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.
The Registry manages your data in three primary ways:
- It creates a searchable, central repository of biological materials across your organization.
- It captures critical properties that define a specific biological material in a structured manner.
- It tracks relationships between different types of biological materials, such as the relationship between specific plasmids and specific strains.
Learn about components of the registry
A schema is a category of biological materials (more technically, a table in a database). We will create schema that define the type of materials that the Registry will track. Examples of typical schema include plasmids, cell lines, strains, and antibodies. Your team could have schema that only your team will use or schema that many teams may reference.
Tip: Often times, existing data sheets are a great starting point. For instance, if you have a plasmid Excel tracker then you will want a plasmid schema.
Schemas often link one another. For example: say we have a cell line schema and a plasmid schema where we track many unique items. In your research process, you use a specific plasmid when transfecting a specific cell line.
Entities and Batches
Unique biological materials of a particular schema are referred to as entities. An entity will have a name and specific values for its fields as defined by the schema.
In the example below, we display a plasmid schema with two fields: Resistance and Promoter.
On the second level, we show two entities of the plasmid schema: p001 and p002. These are unique plasmids with different sequences. For each, we’ve given the values for their resistance and promoter fields.
An optional Enterprise-Only, additional level of data can be recorded as batches. Batches are lots, dilutions, or preps of a specific entity. We show two batches for each entity: batches p001-001 and p001-002 for the p001 entity, and batches p002-001 and p002-002 for the p002 entity.
Batches have additional fields that are used to track information unique to that batch such as prep type and the date created in the example above.
Tip: Batches make sense for things such as DNA sequences (plasmids, targets) or proteins (antibodies, chains) where you might create multiple lots of the sample and the preparation method, concentration, diluent, etc. are valuable to capture. In the example above, p001 has a unique sequence that defines what the plasmid is. p001-001 and p001-002 still have the same sequence, but differ in the way they were prepared.
The Benchling Entry Schema helps organizations tag specific Metadata associated with entries across experiments, project, and groups. Researchers can fill out the Entry Schema fields which can then be queried upon in the Benchling Search. This allows organizations to link entries or to other data together across different departments or groups.
Tip: Entry Schemas can be configured to be required for entry review (please contact your Benchling representative if interested)
Configure your Registry
Open your registry. Navigate to the Registry Settings.
Here you will see a list of Schemas. Select the one you want to edit, or click the "Create" button to create a new one. You will see a screen similar to the one below to configure your schema.
What can be configured
Your schema icon will appear throughout your registry and file listings.
You must select from:
- DNA Sequence: This schema has a native set of DNA bases (i.e gene, plasmid)
- AA Sequence: This schema has a native set of amino acid bases (i.e. single-chain protein, heavy chain)
- Custom Entity: This schema is for anything that doesn’t have bases (i.e. cell line, supernatant, multi-chain protein, full antibody)
- Entry Schema: This schema is for any Entry in the Benchling Notebook (Only for Enterprise)
Schema fields enable standardized data capture and relationship modeling. When you create an entity of the schema, you will fill in these values.
You will need to develop a list of schema fields for both entities and batches (if applicable) per schema.
Tip: Often times, your existing data sheet columns will become schema fields in the Registry.
There are many different types of schema fields in Benchling (Some of these are only available for Enterprise users):
- Text: accepts letters, numbers, and symbols
- Long text: accepts the same input as text but allows more text to be displayed
- Integer: accepts only numbers such as 0, 1, 2
- Floating point: accepts only decimal points such as 1.235
- Date: accepts only a date such as 2019-01-01
- Dropdown: accepts only a choice from a list of predefined values
- Entry link: accepts only a link to an existing Benchling lab notebook entry
- Entity link: accepts only a link to an entity in the Registry of a specific schema
- Batch link: accepts only a link to a batch in the Registry of a specific schema
- Part link: a special type of entity link specific to DNA sequence schema that allows auto-filling (i.e. automatically entity link a resistance entity on a plasmid entity based on sequence)
The most important field to consider is the entity link field. This is how we will model the relationship between two different biological materials of different schema.
Tip: In an example of a plasmid and cell line transfection process, you would include an entity link on the cell line schema to the plasmid schema. This will allow you to link to the specific plasmid you used in the specific cell line you are transfecting.
There are two additional field configurations:
- Required fields: this checkbox will make a field value required at the time an entity is created (i.e. if the field value is blank, then an entity cannot be registered)
- Multi-select fields: this checkbox will enable inputting more than one dropdown option or entity link in a field value
The Registry standardizes the way that you will name each item of a schema.
Each entity will have a Registry ID and descriptive name.
- Registry ID: this is a systematic ID generated by Benchling for every entity based on a prefix defined at the schema level.
- Name: User defined or configured to have Benchling create systematically.
Both the Registry ID and the descriptive name must be unique in the Registry and either can be used to reference and link to the entity.
There are three options to generate batch names. Every batch name is based on the descriptive name or Registry ID of the parent entity.
The options are:
- Registry ID + number: this creates a name based on the entity’s Registry ID and appends -001, -002, etc.
- Registry ID + date: this creates a name based on the entity’s Registry ID and the date the batch was created (i.e. today’s date).
- Name + number: this creates a name based on the entity’s descriptive name and appends -001, -002, etc.
Note: Benchling doesn’t support giving a custom, descriptive name to batches. If a custom name is very important, we may consider thinking about this batch as a different entity schema.
Example of the descriptive name (pBR322 - A.635.G) and Registry ID (TP11696) of a plasmid
You will need to designate a prefix for each schema that will be used to generate the Registry ID. This is often times something like p for plasmid, c for cell line, or something that matches your current naming structure. Every entity will generate a sequential ID based on the prefix (i.e. the first plasmid would be p001, then p002, then p003).
Note: For historical data, if you are using a numbering system, Benchling can generate an ID based on that number to reduce confusion (i.e. if you already have something up to p945, we will use the existing number as the ID and then new plasmids will pick up at p946).
There are several options for the descriptive name of the entity:
- Provide your own name: when you create an entity, you’ll be promoted to provide a descriptive name (this can include text, symbols, numbers)
- Use the Registry ID as the name: this will generate a name based on the systematic Registry ID (they will match exactly). This is useful if you don’t want to have to generate a name.
- Use a name template: Benchling can generate a systematic name based on a combination of field values. For example, if a cell line has fields vendor, organism, and lot number we can generate a name for a specific cell line that is equal to the values of vendor - organism - lot number. This option is useful if you wish to standardize nomenclature and you don’t want to provide your own name.
Entities in the Registry can also have multiple aliases. This is often useful if different people have different names for the same entity. Aliases are searchable and can be used to refer to the entity. They also must be unique.
You can set rules in the registry that ensure uniqueness between different entities of the same schema. The options include:
- Bases: for DNA or AA sequence schema, you can set this constraint to ensure that no two entities have the same sequence.
- Field or combination of fields: you can set a constraint on a certain field or combination of fields to ensure that no two entities have the same combination of links, values, etc. A common example is a constraint on Heavy and Light chains on an Antibody (i.e. no two antibodies can have both the same Heavy and Light chain)
Tip: Constraints give you peace of mind that you are registering a unique entity. When a constraint is set, if you attempt to create an entity that violates the constraint you will be prompted to merge with an existing entity (which will add the name of your new entity as an alias of the existing entity).
Dropdown fields are useful for controlling data input.
For example, if you receive cell lines from a list of vendors, make that a dropdown list instead of a text field. This ensures data integrity between operators and makes it easier to search for this data.
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 Schema Field by clicking into the schema and selecting Dropdown/[Dropdown Name] from the format column.