While LabKey has several locations in which viewing Participants and Specimen data may be available, everything is available in one location within the Clinical and Assay Data tab.
Clinical and Assay Data Tab Overview
Participants, Specimens, custom datasets, and results from the Biobank are all found in this tab. This area is broken down into multiple sections–some which are not available to all projects. Below is a list of sections that may appear under this tab:
- Data Views (always available): the main area that contains a list of all datasets, custom queries, and results tables from the Biobank are found here. They may be organized into sub-categories.
- File Managers (custom availability): this area contains files associated to the study, produced generally by the Biobank. They may have distinct names to further indicate the types of data available.
- Link Assay (custom availability): this area is used specifically by the Biobank and should not be used by other project members.
Data Views
The Data Views section contains the list of datasets (Participants and custom datasets), Specimen grid views (generally broken down by derivative type), and results from assay/instruments as uploaded by the Biobank. Often, sub-categories are created by the LabKey Administrator to help organize the data views. The following screenshot shows a typical Data View section.
The Participants grid is the default table for all Participant data entered into LabKey for any given project.
All Genotyping Results is a custom query provided to project users of LabKey to organize all genotyping results into a single, pivoted table.
Sample Inventory is a custom dataset provided by the Biobank that indicates the latest storage information of each specimen/sample. These can also be viewed in the Specimen-specific views, such as DNA, RNA, Plasma, and Buffy.
Nanodrop, QubitBR, ViiA7, and Microarray reports show the results of the indicated instrument runs in tabular format. Other types of instrument/assay reports may be available, depending on the project requirements.
File Manager
The File Manager section(s) contains a list of stored and downloadable files available to each project team, provided by the Biobank. The purpose of File Managers in LabKey is to store all data in one, central location on the LabKey Server. This replaces the need for individual emailed files (which can lead to file loss in the long term), or for the Biobank staff to be allowed permission on various individual drives as CAMH. Some File Managers contain subfolders in which data is located. Other sections contain only individual files, or a mix of files and subfolders/directories. An example File Manager is shown in the screenshot below.
Note Each File Manager section may be labeled differently, depending on the project. These sections may be named: File Manager, TSPO Reports, mtDNA Sequencing, QC Gel Photos, DSC Forms, among others.
