bio-entrez-fetch
Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.
npx skills add BioTender-max/awesome-bio-agent-skills --skill entrez-fetch --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.efetch)` to check signatures - CLI: `efetch -version` then `efetch -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 Fetch **"Download a record by accession from NCBI"** -> EFetch returns the full record content in a chosen format (FASTA, GenBank, XML, MEDLINE, etc.). ESummary returns a lightweight "docsum" object — much faster when only metadata is needed. The agent's first decision is always: does this workflow need the full record, or just metadata? ESummary is 5-10x cheaper than EFetch for the equivalent record set. For "tell me the organism, length, and definition line for 10,000 accessions", ESummary wins by an order of magnitude. - Python: `Entrez.efetch(db=..., id=..., rettype=..., retmode=...)` (BioPython) - CLI: `efetch -db nucleotide -id NM_007294 -format gb` (Entrez Direct, NBK179288) - R: `entrez_fetch(db=
- Version Compatibility
- Required Setup
- Decision matrix: rettype + retmode per database
- nucleotide / protein
- pubmed
- gene
- sra
- taxonomy
- gds (GEO)
- GI deprecation (still bites in 2026)
- ESummary vs EFetch triage
- XML schema brittleness
- Code patterns
- Single sequence by accession
What does the bio-entrez-fetch skill do?
Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill entrez-fetch --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.