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EFILTER(1) NCBI Entrez Direct User's Manual EFILTER(1)
NCBI "NCBI Entrez Direct User's Manual"

NAME

efilter - filter and/or sort NCBI Entrez search results

SYNOPSIS

efilter (efetch -filter) [-help] [-q[uery] str] [-sort field] [-days N] [-datetype field] [-mindate date] [-maxdate date] [-field field] [-pairs field] [-spell] [-pub type] [-journal name] [-released when] [-country name] [-feature type] [-location type] [-molecule type] [-organism type] [-source type] [-division code] [-status alive] [-type type] [-class class] [-kind pathway] [-pathway type]

DESCRIPTION

efilter filters and/or sorts results from a previous edirect(1) search.

It has two implementations: a shell implementation on top of nquire(1) and a historical Perl implementation that amounts to running edirect -filter, enabled by setting the environment variable USE_NEW_EDIRECT to a false value as described in the ENVIRONMENT section. Some options are implementation-specific, as detailed below.

OPTIONS

Query Specification

Limit results to those matching the given query string.

Document Order

Sort results by the given field.

Date Constraint

Keep only results from the past N days.
Which date field (in abbreviated form) to consider.
Start of date range.
End of date range.

Limit by Field

Query words individually in field.
Query overlapping word pairs.

Spell Check

Correct misspellings in query.

Publication Filters

abstract, clinical, english, free, historical, journal, preprint, review, structured.
pnas, "j bacteriol", ...
last_week, last_month, last_year, prev_years.

Sequence Filters

usa:minnesota, united_kingdom, "pacific ocean", ...
gene, mrna, cds, mat_peptide, ...
mitochondrion, chloroplast, plasmid, plastid.
genomic, mrna, trna, rrna, ncrna.
animals, archaea, bacteria, eukaryotes, fungi, human, insects, mammals, plants, prokaryotes, protists, rodents, viruses, ...
genbank, insd, pdb, pir, refseq, swissprot, tpa
Three-letter GenBank division code: bct, con, env, est, gss, htc, htg, inv, mam, pat, phg, pln, pri, rod, sts, syn, una, vrl, or vrt.

Gene Filters

coding, pseudo.

SNP Filters

acceptor, donor, coding, frameshift, indel, intron, missense, nonsense, synonymous.

Biosystems Filters

reactome, wikipathways.

Miscellaneous Arguments

Print usage information.

ENVIRONMENT

Whether to use the current shell implementation or revert to the historical Perl implementation. Canonical true values are 1, on (case-insensitive), true (case-insensitive), and yes (case-insensitive); canonical false values are 0, off (case-insensitive), false (case-insensitive), and no (case-insensitive).

SEE ALSO

edirect(1), esearch(1), nquire(1), exclude-uid-lists(1).

2021-01-20 NCBI