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 1.2.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for omop-alchemy 1.2.0
File	Size	Uploaded
omop_alchemy-1.2.0.tar.gz	691.7 kB	Sep 18, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for omop-alchemy 1.2.0
File	Interpreter	ABI	Platform	Reset
omop_alchemy-1.2.0-py3-none-any.whl 279.3 kB Sep 18, 2026	Python 3	none	any	Details

Total release size: 971.0 kB

Release files / omop_alchemy-1.2.0.tar.gz

Download URL	omop_alchemy-1.2.0.tar.gz
Size	691.7 kB
Tags	Source
SHA-256 checksum How to use checksums	`689b789e4a39cd63394dea6f2d4bd06f2195744dafee0d42670cabc1dea4339c`
BLAKE2b-256 checksum How to use checksums	`edf16d075fdc151734ec67c678e8ee76c14d6a994e173ac474aceb23af3c671d`
Upload date	Sep 18, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/AustralianCancerDataNetwork/omop-alchemy
Publishing commit: github.com/AustralianCancerDataNetwork/omop-alchemy/tree/54cb20d9a1b2091f2d06730cfcba07fecd6e9811

Workflow

Publishing configuration: github.com/AustralianCancerDataNetwork/omop-alchemy/blob/54cb20d9a1b2091f2d06730cfcba07fecd6e9811/.github/workflows/publish.yml
Publishing logs: github.com/AustralianCancerDataNetwork/omop-alchemy/actions/runs/35293485139/attempts/1

Artifact

Subject: omop_alchemy-1.2.0.tar.gz
SHA-256 checksum: 689b789e4a39cd63394dea6f2d4bd06f2195744dafee0d42670cabc1dea4339c Verifying attestations

Release files / omop_alchemy-1.2.0-py3-none-any.whl

Download URL	omop_alchemy-1.2.0-py3-none-any.whl
Size	279.3 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`9402ad34a011c43609b65a56baff8c50b7d8f3b7ba99f6110d6b2593c1db8995`
BLAKE2b-256 checksum How to use checksums	`75907b34ba5d9ffca12a074a4b5a94ec1dcd9a6bc3ec5f5581736bb56be9b095`
Upload date	Sep 18, 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/54cb20d9a1b2091f2d06730cfcba07fecd6e9811

Workflow

Publishing configuration: github.com/AustralianCancerDataNetwork/omop-alchemy/blob/54cb20d9a1b2091f2d06730cfcba07fecd6e9811/.github/workflows/publish.yml
Publishing logs: github.com/AustralianCancerDataNetwork/omop-alchemy/actions/runs/35293485139/attempts/1

Artifact

Subject: omop_alchemy-1.2.0-py3-none-any.whl
SHA-256 checksum: 9402ad34a011c43609b65a56baff8c50b7d8f3b7ba99f6110d6b2593c1db8995 Verifying attestations