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:

The ‘Enter Sample’ form: this area contains empty fields to enter new sample information.
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:

Field	Data Type	Comments
Participant ID	Dropdown menu (String)	Required. This field will be pre-populated with the most recently added Participant ID if the user has been immediately re-directed to the specimen entry page following entry of a new participant. Otherwise, the Participant ID can be selected from a dropdown menu of all possible participants.
Visit	Integer	Required. Two character maximum. Initial ‘visit’, or the number which corresponds to the time point at which the specimen was collected.
Draw Date	DateTime	Required. This is the date the sample was collected/drawn. Can be entered manually, or by clicking the calendar icon and selecting the appropriate date. Note: Manually entered time should be in the form: MM/DD/YYYY
Draw Time	DateTime	This is the time the sample was collected/drawn. Can be entered manually, or by clicking on the clock icon and selecting the appropriate time. Note: Manually entered time should be in the form: hh:mm: AM/PM
Collection Location (Clinic)	Dropdown menu	Required
Sample Type (Specimen Code)	Dropdown menu	Required
Number of vials	Integer	Required. Enter the total number of vials that will be stored for the initial specimen collected. For example, plasma collected from one vacutainer may be aliquoted into 4 vials after it is spun. The user would enter 4 vials in the vials field. The number of vials must be greater than zero (0).
Comments	Text	Comments entered into this form will show up on each vial (assuming more than one vial is selected above). Individual vial comments can be added/modified when editing specimens.

There are two buttons at the bottom of the page:

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.
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.

Field	Data Type	Comments
Biosample ID	String	Required. Shown in all views. This is the ID of each sample collected by a study team with the format of ParticipantID_VisitId_SampleType_VialNumber.
Participant ID	String	Required. Shown in the default view. This is the ID of the participant from which the sample was collected.
Visit	Integer	Required. Shown in the default view. This is the visit number (or week of the study) when the sample was collected. Unknown visit numbers are required to be zero (0).
Draw Timestamp	DateTime	Shown in all views. This field is required for samples entered using the Enter Sample form. If the timestamp has been left blank, it will show the date as YYYY-MM-DD 00:00
Collection Location	String	Shown in all views. This field is required for samples entered using the Enter Sample form. Indicates where the sample was drawn. This field can be different from the participant's recruitment location.
Receipt Date	DateTime	Shown in all views. This field will be filled in if samples have been received by the CAMH Biobank.
Current Location	String	Shown in all views. This field will be filled in if samples have been received by the CAMH Biobank.
Comments	Multiline String	Shown in all views.
Storage Status	String	Shown in Storage view. If sample is available at the CAMH Biobank, the status will be Available. For samples not available but processed by the Biobank, the status will appear here.
Stored Amount	Double	Shown in Storage view. The amount of sample still remaining at the CAMH Biobank.
Units	String	Shown in Storage view. The unit-type of the remaining amount of sample at the CAMH Biobank.
Storage Location	Multiline String	Shown in Storage view. The fridge/freezer location of the sample stored at the CAMH Biobank.
Rack Slot	String	Shown in Storage view. The exact location of the sample in the storage location.
Tube Barcode	String	Shown in Storage view. The CAMH Biobank barcode used in conjunction to the Biosample ID to label sample tubes.
Oragene Lot Number	String	Shown in Storage view. Not shown in all studies. Studies that collect tubes with OrageneDNA or OrageneRNA can identify each lot number here.

This ‘default’ view can be changed to show other information. By selecting the GRID VIEWS (grid icon) dropdown from the top menu bar shows other predefined filtered views based sample inventory information:

Additional filters and sorts can be conducted by selecting the GRID VIEWS dropdown and selecting Customize Grid. This opens up a Columns tab—a list of all available fields (and subfields resulting from internal SQL JOIN commands) and currently selected fields that are seen in the grid. Each field can be inserted (by using the checkbox in the left column), deleted (by clicking the X in the right column), or reordered (by dragging the field name in the right column).

The filter tab allows users to create filters on all available columns (select them on the left side) with logical constrains in the right-side dropdown menu (e.g. equals, does not equal, contains, etc.). Similarly, the sort tab allows users to determine how to and in what order to sort the data. Multiple filters and sorts are allowed.

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:

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.
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.
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.
Select the Clinic from the dropdown menu. This is the location where each sample was collected.
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.
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).
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).
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:

Study with data to be edited
Biosample ID of sample(s) to be edited
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.

Samples Across Multiple Studies

In certain situations, participants consent to more than one study but only one biosample is collected at the time of the first study. In these cases, please contact the CAMH Biobank to receive the sample list of the original project. These samples will then automatically be viewable in your new study with the original Biosample ID.

Page tree