What is the Registry?

What is the Registry?

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

The Registry manages your data three ways:

• Creates a searchable, central repository of biological materials across your organization using customizable schemas

• Captures critical properties that define a specific biological material in a structured manner

• Tracks relationships between different types of biological materials, such as the relationship between specific plasmids and strains

Schema types

The Registry uses many types of schemas, most of which are classified as entities, except for the mixtures schema. The table below lists all Registry schemas, their definitions, and examples, if applicable.

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: Existing data sheets are often a great starting point. For example, if you have a plasmid Excel tracker then you will want a plasmid schema. 

Schemas often link one another. For example, if we have a cell line schema and a plasmid schema where we track many unique items, you use a specific plasmid in your research process when transfecting a specific cell line.

Entities

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. 

An additional level of data can be recorded as child entities on Enterprise accounts. Child entities are lots, dilutions, or preps of a specific entity. We show two child entities for each entity: batches p001-001 and p001-002 for the p001 entity, and batches p002-001 and p002-002 for the p002 entity.

Child entities 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: Child entities 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. 

Entry Schema

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. 

For additional information on entry schemas, please visit this article.

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

Icon

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

Schema Type

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).

• Oligo: this schema has an oligo, which can be attached to another DNA Sequence type.

• Entry Schema: This schema is for any Entry in the Benchling Notebook (Only for Enterprise).

• Mixtures: this schema is to track chemical solutions comprised of multiple ingredients where the exact quantity of each ingredient must be tracked (media, buffers, formulations).

Schema Fields

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 entities (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 (e.g. -3, 0, or 3).

• Floating point: accepts numbers including decimal points ( e.g. 1.235).

• Date: accepts only a date (e.g. 2019-01-01).

• Datetime: accepts a date and a time (e.g. 2021-01-27 09:30:33 AM).

• Dropdown: accepts only a choice from a list of predefined values.

• Entry link: accepts only a link to an existing Benchling lab notebook entry.

• Translation Link: special link specific to DNA sequence schema; accepts only AA sequences that the DNA sequence translates for.

• Part Link: special link specific to DNA sequence schema, automatically fills an entity link on other DNA entities based DNA sequence.

• Entity Link: accepts a link to entities under a specified schema.

• DNA Entity Link: accepts a link to any entities that are a DNA type.

• AA Entity Link: accepts a link to any entities that are a AA type.

• Custom Entity Link: accepts a link to any entity that is a Custom Entity type (not limited to a specified schema). To accept a link to a specific custom entity schema, refer to Entity Link.

• Mixture Entity Link: accepts a link to any entities that are a Mixture type.

• Blob Link: accepts an uploaded external file.

• Inventory Link: accepts a link to any Inventory item or to a Inventory item under a specified schema

Computed Fields: a special field type created by Benchling personnel. This field type is able to display information harvested through other entity/child entity links.

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 three 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.

• Parent link: this checkbox indicates the entity linked on this line is the parent schema of the current one (i.e. the current schema is a child entity).

Entity Naming

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. 

Child Naming

There are several options to automatically generate names of child entities based on their parent entity. This is only possible if the parent-child relationship has been specified in the schema configuration.

For the child entity Registry IDs, we recommend that you name child entities based on the Registry ID of the parent entity, followed by a unique identifier.

Child Registry ID = Parent Registry ID + Unique Identifier

Above is an example of a parent-child naming schema. This has been configured so the cell line lots are named according to their parent Registry ID - lot number. In the example, samplecellline is the parent cell line name, and 003 designates the lot number.

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 prompted 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. 

Constraints

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). 

Build Dropdowns

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