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Read epidemiology figures in report 12's Prevalence check - #150
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Renames BiochemicalMarker to ClinicalBiomarker and moves the field from Disposition/Serological Markers to Clinical Profile, so biopsy, imaging and physiological tests have a home alongside lab analytes. Adds markerType, markerSensitivity, markerSpecificity and loincCode, types the six T1D markers, and rebuilds twelve retired ARI#132 test findings as biomarkers on their diseases. Data model v4 spreadsheet and OWL updated; report 12's field list follows v4. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
claude/migrate-epidemiology-229 moved prevalence and incidence into EpidemiologyProfile figures and removed the flat fields, but build_research_gaps.py still looked for them, so a rebuild showed the 211 diseases with rates as text-only Partial. The check now counts a disease as Published when a figure linked by hasEpidemiologyProfile has an epiRatePer100k, keeping the ARI_PrevalenceDesc -> Partial fallback. Report 12 is regenerated: Prevalence 211 Published / 9 Partial / 7 Research; Clinical Biomarkers 11 Published. import_prevalence.py is marked superseded and exits, since its import was already migrated and re-running it would write undeclared properties. The reports README describes the figure shape instead of the old field names. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Report 12's Prevalence check still looked for the flat rate fields that
claude/migrate-epidemiology-229(#146) removed. A rebuild would have shown the 211 diseases with rates as text-only Partial. This PR fixes the check and regenerates the report.Changes
notebook/research-gaps/build_research_gaps.py: a disease is Published when at least oneEpidemiologyProfilelinked byhasEpidemiologyProfilehas anepiRatePer100k. The note lists the figure labels, e.g. "Prevalence · US · All". Text only inARI_PrevalenceDescstill counts as Partial.data/4-reports/12_Research_Gaps.xlsxregenerated:notebook/master-list-comparison/import_prevalence.pyis marked superseded and exits immediately. Its 2026-10-08 import has already been migrated into figures. Running it again would write properties the ontology no longer declares.data/4-reports/README.mddescribes that import in the past tense and explains the figure shape.changelog.mdentry added.Verification
python notebook/research-gaps/build_research_gaps.py: Summary counts as above.python .github/scripts/validate_mappings.py: 0 errors. The 5 warnings were there before this change.🤖 Generated with Claude Code