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.
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-count |
Print terms and counts, merging wildcards. |
-counts
Expand wildcards; print individual term counts.
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-query |
Search on words or phrases in Boolean formulas. |
-filter
Filter piped-in output from a previous (quite possibly remote) query.
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-exact |
Strict search for article round-tripping. | ||
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-title |
Exact search limited to indexed title field. | ||
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-link |
Follow links by the given tag (e.g. CITED), merging any duplicates. | ||
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-words |
Combine searches for individual informative words. | ||
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-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
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mesh |
Medline subject headings in general |
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chem |
MeSH chemicals |
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disz |
MeSH diseases |
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gene |
Genes |
and the type may be any of
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Name |
official name |
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Code |
internal identifier |
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Tree |
path within MeSH tree (except for gene) |
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Desc |
description (only for gene) |
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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).