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CDISC Dataset-JSON repository

This project is used to manage the JSON representation for Clinical Datasets (a complement to the Dataset-XML representation). The schema is automatically generated from a LinkML representation of the model.

Developer Instructions

  1. Clone the repository

    git clone https://github.com/cdisc-org/DataExchange-DatasetJson.git

  2. Install required packages (required only once)

    pip install linkml

  3. Create a branch from master for your updates

    git checkout -b feature/<new_facet>

  4. Update the schema by editing the dataset.yaml file

  5. Use Dataset-JSON Notebook to see how to Generate JSON schema from LinkML; this will update file dataset.schema.json in the schema folder.

  6. Push your branch to the upstream repository

    git push -u origin feature/<new_facet>

  7. Raise a Pull Request for the update

Example Data

  • The examples/adam folder contains Dataset-JSON JSON and NDJSON examples of ADaM data

  • The examples/sdtm folder contains Dataset-JSON JSON and NDJSON examples of SDTM data

  • The examples/send folder contains Dataset-JSON JSON and NDJSON examples of SEND data

  • The examples/big_xpt folder contains scripts to create a large XPT file (5Gb) from the XPT file examples/sdtm/lb.xpt.

  • The examples/i18n folder contains an example of a Dataset-JSON file with non-ASCII characters: examples/i18n/ae.json.

  • The examples/extensions folder contains an example of extending the Dataset-JSON schema: examples/extensions/extension.yaml.