Enable Literature Integration to PubMed

Learn how to configure your Vault with a direct connection to the PubMed literature database, so Vault SafetyDocs can automatically search for and import literature articles from PubMed.

About the Feature

With the 25R1 release, Vault SafetyDocs enhances its literature monitoring capabilities by integrating directly with PubMed to support automated literature searches and article intake. This feature improves review efficiency by running scheduled automated PubMed literature searches and then using the search results to automatically create and populate new Literature Review and Literature Article records.

After you have enabled this feature, see the following articles for more information:

• Create Literature Search Groups
• Create Literature Standard Search Terms
• Manage the Literature Review Process

Prerequisites

To enable Literature Integration to PubMed in your Vault, you must:

• Have a PubMed account
• Enable Literature Review Process Management

Overview

Complete the following procedures to enable Literature Integration to PubMed in your Vault:

• Enable the PubMed integration
• Configure Literature Article Automatic Search job settings
• Update object layouts
• Configure Literature Search Term actions

Enable the PubMed Integration

To enable an integration connection between your Vault and the PubMed literature database:

1. Generate an API key using your PubMed (NCBI) account.
2. Copy your newly generated API key.
3. In Vault SafetyDocs, navigate to Admin > Connections > Literature Database: PubMed.
4. In the Details section, select the Literature Database: PubMed record in the Authorization field.
5. From the Client Credential: Literature Database: PubMed page, select Edit.
6. Paste your API key into the Client ID field.
7. Select Save.
8. Navigate back to the parent Connection record by selecting the Literature Database: PubMed link at the top of the page.
9. Within the Details section, ensure the URL field contains the following value: https://eutils.ncbi.nlm.nih.gov/entrez/eutils
10. Update the record’s status to Active.
11. In the dialog that appears, select Yes to confirm the state change and activate the connection.

Configure Literature Article Automatic Search Job Settings

To enable the Literature Article Automatic Search job in your Vault:

1. Navigate to Admin > Operations > Job Definitions > Literature Article Automatic Search Job.
2. Select Edit.
3. In the Status field, select Active.
4. Optional: Update the Vault Time field value to change when Vault runs this job.
5. Optional: Update the Job Owner field value to change to whom Vault sends job notifications.
6. Select Save.

Result

Every day at the specified time, the Literature Article Automatic Search job performs a PubMed database search and creates new SafetyDocs object records using the following flow:

1. Vault compiles a list of all Active-state Literature Standard Search Term records with an Enable Automatic Search field value of Enabled.
2. For each unique Literature Standard Search Term record found, Vault creates a new Literature Review record and populates the fields using data on the originating Literature Standard Search Term record.
3. For each new Literature Review record, Vault creates a child Literature Search Term record and populates its fields using data on the originating Literature Standard Search Term record.
4. For each new Literature Search Term record, Vault searches the PubMed database using its Search Term field value.
5. For each search result, Vault creates a new Literature Article record and populates its fields using data from the PubMed search result and data from the originating Literature Review and Literature Search Term records.
   • If the search result duplicates an existing Literature Article record, Vault updates the newly created Literature Article record’s status and duplicate-related fields to reflect this.
6. Vault uses the current time to update the following field values:
   • The Search Execution Time field value on the Literature Search Term record
   • The Last Search Date field value on the Literature Standard Search Term record

If Vault encounters any errors connecting to PubMed or creating new records, it will send a notification email to the Authorized Connection User on the Literature Database: PubMed Connection record.

Update Object Layouts

To enable Literature Integration to PubMed, update layouts for the following objects:

• Literature Standard Search Term
• Literature Review
• Literature Article
• Literature Search Term

Update the Literature Standard Search Term Layout

To configure the Literature Standard Search Term object layout:

1. Navigate to Admin > Configuration > Objects > Literature Standard Search Term > Layouts > Literature Standard Search Term Detail Page Layout.
2. In the Details section, add the following fields:
   • Search Group
   • Enable Automatic Search
   • Last Search Date
3. Select Save.
4. Select Layout Rules.
5. Select Create and populate the field values as follows:
   • Label: Hide Automatic Search
   • IF this Layout Rule Expression is TRUE: search_database__vr.name__v != 'PubMed'
   • Apply the following display effects:
     • Effect: Hide
     • Type: Fields
     • Values: Enable Automatic Search, Last Search Date
6. Select Save.

Update the Literature Review Layout

To configure the Literature Review object layout:

1. Navigate to Admin > Configuration > Objects > Literature Review > Layouts > Literature Review Detail Page Layout.
2. In the Details section, add the Literature Search Group field.
3. Select Save.

Update the Literature Article Layout

To configure the Literature Article object layout:

1. Navigate to Admin > Configuration > Objects > Literature Article > Layouts > Literature Article Detail Page Layout.
2. In the Article Details section, add the following fields:
   • PubMed ID
   • Medline ID
3. Select Save.

Update the Literature Search Term Layout

To configure the Literature Search Term object layout:

1. Navigate to Admin > Configuration > Objects > Literature Search Term > Layouts > Literature Search Term Detail Page Layout.
2. In the Details section, add the Search Execution Time field.
3. Select Save.

Configure Literature Search Term Actions

To enable Literature Integration to PubMed, configure the following actions on the Literature Search Term object:

• Import Articles From File
• Search Database

Configure the Import Articles From File Action

To configure the Import Articles From File action:

1. Assign the Import Articles From File action to the Literature Search Term object.
2. Add the action as a user action to the Active state of the Literature Search Term Lifecycle.

Configure the Search Database Action

To configure the Search Database action:

1. Assign the Search Database action to the Literature Search Term object.
2. Add the action as a user action to the Active state of the Literature Search Term Lifecycle.