Adding many items to the Benchling Registry manually can take a while. For these situations, you should bulk import items from a spreadsheet.
Set up your spreadsheet
Get an Excel spreadsheet ready with your existing inventory. The first row should specify column headers, which must be unique.
- Entity Name
- One column for each required Schema Field
- One column for each non-required Schema Field
- Sequence (for plasmids / amino acid sequences)
Each row in your spreadsheet corresponds to one registry item in Benchling.
Clean up your data
Before importing your existing data, you’ll need to quickly clean up your spreadsheets.
- Ensure all dropdown field values are among the allowed set in Benchling.
- Ensure any entity or batch link values are exactly the same as they are in Benchling. Tip: Using Registry IDs of linked items can be easier.
- Ensure any date values are in the YYYY-MM-DD format.
- Multiple values in a cell should be separated by a comma (,)
Now you’re ready to import your spreadsheets.
To import files, select the registry button (9 dots) from the left navigation panel. Then, click Import Entities.
In the new window, select the schema (e.g. Cell Line) and registry for your import. You may also designate a folder. Click Next when complete.
To start the import, you may either drag in your Excel file or simply copy and paste your entire spreadsheet (including headers!). Then click Next.
Assign a type for each column in your sheet. The importer will parse through your sheet and import each column. You have 6 types to choose from:
- Entity Name: ID of the file. Each sample must have a unique name.
- Alias: If your lab uses multiple names for an entity, use this type. The file’s alias can be found via search queries
- Schema Field: Required metadata for a file. Hover over the Schema Field type and select the specific schema field that this column represents. In the example below, the column “Resistance” represents the schema field “Antibiotic”. Note: The options in the Schema Field dropdown correspond to the Schema Fields in the Registry settings.
- Custom Field: Optional metadata for a file. Some entities in your inventory may have extra columns that are not crucial for tracking, but still need to be associated with a file.
- Description: Fields from this column go into the description tab of file.
- Ignore: The Benchling importer will ignore this column.
- Bases: This example describes importing files from a custom inventory-type schema. If importing files from a sequence-type schema, the Column Type of “Bases” must be specified. The bases will be used to generate sequence files for each imported entry.
Import columns as file links to access plasmid maps and lineages. Select the appropriate schema field and specify all folders to search for links.
Example: All my lab’s plasmids are located in Benchling in a folder called Example Project. The bacterial strains I’m importing all reference plasmids in this folder; Benchling will automatically create a hyperlink to the plasmid map in the “Plasmid” schema field section of each strain.
Click Next and Benchling will check for any errors. If no errors are detected, click Import to import your inventory into your Registry.