bio-interaction-databases

Version Compatibility

Reference examples tested with: BioPython 1.83+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Interaction Databases

Query protein-protein interaction (PPI) and gene interaction databases to build and analyze biological networks.

"Get protein interactions for a gene list" → Query PPI databases (STRING, BioGRID, IntAct) via REST APIs to retrieve interaction partners and confidence scores.

• Python: requests.get() against STRING/BioGRID REST endpoints + pandas for parsing

STRING API

Query Interactions

import requests
import pandas as pd
from io import StringIO

STRING_API = 'https://version-12-0.string-db.org/api'

def get_string_interactions(genes, species=9606, score_threshold=400):
    '''Fetch PPI from STRING. species: 9606=human, 10090=mouse, 7227=fly'''
    url = f'{STRING_API}/tsv/network'
    params = {
        'identifiers': '%0d'.join(genes),
        'species': species,
        'required_score': score_threshold,
        'caller_identity': 'bioskills'
    }
    response = requests.get(url, params=params)
    return pd.read_csv(StringIO(response.text), sep='\t')

genes = ['TP53', 'BRCA1', 'MDM2', 'ATM', 'CHEK2', 'CDK2']
interactions = get_string_interactions(genes, score_threshold=700)
interactions[['preferredName_A', 'preferredName_B', 'score']].head()

STRING Confidence Score Tiers

Threshold	Tier	Guidance
150	Low	Includes transferred and text-mined; noisy
400	Medium	Default. Balanced sensitivity/specificity
700	High	Recommended for network analysis. Good confidence
900	Highest	Experimentally validated core. Very stringent

Use 700+ for publication-quality networks. Use 400 for exploratory analysis where recall matters.