Draft 1: Update confirmed subclass of evidence in Mondo (#7801)

* Create first draft of subclass sync

This workflow implements our subclass syncining strategy:

1. First, we drop all axiom annotations related to the resources we sync with
2. We add them back

* Update the subclassOf evidence in Mondo

* Add DOID, NCIT, OMIM and ORDO evidence to subclass axioms

* Update .github/workflows/subclass.yaml

Co-authored-by: Trish Whetzel <[email protected]>

* Update src/ontology/mondo.Makefile

Co-authored-by: Trish Whetzel <[email protected]>

---------

Co-authored-by: Trish Whetzel <[email protected]>

.github/workflows/subclass.yaml

@@ -0,0 +1,40 @@
+name: Update Subclass Evidence
+
+on:
+#  schedule:
+#    - cron: '0 14 * * 1'
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5.2
+
+    steps:
+      - name: Checkout main branch
+        uses: actions/checkout@v3
+
+      - name: Update Subclass evidence
+        run: |
+          cd src/ontology
+          make GITHUB_ACTION=true IMP=false PAT=false update-subclass-sync -B
+    
+        # This is important if we are out of sync between Mondo and Mondo Ingest:
+        # We need to eventually add a check to ensure that no subclass axioms have been added or removed
+        # We should consider to create a seperate curation workflows with a table with previously supported and now not anymore supported subclass axioms
+      - name: QC to ensure that nothing other than provenance has changed
+        run: |
+          cd src/ontology
+          make GITHUB_ACTION=true IMP=false PAT=false qc -B
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v5
+        with:
+          branch-suffix: short-commit-hash
+          labels: Automated
+          body: "Update the confirmed subclass axiom annotation."
+          title: "Weekly automated mappings update"
+          base: ${{ github.head_ref }}
+          branch: "mapping_automation"
+          token: ${{ secrets.GH_TOKEN }}
+          reviewers: "sabrinatoro"