index-pubmed

index-pubmed [[-path] dir [[-temp|-work|-working] dir]]

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.

[-path] dir

Place the local archive in dir.

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

archive-pubmed(1), download-ncbi-data(1), download-pubmed(1), fetch-pubmed(1), index-bioc(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).