Feature Comparison Reference

This table maps every major Atlas feature to its Parthenon equivalent, noting current status and any workflow differences. Parthenon extends well beyond Atlas with modules for Genomics, Imaging, HEOR, and FHIR EHR integration that have no Atlas counterpart.

Vocabulary

Atlas Feature	Parthenon Equivalent	Status	Notes
Concept Search	Vocabulary --> Browse Concepts	✅ Full Parity	Full-text + synonym search, AI-powered concept suggestions
Concept Detail (ancestors, descendants)	Concept detail panel	✅ Full Parity
Concept Set Builder	Vocabulary --> Concept Sets --> New	✅ Full Parity	Same flags: descendants, mapped, excluded
Concept Set Import/Export	JSON import/export + CLI	✅ Full Parity	Compatible JSON format
Vocabulary version display	Data Explorer --> Overview	✅ Full Parity
Vocabulary Refresh	Admin --> Vocabulary Management	✅ Implemented	Upload Athena ZIP via admin UI; no manual DB operations needed

Cohort Definitions

Atlas Feature	Parthenon Equivalent	Status	Notes
Cohort Builder UI	Cohorts --> New Cohort Definition	✅ Full Parity	Same CIRCE expression model
Primary event (all domains)	Index Event tab	✅ Full Parity
Inclusion rules	Inclusion Rules tab	✅ Full Parity
Cohort exit strategies	Cohort Exit tab	✅ Full Parity
Cohort generation	Generate button	✅ Full Parity	Async via Horizon queue
Attrition report	Attrition tab post-generation	✅ Full Parity
Cohort overlap report	Cohorts --> Compare	✅ Full Parity
Cohort import/export (JSON)	Import / Export buttons + CLI	✅ Full Parity
Cohort copy/clone	Clone button	✅ Full Parity

Data Sources

Atlas Feature	Parthenon Equivalent	Status	Notes
Source management	Admin --> Data Sources	✅ Full Parity
Daimon configuration	Per-source daimon settings	✅ Full Parity	Same CDM/vocab/results/temp model
WebAPI source import	CLI import-webapi-sources	✅ Full Parity
Connection testing	Test Connection button	✅ Full Parity

Data Explorer (Achilles)

Atlas Feature	Parthenon Equivalent	Status	Notes
Database profile (Achilles results)	Data Explorer --> Overview	✅ Full Parity	6-section CDM characterization dashboard
Condition prevalence	Data Explorer --> Conditions	✅ Full Parity
Drug prevalence	Data Explorer --> Drugs	✅ Full Parity
Measurement distributions	Data Explorer --> Measurements	✅ Full Parity
DQD / Achilles Heel	Data Explorer --> Data Quality + Heel Checks	✅ Full Parity	Full DQD + dedicated Heel checks tab

Analyses

Atlas Feature	Parthenon Equivalent	Status	Notes
Cohort Characterization	Analyses --> Characterization	✅ Full Parity
Incidence Rate Analysis	Analyses --> Incidence Rates	✅ Full Parity
Treatment Pathways (table)	Analyses --> Treatment Pathways	✅ Full Parity	Tabular results; Sankey visualization planned
Population-Level Estimation	Analyses --> Estimation	✅ Configuration UI	Full config forms; R/HADES execution connected
Patient-Level Prediction	Analyses --> Prediction	✅ Configuration UI	Full config forms; R/HADES execution connected
SCCS	Analyses --> SCCS	✅ Full Parity	Self-Controlled Case Series with full configuration
Evidence Synthesis	Analyses --> Evidence Synthesis	✅ Full Parity	Meta-analysis across multiple databases
Negative Controls	Not yet implemented	🔲 Planned	Manual concept set curation available as workaround

Patient Explorer

Atlas Feature	Parthenon Equivalent	Status	Notes
Profile viewer (patient timeline)	Patients --> Patient Timelines	✅ Full Parity	Requires PHI access role

Administration

Atlas Feature	Parthenon Equivalent	Status	Notes
User management	Admin --> Users	✅ Full Parity	Role-based, email-invited, CSV bulk import
Security provider config	Admin --> Authentication Providers	✅ Full Parity	Local, LDAP, SAML 2.0, OIDC --- full admin UI
Source management	Admin --> Data Sources	✅ Full Parity
System health	Admin --> System --> Health	✅ Extended	Real-time 5-service health dashboard with 30s auto-refresh
Audit log	Admin --> Audit Log	✅ Extended	Full CRUD event log, exportable
AI Provider config	Admin --> AI Providers	✅ New	8 AI providers (Ollama, OpenAI, Anthropic, Google, Azure, etc.)
Vocabulary refresh	Admin --> Vocabulary Management	✅ New	Upload Athena ZIP via admin UI

New Capabilities (No Atlas Equivalent)

These features are unique to Parthenon and have no counterpart in OHDSI Atlas.

Genomics

Feature	Parthenon Location	Status	Notes
VCF Upload and Parsing	Genomics --> Uploads	✅ New	Upload VCF files, parse variants, match to OMOP persons
ClinVar Annotation	Genomics --> ClinVar	✅ New	Local ClinVar database with variant pathogenicity lookup
Variant Browser	Genomics --> Variants	✅ New	Search, filter, and explore imported genomic variants
Tumor Board	Genomics --> Tumor Board	✅ New	Per-patient genomic + clinical summary with AI insights
Genomic Cohort Criteria	Cohort Builder --> Genomic Criteria	✅ New	Include/exclude patients by gene, variant, pathogenicity
Survival Analysis by Variant	Genomics --> Analysis	✅ New	Variant-stratified survival curves
Treatment-Variant Matrix	Genomics --> Analysis	✅ New	Treatment response by genomic variant
OMOP Measurement Mapping	Genomics --> Import	✅ New	Map VCF variants to OMOP measurement domain

Imaging (DICOM)

Feature	Parthenon Location	Status	Notes
DICOM Study Browser	Imaging --> Studies	✅ New	Browse, search, and filter imaging studies by modality, date, patient
Built-in DICOM Viewer	Imaging --> Viewer	✅ New	Cornerstone3D-powered viewer with windowing, zoom, pan
DICOMweb Integration	Imaging --> Index from DICOMweb	✅ New	Index studies from Orthanc, dcm4chee, or cloud PACS
Local DICOM Import	Imaging --> Import Local	✅ New	Import DICOM files from server filesystem
WADO-RS Endpoint	/api/v1/imaging/wado/{sopUid}	✅ New	Standard WADO-RS retrieval for viewer integration
Imaging Cohort Criteria	Cohort Builder --> Imaging Criteria	✅ New	Filter cohorts by modality, body part, study count
Population Imaging Analytics	Imaging --> Analytics	✅ New	Modality distribution, temporal trends across populations
NLP Report Extraction	Imaging --> NLP	✅ New	AI-powered structured finding extraction from radiology reports

HEOR (Health Economics and Outcomes Research)

Feature	Parthenon Location	Status	Notes
Cost-Effectiveness Analysis	HEOR --> Analyses	✅ New	CEA with configurable cost models and outcomes
Budget Impact Modeling	HEOR --> Analyses	✅ New	Multi-scenario budget impact projections
Care Gap Identification	HEOR --> Analyses	✅ New	Identify gaps between guidelines and observed care
Sensitivity Analysis	HEOR --> Scenarios	✅ New	Parameter sweeps and scenario comparison
Payer Contract Simulation	HEOR --> Contracts	✅ New	Model rebate structures and value-based contracts

FHIR EHR Integration

Feature	Parthenon Location	Status	Notes
FHIR R4 Connection Management	Admin --> FHIR Connections	✅ New	Connect to Epic, Cerner, and other FHIR R4 servers
SMART Backend Services Auth	Admin --> FHIR Connections	✅ New	JWT-based system-to-system authentication
Bulk Data Export Sync	Admin --> FHIR Connections --> Sync	✅ New	Async NDJSON-based bulk data transfer to OMOP CDM
Incremental Sync	Admin --> FHIR Connections --> Sync	✅ New	Delta sync using _lastUpdated filters
Content Hash Deduplication	Automatic during sync	✅ New	Prevents duplicate CDM records across syncs
Sync Dashboard	Admin --> FHIR Sync Dashboard	✅ New	Aggregated sync status, progress, and error monitoring

AI-Powered Features

Feature	Parthenon Location	Status	Notes
AI Concept Search	Vocabulary search	✅ New	Natural language concept search via MedGemma/Ollama
AI Provider Management	Admin --> AI Providers	✅ New	8 provider backends, encrypted credentials, test endpoints
Contextual Help	In-app help system	✅ New	AI-augmented contextual help throughout the application

WebAPI Compatibility

Parthenon exposes Atlas WebAPI-compatible endpoints for HADES R package integration:

Legacy WebAPI Endpoint	Parthenon Equivalent	Notes
GET /source/sources	GET /api/v1/sources	Source list
GET /cohortdefinition/{id}	GET /api/v1/cohort-definitions/{id}	Cohort definition
POST /cohortdefinition/{id}/generate/{src}	POST /api/v1/cohort-definitions/{id}/generate	Trigger generation
GET /vocabulary/{src}/search	GET /api/v1/vocabulary/search	Concept search
GET /conceptset/{id}/expression	GET /api/v1/concept-sets/{id}/export	Concept set export

HADES packages (CohortMethod, PatientLevelPrediction, CohortGenerator, etc.) can point to Parthenon's API URL and work without modification.

Legend

Symbol	Meaning
✅ Full Parity	Feature fully implemented; Atlas workflows transfer directly
✅ Extended	Feature implemented with enhancements beyond Atlas
✅ Configuration UI	Full configuration interface built; backend execution connected
✅ Implemented	Feature built and operational
✅ New	Capability unique to Parthenon (no Atlas equivalent)
🔲 Planned	Feature on roadmap; not yet available