| name | esearch |
| description | Use when searching NCBI Entrez databases (pubmed, gene, protein, nuccore, snp, geoprofiles) with query strings and field qualifiers to retrieve record UIDs for downstream processing. |
| disable-model-invocation | true |
| user-invocable | true |
esearch
Quick Start
- Command:
esearch -db <database> -query "<query string>"
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/esearch
- Full reference: See references/help.md
When To Use This Tool
- Start an Entrez Direct pipeline by searching for record IDs.
- Search PubMed, Gene, Protein, Nuccore, SRA, and related NCBI databases with field-qualified queries.
- Hand off matching IDs to
efetch, esummary, elink, or xtract.
- Use this whenever you need database-specific search syntax, not a free-form web search.
Common Patterns
esearch -db pubmed -query 'ebola virus[Title/Abstract] AND 2024[pdat]'
esearch -db gene -query 'TP53[gene] AND human[orgn]'
esearch -db assembly -query 'GCF_000001405.40[accn]' | efetch -format docsum
Recommended Workflow
- Pick the Entrez database first, because query fields and sort modes are database-specific.
- Write the query with field tags whenever possible instead of relying on broad keywords.
- Run
esearch, then immediately pipe IDs into efetch, esummary, or elink.
- Use
xtract only after you know what XML structure the downstream command emits.
Guardrails
-db and -query are both required.- Wildcards and unqualified terms can explode result counts; narrow with fields like
[AUTH], [GENE], or [orgn].
- Sort options are database-specific, so do not assume the same
-sort values work everywhere.
esearch gives you IDs, not the final report; plan the next pipeline step before running it at scale.
