Technical Documentation

Phenotype Library Inclusion Criteria

  • Define a disease (e.g. hypertension), life style risk factor (e.g. smoking) or biomarker (e.g. blood pressure)
  • Derive information from one or more electronic health record data sources. This can include national and local sources. The definition of EHR includes administrative data such as billing/claims data, and clinical audits.
  • Have one or more peer-reviewed outputs associated with it e.g. journal publication, scientific conferences, policy white papers etc.
  • Provide evidence of how the phenotyping algorithm was validated.

Specification

Phenotyping algorithms are stored in the Phenotype Library usign a combination of YAML and CSV files. There are two main components to each algorithm:

  • The phenotype definition file (which is defined in a YAML file); and,
  • One or more teminology files (also known as codelists) which can be stored inline within the YAML file or in linked CSV files

Phenotype Definition

The phenotype definition file is a YAML header file. The YAML file is used to record metadata fields capturing information about the algorithm, the data sources, controlled clinical terminologies and other information.

Clinical-Coded Phenotype Template:

Defining a Concept

Existing concepts can be linked to new phenotypes using their concept id and version id, new ones can be uploaded via a csv file.

From an existing concept:

name: The name of the concept

type: existing_concept

concept_id: The concept ID as displayed on the Phenotype Library

concept_version_id: The concent version ID as displayed on the Phenotype Library

Through uploading a csv file:

name: The name of the concept

type: csv

filepath: Location of the csv file, e.g. C:/my/csv/file.csv

code_column: The name of the code column in your csv

description_column: The name of the description column in your csv

How to Submit Data

You can download a sample template file from the repository.

If you have a phenotyping algorithm that meets the eligibility requirements, we invite you to submit your data by one of the following ways: