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
- 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.
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).