gocentral
commented
19 years ago Logged In: YES user_id=436423
Re GO Content requests: Some of these requests have been dealt with; others are outstanding. Still others have not yet been entered in the Curator Requests tracker.
> GO:ammonium transport ; GO:0015696 Need GO > synonym: ammonia transport
not in curator requests
> Should atom binding be synonym for ion binding.
not in curator requests
> SP_KW:Chloride > can we have chloride binding > https://sourceforge.net/tracker/index.php? func=detail&aid=1198232&group_id=36855&atid=440764
done
> Request definition for DNA integration, GO:0015074 > could be mapped to keyword. > https://sourceforge.net/tracker/index.php? func=detail&aid=1198261&group_id=36855&atid=440764
oustanding
> Request new term invertasome, nucleoprotein structure.
not in curator requests
> Should recombinase activity have synonym ; invertase > activity??? > https://sourceforge.net/tracker/index.php? func=detail&aid=1198266&group_id=36855&atid=440764
rejected in SF item
> GO has FAD biosynthesis can we have also FMN > biosynthesis.
GO:0009398
> SP_KW:Guanine-nucleotide releasing factor > > GO:????? What to map too?
GO:0005085
> Could SP_KW: Hemagglutinin be mapped to a broad > term cell adhesion?
mapping question, not a GO content question
> Should heterocyst formation be synonym > of heterocyst cell differentiationGO:0043158 > https://sourceforge.net/tracker/index.php? func=detail&aid=1198266&group_id=36855&atid=440764
done
> SP_KW Hexon-associated protein no mapping..hexon > binding
not in curator requests
> SP_KW: Keratinization, could we have new GO process > term Keratinization
not in curator requests
> GO:lignin catabolism ; GO:0046274.. noticed that a lot > of the catabolism terms are missing a synonym > for degradation, eg. lignin degradation. Or phospholipid > degradation. > https://sourceforge.net/tracker/index.php? func=detail&aid=1198266&group_id=36855&atid=440764
oustanding
> Have mapped SP_KW:Lipoyl > GO:coenzyme binding ; > GO:0050662 but > Should there be a new child of GO:0050662 > called lipoic acid binding (new GO) also > With a parent carboxylic acid binding (new GO) > https://sourceforge.net/tracker/index.php? > func=detail&aid=1198280&group_id=36855&atid=440764
done
> Have mapped SP_KW:Lithium > GO:metal ion binding ; > GO:0046872 but would like new GO term: lithium ion > binding. > https://sourceforge.net/tracker/index.php? func=detail&aid=1198232&group_id=36855&atid=440764
done
> Need new child of GO:0004857; enzyme inhibitor > activity, metalloenzyme inhibitor activity > https://sourceforge.net/tracker/index.php? func=detail&aid=1198289&group_id=36855&atid=440764
oustanding
> Need to map keyword Methotrexate resistance to new > GO term response to methotrexate > https://sourceforge.net/tracker/index.php? func=detail&aid=1198288&group_id=36855&atid=440764
outstanding
> Have mapped SP_KW:Germination > GO:organismal > physiological process ; GO:0050874, > Jen to ask whether generic germination term can be > reinstated. > https://sourceforge.net/tracker/index.php? func=detail&aid=1198276&group_id=36855&atid=440764
oustanding
> Have mapped SP_KW:Oxylipin biosynthesis > > GO:fatty acid biosynthesis ; GO:0006633 > but would like new GO term: oxylipin biosynthesis as > child of GO:0006633. > https://sourceforge.net/tracker/index.php? func=detail&aid=1198287&group_id=36855&atid=440764
done
> Should we have a new GO term for Phytochrome > signaling pathway KW-0607 which is also a keyword. [snip] > https://sourceforge.net/tracker/index.php? func=detail&aid=1198284&group_id=36855&atid=440764
synonym added, so done
> Have mapped SP_KW:Pigment > GO:binding ; > GO:0005488 but would like new GO term: > https://sourceforge.net/tracker/index.php? func=detail&aid=1198282&group_id=36855&atid=440764
done
> Have mapped SP_KW:Plasma > GO:extracellular > region ; GO:0005576 > Bot quite sure whether it should be mapped to > GO:extracellular space
mapping q, not content ... but I think extracellular space would be OK
> Also wondering if acellular should be synonym of > extracellular? > https://sourceforge.net/tracker/index.php? func=detail&aid=1198266&group_id=36855&atid=440764
nope! (see SF item)
> Have mapped SP_KW:Sodium > GO:metal ion binding ; > GO:0046872 could > I have new GO term alkali metal ion binding with a > child sodium ion binding. > https://sourceforge.net/tracker/index.php? func=detail&aid=1198232&group_id=36855&atid=440764
sodium ion binding added; other term not requested
> Need to map Tissue remodeling..> first of all do we [snip] > https://sourceforge.net/tracker/index.php? func=detail&aid=1198273&group_id=36855&atid=440764
outstanding
Original comment by: mah11
SPKW2GO MAPPING: Pending Changes June 2005
Number of UniProt proteins affected are represented in parenthesis [ ]
New/modified mappings:
SP_KW:Actin capping > GO:barbed-end actin filament capping ; GO:0051016[146] SP_KW:Ammonia transport > GO:ammonium transport ; GO:0015696[29] SP_KW:Antiviral defense > GO:response to virus ; GO:0009615[377] SP_KW:Bacterial capsule > GO:capsule (sensu Bacteria) ; GO:0030113[246] SP_KW:Bacteriocin transport > GO:bacteriocin transport ; GO:0043213[39] SP_KW:Capsid maturation > GO:viral procapsid maturation ; GO:0046797 [21] SP_KW:Cell division > GO:cell division ; GO:0051301 [6512] SP_KW:Cell shape > GO:regulation of cell shape ; GO:0008360 [3126] SP_KW:CF(0).AC > GO:proton-transporting ATP synthase complex, coupling factor F(o) ; GO:0045263 [4110] SP_KW:CF(1).AC > GO:proton-transporting ATP synthase complex, coupling factor F(1) ; GO:0045261 [4443] SP_KW:Chlorophyll catabolism > GO: chlorophyll catabolism ; GO:0015996 [10] SP_KW:Chondrogenesis > GO:cartilage development ; GO:0051216 [62] SP_KW:Chylomicron > GO:chylomicron ; GO:0042627 [57] SP_KW:Competence > GO:establishment of competence for transformation ; GO:0030420 [240] SP_KW:Conidiation > GO:conidium formation ; GO:0048315[20] SP_KW:Core protein > GO:viral nucleocapsid ; GO: [17902] SP_KW:Cycloheximide resistance > GO:response to cycloheximide GO:0046898[17] SP_KW:Cyclosporin > GO:peptide binding ; GO:0042277[65] SP_KW:Cytokine > GO:extracellular space ; GO:0005615[1902] SP_KW:DNA invertase >GO:recombinase activity ; GO:0000150[72] SP_KW:DNA synthesis > GO:DNA replication ; GO:0006260[288] SP_KW:Erythrocyte maturation > GO:erythrocyte maturation ; GO:0043249[32] SP_KW:Feather > GO:structural constituent of cutaneous appendage ; GO:0030281[14] SP_KW:Fibrinolysis > GO:fibrinolysis ; GO:0042730 [2050] SP_KW:Folate biosynthesis > GO:folic acid biosynthesis ; GO:0046656[584] SP_KW:Gap protein > GO:segmentation ; GO:0035282 [47] SP_KW:Germination > GO:organismal physiological process ; GO:0050874[121] SP_KW:Golgi stack > GO:Golgi stack ; GO:0005795 [2436] SP_KW:GPI-anchor biosynthesis > GO:GPI anchor biosynthesis ; GO:0006506[54] SP_KW:Hemolymph clotting > GO:hemolymph coagulation ; GO:0042381[10] SP_KW:Heterocyst > GO:heterocyst cell differentiation ; GO:0043158[21] SP_KW:Hibernation > GO:hibernation ; GO:0042750[9] SP_KW:Hydrogen peroxide > GO:hydrogen peroxide catabolism ; GO:0042744[789] SP_KW:Interferon antiviral system evasion > GO:viral evasion of host immune response ; GO:0030683[12] SP_KW:Karyogamy > GO:karyogamy ; GO:0000741[8] SP_KW:Lignin degradation > GO:lignin catabolism ; GO:0046274[330] SP_KW:Lipoyl > GO:coenzyme binding ; GO:0050662 [567] SP_KW:Mast cell degranulation > GO:mast cell degranulation ; GO:0043303[31] SP_KW:Mercury > GO:mercury ion binding ; GO:0045340[291] SP_KW:Metal-binding > GO:metal ion binding ; GO:0046872[53278] SP_KW:Methotrexate resistance > GO:response to antibiotic ; GO:0046677[21] SP_KW:Microtubule > GO:microtubule ; GO:0005874 [4512] SP_KW:Notch signaling pathway > GO:Notch signaling pathway ; GO:0007219[167] SP_KW:Nuclear pore complex > GO:nuclear pore ; GO:0005643[34] SP_KW:Oogenesis > GO:oogenesis ; GO:0048477[63] SP_KW:Osteogenesis > GO:ossification ; GO:0001503 [48] SP_KW:Oxylipin biosynthesis > GO:fatty acid biosynthesis ; GO:0006633[33] SP_KW:Phospholipid degradation > GO:Phospholipid catabolism ; GO:0009395[4] SP_KW:Pigment > GO:binding ; GO:0005488[31] SP_KW:Plasma > GO:extracellular region ; GO:0005576[592] SP_KW:Postsynaptic membrane > GO:postsynaptic membrane ; GO:0045211[1022] SP_KW:Postsynaptic neurotoxin > GO:acetylcholine receptor inhibitor activity ; GO:0030550[190] SP_KW:Proteasome > GO:protein complex ; GO:0043234[1541] SP_KW:Protein splicing > GO:protein splicing ; GO:0030908[77] SP_KW:Pyrogen > GO:fever ; GO:0001660[70] SP_KW:Quinone > GO:quinone binding ; GO:0048038 [403] SP_KW:S-layer > GO:S-layer ; GO:0030115[237] SP_KW:Signal transduction inhibitor > GO:negative regulation of signal transduction ; GO:0009968[185] SP_KW:Sodium > GO:metal ion binding ; GO:0046872 [647] SP_KW:Tegument protein > viral tegument ; GO:0019033[50] SP_KW:Telomere > GO:telomere maintenance ; GO:0000723[91] SP_KW:Threonine protease > GO:threonine endopeptidase activity ; GO:0004298[850] SP_KW:Thyroid hormones biosynthesis > GO:hormone biosynthesis ; GO:0042446[23] SP_KW:Tissue remodeling > GO:histogenesis ; GO:0009888[2050] SP_KW:Transcription antitermination > GO:regulation of transcription ; GO:0045449[89] SP_KW:Vasoactive > GO:regulation of blood vessel size ; GO:0050880[237] SP_KW:Vasoconstrictor > GO:vasoconstriction ; GO:0042310[61] SP_KW:Vasodilator > GO:vasodilation ; GO:0042311 [62] SP_KW:Viral immunoevasion > GO:viral evasion of host immune response ; GO:0030683[122] SP_KW:Viral movement protein > GO:viral spread within host, cell to cell; GO:0046740[94] SP_KW:Vitamin A > GO:vitamin binding ; GO:0019842 [65] SP_KW:Vitamin B12 > GO:vitamin binding ; GO:0019842 [221] SP_KW:Vitamin C > GO:vitamin binding ; GO:0019842 [618] SP_KW:Vitamin D > GO:vitamin D binding ; GO:0005499[16] SP_KW:Xylan degradation > GO:xylan catabolism ; GO:0045493[654] SP_KW:Xylose metabolism > GO:D-xylose metabolism ; GO:0042732[216]
Total No. UniProt entries affected: 115,764
Deleted mapping: (because a more granular mapping can be made)
SP_KW:Bacteriocin transport >GO:transport; GO:0006810 [39] SP_KW:Cell shape > GO:cell morphogenesis ; GO:0000902 [3126] SP_KW:Conidiation > GO:sporulation ; GO:0030435[20] SP_KW:Core protein > GO:virion ; GO:0019012[17902] SP_KW:Cycloheximide resistance > GO:response to antibiotic GO:0046677[17] SP_KW:Folate biosynthesis > GO:folic acid and derivative metabolism ; GO:0006760[584] SP_KW:Golgi stack > GO:Golgi apparatus ; GO:0005794[2436] SP_KW:Lignin degradation > GO:lignin metabolism ; GO:0009808[330] SP_KW:Phospholipid degradation > GO:Phospholipid metabolism ; GO:0006644[4] SP_KW:Pyrogen > GO:inflammatory response ; GO:0006954[70] SP_KW:Signal transduction inhibitor >GO:signal transduction ; GO:0007165[185] SP_KW:Threonine protease > GO:peptidase activity ; GO:0008233[850] SP_KW:Xylan degradation > GO:carbohydrate metabolism ; GO:0005975[654] SP_KW:Xylose metabolism > GO:monosaccharide metabolism ; GO:0005996[216]
Total No. Proteins affected:26433
(because a less granular mapping should be made)
SP_KW:Cell division > GO:cytokinesis ; GO:0000910 [6512] SP_KW:Telomere > GO:telomerase-dependent telomere maintenance ; GO:0007004[91]
Total No. Proteins affected:6603
(because mapping incorrect, new term/path available)
SP_KW:Hemolymph clotting > GO:blood coagulation ; GO:0007596[10] SP_KW:Postsynaptic membrane > GO:synaptic transmission ; GO:0007268[1022] SP_KW:Biotin > GO:biotin binding ; GO:0009374 [307]
Total No. Proteins affected:1339 Grand Total No. Proteins affected:34375
No. Proteins with Re/new mappings (115764) No. of proteins with deleted mappings (34375)= 81389 proteins with new SPKW2GO mappings
Removal of mappings to obsolete GO IDS:
Automatically checked by Daniel for obsoletes and manually corrected by Evelyn This month: None, Amelia must be away!
Requests to UniProt/Swiss-Prot keyword developers (Serenella):
Why is there two separate keywords for calcium and calcium-binding, As for other metal ion binding terms, metal dependency and binding is combined in the description. Would prefer if all these were seprated. Querying Germination usage. Does it include pollen and zygote germination? Tanya suggest kw usage is applied mostly in UniProt to seed germination. CF(0).AC KW-0138 and CF(1).AC KW-0139 SPKW:Repressor can not be mapped to GO because of double usage. Would it be possible to create two new keywords translation repressor and transcription repressor. Is it possible to have a UniProt link as well as expasy in the keyword lists. SPKW Tissue remodeling..not sure if it can be mapped to tissue regeneration GO:0042246
Requests to GO editors: GO:ammonium transport ; GO:0015696 Need GO synonym: ammonia transport
Should atom binding be synonym for ion binding. SP_KW:Chloride > can we have chloride binding https://sourceforge.net/tracker/index.php? func=detail&aid=1198232&group_id=36855&atid=440764
Request definition for DNA integration, GO:0015074 could be mapped to keyword. https://sourceforge.net/tracker/index.php? func=detail&aid=1198261&group_id=36855&atid=440764
Request new term invertasome, nucleoprotein structure.
Should recombinase activity have synonym ; invertase activity??? https://sourceforge.net/tracker/index.php? func=detail&aid=1198266&group_id=36855&atid=440764
GO has FAD biosynthesis can we have also FMN biosynthesis.
SP_KW:Guanine-nucleotide releasing factor > GO:????? What to map too?
Could SP_KW: Hemagglutinin be mapped to a broad term cell adhesion?
Should heterocyst formation be synonym of heterocyst cell differentiationGO:0043158 https://sourceforge.net/tracker/index.php? func=detail&aid=1198266&group_id=36855&atid=440764
SP_KW Hexon-associated protein no mapping..hexon binding
SP_KW: Keratinization, could we have new GO process term Keratinization Possible Def:the process in which the cytoplasm of the outermost cells of the vertebrate epidermis is replaced by keratin. Keratinization occurs in the stratum corneum, feathers, hair,claws, nails, hooves, and horns.
GO:lignin catabolism ; GO:0046274.. noticed that a lot of the catabolism terms are missing a synonym for degradation, eg. lignin degradation. Or phospholipid degradation. https://sourceforge.net/tracker/index.php? func=detail&aid=1198266&group_id=36855&atid=440764
Have mapped SP_KW:Lipoyl > GO:coenzyme binding ; GO:0050662 but Should there be a new child of GO:0050662 called lipoic acid binding (new GO) also With a parent carboxylic acid binding (new GO) https://sourceforge.net/tracker/index.php? func=detail&aid=1198280&group_id=36855&atid=440764
Have mapped SP_KW:Lithium > GO:metal ion binding ; GO:0046872 but would like new GO term: lithium ion binding. https://sourceforge.net/tracker/index.php? func=detail&aid=1198232&group_id=36855&atid=440764
Need new child of GO:0004857; enzyme inhibitor activity, metalloenzyme inhibitor activity https://sourceforge.net/tracker/index.php? func=detail&aid=1198289&group_id=36855&atid=440764
Need to map keyword Methotrexate resistance to new GO term response to methotrexate https://sourceforge.net/tracker/index.php? func=detail&aid=1198288&group_id=36855&atid=440764
Have mapped SP_KW:Germination > GO:organismal physiological process ; GO:0050874, Jen to ask whether generic germination term can be reinstated. https://sourceforge.net/tracker/index.php? func=detail&aid=1198276&group_id=36855&atid=440764
Have mapped SP_KW:Oxylipin biosynthesis > GO:fatty acid biosynthesis ; GO:0006633 but would like new GO term: oxylipin biosynthesis as child of GO:0006633. https://sourceforge.net/tracker/index.php? func=detail&aid=1198287&group_id=36855&atid=440764
Should we have a new GO term for Phytochrome signaling pathway KW-0607 which is also a keyword. KW definition: Protein involved in the relay of information from the activated phytochrome molecule to target genes. Different phytochromes use both separate and common early signaling pathways. These pathways converge downstream in a process of signal integration that regulates photomorphogenesis and the circadian clock. This provides the means by which information from specific wavelengths of light may be amplified and coordinated. https://sourceforge.net/tracker/index.php? func=detail&aid=1198284&group_id=36855&atid=440764
Have mapped SP_KW:Pigment > GO:binding ; GO:0005488 but would like new GO term: pigment binding pos def: Interacting selectively with a pigment or any class of colouring matter, found in animals, plants or microorganisms https://sourceforge.net/tracker/index.php? func=detail&aid=1198282&group_id=36855&atid=440764
Have mapped SP_KW:Plasma > GO:extracellular region ; GO:0005576 Bot quite sure whether it should be mapped to GO:extracellular space Also wondering if acellular should be synonym of extracellular? https://sourceforge.net/tracker/index.php? func=detail&aid=1198266&group_id=36855&atid=440764
Have mapped SP_KW:Sodium > GO:metal ion binding ; GO:0046872 could I have new GO term alkali metal ion binding with a child sodium ion binding. https://sourceforge.net/tracker/index.php? func=detail&aid=1198232&group_id=36855&atid=440764
Discussion in Sourceforge: Should there be a GO term to describe the mechanism of Self-incompatibility for a new keyword mapping. Jen and Emily to resolve. https://sourceforge.net/tracker/index.php? func=detail&aid=1196016&group_id=36855&atid=440764
Need to map Tissue remodeling..> first of all do we need specific GO term or is tissue regeneration useful. Also notice bone remodeling has parent term organismal physiological process but neuronal remodeling is child of development???? Was looking for broad parent of Tissue remodeling to map to, http://www.sciencedaily.com/releases/2004/10/0410010 91737.htm https://sourceforge.net/tracker/index.php? func=detail&aid=1198273&group_id=36855&atid=440764
If you would like to query any of these spkw2go revisions then please contact Evelyn Camon, GOA Coordinator, (camon@ebi.ac.uk). If you find UniProt entries have inappropriate keyword assignments please contact Michele Magrane, UniProt Annotation Coordinator (magrane@ebi.ac.uk)
Reported by: ecamon
Original Ticket: "geneontology/annotation-issues/118":https://sourceforge.net/p/geneontology/annotation-issues/118