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).