ICD11 Ingest #434
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ICD11 Ingest #434
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joeflack4
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joeflack4
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Mar 21, 2024
|
CC @souzadevinicius This PR handles most of the setup for integrating ICD11 with Mondo. You may want to review this to get an idea of how such a thing is handled. |
matentzn
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Mar 29, 2024
| @@ -163,6 +163,18 @@ $(COMPONENTSDIR)/icd10who.owl: $(TMPDIR)/icd10who_relevant_signature.txt | compo | |||
| remove -T config/properties.txt --select complement --select properties --trim true \ | |||
| annotate --ontology-iri $(URIBASE)/mondo/sources/icd10who.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/icd10who.owl -o $@; fi | |||
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| # TODO: complete | |||
| $(COMPONENTSDIR)/icd11foundation.owl: $(TMPDIR)/icd11foundation_relevant_signature.txt | component-download-icd11foundation.owl | |||
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This was referenced Mar 29, 2024
- Rename: ICD11 -> ICD11Foundation - Rename prefix: icd11 -> icd11.foundation - Add prefixes: icd11.schema, icd11.z - Add: intensional exclusions TSV (currently empty) - Add: SPARQL query for selecting all diseases
- Update: mondo-ingest-odk.yaml: New entry for ICD11 in 'components' - Updates from running 'make update_repo': - modified: docs/odk-workflows/ManageDocumentation.md - modified: docs/odk-workflows/RepositoryFileStructure.md - modified: src/ontology/Makefile - modified: src/ontology/run.sh - new file: src/scripts/run-command.sh - modified: src/scripts/update_repo.sh - Add: metadata/icd11.yml - Update: prefixes.csv
This was referenced Apr 3, 2024
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- Update: mondo-ingest.Makefile - Add: $(COMPONENTSDIR)/icd11.owl - Add: config/icd11foundation-property-map.sssom.tsv - Update: ICD11 docs - Update: config/properties.txt - Update: config/context.json - Update: metadata/mondo.sssom.config.yml: added icd11.foundation to subject_prefixes - Update: lexmatch-sssom-compare.py: entry for icd11 - Update: add-new-source.md: Instructions for additional configuration necessities. General - Bugfix: Slurp files were sometimes getting removed because they were considered intermediates and not .PRECIOUS. - Bugfix: reports/*_exclusion_reasons.robot.template.tsv files were getting removed by the build for same reason as above.
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joeflack4
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May 12, 2024
| @@ -476,6 +488,7 @@ slurp/%.tsv: $(COMPONENTSDIR)/%.owl $(TMPDIR)/mondo.sssom.tsv $(REPORTDIR)/%_map | |||
| --mondo-terms-path $(REPORTDIR)/mirror_signature-mondo.tsv \ | |||
| --slurp-dir-path slurp/ \ | |||
| --outpath $@ | |||
| .PRECIOUS: slurp/%.tsv | |||
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More rm issues
-
rm reports/icd11foundation_exclusion_reasons.robot.template.tsv slurp/icd11foundation.tsv -
imports/ro_terms_combined.txtBug fix?:rm imports/ro_terms_combined.txt#477
I checked the build log from last week, and at the end it showed rm reports/icd11foundation_exclusion_reasons.robot.template.tsv slurp/icd11foundation.tsv imports/ro_terms_combined.txt. After adding that 1 .PRECIOUS, now the slurp file is no longer being removed, but the other two still are: rm reports/icd11foundation_exclusion_reasons.robot.template.tsv imports/ro_terms_combined.txt. I think we want these, so I'm going to apply the same fix for both of those as well. I pasted more of the log from build-mondo-ingest below just in case it's of any value.
Log related to (3)
I have the full logs saved as .txt files also if interested
From the build last week:
Release files are now in ../.. - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab
rm reports/icd11foundation_exclusion_reasons.robot.template.tsv slurp/icd11foundation.tsv imports/ro_terms_combined.txt
make[1]: Leaving directory '/work/src/ontology'
Mondo Ingest has been fully completed
From the build today:
Release files are now in ../.. - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab
rm reports/icd11foundation_exclusion_reasons.robot.template.tsv imports/ro_terms_combined.txt
make[1]: Leaving directory '/work/src/ontology'
Mondo Ingest has been fully completed
I've followed up on these two remaining issues here:
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Partially addresses:
Overview
Adds source ICD11 to Mondo.
This will be deemed a success if
build-mondo-ingestis run and ICD11 artefacts are present and look good (e.g. lexmatch with >1k rows).Updates
Pre-merge checklist
docs/have been added/updated ORsh run.sh make build-mondo-ingesthas been run on this branch (after `docker pull obolibrary/odkfull:dev), and no errors occurred OR ICD11 Ingest - Data #471Primary sub-tasks