Benchling's Registry serves as a centralized system for managing and tracking samples such as plasmids, cell lines, and small molecules. It enables teams to standardize data, enforce validation rules, and maintain a comprehensive record of research materials throughout their lifecycle.

This guide provides detailed instructions on utilizing the Registry, including entity registration, data import/export, and schema management.

Navigate the Registry

To access the Registry:

Click on the Registry icon (nine-dot grid) in the left navigation panel.
Use the Search bar at the top to locate entities by name, ID, or metadata.
Utilize filters to narrow down search results by schema, project, or other criteria.

For an expanded view, click the directional arrow icon to open the Registry in full-screen mode, allowing for enhanced browsing and data management.

Register a single entity

Use this method when you need to create a single entity manually for example, when entering a new plasmid or cell line that wasn’t part of a bulk experiment. This approach is ideal for ad hoc additions and quality-controlled data entry. To register an individual entity:

Navigate to the Registry and click the local create icon and select Create Entity
Select the appropriate schema (e.g., Plasmid, Cell Line)
Fill in the required metadata fields
Click Register to add the entity to the Registry

Note: For sequence-based entities, ensure that sequence data is provided once the entity is created. Alternatively for DNA/RNA entities, use the global create tool to input bases, import or upload sequences.

Register entities with Registration tables

Registration tables are best when you are working in a Notebook entry and need to register multiple entities as part of your experimental workflow. This method is common for structured and template-driven data entry.

Click on Insert and select Registration table from the menu
Define the action the Registration table will take, choose between:
- Create new entities
- Register existing entities
Use the Schema dropdown and search bar to select the Registry schema
Use the name and registry ID settings dropdown to choose the settings you want the table to apply
Define the folder location that created items will be associated with, choose between:
- Entry’s project folder – items will be associated with the folder that the Entry is in
- None – items will only be associated with the Registry, not a specific folder
- Choose a folder – select an existing folder that you want items to be associated with
Use the preview to verify the table that you are inserting is what you want to use
Click Insert

Register entities

Enter information into the rows of the Registration table
- Add rows using the Add rows button at the bottom of the table
- Use the + icon to add from a structured table, worklist, or spreadsheet
Click Submit to add entities to the Registry

Entities added to a table via structured tables, worklists, or spreadsheets are added to the first empty cell in the destination column. Entities added to different columns will fill the same rows, if those cells don’t yet have values.

Note: when importing entities in bulk, the order they are created may not follow the order of your spreadsheet. This is due to Benchling’s performance optimizations that may parallelize the creation process. For consistent naming, consider asking your admin to use a naming template with renaming options upon Registration.

Modifications can be made after registration by updating fields and re-submitting. You can both register new entities (in new rows) and update entities (in existing rows) at the same time.

Import Registry data in bulk

Use bulk import when you have large datasets to register - such as after screening campaigns or when onboarding historical data. Spreadsheet-based imports help accelerate entity creation and reduce manual entry errors.

Create schema spreadsheet templates

Schema Spreadsheet Templates help ensure that data imports match the exact format expected by Benchling. Use them to guide your team when preparing registration files and reduce formatting or mapping issues during upload. To generate a template for data import:

Navigate to Feature Settings and select Registry Settings
Select the desired schema
Select Export
Select Spreadsheet template to obtain a spreadsheet formatted with the schema's fields

Use this template to prepare data for bulk import into the Registry.

Import multiple entities into the Registry

Navigate to the Registry and click the + icon and select Import entities
Select the schema corresponding to the entities being imported
Select the project folder
Optional - depending on the schema configuration, choose the Name and registry ID settings
Optional - select Transfer entities to new or existing containers to create inventory data
1. Choose the appropriate schema
Click Next
Upload a spreadsheet formatted according to the schema's template
1. Check the data locale, i.e.numbers and date formatting according to the geographical locale
Click Next
Map the spreadsheet columns to the appropriate schema fields
1. Optional - for large datasets, set a time limit, up to 30 minutes, for the import flow
2. Confirm the location (Registry or folders) where the entities created will be linked
Click Next
Resolve any errors that may be found
1. You may skip the rows with unresolved errors or use a text value for any linked items that cannot be matched
2. Optional - save the column mappings for a future import to streamline the process
Click Import to add the entities to the Registry

Update Registry fields in bulk

The update entities feature is useful when you need to update metadata across many existing entities - for example, correcting a shared field value or adding new metadata. Bulk updates allow you to efficiently maintain data quality over time.

To modify multiple entities simultaneously:

Export the relevant registry data to a spreadsheet
Make the necessary changes to the fields in the spreadsheet
Navigate to the Registry and click local create and select Update Entities from the menu
Upload the updated spreadsheet and map the columns to the appropriate fields
Click Update to apply the changes to the Registry.This process streamlines large-scale data updates

Merge duplicate entities

If duplicate entities are introduced—whether through manual entry or bulk imports—use the merge tool to combine them. This preserves your data integrity and ensures that references and relationships remain intact. To consolidate duplicate entities:

Identify the duplicate entities in the Registry application
Use the checkboxes to select the entities to merge
Click Merge and choose the primary entity to retain
Confirm the merge to consolidate data and references

Merging helps maintain a clean and accurate Registry.

Creating specific entities

Create Mixture entities

Mixtures are used to represent composed materials made from registered components—like buffer solutions or compound blends. Define mixtures to capture both recipes (templates) and preps (specific batch preparations).

Mixtures are entities composed of multiple components with specified quantities:

Create a Mixture schema in the Registry
Register a new mixture entity using this schema
In the mixture's metadata, add components by specifying existing registered entities and their quantities
Save the mixture to record its composition

Mixtures can be categorized as recipes (templates) or preps (actual preparations). Mixtures can also be created with structured tables, for more information on how to use mixture tables read the linked article.

Create Molecule entities

Molecule entities enable your team to model, track, and visualize small molecules in Benchling. Use them in the Registry to model chemical compounds, then search for and visualize your molecules using our chemical structure-based search capabilities.

Molecule entities enable you to create and model chemical compounds captured as chemical entities. With molecule entities, you can:

View calculated physicochemical properties
Find molecules via similarity and substructure search
Visualize chemical structures

For more information on how to create, import, and search for molecule entities, see the linked article.

Note: Molecule entities require chemical awareness capabilities that are an add-on to core Benchling capabilities. To enable this for your organization, contact your CX representative and account manager.

Create oligo duplex and oligo conjugate entities

Modeling the connection of a biologic with small molecules creates both complexity and variability in a system of record. The oligo conjugate and oligo duplex tools in Benchling allow you to model oligo conjugates and oligo duplexes by bringing together oligo entities and molecule entities into a composite entity to visualize, validate, and design new bioconjugates, such as siRNA and ASOs, in a structurally accurate manner.

If you are modeling oligo conjugates or oligo duplexes with the complex polymer schema, that means your team's admin has set up a single schema that defines oligo schema(s) as the backbone and other schemas like molecules as components. Because oligo conjugate and oligo duplex schemas are composites of multiple Benchling schemas, it means that the individual component entities must be created and registered before you can create your oligo conjugate or oligo duplex entity.

Once the component entities are created, you can create your oligo conjugate entity. There are a few steps in that process, which at a high level include:

Setting leaving groups on your molecule entities
Creating the oligo conjugate entity
Creating the attachments in the entity
The process can also include editing attachments as you iterate on your process

For more information on how to create oligo duplex and oligo conjugate entities, see the linked article.

Note: Modeling attachments to complex polymers requires chemical awareness capabilities that are an add-on to core Benchling capabilities. To enable this for your organization, contact your CX representative and account manager.

Export data from the Registry

Exporting Registry data allows you to analyze records externally, share information with collaborators, or back up your current state. You can export by schema or entity type in a structured CSV format.

Navigate to the Registry application
Using the checkboxes in the expanded view, select the entities you’d like to export
Click Export and choose the desired format (e.g., CSV, GenBank)
The exported files will be emailed to you

Archive and edit entities

Benchling provides options to archive and delete data, ensuring flexibility in data management. Use archiving to clean up active workspaces without losing historical context, and permanent deletion for removing obsolete content - while staying compliant with your organization’s retention policies.

Note: European industry users and academics can permanently delete any item after archiving it. All other industry users cannot.

To archive an Entity:

Navigate to the Registry application and find the object you would like to archive
Go to the metadata tab of your object
Click the red icon to archive the object

Alternatively, archive entities in bulk by selecting multiple entities with the checkboxes in the registry application and clicking the archive icon.

Restore archived data

Look for the archived entity
- From the project, registry or global search tool, make sure to set up a filter on the Archived objects
Select the object and go to the metadata tab
In the metadata tab click the icon to Unarchive

Permanently deleting data (EU customers only)

Ensure the object is archived
Open the object and click the info button on the right
Click Delete

Caution: Some data may be restricted from permanent deletion due to compliance policies.

Edit entities

While most Registry interactions focus on registering and importing new entities, you may also need to make updates to existing ones. You can edit metadata fields—like names, tags, or classifications—after registration:

Navigate to the entity’s page in the Registry
Click Edit in the metadata panel
Make the desired changes to editable fields
Click Save to apply updates

Note: Some fields (like IDs or schema-specific system fields) may be locked depending on your schema configuration. If a structural change is needed, consider creating a new entity instead.

Frequently asked questions

Q: Can I change the schema of an entity after registration?
A: No, once an entity is registered under a specific schema, its schema cannot be changed.

Q: How do I handle validation errors during registration?
A: Review the error messages provided during registration to identify and correct issues such as missing required fields or duplicate entries.

Q: Is it possible to import entities without registering them immediately?
A: Yes, you can import entities as unregistered and register them at a later time as needed.

Q: Can I restrict access to certain schemas or entities?
A: Yes, permissions can be configured at the schema and project levels to control user access.

Q: Is there a maximum limit to the number of entities that can be bulk imported?

A: There is a limit of creating 5k entities AND containers. This means if you are registering entities and transferring them into containers at the same time (e.g. has 'Transfer entities to new or existing containers' checked during import), the limit would be 2.5k spreadsheet rows (entity + container creation). Please be mindful that Benchling's performance may be dependent on the complexity and the volume of this entity import.

Q: How do I update the structure of a molecule entity?
A: Navigate to the molecule's metadata page, click Edit, make the necessary changes to the structure, and save the updates.

Create and manage entities with the Registry