- Add DrugAnnotation and DrugAnnotationList models to src/variants.py
- Create new drug_annotation_extraction.py component with detailed field extraction
- Integrate drug annotation extraction into variant association pipeline
- Add comprehensive test script for verification
- Follow existing LLM infrastructure patterns (Generator/Parser)
- Extract detailed pharmacogenomic fields matching provided schema

Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>

- Modified extract_drug_annotations to loop through variants one at a time
- Each variant now gets individual LLM processing for better control
- Added SingleDrugAnnotation model for individual variant processing
- Updated logging to show individual variant processing progress
- Maintains same output quality while providing cleaner extraction per variant
- Updated test script to reflect individual processing approach

Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>

…ation-extraction

Add drug annotation extraction component for variants with drug associations

…-improvements

Efficiency improvements: Cache JSON loading and fix type annotations

…ents

- Add PhenotypeAnnotation and FunctionalAnnotation data models to variants.py
- Create phenotype_annotation_extraction.py with detailed extraction logic
- Create functional_annotation_extraction.py with mechanistic annotation logic
- Update variant_association_pipeline.py to integrate new extraction components
- Follow existing drug annotation extraction patterns
- Use detailed prompt templates from annotation_prompts.md
- Process variants individually for better control and cleaner extraction
- Include proper error handling and logging throughout

Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>

- Move test_imports.py and test_new_annotations.py to tests/ directory
- Clean up temporary converted notebook file
- Follow proper repository structure conventions

Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>

- Fix Python path resolution for tests running from tests/ subdirectory
- Ensure tests can properly import src modules from new location
- Verify all tests pass after organizational changes

Co-Authored-By: Shlok Natarajan <shlok.natarajan@gmail.com>

…functional-extraction

feat: implement phenotype and functional annotation extraction components