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This repository stores theLinkML representation of theCRDC Harmonized Data Model (CRDC-H) produced by theCenter for Cancer Data Harmonization (CCDH).

This repository includesthe LinkML model itself (inYAML format) as well as a number of artifacts produced automatically by LinkML, including a JSON Schema, JSON-LD context, a GraphQL description, a CSV description and ShEx validation shapes.

Model documentation in Markdown can also be generated for this repository, and is currently hosted on GitHub Pages athttps://cancerdhc.github.io/ccdhmodel/. A set of Python Data Classes can also be generated and areavailable for use. Examples of their use are available in theExample Data repository.

All artifacts can be generated by runningmake in this repository.make clean will delete generated existing artifacts, allowing them to be regenerated. This Makefile usesPoetry to manage dependencies.

We usemike to publish documentation to GitHub Pages. Usemike deploy [version] -p to push a new version of the documentation to Google Pages (via thegh-pages branch).mike deploy [version] latest -p -u can be used to indicate that the uploaded version should be used as thelatest version, which will be displayed by default.

The CRDC-H model is currently in development ona Google Sheet,which is converted into a LinkML schema in./model/schema/crdch_model.yaml. If youwould like to use the latest, in-development version of the schema as described in Google Sheets, you will need touse thesheet2linkml package to regenerate this schema to regenerate thisfile by runningmake generate-model.

In order to read a Google Sheet, sheet2linkml will need access to theGoogle Sheets APIin theGoogle Developers Console.Detailed instructions and screenshots are available fromthepygsheets documentation, which is the package sheet2linkml uses to accessGoogle Sheets. Save the file asgoogle_api_credentials.json in the root directory of this project. The first time yourunmake generate-model, you will see a browser page asking you to log in. Follow the instructions. The script willdownload a token and store it locally. You will not need to log in when rerunning this command.