opentargets-database

1# Open Targets Database Skill
2 
3## Overview
4 
5This skill provides access to the Open Targets Platform GraphQL API. It
6aggregates multi-modal evidence from genetics (GWAS/eQTL), pathways, animal
7models, and clinical trials to rank target-disease associations and identify
8druggable genes.
9 
10## Prerequisites
11 
121.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
13    `uv` is installed and on PATH.
142.  **User Notification**: If .licenses/opentargets_database_LICENSE.txt does
15    not already exist in the workspace root directory then (1) prominently
16    notify the user to check the terms at
17    https://platform-docs.opentargets.org/licence, then (2) create the file
18    recording the notification text and timestamp.
19 
20## Core Rules
21 
22-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
23    database rather than accessing the database directly. The scripts
24    automatically enforce fair use and implement retry logic.
25-   **Output Flag**: The `--output` flag is always required as output can be
26    very large. Use `jq` or write your own code to process this JSON file.
27-   **Notification**: If this skill is used, ensure this is mentioned in the
28    output.
29 
30## Quick Reference
31 
32Always use the provided Python script `scripts/query_opentargets.py` to quickly
33query the database. It handles API communication, retries, formatting, and
34automatically truncates overly large responses. NEVER write your own curl or
35similar requests.
36 
37**Usage:**
38…