CellRex Customization
Table of contents
Customization options for CellRex ontology
Multiple levels of customization are available.
The most straightforward approach is to use the default ontology and modify the configuration file (labdata.yml) according to your requirements, such as adding new keywords, species, or drugs. Certain variables have dependencies that are described in the documentation at Parameters
If the file path composition requires alteration, configure the function create_filepath() in cellrex/backend/router/biofiles.py. For reordering operations only, it is possible to provide the function with the list key_order or specify new defaults.
Modifications to the data model can be implemented in the file cellrex/backend/model/biofile.py by adding or modifying the corresponding pydantic classes. It is important to also reflect these changes in cellrex/backend/model/search.py to ensure functionality for searchability. Note that these modifications are not automatically propagated to the frontend. The basic design of the frontend is to structure “pages” with distinct functionalities, such as upload, search, and dashboard. These pages utilize “component”s that are categorized either according to their functional role in a page or by semantic definitions, such as “general” or “device”. Within a component, Streamlit elements and API responses are implemented.