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Set the source of subclass sync to a merged version of edit and owl #607

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@matentzn matentzn commented Jul 5, 2024

I had a dream last night that this might not be necessary because of the way that semsql works. I dont know exactly what semsql does though, and now that Chris is gone it may be not possible to find out.

Here my dream:

  1. semsql is using relationgraph under the hood (that is a fact)
  2. RG may, all by itself, remove the red subclass axiom in the figure below, rendering the change in this PR ineffectual
image

In my view, nothing bad will come of this change, but we need to check manually, later down the line, if subclass assertions in mondo-edit.owl do not get support, even though it exists. We can stem that in a second round I think

Overview

This PR:

  • Changes the source of the subclass sync Mondo DB to a version that contains both the release and edit file axioms
  • This was discussed and agreed in the last tech call

Pre-merge checklist

Documentation

Was the documentation added/updated under docs/?

  • Yes
  • No, updates to the docs were not necessary after careful consideration

QC

Was the full pipeline run before submitting this PR using sh run.sh make build-mondo-ingest on this branch (after
docker pull obolibrary/odkfull:dev), and no errors occurred?

  • Yes
  • No, there are no functional (code-related) changes to the pipeline in the PR, so no re-run is necessary

New Packages

Were any new Python packages added?

Were any other non-Python packages added?

PR Review and Conversations Resolved

Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?

  • Yes
  • No

matentzn added 4 commits June 14, 2024 16:50
To avoid the case that we include non-redundant subclass of links in Mondo, we mondo-edit needs to be the source for subclass sync, not mondo.owl. Here the source is swapped.
@matentzn matentzn marked this pull request as draft July 8, 2024 08:48
@joeflack4 joeflack4 added the enhancement New feature or request label Jul 8, 2024
@twhetzel twhetzel changed the base branch from main to develop November 27, 2024 17:48
- Handled merge conflicts in mondo-ingest.Makefile
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3 participants