bio-entrez-search
Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.
npx skills add BioTender-max/awesome-bio-agent-skills --skill entrez-search --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.esearch)` to check signatures - CLI: `esearch -version` then `esearch -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 Search **"Find NCBI records matching a query"** -> ESearch returns matching record UIDs (not full records) from one NCBI database; EGQuery returns counts across all databases; EInfo describes a database's searchable fields and update timestamp. The single most important fact: ESearch returns *UIDs* (PMIDs, GI numbers, gene IDs, etc.), not records. To get content the agent must call EFetch or ESummary. Forgetting this is the most common Entrez mistake. - Python: `Entrez.esearch(db=..., term=...)` (BioPython) - CLI: `esearch -db pubmed -query 'CRISPR[Title]'` (Entrez Direct, NBK179288) - R: `entrez_search(db=..., term=...)` (rentrez) ## Required Setup ```python from Bio import Entrez import time Entrez.
- Version Compatibility
- Required Setup
- What ESearch actually does
- Decision table: which utility for which question
- retmax silent caps
- History server (WebEnv/QueryKey) semantics
- Index lag
- Field-qualified query patterns (per database)
- Filter properties that newcomers miss
- Organism field gotcha
- Code patterns
- Single search with explicit retmax
- Paged retrieval (only when enumeration without fetching is required)
- History server for downstream EFetch
What does the bio-entrez-search skill do?
Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill entrez-search --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.