cmdr 0.1.0

Core Model for Data Research (Tentative)

CMDR

CMDR (pronunciation: “com-mo-dore” or sometimes “com-man-der”), the Core Model for Data Research, is a LinkML schema/data model for the collection of biological sample data, and its analysis.

The purpose of this schema is to act as a base schema for other LinkML schemas/data models to bootstrap for their specific use case.

The CMDR data model was inspired by the LinkML data model for the INCLUDE project.

Project Setup

1. Clone cmdr project repository

$ git clone https://github.com/linkml/cmdr.git

2. Create virtual environment and install project dependencies

$ make install

3. Create downstream schema artifacts, run unit tests, and also validate examples/instance data against schema

$ make test

4. LinkML transformer mapping between source and target schemas on a class

$ make test_transform

Website

• https://linkml.github.io/cmdr

Repository Structure

• examples/ - example data
• project/ - project files (do not edit these)
• src/ - source files (edit these)
  • cmdr
    • schema -- LinkML schema (edit this)
• datamodel -- Generated python datamodel
• tests - python tests

We've added some HTML visualizastions of data instances!

Developer Documentation

Use the `make` command to generate project artefacts:

• make all: make everything
• make deploy: deploys site

Credits

this project was made with linkml-project-cookiecutter