Competency Queries Tutorials

A collection of tutorials in the form of Jupyter notebooks, detailing how to work with Competency queries in the context of SCKAN/Flatmap.

Jupyter Notebooks Overview

• check_map.ipynb Demo for comparing Neuron Population information from Map and SCKAN.

• fma_nerve.ipynb Explore how nerve structures are represented in the Foundational Model of Anatomy (FMA) ontology.

• pg_human_nerves.ipynb Investigate the Coverage of Nerves in SCKAN/Flatmap Neuron Populations within the Human Scaffold.

• pg_nerves.ipynb Demo for Exposing Neuron Population and Nerve-Related Information from PostgreSQL.

• sckan_nerves.ipynb Demonstrate how to work with SCKAN nerve.

• species_specific.ipynb Demo for retrieving species-specific neuron populations and their supporting evidence.

Running the Tutorials

1. Create a virtual environment:

   python -m venv .venv

2. Activate the virtual environment:

   source .venv/bin/activate

3. Install required libraries:

   pip install -r requirements.txt

4. Start Jupyter Notebook:

   jupyter notebook

5. Open and run the desired notebook.