acr-harmonized-data-model

LinkML Schema for ACR Harmonmized Data.

Tools Required

• Python 3.12 (3.13 support coming for linkml)
• LinkML 1.8.6
• Pydantic 2.10.6
• mkdocs required to generate the documentation website

Tools to install:

pip install linkml
pip install mkdocs
pip install mkdocs-mermaid2-plugin

Users can probably get away with slightly older versions but be aware that later versions of LinkML do require pydantic >= 2.x.x

Checking for convention compliance

It can be helpful to review the schema for compliance with linkml conventions. To run a check for all files against the default standards the following command can be run.

linkml-lint data-model

Creating the anvil project

Here is the command to generate default artifacts if there is a need.

gen-project -d anvil data-model/anvil.yaml

Creating the docs

gen-doc -d docs data-model/anvil.yaml
mkdocs build

Validating Test Data

linkml-validate -s data-model/participant.yaml test-data/participant.csv -C Participant