Activity for Valerie Wood
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Valerie Wood created ticket #73
NTR: glutaminylation ?
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Valerie Wood posted a comment on ticket #130
All three is fine. We can't distinguish as they are identical, and I wnat the annotation to appear as modification on all 3 objects. v
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my fault, I always forget where I can search, so I just searched in teh SF tracker. Can you remind me where I should search ? v
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Hi Darren, yes please methionine removal is fine. I think this should be the defult on all of our moified histnes since the 'active' form is demethylated? Val
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H3 K9me3
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Thanks, you are never slow, believe me. I only created the ticket 2 days ago! This is the fastest tracker! I wanted to capture that dma1 (unubiquitinated) only binds to phosphorylated sid4 to negatively regulated SIN signalling. So the other ref was the correct one for phosphorylated sid4. Thanks for figuring that out. Val
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sid4, dma1
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proline isomerization
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thanks!
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oh gosh. Do you know who maintins PSI-MOD? I don't think I actually requested a PSI-MOD term before. I thought you did both!
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Is this the wrong tracker for PSI-MOD issues?
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It is in our Canto tool. I'll ask Kim to take a look, maybe it is truncated for some reason.
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possible malformed term?
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which term for proline isomerization
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OK thanks we'll update to that.
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OK we'll wait to see what the outcome is. This is the link we are using in our webpages. I think it comes from the GO dbxrefs file so we have these links in the MF part of this page (uncollapsed) https://www.pombase.org/gene/SPAC20G8.05c Ideally the same url will be the one in the GO db xrefs. I will check where we get the base url from.
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Hi Darren should this link work? https://research.bioinformatics.udel.edu/pro/entry/PR%3A000044735/ cheers val
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I guess it would be useful to add all as there a few papers on CTD domain, Im sure we can use them, I can tell everyone that they exist.
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Awesome, that's perfect. v
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rpb1 P36594 CTD S2 phosphorylated
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Thanks, that will do it! val
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S. pombe cdc12 phosphorylated form
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looks good, cheers v
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I was trying to alert our users that the full length protein had a ubiquitin domain but this should be clear when we use the cleavage products in column 17. Although Its a little bit like the ribosome ubiquitin fusion proteins named ribosomal-ubiquitin fusion protein Ubi1 I'm going to change to "intron-specific pre-mRNA splicing-ubiquitin fusion protein" as there is a precendent for naming gene products with a ubiquitin domain that is cleaved in this way.
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Hi Darren, that all seems great except for using the Uniprot description "Telomere maintenance protein SDE2" are these automatically updated when Uniprot names change? I asked for this to be updated to, I called it intron-specific pre-mRNA splicing/ ubiquitin fold protein Sde2 at PomBase (it is actually a splicosome component and the telomere silencing is only a phenotype) Cheers Val
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N and T terminal parts of Sre2
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FYI https://github.com/pombase/website/issues/67
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That's OK, we are all weird here too ;) I'm going to link to this ticket on the relevent tickets on our tracker....our developer (Kim Rutherford) will then be able to assess whether this will do the trick... Basically we are looking for a way to automate sensible display of PRO names on our Gene pages. More later when we get to these tickets. Thanks for looking into this for us. Val
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Hi Darren, Apologies for the very delayed response. This fell ff my radar, but Midori...
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Accessing gene name consistently via PIR ID
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fab, thanks.
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Perfect. I have a question too. We have been using the name: transcription factor...
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Actually Sre2P is the full length (Sre2-precursor) The N-term (cleaved portion) refers...
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711301/figure/F3/ The N-terminal portion...
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cleavage products of pombe sre2
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Thanks, I totally overlooked the "Protein Forms" link...I think because I was concentrating...
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OK, I'll leave it with you. I thought I'd mention these things as it was the first...
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add pombase link to gene/genome
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but thats a link back to this page: http://research.bioinformatics.udel.edu/pro/entry/PR%3A000027506/...
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I found another link to here: http://pir.georgetown.edu/cgi-bin/ipcEntry?id=P06652...
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I found it, I needed to search on 'gene name' So from here http://research.bioinformatics.udel.edu/pro/entry/PR%3A000027506/...
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I am annotating a later paper and I found this ID had already been used, this was...
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fab, thanks
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cdc25 phosphorylated form
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Perfect. Our names are usullay more current and reflect community use ;) , although...
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This should be entitled acetylated form of psm3/Smc3 mitotic cohesin subunit
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lysinated form of psm3/Smc3 mitotic cohesin subunit
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Yep, I don't think it is covalent here. I was being a numpty. val
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Hi, OK I see the mutation is just somehow mimicking GTP bound, so I'm not sure where...
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Hi Darren, The allele is a construct to mimic the GTP bound state. I want the native...
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NTR: GTP bound form fission yeast/pombe Rho3
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Fantastic , thanks Cecila. val
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Hi Cecilia, This is our only GO column17 annotation for which we don't have a PRO...
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Hi Darren, Thanks for your rapid reponse. It ended up that I did not need the PRO...
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Ignore the 2nd part of the request. Upon checking again I only need the rad21 cleavage...
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Ignore the 2nd part of the request. Upon checking again I only need the rad21 cleavage...
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cleavage products of pombe cut1 (separase) and rad21(cohesin, kleisin subunti)
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I'm not sure where we got to with this but can you remind me why this isn't possible:...
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Thanks Darren, Out of curiosity is there an easy way to look up whether a modified...
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fission yeast H3-Lys-9-Me2
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wrong tracker! I'll post on github
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Phew we are back onto this . Antonia has been looking at it again. I now think the...
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I think PCNA is present in archaea and not in prokaryotes There are a couple of 'bacterial'...
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missing "gene" in the navigation menu for single mutants
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gg
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In this case do we need some rules how to name the organism specific variants? For...
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MP GO:0009927 histidine phosphotransfer kinase activity
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ntr: regulation of protein localization to cell division site involved in cell separation after cytokinesis
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refinement of septin ring structures
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refinement of septin ring structures
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At the cell cycle meeting the transition was modelled included some of these events...
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S'okay, I just read. I can now add in term genie?
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Hi David, I am after "ER tubular network membrane organization" http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0098826...
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APC complexed with inhibitor
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force e-mail...
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I also thought that only the transport defs used the phrase 'directed movement'
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protein acetyltransferase activity grouping term
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test
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MP regulation of cyclin-dependent protein serine/threonine pk activity involved in.....
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A related older ticket https://sourceforge.net/p/geneontology/ontology-requests/11118/...
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I agree. It is correct though, A MAPKKK can be involved in the activation of a MAPK,...
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OK I agree and it will be a long time before they all disappear. Comments need to...
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bent vs curved cells
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NTR: ER tubular network membrane organization
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SPAC1F5.04c FYPO:0001904 972 h- not available not available cdc12 14511538 looks...
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allele fixes
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What does "promotes active site reactivity" even mean...I could add that to any enzyme...
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make biogrid evidence code description visible via mouse over
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user interface: interaction evidence workflow
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Table loading is slow - especially the publication tables
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admin interface: Listing publications is slow
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exact duplicate https://sourceforge.net/p/pombase/curation-tool/561/
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has_part is currently ignored https://sourceforge.net/p/pombase/curation-tool/77...
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change the way FYPO has_part links are followed in Canto
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change the way FYPO has_part links are followed in Canto
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Add a way to select curator for annotation in approval mode
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New curation type "protein localization dependency"
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add "back to summary" link button to genotype management page
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question about has_output /output_of
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maybe no action required, still on my list
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