AutoGKB

Goals:

1. Fetch annotated articles from variantAnnotations stored in PharmGKB API
2. Create a general benchmark for an extraction system that can output a score for an extraction system Given: Article, Ground Truth Variants (Manually extracted and recorded in var_drug_ann.tsv:) Input: Extracted Variants Output: Score
3. System for extracting drug related variants annotations from an article. Associations in which the variant affects a drug dose, response, metabolism, etc.
4. Continously fetch new pharmacogenomic articles

Description

This repository contains Python scripts for running and building a Pharmacogenomic Agentic system to annotate and label genetic variants based on their phenotypical associations from journal articles.

Dependencies

We manage a few repos externally:

• PubMed Downloader: This repo is used to download all the markdown files from the PMIDs represented in var_drug_ann.tsv
• Huggingface/AutoGKB: This converts the annotations and article text into a dataset format for benchmarking

System Overview

Downloading the data

pixi run setup-repo

OR

pixi run gdown —-id 1qtQWvi0x_k5_JofgrfsgkWzlIdb6isr9
unzip autogkb-data.zip