Configure Benchling Biologics schemas and formats

Benchling Biologics structures antibody data into searchable, first-class protein entities with 2D structural awareness — domains assembled into chains, informed by a configurable format, and represented visually as a glyph. Registry admins complete this configuration before users begin registering proteins. Use this article to set up component schemas, protein formats, and protein entity schemas on your tenant.

Note: Benchling Biologics requires a separate license. Contact your account manager for details. Before you begin configuration, confirm with Benchling Support that your tenant has been fully set up for Biologics.

Before you begin

Benchling Biologics configuration builds on standard Registry schema concepts. Review Configure Registry schemas before continuing if you're new to creating entity schemas, configuring fieldsets, and setting naming templates in Benchling.

Permissions

Two roles are relevant for Biologics configuration. Registry Admin permissions follow the standard Registry permission model — see Configure Registry schemas for details on how to set those. The Protein Format Admin role is specific to Biologics.

To assign the Protein Format Admin role:

1. Open the tenant admin console
2. Find the relevant user, team, or org
3. Select … then choose Manage roles
4. Check the box next to Protein Format Admin
5. Click Save

Follow the configuration order

We recommend following this order to avoid configuration errors.

1. Create component schemas
2. Create the protein fieldset 
3. Create protein formats 
4. Create protein entity schemas

The sections below walk through each step in detail.

Create component schemas

Component schemas are the building blocks of a protein entity — they represent the domains, chains, variable pairs, and antigens that make up an antibody. Benchling Biologics uses an enforced data model. These schemas include Benchling-managed fields and uniqueness constraints that can't be modified or removed. You can add custom fields alongside the enforced fields, but you can't rename, remove, or change the enforced ones.

For general guidance on naming, fields, and schema configuration options, see Configure Registry schemas.

Create seven component schemas before setting up protein entity schemas. Use the table below to identify the correct entity type and protein component type for each one. You can create these schemas in any order. At least the AA domain and AA chain schemas must exist before you can create protein entity schemas.

To create a component schema:

1. Navigate to Registry settings > Entity schemas
2. Click Create 
3. Select the entity type from the Entity type dropdown — refer to the table above
4. Select the protein component type from the Protein component type dropdown — refer to the table above
5. Set a prefix and unique schema name
6. If your team needs to capture additional metadata alongside the enforced fields, add custom fields — for field configuration options, see Configure Registry schemas
7. Click Next to save the entity settings and proceed to the Access Policies page
8. Configure access policies to control who can create, edit, or manage access to the schema
9. Click Create

Note: Enforced fields are indicated by an antibody-shaped icon in the schema editor. They can't be renamed, removed, or changed. Uniqueness constraints on component schemas are also managed by Benchling and can't be modified.

Note: If you create more than one schema for a given component type, you'll need to manually assign each enforced field to the appropriate schema when setting up protein entity schemas. If you have only one schema per component type, Benchling assigns it automatically.

Note: There's no conversion path from existing AA Sequence, custom entity, or Molecule schemas to the Antigen component type. To designate an existing schema as an Antigen, archive it and recreate it with the Antigen component type selected.

Create the protein fieldset

All protein entity schemas should share a single fieldset. Using a shared fieldset means you configure your naming template, uniqueness constraint, and computed biochemical property fields once and apply them across all formats. For general guidance on creating and managing fieldsets, see Configure Registry schemas.

The protein fieldset should include:

• The Protein structure uniqueness constraint, which evaluates uniqueness as the combination of all chains and domains in a given format
• A prefix (for example, ab# for a consistent numbering convention across all protein entities)
• Computed biochemical property fields, if your team needs them — contact Benchling Support to configure these

Note: Don't add Species, Target, or similar fields to the protein fieldset. These values are inherent to specific component parts and Benchling will compute and surface them on the protein entity automatically in a future release.

To create the protein fieldset:

1. Navigate to Registry settings > Fieldsets
2. Click Create
3. Enter a name and prefix for the fieldset
4. Add the Protein structure uniqueness constraint
5. Click Next to save the fieldset settings and proceed to the Access Policies page
6. Configure access policies to control who can create, edit, or manage access to the fieldset
7. Click Create

Note: You can add custom fields and a naming template to the fieldset to capture additional metadata on protein entities. If adding a naming template, do so after you've created both the fieldset and your first protein entity schema — adding it before the schema is saved can cause a conflict during initial schema creation. For field configuration options, see Configure Registry schemas.

Create protein formats

A format defines the structural blueprint of a protein — its chains, domains, and how they interact. Formats power both the visual glyph and the data shape of each protein entity. You need at least one format before you can create a protein entity schema.

Benchling provides 12 built-in formats out of the box: IgG, Bispecific, Nanobody, scFv, Fab, TCR, Diabody, Triabody, Tetrabody, IgA, IgM Pentamer, and IgM Hexamer. Each built-in format comes with a predefined glyph and a set of chain and domain fields. Built-in formats can't be archived.

For formats not covered by the built-in library, you can create custom formats using VERITAS (Verified Taxonomy for Antibodies), an industry-standard nomenclature published by Amgen.

To create a custom format:

1. Navigate to Registry settings > Entity schemas
2. Click Create
3. Select Protein from the Entity type dropdown — the format picker appears below
4. Click Create new in the format picker
5. Type a VERITAS string into the VERITAS name field

Note: Click How to use VERITAS in the UI for detailed guidance, including Benchling-specific adaptations to the nomenclature.

6. Click Preview to see a real-time rendering of the glyph
7. If you'd like a more user-friendly label, enter a display name — this is what admins and users see throughout the UI, while the VERITAS string remains the canonical identifier
8. Click Create

Note: If an identical format already exists, you'll see an error. Once created, the custom format appears in the format picker alongside built-in formats.

Manage existing formats

Custom formats can be archived, unarchived, and renamed. 

To edit a custom format:

1. Hover over the format in the format picker
2. Click ...
3. Select Edit display name or Archive format

To unarchive a format:

1. Navigate to Registry settings > Entity schemas
2. Click Create and select Protein from the Entity type dropdown — the format picker appears below
3. Select Archived formats from the dropdown next to the format search bar to view archived formats
4. Hover over the format you want to restore
5. Click ...
6. Select Unarchive format

Note: Archiving or unarchiving a format doesn't automatically archive or unarchive its associated schemas.

Create protein entity schemas

You'll create at least one protein entity schema for each format you work with. Note that creating a format alone isn't enough to register proteins — you must create a protein entity schema for each format before registration is possible.

To create a protein entity schema:

1. Navigate to Registry settings > Entity schemas
2. Click Create
3. Select Protein from the Entity type dropdown — the format picker appears below
4. Select a format from the format picker
5. Review the Definition dropdown for each format field — if you have only one schema per component type, Benchling auto-assigns all fields; if you have multiple schemas of the same type, select the appropriate schema for each field manually
6. Add the protein fieldset
7. Enter a name and prefix for the schema
8. Click Next to save the schema settings and proceed to the Access Policies page
9. Configure access policies to control who can create, edit, or manage access to the schema
10. Click Create

Note: Format fields — the chain and domain schema assignments — are locked after saving. If you need to change them, archive the schema and create a new one.