Assay Terminology

  • Assay type: Structure defined by developers for a specific technology or instrument type which functions like a template for creating specific designs. Built-in assay types include Luminex, Elispot, Microarray, etc. There is also a general purpose assay type that can be customized by an administrator to capture any sort of experimental data. A developer may define and add a new assay type if required.
  • Assay design: A specific named instance of an assay type, defined by an administrator and typically customized to include properties specific to a particular use or project. The design is like a pre-prepared map of how to interpret data imported from the instrument.
  • Assay run: Import of data from one instrument run using an assay design. Runs are created by researchers and lab technicians who enter values for properties specified in the design.
  • Assay batch: A set of runs uploaded in a single session. Some properties in a design apply to entire batches of runs.
  • Assay results or assay data: Individual data elements of the run, for example the intensity of a spot or well.

Assay Types and Designs

An assay type (or "provider") corresponds to a class of instrument or file format. For example, the Flow assay type provides a basic framework for capturing experimental results from a flow cytometry instrument. Assay types include a foundational database schema that can be further customized to form a database design.

An assay design is based on an assay type. When you create an assay design, you start with an assay type, and customize it to the specifics of your experiment, so it is capable of capturing the core data, and the contextual data, of your results.

When you import instrument data into LabKey server, the assay design describes how to interpret the uploaded data, and what additional input to request about the run.

Included in the assay design are:

  • the column names
  • the column datatypes (integer, text, etc.)
  • optional validation or parsing/formatting information
  • the contextual data (also known as "metadata") about your assay, such as who ran the assay, on what instrument, and for which client/project.
You can customize one of several basic assay types to create your specific assay design. Each assay type is essentially a template associated with a particular class of assay instrument or diagnostic test. For example, there are assay types for ELISpot, Luminex, and others, each intended to fit the data requirements of the particular assay workflow. There is also a general purpose assay type that you can customize if your assay data is not of one of the pre-defined types.

Note that developers can create their own assay types; administrators can create their own assay designs based on the available types.

To further streamline the process of creating the assay design you need, you can ask LabKey server to infer a best guess design when you upload a representative spreadsheet - then instead of declaring every column from scratch, you might need only edit labels or add non-standard or user-entered metadata fields. The process of inferring an assay design looks like the process for importing data into a list. You upload a file and accept or edit the best guesses LabKey makes.

LabKey Server includes a variety of built in assay types, to simplify creation of designs for specific instrument types, like ELIspot, NAb, and Luminex. Each type can be further customized when creating a specific assay design to suit your data.

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