GO Monthly Release Notes for November 2005 ======================== Generated on Fri Dec 2 11:23:00 2005 Files used: gene_ontology.obo OLD: version 3.1191, 28:10:2005 16:39 NEW: version 3.1219, 29:11:2005 11:55 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 GO-slim term(s) that new term was added under or "obs" if the term is obsolete.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 (47 new terms) GO:0001969 GO:0006950 MGI D regulation of activation of membrane attack complex GO:0008219 GO:0009605 GO:0009607 GO:0001970 GO:0006950 MGI D positive regulation of activation of membrane attack complex GO:0008219 GO:0009605 GO:0009607 GO:0001971 GO:0006950 MGI D negative regulation of activation of membrane attack complex GO:0008219 GO:0009605 GO:0009607 GO:0010262 GO:0000003 TAIR D somatic embryogenesis GO:0009790 GO:0031914 GO:0007267 MAH D 1307985 negative regulation of synaptic plasticity GO:0007582 GO:0031915 GO:0007267 MAH D 1307985 positive regulation of synaptic plasticity GO:0007582 GO:0031916 GO:0007267 MAH D 1307985 regulation of synaptic metaplasticity GO:0007582 GO:0031917 GO:0007267 MAH D 1307985 negative regulation of synaptic metaplasticity GO:0007582 GO:0031918 GO:0007267 MAH D 1307985 positive regulation of synaptic metaplasticity GO:0007582 GO:0031919 GO:0006810 MAH D 1346097 vitamin B6 transport GO:0031920 GO:0006810 MAH D 1346097 pyridoxal transport GO:0031921 GO:0006810 MAH D 1346097 pyridoxal phosphate transport GO:0031922 GO:0006810 MAH D 1346097 pyridoxamine transport GO:0031923 GO:0006810 MAH D 1346097 pyridoxine transport GO:0031929 GO:0007165 MAH D 1365473 TOR signaling pathway GO:0031930 GO:0007165 MAH D 1344197 mitochondrial signaling pathway GO:0031935 GO:0006259 MAH D 1337300 regulation of chromatin silencing GO:0006350 GO:0006996 GO:0040029 GO:0031936 GO:0006259 MAH D 1337300 negative regulation of chromatin silencing GO:0006350 GO:0006996 GO:0040029 GO:0031937 GO:0006259 MAH D 1337300 positive regulation of chromatin silencing GO:0006350 GO:0006996 GO:0040029 GO:0031938 GO:0006259 MAH D 1337300 regulation of chromatin silencing at telomere GO:0006350 GO:0006996 GO:0040029 GO:0031939 GO:0006259 MAH D 1337300 negative regulation of chromatin silencing at telomere GO:0006350 GO:0006996 GO:0040029 GO:0031940 GO:0006259 MAH D 1337300 positive regulation of chromatin silencing at telomere GO:0006350 GO:0006996 GO:0040029 GO:0031943 GO:0006629 MAH D 1359933 regulation of glucocorticoid metabolism GO:0031944 GO:0006629 MAH D 1359933 negative regulation of glucocorticoid metabolism GO:0031945 GO:0006629 MAH D 1359933 positive regulation of glucocorticoid metabolism GO:0031946 GO:0006629 MAH D 1359933 regulation of glucocorticoid biosynthesis GO:0009058 GO:0031947 GO:0006629 MAH D 1359933 negative regulation of glucocorticoid biosynthesis GO:0009058 GO:0031948 GO:0006629 MAH D 1359933 positive regulation of glucocorticoid biosynthesis GO:0009058 GO:0031949 GO:0006629 MAH D 1359933 regulation of glucocorticoid catabolism GO:0009056 GO:0031950 GO:0006629 MAH D 1359933 negative regulation of glucocorticoid catabolism GO:0009056 GO:0031951 GO:0006629 MAH D 1359933 positive regulation of glucocorticoid catabolism GO:0009056 GO:0031952 GO:0006464 MAH D 1363668 regulation of protein amino acid autophosphorylation GO:0031953 GO:0006464 MAH D 1363668 negative regulation of protein amino acid autophosphorylation GO:0006519 GO:0031954 GO:0006464 MAH D 1363668 positive regulation of protein amino acid autophosphorylation GO:0006519 GO:0031958 GO:0007165 MAH D corticosteroid receptor signaling pathway GO:0031959 GO:0007165 MAH D mineralocorticoid receptor signaling pathway GO:0031960 GO:0009628 MAH D response to corticosteroid stimulus GO:0009719 GO:0043523 GO:0008219 JL D 1242965 regulation of neuron apoptosis GO:0043524 GO:0008219 JL D 1242965 negative regulation of neuron apoptosis GO:0043525 GO:0008219 JL D 1242965 positive regulation of neuron apoptosis GO:0043526 GO:0008219 JL D 1363922 neuroprotection GO:0043534 GO:0007582 JL D 1352332 blood vessel endothelial cell migration GO:0007610 GO:0043535 GO:0007582 JL D 1352332 regulation of blood vessel endothelial cell migration GO:0007610 GO:0043536 GO:0007582 JL D 1352332 positive regulation of blood vessel endothelial cell migration GO:0007610 GO:0043537 GO:0007582 JL D 1352332 negative regulation of blood vessel endothelial cell migration GO:0007610 GO:0043538 GO:0006464 JL D 1353217 regulation of actin phosphorylation GO:0007010 GO:0043542 GO:0007582 JL D endothelial cell migration GO:0007610 Term name changes in biological_process ontology GO:0001781: programmed cell death, neutrophils --> neutrophil apoptosis GO:0001783: programmed cell death, B cells --> B cell apoptosis GO:0006924: programmed cell death, activated T cells --> activated T cell apoptosis GO:0006925: programmed cell death, inflammatory cells --> inflammatory cell apoptosis GO:0006926: programmed cell death, virus-infected cells --> virus-infected cell apoptosis GO:0006927: programmed cell death, transformed cells --> transformed cell apoptosis GO:0009765: photosynthesis light harvesting --> photosynthesis, light harvesting GO:0009768: photosynthesis light harvesting in photosystem I --> photosynthesis, light harvesting in photosystem I GO:0009769: photosynthesis light harvesting in photosystem II --> photosynthesis, light harvesting in photosystem II GO:0012503: induction of non-apoptotic programmed cell death --> induction of nonapoptotic programmed cell death GO:0016244: non-apoptotic programmed cell death --> nonapoptotic programmed cell death GO:0035071: salivary gland cell death --> salivary gland cell autophagic cell death GO:0035072: ecdysone-mediated induction of salivary gland cell death --> ecdysone-mediated induction of salivary gland cell autophagic cell death GO:0035096: larval midgut cell death --> larval midgut cell programmed cell death GO:0043070: regulation of non-apoptotic programmed cell death --> regulation of nonapoptotic programmed cell death GO:0043071: positive regulation of non-apoptotic programmed cell death --> positive regulation of nonapoptotic programmed cell death GO:0043072: negative regulation of non-apoptotic programmed cell death --> negative regulation of nonapoptotic programmed cell death GO:0043154: negative regulation of caspase activation --> negative regulation of caspase activity GO:0051402: programmed cell death, neurons --> neuron apoptosis New term merges in biological_process ontology GO:0001719 has been merged into GO:0043154, negative regulation of caspase activity GO:0043026 has been merged into GO:0043281, regulation of caspase activity GO:0046953 has been merged into GO:0042331, phototaxis GO:0046954 has been merged into GO:0046956, positive phototaxis GO:0046955 has been merged into GO:0046957, negative phototaxis GO:0048062 has been merged into GO:0042332, gravitaxis GO:0048063 has been merged into GO:0048060, negative gravitaxis GO:0048064 has been merged into GO:0048061, positive gravitaxis Term movements in biological_process ontology: Terms movements under GO Slim term 'response to stress ; GO:0006950' + GO:0001905, activation of membrane attack complex Terms movements under GO Slim term 'cell-cell signaling ; GO:0007267' + GO:0031637, regulation of neuronal synaptic plasticity in response to neurotrophin + GO:0048167, regulation of synaptic plasticity + GO:0048168, regulation of neuronal synaptic plasticity + GO:0048169, regulation of long-term neuronal synaptic plasticity + GO:0048170, positive regulation of long-term neuronal synaptic plasticity + GO:0048171, negative regulation of long-term neuronal synaptic plasticity + GO:0048172, regulation of short-term neuronal synaptic plasticity + GO:0048173, positive regulation of short-term neuronal synaptic plasticity + GO:0048174, negative regulation of short-term neuronal synaptic plasticity Terms movements under GO Slim term 'development ; GO:0007275' - GO:0031637, regulation of neuronal synaptic plasticity in response to neurotrophin - GO:0048167, regulation of synaptic plasticity - GO:0048168, regulation of neuronal synaptic plasticity - GO:0048169, regulation of long-term neuronal synaptic plasticity - GO:0048172, regulation of short-term neuronal synaptic plasticity Terms movements under GO Slim term 'behavior ; GO:0007610' + GO:0006935, chemotaxis + GO:0009453, energy taxis + GO:0009454, aerotaxis + GO:0009455, redox taxis + GO:0009995, soluble molecule recognition + GO:0042330, taxis + GO:0042331, phototaxis + GO:0042332, gravitaxis + GO:0042333, chemotaxis to oxidizable substrate + GO:0042334, taxis to electron acceptor + GO:0043052, thermotaxis + GO:0043326, chemotaxis to folate + GO:0043327, chemotaxis to cAMP + GO:0046956, positive phototaxis + GO:0046957, negative phototaxis + GO:0048060, negative gravitaxis + GO:0048061, positive gravitaxis + GO:0050918, positive chemotaxis + GO:0050919, negative chemotaxis + GO:0050920, regulation of chemotaxis + GO:0050921, positive regulation of chemotaxis + GO:0050922, negative regulation of chemotaxis + GO:0050923, regulation of negative chemotaxis + GO:0050924, positive regulation of negative chemotaxis + GO:0050925, negative regulation of negative chemotaxis + GO:0050926, regulation of positive chemotaxis + GO:0050927, positive regulation of positive chemotaxis + GO:0050928, negative regulation of positive chemotaxis + GO:0050929, induction of negative chemotaxis + GO:0050930, induction of positive chemotaxis Terms movements under GO Slim term 'biological_process ; GO:0008150' - GO:0043280, positive regulation of caspase activity - GO:0043281, regulation of caspase activity Terms movements under GO Slim term 'cell death ; GO:0008219' + GO:0043280, positive regulation of caspase activity + GO:0043281, regulation of caspase activity Terms movements under GO Slim term 'response to external stimulus ; GO:0009605' + GO:0001905, activation of membrane attack complex Terms movements under GO Slim term 'response to biotic stimulus ; GO:0009607' + GO:0001905, activation of membrane attack complex Terms movements under GO Slim term 'morphogenesis ; GO:0009653' + GO:0000078, cell morphogenesis checkpoint Terms movements under GO Slim term 'cell organization and biogenesis ; GO:0016043' + GO:0000078, cell morphogenesis checkpoint New terms in cellular_component ontology (11 new terms) GO:0031931 GO:0005622 MAH D 1344197 TORC 1 complex GO:0031932 GO:0005622 MAH D 1344197 TORC 2 complex GO:0031933 GO:0005694 MAH D 1337300 telomeric heterochromatin GO:0031934 GO:0005694 MAH D 1337300 mating-type region heterochromatin GO:0031941 GO:0005856 MAH D 1363147 filamentous actin GO:0031942 GO:0005739 MAH D 1361875 i-AAA complex GO:0043527 GO:0005737 JL D 1254824 tRNA methyltransferase complex GO:0043528 GO:0005737 JL D 1254824 tRNA (m2G10) methyltransferase complex GO:0043529 GO:0005783 JL D 1350833 GET complex GO:0043540 GO:0005829 JL D 1358097 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 complex GO:0043541 GO:0005783 JL D 1365149 UDP-N-acetylglucosamine transferase complex Term movements in cellular_component ontology: Terms movements under GO Slim term 'nucleus ; GO:0005634' - GO:0031515, tRNA (m1A) methyltransferase complex Terms movements under GO Slim term 'cytoplasm ; GO:0005737' + GO:0031515, tRNA (m1A) methyltransferase complex New terms in molecular_function ontology (18 new terms) GO:0001972 GO:0005488 MGI D retinoic acid binding GO:0031924 GO:0005215 MAH D 1346097 vitamin B6 transporter activity GO:0031925 GO:0005215 MAH D 1346097 pyridoxal transporter activity GO:0031926 GO:0005215 MAH D 1346097 pyridoxal phosphate transporter activity GO:0031927 GO:0005215 MAH D 1346097 pyridoxamine transporter activity GO:0031928 GO:0005215 MAH D 1346097 pyridoxine transporter activity GO:0031955 GO:0003824 MAH D 1363719 short-chain-fatty-acid-CoA ligase activity GO:0031956 GO:0003824 MAH D 1363719 medium-chain-fatty-acid-CoA ligase activity GO:0031957 GO:0003824 MAH D 1363719 very-long-chain-fatty-acid-CoA ligase activity GO:0031961 GO:0005102 MAH D cortisol receptor binding GO:0031962 GO:0005102 MAH D mineralocorticoid receptor binding GO:0031963 GO:0004872 MAH D cortisol receptor activity GO:0031964 GO:0016787 MAH D 1365477 beta-alanyl-histamine hydrolase activity GO:0043530 GO:0016787 JL D 1351159 adenosine 5'-monophosphoramidase activity GO:0043531 GO:0000166 JL D 1352082 ADP binding GO:0043532 GO:0005515 JL D 1353077 angiostatin binding GO:0043533 GO:0008289 JL D 1353837 inositol 1,3,4,5 tetrakisphosphate binding GO:0043539 GO:0030234 JL D 1356723 protein serine/threonine kinase activator activity Term name changes in molecular_function ontology GO:0008489: UDP-galactose-glucosylceramide beta-1,4-galactosyltransferase activity --> UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity GO:0008499: UDP-galactose beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity --> UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity GO:0015346: ferric triacetylfusarinine [TC:hydrogen symporter activity --> ferric triacetylfusarinine C:hydrogen symporter activity GO:0031559: oxidosqualene cyclase --> oxidosqualene cyclase activity New definitions for molecular_function ontology terms (4 new definitions) GO:0003980, UDP-glucose:glycoprotein glucosyltransferase activity GO:0008489, UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity GO:0008499, UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity GO:0015645, fatty-acid ligase activity SourceForge items closed this month: SF id Resolution SF item title GO ids added, if any 1124304 Works For Me compatible solute biosynthesis GO:0051470 GO:0051471 GO:0051472 GO:0051473 GO:0051474 GO:0051475 GO:0051476 GO:0051477 GO:0051478 GO:0051479 1242965 Accepted child of "regulation of programmed cell death, neurons" GO:0043523 GO:0043524 GO:0043525 GO:0043526 1254824 Accepted ntr: tRNA (m2G10) methyltransferase complex GO:0043527 GO:0043528 1288597 Later interactions between organisms (symbiosis, etc.) [none] 1307985 Accepted new child of synaptogenesis GO:0031914 GO:0031915 GO:0031916 GO:0031917 GO:0031918 1325754 Fixed Term name changes - programmed cell death terms [none] 1337300 Accepted new terms chromatin related GO:0031933 GO:0031934 GO:0031935 GO:0031936 GO:0031937 GO:0031938 GO:0031939 GO:0031940 1340742 Accepted update cell morphogenesis checkpoint [none] 1343828 Works For Me difference intrinsic/integral [none] 1343844 Works For Me possible term merge? [none] 1344197 Accepted ntr: TOR complexes and mitochondrial signaling GO:0031930 GO:0031931 GO:0031932 1344896 Accepted synonym for sphingosine N-acyltransferase activity [none] 1344943 Duplicate apoptosis/programmed cell death term names [none] 1345003 Fixed alpha-1,3-galactosyltransferase [none] 1345941 Fixed update def Cul4A-RING ubiquitin ligase complex [none] 1346097 Accepted pyridoxine/pyridoxal/pyridoxamine GO:0031919 GO:0031920 GO:0031921 GO:0031922 GO:0031923 GO:0031924 GO:0031925 GO:0031926 GO:0031927 GO:0031928 1346291 Fixed exact synonym change for MF GPCR binding [none] 1348617 Fixed wrong parent: hyperphosphorylation of RNA polymerase II? [none] 1348741 Fixed oxidosqualene cyclase [none] 1350833 Accepted GET complex GO:0043529 1351159 Accepted ntr: Adenosine 5'- monophosphoramidase GO:0043530 1352082 Accepted ntr: ADP binding GO:0043531 1352332 Accepted ntr: endothelial cell migration GO:0043534 GO:0043535 GO:0043536 GO:0043537 1353077 Accepted ntr: Angiostatin Binding GO:0043532 1353102 Works For Me NTR: Pos. Reg. of Caspase Activation [none] 1353217 Accepted regulation of actin phosphorylation GO:0043538 1353232 Rejected NTR: response to adriamycin [none] 1353837 Accepted ntr: Inositol 1,3,4,5 tetrakisphosphate binding GO:0043533 1356723 Accepted NTR: protein ser/thr kinase activation activity GO:0043539 1358097 Accepted 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 homodi GO:0043540 1359933 Accepted 'negative regulation of glucocorticoid catabolism' GO:0031943 GO:0031944 GO:0031945 GO:0031946 GO:0031947 GO:0031948 GO:0031949 GO:0031950 GO:0031951 1361875 Accepted NTR: i-AAA complex GO:0031942 1363147 Fixed Actin cytoskeleton: def changes, term moves, and synonyms GO:0031941 1363668 Accepted positive regulation of GO:0046777 GO:0031952 GO:0031953 GO:0031954 1363719 Accepted acyl-CoA ligase activity GO:0031955 GO:0031956 GO:0031957 1363794 Duplicate child of neuroprotection [none] 1364196 Duplicate incorrect definition GO:0042351 ' L-fucose biosynth [none] 1364198 Fixed incorrect definition GO:0042351 de novo GDP-L-fucose biosyn [none] 1365149 Accepted UDP-N-acetylglucosamine transferase complex GO:0043541 1365473 Accepted ntr: TOR signaling pathway GO:0031929 1365477 Accepted NTR: beta-alanyl-histimine hydrolase activity GO:0031964 1368487 Fixed odd def in component term GO:0000214 [none] Statistics: biological_process: 10436 terms, 97.8% defined (10206 terms defined) cellular_component: 1771 terms, 95.3% defined (1687 terms defined) molecular_function: 7862 terms, 91.8% defined (7218 terms defined) Total: 20069 terms, 95.2% defined (19111 terms defined) Term errors none