| name | efilter |
| description | Use when filtering Entrez search results by date, organism, publication type, sequence features, or other database-specific criteria in bioinformatics pipelines. |
| disable-model-invocation | true |
| user-invocable | true |
efilter
Quick Start
- Command:
efilter
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/efilter
- Full reference: See
references/help.md
When To Use This Tool
- Narrow an existing Entrez result set by date, organism, publication type, sequence feature, SNP class, or assembly status.
- Add database-specific shortcuts after
esearch or elink without rewriting the whole query string.
- Prototype filters interactively before folding them back into a single
esearch command.
Common Patterns
esearch -db pubmed -query "opsin gene conversion" \
| efilter -mindate 2015 \
| efetch -format docsum
esearch -db protein -query hemoglobin \
| efilter -organism mammals -source refseq
esearch -db assembly -query "Escherichia coli" \
| efilter -status latest
Recommended Workflow
- Start with an
esearch or elink pipeline that already identifies the right Entrez database.
- Apply only the shortcut family that matches that database category, such as
-pub for PubMed or -organism for sequence databases.
- Inspect counts or summaries if the filter logic is non-obvious.
- Fetch full records only after the filter stage is stable.
Guardrails
- The local executable is just a wrapper around
esearch -filter, so it depends on valid Entrez pipeline state and is not an offline post-processor.
- Shortcut families are database-specific; mixing incompatible groups produces confusing or empty results.
- Many
efilter shortcuts can also be expressed directly in esearch, which is often cleaner once you know the final query.
- In this local install, help output can still emit network-version-check noise from EDirect before printing the real usage text.
