Uberon integration #6
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Uberon integration | |
| on: | |
| # Manual triggering only | |
| workflow_dispatch: | |
| jobs: | |
| uberon_integration: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5 | |
| steps: | |
| - name: Checkout current FBbt | |
| uses: actions/checkout@v4 | |
| with: | |
| path: fbbt | |
| - name: Checkout current Uberon | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: obophenotype/uberon | |
| path: uberon | |
| - name: Checkout current CL | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: obophenotype/cell-ontology | |
| path: cl | |
| - name: Build FBbt | |
| run: | | |
| cd fbbt/src/ontology | |
| make fbbt.owl ../mappings/fbbt.sssom.tsv MIR=false IMP=false PAT=false | |
| - name: Build Uberon | |
| run: | | |
| cd uberon/src/ontology | |
| make uberon.owl MIR=false IMP=false PAT=false BRI=false GH_ACTION=true | |
| - name: Build CL | |
| run: | | |
| cd cl/src/ontology | |
| make cl.owl MIR=false IMP=false PAT=false | |
| - name: Merge all ontologies together | |
| env: | |
| ROBOT_PLUGINS_DIRECTORY: uberon/src/ontology/tmp/plugins | |
| run: | | |
| robot merge -i fbbt/src/ontology/fbbt.owl \ | |
| -i uberon/src/ontology/uberon.owl \ | |
| -i cl/src/ontology/cl.owl \ | |
| sssom:inject --sssom fbbt/src/mappings/fbbt.sssom.tsv \ | |
| --ruleset fbbt/src/scripts/bridging.rules \ | |
| annotate --ontology-iri http://purl.obolibrary.org/obo/fbbt/fbbt-uberon-cl-merge.owl \ | |
| --output fbbt-uberon-cl-merge.owl \ | |
| reason --reasoner ELK | tee merge.log | |
| - name: Upload merged ontology | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: merged-ontology | |
| path: fbbt-uberon-cl-merge.owl | |
| - name: Check and explain unsats | |
| run: | | |
| if grep -q unsat merge.log ; then | |
| robot explain -i fbbt-uberon-cl-merge.owl \ | |
| --reasoner ELK \ | |
| --mode unsatisfiability \ | |
| --unsatisfiable all \ | |
| --explanation unsats.md | |
| exit 1 | |
| fi | |
| - name: Upload explanations | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: explanations | |
| path: unsats.md |