[Go-diff] GO update 12/17/2008
Remote CVS for Gene Ontology
gocvs at genome.stanford.edu
Wed Dec 17 21:30:47 PST 2008
OBODIFF of gene_ontology_write.obo version 1.355 by 1.358
Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0010835
* Created object of type obo:TERM with id GO:0010836
* Created object of type obo:TERM with id GO:0070198
* Created object of type obo:TERM with id GO:0070199
* Created object of type obo:TERM with id GO:0070200
* Created object of type obo:TERM with id GO:0070201
* Created object of type obo:TERM with id GO:0070202
* Created object of type obo:TERM with id GO:0070203
* Created object of type obo:TERM with id GO:0070204
* Created object of type obo:TERM with id GO:0070205
* Created object of type obo:TERM with id GO:0070206
* Created object of type obo:TERM with id GO:0070207
* Created object of type obo:TERM with id GO:0070208
* Populated new object GO:0010835 (macro)
* Changed name of GO:0010835 from "<new term>" to "regulation of protein amino acid ADP-ribosylation"
* Set definition of GO:0010835 to "Any process that modulates the frequency, rate or extent of protein amino acid ADP-ribosylation. Protein amino acid ADP-ribosylation is the transfer, from NAD, of ADP-ribose to protein amino acids."
* Added definition dbxref GOC:dph to GO:0010835
* Added definition dbxref GOC:tb to GO:0010835
* Copied GO:0010835 to GO:0031399 with type OBO_REL:is_a
* Copied GO:0010835 to GO:0006471 with type regulates
* Assigned namespace "biological_process" to GO:0010835
* Populated new object GO:0010836 (macro)
* Changed name of GO:0010836 from "<new term>" to "negative regulation of protein amino acid ADP-ribosylation"
* Set definition of GO:0010836 to "Any process that decreases the frequency, rate or extent of protein amino acid ADP-ribosylation. Protein amino acid ADP-ribosylation is the transfer, from NAD, of ADP-ribose to protein amino acids."
* Added definition dbxref GOC:dph to GO:0010836
* Added definition dbxref GOC:tb to GO:0010836
* Copied GO:0010836 to GO:0031400 with type OBO_REL:is_a
* Copied GO:0010836 to GO:0010835 with type OBO_REL:is_a
* Copied GO:0010836 to GO:0006471 with type negatively_regulates
* Assigned namespace "biological_process" to GO:0010836
* Populated new object GO:0070198 (macro)
* Changed name of GO:0070198 from "<new term>" to "protein localization to telomere"
* Set definition of GO:0070198 to "Any process by which a protein is transported to, or maintained at, the telomeric region of a chromosome."
* Added definition dbxref GOC:mah to GO:0070198
* Added synonym "protein localization to chromosome, telomeric region" to GO:0070198
* Added general dbxref GOC:mah to synonym protein localization to chromosome, telomeric region of GO:0070198
* Changed synonym scope of GO:0070198 from "Related" to "Exact"
* Copied GO:0070198 to GO:0034502 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070198
* Populated new object GO:0070199 (macro)
* Changed name of GO:0070199 from "<new term>" to "establishment of protein localization to chromosome"
* Set definition of GO:0070199 to "The directed movement of a protein to a specific location on a chromosome."
* Added definition dbxref GOC:mah to GO:0070199
* Copied GO:0070199 to GO:0034502 with type OBO_REL:is_a
* Copied GO:0070199 to GO:0045184 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070199
* Populated new object GO:0070200 (macro)
* Changed name of GO:0070200 from "<new term>" to "establishment of protein localization to telomere"
* Set definition of GO:0070200 to "The directed movement of a protein to a specific location in the telomeric region of a chromosome."
* Added definition dbxref GOC:mah to GO:0070200
* Added synonym "establishment of protein localization to chromosome, telomeric region" to GO:0070200
* Added general dbxref GOC:mah to synonym establishment of protein localization to chromosome, telomeric region of GO:0070200
* Changed synonym scope of GO:0070200 from "Related" to "Exact"
* Copied GO:0070200 to GO:0070199 with type OBO_REL:is_a
* Copied GO:0070200 to GO:0070198 with type part_of
* Assigned namespace "biological_process" to GO:0070200
* Populated new object GO:0070201 (macro)
* Changed name of GO:0070201 from "<new term>" to "regulation of establishment of protein localization"
* Set definition of GO:0070201 to "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location."
* Added definition dbxref GOC:mah to GO:0070201
* Copied GO:0070201 to GO:0045184 with type regulates
* Copied GO:0070201 to GO:0032880 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070201
* Populated new object GO:0070202 (macro)
* Changed name of GO:0070202 from "<new term>" to "regulation of establishment of protein localization to chromosome"
* Set definition of GO:0070202 to "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome."
* Added definition dbxref GOC:mah to GO:0070202
* Copied GO:0070202 to GO:0070199 with type regulates
* Copied GO:0070202 to GO:0070201 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070202
* Populated new object GO:0070203 (macro)
* Changed name of GO:0070203 from "<new term>" to "regulation of establishment of protein localization to telomere"
* Set definition of GO:0070203 to "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location in the telomeric region of a chromosome."
* Added definition dbxref GOC:mah to GO:0070203
* Copied GO:0070203 to GO:0070200 with type regulates
* Copied GO:0070203 to GO:0070202 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070203
* Populated new object GO:0070204 (macro)
* Changed name of GO:0070204 from "<new term>" to "2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity"
* Added comment "Note that this function was formerly EC:4.1.3.18."
* Set definition of GO:0070204 to "Catalysis of the reaction: isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate + CO2."
* Added definition dbxref EC:2.2.1.9 to GO:0070204
* Added definition dbxref MetaCyc:2.5.1.64-RXN to GO:0070204
* Added general dbxref EC:2.2.1.9 to GO:0070204
* Added general dbxref MetaCyc:2.5.1.64-RXN to GO:0070204
* Added GO:0070204 to category gosubset_prok
* Added synonym "MenD" to GO:0070204
* Added general dbxref EC:2.2.1.9 to synonym MenD of GO:0070204
* Added synonym "SEPHCHC synthase activity" to GO:0070204
* Added general dbxref EC:2.2.1.9 to synonym SEPHCHC synthase activity of GO:0070204
* Changed synonym scope of GO:0070204 from "Related" to "Exact"
* Copied GO:0070204 to GO:0016744 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0070204
* Populated new object GO:0070205 (macro)
* Changed name of GO:0070205 from "<new term>" to "2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase activity"
* Set definition of GO:0070205 to "Catalysis of the reaction: 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate = (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate + pyruvate."
* Added definition dbxref EC:4.2.99.20 to GO:0070205
* Added definition dbxref MetaCyc:RXN-9310 to GO:0070205
* Added general dbxref EC:4.2.99.20 to GO:0070205
* Added general dbxref MetaCyc:RXN-9310 to GO:0070205
* Added synonym " 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase activity" to GO:0070205
* Added general dbxref EC:4.2.99.20 to synonym 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase activity of GO:0070205
* Changed synonym scope of GO:0070205 from "Related" to "Exact"
* Added synonym "6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate synthase activity" to GO:0070205
* Added general dbxref EC:4.2.99.20 to synonym 6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate synthase activity of GO:0070205
* Changed synonym scope of GO:0070205 from "Related" to "Exact"
* Added synonym "MenH" to GO:0070205
* Added general dbxref EC:4.2.99.20 to synonym MenH of GO:0070205
* Added synonym "SHCHC synthase activity" to GO:0070205
* Added general dbxref EC:4.2.99.20 to synonym SHCHC synthase activity of GO:0070205
* Changed synonym scope of GO:0070205 from "Related" to "Exact"
* Added synonym "YfbB" to GO:0070205
* Added general dbxref EC:4.2.99.20 to synonym YfbB of GO:0070205
* Copied GO:0070205 to GO:0016835 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0070205
* Populated new object GO:0070206 (macro)
* Changed name of GO:0070206 from "<new term>" to "protein trimerization"
* Set definition of GO:0070206 to "The formation of a protein trimer, a macromolecular structure consisting of three noncovalently associated identical or nonidentical subunits."
* Added definition dbxref GOC:hjd to GO:0070206
* Added GO:0070206 to category gosubset_prok
* Added synonym "protein trimer assembly" to GO:0070206
* Added general dbxref GOC:hjd to synonym protein trimer assembly of GO:0070206
* Changed synonym scope of GO:0070206 from "Related" to "Exact"
* Added synonym "protein trimer biosynthesis" to GO:0070206
* Added general dbxref GOC:hjd to synonym protein trimer biosynthesis of GO:0070206
* Changed synonym scope of GO:0070206 from "Related" to "Exact"
* Added synonym "protein trimer biosynthetic process" to GO:0070206
* Added general dbxref GOC:hjd to synonym protein trimer biosynthetic process of GO:0070206
* Changed synonym scope of GO:0070206 from "Related" to "Exact"
* Added synonym "protein trimer formation" to GO:0070206
* Added general dbxref GOC:hjd to synonym protein trimer formation of GO:0070206
* Changed synonym scope of GO:0070206 from "Related" to "Exact"
* Copied GO:0070206 to GO:0051259 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070206
* Populated new object GO:0070207 (macro)
* Changed name of GO:0070207 from "<new term>" to "protein homotrimerization"
* Set definition of GO:0070207 to "The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits."
* Added definition dbxref GOC:hjd to GO:0070207
* Added GO:0070207 to category gosubset_prok
* Added synonym "protein homotrimer assembly" to GO:0070207
* Added general dbxref GOC:hjd to synonym protein homotrimer assembly of GO:0070207
* Changed synonym scope of GO:0070207 from "Related" to "Exact"
* Added synonym "protein homotrimer biosynthesis" to GO:0070207
* Added general dbxref GOC:hjd to synonym protein homotrimer biosynthesis of GO:0070207
* Changed synonym scope of GO:0070207 from "Related" to "Exact"
* Added synonym "protein homotrimer biosynthetic process" to GO:0070207
* Added general dbxref GOC:hjd to synonym protein homotrimer biosynthetic process of GO:0070207
* Changed synonym scope of GO:0070207 from "Related" to "Exact"
* Added synonym "protein homotrimer formation" to GO:0070207
* Added general dbxref GOC:hjd to synonym protein homotrimer formation of GO:0070207
* Changed synonym scope of GO:0070207 from "Related" to "Exact"
* Copied GO:0070207 to GO:0070206 with type OBO_REL:is_a
* Copied GO:0070207 to GO:0051260 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070207
* Populated new object GO:0070208 (macro)
* Changed name of GO:0070208 from "<new term>" to "protein heterotrimerization"
* Set definition of GO:0070208 to "The formation of a protein heterotrimer, a macromolecular structure consisting of three noncovalently associated subunits, of which not all are identical."
* Added definition dbxref GOC:hjd to GO:0070208
* Added GO:0070208 to category gosubset_prok
* Added synonym "protein heterotrimer assembly" to GO:0070208
* Added general dbxref GOC:hjd to synonym protein heterotrimer assembly of GO:0070208
* Changed synonym scope of GO:0070208 from "Related" to "Exact"
* Added synonym "protein heterotrimer biosynthesis" to GO:0070208
* Added general dbxref GOC:hjd to synonym protein heterotrimer biosynthesis of GO:0070208
* Changed synonym scope of GO:0070208 from "Related" to "Exact"
* Added synonym "protein heterotrimer biosynthetic process" to GO:0070208
* Added general dbxref GOC:hjd to synonym protein heterotrimer biosynthetic process of GO:0070208
* Changed synonym scope of GO:0070208 from "Related" to "Exact"
* Added synonym "protein heterotrimer formation" to GO:0070208
* Added general dbxref GOC:hjd to synonym protein heterotrimer formation of GO:0070208
* Changed synonym scope of GO:0070208 from "Related" to "Exact"
* Copied GO:0070208 to GO:0070206 with type OBO_REL:is_a
* Copied GO:0070208 to GO:0051291 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070208
* Deleted GO:0000508 --OBO_REL:is_a--> GO:0000118
* Destroyed object GO:0000508
* Deleted GO:0000509 --OBO_REL:is_a--> GO:0000118
* Destroyed object GO:0000509
* added secondary id GO:0042411 to GO:0010291
* Changed definition of GO:0010291 from "Catalysis of C3-hydroxylation reaction of the beta-ring of various carotenes." to "Catalysis of C3-hydroxylation of the beta-ring of various carotenes."
* Added definition dbxref MetaCyc:MONOMER-12386 to GO:0010291
* Added synonym "beta-carotene hydroxylase activity" to GO:0010291
* Changed synonym scope of GO:0010291 from "Related" to "Narrow"
* added secondary id GO:0000509 to GO:0032221
* Changed definition of GO:0032221 from "A eukaryotically conserved histone deacetylase complex which deacetylates histones preferentially in promoter regions. Composed of a catalytic histone deacetylase subunit, a chromodomain protein, a SIN3 family co-repressor, and a WD repeat protein (Clr6p, Alp13p, Pst2p, and Prw1p respectively in Schizosaccharomyces; homologs thereof in other species)." to "A eukaryotically conserved histone deacetylase complex which deacetylates histones preferentially in promoter regions. Composed of a catalytic histone deacetylase subunit, a chromodomain protein, a SIN3 family co-repressor, and a WD repeat protein (Clr6p, Alp13p, Pst2p, and Prw1p respectively in Schizosaccharomyces; Rpd3p, Sin3p, Ume1p, Rco1p and Eaf3 in Saccharomyces; homologs thereof in other species)."
* Added synonym "Clr6S complex" to GO:0032221
* Added general dbxref PMID:19040720 to synonym Clr6S complex of GO:0032221
* Changed synonym scope of GO:0032221 from "Related" to "Exact"
* Added synonym "Rpd3C(S)" to GO:0032221
* Changed synonym scope of GO:0032221 from "Related" to "Exact"
* Added synonym "Rpd3S complex" to GO:0032221
* Added general dbxref PMID:19040720 to synonym Rpd3S complex of GO:0032221
* Changed synonym scope of GO:0032221 from "Related" to "Exact"
* Copied GO:0032221 to GO:0000790 with type part_of
* added secondary id GO:0000508 to GO:0033698
* Changed definition of GO:0033698 from "A histone deacetylase complex which deacetylates histones across gene coding regions. Composed of a catalytic histone deacetylase subunit, an Sds-3 family protein, a SIN3 family co-repressor, a WD repeat protein, and a zf- PHD finger (Clr6, Sds3, Pst1, Prw1, Png2 in Schizosaccharomyces pombe)." to "A histone deacetylase complex which deacetylates histones across gene coding regions. Composed of a catalytic histone deacetylase subunit, an Sds-3 family protein, a SIN3 family co-repressor, a WD repeat protein, and a zf- PHD finger (Clr6, Sds3, Pst1, Prw1, Png2 in Schizosaccharomyces pombe; Rpd3p, Sin3p, Ume1p, Pho23p, Sap30p, Sds3p, Cti6p, Rxt2p, Rxt3p, Dep1p, Ume6p and Ash1p in Saccharomyces cerevisiae)."
* Added synonym "Clr6L complex" to GO:0033698
* Added general dbxref PMID:19040720 to synonym Clr6L complex of GO:0033698
* Changed synonym scope of GO:0033698 from "Related" to "Exact"
* Added synonym "Rpd3C(L)" to GO:0033698
* Changed synonym scope of GO:0033698 from "Related" to "Exact"
* Added synonym "Rpd3L complex" to GO:0033698
* Added general dbxref PMID:19040720 to synonym Rpd3L complex of GO:0033698
* Changed synonym scope of GO:0033698 from "Related" to "Exact"
* Copied GO:0033698 to GO:0000790 with type OBO_REL:is_a
* Deleted GO:0042411 --OBO_REL:is_a--> GO:0016491
* Destroyed object GO:0042411
* Deleted synonym "2-oxoglutarate decarboxylase/SHCHC synthase activity" from GO:0046410
* Deleted synonym "2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase--alpha-ketoglutarate decarboxylase activity" from GO:0046410
* Deleted synonym "2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase activity" from GO:0046410
* Deleted synonym "6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate synthase activity" from GO:0046410
* Deleted synonym "isochorismate:2-oxoglutarate:cyclodienyltransferase (decarboxylating, pyruvate-forming)" from GO:0046410
* Deleted synonym "SHCHC synthase activity" from GO:0046410
* Deleted GO:0046777 --OBO_REL:is_a--> GO:0016540
* Deleted GO:0051223 --OBO_REL:is_a--> GO:0032880
* Copied GO:0051223 to GO:0070201 with type OBO_REL:is_a
* Changed definition of GO:0051290 from "The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated nonidentical subunits." to "The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical."
* Changed definition of GO:0051291 from "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of nonidentical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." to "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer."
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