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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 ?

We have decided to add other relations in the GAF (including involved_in, and others), but this is not yet the case, so for now all qualifiers other than NOT, contributes_to, and colocalizes_with should be filtered out
sabrinatoro
@sabrinatoro
In the delta-notch pathway: is delta part of the pathway, or is it regulating the pathway? Is there already an agreement on this?
Thanks
Helen Attrill
@hattrill
Hi @sabrinatoro, as the definition includes the ligand, it should be part of the pathway.
sabrinatoro
@sabrinatoro
@hattrill thank you for confirming!
sabrinatoro
@sabrinatoro
Quick questions:
1- what is the update about the users meeting on Monday? Is it happening?
2- It said that we should receive an email with the link to join the GO-meeting. Has this email already been sent?
Thanks!
I'm not sure what is going on with an email at this point.
sabrinatoro
@sabrinatoro
Thank you Seth!
kltm
@kltm
My guess is that it was only distributed to people who had "signed-up".
sabrinatoro
@sabrinatoro
I did sign up and I haven't received anything... Just wandering whether it is 'normal' (i.e. hasn't been sent yet), or I 'fell through the cracks'.
kltm
@kltm
Ah, it looks like it may be getting sent out later today. Let me check on that.
It looks like you should be getting it later today then.
If you do not, ping us and we'll make sure you get the channel/password.
sabrinatoro
@sabrinatoro
OK. Thank you for looking into it!
Eric Douglass
@dougli1sqrd

@dustine32 @vanaukenk I'm looking at the gpad 2.0 spec. For with/from: Pipe-separated entries represent independent evidence; comma-separated entries represent grouped evidence, e.g. two of three genes in a triply mutant organism

We currently only model with/from as a list. Could/should the pipes be treated as different annotations? Like if I had withfrom a|b, this would be the same as 1:a, 2:b? Do we need to update how this is modeled internally?

vanaukenk
@vanaukenk
@dougli1sqrd @dustine32 @ukemi I believe that for the imports Dustin has modeled pipe-separated With/From entries as separate annotations.
kltm
@kltm
It will be good to get on the same page. @vanaukenk If we then output these separate annotations as separate lines in GPAD output, would that weird people out?
dustine32
@dustine32
@dougli1sqrd Yep, gocamgen should be splitting pipe-separated with/from values into separate GO-CAM assertions
vanaukenk
@vanaukenk
@kltm No, I don't think it would weird people out too much. The piped with/from field was really more of a convenience and a way to reduce the number of annotations lines, rather than anything to do with the actual data, iirc.
kltm
@kltm
Okay, that's good to know. It's good to know that intention is maintained.
Eric Douglass
@dougli1sqrd
cool cool thanks everyone