CDISC Conceptual and Operational Standards Metadata Services (COSMoS)

The COSMoS GitHub repository contains working files and other artefacts to support the implementation of Biomedical Concepts (BCs) and Dataset Specializations in the CDISC Library. Below is an overview of the contents of this repository.

• bc_starter_package

  This folder contains a CDISC Biomedical Concepts Starter Package for:

  • users who want to create CDISC BCs and Dataset Specializations
  • Users who want to retrieve and use BCs and Dataset Specializations from the CDISC Library
  • Users who want to provide feedback on BCs and Dataset Specializations

• curation

  The curation folder contains spreadsheets that were used for loading of BCs and SDTM Specializations. These spreadsheets should not be used to download BCs or SDTM Specializations. Instead, use the spreadsheets in the export folder.

• curation/draft

  The curation/draft folder contains draft curation spreadsheets that are still work in progress. The content in these draft spreadsheets is neither validated nor loaded in the CDISC Library.

• export

  The export folder contains spreadsheets with the latest versions of all BCs and SDTM Dataset Specializations in the CDISC Library:

  • Latest CDISC Biomedical Concepts (Excel spreadsheet)
  • Latest SDTM Dataset Specializations (Excel spreadsheet)

• model

  The model folder contains files (cosmos_bc_model.yaml and cosmos_sdtm_bc_model.yaml) according to the LinkML specification. It also contains several other files auto generated from the model:

  • cosmos_bc_model.json amd cosmos_sdtm_bc_model.json: JSON schema files describing the machine-readable YAML files
  • cosmos_bc_model.svg, cosmos_bc_model.yuml, cosmos_sdtm_bc_model.svg, cosmos_sdtm_bc_model.yuml: Entity diagrams
  • cosmos_bc_model.py, cosmos_sdtm_bc_model.py: Python models

• openapi

  The openapi folder contains the OpenAPI definition of the COSMoS API (cosmos.yaml)

  More information about using the CDISC Library API can be found on the CDISC Library API Portal and the Biomedical Concepts and Dataset Specializations Release Notes on the CDISC Wiki. Use your cdiscID credentials to login to the CDISC Library API Portal.

• projects

  The project folder contains various artefacts generated from the LinkML schema, such as JSON-Schema, or the Python object model.

• utilities

  The utilities folder contains utilities to:

  • Validate the curation spreadsheets
  • Generate YAML files from the curation spreadsheets
  • Create Excel spreadsheets from JSON files requested through the API

• yaml

  The yaml folder contains:

  • YAML files generated from the curation spreadsheets
  • Scripts to validate the YAML files

License

Code & Scripts

This project is using the MIT license (see LICENSE) for code and scripts.

Content

The content files like documentation and minutes are released under CC-BY-4.0. This does not include trademark permissions.

Re-use

When you re-use the source, keep or copy the license information also in the source code files. When you re-use the source in proprietary software or distribute binaries (derived or underived), copy additionally the license text to a third-party-licenses file or similar.

When you want to re-use and refer to the content, please do so like the following:

Content based on COSMoS (GitHub) used under the CC-BY-4.0 license.