eric861129/skills_all-in-one/string-database

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/string_api.py) for all STRING REST API operations
2. Comprehensive reference documentation (references/string_reference.md) with detailed API specifications

When users request STRING data, determine which operation is needed and use the appropriate function from scripts/string_api.py.

Core Operations

1. Identifier Mapping (string_map_ids)

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:

from scripts.string_api import string_map_ids
# Map single protein
result = string_map_ids('TP53', species=9606)
# Map multiple proteins
result = string_map_ids(['TP53', 'BRCA1', 'EGFR', 'MDM2'], species=9606)
# Map with multiple matches per query
result = string_map_ids('p53', species=9606, limit=5)

Parameters:

• species: NCBI taxon ID (9606 = human, 10090 = mouse, 7227 = fly)
• limit: Number of matches per identifier (default: 1)
• echo_query: Include query term in output (default: 1)

Best practice: Always map identifiers first for faster subsequent queries.

2. Network Retrieval (string_network)

Get protein-protein interaction network data in tabular format.

When to use: Building interaction networks, analyzing connectivity, retrieving interaction evidence.

Usage:

from scripts.string_api import string_network
# Get network for single protein
network = string_network('9606.ENSP00000269305', species=9606)
# Get network with multiple proteins
proteins = ['9606.ENSP00000269305', '9606.ENSP00000275493']
network = string_network(proteins, required_score=700)
# Expand network with additional interactors
network = string_network('TP53', species=9606, add_nodes=10, required_score=400)
# Physical interactions only
network = string_network('TP53', species=9606, network_type='physical')

Parameters:

• required_score: Confidence threshold (0-1000)
• 150: low confidence (exploratory)
• 400: medium confidence (default, standard analysis)
• 700: high confidence (conservative)
• 900: highest confidence (very stringent)
• network_type: 'functional' (all evidence, default) or 'physical' (direct binding only)
• add_nodes: Add N most connected proteins (0-10)

Output columns: Interaction pairs, confidence scores, and individual evidence scores (neighborhood, fusion, coexpression, experimental, database, text-mining).

3. Network Visualization (string_network_image)

Generate network visualization as PNG image.

When to use: Creating figures, visual exploration, presentations.

Usage:

from scripts.string_api import string_network_image
# Get network image
proteins = ['TP53', 'MDM2', 'ATM', 'CHEK2', 'BRCA1']
img_data = string_network_image(proteins, species=9606, required_score=700)
# Save image
with open('network.png', 'wb') as f:
    f.write(img_data)
# Evidence-colored network
img = string_network_image(proteins, species=9606, network_flavor='evidence')
# Confidence-based visualization
img = string_network_image(proteins, species=9606, network_flavor='confidence')
# Actions network (activation/inhibition)
img = string_network_image(proteins, species=9606, network_flavor='actions')

Network flavors:

• 'evidence': Colored lines show evidence types (default)
• 'confidence': Line thickness represents confidence
• 'actions': Shows activating/inhibiting relationships

4. Interaction Partners (string_interaction_partners)

Find all proteins that interact with given protein(s).

When to use: Discovering novel interactions, finding hub proteins, expanding networks.

Usage:

from scripts.string_api import string_interaction_partners
# Get top 10 interactors of TP53
partners = string_interaction_partners('TP53', species=9606, limit=10)
# Get high-confidence interactors
partners = string_interaction_partners('TP53', species=9606,
                                      limit=20, required_score=700)
# Find interactors for multiple proteins
partners = string_interaction_partners(['TP53', 'MDM2'],
                                      species=9606, limit=15)

Parameters:

• limit: Maximum number of partners to return (default: 10)
• required_score: Confidence threshold (0-1000)

Use cases:

• Hub protein identification
• Network expansion from seed proteins
• Discovering indirect connections

5. Functional Enrichment (string_enrichment)

Perform enrichment analysis across Gene Ontology, KEGG pathways, Pfam domains, and more.

When to use: Interpreting protein lists, pathway analysis, functional characterization, understanding biological processes.

Usage:

from scripts.string_enrichment import string_enrichment
# Enrichment for a protein list
proteins = ['TP53', 'MDM2', 'ATM', 'CHEK2', 'BRCA1', 'ATR', 'TP73']
enrichment = string_enrichment(proteins, species=9606)
# Parse results to find significant terms
import pandas as pd
df = pd.read_csv(io.StringIO(enrichment), sep='\t')
significant = df[df['fdr'] < 0.05]

Enrichment categories:

• Gene Ontology: Biological Process, Molecular Function, Cellular Component
• KEGG Pathways: Metabolic and signaling pathways
• Pfam: Protein domains
• InterPro: Protein families and domains
• SMART: Domain architecture
• UniProt Keywords: Curated functional keywords

Output columns:

• category: Annotation database (e.g., "KEGG Pathways", "GO Biological Process")
• term: Term identifier
• description: Human-readable term description
• number_of_genes: Input proteins with this annotation
• p_value: Uncorrected enrichment p-value
• fdr: False discovery rate (corrected p-value)

Statistical method: Fisher's exact test with Benjamini-Hochberg FDR correction.

Interpretation: FDR < 0.05 indicates statistically significant enrichment.

6. PPI Enrichment (string_ppi_enrichment)

Test if a protein network has significantly more interactions than expected by chance.

When to use: Validating if proteins form functional module, testing network connectivity.

Usage:

from scripts.string_api import string_ppi_enrichment
import json
# Test network connectivity
proteins = ['TP53', 'MDM2', 'ATM', 'CHEK2', 'BRCA1']
result = string_ppi_enrichment(proteins, species=9606, required_score=400)
# Parse JSON result
data = json.loads(result)
print(f"Observed edges: {data['number_of_edges']}")
print(f"Expected edges: {data['expected_number_of_edges']}")
print(f"P-value: {data['p_value']}")

Output fields:

• number_of_nodes: Proteins in network
• number_of_edges: Observed interactions
• expected_number_of_edges: Expected in random network
• p_value: Statistical significance

Interpretation:

• p-value < 0.05: Network is significantly enriched (proteins likely form functional module)
• p-value ≥ 0.05: No significant enrichment (proteins may be unrelated)

7. Homology Scores (string_homology)

Retrieve protein similarity and homology information.

When to use: Identifying protein families, paralog analysis, cross-species comparisons.

Usage:

from scripts.string_api import string_homology
# Get homology between proteins
proteins = ['TP53', 'TP63', 'TP73']  # p53 family
homology = string_homology(proteins, species=9606)

Use cases:

• Protein family identification
• Paralog discovery
• Evolutionary analysis

8. Version Information (string_version)

Get current STRING database version.

When to use: Ensuring reproducibility, documenting methods.

Usage:

from scripts.string_api import string_version
version = string_version()
print(f"STRING version: {version}")

Common Analysis Workflows

Workflow 1: Protein List Analysis (Standard Workflow)

Use case: Analyze a list of proteins from experiment (e.g., differential expression, proteomics).

from scripts.string_api import (string_map_ids, string_network,
                                string_enrichment, string_ppi_enrichment,
                                string_network_image)
# Step 1: Map gene names to STRING IDs
gene_list = ['TP53', 'BRCA1', 'ATM', 'CHEK2', 'MDM2', 'ATR', 'BRCA2']
mapping = string_map_ids(gene_list, species=9606)
# Step 2: Get interaction network
network = string_network(gene_list, species=9606, required_score=400)
# Step 3: Test if network is enriched
ppi_result = string_ppi_enrichment(gene_list, species=9606)
# Step 4: Perform functional enrichment
enrichment = string_enrichment(gene_list, species=9606)
# Step 5: Generate network visualization
img = string_network_image(gene_list, species=9606,
                          network_flavor='evidence', required_score=400)
with open('protein_network.png', 'wb') as f:
    f.write(img)
# Step 6: Parse and interpret results

Workflow 2: Single Protein Investigation

Use case: Deep dive into one protein's interactions and partners.

from scripts.string_api import (string_map_ids, string_interaction_partners,
                                string_network_image)
# Step 1: Map protein name
protein = 'TP53'
mapping = string_map_ids(protein, species=9606)
# Step 2: Get all interaction partners
partners = string_interaction_partners(protein, species=9606,
                                      limit=20, required_score=700)
# Step 3: Visualize expanded network
img = string_network_image(protein, species=9606, add_nodes=15,
                          network_flavor='confidence', required_score=700)
with open('tp53_network.png', 'wb') as f:
    f.write(img)

Workflow 3: Pathway-Centric Analysis

Use case: Identify and visualize proteins in a specific biological pathway.

from scripts.string_api import string_enrichment, string_network
# Step 1: Start with known pathway proteins
dna_repair_proteins = ['TP53', 'ATM', 'ATR', 'CHEK1', 'CHEK2',
                       'BRCA1', 'BRCA2', 'RAD51', 'XRCC1']
# Step 2: Get network
network = string_network(dna_repair_proteins, species=9606,
                        required_score=700, add_nodes=5)
# Step 3: Enrichment to confirm pathway annotation
enrichment = string_enrichment(dna_repair_proteins, species=9606)
# Step 4: Parse enrichment for DNA repair pathways
import pandas as pd
import io
df = pd.read_csv(io.StringIO(enrichment), sep='\t')
dna_repair = df[df['description'].str.contains('DNA repair', case=False)]

Workflow 4: Cross-Species Analysis

Use case: Compare protein interactions across different organisms.

from scripts.string_api import string_network
# Human network
human_network = string_network('TP53', species=9606, required_score=700)
# Mouse network
mouse_network = string_network('Trp53', species=10090, required_score=700)
# Yeast network (if ortholog exists)
yeast_network = string_network('gene_name', species=4932, required_score=700)

Workflow 5: Network Expansion and Discovery