What is the Registry?

The Benchling Registry helps organizations track the entire life cycle of any biological entity across experiments, projects, and groups. Researchers can account for everything that has ever happened to any sample, run structured queries, and mine the data that’s important for their research.

A Registry is tied to an organization in Benchling.

Learn about components of the registry

Collections

We’ve modeled the process of creating and registering files in the Registry around the physical process of creating a new strain in lab, and the journey it takes from a temporary fridge to a shared box the -80°C freezer. In Benchling, a new strain is created in a project and then makes its way to your personal collection and finally the organization’s collection.

  • Projects → Temporary Lab Fridge: Contains strains that you are still modifying.
  • Personal Collection → Personal box a -80°C Freezer: Contains “completed” strains that are in your personal freezer box, usually after sequence verification. Each lab member has their own Personal Collection.
  • Organization Collection → Lab box in the lab’s -80°C Freezer: Contains “completed” strains that are used by the whole lab, usually after someone leaves the lab or after publication.

Registry IDs

As you register your strains into the Registry, each new file will be given a unique ID.

  1. Schema Prefix: This helps identify data types (e.g. “b” for bacteria, “y” for yeast).
  2. Organization Initials: Your lab is assigned initials and files in your Org’s Collection will be assigned those initials upon registration (e.g. “DL” for Darwin’s Lab).
  3. Padded Number: Each newly registered sample will be given a number suffix. Numbering is based on the file type, so the third bacteria strain will be “bDL003” and the third yeast strain will be “yDL003”
  4. Personal Initials: Each lab member is assigned his or her own unique set of initials and files registered in Personal Collections will be assigned those initials. Files in both Org and Personal Collections will retain both IDs.

Set up your Registry

Open your registry. Navigate to the Registry Settings.

Here you will see a list of Schemas. Schemas allow you to define structured information you wish to capture about the different biological types in your lab. You can use schemas to model just about anything, but let's start with the basics.

Schemas for Bacteria Strain and Yeast Strain are included by default, and each have a set of entity fields associated to them.

Configure entity fields

Clicking into the Bacterial Strain schema will take you to the schema's configuration page.

For the Bacterial Strain schema 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.

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

Schema 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…). 

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

Entity Type: This is the type of file that can use your schema. 

  • DNA Sequence: Entities that contain DNA, like plasmids and oligos.
  • AA Sequence: Entities that contain single amino acid components, like heavy chain and light chains.
  • Custom Entity: File type for data outside proteins and sequences, like strains, antibodies, mice, and more.

Field Format: All entities 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.
  • Integer and Floating Point: For numerical values. 
  • Date: Users will be able to select a date from a calendar. 
  • 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).
  • 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 “DNA Sequence Link” format and a “Parent Strain” field might have a “Schema Link / Strain” format). See this article for details about generating new part links.

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 Registry 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.
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