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  • May 24 13:16
    vanaukenk commented #4183
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Petra Fey
@pfey03
In P2GO, we distinguish between AND (comma) and OR (pipe)
Jim Balhoff
@balhoff
Is it legal to have an OR of two ANDs? (a&b) or (x&y)
Petra Fey
@pfey03
Yes I think so. At least it’s possible to do in P2GO
Jim Balhoff
@balhoff
thanks
vanaukenk
@vanaukenk
@balhoff Yes, it is possible to have both commas and pipes in the annotation extensions. The pipes are meant to signify independent extensions, while the commas indicate extensions that, together, provide context for the GO term. I'll double-check our GPX2.0 specs to make sure we're clear on this, but let me know if you want any clarification.
Jim Balhoff
@balhoff
@vanaukenk I need to parse these in a tool so I’m trying to make sure I know exactly what can be there. If both are used in one extension, do commas take precedence over pipes? Is it possible to group using parentheses? I thought I had seen a more explicit grammar doc at one point but I can’t find it since the website overhaul. This page (http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/) isn’t explicit enough.
vanaukenk
@vanaukenk
@balhoff I'm not sure what you mean by precedence. Maybe we could Skype?
At the bottom of the gpad table is the current explanation of annotation extensions format, but we can make this clearer, if needed: https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md
Jim Balhoff
@balhoff
@vanaukenk thanks, that’s what I was looking for
Annotation_Extensions ::= [Extension_Conj] ('|' Extension_Conj)*
vanaukenk
@vanaukenk
Okay; just let me know if you have any other questions.
Jim Balhoff
@balhoff
For precedence I mean you first group by commas, then those groups are OR'd
I think that’s what the spec is saying
vanaukenk
@vanaukenk
Yes, for precedence that's correct: extensions are first grouped by commas, and then those groups are separated by OR.
Petra Fey
@pfey03
Hi All, working on the oligomerization review and we saw and added a few GO:0042802 identical protein binding. The question we have: use IDA orcIPI? I think IDA should be fine as the same protein in the WITH seems just redundant. But there are more IPI out there. Thanks!
Birgit Meldal
@bmeldal
@pfey03 With my interaction head on, if the expt shows physical binding it's IPI... and you need the partner in the WITH field for those who parse the data out. Identical protein binding is very common, hence why I keep saying we need to capture homomeric complexes :) It would be different if it was self-interaction of the same molecule, then you can't have a GP in WITH but I don't know if GO captures that. It would require an exception rule. We do :) (and we may export this data to GO...)
Petra Fey
@pfey03
@bmeldal ok, since nobody else commented I changed mine that I did recently to IPI. All have been shown to self interact
vanaukenk
@vanaukenk
@pfey03 We are recommending that 'identical protein binding' be annotated with IPI and the ID of the same annotated entity be included in the With field for exactly the reasons Birgit states. We need to be consistent in how we capture physical interactions as much as possible, even if the binding is to the same protein. I know in some cases we have said that when we can't assign a specific ID to an interactor, e.g. actin, it is okay to annotate to a term like 'actin binding' using IDA, but I think it'd be good to enumerate these specific cases so there is no confusion about why we think these IDA annotations are okay.
Petra Fey
@pfey03
@vanaukenk Yes, I saw her point and therefore updated those today. But we might have legacy of IDA and I saw others too when I first quickly checked all EXP annotations to GO:0042802. And I agree with the actin example, Dicty has 29 actin genes, 17 make identical proteins.
Birgit Meldal
@bmeldal
We have a discussion here in the office : in 21844191, Fig 7 shows that reelin binding its receptor (binding shown in F6) indirectly activates Dab1 phosphorylation (which is much much weaker if reelin is mutated). I annotated it to GO:0038026 reelin-mediated signaling pathway as IDA (maybe it should be IMP - different discussion!) but Livia questions if we can say this is a direct evidence for reelin's involvement in the pathway. Discuss!
http://www.jbc.org/content/286/40/35247.long
sabrinatoro
@sabrinatoro
I am creating a model which requires a lot of adding individuals and making relationship. Every time I add an individual or creating a new relationship, the view of the whole model changes, and everything is sent WAY far right to the right, making it extremely difficult (and frustrating).
Is there any way around this? Is there a way to stop the "boxes" to change location everytime I do something? Thanks!
kltm
@kltm
@sabrinatoro This is an outstanding issue that we still need to get to: geneontology/noctua#173
In the meantime, there are workbenches that can help rally and control the node layout ("Cytoscape layout tool"). Of things should more-or-less fit on the screen, you can also use "Compact layout" under "Tools".
sabrinatoro
@sabrinatoro
Thank you @kltm . This is not great (as the "compact layout" mix up everything), but it is better that what I have been dealing with.
Does the "Cytoscape layout tool" let you make changes (or is it only a view option)?
kltm
@kltm
You can rubberband, move things as groups, sort however you want, and then save the new layout (as long as you are logged in).
sabrinatoro
@sabrinatoro
OK. Thank you for your help!
kltm
@kltm
NP!
Eric Douglass
@dougli1sqrd

Hello! In GORULE:0000015, we check that when a GAF has two taxon IDs, that they are formed correctly. I had a couple questions to clarify what the intention is. Here's the link to the rule: https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000015.md

Is this rule saying that 1) the first taxon should be attached to the gp, and 2) the second should be the interacting species (is that just what it means, or is there a way to verify this?) 3) the 2 allowed terms that can be used with dual taxons ('GO:0044419 : interspecies interaction between organisms', and 'GO:0044215 : other organism'), is that to mean only those terms are allowed? Or are children terms also allowed?

vanaukenk
@vanaukenk
@dougli1sqrd - As I understand the rule, the first of the pipe-separated taxon IDs should correspond to the taxon of the annotated gp, and the second taxon to that of the other species involved in the process. Children of the two GO terms listed in the description are also allowed for annotation. The statement about ancestor is the relevant part for this: "These annotations should be used only in conjunction with terms that have the biological process term 'GO:0044419 : interspecies interaction between organisms' or the cellular component term 'GO:0044215 : other organism' as an ancestor." Let me know if you want to touch base to discuss further. Thx.
pgaudet
@pgaudet
@dougli1sqrd Which ticket are you working on ?
I put a lot of tickets in the GO-rules projects; I dont recall this was one of them
We really need to start being better at following projects
suzialeksander
@suzialeksander
No annotation call on the GO Calendar, is there no call tomorrow?
vanaukenk
@vanaukenk
That's right, @suzialeksander There is no annotation call tomorrow.
suzialeksander
@suzialeksander
Thanks!!
sabrinatoro
@sabrinatoro
Thanks !
sabrinatoro
@sabrinatoro
Hi! Is Noctua currently down? If so, for how long? (I have a "service unavailable" page, I want to make sure it is not my connection from home)
Thanks
suzialeksander
@suzialeksander
eek, me too
kltm
@kltm
Interesting. The machine is reporting.
I'll look into it.
It should be back now. I'll look into the underlying cause and the lack of restart.
Jim Balhoff
@balhoff
It was quite slow yesterday to load pages
kltm
@kltm
@balhoff Was that for production or dev?
Jim Balhoff
@balhoff
production
sabrinatoro
@sabrinatoro
thank you!
Eric Douglass
@dougli1sqrd
Hi @kltm, @pgaudet, @cmungall, So in ontobio, the tests for qualifers seem to indicate that involved_in should be allowed. But http://geneontology.org/docs/go-annotations/#annotation-qualifiers says only NOT, contributes_to, and colocalizes_with are allowed. I'm making corrections in ontobio to catch the space issue, but I'm not sure how to proceed given the new information here
kltm
@kltm
@dougli1sqrd
It only appears twice:
goa_uniprot_all-src.gaf.gz:2
mgi-src.gaf.gz:12
It may be worth talking to @ukemi
kltm
@kltm
Especially if we are to start booting them, @ukemi should be in the loop.
pgaudet
@pgaudet

So in ontobio, the tests for qualifers seem to indicate that involved_in should be allowed

I am not clear what that means. Surely ontobio is not where the specs are coming from ?