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Build an OMOP Common Data Model Extraction Pipeline for Public Sector Health Care

Municipal employers face escalating healthcare costs due to fragmented, non-standardized claims data. Construct an ETL transformation microservice using Python and DuckDB to extract unstructured clinical billing data and map them into standardized OMOP CDM tables with 98% schema mapping fidelity.

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What you are building

Construct a DuckDB and Python ETL transformation pipeline converting raw public sector health claims to OMOP CDM v5.4 standard.

How work is evaluated

Evaluation

Evaluates schema mapping fidelity and concept translation accuracy for OMOP CDM transformation.

Datasets

Public datasets, plus the private datasets you have access to.

How submissions are scored

Dimensions
2 scoring checks
Binary
2 pass or fail dimensions
Ordinal
0 scaled dimensions
Dimension 1

valid_concept_id_test

Ensures mapped concept ID is non-zero valid OMOP standard concept.

Binary check

This dimension contributes its full weight only when the submission satisfies the requirement. Partial credit is not awarded.

Dimension 2

mapping_accuracy

Accuracy of mapped procedure concept IDs. • target: 0.98 • range: 0-1

Binary check

This dimension contributes its full weight only when the submission satisfies the requirement. Partial credit is not awarded.

Learning goals

  • Design high-speed ETL workflows using DuckDB and PyArrow.

  • Map ICD-10-CM diagnosis codes and CPT procedure codes to OMOP Concept IDs.

  • Construct standardized OMOP `PERSON`, `DRUG_EXPOSURE`, and `PROCEDURE_OCCURRENCE` tables.

Resources

Dataset notes

Dataset of 5,000 raw municipal healthcare claim records with ICD-10 and CPT codes.

Challenge setup

Evaluates schema mapping fidelity and concept translation accuracy for OMOP CDM transformation.

Challenge input

JSON raw claim record

DuckDB

Fast in-process analytical SQL database engine.

OMOP CDM

Standardized observational medical outcome partnership data model.

Evaluated output

JSON compliant with OMOP PROCEDURE_OCCURRENCE standard table row

Evaluation checks
  • Ensures mapped concept ID is non-zero valid OMOP standard concept.
  • Accuracy of mapped procedure concept IDs. • target: 0.98 • range: 0-1
Configured evaluation evidence
  • Benchmark: OMOP-Bench
  • Mapping Accuracy target: 0.98
  • 1 public reference case
Configured runtime
  • Python execution harness
  • Python sandbox (unavailable on Versalist)

Shows the first task, up to three tools, and up to three evidence items.

View technical recipe

Configured tools

Action Space
  • Zed · Required
  • Aim · Optional
Policy Serving
  • Hunyuan · Optional

Evaluation contract

  • valid_concept_id_test · Weight 1
  • mapping_accuracy · Weight 1

Metrics

  • mapping_accuracy · Target 0.98

Benchmarks

  • OMOP-Bench
  • biotech

Reference cases

  • 1 public reference case

Workflow tasks

  1. Task 1

    Input: JSON raw claim record

    Output: JSON compliant with OMOP PROCEDURE_OCCURRENCE standard table row

    Execution harness: Python

Evaluation tools

  • DuckDB · database_engine
  • OMOP CDM · data_standard

Recipe freeze marker

No recipe freeze time is recorded.

Frequently Asked Questions about Build an OMOP Common Data Model Extraction Pipeline for Public Sector Health Care