Setting up your Bioregistry

Create your Bioregistry

Click here to create your organization’s bioregistry. You’ll be asked to set up an organization (if you don’t have one) and assign initials for your team.

Establish Standard Schemas

Once you’ve created your registry, you can create establish standard naming schemes to make searching, tracking, and sharing more streamlined.

You can set up schemas for the biological entities you want to track. Click the registry panel on the left navigation bar and then the gear icon to open the settings page.

Schemas are customizable for the lab, but we’ve started you off with default schemas for Bacterial Strain and Yeast Strain below.

Note: Schemas are set globally - all members in your organization will see new schemas and the corresponding File Fields.

Configure File Fields

Clicking into the Bacterial Strain will take you to the File Field page below, where you can can set the required meta data for your entities.

For the Bacterial Strain file field below, all members in your organization will be required to include information about the host strain, embedded plasmid, resistance marker, and box location for every new bacterial strain.

Components of the File Field page:

• Icon: Your schema icon will appear throughout your registry and file listings.

• Prefix: Schema prefixes help quickly identify sample types. For example, each new registered bacterial strains will have a “b” in its ID prefix (e.g. bNN001, bNN002, bNN003….). My yeast strains will have a y in its ID prefix (e.g. yNN001, yNN002, yNN003…). We recommend that prefixes are lowercase.

• Name: The schema name will appear in filtering and file creation options.

• File Type: This is the type of file that can use your schema. This can be an existing file type, or one that you create yourself.
  • Sequence: Entities that contain DNA, like plasmids and oligos.
  • Protein: Entities that contain single amino acid components, like heavy chain and light chains.
  • Custom Inventory: File type for data outside proteins and sequences, like strains, antibodies, mice, and more.
  • Note: The Benchling Bioregistry is currently optimized for strains, but we’ll be adding improvements soon to streamline oligo, protein, and plasmid tracking.
• Format: All files with this schema will receive these fields and their respective formats. Possible formats are:
  • Text: A text field ideal for short text (e.g. DH10B)
  • Long Text: A text field ideal for longer text, genotype description.
  • Links: These allow linking to other files in Benchling. DNA and Protein links allow searching for files of those types, and Schema links allow searching for a file matching the selected schema. (ex. a “Gene” field might have a “Sequence Link” format and a “Parent Strain” field might have a “Schema Link / Strain” format)
  • Dropdowns: These allow picking a value from a list. Dropdown values can be created in the “Dropdowns” section below (ex. a list of antibiotic resistances).

Build Dropdowns

Use dropdowns to keep the lab standardized on spelling and naming conventions, especially for important metadata like resistance markers.

• Access dropdowns from the Bioregistry Settings page. We’ve set you up with two default dropdowns, but you can create your own by selecting Create.

• Assign dropdowns to a File Field by clicking into the schema and selecting Dropdown/[Dropdown Name] from the format column. See the Schema Field section above.