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Data Tools & Services

Supporting data tooling and services for the warehouse: dbt, the Glue Catalog, and the (decommissioned) Vocabulary Service.

Data Build Tool (dbt)

dbt is the canonical authoring tool for everything in CLINICOGENOMICS — staging views, intermediate Dynamic Tables, and partner cohort marts all live as dbt models. Deployment to each environment is automated through GitLab CI/CD on merge to master.

bash
uv tool install dbt-core==1.11.8 --with dbt-snowflake==1.11.4 --python 3.13

For the repository structure, materializations, and the full build pipeline, see dbt & Build Pipeline.

Glue Catalog

The AWS Glue Catalog provides table metadata and schema discovery for data assets outside the Snowflake warehouse. It complements the Snowflake-native Schema Reference for the broader data platform.

Vocabulary Service

It was a standalone term-mapping service (fuzzy matching, common ancestors, level alignment) fronting a SciGraph graph database and a Postgres similarity store. Vocabulary and code-mapping now live in the cgdb/clinical-llm repo and dbt models under cgdb/snowflake/dbt/models/.