Add two new annotation extension relations to gpad-extensions.rq

[vanaukenk]

@balhoff

Please add these two new annotation extension relations from RO to the gpad-extensions.rq file so we can start exporting them from GO-CAM models. Thx.

http://purl.obolibrary.org/obo/RO_0002490 http://purl.obolibrary.org/obo/RO_0002491

@suzialeksander @ukemi @dustine32

[balhoff]

@vanaukenk this is on the dev branch now. Want to test there first?

[kltm]

If merged on dev, I would recommend putting this up during the outage tomorrow (or sooner--I'll be out Friday).

[vanaukenk]

@balhoff - sure, we can test on dev. Would that involved looking at the Annotation Preview and GPAD export? Or something else?

I have a test model here: http://noctua-dev.berkeleybop.org/editor/graph/gomodel:6112f4bf00000119

Note that this model URI above no longer returns anything with searches in noctua-dev :-(

[kltm]

I've restarted with the new code (but not rebuilt the triplestore).

[balhoff]

@vanaukenk I think your test model may need a matching PMID added on the existence overlaps edge.

[ukemi]

MGI has annotation using RO_0002491.

[ukemi]

MGI:MGI:97621 |   | RO:0001025 | GO:0000775 | MGI:MGI:5882483|PMID:26919979 | ECO:0000314 |   |   | 2021-06-02 | MGI | RO:0002491(GO:0000236)|RO:0002491(GO:0000278) | creation-date=2020-05-05|modification-

[dustine32]

This could be a gocamgen bug in the translation code. I'll debug using your example @ukemi.

[ukemi]

There are several annotations in the MGI GPAD file that use RO:0002491 in annotation extensions.

[dustine32]

Ah, the relation "existence starts and ends during" isn't in the current noctua-dev MGI models because they were generated before @vanaukenk's relations.py change was merged.

I did a quick before-and-after test generating the MGI:MGI:97621 model with the latest ontobio vs the version used on 2021-08-09. The current ontobio emits the relation while the older code does not. So, this will be fixed when I regenerate the MGI models tomorrow.

[ukemi]

I still don't see these in the new file that Dustin released.

[ukemi]

My bad! I was looking for the RO identifers:

MGI MGI:88311 located_in GO:0005737 PMID:23541922 ECO:0000314 20200429 MGI existence_overlaps(GO:0051331) model-state=production|contributor=https://orcid.org/0000-0002-9796-7693|noctua-model-id=gomodel:5e72450500002902

This one is ready to go to production.

[vanaukenk]

@ukemi I think we are okay to close this ticket, right? The extensions are visible in the GPAD output.

Just noting here that there is a separate issue with display of life stage terms in the Noctua form table that has to do with root types of life stages. https://github.com/geneontology/minerva/issues/428

[ukemi]

Is it in production? I haven't been closing them until the changes go to production. I have a column for that in the MGI imports project.

[ukemi]

I fear that if we close them without making sure they went over the fence, we may miss some. Maybe it's not a valid fear.

[vanaukenk]

No, you're right. I thought this had gone into production, but it's not there yet. I'll check with @kltm about our scheduling options here.

[ukemi]

Maybe an obvious question, but maybe not obvious. Who's responsibility is it to close the ticket in the end? Do we want to check it in production one last time or should whoever throws the production switch close the ticket and move it along in the projects?

[kltm]

We can do an minerva update any time there is an outage for production. As long as minerva dev and minerva master and API-compatible, it is just a "quick" PR and restart.