odiop88/omop-covid19-iressef: v1.0.0 — ETL Materials for OMOP CDM Standardization of COVID-19 Surveillance Data from Senegal
Domain:
healthcareRecord type:
OMOP CDM COVID-19 ETL Materials — First Public Release
This is the first public release of all Extract–Transform–Load (ETL) materials used to standardize a multi-source COVID-19 surveillance dataset from Senegal into the OMOP Common Data Model version 5.4.
Associated publication: Diop O, Odhiambo R, Momanyi R, Ochola M, Diouf O, Diallo AS, et al. Standardizing multi-source COVID-19 surveillance data into the OMOP Common Data Model: a first implementation case study from Senegal. PLOS ONE. 2026. (submitted)
Contents
This release includes the complete set of reproducible ETL artifacts:
| Folder | Content |
|---|---|
| 1. Scan report/ | WhiteRabbit automated profiling of the source COVID-19 surveillance flat file |
| 2. Source Code list/ | Source variable codebook with French-language labels, categories, and value dictionaries |
| 3. Usagi concept code list/ | Usagi semi-automated concept mapping outputs (SNOMED CT, LOINC, RxNorm mappings with match scores) |
| 4. Mapping/ | Rabbit-in-a-Hat mapping specifications documenting source-to-OMOP CDM v5.4 table and field-level mappings |
| 5. SQL scripts/ | SQL transformation and loading scripts for populating OMOP CDM tables in PostgreSQL |
| 6. DQD/ | OHDSI Data Quality Dashboard v2.6.1 assessment results (97% overall pass rate, 98% corrected) |
| 7. Atlas/ | ATLAS cohort characterization outputs (demographics, symptom prevalence, drug exposures, mortality) |
Key figures
- 13,090 individuals standardized into the OMOP Person table
- 13,403 RT-PCR measurement records
- 22,025 condition and observation records
- 52 death records
- 97% DQD overall pass rate (98% corrected)
Source data
The source surveillance dataset cannot be included in this release due to ethical and legal restrictions (Loi n° 2008-12 du 25 janvier 2008, Senegal; CNERS approval). Access requests from qualified researchers may be directed to: ousmane.diop@iressef.org.
How to cite
Diop O, Odhiambo R, Momanyi R, Ochola M, Diouf O, Diallo AS, et al. OMOP CDM Standardization of COVID-19 Surveillance Data from Senegal — ETL Materials and Scripts (v1.0.0). Zenodo. 2026. doi.org
License
MIT License — see LICENSE for details.