string-database

Topics in the source

• STRING Database
• Overview
• When to Use This Skill
• Quick Start
• Core Operations
• 1. Identifier Mapping (stringmapids)
• 2. Network Retrieval (stringnetwork)
• 3. Network Visualization (stringnetworkimage)

STRING is a comprehensive database of known and predicted protein-protein interactions covering 59M proteins and 20B+ interactions across 5000+ organisms. Query interaction networks, perform functional enrichment, discover partners via REST API for systems biology and pathway analysis. This skill should be used when: Retrieving protein-protein interaction networks for single or multiple proteins Performing functional enrichment analysis (GO, KEGG, Pfam) on protein lists Discovering interaction partners and expanding protein networks Testing if proteins form significantly enriched functional modules Generating network visualizations with evidence-based coloring Analyzing homology and protein family relationships Conducting cross-species protein interaction comparisons Identifying hub proteins and network connectivity patterns The skill provides: 1. Python helper functions (scripts/stringapi.py) for all STRING REST API operations 2. Comprehensive reference documentation (references/stringreference.md) with detailed API specifications When users request STRING data, determine which operation is needed and use the appropriate function from scripts/stringapi.py. Convert gene names, prot

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