GO Monthly Release Notes for August 2004 ======================== Generated on Mon Jan 24 12:50:12 2005 Files used: gene_ontology.obo OLD: version 3.401, 30:07:2004 15:05 NEW: version 3.459, 31:08:2004 16:38 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 GO-slim term(s) that new term was added under or "obs" if the term is obsolete.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 component ontology (7 new terms) GO:0035230 GO:0005623 FB D 999586 cytoneme GO:0043202 GO:0005764 JL D 1035336 lysosomal lumen GO:0043203 GO:0005623 JL D 1035336 axon hillock GO:0043204 GO:0005623 JL D 1035336 perikaryon GO:0043205 GO:0005578 JL D 1035336 fibril GO:0048500 GO:0005737 JIC D 991995 signal recognition particle GO:0048501 GO:0005737 JIC D 991995 signal recognition particle (sensu Bacteria and Archaea) New obsoletions in component ontology GO:0030074, thylakoid (sensu Proteobacteria): thylakoids are not found in organisms of the Phylum Proteobacteria. Term name changes in component ontology GO:0000808: origin of replication recognition complex --> origin recognition complex GO:0005786: signal recognition particle --> signal recognition particle (sensu Eukaryota) GO:0043025: cell body --> cell soma GO:0048494: ribulose bisphosphate carboxylase complex (sensu Proteobacteria) --> ribulose bisphosphate carboxylase complex (sensu Proteobacteria, Chloroflexaceae and Chlorobiaceae) New definitions for component ontology terms (1 new definitions) GO:0008328, ionotropic glutamate receptor complex Term movements in component ontology: Terms movements under GO Slim term 'intracellular ; GO:0005622' + GO:0005956, protein kinase CK2 complex Terms movements under GO Slim term 'cytoplasm ; GO:0005737' + GO:0009348, ornithine carbamoyltransferase complex + GO:0017109, glutamate-cysteine ligase complex Terms movements under GO Slim term 'plasma membrane ; GO:0005886' - GO:0030078, light-harvesting complex, core complex - GO:0030079, light-harvesting complex, peripheral complex - GO:0030080, B875 antenna complex - GO:0030081, B800-820 antenna complex - GO:0030082, B800-850 antenna complex - GO:0030090, reaction center (sensu Proteobacteria) Terms movements under GO Slim term 'unlocalized ; GO:0005941' - GO:0005956, protein kinase CK2 complex - GO:0009348, ornithine carbamoyltransferase complex - GO:0017109, glutamate-cysteine ligase complex New terms in function ontology (14 new terms) GO:0030973 GO:0005488 MAH D 1035336 molybdate ion binding GO:0030975 GO:0005488 MAH D 1035336 thiamin binding GO:0030976 GO:0005488 MAH D 1035336 thiamin pyrophosphate binding GO:0030977 GO:0005488 MAH D 1035336 taurine binding GO:0035226 GO:0005515 FB D 1035336 glutamate-cysteine ligase catalytic subunit binding GO:0035236 GO:0004872 FB D 1035336 proctolin receptor activity GO:0005488 GO:0035237 GO:0004872 FB D 1035336 corazonin receptor activity GO:0005488 GO:0048495 GO:0005102 JIC D 1035336 Roundabout binding GO:0048502 GO:0016787 JIC D 1035336 thiamin-transporting ATPase activity GO:0048503 GO:0008289 JIC D 1035336 GPI anchor binding GO:0051116 GO:0003824 AI D 1035336 cobaltochelatase activity GO:0051117 GO:0005515 AI D 1035336 ATPase binding GO:0051118 GO:0016787 AI D 1035336 glucan endo-1,3-alpha-glucosidase activity GO:0051120 GO:0003824 AI D 1035336 hepoxilin A3 synthase activity Term name changes in function ontology GO:0001884: pyrmidine nucleoside binding --> pyrimidine nucleoside binding GO:0004970: inotropic glutamate receptor activity --> ionotropic glutamate receptor activity GO:0015619: thiamin pyrophosphate porter activity --> thiamin pyrophosphate-transporting ATPase activity GO:0016852: cobalt chelatase activity --> sirohydrochlorin cobaltochelatase activity New definitions for function ontology terms (8 new definitions) GO:0004153, dihydropterin deaminase activity GO:0004980, melanocyte stimulating hormone receptor activity GO:0008320, protein carrier activity GO:0009031, thiol peroxidase activity GO:0016832, aldehyde-lyase activity GO:0017173, DRAP deaminase activity GO:0019239, deaminase activity GO:0019793, ISG15 carrier activity New term merges in function ontology GO:0016228 has been merged into GO:0016832, aldehyde-lyase activity Term movements in function ontology: Terms movements under GO Slim term 'nucleotide binding ; GO:0000166' + GO:0010181, FMN binding + GO:0050660, FAD binding Terms movements under GO Slim term 'transporter activity ; GO:0005215' + GO:0019793, ISG15 carrier activity Terms movements under GO Slim term 'binding ; GO:0005488' - GO:0005539, glycosaminoglycan binding - GO:0005540, hyaluronic acid binding - GO:0008201, heparin binding - GO:0010181, FMN binding - GO:0030492, hemoglobin binding - GO:0050660, FAD binding Terms movements under GO Slim term 'protein binding ; GO:0005515' + GO:0030492, hemoglobin binding + GO:0042809, vitamin D receptor binding + GO:0042974, retinoic acid receptor binding + GO:0046966, thyroid hormone receptor binding - GO:0048156, tau protein binding Terms movements under GO Slim term 'cytoskeletal protein binding ; GO:0008092' + GO:0048156, tau protein binding Terms movements under GO Slim term 'antioxidant activity ; GO:0016209' + GO:0004096, catalase activity + GO:0004130, cytochrome-c peroxidase activity + GO:0004447, iodide peroxidase activity + GO:0004602, glutathione peroxidase activity + GO:0008379, thioredoxin peroxidase activity + GO:0009031, thiol peroxidase activity + GO:0016224, non-selenium glutathione peroxidase activity + GO:0016688, L-ascorbate peroxidase activity + GO:0016689, manganese peroxidase activity + GO:0016690, diarylpropane peroxidase activity + GO:0016691, chloride peroxidase activity + GO:0016692, NADH peroxidase activity + GO:0016693, secretory plant peroxidase activity + GO:0016952, heme catalase activity + GO:0016953, manganese catalase activity + GO:0016955, heme chloroperoxidase activity + GO:0016956, cofactor-free chloroperoxidase activity + GO:0016957, vanadium chloroperoxidase activity + GO:0016958, flavin-heme chloroperoxidase activity + GO:0019806, bromide peroxidase activity + GO:0047066, phospholipid-hydroperoxide glutathione peroxidase activity + GO:0047888, fatty-acid peroxidase activity + GO:0050137, NADPH peroxidase activity Terms movements under GO Slim term 'carbohydrate binding ; GO:0030246' + GO:0005539, glycosaminoglycan binding + GO:0005540, hyaluronic acid binding + GO:0008201, heparin binding New terms in process ontology (18 new terms) GO:0001885 GO:0030154 MGI D 1035336 endothelial cell development GO:0001886 GO:0009653 MGI D 1035336 endothelial cell morphogenesis GO:0016043 GO:0030154 GO:0030974 GO:0006810 MAH D 1035336 thiamin pyrophosphate transport GO:0035227 GO:0008150 FB D 1035336 regulation of glutamate-cysteine ligase activity GO:0035228 GO:0008150 FB D 1035336 negative regulation of glutamate-cysteine ligase activity GO:0035229 GO:0008150 FB D 1035336 positive regulation of glutamate-cysteine ligase activity GO:0035231 GO:0009653 FB D 999586 cytoneme biogenesis GO:0016043 GO:0035232 GO:0000003 FB D 975352 germ cell attraction GO:0009628 GO:0035233 GO:0000003 FB D 975352 germ cell repulsion GO:0009628 GO:0035234 GO:0000003 FB D 975352 germ cell programmed cell death GO:0008219 GO:0035235 GO:0007165 FB D 1035336 ionotropic glutamate receptor signaling pathway GO:0043206 GO:0007582 JL D 1035336 fibril organization and biogenesis GO:0048496 GO:0009653 JIC D 951331 maintenance of organ identity GO:0048497 GO:0009653 JIC D 951331 maintenance of floral organ identity GO:0048498 GO:0007275 JIC D 1035336 establishment of petal orientation GO:0048499 GO:0016043 JIC D 931797 synaptic vesicle membrane organization and biogenesis GO:0051121 GO:0006629 AI D 1035336 hepoxilin metabolism GO:0051122 GO:0006629 AI D 1035336 hepoxilin biosynthesis GO:0009058 Term name changes in process ontology GO:0007265: RAS protein signal transduction --> Ras protein signal transduction GO:0008608: microtubule/kinetochore interaction --> spindle kinetochore attachment GO:0009755: hormone mediated signaling --> hormone-mediated signaling GO:0016601: RAC protein signal transduction --> Rac protein signal transduction GO:0035020: regulation of RAC protein signal transduction --> regulation of Rac protein signal transduction GO:0035021: negative regulation of RAC protein signal transduction --> negative regulation of Rac protein signal transduction GO:0035022: positive regulation of RAC protein signal transduction --> positive regulation of Rac protein signal transduction GO:0035172: hemocyte proliferation (sensu Arthropda) --> hemocyte proliferation (sensu Arthropoda) GO:0035206: regulation of hemocyte proliferation (sensu Arthropda) --> regulation of hemocyte proliferation (sensu Arthropoda) GO:0035207: negative regulation of hemocyte proliferation (sensu Arthropda) --> negative regulation of hemocyte proliferation (sensu Arthropoda) GO:0035208: positive regulation of hemocyte proliferation (sensu Arthropda) --> positive regulation of hemocyte proliferation (sensu Arthropoda) GO:0043193: positive regulation of gene transcription --> positive regulation of gene-specific transcription GO:0046578: regulation of RAS protein signal transduction --> regulation of Ras protein signal transduction GO:0046579: positive regulation of RAS protein signal transduction --> positive regulation of Ras protein signal transduction GO:0046580: negative regulation of RAS protein signal transduction --> negative regulation of Ras protein signal transduction GO:0050901: leukocyte tethering / rolling --> leukocyte tethering or rolling New definitions for process ontology terms (11 new definitions) GO:0007264, small GTPase mediated signal transduction GO:0007405, neuroblast proliferation GO:0007566, embryo implantation GO:0019932, second-messenger-mediated signaling GO:0019933, cAMP-mediated signaling GO:0019934, cGMP-mediated signaling GO:0030467, establishment and/or maintenance of cell polarity (sensu Fungi) GO:0030468, establishment of cell polarity (sensu Fungi) GO:0030469, maintenance of cell polarity (sensu Fungi) GO:0030471, spindle pole body and microtubule cycle (sensu Fungi) GO:0030473, nuclear migration (sensu Fungi) New term merges in process ontology GO:0000065 has been merged into GO:0030473, nuclear migration (sensu Fungi) GO:0000283 has been merged into GO:0030468, establishment of cell polarity (sensu Fungi) GO:0007102 has been merged into GO:0030471, spindle pole body and microtubule cycle (sensu Fungi) GO:0030012 has been merged into GO:0030467, establishment and/or maintenance of cell polarity (sensu Fungi) GO:0030013 has been merged into GO:0030469, maintenance of cell polarity (sensu Fungi) Term movements in process ontology: Terms movements under GO Slim term 'reproduction ; GO:0000003' + GO:0007280, pole cell migration Terms movements under GO Slim term 'cell proliferation ; GO:0008283' + GO:0007405, neuroblast proliferation + GO:0007406, negative regulation of neuroblast proliferation SourceForge items closed this month: SF id Resolution SF item title GO ids added, if any 1000792 Fixed glutamate-cysteine ligase regulator GO:0035226-35229 1002063 Accepted Roundabout binding GO:0048495 1002576 Accepted ATPase binding GO:0051117 1003616 Accepted thiamine-transporting ATPase GO:0048502 1003877 Accepted new children of neuropeptide receptor activity GO:0035236-35237 1004085 Accepted GO:0001569 patterning of blood vessels parent [none] 1004527 Works For Me tpv: children of axon cargo transport [none] 1004636 Later utilization standard def [none] 1004718 Accepted ntr: GPI anchor binding GO:0048503 1004721 Accepted add isthmus as synonym for midbrain hindbrain boundary [none] 1006596 Accepted lysosomal lumen GO:0043202 1006846 Accepted fibril GO:0043205-43206 1007061 Duplicate tpv: polarisome [none] 1007156 Accepted add synonym:4-alpha-hydroxytetrahydrobiopterin dehydratas [none] 1007169 Fixed ntr:dolichyl pyrophosphate (Dol-P-P) phosphatase [none] 1007200 Accepted sensu terms archaea [none] 1007203 Accepted ntr: glucan endo-1,3-alpha-glucosidase activity GO:0051118 1007922 Accepted hepoxilin A(3) synthase activity GO:0051120-51122 1011343 Fixed (*:* antiporter/symporter activity) wrong parents [none] 1011349 Fixed Organic anion transporter activity - wrong definition [none] 1012284 Fixed term name ORC [none] 1012527 Accepted molybdate ion binding GO:0030973 1013152 Fixed GO:0020011 : apicoplast - modify definition [none] 1017038 Accepted taurine-transporting ATPase activity GO:0030977 1017045 Fixed thiamin-transporting ATPase parent change [none] 1017057 Accepted thiamin/thiamin pyrophosphate binding GO:0030975-30976 1017065 Accepted thiamin pyrophosphate transport GO:0030974 1017223 Fixed GO:0006415 : translational termination - modify definition [none] 1019373 Fixed defs GO:30175/GO:46847- filopodium/filopodium formation [none] 854880 Fixed NADH-quinone oxidoreductase GO:0030964-30966 877591 Fixed Equivalent terms? [none] 913225 Fixed term merges, new defs from SGD [none] 950151 Later merge trichome morphogenesis [none] 951166 Fixed standard def for signaling pathways? [none] 951331 Accepted Dicot Flower development GO:0048479-48482 GO:0048496-48497 955149 Works For Me missing relationships: obol [none] 960898 Out of Date Cytolysis terms [none] 975352 Accepted [primordial] germ cell migration GO:0035232-35234 997949 Works For Me New IsA links in binding (GO:0005488) (II) [none] 997982 Rejected children of sensu terms [none] 998107 Accepted nucleoside binding and children GO:0001882-01884 998597 Fixed parentage of metamorphosis ; GO:0007552 [none] 999586 Accepted cytoneme/cytoneme biogenesis GO:0035230-35231 Statistics: component: 1448 terms, 90.3% defined (1307 terms defined) function: 7401 terms, 88.7% defined (6565 terms defined) process: 8885 terms, 94.3% defined (8381 terms defined) Total: 17734 terms, 91.6% defined (16253 terms defined) Term errors GO:0030959, peptide cross-linking via 3'-(3'-L-tyrosinyl)-L-tyrosine - moved from component ontology to process.