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 GO-slim term(s) that new term was added under or "obs" if the term is obsolete.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