/bio-entrez-link

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--- name: bio-entrez-link description: Find cross-references between NCBI databases using Biopython Bio.Entrez. Use when navigating from genes to proteins, sequences to publications, finding related records, or discovering database relationships. tool_type: python primary_tool: Bio.Entrez measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

• read_file
• run_shell_command

---

Entrez Link

Navigate between NCBI databases using Biopython's Entrez module (ELink utility).

Required Setup

from Bio import Entrez

Entrez.email = 'your.email@example.com'  # Required by NCBI
Entrez.api_key = 'your_api_key'          # Optional, raises rate limit

Core Function

Entrez.elink() - Cross-Database Links

Find related records in the same or different databases.

# Find proteins linked to a gene
handle = Entrez.elink(dbfrom='gene', db='protein', id='672')
record = Entrez.read(handle)
handle.close()

# Extract linked IDs
linkset = record[0]
if linkset['LinkSetDb']:
    links = linkset['LinkSetDb'][0]['Link']
    protein_ids = [link['Id'] for link in links]
    print(f"Found {len(protein_ids)} linked proteins")

**Key Parameters:** | Parameter | Description | Example | |-----------|-------------|---------| | `dbfrom` | Source database | `'gene'` | | `db` | Target database | `'protein'` | | `id` | Source record ID(s) | `'672'` or `'672,675'` | | `linkname` | Specific link type | `'gene_protein_refseq'` | | `cmd` | Link command | `'neighbor'`, `'neighbor_score'` |

ELink Result Structure

record[0]                          # First linkset
record[0]['DbFrom']                # Source database
record[0]['IdList']                # Input IDs
record[0]['LinkSetDb']             # List of link results
record[0]['LinkSetDb'][0]['DbTo']  # Target database
record[0]['LinkSetDb'][0]['LinkName']  # Link name
record[0]['LinkSetDb'][0]['Link']  # List of linked records
record[0]['LinkSetDb'][0]['Link'][0]['Id']  # Linked ID

Common Link Paths

Gene to Other Databases

| From | To | Link Name | Description | |------|-----|-----------|-------------| | gene | protein | `gene_protein` | All proteins | | gene | protein | `gene_protein_refseq` | RefSeq proteins only | | gene | nucleotide | `gene_nuccore` | Nucleotide sequences | | gene | nucleotide | `gene_nuccore_refseqrna` | RefSeq mRNA | | gene | pubmed | `gene_pubmed` | Related publications | | gene | homologene | `gene_homologene` | Homologs | | gene | snp | `gene_snp` | SNPs in gene | | gene | clinvar | `gene_clinvar` | Clinical variants |

Nucleotide to Other Databases

| From | To | Link Name | Description | |------|-----|-----------|-------------| | nucleotide | protein | `nuccore_protein` | Encoded proteins | | nucleotide | gene | `nuccore_gene` | Gene records | | nucleotide | pubmed | `nuccore_pubmed` | Publications | | nucleotide | taxonomy | `nuccore_taxonomy` | Organism taxonomy | | nucleotide | biosample | `nuccore_biosample` | Sample info | | nucleotide | sra | `nuccore_sra` | Related SRA data |

Protein to Other Databases

| From | To | Link Name | Description | |------|-----|-----------|-------------| | protein | nucleotide | `protein_nuccore` | Coding sequences | | protein | gene | `protein_gene` | Gene records | | protein | pubmed | `protein_pubmed` | Publications | | protein | structure | `protein_structure` | 3D structures | | protein | cdd | `protein_cdd` | Conserved domains |

PubMed Links

| From | To | Link Name | Description | |------|-----|-----------|-------------| | pubmed | pubmed | `pubmed_pubmed` | Related articles | | pubmed | gene | `pubmed_gene` | Mentioned genes | | pubmed | protein | `pubmed_protein` | Mentioned proteins | | pubmed | nucleotide | `pubmed_nuccore` | Mentioned sequences |

Code Patterns

Gene to Protein

from Bio import Entrez

Entrez.email = 'your.email@example.com'

def get_proteins_for_gene(gene_id):
    handle = Entrez.elink(dbfrom='gene', db='protein', id=gene_id, linkname='gene_protein_refseq')
    record = Entrez.read(handle)
    handle.close()

    if not record[0]['LinkSetDb']:
        return []
    return [link['Id'] for link in record[0]['LinkSetDb'][0]['Link']]

protein_ids = get_proteins_for_gene('672')  # BRCA1
print(f"RefSeq proteins: {protein_ids[:5]}")

Nucleotide to Gene

def get_gene_for_nucleotide(nuc_id):
    handle = Entrez.elink(dbfrom='nucleotide', db='gene', id=nuc_id)
    record = Entrez.read(handle)
    handle.close()

    if not record[0]['LinkSetDb']:
        return None
    return record[0]['LinkSetDb'][0]['Link'][0]['Id']

gene_id = get_gene_for_nucleotide('NM_007294')
print(f"Gene ID: {gene_id}")

Find Related PubMed Articles

def get_related_articles(pmid, max_results=10):
    handle = Entrez.elink(dbfrom='pubmed', db='pubmed', id=pmid, linkname='pubmed_pubmed')
    record = Entrez.read(handle)
    handle.close()

    if not record[0]['LinkSetDb']:
        return []
    links = record[0]['LinkSetDb'][0]['Link']
    return [link['Id'] for link in links[:max_results]]

related = get_related_articles('35412348')
print(f"Related articles: {related}")

Get All Available Links

def discover_links(db, record_id):
    handle = Entrez.elink(dbfrom=db, id=record_id, cmd='acheck')
    record = Entrez.read(handle)
    handle.close()

    links = {}
    for linkset in record[0].get('LinkSetDb', []):
        links[linkset['LinkName']] = linkset['DbTo']
    return links

available = discover_links('gene', '672')
for name, target in available.items():
    print(f"