archive-pubmed, index-pubmed - maintain a local NCBI PubMed archive
archive-pubmed [[
-]
pma2pme|[
-]
asn[[
.]
1]] [[
-]
daily|[
-][
re]
index] [[
-]
clean|[
-]
clear|[
-]
scrub] [[
-]
biocoll|[
-]
extras|[
-]
bioconcepts|[
-]
generifs] [[
-]
nihocc] [
-ftp|
-http[
s]] [[
-path]
dir [[
-temp|
-work[
ing]]
dir]]
index-pubmed
archive-pubmed prepares a directory to hold a local PubMed archive, then
downloads a full database dump and auxiliary vocabulary data from NCBI's
servers, organizes the dump into an
rchive(1) trie, and refreshes the
versioned records.
index-pubmed is shorthand for
archive-pubmed -index, and takes no
options.
- [-]pma2pme|[-]asn[[.]1]
- Additionally support retrieval in text ASN.1 Pubmed-entry
format.
- [-]daily
- Additionally produce or update an inverted index.
- [-][re]index
- Fully reindex, complete with an inverted index.
- [-]clean|[-]clear
- Delete Indices contents and Increment
files.
- [-]scrub
- Delete Indices contents, Increment files, and
Postings directories.
- [-]biocoll|[-]extras|[-]bioconcepts|[-]generifs
- Download or update auxiliary BioConcept and GeneRIF
data.
- [-]nihocc
- Incorporate NIH Open Citation Collection data from a
user-supplied Extras/open_citation_collection.zip.
- -ftp
- Download needed data via FTP (default).
-
-http[s]
- Download needed data via HTTPS.
- [-path] dir
- Place the local archive in dir.
- [-temp|-work[ing]] dir
- Place intermediate subtrees in dir.
- EDIRECT_PUBMED_MASTER
- Local archive directory to use in the absence of
-path. Expected to hold an absolute path; mandatory when not
supplying a path on the command line.
- EDIRECT_PUBMED_WORKING
- Directory to hold intermediate subtrees in the absence of
-temp|-work[ing]. Expected to hold an absolute path.
Defaults to the primary local archive directory when not set.
archive-pmc(1),
download-ncbi-data(1),
download-pubmed(1),
edict(1),
expand-current(1),
fetch-pubmed(1),
phrase-search(1),
pm-prepare(1),
pm-refresh(1),
rchive(1),
ref2pmid(1),
xtract(1).