dalmeidaayite-dev/pan-african-ehr-omop-etl

ETL pipeline and data quality framework for standardizing multilingual Pan-African EHR medication data into the OMOP CDM v5.4 # pan-african-ehr-omop Review, cleaning, and OHDSI OMOP CDM standardization of a multi-country Pan-African EHR medication extract (10,000 rows · 10 countries · 13 unique raw drug strings). ## Source data `data/raw/pan_african_ehr_10000.csv` - `patient_id`, `country_code` (AGO CIV EGY ETH KEN MOZ NGA RWA SEN ZAF), `facility_code` - `raw_med_string` — free text in English, French, Portuguese, Arabic, Amharic, Swahili - `sync_date` — contains `1970-01-01` Unix-epoch artifacts (= missing date) ## Pipeline 1. **Review & profiling** — pandas / OHDSI White Rabbit scan report 2. **Cleaning** — epoch dates → `NaT`, typo fix (`uknown ARVs`), duplicate key audit 3. **Vocabulary mapping** — Usagi source-to-concept mapping (RxNorm / ATC) 4. **ETL to OMOP CDM v5.4** — `PERSON`, `OBSERVATION_PERIOD`, `CARE_SITE`, `LOCATION`, `DRUG_EXPOSURE` 5. **DQA** — OHDSI DataQualityDashboard + Achilles ## Core mapping dictionary (v0.1) | raw_med_string | Meaning | Target | |---|---|---| | TLD 300/300/50 | Tenofovir/Lamivudine/Dolutegravir | RxNorm combo | | RHZE phase intensive | Rifampicin/Isoniazid/Pyrazinamide/Ethambutol | RxNorm combo | | CTX prophylaxis | Cotrimoxazole | RxNorm | | SP pour CIP | Sulfadoxine/Pyrimethamine | RxNorm | | Coartem tabs | Artemether/Lumefantrine | RxNorm | | Artesunato IV | Artesunate injectable | RxNorm | | paracétamol 500 / حبوب الباراسيتامول 500 | Paracetamol 500 mg | RxNorm (Acetaminophen) | | amoxicilline 500mg gélule | Amoxicillin 500 mg capsule | RxNorm | | xarope de tosse / dawa ya kikohozi | Cough medicine | ATC class (R05) | | የወባ መድሀኒት | "Malaria medicine" (Amharic) | ATC class (P01) | | uknown ARVs | Unspecified antiretrovirals | ATC class (J05) | ## Rules - `sync_date == 1970-01-01` → treated as **missing**, never loaded as a real exposure date - Raw strings always preserved in `drug_source_value` (full traceability) ## License Apache-2.0