---
name: "index-pubmed"
section: "1"
platform: "linux"
package: "ncbi-entrez-direct"
version: "19.0.20230216+dfsg-2+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/archive-pubmed"
---

# index-pubmed(1)

maintain a local NCBI PubMed archive

Part of [archive-pubmed(1)](/archive-pubmed/1.md).

## 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)](/rchive/1.md) 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 from a user-supplied **Extras/open\_citation\_collection.zip**.

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