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Pipeline currently mis-maps IEAs around GOlr, likely related to owltools or its environment #251
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GOlr build step runs with> java \
-Xms$LOADER_MEM \
-Xmx$LOADER_MEM \
-DentityExpansionLimit=8172000 \
-Djava.awt.headless=true \
-jar /srv/amigo/java/lib/owltools-runner-all.jar \
$ONTOLOGIES \
--log-info \
--solr-config /srv/amigo/metadata/ont-config.yaml \
--merge-support-ontologies \
--merge-imports-closure \
--remove-subset-entities upperlevel \
--remove-disjoints \
--silence-elk \
--reasoner elk \
--solr-taxon-subset-name amigo_grouping_subset \
--solr-eco-subset-name go_groupings \
--solr-url http://localhost:8080/solr/ \
--solr-log /tmp/golr_timestamp.log \
--solr-load-ontology \
--solr-load-ontology-general \
--read-panther /tmp/panther_data/ \
--solr-load-gafs $GAFS \
--solr-load-panther \
--solr-load-panther-general \
--solr-optimize The only explicit ECO reference is |
Noting: IEA ECO:0000501 switched to ECO:0007669 |
Raw access to "IEA" annotations in production AmiGO: |
Getting a little more cute with AmiGO, we can see that the annotations are more or less there:
|
…co tests; add some testing for IEAs; attempting clarifying work on work on geneontology/pipeline#251
Attempt at quick recreation of possible issue, after doing some small updates of owltools ECO tests (see owlcollab/owltools#321); unfortunately, testing cleanly with fixes: I'm having a little trouble figuring out where to go next. Maybe need to dig in more around the GAF document loader? |
Noting that the far upstream origin of this issue is likely evidenceontology/evidenceontology#251 |
…etClassesForGoCode; work on geneontology/pipeline#251
I can now hit a problem spot with: Appearing in the GOlr loader here: |
@cmungall @balhoff, with the context right above here (#251 (comment)), I was wondering if you could easily spot what might be going wrong? I can start working through getClassesForGoCode, I could also switch to using getClassesForCode, which seems to be giving results that are more inline with what is expected (unsure why these choices were made). Any thoughts here? |
@balhoff @cmungall To resummarize where I'm at:
With that, my questions are, in order of utility towards fixing this:
|
Talking with @pgaudet @mgiglio99 et al. this morning, the current plan is to: have eco / mapping for IEA to revert to its previous state for the time being, get a release out, and continue to move forward on finding a fix with an eye for the next release out. |
I believe we've cleared other issues blocking the pipeline and am restarting the |
I'm assuming this is closed for now. |
There are 128276 more annotations on release than were on the candidate. Looking at AmiGO, it seems like "evidence used in automatic assertion" (ECO:0000501) has entirely disappeared. Strangely, a very small numberof IEA annotations did manage to find their way in:
https://amigo-staging.geneontology.io/amigo/search/annotation?q=IEA*&fq=-evidence_subset_closure_label:%22genetic%20interaction%20evidence%20used%20in%20manual%20assertion%22&fq=-evidence_subset_closure_label:%22biological%20aspect%20of%20ancestor%20evidence%20used%20in%20manual%20assertion%22&sfq=document_category:%22annotation%22
That's weird.
I'm putting a pin in that for now.
That leaves us with two paths for data to be dropped, assuming that we are at issue and not upstream: ontobio and owltools.
Checking around for a data set let's arbitrarily select the MGI GAF as an example, specifically the IEAs:
snapshot | release
src: 73326 | 73829
valid: 73318 | 73821
So, that is a small change in the src/valid numbers. In AmiGO, filtering for just species "mouse" annotations, there are actually /more/ in the snapshot...so hm.
My guess for the moment is that there is something going on in either owltools or the docker mechanism around it (possibly cached old files) that is causing a problem here. I'll do a bit more digging to try and get at what's going on.
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