New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Outage tasks for 2022-12-15 #807
Comments
@vanaukenk The report is completed |
I've checked over the diff and most of the updates are okay and consistent with the work in these two ontology tickets: However, we also have two automatic model updates in which a BP term is being replaced by an MF term, as a result of the work in this ticket: This update will result in either logically incorrect models or models with possibly incorrect biological information. For the Reactome model, presumably this will be corrected with the next Reactome import, but for the second, mouse model, I think an MGI curator will need to review the model after the update to fix it. I'm not sure how we should handle these types of replacements, i.e. MF for BP, in the future as they will likely result in similarly incorrect models. |
@vanaukenk I think you might be thinking more of the day-to-day but, not to sound like a broken record, this would be in the scope of geneontology/project-management#47. Theoretically, I assume that we'd go ahead with the breakages, but have fixing them be a high priority; larger changes would be shelved until there was enough resources to accomplish them. We would also be able to continuously run these checks against new versions of the ontology, so there would be more lead time and a way of testing changes. |
@kltm I'm actually thinking more about the consequence of replacing a term from one ontology with another, i.e. BP with MF, and whether we should do that in the ontology or whether these types of changes should instead make use of the 'consider' tag. |
@vanaukenk Is a main consequence under consideration that we'd be building up a body of "broken" (i.e. shex-illegal) models and what to do with them? Or is this purely a best practices for the ontology and how migrations operate? (If the latter, I'll hide this off-topic subthread.) |
@kltm and I talked about this. |
I shouldnt have replaced a BP by a MF, I'll change that |
Thanks @pgaudet |
I went in and removed the mouse annotations. |
See also: geneontology/go-ontology#24546 (comment) |
For Reactome see comment in #26546 |
http://skyhook.berkeleybop.org/noctua-models-migrations/reports/
master
replaced_by
term update on blazegraph (@vanaukenk)Update NEOontology build outages
The text was updated successfully, but these errors were encountered: