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bio-entrez-link
Maintainer FreedomIntelligence · Last updated April 1, 2026
Retrieve linked records across NCBI Entrez databases.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-entrez-link
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Navigate between NCBI databases using Biopython's Entrez module (ELink utility).
- handle = Entrez.elink(dbfrom='gene', db='protein', id='672') record = Entrez.read(handle) handle.close().
Source Doc
Excerpt From SKILL.md
Entrez.elink() - Cross-Database Links
Find related records in the same or different databases.
## 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' |
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 |
Use cases
- Use bio-entrez-link in research workflows aligned with this subject area.
- Follow the upstream documentation for the full working procedure.
Not for
- Do not assume this entry replaces the original database documentation or API notes.
Upstream Related Skills
- entrez-search - Search databases before linking
- entrez-fetch - Retrieve records after finding linked IDs
- batch-downloads - Download many linked records efficiently
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