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


index-pubmed - populate and index a local NCBI PubMed archive from scratch


index-pubmed [-collect|-index|-invert|-merge|-promote] [-extras] [[-]pma2pme|[-]asn[[.]1]] [[-pathdir [[-temp|-work|-workingdir]]


index-pubmed prepares a directory to hold a local PubMed archive, then downloads a full database dump from NCBI's servers (along with MeSH data), organizes it into an rchive(1) trie, refreshes and collects the versioned records, and fully indexes the resulting archive. It can optionally pick up partway through by explicit request.


Skip initial preparation and download, and start with forming an rchive(1) trie.
Skip everything up through running rchive(1) and just perform full indexing.
Skip everything through the first indexing pass and start with calculating inverted indices.
Skip everything through calculating inverted indices and start with merging them.
Skip everything through merging inverted indices and just produce final postins files.
Index extra fields.
Additionally support retrieval in text ASN.1 Pubmed-entry format.
Place the local archive in 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|-working. Expected to hold an absolute path. Defaults to the primary local archive directory when not set.


archive-pubmed(1), custom-index(1), download-ncbi-data(1), download-pubmed(1), expand-current(1), fetch-pubmed(1), index-extras(1), phrase-search(1), pm-collect(1), pm-index(1), pm-invert(1), pm-merge(1), pm-prepare(1), pm-promote(1), pm-refresh(1), pm-stash(1), rchive(1), xtract(1).

2023-02-11 NCBI