Is it possible to visualize the networks?

Yes, the skill can generate and save PNG images of interaction networks with customizable coloring based on evidence types, confidence levels, or biological actions.

What types of interaction evidence are provided?

The skill retrieves evidence scores from multiple sources, including genomic neighborhood, gene fusion, co-occurrence, co-expression, experimental data, curated databases, and text-mining.

Can I use this skill to perform pathway analysis?

Yes, the skill includes functional enrichment for KEGG pathways, Gene Ontology (GO), and Pfam domains to characterize protein lists.

What organisms does the STRING database skill support?

It supports over 5000 species, including humans (NCBI taxon 9606), mice (10090), and fruit flies (7227).

How does the skill handle different protein identifiers?

It includes a dedicated mapping operation that converts common gene names, protein names, and external IDs into canonical STRING identifiers for accurate querying.

STRING Protein Interaction Database

Name: STRING Protein Interaction Database
Author: ricable

byricable

•

Data Science & ML

Accesses the STRING database to analyze protein-protein interaction networks and perform functional enrichment for systems biology.

The STRING Database skill integrates the comprehensive STRING API into the Claude Code environment, allowing researchers and bioinformaticians to map protein identifiers, retrieve complex interaction networks, and perform statistical enrichment analysis. Covering over 5000 species and billions of interactions, it facilitates the discovery of protein partners, pathway analysis, and network visualization directly within a development or analysis workflow, streamlining the interpretation of proteomics and genomics data.

Key Features

01Conducts PPI enrichment tests to determine statistical significance of network modules

02Maps gene and protein identifiers to canonical STRING IDs across 5000+ species

03Performs functional enrichment analysis using GO, KEGG, Pfam, and InterPro databases

04Retrieves high-confidence protein-protein interaction (PPI) networks with evidence scores

05Generates evidence-based network visualizations in PNG format

061 GitHub stars

Use Cases

01Identifying hub proteins and novel interaction partners for specific biological targets

02Analyzing differentially expressed protein lists from proteomics or transcriptomics experiments

03Validating the functional connectivity of protein clusters using statistical enrichment analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ricable/ultimate-ai-agent string-database

For use in Claude.ai and ChatGPT

Download Skill