tools-only Entrez Link - Usage Guide
Overview
This skill enables AI agents to help you navigate between NCBI databases, finding related records across different data types (genes, proteins, sequences, publications).
Prerequisites
pip install biopython
Quick Start
Tell your AI agent what you want to do:
- "Find all proteins encoded by gene ID 672"
- "What publications mention this sequence?"
- "Get the gene record for accession NM_007294"
- "Find 3D structures for BRCA1 protein"
Example Prompts
Gene to Protein
"Get the RefSeq proteins for human BRCA1 (gene ID 672)"
Sequence to Gene
"What gene does NM_007294 belong to?"
Related Publications
"Find PubMed articles related to PMID 35412348"
Multi-Database Navigation
"Start with gene TP53, find its proteins, then get any 3D structures"
Discover Links
"What other databases can I link to from a gene record?"
What the Agent Will Do
- Import Bio.Entrez and set up authentication
- Use elink() to find cross-references
- Parse the LinkSetDb results
- Chain multiple links if navigating several databases
- Return the linked record IDs for further use
Common Link Paths
- Gene -> Protein: Find encoded proteins
- Gene -> Nucleotide: Find mRNA sequences
- Nucleotide -> Gene: Find the gene a sequence belongs to
- Any -> PubMed: Find related publications
- Protein -> Structure: Find 3D structures
Tips
- Provide the record ID when you have it
- Specify which database you're starting from
- Mention the target database or data type you need
- For complex navigations, describe the path you want
- Remember that elink returns IDs - use efetch to get actual records