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ARCHIVE-PUBMED(1) NCBI Entrez Direct User's Manual ARCHIVE-PUBMED(1)


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]] [[-pathdir [[-temp|-work[ing]] dir]]



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.


Additionally support retrieval in text ASN.1 Pubmed-entry format.
Additionally produce or update an inverted index.
Fully reindex, complete with an inverted index.
Delete Indices contents and Increment files.
Delete Indices contents, Increment files, and Postings directories.
Download or update auxiliary BioConcept and GeneRIF data.
Incorporate NIH Open Citation Collection data from a user-supplied Extras/
Download needed data via FTP (default).
Download needed data via HTTPS.
Place the local archive in dir.
[-temp|-work[ing]] dir
Place intermediate subtrees in dir.


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.
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).

2023-02-26 NCBI