name: life-sciences-connector description: Query PubMed and scientific databases for protocols, analyze biological data with Biopython, handle HIPAA-compliant data. Use for biology research, protocol searches, sequence analysis, or scientific data handling. Cross-validates sources for high accuracy. Triggers on "PubMed", "biology", "scientific data", "sequences", "protocols", "life sciences", "HIPAA".
Life Sciences Connector
Purpose
Connect to scientific databases (PubMed, Benchling) for protocol queries and biological data analysis with Biopython integration.
When to Use
- Biology research tasks
- Protocol searches
- Scientific data handling
- Sequence analysis
- Lab data integration
- HIPAA-compliant workflows
Core Instructions
PubMed Query
from Bio import Entrez
Entrez.email = "your.email@example.com"
def search_pubmed(term, retmax=5):
"""Search PubMed for articles"""
handle = Entrez.esearch(db="pubmed", term=term, retmax=retmax)
record = Entrez.read(handle)
return record['IdList']
def fetch_article(pmid):
"""Fetch article details"""
handle = Entrez.efetch(db="pubmed", id=pmid, rettype="xml")
return Entrez.read(handle)
# Usage
results = search_pubmed("CRISPR protocol")
for pmid in results:
article = fetch_article(pmid)
print(article['Title'])
Sequence Analysis
from Bio import SeqIO
from Bio.Align import PairwiseAligner
# Parse FASTA
sequences = list(SeqIO.parse("sequences.fasta", "fasta"))
# Align sequences
aligner = PairwiseAligner()
alignments = aligner.align(sequences[0].seq, sequences[1].seq)
print(f"Alignment score: {alignments[0].score}")
HIPAA Compliance
def anonymize_patient_data(data):
"""
Anonymize patient information (HIPAA)
"""
# Remove PHI (Protected Health Information)
phi_fields = [
'name', 'address', 'phone', 'email',
'ssn', 'medical_record_number'
]
anonymized = data.copy()
for field in phi_fields:
if field in anonymized:
anonymized[field] = hash_or_remove(field, data[field])
return anonymized
Guidelines
- Accuracy: Cross-validate sources
- Privacy: Anonymize patient data (HIPAA)
- Citations: Always cite sources
- Verification: Cross-check protocols
Dependencies
- Python 3.8+
- biopython
- requests
- PubMed Entrez API access
Version
v1.0.0 (2025-10-23)