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 GO-slim term(s) that new term was added under or "obs" if the term is obsolete.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