phrase-search1

Usage

Overview

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

mesh

Medline subject headings in general

chem

MeSH chemicals

disz

MeSH diseases

gene

Genes

and the type may be any of

Name

official name

Code

internal identifier

Tree

path within MeSH tree (except for gene)

Desc

description (only for gene)

Term

synonym (except for gene)

-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.