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.
index-pubmed1
Maintain a local ncbi pubmed archive
Part of archive-pubmed(1).
Usage
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
Overview
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
Indicescontents andIncrementfiles.
- [
-]scrub -
Delete
Indicescontents,Incrementfiles, andPostingsdirectories.
- [
-]biocoll|[-]extras|[-]bioconcepts|[-]generifs -
Download or update auxiliary BioConcept and GeneRIF data.
- [
-]nihocc -
Incorporate NIH Open Citation Collection data from a user-supplied
Extras/open_citation_collection.zip.
-
-ftp -
Download needed data via FTP (default).
-
-http[s] -
Download needed data via HTTPS.
[
|
Place the local archive in dir. |
|---|---|
[
|
Place intermediate subtrees in dir. |
Environment
-
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.
Releases
3 releases since Debian 10 (Buster); the text changed 2 times.
-ftp since Debian 12 (Bookworm);
-http since Debian 12 (Bookworm).
-collect until Debian 11 (Bullseye);
-index until Debian 11 (Bullseye);
-invert until Debian 11 (Bullseye);
-merge until Debian 11 (Bullseye);
-promote until Debian 11 (Bullseye).