NAME¶

phrase-search - search an indexed local NCBI PubMed archive

SYNOPSIS¶

phrase-search [-h|-help|--help] [-path dir] -count|-counts|-query|-filter|-link|-exact|-title|-words|-pairs|-fields|-terms|-totals query...|-convert dbas type type [key]|-lookup tag theme...

DESCRIPTION¶

phrase-search searches an indexed local NCBI PubMed archive (as prepared by index-pubmed(1)).

OPTIONS¶

-h|-help|--help

Print usage information.

-path dir

Search the local archive in dir.

-count

Print terms and counts, merging wildcards.

-counts

Expand wildcards; print individual term counts.

-query

Search on words or phrases in Boolean formulas.

-filter

Filter piped-in output from a previous (quite possibly remote) query.

-exact

Strict search for article round-tripping.

-title

Exact search limited to indexed title field.

-link

Follow links by the given tag (e.g. CITED), merging any duplicates.

-words

Combine searches for individual informative words.

-pairs

Combine searches for pairs of adjacent informative words.

-fields|-terms

Interpret the query as a field name, and list that field's known terms. With an empty query, list supported fields.

-totals

Like -fields, but with term counts.

query...

What to search for in the above modes; may contain standard Boolean operators AND, OR, and NOT, using parentheses as needed for grouping.

-convert dbas type type [key]

Convert identifiers in the specified database from one type to another, accepting either a single identifier on the command line or a newline-delimited list on standard input. The database may be any of

-lookup tag theme...

Look up cross references between internal identifiers read from standard input, where tag identifies a pair of databases (e.g., chdi for chemicals and diseases) and theme... are theme codes of particular interest (with p and m standing in for + and - respectively).

ENVIRONMENT¶

EDIRECT_PUBMED_MASTER

Local archive directory to use in the absence of -path/-master. Expected to hold an absolute path; mandatory when not supplying a path on the command line.

SEE ALSO¶

cit2pmid(1), download-ncbi-data(1), edict(1), fetch-pubmed(1), filter-stop-words(1), index-pubmed(1), rchive(1), theme-aliases(1), word-at-a-time(1), xtract(1).