Add source adapter layer for IBM MarketScan, IBM LCED, and CPRD GOLD#235
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xushenbo wants to merge 2 commits into
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Add source adapter layer for IBM MarketScan, IBM LCED, and CPRD GOLD#235xushenbo wants to merge 2 commits into
xushenbo wants to merge 2 commits into
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- Three ETL adapters (marketscan, lced, cprd) producing canonical tables
- Vocabulary loaders: NDC, RxNorm, LOINC, Read code, prodcode, ICD GEM/CCS stubs
- to_ehrdata() bridge converting canonical tables to EHRData
- 327 tests across all modules
- Reference docs: docs/sources/{marketscan,lced,cprd}.md
- Tutorial notebooks: CPRD overview, LOINC mapping, ICD mapping, LCED cohort
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Summary
This PR migrates three EHR ETL pipelines into a new
ehrdata.io.sourcePython layer, providing a unified adapter interface for IBM MarketScan, IBM LCED, and CPRD GOLD.New modules
ehrdata.io.source.adapters.marketscan— US commercial claims (diagnosis, therapy, procedure, patinfo, insurance, provider)ehrdata.io.source.adapters.lced— IBM LCED linked claims-EMR data (diagnosis, therapy, lab test, habit, patinfo)ehrdata.io.source.adapters.cprd— CPRD GOLD UK primary-care data (diagnosis, therapy, lab test, patinfo); supports Read code and prodcode vocabulary translationehrdata.io.source.vocab— vocabulary loaders for NDC→ingredient, RxNorm→ingredient, LOINC, Read code (medcode→readcode), and prodcode mappingsehrdata.io.source.to_ehrdata— bridge that converts any combination of canonical source tables into anEHRDataobjectDocumentation
docs/sources/docs/tutorials/: CPRD overview and EDA, LOINC mapping, ICD version inference and mapping, LCED T2D cohort studyTests
327 new tests covering all adapters, vocab loaders, normalisation utilities, and the
to_ehrdatabridge.Test plan
pytest tests/io/test_source_*.py— 327 tests, all passinghatch run docs:build— docs build cleanly