GO Monthly Release Notes for June 2006 ======================== Generated on Mon Jul 3 14:59:26 2006 Files used: gene_ontology.obo OLD: version 3.1479, 31:05:2006 17:24 NEW: version 4.18, 30:06:2006 17:04 goslim_generic 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 GO-slim term(s) that new term was added under or "obs" if the term is obsolete.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 biological_process ontology (58 new terms) GO:0002064 GO:0009653 MGI D epithelial cell development GO:0030154 GO:0002065 GO:0009653 MGI D columnar/cuboidal epithelial cell differentiation GO:0030154 GO:0002066 GO:0009653 MGI D columnar/cuboidal epithelial cell development GO:0030154 GO:0002067 GO:0009653 MGI D glandular epithelial cell differentiation GO:0030154 GO:0002068 GO:0009653 MGI D glandular epithelial cell development GO:0030154 GO:0002069 GO:0009653 MGI D columnar/cuboidal epithelial cell maturation GO:0030154 GO:0002070 GO:0009653 MGI D epithelial cell maturation GO:0030154 GO:0002071 GO:0009653 MGI D glandular epithelial cell maturation GO:0030154 GO:0002072 GO:0009653 MGI D optic cup morphogenesis (sensu mammalia) GO:0009790 GO:0002073 GO:0007275 MGI D retina development (sensu mammalia) GO:0032069 GO:0050789 MAH D 1498539 regulation of nuclease activity GO:0032070 GO:0050789 MAH D 1498539 regulation of deoxyribonuclease activity GO:0032071 GO:0050789 MAH D 1498539 regulation of endodeoxyribonuclease activity GO:0032072 GO:0050789 MAH D 1498539 regulation of restriction endodeoxyribonuclease activity GO:0032073 GO:0050789 MAH D 1498539 negative regulation of restriction endodeoxyribonuclease activity GO:0032074 GO:0050789 MAH D 1498539 negative regulation of nuclease activity GO:0032075 GO:0050789 MAH D 1498539 positive regulation of nuclease activity GO:0032076 GO:0050789 MAH D 1498539 negative regulation of deoxyribonuclease activity GO:0032077 GO:0050789 MAH D 1498539 positive regulation of deoxyribonuclease activity GO:0032078 GO:0050789 MAH D 1498539 negative regulation of endodeoxyribonuclease activity GO:0032079 GO:0050789 MAH D 1498539 positive regulation of endodeoxyribonuclease activity GO:0032080 GO:0050789 MAH D 1498539 negative regulation of Type I restriction endodeoxyribonuclease activity GO:0032081 GO:0050789 MAH D 1498539 negative regulation of Type II restriction endodeoxyribonuclease activity GO:0032082 GO:0050789 MAH D 1498539 negative regulation of Type III restriction endodeoxyribonuclease activity GO:0032083 GO:0050789 MAH D 1498539 negative regulation of Type IV restriction endodeoxyribonuclease activity GO:0032084 GO:0050789 MAH D 1498539 regulation of Type I restriction endodeoxyribonuclease activity GO:0032085 GO:0050789 MAH D 1498539 regulation of Type II restriction endodeoxyribonuclease activity GO:0032086 GO:0050789 MAH D 1498539 regulation of Type III restriction endodeoxyribonuclease activity GO:0032087 GO:0050789 MAH D 1498539 regulation of Type IV restriction endodeoxyribonuclease activity GO:0032088 GO:0006350 MAH D 1495413 inhibition of NF-kappaB transcription factor GO:0050789 GO:0032091 GO:0050789 MAH D 1502976 negative regulation of protein binding GO:0032092 GO:0050789 MAH D 1502976 positive regulation of protein binding GO:0032094 GO:0007154 MAH D 1447142 response to food GO:0007582 GO:0009605 GO:0032095 GO:0007154 MAH D 1447142 regulation of response to food GO:0007582 GO:0009605 GO:0050789 GO:0032096 GO:0007154 MAH D 1447142 negative regulation of response to food GO:0007582 GO:0009605 GO:0050789 GO:0032097 GO:0007154 MAH D 1447142 positive regulation of response to food GO:0007582 GO:0009605 GO:0050789 GO:0032098 GO:0007154 MAH D 1447142 regulation of appetite GO:0007582 GO:0009605 GO:0050789 GO:0032099 GO:0007154 MAH D 1447142 negative regulation of appetite GO:0007582 GO:0009605 GO:0050789 GO:0032100 GO:0007154 MAH D 1447142 positive regulation of appetite GO:0007582 GO:0009605 GO:0050789 GO:0032101 GO:0009605 MAH D 1447142 regulation of response to external stimulus GO:0050789 GO:0032102 GO:0009605 MAH D 1447142 negative regulation of response to external stimulus GO:0050789 GO:0032103 GO:0009605 MAH D 1447142 positive regulation of response to external stimulus GO:0050789 GO:0032104 GO:0007154 MAH D 1447142 regulation of response to extracellular stimulus GO:0007582 GO:0009605 GO:0050789 GO:0032105 GO:0007154 MAH D 1447142 negative regulation of response to extracellular stimulus GO:0007582 GO:0009605 GO:0050789 GO:0032106 GO:0007154 MAH D 1447142 positive regulation of response to extracellular stimulus GO:0007582 GO:0009605 GO:0050789 GO:0032107 GO:0007154 MAH 1447142 regulation of response to nutrient levels GO:0007582 GO:0009605 GO:0050789 GO:0032108 GO:0007154 MAH 1447142 negative regulation of response to nutrient levels GO:0007582 GO:0009605 GO:0050789 GO:0032109 GO:0007154 MAH 1447142 positive regulation of response to nutrient levels GO:0007582 GO:0009605 GO:0050789 GO:0032110 GO:0050789 MAH D 1234861 regulation of protein histidine kinase activity GO:0032111 GO:0050789 MAH D 1234861 activation of protein histidine kinase activity GO:0032112 GO:0050789 MAH D 1234861 negative regulation of protein histidine kinase activity GO:0032113 GO:0050789 MAH D 1515374 regulation of carbohydrate phosphatase activity GO:0032114 GO:0050789 MAH D 1511525 regulation of glucose-6-phosphatase activity GO:0048839 GO:0007275 JIC D 1510969 inner ear development GO:0048840 GO:0007275 JIC D 1510969 otolith development GO:0048841 GO:0009653 JIC D 1509593 regulation of axon extension involved in axon guidance GO:0016043 GO:0030154 GO:0050789 GO:0048842 GO:0009653 JIC D 1509593 positive regulation of axon extension involved in axon guidance GO:0016043 GO:0030154 GO:0050789 GO:0048843 GO:0009653 JIC D 1509593 negative regulation of axon extension involved in axon guidance GO:0016043 GO:0030154 GO:0050789 New definitions for biological_process ontology terms (1 new definitions) GO:0009650, UV protection Term movements in biological_process ontology: Terms movements under GO Slim term 'DNA metabolism ; GO:0006259' - GO:0043388, positive regulation of DNA binding - GO:0043392, negative regulation of DNA binding - GO:0051101, regulation of DNA binding Terms movements under GO Slim term 'protein modification ; GO:0006464' + GO:0006511, ubiquitin-dependent protein catabolism + GO:0007092, anaphase-promoting complex activation during mitotic cell cycle + GO:0008054, cyclin catabolism + GO:0030433, ER-associated protein catabolism + GO:0030579, ubiquitin-dependent SMAD protein catabolism + GO:0031145, anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolism + GO:0031146, SCF-dependent proteasomal ubiquitin-dependent protein catabolism + GO:0043161, proteasomal ubiquitin-dependent protein catabolism + GO:0043162, ubiquitin-dependent protein catabolism via the multivesicular body pathway + GO:0043328, protein targeting to vacuole during ubiquitin-dependent protein catabolism via the MVB pathway + GO:0043329, protein targeting to membrane during ubiquitin-dependent protein catabolism via the MVB pathway Terms movements under GO Slim term 'development ; GO:0007275' + GO:0031173, otolith mineralization (sensu Tetrapoda) + GO:0031174, otolith mineralization (sensu Actinopterygii) + GO:0045299, otolith mineralization Terms movements under GO Slim term 'physiological process ; GO:0007582' + GO:0001300, chronological cell aging + GO:0001301, progressive alteration of chromatin during cell aging + GO:0001302, replicative cell aging + GO:0001304, progressive alteration of chromatin during replicative cell aging + GO:0001305, progressive alteration of chromatin during chronological cell aging + GO:0001307, extrachromosomal circular DNA accumulation during replicative cell aging + GO:0001309, age-dependent telomere shortening + GO:0001310, extrachromosomal rDNA circle accumulation during replicative cell aging + GO:0001321, age-dependent general metabolic decline during replicative cell aging + GO:0001323, age-dependent general metabolic decline during chronological cell aging + GO:0007568, aging + GO:0007569, cell aging + GO:0007571, age-dependent general metabolic decline + GO:0007580, extrachromosomal circular DNA accumulation during cell aging + GO:0008340, determination of adult life span + GO:0010149, senescence (sensu Magnoliophyta) + GO:0010150, leaf senescence + GO:0010259, organismal aging + GO:0010260, organ senescence + GO:0010261, organ senescence (sensu Magnoliophyta) + GO:0042697, menopause - GO:0043516, regulation of DNA damage response, signal transduction by p53 class mediator - GO:0043517, positive regulation of DNA damage response, signal transduction by p53 class mediator - GO:0043518, negative regulation of DNA damage response, signal transduction by p53 class mediator - GO:0048576, positive regulation of short-day photoperiodism, flowering - GO:0048577, negative regulation of short-day photoperiodism, flowering - GO:0048578, positive regulation of long-day photoperiodism, flowering - GO:0048579, negative regulation of long-day photoperiodism, flowering - GO:0048583, regulation of response to stimulus - GO:0048584, positive regulation of response to stimulus - GO:0048585, negative regulation of response to stimulus - GO:0048586, regulation of long-day photoperiodism, flowering - GO:0048587, regulation of short-day photoperiodism, flowering Terms movements under GO Slim term 'cell death ; GO:0008219' - GO:0001300, chronological cell aging - GO:0001301, progressive alteration of chromatin during cell aging - GO:0001302, replicative cell aging - GO:0001303, nucleolar fragmentation during replicative aging - GO:0001304, progressive alteration of chromatin during replicative cell aging - GO:0001305, progressive alteration of chromatin during chronological cell aging - GO:0001306, age-dependent response to oxidative stress - GO:0001307, extrachromosomal circular DNA accumulation during replicative cell aging - GO:0001308, loss of chromatin silencing during replicative cell aging - GO:0001309, age-dependent telomere shortening - GO:0001310, extrachromosomal rDNA circle accumulation during replicative cell aging - GO:0001311, formation of extrachromosomal circular rDNA by homologous recombination during replicative cell aging - GO:0001312, replication of extrachromosomal rDNA circles during replicative cell aging - GO:0001313, formation of extrachromosomal circular DNA during replicative cell aging - GO:0001314, replication of extrachromosomal circular DNA during replicative cell aging - GO:0001316, age-dependent response to reactive oxygen species during replicative cell aging - GO:0001317, accumulation of oxidatively modified proteins during replicative cell aging - GO:0001318, formation of oxidatively modified proteins during replicative cell aging - GO:0001319, inheritance of oxidatively modified proteins during replicative cell aging - GO:0001320, age-dependent response to reactive oxygen species during chronological cell aging - GO:0001321, age-dependent general metabolic decline during replicative cell aging - GO:0001322, age-dependent response to oxidative stress during replicative cell aging - GO:0001323, age-dependent general metabolic decline during chronological cell aging - GO:0001324, age-dependent response to oxidative stress during chronological cell aging - GO:0007569, cell aging - GO:0007571, age-dependent general metabolic decline - GO:0007576, nucleolar fragmentation - GO:0007580, extrachromosomal circular DNA accumulation during cell aging Terms movements under GO Slim term 'morphogenesis ; GO:0009653' - GO:0031173, otolith mineralization (sensu Tetrapoda) - GO:0031174, otolith mineralization (sensu Actinopterygii) - GO:0045299, otolith mineralization Terms movements under GO Slim term 'embryonic development ; GO:0009790' - GO:0031173, otolith mineralization (sensu Tetrapoda) - GO:0031174, otolith mineralization (sensu Actinopterygii) - GO:0045299, otolith mineralization Terms movements under GO Slim term 'cell growth ; GO:0016049' + GO:0001403, invasive growth (sensu Saccharomyces) + GO:0007124, pseudohyphal growth Terms movements under GO Slim term 'death ; GO:0016265' - GO:0007568, aging - GO:0008340, determination of adult life span - GO:0010149, senescence (sensu Magnoliophyta) - GO:0010150, leaf senescence - GO:0010259, organismal aging - GO:0010260, organ senescence - GO:0010261, organ senescence (sensu Magnoliophyta) - GO:0042697, menopause Terms movements under GO Slim term 'protein metabolism ; GO:0019538' - GO:0006511, ubiquitin-dependent protein catabolism - GO:0007092, anaphase-promoting complex activation during mitotic cell cycle - GO:0008054, cyclin catabolism - GO:0030433, ER-associated protein catabolism - GO:0030579, ubiquitin-dependent SMAD protein catabolism - GO:0031145, anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolism - GO:0031146, SCF-dependent proteasomal ubiquitin-dependent protein catabolism - GO:0043161, proteasomal ubiquitin-dependent protein catabolism - GO:0043162, ubiquitin-dependent protein catabolism via the multivesicular body pathway - GO:0043328, protein targeting to vacuole during ubiquitin-dependent protein catabolism via the MVB pathway - GO:0043329, protein targeting to membrane during ubiquitin-dependent protein catabolism via the MVB pathway Terms movements under GO Slim term 'growth ; GO:0040007' - GO:0001403, invasive growth (sensu Saccharomyces) - GO:0007124, pseudohyphal growth New terms in cellular_component ontology (7 new terms) GO:0032068 GO:0005737 MAH D 1499764 Type IV site-specific deoxyribonuclease complex GO:0043234 GO:0032153 GO:0005623 MAH D 994121 cell division plane GO:0032154 GO:0005623 MAH D 994121 cleavage furrow GO:0032155 GO:0005623 MAH D 994121 cell division plane part GO:0043655 GO:0005576 JL D 1504668 extracellular space of host GO:0043656 GO:0005576 JL D 1504668 intracellular region of host GO:0043657 GO:0005576 JL D 1504668 host cell Term name changes in cellular_component ontology GO:0009359: type II site-specific deoxyribonuclease complex --> Type II site-specific deoxyribonuclease complex GO:0019812: type I site-specific deoxyribonuclease complex --> Type I site-specific deoxyribonuclease complex GO:0019813: type III site-specific deoxyribonuclease complex --> Type III site-specific deoxyribonuclease complex New definitions for cellular_component ontology terms (3 new definitions) GO:0009359, Type II site-specific deoxyribonuclease complex GO:0015050, methane monooxygenase complex GO:0019812, Type I site-specific deoxyribonuclease complex Term movements in cellular_component ontology: Terms movements under GO Slim term 'extracellular space ; GO:0005615' - GO:0008247, 2-acetyl-1-alkylglycerophosphocholine esterase complex Terms movements under GO Slim term 'intracellular ; GO:0005622' + GO:0000159, protein phosphatase type 2A complex + GO:0005955, calcineurin complex - GO:0019813, Type III site-specific deoxyribonuclease complex + GO:0030289, protein phosphatase 4 complex + GO:0031501, mannosyltransferase complex Terms movements under GO Slim term 'cell ; GO:0005623' + GO:0008287, protein serine/threonine phosphatase complex + GO:0009367, prepilin peptidase complex + GO:0015050, methane monooxygenase complex + GO:0017023, myosin phosphatase complex Terms movements under GO Slim term 'cytoplasm ; GO:0005737' + GO:0000164, protein phosphatase type 1 complex + GO:0009359, Type II site-specific deoxyribonuclease complex + GO:0019804, quinolinate synthetase complex + GO:0019812, Type I site-specific deoxyribonuclease complex + GO:0019813, Type III site-specific deoxyribonuclease complex Terms movements under GO Slim term 'unlocalized protein complex ; GO:0005941' - GO:0000136, alpha-1,6-mannosyltransferase complex - GO:0000159, protein phosphatase type 2A complex - GO:0000164, protein phosphatase type 1 complex - GO:0005955, calcineurin complex - GO:0008287, protein serine/threonine phosphatase complex - GO:0009359, Type II site-specific deoxyribonuclease complex - GO:0009367, prepilin peptidase complex - GO:0015050, methane monooxygenase complex - GO:0017023, myosin phosphatase complex - GO:0019804, quinolinate synthetase complex - GO:0019812, Type I site-specific deoxyribonuclease complex - GO:0030289, protein phosphatase 4 complex - GO:0031501, mannosyltransferase complex - GO:0031502, dolichyl-phosphate-mannose-protein mannosyltransferase complex Terms movements under GO Slim term 'protein complex ; GO:0043234' + GO:0000136, alpha-1,6-mannosyltransferase complex + GO:0000159, protein phosphatase type 2A complex + GO:0000164, protein phosphatase type 1 complex + GO:0005955, calcineurin complex + GO:0008287, protein serine/threonine phosphatase complex + GO:0009359, Type II site-specific deoxyribonuclease complex + GO:0009367, prepilin peptidase complex + GO:0015050, methane monooxygenase complex + GO:0017023, myosin phosphatase complex + GO:0019804, quinolinate synthetase complex + GO:0019812, Type I site-specific deoxyribonuclease complex + GO:0030289, protein phosphatase 4 complex + GO:0031501, mannosyltransferase complex + GO:0031502, dolichyl-phosphate-mannose-protein mannosyltransferase complex New terms in molecular_function ontology (5 new terms) GO:0032067 GO:0004518 MAH D 1498533 Type IV site-specific deoxyribonuclease activity GO:0032089 GO:0005515 MAH D 1494869 NACHT domain binding GO:0032090 GO:0005515 MAH D 1494869 Pyrin domain binding GO:0032093 GO:0005515 MAH D 1506896 SAM domain binding GO:0032115 GO:0003824 MAH D 1512265 sorbose reductase activity Term name changes in molecular_function ontology GO:0009035: type I site-specific deoxyribonuclease activity --> Type I site-specific deoxyribonuclease activity GO:0009036: type II site-specific deoxyribonuclease activity --> Type II site-specific deoxyribonuclease activity GO:0015668: type III site-specific deoxyribonuclease activity --> Type III site-specific deoxyribonuclease activity New definitions for molecular_function ontology terms (2 new definitions) GO:0015666, restriction endodeoxyribonuclease activity GO:0019203, carbohydrate phosphatase activity New term merges in molecular_function ontology GO:0030376 has been merged into GO:0043022, ribosome binding SourceForge items closed this month: SF id Resolution SF item title GO ids added, if any 1065289 Accepted organ morphogenesis terms 2 [none] 1203227 Accepted male germ cell in plants [none] 1234861 Accepted ntr: protein histidine kinase inhibitor activity GO:0032110 GO:0032111 GO:0032112 1432216 Fixed tpv: conjugation [none] 1447142 Accepted positive regulation of appetite GO:0032094 GO:0032095 GO:0032096 GO:0032097 GO:0032098 GO:0032099 GO:0032100 GO:0032101 GO:0032102 GO:0032103 GO:0032104 GO:0032105 GO:0032106 GO:0032107 GO:0032108 GO:0032109 1468304 Rejected liposome [none] 1468305 Rejected proteoliposome [none] 1475427 Accepted update def?: RSC complex [none] 1479867 Fixed GO:0004687 : MLCK activity - parentage [none] 1490151 Fixed bipolar attachment related [none] 1490281 Accepted nucleobase binding GO:0002054 GO:0002055 GO:0002056 GO:0002057 GO:0002058 GO:0002059 GO:0002060 GO:0002061 1490810 Accepted mp: proteasomal ubiquitin-dependent protein catabolism [none] 1495413 Accepted nhibition of NF-kappaB GO:0032088 1495603 Accepted Additional parentage for growth terms [none] 1498533 Accepted restriction enzyme activities GO:0032067 1498539 Accepted ntr: inhibitors of restriction enzymes GO:0032069 GO:0032070 GO:0032071 GO:0032072 GO:0032073 GO:0032074 GO:0032075 GO:0032076 GO:0032077 GO:0032078 GO:0032079 GO:0032080 GO:0032081 GO:0032082 GO:0032083 GO:0032084 GO:0032085 GO:0032086 GO:0032087 1499764 Accepted defs for restriction enzyme complexes GO:0032068 1499777 Fixed weird placement of reg of DNA binding [none] 1501597 None NTR: Rhoptry (CC) [none] 1502916 Fixed definition for fibroblast growth factor binding [none] 1502976 Accepted children of regulation of protein binding GO:0032091 GO:0032092 1506896 Accepted ntr: SAM domain binding GO:0032093 1508450 Fixed tpv /etc GO:0030376/ribosome receptor activity [none] 1508679 Fixed remove parent 2-acetyl-1-alkylglycerophosphocholine esterase [none] 1510969 Accepted inner ear development GO:0048839 GO:0048840 1511525 Accepted ntr: regulation of glucose-6-phosphatase activity GO:0032113 GO:0032114 1512265 Accepted ntr: sorbose reductase GO:0032115 Statistics: biological_process: 11074 terms, 98.0% defined (10856 terms defined) cellular_component: 1873 terms, 96.6% defined (1810 terms defined) molecular_function: 7960 terms, 92.2% defined (7338 terms defined) Total: 20907 terms, 95.7% defined (20004 terms defined) Term errors none