[Go-diff] GO update 04/22/2009
Remote CVS for Gene Ontology
gocvs at genome.stanford.edu
Wed Apr 22 21:30:55 PDT 2009
OBODIFF of gene_ontology_write.obo version 1.553 by 1.560
Starting obodiff at /share/go/bin/oboedit/current using 256M of memory
* Created object of type obo:TERM with id GO:0002137
* Created object of type obo:TERM with id GO:0010945
* Created object of type obo:TERM with id GO:0044094
* Created object of type obo:TERM with id GO:0044095
* Created object of type obo:TERM with id GO:0044096
* Created object of type obo:TERM with id GO:0070578
* Created object of type obo:TERM with id GO:0070579
* Created object of type obo:TERM with id GO:0070580
* Created object of type obo:TERM with id GO:0070581
* Created object of type obo:TERM with id GO:0070582
* Created object of type obo:TERM with id GO:0080084
* Created object of type obo:TERM with id GO:0080085
* Created object of type obo:TERM with id GO:0080086
* Created object of type obo:TERM with id GO:0080087
* Created object of type obo:TERM with id GO:0080088
* Created object of type obo:TERM with id GO:0080089
* Created object of type obo:TERM with id GO:0080090
* Created object of type obo:TERM with id GO:0080091
* Created object of type obo:TERM with id GO:0080092
* Created object of type obo:TERM with id GO:0080093
* Created object of type obo:TERM with id GO:0080094
* Populated new object GO:0002137 (macro)
* Changed name of GO:0002137 from "<new term>" to "nuclear cluster"
* Set definition of GO:0002137 to "Discrete hetero-chromatin-containing foci in interphase nuclei, which comprise clusters of centromeric DNA (as defined by gamma-satellite sequences and the abundance of heterochromatin protein 1 (HP-1) ."
* Added definition dbxref PMID:9413993 to GO:0002137
* Copied GO:0002137 to GO:0031618 with type part_of
* Copied GO:0002137 to GO:0044428 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0002137
* Populated new object GO:0010945 (macro)
* Changed name of GO:0010945 from "<new term>" to "CoA pyrophosphatase activity"
* Set definition of GO:0010945 to "Catalysis of the reaction: coenzyme A + H20 = 3',5'-ADP + 4'-phosphopantetheine."
* Added definition dbxref GOC:tb to GO:0010945
* Copied GO:0010945 to GO:0016462 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0010945
* Populated new object GO:0044094 (macro)
* Changed name of GO:0044094 from "<new term>" to "host cell nuclear part"
* Set definition of GO:0044094 to "Any constituent part of a host cell's nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. The host is the larger of the organisms involved in a symbiotic interaction."
* Added definition dbxref GOC:ed to GO:0044094
* Added GO:0044094 to category gosubset_prok
* Copied GO:0044094 to GO:0042025 with type part_of
* Copied GO:0044094 to GO:0033646 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0044094
* Populated new object GO:0044095 (macro)
* Changed name of GO:0044095 from "<new term>" to "host cell nucleoplasm"
* Set definition of GO:0044095 to "That part of a host cell's nuclear content other than the chromosomes or the nucleolus. The host is the larger of the organisms involved in a symbiotic interaction."
* Added definition dbxref GOC:ed to GO:0044095
* Added GO:0044095 to category gosubset_prok
* Copied GO:0044095 to GO:0044094 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0044095
* Populated new object GO:0044096 (macro)
* Changed name of GO:0044096 from "<new term>" to "type IV pilus"
* Set definition of GO:0044096 to "A short filamentous structure on the surface of a bacterial cell distinguished from other pili by post-translational N-methylation of the pilin monomers."
* Added definition dbxref GOC:pamgo_curators to GO:0044096
* Added GO:0044096 to category gosubset_prok
* Added synonym "TFP" to GO:0044096
* Changed synonym scope of GO:0044096 from "Related" to "Exact"
* Added synonym "type 4 pilus" to GO:0044096
* Changed synonym scope of GO:0044096 from "Related" to "Exact"
* Added synonym "type IV fimbriae" to GO:0044096
* Changed synonym scope of GO:0044096 from "Related" to "Exact"
* Copied GO:0044096 to GO:0009289 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0044096
* Populated new object GO:0070578 (macro)
* Changed name of GO:0070578 from "<new term>" to "RISC-loading complex"
* Set definition of GO:0070578 to "A trimeric ribonucleoprotein complex that and is required for the formation of a mature RNA induced silencing complex (RISC). In humans the complex is composed of the endonuclease Dicer (DICER1) and TRBP (TARBP2) in association with the Argonaute protein Ago2 (EIF2C2/AGO2). Within the complex, Dicer and TRBP are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto Ago2. Ago2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from Dicer and TRBP."
* Added definition dbxref GOC:ab to GO:0070578
* Added definition dbxref PMID:18178619 to GO:0070578
* Added synonym "microRNA loading complex" to GO:0070578
* Added general dbxref GOC:ab to synonym microRNA loading complex of GO:0070578
* Changed synonym scope of GO:0070578 from "Related" to "Exact"
* Added synonym "miRLC" to GO:0070578
* Added general dbxref GOC:ab to synonym miRLC of GO:0070578
* Changed synonym scope of GO:0070578 from "Related" to "Exact"
* Added synonym "RLC" to GO:0070578
* Added general dbxref GOC:mah to synonym RLC of GO:0070578
* Added general dbxref GOC:ab to synonym RLC of GO:0070578
* Copied GO:0070578 to GO:0030529 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0070578
* Populated new object GO:0070579 (macro)
* Changed name of GO:0070579 from "<new term>" to "methylcytosine dioxygenase activity"
* Set definition of GO:0070579 to "Catalysis of the reaction: methylcytosine + 2-oxoglutarate + O2 = 5-hydroxymethylcytosine + succinate + CO2."
* Added definition dbxref PMID:19372391 to GO:0070579
* Copied GO:0070579 to GO:0016706 with type OBO_REL:is_a
* Copied GO:0070579 to GO:0051213 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0070579
* Populated new object GO:0070580 (macro)
* Changed name of GO:0070580 from "<new term>" to "base J metabolic process"
* Set definition of GO:0070580 to "The chemical reactions and pathways involving base J (beta-D-glucosyl-hydroxymethyluracil), a hypermodified thymidine residue found in the genome of kinetoplastid parasites. This modified base is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. The base is synthesized in a two-step pathway. Initially, a thymidine residue in DNA is hydroxylated by a thymidine hydroxylase (TH) to form the intermediate hydroxymethyluracil, which is then glucosylated to form base J."
* Added definition dbxref PMID:19114062 to GO:0070580
* Added synonym "base J metabolism" to GO:0070580
* Added general dbxref GOC:mah to synonym base J metabolism of GO:0070580
* Changed synonym scope of GO:0070580 from "Related" to "Exact"
* Added synonym "beta-D-glucosyl-HOMedU metabolic process" to GO:0070580
* Added general dbxref GOC:mah to synonym beta-D-glucosyl-HOMedU metabolic process of GO:0070580
* Changed synonym scope of GO:0070580 from "Related" to "Exact"
* Added synonym "beta-D-glucosyl-hydroxymethyluracil metabolism" to GO:0070580
* Added general dbxref PMID:19114062 to synonym beta-D-glucosyl-hydroxymethyluracil metabolism of GO:0070580
* Changed synonym scope of GO:0070580 from "Related" to "Exact"
* Copied GO:0070580 to GO:0006206 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070580
* Populated new object GO:0070581 (macro)
* Changed name of GO:0070581 from "<new term>" to "rolling circle DNA replication"
* Set definition of GO:0070581 to "A DNA-dependent DNA replication process in which a single-stranded DNA molecule is synthesized from a circular duplex template. Replication typically does not cease when one circumference has been replicated, but continues around the circumference several more times, producing a long single strand comprising multimers of the replicon."
* Added definition dbxref GOC:cb to GO:0070581
* Added definition dbxref GOC:mah to GO:0070581
* Added definition dbxref ISBN:0198506732 to GO:0070581
* Added synonym "rolling circle replication" to GO:0070581
* Added general dbxref GOC:cb to synonym rolling circle replication of GO:0070581
* Changed synonym scope of GO:0070581 from "Related" to "Exact"
* Copied GO:0070581 to GO:0006261 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070581
* Populated new object GO:0070582 (macro)
* Changed name of GO:0070582 from "<new term>" to "theta DNA replication"
* Set definition of GO:0070582 to "A DNA-dependent DNA replication process in which a double-stranded DNA molecule is synthesized from a circular duplex template."
* Added definition dbxref GOC:cb to GO:0070582
* Added definition dbxref GOC:mah to GO:0070582
* Added definition dbxref ISBN:0198506732 to GO:0070582
* Added synonym "theta replication" to GO:0070582
* Added general dbxref GOC:cb to synonym theta replication of GO:0070582
* Changed synonym scope of GO:0070582 from "Related" to "Exact"
* Copied GO:0070582 to GO:0006261 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0070582
* Populated new object GO:0080084 (macro)
* Changed name of GO:0080084 from "<new term>" to "5S rDNA binding"
* Set definition of GO:0080084 to "Interacting selectively with the 5S rDNA sequence encoding ribosomal 5S rRNA, which is individually transcribed by RNA polymerase III, rather than by RNA polymerase I, in species where it exists."
* Added definition dbxref PMID:12711688 to GO:0080084
* Copied GO:0080084 to GO:0000182 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0080084
* Populated new object GO:0080085 (macro)
* Changed name of GO:0080085 from "<new term>" to "signal recognition particle, chloroplast targeting"
* Set definition of GO:0080085 to "A complex consisting of a protein and RNA component which binds the signal sequence of some proteins and facilitates their export to the chloroplast."
* Added definition dbxref PMID:17513500 to GO:0080085
* Copied GO:0080085 to GO:0048500 with type OBO_REL:is_a
* Assigned namespace "cellular_component" to GO:0080085
* Populated new object GO:0080086 (macro)
* Changed name of GO:0080086 from "<new term>" to "stamen filament development"
* Set definition of GO:0080086 to "The process whose specific outcome is the progression of the filament over time, from its formation to the mature structure. Filament is the stalk of a stamen."
* Added definition dbxref PMID:19139039 to GO:0080086
* Added definition dbxref PO:0009067 to GO:0080086
* Added synonym "filament development" to GO:0080086
* Changed synonym scope of GO:0080086 from "Related" to "Exact"
* Copied GO:0080086 to GO:0048856 with type OBO_REL:is_a
* Copied GO:0080086 to GO:0048443 with type part_of
* Assigned namespace "biological_process" to GO:0080086
* Populated new object GO:0080087 (macro)
* Changed name of GO:0080087 from "<new term>" to "callose binding"
* Set definition of GO:0080087 to "Interacting selectively with callose. Callose is a linear 1,3-beta-D-glucan formed from UDP-glucose and is found in certain plant cell walls."
* Added definition dbxref GOC:DHL to GO:0080087
* Copied GO:0080087 to GO:0030247 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0080087
* Populated new object GO:0080088 (macro)
* Changed name of GO:0080088 from "<new term>" to "spermidine hydroxycinnamate conjugate biosynthetic process"
* Set definition of GO:0080088 to "The chemical reactions and pathways resulting in the formation of spermidine hydroxycinnamate conjugates."
* Added definition dbxref PMID:19077165 to GO:0080088
* Copied GO:0080088 to GO:0006596 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0080088
* Populated new object GO:0080089 (macro)
* Changed name of GO:0080089 from "<new term>" to "sinapoyl spermidine:sinapoyl CoA N-acyltransferase activity"
* Set definition of GO:0080089 to "Catalysis of the transfer of a sinapoyl group to a nitrogen atom on the spermidine molecule."
* Added definition dbxref PMID:19168716 to GO:0080089
* Copied GO:0080089 to GO:0016410 with type OBO_REL:is_a
* Assigned namespace "molecular_function" to GO:0080089
* Populated new object GO:0080090 (macro)
* Changed name of GO:0080090 from "<new term>" to "regulation of primary metabolic process"
* Set definition of GO:0080090 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism."
* Added definition dbxref PMID:19211694 to GO:0080090
* Copied GO:0080090 to GO:0044238 with type regulates
* Copied GO:0080090 to GO:0019222 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0080090
* Populated new object GO:0080091 (macro)
* Changed name of GO:0080091 from "<new term>" to "regulation of raffinose metabolic process"
* Set definition of GO:0080091 to "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving raffinose."
* Added definition dbxref PMID:19211694 to GO:0080091
* Copied GO:0080091 to GO:0006109 with type OBO_REL:is_a
* Copied GO:0080091 to GO:0033530 with type regulates
* Assigned namespace "biological_process" to GO:0080091
* Populated new object GO:0080092 (macro)
* Changed name of GO:0080092 from "<new term>" to "regulation of pollen tube growth"
* Set definition of GO:0080092 to "Any process that modulates the frequency, rate or extent of pollen tube growth."
* Added definition dbxref PMID:19208902 to GO:0080092
* Copied GO:0080092 to GO:0001558 with type OBO_REL:is_a
* Copied GO:0080092 to GO:0009860 with type regulates
* Assigned namespace "biological_process" to GO:0080092
* Populated new object GO:0080093 (macro)
* Changed name of GO:0080093 from "<new term>" to "regulation of photorespiration"
* Set definition of GO:0080093 to "Any process that modulates the rate, frequency or extent of photorespiration. Photorespiration is a light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved."
* Added definition dbxref GOC:tb to GO:0080093
* Copied GO:0080093 to GO:0031323 with type OBO_REL:is_a
* Copied GO:0080093 to GO:0009853 with type regulates
* Assigned namespace "biological_process" to GO:0080093
* Populated new object GO:0080094 (macro)
* Changed name of GO:0080094 from "<new term>" to "response to trehalose-6-phosphate stimulus"
* Set definition of GO:0080094 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 trehalose-6-phosphate stimulus."
* Added definition dbxref PMID:19193861 to GO:0080094
* Copied GO:0080094 to GO:0034285 with type OBO_REL:is_a
* Assigned namespace "biological_process" to GO:0080094
* Changed definition of GO:0005829 from "That part of the cytoplasm that does not contain membranous or particulate subcellular components." to "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes."
* Deleted definition dbxref ISBN:0198547684 from GO:0005829
* Added definition dbxref GOC:hgd to GO:0005829
* Added definition dbxref GOC:jl to GO:0005829
* Changed name of GO:0009289 from "fimbrium" to "pilus"
* Changed definition of GO:0009289 from "A proteinaceous hair-like appendage on the surface of bacteria; range from 2-8 nm in diameter." to "A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter."
* Deleted definition dbxref ISBN:0598034692 from GO:0009289
* Added definition dbxref GOC:pamgo_curators to GO:0009289
* Changed synonym scope of GO:0009289 from "Broad" to "Exact"
* Deleted synonym "pilus" from GO:0009289
* Added synonym "fimbrium" to GO:0009289
* Changed synonym scope of GO:0009289 from "Related" to "Exact"
* Added synonym "pili" to GO:0009289
* Changed synonym scope of GO:0009289 from "Related" to "Exact"
* Changed name of GO:0009418 from "fimbrial shaft" to "pilus shaft"
* Changed definition of GO:0009418 from "The long, slender, mid section of a fimbrium." to "The long, slender, mid section of a pilus."
* Added synonym "fimbrial shaft" to GO:0009418
* Changed synonym scope of GO:0009418 from "Related" to "Exact"
* Changed name of GO:0009419 from "fimbrial tip" to "pilus tip"
* Changed definition of GO:0009419 from "The pointed extremity furthest from the cell of a fimbrium." to "The pointed extremity furthest from the cell of a pilus."
* Added synonym "fimbrial tip" to GO:0009419
* Changed synonym scope of GO:0009419 from "Related" to "Exact"
* Added synonym "host cell intracellular part" to GO:0033646
* Changed synonym scope of GO:0033646 from "Related" to "Exact"
* Changed name of GO:0044443 from "fimbrial part" to "pilus part"
* Changed definition of GO:0044443 from "Any constituent part of a fimbrium, a proteinaceous hair-like appendage on the surface of bacteria; range from 2-8 nm in diameter." to "Any constituent part of a pilus, a proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter."
* Deleted definition dbxref GOC:jl from GO:0044443
* Added definition dbxref GOC:pamgo_curators to GO:0044443
* Added synonym "fimbrial part" to GO:0044443
* Changed synonym scope of GO:0044443 from "Related" to "Exact"
* Added synonym "pilus component" to GO:0044443
* Changed synonym scope of GO:0044443 from "Related" to "Exact"
* Changed definition of GO:0070449 from "A transcription elongation factor complex that suppresses RNA polymerase II pausing, and may act by promoting proper alignment of the 3?-end of nascent transcripts with the polymerase catalytic site. Consists of of a transcriptionally active Elongin A subunit (abut 100 kDa)and two smaller Elongin B (about 18 kDa) and Elongin C (about 15 kDa)subunits." to "A transcription elongation factor complex that suppresses RNA polymerase II pausing, and may act by promoting proper alignment of the 3?-end of nascent transcripts with the polymerase catalytic site. Consists of a transcriptionally active Elongin A subunit (abut 100 kDa)and two smaller Elongin B (about 18 kDa) and Elongin C (about 15 kDa)subunits."
* Added definition dbxref GOC:ab to GO:0070545
* Deleted GO:0075341 --OBO_REL:is_a--> GO:0033655
* Deleted GO:0075341 --part_of--> GO:0042025
* Copied GO:0075341 to GO:0044094 with type OBO_REL:is_a
* Changed name of GO:0080075 from "spermidine:feruloyl CoA N-acyltransferasehttp://goweb-dev.stanford.edu/cgi-bin/amigo/amigo?mode=homolset_graph&set=1&format=svg" to "spermidine:feruloyl CoA N-acyltransferase activity"
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