Camino Frances
A UCLH data pipeline for anti-microbial stewardship and decision making
Camino
Camino is a data extraction tool for retrieving antibiotic prescribing and resistance data from Epic's Clarity data warehouse at UCLH. Camino is built to serve the RADIX translational research project, other usage of the data may be possible but is unsupported.
Camino is comprised of four main components:
Passport: Extracts data from Clarity into Parquet staging files.
Pilgrimage: Ingests data from Parquet staging files into a DuckLake
Planning: Camino orchestration and scheduling with Prefect.
Data Model
The dataset is modelled around the concept of a prescribing encounter, i.e. an inpatient hospital encounter during which a patient was prescribed an antibiotic with additional dimensions on the patient, the encounter, orders placed and results received during the encounter.
The dataset is constructed from Epic's Clarity data warehouse via the Camino passport and Pilgrimage.
Prescribing encounters from 2020-01-01 onwards are included in the full dataset although the "historical" tables go back as far as 2019-04-01.
Camino Portal
These instructions are for researchers in the RADIX translational research project with access to the UCLH network.
How to access RStudio for Rtisans
Camino core: Passport, Pilgrimage and Planning
We maintain a separate and private Book of Camino because the code and content for Passport, and Pilgramage is intertwined with Epic's intellectual property.
Please get in touch if you think you should have access.
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