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Export From Atlas

Before importing into Parthenon, you need to export your Atlas artefacts. All Atlas exports use standard OHDSI JSON formats that Parthenon accepts directly.

2.1 Exporting Cohort Definitions​

Via the Atlas UI (per cohort)​

  1. Open Atlas and navigate to Cohort Definitions.
  2. Open any cohort definition.
  3. Click Export (the download icon in the top-right toolbar).
  4. Select JSON format and save the file.

The exported JSON has the format:

{
  "name": "T2DM New Users",
  "description": "...",
  "expression": { ... }
}

Via the Atlas UI (bulk)​

Atlas does not have a native bulk export button, but you can export all cohort definitions programmatically using the WebAPI:

# Export all cohort definitions from Atlas WebAPI
ATLAS_URL="https://atlas.yourorg.net/WebAPI"
mkdir -p atlas-exports/cohorts

# Get list of all cohort IDs
curl -s "${ATLAS_URL}/cohortdefinition/" | jq -r '.[].id' | while read id; do
  name=$(curl -s "${ATLAS_URL}/cohortdefinition/${id}" | jq -r '.name' | tr '/ ' '--')
  echo "Exporting cohort ${id}: ${name}"
  curl -s "${ATLAS_URL}/cohortdefinition/${id}" \
    > "atlas-exports/cohorts/${id}-${name}.json"
done

echo "Exported $(ls atlas-exports/cohorts/ | wc -l) cohort definitions"

If your WebAPI requires authentication, add -H "Authorization: Bearer YOUR_TOKEN" to each curl command.

2.2 Exporting Concept Sets​

Via the Atlas UI (per concept set)​

  1. Navigate to Concept Sets in Atlas.
  2. Open a concept set.
  3. Click Export --> JSON.

Via the WebAPI (bulk)​

mkdir -p atlas-exports/concept-sets

curl -s "${ATLAS_URL}/conceptset/" | jq -r '.[].id' | while read id; do
  name=$(curl -s "${ATLAS_URL}/conceptset/${id}" | jq -r '.name' | tr '/ ' '--')
  echo "Exporting concept set ${id}: ${name}"
  curl -s "${ATLAS_URL}/conceptset/${id}/expression" \
    | jq --arg name "$(curl -s "${ATLAS_URL}/conceptset/${id}" | jq -r '.name')" \
         '{name: $name, expression: .}' \
    > "atlas-exports/concept-sets/${id}-${name}.json"
done

echo "Exported $(ls atlas-exports/concept-sets/ | wc -l) concept sets"

2.3 Exporting IR and Characterization Analysis Definitions​

Atlas stores incidence rate and characterization analysis definitions in its application database. Export them via WebAPI:

mkdir -p atlas-exports/analyses

# Incidence rate analyses
curl -s "${ATLAS_URL}/ir/" > atlas-exports/analyses/incidence-rates.json

# Characterization analyses
curl -s "${ATLAS_URL}/cohortcharacterization/" > atlas-exports/analyses/characterizations.json
note

Parthenon does not currently import these analysis definitions automatically. Export them for reference --- you will recreate them manually using the imported cohorts as inputs. The analysis definition format is simpler in Parthenon's UI, and Parthenon supports additional analysis types (SCCS, Evidence Synthesis, PLE, PLP) that can be configured during recreation.

2.4 Recording Your WebAPI Source Configuration​

The WebAPI source configuration (which CDM schema, vocabulary schema, and results schema your Atlas instance connects to) is needed to set up the matching Parthenon Data Source.

Export it:

curl -s "${ATLAS_URL}/source/sources" > atlas-exports/sources.json
cat atlas-exports/sources.json | jq '.[] | {sourceKey, sourceName, daimons: .daimons}'

Save the source keys and schema names. You will need these in Chapter 3.

File Organization​

After export, your directory should look like:

atlas-exports/
  cohorts/
    1-T2DM-New-Users.json
    2-GI-Hemorrhage.json
    ...
  concept-sets/
    1-Type-2-Diabetes.json
    2-Metformin.json
    ...
  analyses/
    incidence-rates.json
    characterizations.json
  sources.json

Keep this export directory --- it serves as a backup of your Atlas configuration.