Drug Side Effect Study

Bio-IT World 2026 FAIR Data Hackathon — Project 4

A proof-of-concept pipeline that integrates CFDE-linked resources (DrugCentral, Pharos, KEGG, Reactome, WikiPathways) to investigate the molecular basis of drug side effects. This repository is intended as a starting point for hackathon participants — not a finished tool.

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Pipeline Overview

Given a side effect, the pipeline:

1. DrugCentral — Find drugs associated with the side effect; identify shared protein targets after physicochemical filtering (pAct ≥ 7, CLogP ≥ 1, LogSw ≥ -6)
2. Anatomy Mapping — Map the side effect to an anatomical location using a local LLM (BioMistral via Ollama)
3. Pharos — Confirm target expression at the anatomical location
4. Pathway Validation — Query KEGG, Reactome, and WikiPathways for pathway-level support
5. Evidence Assembly — Compile results with confidence tiers (strong / moderate / weak)

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Setup

# Create environment
conda create -n sideeffects python=3.11 -y
conda activate sideeffects

# Install dependencies
pip install -r requirements.txt

# Configure
cp .env.example .env
# Edit .env if needed

For Step 2 (anatomy mapping), install Ollama and pull BioMistral:

ollama pull biomistral:latest

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Usage

Run on a single side effect:

python scripts/run_pipeline.py "Parkinsonism"

Run on the batch validation set (40 side effects):

python scripts/run_batch_validation.py

Results are written to results/ and outputs/.

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Key Resources for Participants

Resource	Endpoint
DrugCentral API	https://uxn2ycvimg.us-east-2.awsapprunner.com/docs
Pharos (UNM team)	https://qjempg3k6t.us-east-2.awsapprunner.com/docs
Pharos (NCATS)	https://pharos-api.ncats.io/graphql
KEGG REST	https://rest.kegg.jp
Reactome Content Service	https://reactome.org/ContentService
WikiPathways SPARQL	https://sparql.wikipathways.org/sparql

See the Resource Guide for the full setup walkthrough.

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Where Participants Can Extend This

Team

• Jeremy Yang (Co-lead, UNM) — jjyang@unm.edu
• Tudor Oprea (Co-lead) — tudorzinho@gmail.com
• Manjil Pradhan (CS graduate student, UNM)
• Bivek Acharya (DrugCentral developer)

Affiliation: UNM / IDG (Illuminating the Druggable Genome)

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