NAME

       archive-pubmed, index-pubmed - maintain a local NCBI PubMed archive

SYNOPSIS

       archive-pubmed              [[-]pma2pme|[-]asn[[.]1]]              [[-]daily|[-][re]index]
       [[-]clean|[-]clear|[-]scrub] [[-]biocoll|[-]extras|[-]bioconcepts|[-]generifs] [[-]nihocc]
       [-ftp|-http[s]] [[-path] dir [[-temp|-work[ing]] dir]]

       index-pubmed

DESCRIPTION

       archive-pubmed  prepares a directory to hold a local PubMed archive, then downloads a full
       database dump and auxiliary vocabulary data from NCBI's servers, organizes the  dump  into
       an rchive(1) trie, and refreshes the versioned records.

       index-pubmed is shorthand for archive-pubmed -index, and takes no options.

OPTIONS

       [-]pma2pme|[-]asn[[.]1]
              Additionally support retrieval in text ASN.1 Pubmed-entry format.

       [-]daily
              Additionally produce or update an inverted index.

       [-][re]index
              Fully reindex, complete with an inverted index.

       [-]clean|[-]clear
              Delete Indices contents and Increment files.

       [-]scrub
              Delete Indices contents, Increment files, and Postings directories.

       [-]biocoll|[-]extras|[-]bioconcepts|[-]generifs
              Download or update auxiliary BioConcept and GeneRIF data.

       [-]nihocc
              Incorporate NIH Open Citation Collection data, downloaded as needed.

       -ftp   Download needed data via FTP (default).

       -http[s]
              Download needed data via HTTPS.

       [-path] dir
              Place the local archive in dir.

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

SEE ALSO

       archive-pmc(1), download-ncbi-data(1),  download-pubmed(1),  edict(1),  expand-current(1),
       fetch-pubmed(1),  phrase-search(1),  pm-prepare(1), pm-refresh(1), rchive(1), ref2pmid(1),
       xtract(1).