---
name: "index-extras"
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/index-extras"
---

# index-extras(1)

populate and index local BioConcepts, GeneRifs, and theme data

## NAME

index-extras - populate and index local BioConcepts, GeneRifs, and theme data

## SYNOPSIS

**index-extras** \[\[**-path**\] *dir* \[\[**-temp**\|**-work**\|**-working**\] *dir*\]\]

## DESCRIPTION

**index-extras** prepares a directory to hold local BioConcepts, GeneRifs, and Percha-Altman theme data, then downloads full dumps from NCBI and Zenodo servers, organizes the data into an [**rchive**(1)](/rchive/1.md) trie, and fully indexes the resulting archive.

## OPTIONS

- \[**-path**\] *dir*

  Place the local archive in *dir*.

- \[**-temp**\|**-work**\|**-working**\] *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**\|**-working**. Expected to hold an absolute path. Defaults to the primary local archive directory when not set.

## SEE ALSO

[**custom-index**(1)](/custom-index/1.md), [**download-ncbi-data**(1)](/download-ncbi-data/1.md), [**index-pubmed**(1)](/index-pubmed/1.md), [**rchive**(1)](/rchive/1.md), [**theme-aliases**(1)](/theme-aliases/1.md), [**xtract**(1)](/xtract/1.md).