Activity for rach_huntley
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rach_huntley posted a comment on ticket #11776
Hi Chris, David, Is is possible to get this done ASAP because my student needs to...
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NTR: reduced folate transmembrane transport
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NT: Intestinal folic acid absorption
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Hi Leonore, Thanks for the document, it all makes sense. For the transcription factors,...
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Hi Leonore, Was there an attachment? I can't seem to see it. Thanks, Rachael.
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Hi Leonore, I have made a diagram for the plant miRNA biogenesis pathway (attached...
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Hi David, "Maybe reposition as a child of 'primary miRNA methylation'?" I don't think...
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NTR: "miRNA export from nucleus" and "miRNA transporter activity"
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NTR: miRNA 2'-O-methylation
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NTR: Thymidylate synthase inhibitor binding
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NTR: folic acid receptor activity
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Parentage of methotrexate binding
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Hi David, There is no indication that they are talking about neuropores, so I think...
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Possible NTR: anterior neural tube closure
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Hi Leonore, OK, thanks. If you can send me what you can, I will try to work on the...
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Hi Kimberly, Just to let you know this was dealt with in this SF ticket https://sourceforge.net/p/geneontology/ontology-requests/11638/...
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Hi Leonore, Have you had chance to work on the plant miRNA section and figure? I...
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Definition of 'deadenylation involved in gene silencing by miRNA'
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Protein2GO report not working
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Val, see https://sourceforge.net/p/geneontology/annotation-issues/1317/
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Above list of annotations with curation groups identified; mRNA cleavage involved...
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Hi David, Is the above proposed solution agreed now? I would like to update my guidelines...
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It is (see screenshot) - am I missing something?
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Hi David, Karen, I think I understand what you mean, just to confirm - you are saying...
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Figure 1 Powerpoint file here
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Hi Leonore, Thanks very much for putting together the annotations for the plant pathway....
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Here is some feedback from Dmitry from MGI. My responses are prefixed with a 'RH>'....
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Thanks for your reply Karen, I thought the removal of the part_of relation between...
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Hi Leonore, Just to say thanks for this, I am going through this now so I'll send...
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GO:0035068 micro-ribonucleoprotein complex parentage
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I think the proposed solution looks OK. You would then have the major mechanisms...
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Update on miPEP sequences: UniProt have now included the miPEP sequences from Lauressergues,...
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Hi David, Would the simplest solution be to broaden the definition of mRNA processing...
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I have made a decision tree to replace Table 2 in the guidelines (attached at the...
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miRNA annotation guidelines
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I have made a decision tree to replace Table 2 in the guidelines. Feel free to add...
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Gene silencing definition too narrow.
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Hi Kimberly, That's a good point, I hadn't looked closely at the parent. The gene...
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Hi Tanya, I will take a look at converting the table into a decision tree. Thanks...
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Hi Leonore, Firstly, thank you very much for reading the document and providing feedback....
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Ensembl name lookup
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miRNA annotation guidelines
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Additional parent for mature miRNA 3'end processing
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OK, thanks Val, that makes it clear. Then the new term I guess should be ³pre-miRNA...
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Hi Val, I¹m not sure I get the distinction. Transmembrane transporter activity "Enables...
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NTR: pre-miRNA transmembrane transporter activity
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Missing parent for S-adenosylmethionine cycle
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Parentage of GO:0000981
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Update to GOrel to enable use of RNAcentral IDs in extensions
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NTR: mRNA cleavage involved in gene silencing by siRNA
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NTR: mRNA cleavage involved in gene silencing by siRNA
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NTR: endoribonuclease activity, cleaving miRNA-paired mRNA
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Query parentage of GO:0060969 neg. reg. gene silencing
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Hi Paola, Thanks for this. Can you set my dbxrf the same as for Nancy Campbell and...
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Hi Paola, I think your suggestion is good. Since the alternative pathway has only...
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Hi Paola, This paper is quite recent http://www.ncbi.nlm.nih.gov/pubmed/?term=24837021....
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Hi Paola, I guess it could be a sub-type, but it depends what GO:0006303 is describing....
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NTR: DSB repair via alternative non homologous end joining
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Taxon constraint:GO:0042574
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Also GO:0005503 all-trans retinal binding has the same constraint.
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Taxon constraint:GO:0042574
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I would hope that Chris will bring this to an annotation call as we have already...
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Hi, Wouldn't the correct way to annotate be to use a specific ECO term for the assay?...
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UniProt annotations; P12979 appears to be involved in muscle atrophy normally. For...
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SP_KW:KW-0346
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Yes, good point, this term should only be used for electronic annotations when nothing...
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Annot. to GO:0010421 hydrogen peroxide-mediated programmed
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Ah, OK. I see the distinction - I was thinking of other organism as other species...
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Bad E. coli annotations
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Hi Jim, This annotation is not visible anymore, so your fix has worked. Rachael....
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Hi Val, Can you tell us which gene this refers to? Rachael.
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SP_KW:KW-0238 DNA binding
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Keyword is still present only on these; P20433 Q8VC56 Q80XJ2 Sent to UniProt.
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Sent to UniProt.
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Hi Paola, I'm looking into this and it looks like the cell death is from the same...
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Sent to UniProt
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Only P04910 still has the DNA repair keyword. Sent to UniProt.
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Sent to UniProt
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SL-0455 should be removed from the following entries; O13729 pun1 O14014 rga3 O14248...
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Duplicate of https://sourceforge.net/p/geneontology/annotation-issues/813/ However,...
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SPKW mapping to protein folding UniProtKB-KW:KW-0697
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problem mapping for glutamate--cysteine ligase regulatory s
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This annotation has disappeared.
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It seems that the is_a relation to iron ion binding was deleted in 2012. However,...
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I can't see any PAINT annotations to this term, but there are manual annotations...
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DPAGT1 is GO:0031227 or GO:0005789, not GO:0016021
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I think Ruth was querying P05121, which now does not have the annotation from KW-0617....
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Hi Val, We are not getting any GO annotations for pombe from this mapping anymore...
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Reactome mapping to wrong yeast
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Annotation has been removed.
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O14012 incorrect annotation
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I'm going to delete all the TAS annotations from this paper as it's a review. By...
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I'm going to delete all the TAS annotations from this paper as it's a review. By...
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PKA regulatory subunit maps to 'kinase activity' in spkw2go
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Q6NW93 still has two GO annotations derived from KW-0418. Have submitted to the UniProt...
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Both of these proteins now have manual annotations to this term. The yeast is IMP...
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Sent to UniProt.
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Hi Val, Is this still an issue? InterPro:IPR001719 doesn't have this mapping anymore...
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E. coli NuoE annotated to mitochondrial complex
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This annotation no longer exists.
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