InterPro Database Access

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/interpro_database_LICENSE.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/interpro/ and https://www.ebi.ac.uk/about/terms-of-use/, then (2) create the file recording the notification text and timestamp.

Overview

InterPro combines signatures from multiple, diverse databases into a single searchable resource, reducing redundancy and helping users interpret their sequence analysis results. By uniting these member databases (e.g., Pfam, CDD, SMART), InterPro capitalises on their individual strengths to produce a powerful diagnostic tool and integrated resource.

Use interpro-database to:

• Identify what domains, families, and sites are found in a particular protein.
• Identify all proteins that belong to a protein family or contain a particular domain, even when the names and activities of the proteins are highly variable.
• Examine the species in which a particular protein family or domain is found.
• Annotate genomes with protein family information and Gene Ontology (GO) terms.

This skill provides a robust utility, interpro_client.py, to interact with the InterPro API seamlessly. It natively handles rate limiting (HTTP 429), background query sleep tracking (HTTP 408), terminal errors (HTTP 404/410), and lazy pagination.

Core Rules