BioReason/data/README.md

BioReasoning Data Curation

Jupyter notebooks for processing genetic variant data and creating ML datasets for biological reasoning tasks.

Notebooks

Core Analysis

• BioReasoning_DataCuration_KEGG.ipynb - KEGG pathway analysis with Claude API
• Clinvar_Coding.ipynb - ClinVar variant processing and gene mapping
• Clinvar_SNV_Non_SNV.ipynb - SNV/structural variant datasets with VEP annotations

KEGG Pipeline

• KEGG_Data_1.ipynb - KEGG network data processing and variant identification
• KEGG_Data_2.ipynb - Variant parsing and sequence generation
• KEGG_Data_3.ipynb - Final ML dataset creation with Q&A pairs

Variant Prediction

• VEP.ipynb - Variant effect prediction datasets (ClinVar, OMIM, eQTL)

Setup

brew install brewsci/bio/edirect  # For ClinVar (macOS)
export ANTHROPIC_API_KEY="your-key"  # For KEGG analysis

Usage

Each notebook has a configuration section - update paths/keys as needed, then run sequentially.

Key Outputs:

• KEGG biological reasoning datasets
• ClinVar variant-disease associations
• VEP prediction task datasets
• Genomic sequences with variant context