We have encoded the coderdata schema in linkML, a schema definition language that allows for easy operability with Python, OWL, JSONSchema, and other schema definition libraries.
To validate any files you choose to add, you have to download the linkml-validate python package:
pip install linkml-validate
Then you can choose to validate any of the schema classes in our model. Currently we have the following objects in our model:
| Object | Description |
|---|---|
| Gene | Human gene identifiers |
| Samples | Samples in which omics and drugs are measured |
| Drugs | Drugs evaluated on samples |
| Drug Descriptor | Computational descriptions of drug properties |
| Transcriptomics | Gene exrpression data |
| Mutations | Gene mutation data |
| Copy Number | Copy number data |
| Proteomics | Proteomics data |
| Experiments | Drug experiments that measure the viability of the cell |
| Perturbations | Experiments that measure molecular changes of the cell |
| Combinations | Synergy calculations from pairs of drugs |
The data model is shown here:
