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  • 13:07
    marcfeuermann closed #4326
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    marcfeuermann commented #4326
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    AndreaAuchincloss assigned #4326
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  • Oct 06 20:04
    ValWood closed #4311
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    ValWood opened #4324
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  • Oct 05 17:56
    ValWood commented #4302
  • Oct 05 16:55
    ValWood edited #4323
Chris Mungall
@cmungall
I would like to move towards having a single relation used for all development terms->uberon. There are some technical reasons why we can’t do that yet (maybe we can revisit this at the Geneva meeting?).
For now, you have to use the same design pattern as we use in the ontology, and use the same relation (results_in_development_of), IF you want to post-compose.
I think that given we have some many pre-composed development terms we should just go ahead and add this one too
sabrinatoro
@sabrinatoro
Thank you @cmungall , I'll ask for a new term.
sabrinatoro
@sabrinatoro
I am trying to capture the ligand for "nuclear receptors" using a Noctua model. (geneontology/go-ontology#16540)
Which relationship should I use between "nulcear receptor activity" and the Chebi term?
"directly activates" gives an "inconcistency" error.
Thanks!
sabrinatoro
@sabrinatoro
I am still having some inconcistency error...
I used "has input" Chebi# ...
Is a Chebi# not allowed for "has input" relationship?
Here is the model link: http://noctua.geneontology.org/editor/graph/gomodel:5b91dbd100001025
Jim Balhoff
@balhoff
I think this is an issue with ChEBI material entity vs role
androgen is a role
same with thyroid hormone
You can make an intermediate node of type something like ‘chemical entity'
and relate it to the ‘androgen’ node using ‘has role'
I would be curious if any GO editors have other suggestions
suzialeksander
@suzialeksander
How do I make a “contributes to” annotation in Noctua? I have two different proteins required to enable an activity (transmembrane transporter activity). Related to geneontology/noctua#438 but there hasn’t been any response in a while
kltm
@kltm
@vanaukenk seems to be on this channel, but it seems like some people, like @ukemi are not and I cannot add them automatically. I've tried manually. (I was figuring that one of them might provide the answer you want.)
suzialeksander
@suzialeksander
OK, I’ll @ them in that ticket. Thanks
suzialeksander
@suzialeksander
What relation would I use in Noctua to add a target of a process? In gomodel:5b91dbd100001972, a specific portion of Bre1 is needed to prevent Lge1 from degradation. I don’t have any reliable info that Lge1 directly binds Bre1, although that is the implication and extremely likely. I have the annotation to Bre1/neg reg of protein catabolic proc, is there a way to include Lge1 in the output?
cerivs
@cerivs
Hi, I'm looking for a term to use for cellular response to RNA repeats. Transcription of genes that have over a certain number of repeats causes RNA metabolic processes to occur, often called "repeat RNA toxicity"". I'm looking at a paper that characterizes the genetic responses to a specific RNA repeat 35+ poly[GGGGCC] and can't find a GO term. @vanaukenk and @ValWood do you know where in the tree I should start looking?
Any process involved in sustaining the fidelity and copy number of rDNA repeats. PMID:14528010
I think this is probably the process you need. I would avaid "cellular response to..." as these are largely describing phenotypes and probably shouldn't be in GO...
"maintenance of rDNA"
@suzialeksander @suzialeksander
@suzialeksander We have used "has_regulation_target" for the regulatory input on process annotations when can't be sure that the input is 'direct'
Val Wood
@ValWood
Sorry everyone. I can't figure out how to reply to specific messages.
cerivs
@cerivs
This is a gene that binds transcripts that have expanded repeat sequences and then interacts with other proteins that do something, probably take the bound transcripts & target for destruction
suzialeksander
@suzialeksander
Ah no I think responding to everyone is great, lets everyone see what is decided! thanks
cerivs
@cerivs
So this protein is acting on mRNA not rDNA or rRNA. It is a normal process in response to repeat expansion in a single protein coding gene.
@ValWood
suzialeksander
@suzialeksander
Is there a “has_regulation_target” equivalent that’s available in Noctua?
cerivs
@cerivs
I can use "is acted upon" for MF for interactions between the 2 proteins. but I can't find an appropriate term for the specific RNA binding function of protein 1, nor can I find the appropriate BP term for the process so I figured others might have good suggestions since I don't annotate in this branch very often. I appreciate all the suggestions @ValWood @suzialeksander Right now I'm looking at single stranded RNA binding for the MF but that leaves out the RNA repeats part of the equation. I could request a new ChEBI term to use or maybe make a NTR for GO
cerivs
@cerivs
I found RNA surveillance which is probably ok
suzialeksander
@suzialeksander
@cerivs there are also terms around GO:1903231
mRNA binding involved in posttranscriptional gene silencing, that may be somewhere to look
Val Wood
@ValWood
RNA surveillance or a descendant sounds corrct.
@cerivs which paper is it, I'm curious..
@suzialeksander has_regulation_target might be our user facing term name... I'll check what the official name is
Val Wood
@ValWood
OK has_regulation_target is the official name.
cerivs
@cerivs
@ValWood PMID:29302778 A zebrafish model for C9orf72 ALS reveals RNA toxicity as a pathogenic mechanism
Petra Fey
@pfey03
hello glitterers
suzialeksander
@suzialeksander
Hi @pfey03!
Stacia Engel
@srengel
Petra!
sabrinatoro
@sabrinatoro
Hi everyone! I have a question about protein binding curation using Noctua.
What we want to curate is that protein A binds to protein B. There is no evidence of these proteins function together as a complex. Can we (should we) curate this using Noctua? If so how? Should we say "protein A - protein binding" with proteinB in the "with" field? (consistent with conventional annoations?) or should we say "protein A-protein binding-has input proteinB"? Or create a macromolecular complex with both protein (and link it to nothing since we don't know the function of the complex)
If this is a larger discussion, we can talk about it at one of our call.
Thanks!
goodb
@goodb
Screen Shot 2019-04-22 at 1.56.24 PM.png
Hi @sabrinatoro what do you think of modeling it like this ?
sabrinatoro
@sabrinatoro
@goodb That works for me.
@vanaukenk @ukemi : is this is the official convention?
vanaukenk
@vanaukenk
@sabrinatoro - afaik, we are still modeling this using the enabled_by relation for the MF. In that case, I would make two separate protein binding annotations with each protein as the enabler and the interacting protein as the has_input.
goodb
@goodb
@vanaukenk is there documentation on this on the wiki somewhere ?
vanaukenk
@vanaukenk
@goodb - specifically for the protein binding MF annotations, no.
goodb
@goodb
@vanaukenk seems a little wonky to use enables on this to me. Out of curiosity is that choice made because it results in gpad output? the has_input structure above won’t produce any gpad as things stand.
vanaukenk
@vanaukenk
@goodb - yes, that is currently the only way we'll get the expected GPAD output, although that's not to say we can't re-visit the rules for this.
sabrinatoro
@sabrinatoro
@vanaukenk Thank you!