bio-entrez-link
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.
npx skills add majiayu000/claude-skill-registry --skill entrez-link-gptomics-bioskills --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Entrez Link Navigate between NCBI databases using Biopython's Entrez module (ELink utility). ## Required Setup ```python 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. ```python # 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 ```python record[0] # First linkset record[0]['DbFrom'] # Source database r
- Required Setup
- Core Function
- Entrez.elink() - Cross-Database Links
- ELink Result Structure
- Common Link Paths
- Gene to Other Databases
- Nucleotide to Other Databases
- Protein to Other Databases
- PubMed Links
- Code Patterns
- Gene to Protein
- Nucleotide to Gene
- Find Related PubMed Articles
- Get All Available Links
What does the bio-entrez-link skill do?
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.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill entrez-link-gptomics-bioskills --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.