lamm-mit/skills/interpro-database

InterPro Database Skill Documentation

Overview

InterPro is a comprehensive protein annotation resource maintained by EMBL-EBI that integrates signatures from 13 member databases. It classifies proteins into families, domains, homologous superfamilies, repeats, and functional sites, covering over 100 million protein sequences.

Primary Use Cases

• Predicting functions of uncharacterized proteins
• Analyzing domain architecture and composition
• Classifying proteins into evolutionary families
• Mapping Gene Ontology terms to sequences
• Conducting evolutionary and structural analyses

Core API Functions

Protein Lookup: Query InterPro entries for any UniProt identifier using the /protein/UniProt/{id}/entry/InterPro/ endpoint.

Entry Details: Retrieve comprehensive information about specific InterPro entries through /entry/InterPro/{id}/ or member database-specific endpoints.

Reverse Lookup: "Get all proteins annotated with an InterPro entry" via /entry/InterPro/{id}/protein/UniProt/ to discover related sequences.

Domain Architecture: Obtain complete positional mapping of domains across a protein sequence.

GO Term Mapping: Extract Gene Ontology annotations embedded within InterPro entry metadata.

Integration Strategy

• Utilize UniProt accession numbers for reliable queries
• Distinguish between broad family classifications and specific structural domains
• Implement rate limiting (0.3 seconds between requests) for batch operations
• Combine results with UniProt and PDB data for enriched biological context

Technical Implementation

All queries use the REST API at https://www.ebi.ac.uk/interpro/api/ with JSON responses. Python implementations employ the requests library with appropriate headers and error handling.