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


fetch-pubmed - fetch records from a local NCBI PubMed archive by UID


fetch-pubmed [-strict|-mixed] [[-path] dir] [-all] [-fresh] [-asn|-xml|-pme] [-turbo]


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.


Run rchive(1) with -flag strict or -flag mixed, respectively.
Use the local archive in dir.
Dump the entire archive.
Dump the entire archive into filenames of the form pubmed001.xml.gz, using any existing such files as a starting point.
Retrieve ASN.1.
Retrieve XML (default).
Produce ASN.1 on the fly, via pma2pme.
Add NEXT_RECORD_SIZE nodes to speed navigation.


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), cit2pmid(1), ds2pme(1), edict(1), phrase-search(1), pma2pme(1), rchive(1), stream-pubmed(1), xtract(1).

2023-02-20 NCBI