NAME
archive-pubmed, index-pubmed - maintain a local NCBI PubMed archive
SYNOPSIS
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
DESCRIPTION
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.
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.
ENVIRONMENT
- 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.
SEE ALSO
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).