Sentinel CDM

Category: Distributed health-data network CDM

The Sentinel Common Data Model standardizes health-data tables across participating data partners. Convert-Pheno reads exported Sentinel CDM tables; it does not query a live partner database. The tests use synthetic exports; data-partner conventions outside those fixtures may need further mapping work.

RoleInput

Accepted inputCSV/TSV tables, directory, or ZIP package

Main outputBFF, PXF, OMOP-CDM

ProcessingGrouped by PATID in memory

Data-partner tables are joined to DEMOGRAPHIC by PATID before target conversion

What You Need

Provide UTF-8 CSV or TSV table exports, either individually, in a directory, or inside one ZIP package. Gzip-compressed table files are also accepted. DEMOGRAPHIC is required.

Table group	Supported tables
person	DEMOGRAPHIC, DEATH
encounters and diagnoses	ENCOUNTER, DIAGNOSIS
procedures	PROCEDURE
laboratory and vital signs	LAB_RESULT, VITAL_SIGNS
medications	PRESCRIBING, DISPENSING, INPATIENT_PHARMACY

convert-pheno \
  -isentinel sentinel-export/ \
  -obff individuals.json

Use -opxf phenopackets.json for PXF, or -oomop --out-dir omop_out/ --ohdsi-db for OMOP-CDM tables. The clinical mapping is built in. For entity-aware BFF output, an optional compact Mapping V2 file can name the synthesized dataset and cohort.

What Is Converted

Sentinel content	Main BFF target
DEMOGRAPHIC, DEATH	individual identity, demographics, and vital status
DIAGNOSIS	diseases
PROCEDURE	interventionsOrProcedures
LAB_RESULT, VITAL_SIGNS	measures
medication tables	treatments
encounter links	private _visit context on mapped events

HISPANIC or another explicit ethnicity field can populate BFF ethnicity. RACE remains in source provenance because race and ethnicity are not treated as interchangeable concepts.

Terminology And Source Data

Recognized code systems are retained as CURIEs. Source-specific or ambiguous codes remain Sentinel: terms rather than receiving a guessed crosswalk. For OMOP output, use --term-audit terminology.xlsx to review OHDSI vocabulary resolution.

Raw rows are retained under info.sentinel by default. Use --no-source-info to omit them while retaining the converted fields.

Current Boundaries

Input is non-streaming and must fit in memory. Support follows the listed Sentinel tables and their standard columns; data-partner extensions require independent review.

For the field-level contract, see Sentinel CDM to BFF.