Documentation

Documentation for the engineers who run Clinical Extract.

Clinical Extract is one container in your environment, installed by our engineers. It authorizes with a signed JWT, runs one Group export for the study cohort, downloads the NDJSON files and writes study.csv and its data dictionary. The three pages below cover deployment, the output files and EHR registration.

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1 The pages

Documentation pages.

  1. Deployment in your environment: We install one container on your compute, built from the release source with the Dockerfile; the settings, the key store, the network, the storage and the log.
  2. Output format: study.csv, data-dictionary.json and the manifest the EHR returned: the rules for every file and field.
  3. EHR registration: Registering the backend app with your EHR vendor once: the app type, the JWKS, the scopes, the Group; then each vendor’s own terms.

2 In brief

What is already built.

Authorization
SMART Backend Services: an RS384-signed JWT for a token with system/<Resource>.read scopes, the private key in your key store, the public key at the JWKS URL the container serves.
The export
Group/{id}/$export with _type, status polling with Retry-After, NDJSON downloads with the bearer token, retries on a failed file, and the status URL deleted after.
The output
study.csv (one row per patient, one column per approved variable), data-dictionary.json (description, fhirSource, example per column) and the manifest as the EHR returned it.
The connections
One backend app registration per EHR; Epic, Oracle Health, eClinicalWorks, athenahealth, MEDITECH, NextGen and Veradigm in their own terms on the EHR pages.
The tools
The cohort builder (criteria to a Group, with counts), roster pull (a patient list to graded matches), the oncology lens (biomarkers and staging as columns).
Operations
Health at /healthz, version at /api/version, a size-rotated server log with each run step and JWKS fetch.

Every header and manifest field, in the bulk export guide

Next

See Clinical Extract run on one of your studies.

Tell us which EHR you run and what the study or registry needs. We reply within one business day to set a meeting time.

Request a demo