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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
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Unable to add CC as AE without appearing as individual CC annotation #584

Open suzialeksander opened 6 years ago

suzialeksander commented 6 years ago

http://noctua.geneontology.org/editor/graph/gomodel:5b91dbd100000065

In this model, I'm trying to state the MF occurs_in the GO:0005775 vacuolar lumen as an an extension (in Protein2GO under PMID:29514932). We don't want to add a separate CC annotation, necessarily: in the scenario where we have a dozen annotations to "cytoplasm", we don't want to be forced to add "cytoplasm" every time we make a F annotation as well.

Is there a way to state

ATG42 Scer enables serine-type carboxypeptidase activity PMID:29514932 genetic interaction evidence used in manual assertion PRC1 Scer   20180912 SGD occurs_in(vacuolar lumen),happens_during(cellular response to nitrogen starvation),has_input(PRB1 Scer),has_input(APE1 Scer)

without adding

PRC1 Scer part_of vacuolar lumen PMID:29514932 genetic interaction evidence used in manual assertion ATG42 Scer  
balhoff commented 6 years ago

Is this a question about the inferred GPAD output? As in you want to suppress the CC annotation that is being generated by the GPAD inference?

suzialeksander commented 6 years ago

Yes, exactly. Is there any way to do that?

balhoff commented 6 years ago

I tried to think of some tricks you could do with leaving off evidence on the edge to 'vacuolar lumen', however I think that would also remove the term from the annotation extension in the MF annotation. I don't think there's a way to do this at the moment.

balhoff commented 6 years ago

We should discuss this in a Noctua call @vanaukenk @ukemi.

vanaukenk commented 6 years ago

@suzialeksander Is the issue that you don't want redundant annotations to the CC term in the GPAD output or that you don't want any of the CC annotations? If the former, then maybe that's something we could address with the GPAD output. Before we go further, though, I have some other questions about the model, so maybe we could Skype chat?

vanaukenk commented 5 years ago

@suzialeksander - would you like to keep this issue open? If so, please just comment on what still needs to be addressed. Thanks!

suzialeksander commented 5 years ago

Hi @vanaukenk, the issue was we don't want duplicate annotations in the GPAD. It seems from other conversations that duplicates may be an issue in the pipeline overall: with some annotations from Protein2GO, some from Noctua, and up to a month-ish delay before we can easily search models in https://geneontology.cloud/home, there may be curators inadvertently overlapping newly made annots. Not sure the best way to address this.

Bottom line, SGD policy is to not "stack" annotations- we want just 1 to 'vacuolar lumen', not a half dozen, so we don't want to import 'vacuolar lumen' if that's not what we wanted out of the model.

From conversations with @kltm it seems like this filtering has to be done on our end after we've retrieved the NOCTUA GPAD, does this sound correct? If there's no other way to do this and no plans this ticket can close. We really would like an upstream solution though.

pgaudet commented 5 years ago

I think we want to produce GAFs with non-redundant annotations, but we are not that close from doing it - we first need to define specs. How urgent is this for you @suzialeksander ?

suzialeksander commented 5 years ago

At this moment, not very. We are waiting for our very first production models to make a full trip (NOCTUA -> display on SGD pages), but this is a valid concern due to multiple curators working on the same corpus of literature.
Maybe this is wishlist for now?

srengel commented 5 years ago

it's important enough that it's stopping us from adopting Noctua.

suzialeksander commented 5 years ago

As a sort of follow up, is there any reason that another group would be propagating our Noctua annotations appearing in our (future) noctua_fb.gpad? Asking because Noctua is inferring other annotations that we don't necessarily want, this time a P: http://noctua.geneontology.org/workbench/annpreview/?model_id=gomodel:5b91dbd100001818

(Even though this isn't a production model, we wouldn't want the vague "macromolecule metabolic process" ).

Would be happy to talk to @vanaukenk about any of our models, there area few things we're definitely still working on.

Note: our handful of prod models are currently packaged in the Uniprot noctua gpad (https://github.com/geneontology/neo/issues/36); should be resolved soon.

cmungall commented 5 years ago

If there is GOC-wide agreement then we can add this to the do_not_manually_annotate subset, otherwise the filter could be implemented on the SGD end

ukemi commented 5 years ago

I would be comfortable as having this do not manually annotate.

vanaukenk commented 5 years ago

I would also be fine with having a 'do not manually annotate' flag on terms like these, but if I'm reading the inference explanation correctly on this model, the macromolecule referenced in this annotation is actually the gene product, GPC1, since it is classified as an information biomacromolecule and is a participant in the metabolic process. I don't yet see a ticket in the RO tracker for our has_participant proposal from Geneva.
@ukemi @cmungall - how would you like to proceed with that?

cmungall commented 5 years ago

Can you make a new ticket on the RO tracker (there are existing tickets but they are tied up with other things, I will link them)

vanaukenk commented 5 years ago

Okay, just to be sure, this is what I have from the whiteboard in Geneva:

has participant proposal

has participant -has primary input or output NEW --has primary input NEW --has primary output NEW -enabled by (new parentage) -has input --has primary input NEW -has output --has primary output NEW functionally related to -enabled by

The 'primary' terms still need definitions.

ukemi commented 5 years ago

https://github.com/oborel/obo-relations/pull/291

I think the best we can do for now with the primary terms is to create a subjective distinction of participants. The primary participants are those that are the focus of the occurent. For example in named processes, they are the participants that are specified in the label. Do we really want these for Noctua or will they only be used in the ontology?

vanaukenk commented 5 years ago

Thanks @ukemi If you have time to go over that pull request, that'd be great.

vanaukenk commented 5 years ago

@suzialeksander Yes, I'd be happy to go over models with you some time. Let's set up a time after the holidays.

ukemi commented 5 years ago

It is one that was added by @cmungall in Geneva.

suzialeksander commented 2 years ago

Created http://noctua.geneontology.org/workbench/noctua-form/?model_id=gomodel%3A62b4ffe300002236 as a reference for this ticket.

Note to self- we made the desired annot here in P2GO so this model can be discarded.

suzialeksander commented 7 months ago

Bumping as this probably is an issue in the SGD import, discussed after Feb 8 Noctua outage and on a Feb 9 call with @dustine32 @kltm @balhoff @vanaukenk