Benchling In Vivo Sync App Configurations

Adding a Custom Metadata Field to the In Vivo Sync App

Follow the instructions below to create and map new metadata from In Vivo to Benchling.

1. In In Vivo, add the desired metadata to the corresponding schema in the Glossary
   1. 1. Copy the slug name and store it for later use in this process

2. In Benchling, add the same desired metadata on the related schema (ex. In Vivo Study for Study, In Vivo Animal for Animal)
   1. 1. Copy the field’s API ID and store it for later use in this process

3. In Benchling, select the Connection icon on the left navigation bar
4. Select the Apps tab and open the In Vivo Sync app

5. In the app, select the Configuration sub-tab
6. Scroll to find the relevant schema section (ex. Study Schema, Animal Schema) for the new metadata field that was added to In Vivo
7. In the associated Metadata Mapping JSON box, add the appropriate JSON code to map the new metadata field to the In Vivo Sync App. The JSON should be written as follows: {“benchling_registry_field_API_ID”:“in_vivo_slug_name”}
   1. 1. Enter the Benchling Registry’s field API ID and the In Vivo slug name in the respective locations
      2. If mapping more than one field Separate each JSON line using a comma

8. Press the submit button in the upper right-hand corner of the app. This is critical for the changes to save!

Please note that adding metadata after items have started syncing will not automatically backfill the new metadata field for existing entities. If a backfill is desired, see the section below for information on running a backfill.

1. Update the metadata field for the “Benchling Integration Folder” on the Study or studies you would like backfilled within In Vivo under the “Settings” Section of the study.
   1. 1. Create a folder within Benchling
      2. Copy the API ID of that folder
      3. Paste it into to the “Benchling Integration Folder” field
2. Navigate to the In Vivo Sync App within Benchling and set the date in which studies will be backfilled for after that date
3. Select Run In Vivo Backfill

Removing a Custom Metadata Field from the In Vivo Sync App

Follow the instructions below to remove custom metadata syncing from In Vivo to Benchling.

1. In In Vivo, navigate to the field in the Glossary
2. Select archive
3. In Benchling, navigate to the corresponding Registry field
4. Select archive
5. In Benchling, select the Connection icon on the left navigation bar
6. Select the Apps tab and open the In Vivo Sync app

7. In the app, select the Configuration sub-tab
8. Scroll to find the relevant schema section (ex. Study Schema, Animal Schema) for the new metadata field that was added to In Vivo
9. In the associated Metadata Mapping JSON box, find the appropriate JSON code that maps the metadata fields in the In Vivo Sync App. The JSON should be written as follows: {“benchling_registry_field_API_ID”:“in_vivo_slug_name”}. You can use the field API ID and/or the slug name to help locate the applicable code.
10. Delete the applicable JSON code, being sure to check for appropriate syntax after updating (ex. Remove unnecessary commas, ensure brackets are present)
11. Press the submit button in the upper right-hand corner of the app. This is critical for the changes to save!

Remapping an Existing Custom Metadata Field in the In Vivo Sync App

Follow the instructions below to archive an existing field in In Vivo, create a new field in In Vivo, and re-map the field to successfully sync from In Vivo to Benchling.

1. In In Vivo, navigate to the field in the Glossary
   1. 1. Copy the slug name and store it for later use in this process

2. Select archive
3. In In Vivo, create the new desired field if not already created
   1. 1. Copy the slug name and store it for later use in this process
4. In Benchling, select the Connection icon on the left navigation bar
5. Select the Apps tab and open the In Vivo Sync app

6. In the app, select the Configuration sub-tab
7. Scroll to find the relevant schema section (ex. Study Schema, Animal Schema) for the new metadata field that was added to In Vivo
8. In the associated Metadata Mapping JSON box, find the appropriate JSON code that maps the metadata fields in the In Vivo Sync App. The JSON should be written as follows: {“benchling_registry_field_API_ID”:“in_vivo_slug_name”}. You can use the field API ID and/or the slug name to help locate the applicable code.
9. Replace the applicable “in_vivo_slug_name” from the archived In Vivo field with the “in_vivo_slug_name” from the new field, being sure to check for appropriate syntax after updating (ex. Ensure quotation marks are present, ensure brackets are present)

10. Press the submit button in the upper right-hand corner of the app. This is critical for the changes to save!