Agent skill · research science · aiskillstore
string-database
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
Why this skill is useful
Adds Python scripts for querying the STRING API, enabling advanced protein interaction analysis and visualization that the AI cannot generate on its own.
What it needs
Requires python installed locally. About 8k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
STRING Database Overview 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. When to Use This Skill 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 Quick Start 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. Core Operations 1. Identifier Mapping (stringmapids) Convert gene names, protein names, and external IDs to STRING identifiers. When to use: Starting any STRING analysis, validating protein names, finding canonical identifiers. Usage: Parameters: species: NCBI taxon ID (9606 = human, 10090 = mouse, 7227 = fly) limit: Number of matches per identifier (default: 1) echoquery: Include query term in output (default: 1) Best practice: Always map identifiers first for faster subsequent queries. 2. Network Retrieval (stringnetwork) Get protein-protein interaction network data in tabular format. When to use: Building interaction networks, analyzing connectivity, retrieving interaction evidence. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/string-database