GO Monthly Release Notes for June 2004 ======================== Generated on Mon Aug 9 15:57:51 2004 Files used: component old: 3.49 new: 3.69 function old: 3.49 new: 3.69 process old: 3.49 new: 3.69 definitions old: 3.49 new: 3.69 GO Slim: Generic.0208 Key: |----1----||----2-----||-3--||4||----5----||-----------6-----------| GO:0009941 GO:0009536 TAIR D SF:575119 chloroplast envelope (obs) 1. GO ID number 2. GO-slim term(s) that new term was added under or "obs" if the term is obsolete. Terms with more than one GO-slim parent have further parents listed underneath the first parent. 3. Database that added term 4. indicates the existence of a definition for the term 5. the sourceforge request ID the term was added in response to 6. term name Columns are tab-delimited and can be imported into Excel for ease of reading. New terms in component ontology (7 new terms) GO:0030956 GO:0005622 MAH D 965350 glutamyl-tRNA(Gln) amidotransferase complex GO:0030958 GO:0005694 MAH D 971071 RITS complex GO:0035182 GO:0005576 FB D 959484 ring canal outer rim GO:0035183 GO:0005576 FB D 959484 ring canal inner rim GO:0035189 GO:0005654 FB D 968306 Rb-E2F complex GO:0048471 GO:0005737 JIC D 969611 perinuclear region GO:0051077 GO:0005623 AI D 975485 secondary septum (sensu Fungi) Term name changes in component ontology GO:0045203: integral to external membrane (sensu Gram-negative Bacteria) --> integral to outer membrane (sensu Gram-negative Bacteria) New definitions for component ontology terms (1 new definitions) GO:0017102, methionyl glutamyl tRNA synthetase complex New term merges in component ontology GO:0005653 has been merged into GO:0005641, nuclear membrane lumen New terms in function ontology (18 new terms) GO:0001406 GO:0005215 SGD D 956845 glycerophosphodiester transporter activity GO:0001409 GO:0005215 SGD D 952566 guanine nucleotide transporter activity GO:0030957 GO:0005515 MAH D 961450 Tat protein binding GO:0035184 GO:0004672 FB D 966481 histone-threonine kinase activity GO:0043166 GO:0003824 JL D 845102 H4/H2A histone acetyltransferase activity GO:0048472 GO:0003824 JIC D 974032 threonine-phosphate decarboxylase activity GO:0048474 GO:0005215 JIC D 974279 D-methionine transporter activity GO:0051059 GO:0005515 AI D 964875 NF-kappaB binding GO:0051060 GO:0003824 AI D 965183 pullulanase activity GO:0051061 GO:0003824 AI D ADP reductase activity GO:0051062 GO:0003824 AI D UDP reductase activity GO:0051063 GO:0003824 AI D CDP reductase activity GO:0051064 GO:0003824 AI D TTP reductase activity GO:0051065 GO:0003824 AI D CTP reductase activity GO:0051073 GO:0003824 AI D 974054 adenosylcobinamide-GDP ribazoletransferase activity GO:0051074 GO:0005515 AI D 968834 protein tetramerization activity GO:0051075 GO:0003824 AI D 970659 S-adenosylmethionine:tRNA ribosyltransferase-isomerase activity GO:0051076 GO:0005488 AI D 969520 Gram-positive bacterial binding Term name changes in function ontology GO:0003875: ADPribosylarginine hydrolase activity --> ADP-ribosylarginine hydrolase activity GO:0003956: NAD(P)+-arginine ADP-ribosyltransferase activity --> NAD(P)+-protein-arginine ADP-ribosyltransferase activity GO:0008685: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity --> 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity GO:0008817: cob(I)alamin adenosyltransferase activity --> cob(I)yrinic acid a,c-diamide adenosyltransferase activity GO:0008818: cobalamin [5'-phosphate] synthase activity --> cobalamin 5'-phosphate synthase activity GO:0016994: precorrin-6X reductase activity --> precorrin-6A reductase activity GO:0017061: 5'-methylthioadenosine phosphorylase activity --> S-methyl-5-thioadenosine phosphorylase activity GO:0035175: histone-serine kinase activity (H3-K10 specific) --> histone-serine kinase activity (H3-S10 specific) GO:0046429: 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase activity --> 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity GO:0046522: 5-methylthioribose kinase activity --> S-methyl-5-thioribose kinase activity GO:0046523: 5-methylthioribose-1-phosphate isomerase activity --> S-methyl-5-thioribose-1-phosphate isomerase activity GO:0046972: histone lysine acetyltransferase activity (H4-K16 specific) --> histone acetyltransferase activity (H4-K16 specific) GO:0047179: platelet activating factor acetyltransferase activity --> platelet-activating factor acetyltransferase activity GO:0047290: alpha-N-acetylneuraminyl-2,3-alpha-galactosyl-1,3-N-acetyl-galactosaminide alpha-2,6-sialyltransferase activity --> (alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity GO:0050079: malonate-semialdehyde dehydratase activity --> acetylenecarboxylate hydratase activity New definitions for function ontology terms (4 new definitions) GO:0004405, H2A/H2B histone acetyltransferase activity GO:0004406, H3/H4 histone acetyltransferase activity GO:0008685, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity GO:0015605, organophosphate ester transporter activity New term merges in function ontology GO:0016967 has been merged into GO:0016966, nitric oxide reductase activity GO:0016968 has been merged into GO:0016966, nitric oxide reductase activity GO:0046971 has been merged into GO:0004402, histone acetyltransferase activity GO:0047314 has been merged into GO:0047305, (R)-3-amino-2-methylpropionate-pyruvate transaminase activity GO:0047607 has been merged into GO:0050079, acetylenecarboxylate hydratase activity GO:0050443 has been merged into GO:0047930, glucosaminate ammonia-lyase activity Term movements in function ontology: Terms movements under GO Slim term 'binding ; GO:0005488' + GO:0001872, zymosan binding + GO:0001873, polysaccharide receptor activity + GO:0001874, zymosan receptor activity + GO:0008061, chitin binding + GO:0030247, polysaccharide binding + GO:0030248, cellulose binding + GO:0048028, galacturonan binding New terms in process ontology (31 new terms) GO:0000819 GO:0007049 SGD D 848985 sister chromatid segregation GO:0001407 GO:0006811 SGD D 956845 glycerophosphodiester transport GO:0001408 GO:0006810 SGD D 952572 guanine nucleotide transport GO:0030959 GO:0006464 MAH D 981877 peptide cross-linking via 3'-(3'-L-tyrosinyl)-L-tyrosine GO:0030960 GO:0006464 MAH D 981877 peptide cross-linking via 3'-(O4'-L-tyrosinyl)-L-tyrosine GO:0030961 GO:0006464 MAH D 981877 peptidyl-arginine hydroxylation GO:0030962 GO:0006464 MAH D 981877 peptidyl-arginine dihydroxylation to peptidyl-3,4-dihydroxy-L-arginine GO:0030963 GO:0006464 MAH D 981877 peptidyl-lysine dihydroxylation to 4,5-dihydroxy-L-lysine GO:0035185 GO:0007049 FB D 964417 preblastoderm mitotic cell cycle GO:0035186 GO:0007049 FB D 964417 syncytial blastoderm mitotic cell cycle GO:0035187 GO:0007275 FB D 970518 hatching behavior GO:0007610 GO:0035188 GO:0007275 FB D 970518 hatching GO:0035190 GO:0007049 FB D 960722 syncytial nuclear migration GO:0007275 GO:0035191 GO:0007049 FB D 960722 nuclear axial expansion GO:0007275 GO:0035192 GO:0007049 FB D 960722 nuclear cortical migration GO:0007275 GO:0043163 GO:0016043 JL D cell envelope organization and biogenesis GO:0043164 GO:0009058 JL D cell wall biosynthesis (sensu Gram-negative Bacteria) GO:0016043 GO:0043165 GO:0016043 JL D outer membrane biogenesis (sensu Gram-negative Bacteria) GO:0048470 GO:0007582 JIC D 944692 synergid degeneration GO:0048473 GO:0006810 JIC D 974279 D-methionine transport GO:0051066 GO:0008152 AI D dihydrobiopterin metabolism GO:0051067 GO:0008152 AI D dihydropteridine metabolism GO:0051068 GO:0006731 AI D dihydrolipoamide metabolism GO:0051069 GO:0005975 AI D 966437 galactomannan metabolism GO:0051070 GO:0005975 AI D 966437 galactomannan biosynthesis GO:0051071 GO:0005975 AI D 966437 4,6-pyruvylated galactose residue metabolism GO:0051072 GO:0005975 AI D 966437 4,6-pyruvylated galactose residue biosynthesis GO:0009058 GO:0051078 GO:0007049 AI D 970369 meiotic nuclear envelope disassembly GO:0016043 GO:0051079 GO:0007049 AI D 970369 meiosis I nuclear envelope disassembly GO:0016043 GO:0051080 GO:0007049 AI D 970369 meiosis II nuclear envelope disassembly GO:0016043 GO:0051081 GO:0016043 AI D 970369 nuclear envelope disassembly New obsoletions in process ontology GO:0006128, oxidized glutathione reduction: the term string represents a molecular function and not a biological pathway. GO:0006129, protein-disulfide reduction: represents a molecular function rather than a biological process. GO:0006131, dihydrolipoamide reduction: represents a molecular function rather than a biological process. GO:0006132, dihydrolipoylprotein reduction: represents a molecular function rather than a biological process. GO:0006134, dihydrobiopterin reduction: represents a molecular function rather than a biological process. GO:0006135, dihydropteridine reduction: represents a molecular function rather than a biological process. GO:0006162, purine/pyrimidine nucleoside diphosphate reduction: represents a molecular function rather than a biological process. GO:0006199, ADP reduction: represents a molecular function rather than a biological process. GO:0006247, TTP reduction: represents a molecular function rather than a biological process. GO:0006250, CDP reduction: represents a molecular function rather than a biological process. GO:0006252, CTP reduction: represents a molecular function rather than a biological process. GO:0006255, UDP reduction: represents a molecular function rather than a biological process. GO:0006762, dihydrofolate reduction: represents a molecular function rather than a biological process. GO:0006774, vitamin B12 reduction: represents a molecular function rather than a biological process. GO:0010153, polar cell elongation: did not represent a concept discrete from its sibling terms. Term name changes in process ontology GO:0000070: mitotic chromosome segregation --> mitotic sister chromatid segregation GO:0007077: mitotic nuclear envelope breakdown --> mitotic nuclear envelope disassembly GO:0007084: nuclear envelope reassembly --> mitotic nuclear envelope reassembly GO:0007087: nuclear pore complex reassembly --> mitotic nuclear pore complex reassembly GO:0007261: STAT protein dimerization --> JAK-induced STAT protein dimerization GO:0009825: cell expansion --> multidimensional cell growth GO:0009826: cell elongation --> unidimensional cell growth GO:0010223: seondary shoot formation --> secondary shoot formation GO:0010227: floral organ abcission --> floral organ abscission GO:0018102: peptidyl-arginine hydroxylation --> peptidyl-arginine hydroxylation to peptidyl-4-hydroxy-L-arginine GO:0030397: membrane degradation --> membrane disassembly GO:0030398: peroxisomal membrane degradation --> peroxisomal membrane disassembly GO:0030399: autophagic membrane degradation --> autophagic membrane disassembly GO:0035045: sperm plasma membrane breakdown --> sperm plasma membrane disassembly GO:0045143: meiosis I, chromosome segregation --> homologous chromosome segregation GO:0045144: meiosis II, chromosome segregation --> meiotic sister chromatid segregation GO:0048386: positive regulation of retinoic acic receptor signaling pathway --> positive regulation of retinoic acid receptor signaling pathway New definitions for process ontology terms (51 new definitions) GO:0000083, G1/S-specific transcription in mitotic cell cycle GO:0000114, G1-specific transcription in mitotic cell cycle GO:0000115, S-phase-specific transcription in mitotic cell cycle GO:0000116, G2-specific transcription in mitotic cell cycle GO:0000117, G2/M-specific transcription in mitotic cell cycle GO:0006099, tricarboxylic acid cycle GO:0006128, oxidized glutathione reduction GO:0006129, protein-disulfide reduction GO:0006131, dihydrolipoamide reduction GO:0006132, dihydrolipoylprotein reduction GO:0006134, dihydrobiopterin reduction GO:0006135, dihydropteridine reduction GO:0006162, purine/pyrimidine nucleoside diphosphate reduction GO:0006199, ADP reduction GO:0006247, TTP reduction GO:0006250, CDP reduction GO:0006252, CTP reduction GO:0006255, UDP reduction GO:0006419, alanyl-tRNA aminoacylation GO:0006420, arginyl-tRNA aminoacylation GO:0006421, asparaginyl-tRNA aminoacylation GO:0006423, cysteinyl-tRNA aminoacylation GO:0006424, glutamyl-tRNA aminoacylation GO:0006425, glutaminyl-tRNA aminoacylation GO:0006426, glycyl-tRNA aminoacylation GO:0006427, histidyl-tRNA aminoacylation GO:0006428, isoleucyl-tRNA aminoacylation GO:0006429, leucyl-tRNA aminoacylation GO:0006430, lysyl-tRNA aminoacylation GO:0006431, methionyl-tRNA aminoacylation GO:0006432, phenylalanyl-tRNA aminoacylation GO:0006434, seryl-tRNA aminoacylation GO:0006435, threonyl-tRNA aminoacylation GO:0006436, tryptophanyl-tRNA aminoacylation GO:0006437, tyrosyl-tRNA aminoacylation GO:0006438, valyl-tRNA aminoacylation GO:0006762, dihydrofolate reduction GO:0006774, vitamin B12 reduction GO:0007077, mitotic nuclear envelope disassembly GO:0007084, mitotic nuclear envelope reassembly GO:0007087, mitotic nuclear pore complex reassembly GO:0007167, enzyme linked receptor protein signaling pathway GO:0007168, receptor guanylyl cyclase signaling pathway GO:0007178, transmembrane receptor protein serine/threonine kinase signaling pathway GO:0007179, transforming growth factor beta receptor signaling pathway GO:0007185, transmembrane receptor protein tyrosine phosphatase signaling pathway GO:0007186, G-protein coupled receptor protein signaling pathway GO:0009865, pollen tube adhesion GO:0009934, regulation of meristem organization GO:0015748, organophosphate ester transport GO:0048113, pole plasm assembly (sensu Insecta) New term merges in process ontology GO:0007061 has been merged into GO:0045143, homologous chromosome segregation GO:0016359 has been merged into GO:0000070, mitotic sister chromatid segregation Term movements in process ontology: Terms movements under GO Slim term 'electron transport ; GO:0006118' - GO:0006128, oxidized glutathione reduction - GO:0006129, protein-disulfide reduction - GO:0006131, dihydrolipoamide reduction - GO:0006132, dihydrolipoylprotein reduction - GO:0006134, dihydrobiopterin reduction - GO:0006135, dihydropteridine reduction Terms movements under GO Slim term 'coenzyme and prosthetic group metabolism ; GO:0006731' - GO:0006762, dihydrofolate reduction - GO:0006774, vitamin B12 reduction Terms movements under GO Slim term 'response to stress ; GO:0006950' + GO:0001879, detection of yeast Terms movements under GO Slim term 'physiological process ; GO:0007582' + GO:0001776, immune cell homeostasis + GO:0001780, neutrophil homeostasis + GO:0001781, programmed cell death, neutrophils + GO:0001782, B-cell homeostasis + GO:0001783, programmed cell death, B-cells + GO:0006924, programmed cell death, activated T-cells + GO:0009857, pollen recognition + GO:0009859, pollen hydration + GO:0009865, pollen tube adhesion + GO:0009876, pollen adhesion + GO:0043029, T-cell homeostasis Terms movements under GO Slim term 'metabolism ; GO:0008152' - GO:0006134, dihydrobiopterin reduction - GO:0006135, dihydropteridine reduction - GO:0006162, purine/pyrimidine nucleoside diphosphate reduction - GO:0006199, ADP reduction - GO:0006247, TTP reduction - GO:0006250, CDP reduction - GO:0006252, CTP reduction - GO:0006255, UDP reduction - GO:0006762, dihydrofolate reduction - GO:0006774, vitamin B12 reduction Terms movements under GO Slim term 'catabolism ; GO:0009056' - GO:0006199, ADP reduction - GO:0006247, TTP reduction - GO:0006250, CDP reduction - GO:0006252, CTP reduction - GO:0006255, UDP reduction Terms movements under GO Slim term 'cell organization and biogenesis ; GO:0016043' + GO:0007077, mitotic nuclear envelope disassembly + GO:0007078, lamin depolymerization + GO:0007084, mitotic nuclear envelope reassembly + GO:0007085, nuclear membrane vesicle binding to chromatin + GO:0007086, vesicle fusion with nuclear membrane + GO:0007087, mitotic nuclear pore complex reassembly + GO:0035045, sperm plasma membrane disassembly Terms movements under GO Slim term 'cell growth ; GO:0016049' - GO:0010153, polar cell elongation Terms movements under GO Slim term 'cell homeostasis ; GO:0019725' - GO:0001776, immune cell homeostasis - GO:0001777, T-cell homeostatic proliferation - GO:0001780, neutrophil homeostasis - GO:0001781, programmed cell death, neutrophils - GO:0001782, B-cell homeostasis - GO:0001783, programmed cell death, B-cells - GO:0006924, programmed cell death, activated T-cells - GO:0042103, positive regulation of T-cell homeostatic proliferation - GO:0043029, T-cell homeostasis - GO:0046013, regulation of T-cell homeostatic proliferation - GO:0046014, negative regulation of T-cell homeostatic proliferation Terms movements under GO Slim term 'growth ; GO:0040007' + GO:0009860, pollen tube growth SourceForge items closed this month: SF id Resolution SF item title GO ids added, if any 848985 None query chromosome segregation GO:0000819 874063 Fixed teleost adrenals don't fit under organogenesis->adrenal glan [none] 877837 Later inflorescence development (+more) GO:0048409-48467 907413 Later query term name G1 phase of mitotic cell cycle [none] 930414 Accepted odd parentage of tubulin folding and new term GO:0030953-30954 937897 Accepted New Defs from SGD [none] 944692 Accepted pollination GO:0048470 951222 Accepted mesoderm development 2 GO:0048389-48402 952566 Accepted new term: guanine nucleotide transporter activity GO:0001409 952572 Accepted new term: guanine nucleotide transport GO:0001408 956633 Fixed nitric oxide reductases [none] 956845 Accepted new transport/transporter terms GO:0001406-01407 957037 Accepted correction of axon definition [none] 957337 Invalid consistency ATP binding/ATP-binding [none] 959484 Accepted children of ring canal GO:0035182-35183 959616 Invalid new term: threo-3-hydroxy-L-aspartate ammonia-lyase [none] 960829 Fixed missing relationship? protein carrier [none] 961450 Accepted HIV Tat protein binding GO:0030957 964330 Accepted synonym for GO:0030288 [none] 964417 Accepted preblastoderm and syncytial blastoderm mitotic cell cycles GO:0035185-35186 964875 Accepted NF-kappaB binding GO:0051059 965142 Duplicate NF-kappaB binding [none] 965183 Accepted new term: pullulanase GO:0051060 965350 Accepted glutamyl-tRNA(Gln) amidotransferase complex GO:0030956 965631 Invalid ntr: phytochelatin synthetase avtivity [none] 966437 Accepted ntr: pyruvylate galactose-beta-1,3-galactose biosynt GO:0051069-51072 966481 Accepted histone-threonine kinase activity GO:0035184 966752 Fixed Semaphorin receptor binding activity - def modification [none] 966798 Accepted modified definition for incorrect one for GO:0030255 [none] 966801 Accepted expanded definition for incomplete one for GO:0015628 [none] 966807 Accepted suggested expansion to definition for GO:0030254 [none] 968306 Accepted Rb-E2F complex GO:0035189 968828 Fixed synonym for cell aging [none] 968834 Accepted protein tetramerization activity GO:0051074 969520 Accepted Gram-positive bacterial binding GO:0051076 969611 Accepted perinuclear region GO:0048471 970369 Accepted meiotic nuclear envelope breakdown GO:0051078-51081 970518 Accepted hatching behavior GO:0035187-35188 970615 Fixed synonyms for GO:0004655 [none] 970659 Accepted S-adenosylmethionine:tRNA ribosyltransferase-isomerase GO:0051075 970691 Fixed synonym for GO:0046429 [none] 971071 Accepted ntr: RITs complex GO:0030958 973111 Fixed Intercellular bridge vs intercellular junction [none] 973473 Accepted synonym for GO:0008834 [none] 973500 Fixed name change [none] 974054 Accepted GO:0008818 GO:0051073 974133 Accepted add EC 4.6.1.12 to GO:0008685 [none] 974279 Accepted D-methionine transport GO:0048473-48474 975405 Fixed hydrogen-exporting ATPase relationship [none] 975434 None biotin transporter activity synonym [none] 975485 Accepted ntr: secondary septum GO:0051077 977506 Fixed STAT dimerization [none] 979615 Accepted cant find: alpha glucanase GO:0051082 979684 Fixed Minor syntax irregularity in obsolete term [none] 979698 Invalid ntr: prospore membrane formation [none] 979946 Fixed def of GO:0016998 cell wall catabolism [none] 981156 Accepted add synonym: CDK inhibitor [none] 981877 Accepted Four New RESID GO Xrefs GO:0030959-30963 Statistics: Component: 1421 terms, 89.0% defined (1265 terms defined) Function: 7376 terms, 88.4% defined (6519 terms defined) Process: 8810 terms, 93.1% defined (8200 terms defined) Total: 17607 terms, 90.8% defined (15984 terms defined) Term errors GO:0007315, pole plasm assembly - definition removed