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.
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).