NAME
fetch-pubmed - fetch records from a local NCBI PubMed archive by UID
SYNOPSIS
fetch-pubmed [-strict|-mixed] [[-path] dir] [-all] [-fresh] [-asn|-xml|-pme] [-turbo]
DESCRIPTION
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.
OPTIONS
- -strict|-mixed
-
Run rchive(1) with -flag strict or -flag mixed, respectively.
- [-path] dir
-
Use 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.
- -asn
-
Retrieve ASN.1.
- -xml
-
Retrieve XML (default).
- -pme
-
Produce ASN.1 on the fly, via pma2pme.
- -turbo
-
Add NEXT_RECORD_SIZE nodes to speed navigation.
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.
SEE ALSO
archive-pubmed(1), cit2pmid(1), ds2pme(1), edict(1), phrase-search(1), pma2pme(1), rchive(1), stream-pubmed(1), xtract(1).