STRING Database — Protein-Protein Interactions

STRING Database — Protein-Protein Interactions

Overview

Query the STRING protein-protein interaction database (59M proteins, 20B+ interactions, 5000+ species) via REST API. Covers network retrieval, functional enrichment (GO, KEGG, Pfam), interaction partner discovery, PPI enrichment testing, network visualization, and homology analysis.

When to Use

• Retrieving protein-protein interaction networks for one or multiple proteins
• Performing functional enrichment analysis (GO, KEGG, Pfam, InterPro) on protein lists
• Discovering interaction partners and expanding protein networks from seed proteins
• Testing whether a set of proteins forms a significantly enriched functional module
• Generating network visualizations with evidence-based coloring
• Analyzing homology and protein family relationships across species
• Identifying hub proteins and network connectivity patterns
• For chemical compound interactions use chembl-database-bioactivity instead; for pathway-centric queries use kegg-database

Prerequisites

uv pip install requests pandas

Rate limiting: No strict rate limit, but wait ~1 second between API calls. For proteome-scale analyses, use bulk downloads from https://string-db.org/cgi/download instead of the API.

Quick Start

import requests
import time

STRING_API = "https://string-db.org/api"

def string_query(endpoint, params, fmt="tsv"):
    """Reusable helper for all STRING API calls."""
    url = f"{STRING_API}/{fmt}/{endpoint}"
    params.setdefault("caller_identity", "python_script")
    response = requests.get(url, params=params)
    response.raise_for_status()
    return response.text