density lipoproteins, also known as beta lipoproteins, one of the classes of lipoproteins found in the bloodstream of animals, acting as a carrier for cholesterol and fats." to "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of low-density lipoproteins, also known as beta lipoproteins, one of the classes of lipoproteins found in the bloodstream of animals, acting as a carrier for cholesterol and fats."
* Deleted GO:0045192 --OBO_REL:is_a--> GO:0042159
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 11b9972
* Added comment "This term was made obsolete because low-density lipoprotein is a macromolecular complex, not a single class of molecule; its degradation involves the dissociation of non-covalently attached constituents as well as some breaking and reforming of covalent bonds."
* Changed definition of GO:0045193 from "The chemical reactions and pathways resulting in the breakdown of acetylated low-density lipoproteins." to "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of acetylated low-density lipoproteins."
* Deleted GO:0045193 --OBO_REL:is_a--> GO:0045192
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at f73f39
* Added comment "This term was made obsolete because low-density lipoprotein is a macromolecular complex, not a single class of molecule; its degradation involves the dissociation of non-covalently attached constituents as well as some breaking and reforming of covalent bonds."
* Changed definition of GO:0045194 from "The chemical reactions and pathways resulting in the breakdown of oxidized low-density lipoproteins." to "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of oxidized low-density lipoproteins."
* Deleted GO:0045194 --OBO_REL:is_a--> GO:0045192
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 57f433
* Added comment "This term was made obsolete because it has been widely, and incorrectly, used to annotate proteins that have GPI anchors covalently attached. A new term has been created that can be used to annotate gene products that interact non-covalently with GPI anchors."
* Changed definition of GO:0048503 from "Interacting selectively with any glycosylphosphatidylinositol anchor. GPI anchors serve to attach membrane proteins to the lipid bilayer of cell membranes." to "OBSOLETE. Interacting selectively with any glycosylphosphatidylinositol anchor. GPI anchors serve to attach membrane proteins to the lipid bilayer of cell membranes."
* Deleted GO:0048503 --OBO_REL:is_a--> GO:0035091
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 6172b5
* Deleted GO:0048548 --OBO_REL:is_a--> GO:0006907
* Copied GO:0048548 to GO:0006907 with type part_of
* Deleted GO:0051037 --part_of--> GO:0007126
* Copied GO:0051205 to GO:0032594 with type OBO_REL:is_a
* Copied GO:0051925 to GO:0032412 with type OBO_REL:is_a
* Deleted synonym "negative regulation of voltage gated calcium channel activity" from GO:0051927
* Added synonym "negative regulation of voltage-gated calcium channel activity" to GO:0051927
* Changed synonym scope of GO:0051927 from "Related" to "Exact"
* Copied GO:0051927 to GO:0032413 with type OBO_REL:is_a
* Deleted synonym "positive regulation of voltage gated calcium channel activity" from GO:0051929
* Added synonym "positive regulation of voltage-gated calcium channel activity" to GO:0051929
* Changed synonym scope of GO:0051929 from "Related" to "Exact"
* Copied GO:0051929 to GO:0032414 with type OBO_REL:is_a
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