Managing Samples

Note Samples have now replaced Specimens in LabKey. Please note the terminology change.

Note Please remember that LabKey is not compatible with Internet Explorer. Please have JavaScript enabled to use all features of Managing Samples.

What are Samples?

Biological materials collected from participants are tracked in LabKey as Samples. These may include materials such as products from blood draws, lymphoblasts, and saliva. A full list of possible sample types is found below under Sample Types (previous terminology: Specimen Codes).

Samples Tab Overview

The Specimen Data page has two associated frames:

1. The ‘Enter Sample’ form: this area contains empty fields to enter new sample information.
2. The ‘Sample’ grid view: this area allows users to view all existing Samples and related information entered into the study.

Enter Sample Form

Individual sample entry is done through the Enter Sample form. Most fields are required to be completed in order to successfully add an entry into LabKey. Please note, each sample type collected per visit will have to be entered separately for a given participant. For example, if blood and saliva are collected at the same visit for participant A, the study team will have to complete the sample form once for the blood sample(s) and once for the saliva sample(s).

The following table indicates each possible entry field and their expected data types:

There are two buttons at the bottom of the page:

1. Submit will insert the new Sample entry(ies) directly into the Sample query (assuming all required fields are entered, and optional fields are of the correct data type as indicated in the above table). For vial numbers greater than one (1), multiple records will be created, differentiated only by vial number. The user will then be prompted with a confirmation box in the browser to add more samples. Clicking OK will return to the Enter Sample form.
2. The Cancel button will clear the form and return the user to the Overview tab. Click cancel after the last sample has been added for a specific participant visit.

Sample Grid

The Sample grid is a built-in, visual representation of querying the Sample datasets. The default view shows all entered samples, the participant of which the samples are derived, the Biosample ID of each vial, primary, derivative, and additive types, among many other fields. A list of all properties contained in the Sample grid is explained below.

Entering Samples

Samples can be entered individually, or in bulk. Bulk uploading of Samples can currently only be done by Biobank staff or by a LabKey Administrator, unless a study team is managing their own samples. For information regarding Sample Manager, please contact the LabKey Administrator.

The process for entering single (multiple vial records may be created from a single sample) sample is as follows:

1. From the Enter Sample form, select the Participant ID from which the sample is derived from the dropdown menu.
   1. Note that if a user has been redirected from the Enter Participants page, the Participant ID becomes non-selectable. If another participant is desired, reload the page by navigating to the Cancel button, and returning to the Specimen Data tab.
2. Add a visit number. All initial sample entries should begin at one (1), and increment by 1 sequentially. Note that LabKey does not allow non-numeric values for the Visit field.
3. Select the Draw Date and Time—the date the sample was collected from the participant by filling in date values (MM/DD/YYYY) or by selecting the calendar icon. The time the sample was collected (hh:mm AM||PM) or by selecting the clock icon. The Draw Date is mandatory, while the Draw Time is optional.
4. Select the Clinic from the dropdown menu. This is the location where each sample was collected.
5. Select the Sample Type (Specimen Code) from the dropdown menu. The selection will populate the primary, derivative, and additive type of the sample automatically. Refer to the Sample Type lookup table here.
6. Select the number of vials created for this sample and visit number. At least one (1) vial must exist to enter the sample into LabKey. The maximum number of vials that can be added is ten (10).
7. Optionally, enter any comments relevant to the sample collection. Note that any comments entered at this step will be associated with each vial (assuming more than one vial is selected).
8. Ensure that all entered information is correct and press Submit. Upon a successful submit of the sample data into LabKey, the browser will open a confirmation box.
   1. Selecting OK from the confirmation box will allow users to continue adding specimens in the Enter Sample form.
   2. Selecting Cancel will redirect users to view all entered samples in the Sample grid view.

The process for entering samples in bulk is as follows:

Note Entering samples in bulk has been discontinued. If Samples need to be added in bulk, please contact the LabKey Administrator or Biobank staff.

Editing Samples

Note Editing samples by users has been discontinued. If edits need to be made, please contact the LabKey Administrator or Biobank with the following information:

1. Study with data to be edited
2. Biosample ID of sample(s) to be edited
3. Nature of edit (change in ID, sample type, draw date/time, etc.)

The Administrator or Biobank staff will then add a comment explaining the change request.

Deleting Samples

Note Deleting samples by users has been discontinued. If deletions need to be made, please contact the LabKey Administrator or Biobank staff.