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ppi-string-query

Retrieves protein-protein interaction data from the STRING database with confidence scores.

1.1k|132|Updated Apr 13, 2023
Search Tags:#bioinformatics#network-analysis#uniprot#string#ppi#protein-interaction
One-click install
npx skills add https://github.com/PharMolix/OpenBioMed --skill ppi-string-query
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ppi-string-query
Source: https://github.com/PharMolix/OpenBioMed/tree/main/skills/ppi-string-query
Command: npx skills add https://github.com/PharMolix/OpenBioMed --skill ppi-string-query

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Retrieves protein-protein interaction data from the STRING database with confidence scores.

Core Features & Use Cases

  • Retrieve interaction partners for a given UniProt ID.
  • Access multi-channel confidence scores (experimental, text mining, database, etc.) and combined scores.
  • Build protein interaction networks for pathway analysis or functional inference.

Quick Start

Run a STRING query for a UniProt ID and return top interactions.

Frequently Asked Questions about ppi-string-query

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve protein-protein interaction data from the STRING database using a UniProt ID?▼

To retrieve protein-protein interaction data from STRING, query the database using a UniProt ID. The Skill returns interaction partners and multi-channel confidence scores, including experimental, text mining, and database evidence.

Can I filter STRING protein interactions by confidence score for pathway analysis?▼

Yes, you can filter STRING protein interactions by confidence score. Use the required_score parameter to set a minimum threshold, ensuring you only retrieve interaction networks with sufficient evidence for pathway analysis.

What multi-channel confidence scores are available when querying STRING interaction networks?▼

Querying STRING interaction networks provides multi-channel confidence scores, including experimental, text mining, database, and combined scores. These channels help evaluate the reliability of protein interaction partners for functional inference.

How do I limit the number of interaction partners returned for a protein-protein interaction query?▼

Use the limit parameter to restrict the number of interaction partners returned by a STRING query. This helps manage result size when building large protein interaction networks for a given UniProt ID.

Does querying STRING for protein interactions require specifying the species?▼

Yes, querying STRING for protein interactions supports the species parameter. Specifying the species ensures the retrieved interaction data and confidence scores are accurate for the target organism's protein interaction network.

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