Closed ukemi closed 1 year ago
@deustp01 and @dustine32 we need to add dates to the task list above. All of the things under 5 should get turned into tickets. If we can do incremental testing, we can check them off as we go.
Do we have the release 82 BioPAX Homo_sapiens.owl file available now?
Do we have the release 82 BioPAX Homo_sapiens.owl file available now?
Not yet. Should be available next week, maybe as early as 9/12. Note that getting a draft version of a BioPAX to use to generate a draft set of GO-CAMs to be checked while the Reactome source material is still available for updating, as outlined in the bulleted list at the top of this ticket is still something for the future. We hope to have that available in time for use for a coordinated release of Reactome version 83 both as Reactome pathway pages and as GO-CAMs, but that is a work in progress and depends on some machine upgrades and scripting that are still to be done.
@deustp01 Thanks! I can just wait until that's available and then push the new models to noctua-dev for testing.
Thanks guys. So Wednesday we will need to talk about a modification of our SOP for the new loads since the BioPax isn't available until the release.
new loads since the BioPax isn't available until the release.
In the future, maybe as soon as the next release, we should have the BioPAX in advance, as planned, so I hope we are looking at a delay in our plans, not a change.
Cris Mungall question on pathways2GO call about intersection of Java versions and generation of BioPAX files, and the possibility that he / Dustin may already have code to get around the current Reactome problem.
@ukemi @deustp01 ShEx and OWL consistency checks have been run. 5 models failed ShEx, all are logically consistent. Full main_report.txt
is below along with explanations.txt
for the failures:
main_report.txt
explanations.txt
You can find the five ShEx failing models in main_report.txt
by sorting the shex_valid
column. Here are model links for your convenience:
http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-9670095
http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-9708296
http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-1474151
http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-4615885
http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-2514859
I've gone through these and here is what I think. I should probably still tweak the models and not save to see if I am right. @dustine32 There are a couple cases below where I don't see why some Reacto entities aren't passing.
http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-9670095 Annotation to an obsolete term. This should be corrected? http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-9708296 Endoribonuclease activity input and output of REACTO_R-HSA-9708818 and REACTO_R-HSA-9708815 are not typed as chemical entities or complexes. Why? http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-1474151 oxidoreductase activity has input REACTO_R-HSA-9693721. This should be CHEBI:17804. Why isn't it? http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-4615885 RANBP2 SUMOylates CDCA8 (Borealin) and PIAS3 SUMOylates AURKB (Aurora-B). This is a black box reaction with two catalysts. I suspect this is what is causing the Shex failure. Both are mapped to SUMO transferase activity. MFs should only have one enabler. http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-2514859 glycine N-acyltransferase activity has an input of obo:go/shapes/ProteinContainingComplex, obo:go/shapes/InformationBiomacromolecule, but this reaction also has an input of Acyl-CoA. @vanaukenk, we might want to modify the Shex here and make the target proteins a primary input. These kinds of enzymes will have molecules other than the target protein/complex being modified.
Thank you @ukemi for testing and the feedback! Sorry for the delay in responding. This was quite the learning experience and my responses below went through several iterations of "ohhhh!" and then having to rewrite what's going on.
So, for our failing models:
term replaced by
(IAO:0100001
) annotation in the GO ontology, which is currently required by the conversion code. There two "consider" terms. To fix, should the conversion code be looking at these "consider" annotations or should the term get updated in the GO with the usual term replaced by
?reacto.owl
, these classes do not have any subClassOf
relationship to CHEBI or GO terms that ShEx could use to infer they are either a ChemicalEntity
or ProteinContainingComplex
. I wonder if there are other models that use sets w/o issue.CHEBI:17804
xref'd to its entityReference
(in the External Reference Information section). However, the conversion code currently doesn't look at xrefs from entityReference
elements on a SmallMolecule object and instead just uses its Reactome ID. Same with output sepiapterin and likely every other small molecule in Reactome GO-CAMs. We can open a ticket to change this behavior to always fetch the CHEBI if that is desired.reacto.owl
, R-HSA-9693721 only has subClassOf
continuant, which is not specific enough to be inferred as either InformationBiomacromolecule or ProteinContainingComplex.subClassOf continuant
in reacto.owl
.@dustine32 thanks for the follow up.
@dustine32 I just met with @deustp01 and he reminded me of some things we had done with other models. He will comment here, but in the meantime don't work on my suggestion to use ChEBI just yet.
@dustine32 and @deustp01 Having a night to think this over, I think we should adopt a strategy to use the ChEBI identifiers. Peter, after our conversation yesterday the realization struck me that when I use the model copy functionality all of the Reactome chemicals get copied over to my models. See http://noctua.geneontology.org/editor/graph/gomodel:633b013300001469? This means that I need to go in and clean up all my models where I've used model copy. Less than an ideal situation.
@dustine32 and @ukemi Still thinking here about the correct role for ChEBI identifiers in these models - needs more discussion.
On the five models that failed ShEX and OWL, it looks like all have straightforward, known errors in the Reactome annotation / BioPAX export that are easy enough to fix on the Reactome side so that, if such turned up at QA time in a future fast Reactome-to-GO-CAM export, we could make the fixes within the seven-day window that should be available. Here, I have fixed four already; the fifth requires strong-arming a curator. Detailed comments for each are interpolated into Dustin's comment on 10/14.
OK, great! Thanks @deustp01 @ukemi for summing up the actions. If we decide to switch to extracting CHEBI IDs we can work off of that new code change ticket.
@deustp01, should we move forward? @dustine32, during a weeds call last week, we decided that we should go ahead and try to import the ChEBI identifiers that are xref'd in Reactome. The main reason for this is consistency. Right now if I copy a model to make the mouse version, the Reactome entities come into my model. If I then make the model production, the Reactome entities end up on the Alliance view. This wouldn't be terrible if we could link them back to Reactome from there, but the group decided that it would be better if they linked to ChEBI because the ChEBI entities are the ones that are used by curators when they make de novo models. I will open a new ticket for this task. Meanwhile, I think the next thing to do is to sanity check the models that are on dev? and determine whether or not we can push the new load to production. Is everyone good with that?
Is everyone good with that?
I'm good with both (replace Reactome IDs for localized small molecules with ChEBI ID coupled if possible to GO CC term) and doing sanity checks on latest models before push to production.
@ukemi Yep, good with both as well. Let me know when/if you are good with the models in noctua-dev and I can make a PR with the new models to noctua-models/master
. This PR will then get merged/loaded to Noctua prod during the next Noctua maintenance outage (most likely 2022-11-10).
Models to check:
Notes for future work in release 83:
OK @dustine32, I checked the above four models as well as the ones that failed the Shex and didn't spot any glaring issues with the import. I made a couple of notes above just so that I can remember them. There are now only two tasks left in this ticket, both in your court:
@ukemi Great! I just found code specifically for the Venn diagram numbers in garage/Manuscript.java that I can revive.
@dustine32 I'm wondering where we stand on this release since @deustp01 might want to report on the status at tomorrow's PI meeting.
@ukemi @deustp01 I figured out the dang stats!!
First, here's the Venn diagram based on the latest GO-CAM load of Reactome 82 going into Noctua prod today:
Note this Venn diagram is created by a free web tool at https://bioinformatics.psb.ugent.be/webtools/Venn/.
The commands to generate the input for this diagram tool are now incorporated into the Reactome -> GO-CAM conversion pipeline (along with the ShEx checks).
Great! I will align with the published diagram.
Release 82 has been moved to the 'Done" column. Onward to 83.