Open Targets Database Skill

Overview

This skill provides access to the Open Targets Platform GraphQL API. It aggregates multi-modal evidence from genetics (GWAS/eQTL), pathways, animal models, and clinical trials to rank target-disease associations and identify druggable genes.

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
2. User Notification: If .licenses/opentargets_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://platform-docs.opentargets.org/licence, then (2) create the file recording the notification text and timestamp.

Core Rules

• Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce fair use and implement retry logic.
• Output Flag: The --output flag is always required as output can be very large. Use jq or write your own code to process this JSON file.
• Notification: If this skill is used, ensure this is mentioned in the output.

Quick Reference

Always use the provided Python script scripts/query_opentargets.py to quickly query the database. It handles API communication, retries, formatting, and automatically truncates overly large responses. NEVER write your own curl or similar requests.

Usage:

uv run scripts/query_opentargets.py --output /tmp/opentargets_results.json [OPTIONS] COMMAND [ARGS]...

Common Options:

• --output PATH: Required. Path to write the JSON output file.
• --limit N: Limit the number of items returned in arrays (default is 50). Use a smaller number like 10 when doing preliminary exploration.
• --page-size N: Set the API pagination size (default is 200). Increase if you need more results (e.g., a study with many credible sets).