From: <cj...@yu...> - 2011-08-20 00:01:32
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Starting obodiff at /users/cjm/cvs/geneontology/oboedit/launch_scripts using 1024M of memory [INFO] Reading [obo-all/biological_process_prerelease/biological_process_prerelease.obo.CURRENT] (allowDangling = true) (followImports = true) [INFO] Reading [obo-all/biological_process_prerelease/biological_process_prerelease.obo] (allowDangling = true) (followImports = true) * Created object of type obo:TERM with id GO:0035977 * [Changed name of GO:0035977 from "null" to "protein deglycosylation involved in glycoprotein catabolic process", Set definition of GO:0035977 to "The removal of sugar residues from a glycosylated protein that contributes to the breakdown of a glycoprotein.", Added definition dbxref GOC:bf to GO:0035977, Added definition dbxref GOC:vw to GO:0035977, Created link GO:0035977 -part_of-> GO:0006516, Created link GO:0035977 -OBO_REL:is_a-> GO:0006517, Assigned namespace "biological_process" to GO:0035977] * Changed name of GO:0035977 from "null" to "protein deglycosylation involved in glycoprotein catabolic process" * Set definition of GO:0035977 to "The removal of sugar residues from a glycosylated protein that contributes to the breakdown of a glycoprotein." * Added definition dbxref GOC:bf to GO:0035977 * Added definition dbxref GOC:vw to GO:0035977 * Created link GO:0035977 -part_of-> GO:0006516 * Created link GO:0035977 -OBO_REL:is_a-> GO:0006517 * Assigned namespace "biological_process" to GO:0035977 * added secondary id GO:0000420 to GO:0000418 * Changed definition of GO:0000418 from "RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants. In addition to RNA polymerases I, II, and III, the essential RNA polymerases present in all eukaryotes, plants have two additional nuclear RNA polymerases, Pol IV and Pol V, that play nonredundant roles in siRNA-directed DNA methylation and gene silencing. Pol IV is required for siRNA production and Pol V is required for generating noncoding transcripts at target loci. Pol IV is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol IV are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases." to "RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeate d sequences. Pol IV is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol IV are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase V, while the largest subunit is found only in RNAP IV complex." * Added synonym "DNA-directed RNA polymerase IVa complex" to GO:0000418 * Changed synonym scope of GO:0000418 from "Related" to "Exact" * Changed name of GO:0000419 from "DNA-directed RNA polymerase IVb complex" to "DNA-directed RNA polymerase V complex" * added secondary id GO:0080137 to GO:0000419 * Changed definition of GO:0000419 from "RNA polymerase IVb is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits." to "RNA polymerase V is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol V is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits." * Added definition dbxref PMID:19110459 to GO:0000419 * Added synonym "DNA-directed RNA polymerase IVb complex" to GO:0000419 * Changed synonym scope of GO:0000419 from "Related" to "Exact" * Deleted GO:0000419 --OBO_REL:is_a--> GO:0000418 * Created link GO:0000419 -OBO_REL:is_a-> GO:0055029 * Deleted GO:0000420 --OBO_REL:is_a--> GO:0000418 * Destroyed object GO:0000420 * Changed definition of GO:0000988 from "Interacting selectively and non-covalently with two or more protein molecules, or a protein and another macromolecule or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." to "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." * Changed definition of GO:0000989 from "Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." to "Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." * Changed definition of GO:0000990 from "Interacting selectively and non-covalently with an RNA polymerase and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." to "Interacting selectively and non-covalently with an RNA polymerase in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." * Changed definition of GO:0000991 from "Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." to "Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." * Changed definition of GO:0000995 from "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." to "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." * Changed definition of GO:0001007 from "Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." to "Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." * Changed definition of GO:0001076 from "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." to "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." * Changed definition of GO:0001083 from "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor, which may be a single protein or a complex, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." to "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." * Added synonym "RNA polymerase I CORE element sequence-specific DNA binding" to GO:0001164 * Changed synonym scope of GO:0001164 from "Related" to "Exact" * Added synonym "RNA polymerase I CORE element sequence-specific DNA binding transcription factor activity" to GO:0001169 * Changed synonym scope of GO:0001169 from "Related" to "Exact" * Added synonym "pseudouridine-5'-phosphate glycosidase activity" to GO:0004730 * Changed synonym scope of GO:0004730 from "Related" to "Exact" * Deleted GO:0006517 --OBO_REL:is_a--> GO:0006516 * Added general dbxref GOC:mah to synonym forebrain dorsal-ventral pattern formation of GO:0021798 * Changed name of GO:0032905 from "transforming growth factor-beta1 production" to "transforming growth factor beta1 production" * Added synonym "transforming growth factor-beta1 production" to GO:0032905 * Added general dbxref GOC:bf to synonym transforming growth factor-beta1 production of GO:0032905 * Changed synonym scope of GO:0032905 from "Related" to "Exact" * Changed name of GO:0032906 from "transforming growth factor-beta2 production" to "transforming growth factor beta2 production" * Added synonym "transforming growth factor-beta2 production" to GO:0032906 * Added general dbxref GOC:bf to synonym transforming growth factor-beta2 production of GO:0032906 * Changed synonym scope of GO:0032906 from "Related" to "Exact" * Changed name of GO:0032907 from "transforming growth factor-beta3 production" to "transforming growth factor beta3 production" * Added synonym "transforming growth factor-beta3 production" to GO:0032907 * Added general dbxref GOC:bf to synonym transforming growth factor-beta3 production of GO:0032907 * Changed synonym scope of GO:0032907 from "Related" to "Exact" * Changed name of GO:0032908 from "regulation of transforming growth factor-beta1 production" to "regulation of transforming growth factor beta1 production" * Added synonym "regulation of transforming growth factor-beta1 production" to GO:0032908 * Added general dbxref GOC:bf to synonym regulation of transforming growth factor-beta1 production of GO:0032908 * Changed synonym scope of GO:0032908 from "Related" to "Exact" * Changed name of GO:0032909 from "regulation of transforming growth factor-beta2 production" to "regulation of transforming growth factor beta2 production" * Added synonym "regulation of transforming growth factor beta2 production" to GO:0032909 * Added general dbxref GOC:bf to synonym regulation of transforming growth factor beta2 production of GO:0032909 * Changed synonym scope of GO:0032909 from "Related" to "Exact" * Changed name of GO:0032910 from "regulation of transforming growth factor-beta3 production" to "regulation of transforming growth factor beta3 production" * Added synonym "regulation of transforming growth factor-beta3 production" to GO:0032910 * Added general dbxref GOC:bf to synonym regulation of transforming growth factor-beta3 production of GO:0032910 * Changed synonym scope of GO:0032910 from "Related" to "Exact" * Changed name of GO:0032911 from "negative regulation of transforming growth factor-beta1 production" to "negative regulation of transforming growth factor beta1 production" * Added synonym "negative regulation of transforming growth factor-beta1 production" to GO:0032911 * Added general dbxref GOC:bf to synonym negative regulation of transforming growth factor-beta1 production of GO:0032911 * Changed synonym scope of GO:0032911 from "Related" to "Exact" * Changed name of GO:0032912 from "negative regulation of transforming growth factor-beta2 production" to "negative regulation of transforming growth factor beta2 production" * Added synonym "negative regulation of transforming growth factor-beta2 production" to GO:0032912 * Added general dbxref GOC:bf to synonym negative regulation of transforming growth factor-beta2 production of GO:0032912 * Changed synonym scope of GO:0032912 from "Related" to "Exact" * Changed name of GO:0032913 from "negative regulation of transforming growth factor-beta3 production" to "negative regulation of transforming growth factor beta3 production" * Added synonym "negative regulation of transforming growth factor-beta3 production" to GO:0032913 * Added general dbxref GOC:bf to synonym negative regulation of transforming growth factor-beta3 production of GO:0032913 * Changed synonym scope of GO:0032913 from "Related" to "Exact" * Changed name of GO:0032914 from "positive regulation of transforming growth factor-beta1 production" to "positive regulation of transforming growth factor beta1 production" * Added general dbxref GOC:bf to synonym activation of transforming growth factor-beta1 production of GO:0032914 * Changed name of GO:0032915 from "positive regulation of transforming growth factor-beta2 production" to "positive regulation of transforming growth factor beta2 production" * Added synonym "positive regulation of transforming growth factor beta2 production" to GO:0032915 * Added general dbxref GOC:bf to synonym positive regulation of transforming growth factor beta2 production of GO:0032915 * Changed synonym scope of GO:0032915 from "Related" to "Exact" * Changed name of GO:0032916 from "positive regulation of transforming growth factor-beta3 production" to "positive regulation of transforming growth factor beta3 production" * Added synonym "positive regulation of transforming growth factor beta3 production" to GO:0032916 * Added general dbxref GOC:bf to synonym positive regulation of transforming growth factor beta3 production of GO:0032916 * Changed synonym scope of GO:0032916 from "Related" to "Exact" * Deleted general dbxref KEGG:R04002 from synonym ATP:branched-chain-fatty-acid 1-phosphotransferase activity of GO:0047758 * Added general dbxref EC:2.7.2.14 to synonym ATP:branched-chain-fatty-acid 1-phosphotransferase activity of GO:0047758 * Changed synonym scope of GO:0047758 from "Broad" to "Exact" * Changed name of GO:0071604 from "transforming growth factor-beta production" to "transforming growth factor beta production" * Added synonym "transforming growth factor-beta production" to GO:0071604 * Added general dbxref GOC:bf to synonym transforming growth factor-beta production of GO:0071604 * Changed synonym scope of GO:0071604 from "Related" to "Exact" * Changed name of GO:0071634 from "regulation of transforming growth factor-beta production" to "regulation of transforming growth factor beta production" * Added synonym "regulation of transforming growth factor-beta production" to GO:0071634 * Added general dbxref GOC:bf to synonym regulation of transforming growth factor-beta production of GO:0071634 * Changed synonym scope of GO:0071634 from "Related" to "Exact" * Changed name of GO:0071635 from "negative regulation of transforming growth factor-beta production" to "negative regulation of transforming growth factor beta production" * Added synonym "negative regulation of transforming growth factor-beta production" to GO:0071635 * Added general dbxref GOC:bf to synonym negative regulation of transforming growth factor-beta production of GO:0071635 * Changed synonym scope of GO:0071635 from "Related" to "Exact" * Changed name of GO:0071636 from "positive regulation of transforming growth factor-beta production" to "positive regulation of transforming growth factor beta production" * Added synonym "positive regulation of transforming growth factor-beta production" to GO:0071636 * Added general dbxref GOC:bf to synonym positive regulation of transforming growth factor-beta production of GO:0071636 * Changed synonym scope of GO:0071636 from "Related" to "Exact" * Deleted GO:0080137 --OBO_REL:is_a--> GO:0055029 * Destroyed object GO:0080137 * Created link occurs_in -transitive_over-> part_of |