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Move prevalence and incidence rates into figures (#229) - #146
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The editor reads prevalence and incidence as EpidemiologyProfile figures since KrishnaTO/ARI-metadata-manager#236, so every disease showed no figures while the ontology still held the twelve flat rate/year/source fields. Ran the app's scripts/migrate_epidemiology.py: 371 figures on 211 diseases, one per flat rate, with a change-log line on each disease. The flat properties and their declarations are removed. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
This was referenced Oct 16, 2026
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Since KrishnaTO/ARI-metadata-manager#236 (for KrishnaTO/ARI-metadata-manager#229), the editor reads prevalence and incidence as
EpidemiologyProfilefigures. This ontology still held the twelve flat fields, so the editor showed "No prevalence or incidence figures yet." for every disease. This PR is the data migration that #236 needs.What changed
scripts/migrate_epidemiology.pyonontologies/ari_t1d.owl. Each flat rate became one figure linked byhasEpidemiologyProfile, holding the measure, the region, sex "All", the rate, and the year and sources that sat beside the rate.prevalenceValue(estimated US cases) stays on the disease.ARI_ChangeLogline listing the rates it moved.Checked
OntologyService. Every disease'sget_disease_detail()["epidemiology"]gives the counts above, and Type 1 diabetes shows 299.9 (US) and 150.0 (worldwide) /100k, the same as the old fields.*Per100k/*Year/*Sourceproperty elements are left. The old names appear only as text in earlier change-log entries.python .github/scripts/validate_mappings.py --since origin/main: 0 errors, 0 warnings.Not in this PR
notebook/master-list-comparison/import_prevalence.py,notebook/research-gaps/build_research_gaps.pyanddata/4-reports/README.mdstill use the flat property names. Ifimport_prevalence.pyis re-run unchanged, it writes fields the editor no longer reads. They need a follow-up.🤖 Generated with Claude Code