Brain Knowledge Base Interaction Toolkit

This package contains Pydantic version of the BICAN Knowledgebase Data Models, along with tools to interact with the models and the data they represent.

This project is still under development, and we encourage everyone to provide feedback and join the project.

Models

All models are located in the models directory. Currently, we support the following models:

• Library Generation Model
• Anatomical Structure Model
• Genome Annotation Model

Tools to interact with the models

• Tools to extract data, validate against the current model, and create JSON-LD representations
• Converter from spreadsheets to LinkML YAML files
• Tools to edit LinkML YAML files

Installation

Installation from PyPI

pip install bkbit

Temporary fix: updating to new schemasheets version from GitHub:

pip install git+https://github.com/linkml/schemasheets

Instructions for developers:

• Fork the repository
• Clone your fork
• Navigate to the main project directory: cd bkbit
• Install in editable mode: pip install -e .[all]
• Install newer version of schemasheets (temporary fix): pip install git+https://github.com/linkml/schemasheets