You design an assay by creating a named instance of either the flexible "Standard" type or of a built-in "Specialty" assay type. In an assay design, you describe the structure of the data you will be importing and can customize it adding and modifying fields and properties as needed. This topic covers properties and fields available for Standard assay designs.

Assay Properties

Assay properties describe attributes of an assay design that are common to all runs and batches imported using it. Every assay design must have a unique Name; other properties are optional and depend on the needs of the group using it. When you define an assay, the first panel includes properties in the following categories:

Basic Properties

  • Name (Required): Text. Each assay design must have a unique name.
  • Description: Optional text with a more verbose description.
  • QC States: (Premium Feature/Available in Standard assays) Check to enable defining and using assay QC states for this assay design.
  • Plate Metadata (Standard assay type only): Check the box to use plate data with a Standard assay. Learn more in this topic: Standard Plate-Based Assays

Editing Settings

By default, assay data cannot be edited after import into LabKey Server. It's often the case that the instrument generates the final, authoritative form of the data, which should not be changed after the fact. In cases where you want to allow authorized users to change assay run information or result data after import to the server, you can use these settings:

  • Editable Runs: If enabled, users with sufficient permissions can edit values at the run level after the initial import is complete. These changes will be audited.
  • Editable Results: If enabled, users with sufficient permissions can edit and delete at the individual results row level after the initial import is complete. These changes will be audited. New result rows cannot be added to existing runs.
Can Batch fields be edited? Yes, but only if you re-import a run. The import wizard allows you to update any batch fields.

Import Settings

  • Import in Background: If enabled, assay imports will be processed as jobs in the data pipeline. If there are any errors during import, they can be viewed from the log file for that job.

Transform Script Options (For Developers)

Users with the "Platform Developer" role will have additional options in the Import Settings section for using transform scripts with their assay designs. Transform scripts run before the assay data is imported and can reshape the data file to match the expected import format. Learn more in this topic: Transform Scripts.

  • Transform Scripts: Click Add Script to provide the full path to the transform script file.
  • Save Script Data for Debugging: Typically transform and validation script data files are deleted on script completion. For debug purposes, it can be helpful to be able to view the files generated by the server that are passed to the script. If this checkbox is checked, files will be saved to a subfolder named: "TransformAndValidationFiles", located in the same folder that the original script is located.

Link to Study Settings

  • Auto-link Data to Study: If a target study is selected, then when new runs are imported, data rows are automatically linked to the specified target study (if they include subject and visit/date information). Learn more here: Link Assay Data into a Study
  • Linked Dataset Category: Specify the desired category for the Assay Dataset that will be created (or appended to) in the target study when rows are linked. Learn more here: Manage Categories.

Batch Fields

The user is prompted for batch properties once for each set of runs during import. The batch is a convenience to let users set properties once and import many runs using the same suite of properties. Typically, batch properties are properties that rarely change. Default properties:

  • Participant Visit Resolver This field records the method used to associate the assay with participant/visit pairs. The user chooses a method of association during the assay import process. See also Participant/Visit Resolver Field.
  • TargetStudy. If this assay data is linked to a study, it will go to this study. This is the only pre-defined Batch property field for Standard Assays. It is optional, but including it simplifies the link-to-study process. Alternatively, you can create a property with the same name and type at the run level so you can then publish each run to a different study. Note that "TargetStudy" is a special property which is handled differently than other properties.

Run Fields

Run properties are set once for all data records imported as part of a given run. An example run property might be the ID of the instrument or the operator performing the upload.

No default run properties are defined for Standard Assays.

Results Fields

Results fields (also can be called data properties) apply to individual rows within the imported run.

The pre-defined Results Fields fields for Standard Assays are:

  • SpecimenID
  • ParticipantID
  • VisitID
  • Date
These properties are used to associate assay data with other data from the same source material. For more, see Participant/Visit Resolver Field.

Files and Attachments

Assay designs support associating a given row of data with a file using either a run field or results field of one of these types:

  • File: A field that creates a link to a file. The file will be stored in the file root on the server, and will be associated with an assay result.
  • Attachment: A field that will associate an image file with a row of data in a list.
These files might contain images or rectangular data. For example, to index microscopy files, you might create an assay design with metadata and descriptive fields (such as content, timing, staining) and then include an attachment file with the image.

Related Topics

For assay-specific properties and fields see the following pages:

Discussion

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