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 GO-slim term(s) that new term was added under or "obs" if the term is obsolete.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