Enable Literature Integration to PubMed

With the 25R1 release, SafetyDocs enhances its literature monitoring capabilities by integrating directly with the PubMed literature database 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 Reviews and Literature Articles.

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

26R1 Update: Literature Integration to PubMed Enhancements

With the 26R1 release, SafetyDocs enhances Literature Integration to PubMed by:

• Introducing weekly and monthly literature article search jobs
• Populating the URL on Literature Articles sourced from PubMed
• Adding warnings on the Search Term field of Literature Search Terms to reduce errors during automated searches

See Configure Literature PubMed Integration Enhancements to configure your Vault for this feature.

Prerequisites

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

• Have a PubMed account
• Enable Literature Review Process Management

Overview

To enable Literature Integration to PubMed in your Vault:

• Enable the PubMed integration
• Configure the daily, weekly, or monthly Literature Article Search job, depending on your organization’s business needs¹
• Update object layouts
• Configure the Search Database action
• Grant Literature Search Group object permissions

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 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. Optional: In the Authorized Connection User field, select a user to receive notifications if Vault encounters any PubMed connection errors.
11. Update the record’s status to Active.
12. In the dialog that appears, select Yes to confirm the state change and activate the connection.

Optional: Configure the Literature Article Daily Search Job

To enable the Literature Article Daily Search Job¹ in your Vault:

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

Every day at the specified time, the Literature Article Daily Search job searches the PubMed database and creates new object records using the following flow:

1. Vault compiles a list of all Active-state Literature Standard Search Terms with an Enable Automatic Search field value of Enabled.
2. For each unique Literature Standard Search Term found, Vault creates a new Literature Review and populates the fields using data on the originating Literature Standard Search Term.
3. For each new Literature Review, Vault creates a child Literature Search Term and populates its fields using data on the originating Literature Standard Search Term.
4. For each new Literature Search Term, Vault searches the PubMed database using its Search Term field value.
5. For each search result, Vault creates a new Literature Article and populates its fields using data from the PubMed search result and data from the originating Literature Review and Literature Search Term.
   • If the search result duplicates an existing Literature Article, Vault updates the newly created Literature Article’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
   • The Last Search Date field value on the Literature Standard Search Term

If Vault encounters any errors connecting to PubMed or creating new records, a notification email is sent 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 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.

Grant Literature Search Group Object Permissions

Ensure your permission sets are updated to grant the appropriate level of access for users to the Literature Search Group object according to your organization’s process. Manage object permissions from Admin > Users & Groups > Permission Sets > Literature Actions > Objects > Literature Search Group.

We recommend granting the following Literature Search Group object permissions:

• Read
• Create
• Edit

(26R1) Configure Literature Integration to PubMed Enhancements

To configure Literature Integration to PubMed Enhancements in your Vault:

• Update the Literature Search Term object layout
• Configure field defaults for the Literature Search Term object
• Update the custom Literature Actions permission set
• Configure the daily, weekly, or monthly Literature Article Search job, depending on your organization’s business needs¹

Update the Literature Search Term Object Layout

To update the Literature Search Term object layout:

1. Copy the standard layout for the Literature Search Term object and ensure the new layout is active.
2. Within the copied layout, activate the Standard Search Term Selected layout rule.
3. Set the copied layout as the default.
4. Delete any other existing custom layouts.

Configure Field Defaults for the Literature Search Term Object

Configure field defaults on the Literature Search Term object as follows:

• Literature Database: Enter standard_search_term__vr.search_database__v
• Product: Enter standard_search_term__vr.product__v
• Product Family: Enter standard_search_term__vr.product_family__v
• Search Term: Enter standard_search_term__vr.search_term__v

Update the Custom Literature Actions Permission Set

Ensure your permission sets are updated to grant the appropriate level of access for users according to your organization’s process:

1. Navigate to Admin > Users & Groups > Permission Sets and select the custom Literature Actions permission set.
2. Navigate to the Objects tab and select the Literature Search Term object.
3. Under the Object Control Permissions section, select Edit, then add View permissions for the Search Term object control.
4. Select Save.

Optional: Configure the Literature Article Weekly Search Job

To enable the Literature Article Weekly Search Job¹ in your Vault:

1. Navigate to Admin > Operations > Job Definitions > Literature Article Weekly Search Job.
2. Select Edit.
3. In the Status drop-down, select Active.
4. Optional: Update the Job Owner value to change to whom Vault sends job notifications.
5. Optional: Update the Days of the Week checkboxes to change the day on which Vault runs this job.
6. Optional: Update the Vault Time value to change when on the selected days Vault runs this job.
7. Select Save.

Every week on the specified day and time, the Literature Article Weekly Search Job searches the PubMed database and creates new object records following the same logic as the Literature Article Daily Search Job.

Optional: Configure the Literature Article Monthly Search Job

To enable the Literature Article Monthly Search Job¹ in your Vault:

1. Navigate to Admin > Operations > Job Definitions > Literature Article Monthly Search Job.
2. Select Edit.
3. In the Status drop-down, select Active.
4. Optional: Update the Job Owner value to change to whom Vault sends job notifications.
5. Optional: Update the Repeat By value to define whether Vault runs this job on a specified day of the week or day of the month.
   • If you select Day of Month, select a value from the Repeat on Day drop-down to define the specific day of the month.
   • If you select Day of the Week, select values in the Repeat on drop-downs to define the specific day of the week.
6. Optional: Update the Vault Time value to change when on the selected day Vault runs this job.
7. Select Save.

Every month on the specified day and time, the Literature Article Monthly Search Job searches the PubMed database and creates new object records following the same logic as the Literature Article Daily Search Job.