GO Monthly Release Notes for September 2007 ======================== Generated on Mon Oct 1 16:55:43 2007 Files used: gene_ontology.obo OLD: version 4.309, 30:08:2007 19:30 NEW: version 4.322, 29:09:2007 19:30 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 GO-slim term(s) that new term was added under or "obs" if the term is obsolete.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 (3 new terms) GO:0032581 GO:0006996 MAH D ER-dependent peroxisome biogenesis GO:0032582 GO:0006350 MAH D negative regulation of gene-specific transcription GO:0050789 GO:0032583 GO:0006350 MAH D regulation of gene-specific transcription GO:0050789 Term name changes in biological_process ontology GO:0006349: imprinting --> genetic imprinting GO:0051460: negative regulation of adrenocorticotropin hormone secretion --> negative regulation of adrenocorticotropic hormone secretion GO:0051461: positive regulation of adrenocorticotropin hormone secretion --> positive regulation of adrenocorticotropic hormone secretion GO:0052548: regulation of protease activity --> regulation of endopeptidase activity New term merges in biological_process ontology GO:0000283 has been merged into GO:0030010, establishment of cell polarity GO:0030012 has been merged into GO:0007163, establishment and/or maintenance of cell polarity GO:0030013 has been merged into GO:0030011, maintenance of cell polarity GO:0030467 has been merged into GO:0007163, establishment and/or maintenance of cell polarity GO:0030468 has been merged into GO:0030010, establishment of cell polarity GO:0030469 has been merged into GO:0030011, maintenance of cell polarity Term movements in biological_process ontology: Terms movements under GO Slim term 'mitochondrion organization and biogenesis ; GO:0007005' + GO:0032981, mitochondrial respiratory chain complex I assembly + GO:0033108, mitochondrial respiratory chain complex assembly Terms movements under GO Slim term 'cell communication ; GO:0007154' - GO:0000409, regulation of transcription by galactose - GO:0000410, negative regulation of transcription by galactose - GO:0000411, positive regulation of transcription by galactose - GO:0000429, regulation of transcription from RNA polymerase II promoter by carbon catabolites - GO:0000430, regulation of transcription from RNA polymerase II promoter by glucose - GO:0000431, regulation of transcription from RNA polymerase II promoter by galactose - GO:0000432, positive regulation of transcription from RNA polymerase II promoter by glucose - GO:0000433, negative regulation of transcription from RNA polymerase II promoter by glucose - GO:0000434, negative regulation of transcription from RNA polymerase II promoter by galactose - GO:0000435, positive regulation of transcription from RNA polymerase II promoter by galactose - GO:0000436, positive regulation of transcription from RNA polymerase II promoter by carbon catabolites - GO:0000437, negative regulation of transcription from RNA polymerase II promoter by carbon catabolites - GO:0007584, response to nutrient - GO:0007637, proboscis extension reflex - GO:0009594, detection of nutrient - GO:0009991, response to extracellular stimulus - GO:0010266, response to vitamin B1 - GO:0030587, fruiting body development (sensu Dictyosteliida) - GO:0031149, stalk cell differentiation - GO:0031150, stalk development (sensu Dictyosteliida) - GO:0031152, aggregation during fruiting body development - GO:0031153, slug development during fruiting body development - GO:0031154, culmination during fruiting body development - GO:0031156, regulation of fruiting body development (sensu Dictyosteliida) - GO:0031157, regulation of aggregate size - GO:0031158, negative regulation of aggregate size - GO:0031159, positive regulation of aggregate size - GO:0031285, regulation of stalk cell differentiation - GO:0031286, negative regulation of stalk cell differentiation - GO:0031287, positive regulation of stalk cell differentiation - GO:0031288, fruiting body morphogenesis (sensu Dictyosteliida) - GO:0031667, response to nutrient levels - GO:0032094, response to food - GO:0032095, regulation of response to food - GO:0032096, negative regulation of response to food - GO:0032097, positive regulation of response to food - GO:0032098, regulation of appetite - GO:0032099, negative regulation of appetite - GO:0032100, positive regulation of appetite - GO:0032104, regulation of response to extracellular stimulus - GO:0032105, negative regulation of response to extracellular stimulus - GO:0032106, positive regulation of response to extracellular stimulus - GO:0032107, regulation of response to nutrient levels - GO:0032108, negative regulation of response to nutrient levels - GO:0032109, positive regulation of response to nutrient levels - GO:0032526, response to retinoic acid - GO:0032571, response to vitamin K - GO:0032572, response to menaquinone - GO:0032573, response to phylloquinone - GO:0033189, response to vitamin A - GO:0033197, response to vitamin E - GO:0033273, response to vitamin - GO:0033274, response to vitamin B2 - GO:0033280, response to vitamin D - GO:0033552, response to vitamin B3 - GO:0033590, response to cobalamin - GO:0033591, response to L-ascorbic acid - GO:0042594, response to starvation - GO:0042595, behavioral response to starvation - GO:0045013, negative regulation of transcription by carbon catabolites - GO:0045014, negative regulation of transcription by glucose - GO:0045990, regulation of transcription by carbon catabolites - GO:0045991, positive regulation of transcription by carbon catabolites - GO:0046015, regulation of transcription by glucose - GO:0046016, positive regulation of transcription by glucose - GO:0048837, sorus development - GO:0051780, behavioral response to nutrient Terms movements under GO Slim term 'cellular component organization and biogenesis ; GO:0016043' - GO:0032981, mitochondrial respiratory chain complex I assembly - GO:0033108, mitochondrial respiratory chain complex assembly New terms in cellular_component ontology (12 new terms) GO:0032578 GO:0016023 MAH D aleurone grain membrane GO:0032579 GO:0005578 MAH D apical lamina of hyaline layer GO:0032580 GO:0005794 MAH D Golgi cisterna membrane GO:0032584 GO:0005886 MAH D growth cone membrane GO:0032585 GO:0005768 MAH D multivesicular body membrane GO:0032586 GO:0005773 MAH D protein storage vacuole membrane GO:0032587 GO:0005886 MAH D ruffle membrane GO:0032588 GO:0005794 MAH D trans-Golgi network membrane GO:0032589 GO:0005886 MAH D neuron projection membrane GO:0032590 GO:0005886 MAH D dendrite membrane GO:0032591 GO:0005886 MAH D dendritic spine membrane GO:0032592 GO:0005794 MAH D integral to mitochodrial membrane Term name changes in cellular_component ontology GO:0002111: BRAC2-BRAF35 complex --> BRCA2-BRAF35 complex Term movements in cellular_component ontology: Terms movements under GO Slim term 'cell ; GO:0005623' - GO:0030673, axolemma Terms movements under GO Slim term 'Golgi apparatus ; GO:0005794' + GO:0031305, integral to mitochondrial inner membrane + GO:0031307, integral to mitochondrial outer membrane Terms movements under GO Slim term 'plasma membrane ; GO:0005886' + GO:0030673, axolemma New terms in molecular_function ontology (2 new terms) GO:0032576 GO:0016740 MAH D O-linoleoyltransferase activity GO:0032577 GO:0016740 MAH D phosphatidylcholine:cardiolipin O-linoleoyltransferase Term name changes in molecular_function ontology GO:0004198: calpain activity --> calcium-dependent cysteine-type endopeptidase activity GO:0004712: protein threonine/tyrosine kinase activity --> protein serine/threonine/tyrosine kinase activity GO:0043138: 3' to 5' DNA helicase activity --> 3'-5' DNA helicase activity GO:0043139: 5' to 3' DNA helicase activity --> 5'-3' DNA helicase activity GO:0043140: ATP-dependent 3' to 5' DNA helicase activity --> ATP-dependent 3'-5' DNA helicase activity GO:0043141: ATP-dependent 5' to 3' DNA helicase activity --> ATP-dependent 5'-3' DNA helicase activity New definitions for molecular_function ontology terms (5 new definitions) GO:0004677, DNA-dependent protein kinase activity GO:0004697, protein kinase C activity GO:0004698, calcium-dependent protein kinase C activity GO:0004699, calcium-independent protein kinase C activity GO:0004714, transmembrane receptor protein tyrosine kinase activity New term merges in molecular_function ontology GO:0004701 has been merged into GO:0004697, protein kinase C activity SourceForge items closed this month: SF id Resolution SF item title GO ids added, if any 1073073 Out of Date morphogenesis is_a development 1081679 Accepted updates for gap junction terms 1428209 Fixed sensu syntax 1711143 Accepted mosquito - human behaviour 1723526 Accepted ntr: cysteine export terms 1724459 Fixed neuroblast division term defs need tweaks 1743484 Fixed Protein-serine/threonine kinases 1768067 Fixed fruiting body development / sensus 1775791 Accepted RG: BRAC2-BRAF35 Complex 1778812 Accepted regulation of smooth muscle cell migration 1779479 Fixed response to extracellular stimulus GO:0009991 1785486 Accepted Polysemy of "imprinting" (GO:0006349) 1786600 Accepted add synonym calcium ion transport 1787119 Fixed helicase consistency (quick) 1787600 Works For Me primary metabolic process meaning.... 1787665 Accepted NTR: new type of transacylase 1787995 Rejected electron-transferring-flavoprotein dehydrogenase 1788310 Duplicate electron-transferring-flavoprotein dehydrogenase 1789569 Fixed GO:0052548 regulation of protease activity 1790209 Fixed update EC numbers 1790293 Accepted di/tri oligo peptide transport 1791458 Fixed synonym for narrow pore, gated channel activity (GO:0022831) 1792358 Accepted aleurone grain membrane 1792396 Accepted apical lamina of hyaline layer 1792470 Accepted Golgi stack membrane 1793816 Accepted synonym for sulfuric ester hydrolase activity (GO:0008484) 1794791 Works For Me mp : iron sufur cluster assembly 1795419 Works For Me q secretory pathway 1796071 Accepted sensu /cell polarity suggestion 1797146 Accepted NTR: ER-dependent peroxisome biogenesis 1797848 Accepted rg: NTR: -ve reg gene-specific transcription 1798477 Fixed hemolysis definitions 1798777 Fixed mp: pyridoxamine transmembrane 1798779 Fixed mp: nicotinamide mononucleotide transmembrane trans 1801003 Accepted rg: add synonym to GO:0008611 1801213 Accepted NTR: Growth cone membrane 1801237 Accepted NTR: Multivesicular body membrane 1801286 Accepted NTR: Protein storage vacuole membrane 1802550 Accepted NTR: Ruffle membrane 1802598 Accepted NTR: trans-Golgi network membrane 1802599 Accepted Add synonym to Uropod 1803144 Accepted add parentage to GO:0033108 1803376 Accepted NTR: Dendritic spine membrane 1804141 Accepted add parentage to GO:0031307 1804300 Accepted new mito membrane term 703326 Accepted Transporter Ontology Revamp 923627 Out of Date GO:0010196 : nonphotochemical quenching Statistics: biological_process: 14375 terms, 98.9% defined (14216 terms defined) cellular_component: 2133 terms, 100.0% defined (2133 terms defined) molecular_function: 8435 terms, 95.4% defined (8048 terms defined) Total: 24943 terms, 97.8% defined (24397 terms defined) Term errors none