GO Monthly Release Notes for June 2001 ======================== Generated on Mon Oct 27 12:26:41 2003 Files used: component old: 2.23 new: 2.37 function old: 2.45 new: 2.64 process old: 2.35 new: 2.49 definitions old: 2.37 new: 2.55 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 GO-slim term(s) that new term was added under or "obs" if the term is obsolete.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 (20 new terms) GO:0001534 GO:0005929 MGI D radial spoke GO:0001535 GO:0005929 MGI D radial spokehead GO:0001536 GO:0005929 MGI D radial spoke stalk GO:0016363 GO:0005634 FB D nuclear matrix GO:0017101 GO:0005941 FB D aminoacyl-tRNA synthetase multienzyme complex GO:0017102 GO:0005941 FB D methionyl glutamyl tRNA synthetase complex GO:0017109 GO:0005941 FB D glutamate--cysteine ligase GO:0017117 GO:0005634 FB D single-stranded DNA dependent ATP dependent DNA helicase GO:0017119 GO:0005794 FB D Golgi transport complex GO:0016023 GO:0017122 GO:0005941 FB D UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase GO:0017133 GO:0005739 FB D electron transfer flavoprotein GO:0017146 GO:0005575 FB D N-methyl-D-aspartate selective glutamate receptor complex GO:0005886 GO:0030027 GO:0005886 MAH D lamellipodium GO:0030028 GO:0005886 MAH D microspike GO:0030054 GO:0005886 MAH D cell junction GO:0030055 GO:0005886 MAH D cell-matrix junction GO:0030056 GO:0005886 MAH D hemidesmosome GO:0030057 GO:0005886 MAH D desmosome GO:0030061 GO:0005575 MAH D mitochondrial crista GO:0005739 GO:0030062 GO:0005739 MAH D TCA cycle enzyme complex Term name changes in component ontology GO:0000275: hydrogen-transporting ATP synthase, F1 sector --> proton-transporting ATP synthase complex, catalytic core F(1) GO:0000276: hydrogen-transporting ATP synthase, F0 sector --> proton-transporting ATP synthase complex, coupling factor F(0) GO:0005746: respiratory chain complex --> mitochondrial electron transport chain complex GO:0005753: hydrogen-transporting ATP synthase --> proton-transporting ATP synthase complex GO:0005757: mitochondrial PT pore --> mitochondrial permeability transition pore GO:0005760: mitochondrial (gamma) DNA-directed DNA polymerase --> gamma DNA polymerase GO:0005762: mitochondrial large ribosomal-subunit --> mitochondrial large ribosomal subunit GO:0005763: mitochondrial small ribosomal-subunit --> mitochondrial small ribosomal subunit GO:0005842: cytosolic large ribosomal (60S)-subunit --> cytosolic large ribosomal (60S) subunit GO:0005843: cytosolic small ribosomal (40S)-subunit --> cytosolic small ribosomal (40S) subunit GO:0005902: microvilli --> microvillus GO:0005925: hemi adherens junction --> focal adhesion GO:0005926: connecting hemi adherens junction --> connecting hemiadherens junction GO:0005928: apical hemi adherens junction --> apical hemiadherens junction GO:0005947: alpha-ketoacid dehydrogenase complex --> alpha-ketoglutarate dehydrogenase complex GO:0009282: prokaryotic large ribosomal (50S)-subunit --> prokaryotic large ribosomal (50S) subunit GO:0009283: prokaryotic small ribosomal (30S)-subunit --> prokaryotic small ribosomal (30S) subunit New definitions for component ontology terms (10 new definitions) GO:0005902, microvillus GO:0005911, intercellular junction GO:0005912, adherens junction GO:0005913, cell-cell adherens junction GO:0005915, zonula adherens GO:0005918, septate junction GO:0005921, gap junction GO:0005923, tight junction GO:0005924, cell-substrate adherens junction GO:0005925, focal adhesion New term merges in component ontology GO:0008357 has been merged into GO:0005925, focal adhesion Term movements in component ontology: Terms movements under GO Slim term 'cellular_component ; GO:0005575' - GO:0008325, succinate--CoA ligase (GDP-forming) Terms movements under GO Slim term 'cell ; GO:0005623' - GO:0005911, intercellular junction - GO:0005912, adherens junction - GO:0005913, cell-cell adherens junction - GO:0005914, spot adherens junction - GO:0005915, zonula adherens - GO:0005916, fascia adherens - GO:0005917, nephrocyte junction - GO:0005918, septate junction - GO:0005919, pleated septate junction - GO:0005920, smooth septate junction - GO:0005921, gap junction - GO:0005922, connexon - GO:0005923, tight junction - GO:0009506, plasmodesma - GO:0009510, plasmodesmatal desmotubule - GO:0009511, plasmodesmatal endoplasmic reticulum - GO:0009546, plasmodesmatal cytoplasmic sleeve - GO:0009548, plasmodesmatal plasma membrane - GO:0009572, desmotubule central rod Terms movements under GO Slim term 'mitochondrion ; GO:0005739' + GO:0005947, alpha-ketoglutarate dehydrogenase complex + GO:0005962, isocitrate dehydrogenase (NAD+) + GO:0005967, pyruvate dehydrogenase complex Terms movements under GO Slim term 'plasma membrane ; GO:0005886' + GO:0005911, intercellular junction + GO:0009506, plasmodesma + GO:0009510, plasmodesmatal desmotubule + GO:0009511, plasmodesmatal endoplasmic reticulum + GO:0009546, plasmodesmatal cytoplasmic sleeve + GO:0009572, desmotubule central rod Terms movements under GO Slim term 'unlocalized ; GO:0005941' - GO:0005947, alpha-ketoglutarate dehydrogenase complex - GO:0005962, isocitrate dehydrogenase (NAD+) - GO:0005967, pyruvate dehydrogenase complex New terms in function ontology (57 new terms) GO:0001537 GO:0003824 MGI D N-acetylgalactosamine-4-O-sulfotransferase GO:0001538 GO:0005194 MGI D cadherin GO:0016361 GO:0004672 FB D type I activin receptor GO:0004872 GO:0016362 GO:0004672 FB D type II activin receptor GO:0004872 GO:0017096 GO:0003824 FB D acetylserotonin O-methyltransferase GO:0017097 GO:0003824 FB D acetylserotonin N-methyltransferase GO:0017098 GO:0005102 FB D sulfonylurea receptor ligand GO:0017099 GO:0003824 FB D very long-chain acyl-CoA dehydrogenase GO:0017100 GO:0003824 FB D aminoacyl-tRNA synthetase auxiliary protein GO:0017103 GO:0003824 FB D UTP--galactose-1-phosphate uridylyltransferase GO:0017105 GO:0003824 FB D acyl-CoA delta(11)-desaturase GO:0017106 GO:0004871 FB D activin inhibitor GO:0017107 GO:0005215 FB D anion exchanger adapter GO:0017108 GO:0004518 FB D flap endonuclease GO:0017110 GO:0003824 FB D nucleoside diphosphatase GO:0017111 GO:0003824 FB D nucleoside triphosphatase GO:0017112 GO:0004871 FB D RAB guanyl-nucleotide exchange factor GO:0017113 GO:0003824 FB D dihydropyrimidine dehydrogenase GO:0017114 GO:0003824 FB D wide-spectrum proteinase inhibitor GO:0017115 GO:0003824 FB D SUMO activating enzyme GO:0017116 GO:0003824 FB D single-stranded DNA dependent ATP dependent DNA helicase GO:0017118 GO:0003824 FB D lipoyltransferase GO:0017120 GO:0003824 FB D polyphosphoinositide phosphatase GO:0017123 GO:0003824 FB D RAL GTPase activator GO:0004871 GO:0017124 GO:0005515 FB D SH3-domain binding GO:0017125 GO:0003824 FB D deoxycytidyl transferase GO:0017127 GO:0005215 FB D cholesterol transporter GO:0017128 GO:0005215 FB D phospholipid scramblase GO:0017129 GO:0008289 FB D triglyceride binding GO:0017130 GO:0003723 FB D poly(rC) binding GO:0017131 GO:0003723 FB D uridine-rich cytoplasmic polyadenylation element binding GO:0017132 GO:0004871 FB D cyclic nucleotide dependent guanyl-nucleotide exchange factor GO:0017134 GO:0005515 FB D fibroblast growth factor binding GO:0017135 GO:0005515 FB D membrane-associated protein with guanylate kinase activity interacting GO:0017136 GO:0003824 FB D NAD-dependent histone deacetylase GO:0017137 GO:0004871 FB D RAB interactor GO:0017140 GO:0003824 FB D lipoic acid synthase GO:0017147 GO:0005515 FB D Wnt-protein binding GO:0017149 GO:0003824 FB D protein biosynthesis inhibitor GO:0017150 GO:0003824 FB D tRNA dihydrouridine synthase GO:0017151 GO:0005515 FB D DEAD/H-box RNA helicase binding GO:0017153 GO:0005215 FB D sodium:dicarboxylate cotransporter GO:0017154 GO:0004872 FB D semaphorin receptor GO:0017155 GO:0005215 FB D sodium:hydrogen antiporter regulator GO:0017159 GO:0003824 FB D pantetheinase GO:0017160 GO:0004871 FB D RAL interactor GO:0017161 GO:0003824 FB D inositol-1,3,4-triphosphate 4-phosphatase GO:0017162 GO:0005515 FB D aryl hydrocarbon-receptor binding GO:0017163 GO:0003700 FB D negative regulator of basal transcription GO:0017164 GO:0004872 FB D nicotinic acetylcholine receptor-associated protein GO:0030039 GO:0003677 MAH D DNA unwinding factor GO:0030051 GO:0003754 MAH D FK506-binding isomerase GO:0003824 GO:0005488 GO:0030052 GO:0003754 MAH D parvulin GO:0003824 GO:0030053 GO:0003754 MAH D immunophilin GO:0003824 GO:0030058 GO:0003824 MAH D amine dehydrogenase GO:0030059 GO:0003824 MAH D aralkylamine dehydrogenase GO:0030060 GO:0003824 MAH D malate dehydrogenase 1 New obsoletions in function ontology GO:0008498, phospholipid scrambling: No reason given. Term name changes in function ontology GO:0003795: antimicrobial response protein --> antimicrobial peptide GO:0003797: antibacterial response protein --> antibacterial peptide GO:0003798: male-specific antibacterial response protein --> male-specific antibacterial peptide GO:0003799: antifungal response protein --> antifungal peptide GO:0008224: gram-positive antibacterial response protein --> gram-positive antibacterial peptide GO:0008225: gram-negative antibacterial response protein --> gram-negative antibacterial peptide New definitions for function ontology terms (12 new definitions) GO:0003795, antimicrobial peptide GO:0003797, antibacterial peptide GO:0003798, male-specific antibacterial peptide GO:0003799, antifungal peptide GO:0004470, malic enzyme GO:0004471, malate dehydrogenase (decarboxylating) GO:0004473, malate dehydrogenase (oxaloacetate decarboxylating) (NADP+) GO:0008224, gram-positive antibacterial peptide GO:0008225, gram-negative antibacterial peptide GO:0008526, phosphatidylinositol transporter GO:0016615, malate dehydrogenase GO:0016619, malate dehydrogenase (oxaloacetate decarboxylating) New term merges in function ontology GO:0004752 has been merged into GO:0003755, peptidylprolyl isomerase GO:0008032 has been merged into GO:0005041, low-density lipoprotein receptor Term movements in function ontology: Terms movements under GO Slim term 'nucleotide binding ; GO:0000166' + GO:0008327, methyl-CpG binding Terms movements under GO Slim term 'chaperone ; GO:0003754' - GO:0003756, protein disulfide isomerase Terms movements under GO Slim term 'transporter ; GO:0005215' - GO:0008498, phospholipid scrambling Terms movements under GO Slim term 'ligand binding or carrier ; GO:0005488' - GO:0008327, methyl-CpG binding New terms in process ontology (40 new terms) GO:0000288 GO:0008152 SGD D deadenylation-dependent mRNA decay GO:0009056 GO:0000289 GO:0008152 SGD D poly(A) tail shortening GO:0009056 GO:0000290 GO:0008152 SGD D deadenylation-dependent decapping GO:0009056 GO:0000291 GO:0008152 SGD D exonucleolytic degradation of mRNA GO:0009056 GO:0000294 GO:0008152 SGD D endonucleolytic mRNA decay GO:0009056 GO:0016360 GO:0007275 FB D determination of sensory organ precursor cell fate GO:0017085 GO:0009628 FB D insecticide response GO:0017121 GO:0006996 FB D phospholipid scrambling GO:0016043 GO:0017126 GO:0016043 FB D nucleologenesis GO:0017139 GO:0006950 FB D arsenate sensitivity/resistance GO:0009628 GO:0017141 GO:0009628 FB D antibiotic susceptibility/resistance GO:0017142 GO:0009628 FB D toxin susceptibility/resistance GO:0017143 GO:0008152 FB D insecticide metabolism GO:0009628 GO:0017144 GO:0008152 FB D drug metabolism GO:0009628 GO:0017145 GO:0007049 FB D stem cell renewal GO:0017148 GO:0006412 FB D protein biosynthesis inhibition GO:0017156 GO:0008151 FB D calcium ion dependent exocytosis GO:0017157 GO:0008151 FB D regulation of exocytosis GO:0017158 GO:0008151 FB D regulation of calcium ion dependent exocytosis GO:0030026 GO:0008151 MAH D manganese homeostasis GO:0030029 GO:0007010 MAH D actin filament-based process GO:0030030 GO:0016043 MAH D cell surface structure organization and biogenesis GO:0030031 GO:0016043 MAH D formation of a cell surface projection GO:0030032 GO:0016043 MAH D lamellipodium formation GO:0030033 GO:0016043 MAH D microvillus assembly GO:0030034 GO:0016043 MAH D microvillar actin bundle formation GO:0030035 GO:0016043 MAH D microspike formation GO:0030036 GO:0007010 MAH D actin cytoskeleton organization and biogenesis GO:0030037 GO:0007010 MAH D cell cycle dependent actin filament reorganization GO:0007049 GO:0030038 GO:0007010 MAH D contractile actin filament bundle formation GO:0030041 GO:0007010 MAH D actin filament polymerization GO:0030042 GO:0007010 MAH D actin filament depolymerization GO:0030043 GO:0007010 MAH D actin filament fragmentation GO:0030044 GO:0007010 MAH D actin filament stabilization GO:0030045 GO:0007010 MAH D actin filament destabilization GO:0030046 GO:0007010 MAH D parallel actin filament bundle formation GO:0030047 GO:0006464 MAH D actin modification GO:0007010 GO:0030048 GO:0007010 MAH D actin filament-based movement GO:0030049 GO:0007010 MAH D muscle filament sliding GO:0008151 GO:0030050 GO:0007010 MAH D vesicle transport along actin filament New obsoletions in process ontology GO:0007012, actin cytoskeleton reorganization: No reason given. GO:0007013, actin modification: No reason given. Term name changes in process ontology GO:0008154: actin polymerization/depolymerization --> actin polymerization and/or depolymerization GO:0009634: heavy metal resistance --> heavy metal sensitivity/resistance GO:0009635: response to herbicides --> herbicide response GO:0016351: drug susceptibility --> drug susceptibility/resistance GO:0016352: insecticide susceptibility --> insecticide susceptibility/resistance GO:0016353: carbamate susceptibility --> carbamate susceptibility/resistance GO:0016354: cyclodiene susceptibility --> cyclodiene susceptibility/resistance GO:0016355: DDT susceptibility --> DDT susceptibility/resistance GO:0016356: organophosphosphorous susceptibility --> organophosphosphorous susceptibility/resistance GO:0016357: pyrethroid susceptibility --> pyrethroid susceptibility/resistance New definitions for process ontology terms (8 new definitions) GO:0000147, actin cortical patch assembly GO:0006805, xenobiotic metabolism GO:0007015, actin filament organization GO:0008064, actin polymerization/depolymerization regulation GO:0008154, actin polymerization and/or depolymerization GO:0009404, toxin metabolism GO:0009636, detoxification response GO:0016999, antibiotic metabolism Term movements in process ontology: Terms movements under GO Slim term 'protein modification ; GO:0006464' + GO:0007014, indirect flight muscle actin ubiquitylation Terms movements under GO Slim term 'organelle organization and biogenesis ; GO:0006996' + GO:0000011, vacuole inheritance + GO:0006895, Golgi to endosome transport - GO:0006997, nuclear organization and biogenesis - GO:0006998, nuclear membrane organization and biogenesis - GO:0006999, nuclear pore organization and biogenesis - GO:0007000, nucleolus organization and biogenesis - GO:0007001, chromosome organization and biogenesis - GO:0007004, telomere maintenance + GO:0007029, ER organization and biogenesis + GO:0007030, Golgi organization and biogenesis + GO:0007031, peroxisome organization and biogenesis + GO:0007032, endosome organization and biogenesis + GO:0007033, vacuole organization and biogenesis + GO:0007034, vacuolar transport + GO:0007035, vacuolar acidification + GO:0007037, vacuolar phosphate transport + GO:0007038, delivery of endocytosed proteins to the vacuole + GO:0007039, vacuolar protein degradation + GO:0007040, lysosome organization and biogenesis + GO:0007041, lysosomal transport + GO:0007042, lysosomal lumen acidification + GO:0008333, endosome to lysosome transport + GO:0016050, vesicle organization and biogenesis + GO:0016182, endosome to synaptic vesicle budding + GO:0016189, synaptic vesicle to endosome fusion + GO:0016197, endosome traffic - GO:0016233, telomere capping + GO:0016557, peroxisome membrane biogenesis + GO:0016558, peroxisome matrix protein import + GO:0016559, peroxisome division + GO:0016560, peroxisome receptor docking + GO:0016561, peroxisome receptor translocation + GO:0016562, peroxisome receptor recycling Terms movements under GO Slim term 'cytoskeleton organization and biogenesis ; GO:0007010' - GO:0007012, actin cytoskeleton reorganization - GO:0007013, actin modification Terms movements under GO Slim term 'cytoplasm organization and biogenesis ; GO:0007028' - GO:0000011, vacuole inheritance - GO:0006895, Golgi to endosome transport - GO:0007029, ER organization and biogenesis - GO:0007030, Golgi organization and biogenesis - GO:0007031, peroxisome organization and biogenesis - GO:0007032, endosome organization and biogenesis - GO:0007033, vacuole organization and biogenesis - GO:0007034, vacuolar transport - GO:0007035, vacuolar acidification - GO:0007037, vacuolar phosphate transport - GO:0007038, delivery of endocytosed proteins to the vacuole - GO:0007039, vacuolar protein degradation - GO:0007040, lysosome organization and biogenesis - GO:0007041, lysosomal transport - GO:0007042, lysosomal lumen acidification - GO:0008333, endosome to lysosome transport - GO:0016050, vesicle organization and biogenesis - GO:0016182, endosome to synaptic vesicle budding - GO:0016189, synaptic vesicle to endosome fusion - GO:0016197, endosome traffic - GO:0016557, peroxisome membrane biogenesis - GO:0016558, peroxisome matrix protein import - GO:0016559, peroxisome division - GO:0016560, peroxisome receptor docking - GO:0016561, peroxisome receptor translocation - GO:0016562, peroxisome receptor recycling Terms movements under GO Slim term 'cell cycle ; GO:0007049' - GO:0000147, actin cortical patch assembly - GO:0007012, actin cytoskeleton reorganization - GO:0007015, actin filament organization + GO:0007284, spermatogonial cell division - GO:0008302, ring canal formation, actin assembly Terms movements under GO Slim term 'metabolism ; GO:0008152' + GO:0007014, indirect flight muscle actin ubiquitylation Terms movements under GO Slim term 'catabolism ; GO:0009056' + GO:0007014, indirect flight muscle actin ubiquitylation + GO:0016998, cell wall degradation Terms movements under GO Slim term 'response to abiotic stimulus ; GO:0009628' + GO:0009402, toxin resistance + GO:0009403, toxin biosynthesis + GO:0009404, toxin metabolism + GO:0009407, toxin catabolism + GO:0016999, antibiotic metabolism + GO:0017000, antibiotic biosynthesis + GO:0017001, antibiotic catabolism Terms movements under GO Slim term 'cell organization and biogenesis ; GO:0016043' + GO:0006997, nuclear organization and biogenesis + GO:0006999, nuclear pore organization and biogenesis + GO:0007000, nucleolus organization and biogenesis + GO:0007001, chromosome organization and biogenesis + GO:0007004, telomere maintenance + GO:0016233, telomere capping SourceForge items closed this month: SF id Resolution SF item title GO ids added, if any none Statistics: Component: 763 terms, 34.3% defined (262 terms defined) Function: 4020 terms, 8.7% defined (351 terms defined) Process: 3020 terms, 14.2% defined (428 terms defined) Total: 7803 terms, 13.3% defined (1041 terms defined) Term errors GO:0005201, extracellular matrix structural protein - definition removed GO:0016358, dendrite morphogenesis - definition removed GO:0016359, mitotic sister chromatid separation - definition removed GO:0030020, extracellular matrix structural protein conferring tensile strength - definition removed GO:0030021, extracellular matrix structural protein conferring compression resistance - definition removed GO:0030022, extracellular matrix protein, adhesive - definition removed GO:0030023, extracellular matrix protein conferring elasticity - definition removed GO:0030024, NADH:plastoquinone reductase - definition removed GO:0030025, NADH:plastoquinone reductase - definition removed