https://github.com/linkml/cmdr
https://github.com/linkml/cmdr
Last synced: 11 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/linkml/cmdr
- Owner: linkml
- License: mit
- Created: 2023-03-06T21:14:18.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-01-07T21:38:16.000Z (over 1 year ago)
- Last Synced: 2025-07-11T12:55:45.370Z (12 months ago)
- Language: Python
- Homepage: https://linkml.io/cmdr/
- Size: 1.36 MB
- Stars: 6
- Watchers: 7
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
# 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](https://github.com/include-dcc/include_linkml) 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](https://linkml.github.io/cmdr)
## Repository Structure
* [examples/](examples/) - example data
* [project/](project/) - project files (do not edit these)
* [src/](src/) - source files (edit these)
* [cmdr](src/cmdr)
* [schema](src/cmdr/schema) -- LinkML schema (edit this)
* [datamodel](src/cmdr/datamodel) -- Generated python datamodel
* [tests](tests/) - python tests
We've added
some [HTML visualizastions of data instances](https://htmlpreview.github.io/?https://github.com/linkml/cmdr/blob/master/examples/Container-material-entities.html)!
## 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](https://github.com/linkml/linkml-project-cookiecutter)