NAME¶

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

SYNOPSIS¶

index-pubmed [-collect|-index|-invert|-merge|-promote] [-extras] [[-]pma2pme|[-]asn[[.]1]] [[-path] dir [[-temp|-work|-working] dir]]

DESCRIPTION¶

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.

OPTIONS¶

-collect

Skip initial preparation and download, and start with forming an rchive(1) trie.

-index

Skip everything up through running rchive(1) and just perform full indexing.

-invert

Skip everything through the first indexing pass and start with calculating inverted indices.

-merge

Skip everything through calculating inverted indices and start with merging them.

-promote

Skip everything through merging inverted indices and just produce final postins files.

-extras

Index extra fields.

[-]pma2pme|[-]asn[[.]1]

Additionally support retrieval in text ASN.1 Pubmed-entry format.

[-path] dir

Place the local archive in dir.

[-temp|-work|-working] 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|-working. Expected to hold an absolute path. Defaults to the primary local archive directory when not set.

SEE ALSO¶

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).