quickgo-database

1# QuickGO Database Skill
2 
3GO (Gene Ontology) annotations are one of the main ways to label a gene's
4function. QuickGO is a fast, web-based browser for the GO and Evidence &
5Conclusion Ontology (ECO), maintained by the Gene Ontology Annotation (GOA)
6group at EMBL-EBI.
7 
8It provides a centralised resource to explore the functional attributes of gene
9products (proteins, RNA, and complexes). It is a primary tool for functional
10annotation mapping since it allows you to link a gene (e.g., USH2A) to its
11specific biological processes (e.g. sensory perception of light stimulus),
12molecular functions, and cellular components.
13 
14## Prerequisites
15 
161.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
17    `uv` is installed and on PATH.
182.  **User Notification**: If .licenses/quickgo_database_LICENSE.txt does not
19    already exist in the workspace root directory then (1) prominently notify
20    the user to check the terms at https://www.ebi.ac.uk/QuickGO/ and
21    https://www.ebi.ac.uk/QuickGO/api/index.html, then (2) create the file
22    recording the notification text and timestamp.
23 
24## Usage
25 
26This skill provides a Python CLI wrapper `scripts/quickgo_tool.py` that queries
27the QuickGO REST API. It handles formatting the requests, respecting rate
28limits, and safely storing the potentially large JSON responses.
29 
30## Core Rules
31 
32-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
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