> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management.md).

# Organization DB management

Use the **Organization DB Management** card to review, configure, search, and download [organization databases](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/organization-databases.md). Organization databases provide custom variant or region [annotations](/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/annotations-from-organization-databases.md) for case analysis.

<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-32aa330f801564465e516c6eab39c0804dd842d2%2Fimage%20(48).png?alt=media" alt=""><figcaption><p><strong>Organization DB management card.</strong></p></figcaption></figure>

## Configure databases

[Configure](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database.md) historic, noise, curated, and custom BED annotation databases. You can also [modify](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/modifying-database-settings.md) the settings of a registered database.

{% hint style="info" %}
Configuring a database and modifying its settings require special [permissions](/emedgene/emedgene-analyze-manual/settings/user_roles/iam-scopes-emedgene-roles.md). Users without these permissions can still review the database table.
{% endhint %}

## Review database details

The table in the **Organization DB management** card lists the following details for each database:

* **DB name**
* **DB type**
* **File name**
* **Human ref**: Genome reference
* **Variant type**
* For CNV databases: **Candidate (C) and annotation (A)** [**overlap percentages**](/emedgene/emedgene-analyze-manual/variant_page/related_cases_section/cnv_overlap_percentage.md) used to compare case variants with the database.
* **Fields**
* **Last edited**
* **AI Shortlist** (On/Off): Indicates whether the **AI Shortlist** factors in allele frequencies from the database. When enabled, variants with an allele frequency above 10% are excluded from the list.
* **Active** (On/Off): Indicates whether annotation from the database is applied to variants in new and reanalyzed cases.

{% hint style="info" %}
For custom BED annotation databases, **Variant type**, **Overlap**, and **Fields** are `N/A`, and **AI Shortlist** setting is always off.
{% endhint %}

## Search for a database

Use the search bar above the table to find a database by name.

## Download a database

Select the **Download** (<i class="fa-arrow-down-from-line">:arrow-down-from-line:</i>) icon on the right of a database row.

* Historic, noise, and curated databases download as VCF files.
* Custom BED annotation databases download as BED files.

## Learn more

<table data-view="cards"><thead><tr><th></th><th></th><th></th></tr></thead><tbody><tr><td><strong>Organization databases</strong></td><td>Learn about historic, noise, curated, and custom BED Annotation databases.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/organization-databases.md">Learn more</a></td></tr><tr><td><strong>Configuring an organization database</strong></td><td>Create, register, and configure an organization database.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database.md">Learn more</a></td></tr><tr><td><strong>Annotations from organization databases</strong></td><td>Learn how organization databases provide custom variant and region annotations.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/annotations-from-organization-databases.md">Learn more</a></td></tr></tbody></table>


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