Atlas to Parthenon Migration Guide
This guide helps informatics teams migrate an institution from a running OHDSI Atlas + WebAPI installation to Parthenon. The process is designed to be low-risk and fully reversible: you can run both systems in parallel until validation is complete, then cut over at a scheduled time.
What Transfers Automatically
| Artefact | How it migrates |
|---|---|
| Cohort definitions | CLI import or UI bulk upload from Atlas JSON exports |
| Concept sets | CLI import or UI bulk upload from Atlas JSON exports |
| Data source connections | CLI import from live WebAPI instance |
| Vocabulary | Shared --- Parthenon connects to the same CDM/vocab schema as Atlas |
| Achilles results | Shared --- Parthenon reads the same results schema |
What Requires Manual Work
| Artefact | Notes |
|---|---|
| User accounts | Must be recreated in Parthenon (bulk CSV import supported) |
| Analysis results (IR, characterization) | Re-run analyses after import |
| Atlas bookmarks / saved searches | Not migrated; document and recreate in Parthenon |
| Custom Atlas plugins / visualisations | Evaluate Parthenon equivalent features |
New Capabilities After Migration
After migrating to Parthenon, your team gains access to capabilities that have no Atlas equivalent:
- Genomics --- VCF upload, ClinVar annotation, variant browsing, tumor board, genomic cohort criteria
- Imaging --- DICOM study browser, built-in Cornerstone3D viewer, imaging cohort criteria, population analytics
- HEOR --- Cost-effectiveness analysis, budget impact modeling, care gap identification, payer contract simulation
- FHIR EHR Integration --- Connect to Epic, Cerner, and other FHIR R4 servers for automated data sync
- AI-Powered Search --- Natural language concept search, contextual help, clinical text summarization
- Expanded Analyses --- SCCS, Evidence Synthesis, PLE and PLP configuration UIs with R/HADES execution
See Chapter 6 --- Feature Comparison for the complete feature-by-feature mapping.
Estimated Timeline
| Activity | Typical duration |
|---|---|
| Parthenon instance setup | 1--2 days (use the Python installer) |
| Atlas export | 1--4 hours |
| Import and validation | 1--2 days |
| User onboarding | 1 week (staggered) |
| Parallel operation period | 2--4 weeks |
| Atlas decommission | 1 day |
Prerequisites
Before starting migration:
- Parthenon is running and accessible at its production URL.
- CDM source is connected --- at least one Source with CDM, Vocabulary, and Results daimons configured.
- Atlas is accessible --- you have admin access to the Atlas instance and know its WebAPI URL.
- PHP CLI access --- you can run
php artisancommands inside the Parthenon container or on the host.
See Chapter 1 --- Before You Begin for the full prerequisite checklist.