Molecular Characterization Initiative (MCI) Knowledge Pilot

This repository contains a pilot effort to transform semi-structured somatic cancer variant classification knowledge into computable clinical assertions using GA4GH Genomic Knowledge Standards (GKS).

Previously captured clinical significance classifications from spreadsheets were programmatically mapped to the GA4GH Variant Annotation Specification (VA-Spec) to evaluate approaches for reducing knowledge silos and improving interoperability.

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Development

Clone the repo and create a virtual environment:

git clone https://github.com/genomicmedlab/mci_knowledge_pilot
cd mci_knowledge_pilot
python3 -m virtualenv venv
source venv/bin/activate

Install development dependencies and prek:

python3 -m pip install -e '.[dev]'
prek install

Check style with ruff:

python3 -m ruff format . && python3 -m ruff check --fix .