OMOP Alchemy

OMOP Alchemy provides a canonical, typed, SQLAlchemy-first representation of the OHDSI OMOP Common Data Model (CDM).

It is designed to support fluency for research-ready analytics, validation, and exploration of OMOP data using modern Python tooling, without imposing ETL conventions or execution-time side effects.

Design goals

OMOP Alchemy is intentionally:

Declarative
Defines tables, columns, relationships, and constraints
Typed and inspectable
Models are fully typed and introspectable for validation, tooling, and IDE support.
Backend-agnostic
Layered abstractions for adding in new supported backend behaviours.

Core features

SQLAlchemy ORM models for OMOP CDM tables
Explicit foreign key and relationship definitions
Lightweight mapper versions to provide simple model validation against CDM for use in ETL loops without side-effects or performance hit that can come from relationship instantiation within the runtime
Read-only View classes for safe navigation and analytics that include complex multi-table objects such as conditions with their modifiers, episodes with their events
Domain validation helpers for OMOP concept integrity

from omop_alchemy.cdm.model.vocabulary.concept import ConceptView

concept = session.get(ConceptView, 320128)  # Lung cancer
concept.domain.domain_id                    # "Condition"
concept.vocabulary.vocabulary_id            # "SNOMED"
concept.is_standard                         # True

Status

The core API under cdm/ should be considered stable as of the 1.x release.

The toolkit API is experimental and carries no compatibility guarantees. Feedback and issues are welcome.

Some additional background

This work builds on earlier research and tooling presented at the 2023 OHDSI APAC Symposium

see background paper.

Configuration

OMOP Alchemy reads all database connection and schema settings from oa-configurator. No .env files or ENGINE environment variables are needed.

Run once after installation:

omop-config init
omop-config configure omop_alchemy

See Configuration for full details.

Metadata

Release files for omop-alchemy 2.0.0

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Source distribution (sdist)

Source distribution for omop-alchemy 2.0.0
File	Size	Uploaded
omop_alchemy-2.0.0.tar.gz	734.8 kB	Oct 10, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for omop-alchemy 2.0.0
File	Interpreter	ABI	Platform	Reset
omop_alchemy-2.0.0-py3-none-any.whl 298.0 kB Oct 10, 2026	Python 3	none	any	Details

Total release size: 1.0 MB

Release files / omop_alchemy-2.0.0.tar.gz

Download URL	omop_alchemy-2.0.0.tar.gz
Size	734.8 kB
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Publishing platform: GitHub Actions
Publishing repository: github.com/AustralianCancerDataNetwork/omop-alchemy
Publishing commit: github.com/AustralianCancerDataNetwork/omop-alchemy/tree/7c28cfde00f3a1e9e1ed8b1f6392b1304de100ac

Workflow

Publishing configuration: github.com/AustralianCancerDataNetwork/omop-alchemy/blob/7c28cfde00f3a1e9e1ed8b1f6392b1304de100ac/.github/workflows/publish.yml
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Release files / omop_alchemy-2.0.0-py3-none-any.whl

Download URL	omop_alchemy-2.0.0-py3-none-any.whl
Size	298.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`17cdbf3d901f23da339b7e4d4598f22f178499733fa326884de6e0de40c78f02`
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Upload date	Oct 10, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/AustralianCancerDataNetwork/omop-alchemy
Publishing commit: github.com/AustralianCancerDataNetwork/omop-alchemy/tree/7c28cfde00f3a1e9e1ed8b1f6392b1304de100ac

Workflow

Publishing configuration: github.com/AustralianCancerDataNetwork/omop-alchemy/blob/7c28cfde00f3a1e9e1ed8b1f6392b1304de100ac/.github/workflows/publish.yml
Publishing logs: github.com/AustralianCancerDataNetwork/omop-alchemy/actions/runs/38095749159/attempts/1

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Subject: omop_alchemy-2.0.0-py3-none-any.whl
SHA-256 checksum: 17cdbf3d901f23da339b7e4d4598f22f178499733fa326884de6e0de40c78f02 Verifying attestations