[go-diff] GO update 12/14/2007
Remote CVS for Gene Ontology
gocvs at genome.Stanford.EDU
Fri Dec 14 21:30:44 PST 2007
OBODIFF of gene_ontology_edit.obo version 5.614 by 5.622
Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010496
* Created object of type obo:TERM with id GO:0010497
* Created object of type obo:TERM with id GO:0010498
* Created object of type obo:TERM with id GO:0010499
* Created object of type obo:TERM with id GO:0010500
* Created object of type obo:TERM with id GO:0033955
* Created object of type obo:TERM with id GO:0033962
* Created object of type obo:TERM with id GO:0033967
* Created object of type obo:TERM with id GO:0033979
* Created object of type obo:TERM with id GO:0033985
* Created object of type obo:TERM with id GO:0033986
* Created object of type obo:TERM with id GO:0033993
* Created object of type obo:TERM with id GO:0034014
* Created object of type obo:TERM with id GO:0034021
* Created object of type obo:TERM with id GO:0034046
* Created object of type obo:TERM with id GO:0034047
* Created object of type obo:TERM with id GO:0034048
* Created object of type obo:TERM with id GO:0034049
* Created object of type obo:TERM with id GO:0055107
* Created object of type obo:TERM with id GO:0055108
* Populated new object GO:0010496 (macro)
* Changed name of GO:0010496 from "<new term>" to "intercellular transport"
* Set definition of GO:0010496 to "The movement of substances between cells in a multicellular organism."
* Added definition dbxref GOC:DL to GO:0010496
* Copied GO:0010496 to GO:0032501 with type OBO_REL:is_a
* Copied GO:0010496 to GO:0006810 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010496
* Populated new object GO:0010497 (macro)
* Changed name of GO:0010497 from "<new term>" to "plasmodesmata-mediated intercellular transport"
* Set definition of GO:0010497 to "The movement of substances between cells via plasmodesmata. Plasmodesmata is a fine cytoplasmic channel, found in all higher plants, that connects the cytoplasm of one cell to that of an adjacent cell."
* Added definition dbxref PMID:17601829 to GO:0010497
* Added synonym "plasmodesma-mediated cell-to-cell transport" to GO:0010497
* Added synonym "plasmodesma-mediated intercellular transport" to GO:0010497
* Added synonym "plasmodesmata-mediated cell-to-cell transport" to GO:0010497
* Copied GO:0010497 to GO:0010496 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010497
* Populated new object GO:0010498 (macro)
* Changed name of GO:0010498 from "<new term>" to "proteasomal protein catabolic process"
* Set definition of GO:0010498 to "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome."
* Added definition dbxref GOC:tb to GO:0010498
* Copied GO:0010498 to GO:0051603 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010498
* Populated new object GO:0010499 (macro)
* Changed name of GO:0010499 from "<new term>" to "proteasomal ubiquitin-independent protein catabolic process"
* Set definition of GO:0010499 to "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome but do not involve ubiquitin."
* Added definition dbxref GOC:tb to GO:0010499
* Copied GO:0010499 to GO:0010498 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010499
* Populated new object GO:0010500 (macro)
* Changed name of GO:0010500 from "<new term>" to "transmitting tissue development"
* Set definition of GO:0010500 to "The process whose specific outcome is the progression of the transmitting tract over time, from its formation to the mature structure. The transmitting tissue is the tissue in the style of a carpel through which the pollen tube grows; it connects the stigma and the inside of ovary."
* Added definition dbxref PMID:17855426 to GO:0010500
* Copied GO:0010500 to GO:0048467 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0010500
* Populated new object GO:0033955 (macro)
* Changed name of GO:0033955 from "<new term>" to "mitochondrial DNA inheritance"
* Set definition of GO:0033955 to "The process by which copies of the mitochondrial genome are segregated or distributed into daughter mitochondria upon mitochondrial fission."
* Added definition dbxref GOC:mah to GO:0033955
* Added synonym "mitochondrial chromosome segregation" to GO:0033955
* Added synonym "mitochondrial DNA segregation" to GO:0033955
* Copied GO:0033955 to GO:0000001 with type part_of
* Copied GO:0033955 to GO:0000002 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0033955
* Populated new object GO:0033962 (macro)
* Changed name of GO:0033962 from "<new term>" to "cytoplasmic mRNA processing body assembly"
* Set definition of GO:0033962 to "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body."
* Added definition dbxref GOC:mah to GO:0033962
* Added definition dbxref PMID:17429074 to GO:0033962
* Added synonym "P body assembly" to GO:0033962
* Changed synonym scope of GO:0033962 from "Related" to "Exact"
* Added synonym "P body biogenesis" to GO:0033962
* Added synonym "P-body assembly" to GO:0033962
* Changed synonym scope of GO:0033962 from "Related" to "Exact"
* Copied GO:0033962 to GO:0022618 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0033962
* Populated new object GO:0033967 (macro)
* Changed name of GO:0033967 from "<new term>" to "box C/D snoRNA metabolic process"
* Set definition of GO:0033967 to "The chemical reactions and pathways involving box C/D type small nucleolar RNA."
* Added definition dbxref GOC:mah to GO:0033967
* Copied GO:0033967 to GO:0016074 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0033967
* Populated new object GO:0033979 (macro)
* Changed name of GO:0033979 from "<new term>" to "box H/ACA snoRNA metabolic process"
* Set definition of GO:0033979 to "The chemical reactions and pathways involving box H/ACA type small nucleolar RNA."
* Added definition dbxref GOC:mah to GO:0033979
* Copied GO:0033979 to GO:0016074 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0033979
* Populated new object GO:0033985 (macro)
* Changed name of GO:0033985 from "<new term>" to "acidocalcisome lumen"
* Set definition of GO:0033985 to "The volume enclosed by the membranes of an acidocalcisome."
* Added definition dbxref GOC:mah to GO:0033985
* Copied GO:0033985 to GO:0043233 with type OBO_REL:is_a
* Copied GO:0033985 to GO:0020022 with type part_of
* Assigned namespace "cellular_component" to GO:0033985
* Populated new object GO:0033986 (macro)
* Changed name of GO:0033986 from "<new term>" to "response to methanol"
* Set definition of GO:0033986 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 methanol stimulus."
* Added definition dbxref GOC:sl to GO:0033986
* Copied GO:0033986 to GO:0010033 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0033986
* Populated new object GO:0033993 (macro)
* Changed name of GO:0033993 from "<new term>" to "response to lipid"
* Set definition of GO:0033993 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 lipid stimulus."
* Added definition dbxref GOC:sl to GO:0033993
* Copied GO:0033993 to GO:0010033 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0033993
* Populated new object GO:0034014 (macro)
* Changed name of GO:0034014 from "<new term>" to "response to triglyceride"
* Set definition of GO:0034014 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 triglyceride stimulus."
* Added definition dbxref GOC:sl to GO:0034014
* Added synonym "response to triacylglyceride" to GO:0034014
* Changed synonym scope of GO:0034014 from "Related" to "Exact"
* Added synonym "response to triacylglycerol" to GO:0034014
* Changed synonym scope of GO:0034014 from "Related" to "Exact"
* Copied GO:0034014 to GO:0033993 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0034014
* Populated new object GO:0034021 (macro)
* Changed name of GO:0034021 from "<new term>" to "response to silicon dioxide"
* Set definition of GO:0034021 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 silicon dioxide stimulus."
* Added definition dbxref GOC:sl to GO:0034021
* Added synonym "response to silica" to GO:0034021
* Changed synonym scope of GO:0034021 from "Related" to "Exact"
* Added synonym "response to silox" to GO:0034021
* Changed synonym scope of GO:0034021 from "Related" to "Exact"
* Copied GO:0034021 to GO:0010035 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0034021
* Populated new object GO:0034046 (macro)
* Changed name of GO:0034046 from "<new term>" to "poly(rG) binding"
* Set definition of GO:0034046 to "Interacting selectively with a sequence of guanine residues in an RNA molecule."
* Added definition dbxref GOC:mah to GO:0034046
* Added synonym "poly(G) binding" to GO:0034046
* Changed synonym scope of GO:0034046 from "Related" to "Broad"
* Copied GO:0034046 to GO:0003727 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0034046
* Populated new object GO:0034047 (macro)
* Changed name of GO:0034047 from "<new term>" to "regulation of protein phosphatase type 2A activity"
* Set definition of GO:0034047 to "Any process that modulates the activity of the enzyme protein phosphatase type 2A."
* Added definition dbxref GOC:mah to GO:0034047
* Copied GO:0034047 to GO:0043666 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0034047
* Populated new object GO:0034048 (macro)
* Changed name of GO:0034048 from "<new term>" to "negative regulation of protein phosphatase type 2A activity"
* Set definition of GO:0034048 to "Any process that stops or reduces the activity of the enzyme protein phosphatase type 2A."
* Added definition dbxref GOC:mah to GO:0034048
* Added GO:0034048 to category gosubset_prok
* Added synonym "down regulation of protein phosphatase type 2A activity" to GO:0034048
* Changed synonym scope of GO:0034048 from "Related" to "Exact"
* Added synonym "down-regulation of protein phosphatase type 2A activity" to GO:0034048
* Changed synonym scope of GO:0034048 from "Related" to "Exact"
* Added synonym "downregulation of protein phosphatase type 2A activity" to GO:0034048
* Changed synonym scope of GO:0034048 from "Related" to "Exact"
* Added synonym "inhibition of protein phosphatase type 2A activity" to GO:0034048
* Changed synonym scope of GO:0034048 from "Related" to "Narrow"
* Copied GO:0034048 to GO:0034047 with type OBO_REL:is_a
* Copied GO:0034048 to GO:0032515 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0034048
* Populated new object GO:0034049 (macro)
* Changed name of GO:0034049 from "<new term>" to "positive regulation of protein phosphatase type 2A activity"
* Set definition of GO:0034049 to "Any process that activates or increases the activity of the enzyme protein phosphatase type 2A."
* Added definition dbxref GOC:mah to GO:0034049
* Added GO:0034049 to category gosubset_prok
* Added synonym "activation of protein phosphatase type 2A activity" to GO:0034049
* Changed synonym scope of GO:0034049 from "Related" to "Narrow"
* Added synonym "stimulation of protein phosphatase type 2A activity" to GO:0034049
* Changed synonym scope of GO:0034049 from "Related" to "Narrow"
* Added synonym "up regulation of protein phosphatase type 2A activity" to GO:0034049
* Changed synonym scope of GO:0034049 from "Related" to "Exact"
* Added synonym "up-regulation of protein phosphatase type 2A activity" to GO:0034049
* Changed synonym scope of GO:0034049 from "Related" to "Exact"
* Added synonym "upregulation of protein phosphatase type 2A activity" to GO:0034049
* Changed synonym scope of GO:0034049 from "Related" to "Exact"
* Copied GO:0034049 to GO:0032516 with type OBO_REL:is_a
* Copied GO:0034049 to GO:0034047 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0034049
* Populated new object GO:0055107 (macro)
* Changed name of GO:0055107 from "<new term>" to "Golgi to secretory granule transport"
* Set definition of GO:0055107 to "The directed movement of proteins from the Golgi to a secretory granule. The secretory granule is a membrane-bound particle, usually protein, formed in the granular endoplasmic reticulum and the Golgi complex."
* Added definition dbxref GOC:jid to GO:0055107
* Added definition dbxref http://cancerweb.ncl.ac.uk to GO:0055107
* Copied GO:0055107 to GO:0046907 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0055107
* Populated new object GO:0055108 (macro)
* Changed name of GO:0055108 from "<new term>" to "Golgi to transport vesicle transport"
* Set definition of GO:0055108 to "The directed movement of proteins from the Golgi to a transport vesicle. Continuously secreted proteins are sorted into transport vesicles that fuse with the plasma membrane, releasing their contents by exocytosis."
* Added definition dbxref GOC:jid to GO:0055108
* Copied GO:0055108 to GO:0048193 with type part_of
* Copied GO:0055108 to GO:0046907 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0055108
* Copied GO:0000494 to GO:0033967 with type OBO_REL:is_a
* Copied GO:0000495 to GO:0033979 with type OBO_REL:is_a
* Added synonym "P-body" to GO:0000932
* Changed synonym scope of GO:0000932 from "Related" to "Exact"
* Deleted GO:0000932 --OBO_REL:is_a--> GO:0043234
* Copied GO:0000932 to GO:0030529 with type OBO_REL:is_a
* Changed name of GO:0002117 from "larval development (sensu Amphibia)" to "amphibian larval development"
* Changed definition of GO:0002117 from "The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. As in, but not restricted to, the amphibia (Amphibia, ncbi_taxonomy_id:8292)." to "The process whose specific outcome is the progression of the amphibian larva over time, from its formation to the mature structure. Amphibian larvae, sometimes called pollywogs or tadpoles, hatch from eggs and begin to grow limbs and other adult physical features at various times, depending on the species, before they metamorphose into the adult form."
* Added definition dbxref GOC:rf to GO:0002117
* Added definition dbxref http://www.livingunderworld.org/biology/ to GO:0002117
* Added synonym "larval development (sensu Amphibia)" to GO:0002117
* Changed synonym scope of GO:0002117 from "Related" to "Exact"
* Changed name of GO:0002119 from "larval development (sensu Nematoda)" to "nematode larval development"
* Changed definition of GO:0002119 from "The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. This begins with the newly hatched first-stage larva and ends with the end of the last larval stage (e.g. fourth-stage in C. elegans) before molting to adulthood. As in, but not restricted to, the roundworms (Nematoda, ncbi_taxonomy_id:6231)." to "The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (fr example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew."
* Added definition dbxref GOC:kva to GO:0002119
* Added synonym "larval development (sensu Nematoda)" to GO:0002119
* Changed synonym scope of GO:0002119 from "Related" to "Exact"
* Deleted GO:0003726 --OBO_REL:is_a--> GO:0003969
* Added comment "This term was made obsolete because it describes a biological process."
* Set definition of GO:0003969 to "OBSOLETE (was not defined before being made obsolete)."
* Added definition dbxref GOC:mah to GO:0003969
* Deleted GO:0003969 --OBO_REL:is_a--> GO:0003824
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 2ef22e
* Copied GO:0004465 to GO:0004091 with type OBO_REL:is_a
* Copied GO:0004622 to GO:0004091 with type OBO_REL:is_a
* Copied GO:0004623 to GO:0004091 with type OBO_REL:is_a
* Deleted GO:0004630 --OBO_REL:is_a--> GO:0016791
* Copied GO:0004767 to GO:0004620 with type OBO_REL:is_a
* Copied GO:0004806 to GO:0004091 with type OBO_REL:is_a
* Added GO:0006457 to category goslim_yeast
* Added GO:0006725 to category goslim_yeast
* Added comment "This term was made obsolete because it mixes two processes that can be better captured in separate terms."
* Changed definition of GO:0006894 from "The directed movement of proteins from the Golgi to one of two types of secretory vesicle. Continuously secreted proteins are sorted into transport vesicles that fuse with the plasma membrane, releasing their contents by exocytosis. Specialized secretory cells have a second secretory pathway in which soluble proteins and other substances are initially stored in secretory vesicles for later release." to "OBSOLETE. The directed movement of proteins from the Golgi to one of two types of secretory vesicle. Continuously secreted proteins are sorted into transport vesicles that fuse with the plasma membrane, releasing their contents by exocytosis. Specialized secretory cells have a second secretory pathway in which soluble proteins and other substances are initially stored in secretory vesicles for later release."
* Deleted GO:0006894 --OBO_REL:is_a--> GO:0006892
* org.geneontology.oboedit.datamodel.history.ObsoleteObjectHistoryItem at 1db770
* Deleted GO:0008251 --OBO_REL:is_a--> GO:0003969
* Added GO:0008289 to category goslim_yeast
* Changed definition of GO:0008970 from "Catalysis of the reaction: phosphatidylcholine + H2O = 2-acylglycerophosphocholine + a fatty acid anion." to "Catalysis of the reaction: phosphatidylcholine + H2O = 2-acylglycerophosphocholine + a carboxylate."
* Copied GO:0008970 to GO:0004091 with type OBO_REL:is_a
* Changed name of GO:0014023 from "neural rod formation (sensu Teleost)" to "neural rod formation"
* Added synonym "neural rod formation (sensu Teleost)" to GO:0014023
* Changed synonym scope of GO:0014023 from "Related" to "Exact"
* Changed name of GO:0014024 from "neural rod cavitation (sensu Teleost)" to "neural rod cavitation"
* Added synonym "neural rod cavitation (sensu Teleost)" to GO:0014024
* Changed synonym scope of GO:0014024 from "Related" to "Exact"
* Deleted GO:0016298 --OBO_REL:is_a--> GO:0004091
* Copied GO:0016298 to GO:0016788 with type OBO_REL:is_a
* Added GO:0030533 to category goslim_yeast
* Added GO:0032196 to category goslim_yeast
* Changed synonym scope of GO:0033920 from "Broad" to "Exact"
* Deleted general dbxref :N-substituted formamide deformylase activit from GO:0033966
* Changed definition of GO:0035300 from "Catalysis of the reactions: ATP + 1D-myo-inositol 1,3,4-trisphosphate = ADP + 1D-myo-inositol 1,3,4,5-tetrakisphosphate.ATP + 1D-myo-inositol 1,3,4-trisphosphate = ADP + 1D-myo-inositol 1,3,4,6-tetrakisphosphate." to "Catalysis of the reactions: ATP + 1D-myo-inositol 1,3,4-trisphosphate = ADP + 1D-myo-inositol 1,3,4,5-tetrakisphosphate and ATP + 1D-myo-inositol 1,3,4-trisphosphate = ADP + 1D-myo-inositol 1,3,4,6-tetrakisphosphate."
* Added GO:0042221 to category goslim_yeast
* Copied GO:0043161 to GO:0010498 with type OBO_REL:is_a
* Added GO:0046483 to category goslim_yeast
* Copied GO:0047372 to GO:0004091 with type OBO_REL:is_a
* Copied GO:0047714 to GO:0004091 with type OBO_REL:is_a
* Copied GO:0050290 to GO:0004620 with type OBO_REL:is_a
* Added GO:0051186 to category goslim_yeast
More information about the Go-diff
mailing list