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