.TH INDEX-PUBMED 1 2023-02-11 NCBI "NCBI Entrez Direct User's Manual"
.SH NAME
index\-pubmed \- populate and index a local NCBI PubMed archive from scratch
.SH SYNOPSIS
.B index\-pubmed
.RB [\| \-collect | \-index | \-invert | \-merge | \-promote \|]
[\|\fB\-extras\fP\|]
[\|[\|\fB\-\fP\|]\fBpma2pme\fP|\
[\|\fB\-\fP\|]\fBasn\fP[\|[\|\fB.\fP\|]\fB1\fP\|]\|]
[\|[\|\fB\-path\fP\|]\ \fIdir\fP
[\|[\|\fB\-temp\fP|\fB\-work\fP|\fB\-working\fP\|]\ \fIdir\fP\|]\|]
.SH DESCRIPTION
\fBindex\-pubmed\fP prepares a directory
to hold a local PubMed archive,
then downloads a full database dump from NCBI's servers
(along with MeSH data),
organizes it into an \fBrchive\fP(1) trie,
refreshes and collects the versioned records,
and fully indexes the resulting archive.
It can optionally pick up partway through by explicit request.
.SH OPTIONS
.TP
\fB\-collect\fP
Skip initial preparation and download,
and start with forming an \fBrchive\fP(1) trie.
.TP
\fB\-index\fP
Skip everything up through running \fBrchive\fP(1)
and just perform full indexing.
.TP
\fB\-invert\fP
Skip everything through the first indexing pass
and start with calculating inverted indices.
.TP
\fB\-merge\fP
Skip everything through calculating inverted indices
and start with merging them.
.TP
\fB\-promote\fP
Skip everything through merging inverted indices
and just produce final postins files.
.TP
\fB\-extras\fP
Index extra fields.
.TP
[\|\fB\-\fP\|]\fBpma2pme\fP|[\|\fB\-\fP\|]\fBasn\fP[\|[\|\fB.\fP\|]\fB1\fP\|]
Additionally support retrieval in text ASN.1 Pubmed\-entry format.
.TP
[\|\fB\-path\fP\|]\ \fIdir\fP
Place the local archive in \fIdir\fP.
.TP
[\|\fB\-temp\fP|\fB\-work\fP|\fB\-working\fP\|]\ \fIdir\fP
Place intermediate subtrees in \fIdir\fP.
.SH ENVIRONMENT
.TP
.B EDIRECT_PUBMED_MASTER
Local archive directory to use in the absence of \fB\-path\fP.
Expected to hold an absolute path;
mandatory when not supplying a path on the command line.
.TP
.B EDIRECT_PUBMED_WORKING
Directory to hold intermediate subtrees
in the absence of \fB\-temp\fP|\fB\-work\fP|\fB\-working\fP.
Expected to hold an absolute path.
Defaults to the primary local archive directory when not set.
.SH SEE ALSO
.BR archive\-pubmed (1),
.BR custom\-index (1),
.BR download\-ncbi\-data (1),
.BR download\-pubmed (1),
.BR expand\-current (1),
.BR fetch\-pubmed (1),
.BR index\-extras (1),
.BR phrase\-search (1),
.BR pm\-collect (1),
.BR pm\-index (1),
.BR pm\-invert (1),
.BR pm\-merge (1),
.BR pm\-prepare (1),
.BR pm\-promote (1),
.BR pm\-refresh (1),
.BR pm\-stash (1),
.BR rchive (1),
.BR xtract (1).