refactor: Move hardcoded values to config files

[berntpopp]

Description:

Several hardcoded values are currently embedded within various scripts, including ontology-functions.R. To improve maintainability and flexibility, these values should be moved into configuration files to allow for easier updates and environment-specific settings.

Tasks:

• Identify all scripts with hardcoded values (e.g., ontology-functions.R).
• Refactor the code to replace hardcoded values with configurable parameters.
• Create a configuration file (or enhance the existing one) to store these parameters.
• Update documentation to reflect the changes in configuration management.

Rationale:
Moving hardcoded values to config files will make the application more adaptable to different environments, reducing the need for code changes in deployment.