archive-taxonomy(1)

Usage

archive-taxonomy [{[-] daily | [-] [re] index}] [{[-] clean | [-] clear | [-] scrub | [-] scour | [-] erase | [-] zap}] [-info] [{-ftp | -http [s]}]

Overview

archive-taxonomy prepares a directory to hold a local taxonomy 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: Delete Indices contents and Increment files.

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

[-]scour: Delete Indices contents, Increment files, and Postings, Data, Archive, and Sentinel directories.

[-]erase: Delete Indices contents, Increment files, Postings, Data, Archive, and Sentinel directories, and Extras directory contents.

[-]zap: Delete entire archive.

-info: Check whether the archive is complete and up to date; report what's wrong if it isn't.

-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_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.

archive-nihocc(1) maintain a local NIH Open Citation Collection archive archive-nlmnlp(1) maintain a local BioConcepts (PubTator) and GeneRifs archive archive-nmcds(1) maintain a local NCBI RefSeq human mRNA archive archive-pids(1) maintain a local NCBI PubMed / PubMed Central ID map archive-pmc(1) maintain a local NCBI PubMed Central archive archive-pubmed(1) maintain a local NCBI PubMed archive download-ncbi-data(1) download specific data from NCBI's FTP site nquire(1) query NCBI Entrez Utilities, other parameter-based web services, or FTP pm-clean(1) clean a local NCBI Entrez Direct archive pm-prepare(1) prepare directories to hold a local NCBI Entrez Direct archive pm-setup(1) create directories to hold a local NCBI Entrez Direct archive rchive(1) work with a local archive of Entrez document summaries xfetch(1) fetch records from a local NCBI Entrez Direct archive by UID xfilter(1) filter local NCBI Entrez Direct archive search results xinfo(1) output information about the current X setup xlink(1) look up related local NCBI Entrez Direct archive search results xsearch(1) search an indexed local NCBI Entrez Direct archive xtract(1) NCBI Entrez Direct XML conversion and transformation tool

Referred to by

Usage

Overview

Options

Environment

See also

Referred to by