fetch-pubmed

fetch-pubmed [-strict|-mixed] [[-path] dir] [-all] [-fresh]

fetch-pubmed reads a list of record IDs from standard input and prints to standard output the corresponding portions of a local NCBI PubMed archive produced by archive-pubmed(1), typically for further processing by xtract(1) or the like.

[-strict|-mixed]

Run rchive(1) with -flag strict or -flag mixed, respectively.

[-path] dir

Place the local archive in dir.

-all

Dump the entire archive.

-fresh

Dump the entire archive into filenames of the form pubmed001.xml.gz, using any existing such files as a starting point.

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.

archive-pubmed(1), phrase-search(1), rchive(1), stream-pubmed(1), xtract(1).