Toolkit

omop_alchemy.cdm gives you the OMOP CDM schema as SQLAlchemy models. The toolkit is what you build with them: vocabulary resolution, patient timelines, episode traversal, domain analytics, and outbound export.

Experimental

The toolkit is newer and less battle-tested than the CDM models it sits on top of. Module paths below an area (anything past toolkit.<tier>.<area>) may still move; the area itself is the stable import surface. The CDM models themselves are not affected by anything here.

Four tiers

Each tier may depend only on the tiers before it in this list — core knows nothing of episodes or clinical domains, and nothing depends on integrations.

Tier	Answers	Assumes a clinical domain?
core	Resolve concepts, build a patient timeline, convert units	No
episodes	Build episodes, retrieve what belongs to one	No
analytics	What does this value mean clinically?	Yes, one subpackage per domain
integrations	Export to an external data standard	No

A worked example

Querying an oncology episode pulls together all four tiers without you having to think about the seams between them: concept resolution and timelines from core, drug retrieval from episodes, oncology classification from analytics.

from sqlalchemy.orm import Session
from omop_alchemy.toolkit.analytics.oncology import OncologyEpisode

with Session(engine) as session:
    episode = session.get(OncologyEpisode, episode_id)

    episode.structural_modality        # OncologyModality.SACT, .RADIOTHERAPY, ...
    episode.drug_exposures              # linked Drug_Exposure rows
    episode.rt_dose_summary             # RTDoseSummary, if any RT was given
    episode.critical_weight_loss_grade  # graded against Martin/CTCAE criteria

Import surface

Import from the area subpackage — omop_alchemy.toolkit.<tier>.<area> — not from a specific module beneath it:

from omop_alchemy.toolkit.core.concepts import make_concept_resolver
from omop_alchemy.toolkit.analytics.oncology import OncologyEpisode

Each area's __init__.py re-exports its public names, and that's the part of the path that stays stable. Files beneath it are free to move.