NAME¶

archive-nlmnlp - maintain a local BioConcepts (PubTator) and GeneRifs archive

SYNOPSIS¶

archive-nlmnlp [[-]daily|[-][re]index] [[-]clean|[-]clear|[-]scrub|[-]scour|[-]scratch|[-]erase] [-ftp|-http[s]]

DESCRIPTION¶

archive-nlmnlp prepares a directory to hold a local BioConcepts (PubTator) and GeneRifs archive, then downloads a full database dump from NCBI's servers, organizes the dump into an rchive(1) trie, and refreshes the versioned records.

OPTIONS¶

[-]daily

Additionally produce or update an inverted index.

[-][re]index

Fully reindex, complete with an inverted index.

[-]clean|[-]clear|[-]scrub|[-]scour|[-]scratch|[-]erase

Delete Scratch directories.

-ftp

Download needed data via FTP (default).

-http[s]

Download needed data via HTTPS.

ENVIRONMENT¶

EDIRECT_LOCAL_ARCHIVE

Local archive directory to use; expected to hold an absolute path.

EDIRECT_LOCAL_WORKING

Directory to hold intermediate subtrees; expected to hold an absolute path. Defaults to the local archive directory when not set.

SEE ALSO¶

archive-nihocc(1), archive-nmcds(1), archive-pids(1), archive-pmc(1), archive-pubmed(1), archive-taxonomy(1), nquire(1), pm-clean(1), pm-prepare(1), pm-setup(1), rchive(1), xfetch(1), xfilter(1), xinfo(1), xlink(1), xsearch(1), xtract(1).