...
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.
...
- From the Enter Sample form, select the Participant ID from which the sample is derived from the dropdown menu.
- 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.
- Selecting OK from the confirmation box will allow users to continue adding specimens in the Enter Sample form.
- Selecting Cancel will redirect users to view all entered samples in the Sample grid view.
- Selecting OK from the confirmation box will allow users to continue adding specimens in the Enter Sample form.
...
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.