Agent skill · research science · google-deepmind
quickgo-database
Query the QuickGO and Evidence & Conclusion Ontology (ECO) REST API. Use this when you need to map genes to biological processes, molecular functions, or cellular components, find genes associated with a specific pathway/GO term, or explore the Gene Ontology hierarchy. Do not use for querying drug targets (use OpenTargets) or mechanistic signaling pathway diagrams (use KEGG).
Why this skill is useful
Adds a Python CLI wrapper for querying the QuickGO REST API with specific commands and rate limit handling that the AI wouldn't reliably generate on its own.
What it needs
Requires uv installed locally. About 3k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
QuickGO Database Skill GO (Gene Ontology) annotations are one of the main ways to label a gene's function. QuickGO is a fast, web-based browser for the GO and Evidence & Conclusion Ontology (ECO), maintained by the Gene Ontology Annotation (GOA) group at EMBL-EBI. It provides a centralised resource to explore the functional attributes of gene products (proteins, RNA, and complexes). It is a primary tool for functional annotation mapping since it allows you to link a gene (e.g., USH2A) to its specific biological processes (e.g. sensory perception of light stimulus), molecular functions, and cellular components. 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/quickgodatabaseLICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.ebi.ac.uk/QuickGO/ and https://www.ebi.ac.uk/QuickGO/api/index.html, then (2) create the file recording the notification text and timestamp. Usage This skill provides a Python CLI wrapper scripts/quickgotool.py that queries the QuickGO REST API. It handles formatting the requests, respecting rate limits, and safely storing the potentially large JSON responses. 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 the required rate limit gracefully. Pagination & Limits: Restrict endpoints to a maximum of 100 results per page using --limit 100 and the --page parameter for larger datasets. Output Files: Always use the --output flag to save responses to a file incrementally or parse via jq. Evidence Codes: Prioritize experimental evidence (ECO:0000269) over electronic (ECO:0000501) to avoid noisy predictions. Taxon Filtering: Use --taxonId 9606 to restrict results to Human when analysing clinical or human genomic data. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/quickgo_database