Esearch

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

# 1) PubMed literature search
esearch -db pubmed -query 'ebola virus[Title/Abstract] AND 2024[pdat]'

# 2) Gene search with field qualifiers
esearch -db gene -query 'TP53[gene] AND human[orgn]'

# 3) Search and immediately fetch document summaries
esearch -db assembly -query 'GCF_000001405.40[accn]' | efetch -format docsum

Recommended Workflow

1. Pick the Entrez database first, because query fields and sort modes are database-specific.
2. Write the query with field tags whenever possible instead of relying on broad keywords.
3. Run esearch, then immediately pipe IDs into efetch, esummary, or elink.
4. 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.