bio-entrez-link
Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.
npx skills add BioTender-max/awesome-bio-agent-skills --skill entrez-link --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.
## Version Compatibility Reference examples tested with: BioPython 1.83+, Entrez Direct 21.0+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show biopython` then `help(Bio.Entrez.elink)` to check signatures - CLI: `elink -version` then `elink -help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Entrez Link **"Find records linked to this record in another NCBI database"** -> ELink walks the curated, weekly-maintained link tables between Entrez databases. A link is an asserted relationship (e.g. "this PubMed article describes this nucleotide sequence"), not a similarity hit. ELink is the navigation layer of Entrez. The decision that matters most is **which `linkname` to use** — not which databases. A single (`dbfrom`, `db`) pair can have a dozen `linkname` variants distinguishing curation level, evidence type, and direction. Picking the wrong one is the difference between 5 high-confidence matches and 500 noisy automated assertions. - Python: `Entrez.elink(dbfrom=..., db=..., id=..., linkname=...)` (BioPyt
- Version Compatibility
- Required Setup
- The linkname decision (most important)
- gene -> protein (representative example)
- pubmed -> gene
- nucleotide -> protein
- Discover what link names exist for a pair
- Decision table: which cmd for which goal
- Asymmetric link warning
- Per-database link catalog (curated subset)
- gene
- nuccore / nucleotide
- protein
- pubmed
What does the bio-entrez-link skill do?
Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill entrez-link --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.