A study can integrate experimental and laboratory data with the clinical and demographic data you have already uploaded. In addition to participant/date pairs being used to make the correct associations, specimen (or assay) data can have multiple rows for any given participant/date pair.
In this tutorial step, you will import a simple specimen archive which contains (fictional) data that might have been from specimens collected from a few of the participants in our tutorial study at some of their visits.
Import Specimen Data
- Click the Specimen Data tab.
- In the Specimens web part, click Import Specimens.
- In Excel, open [LabKeyDemoFiles]/Specimens/SimpleSpecimenRepository.xls you downloaded earlier.
- Select the entire spreadsheet, including column headings.
- Copy and paste the contents into the Upload Specimens window
- Click Submit.
- When you see the message "Specimens uploaded successfully," click Specimens to see the data.
- Notice that all the first rows are for participant "101" including 2 blood samples and one of urine all collected on 2008-05-17 (the date is encoded in the "SequenceNum" column in this example). Each row represents a group of one or more vials - if you scroll to the right you can see the total number of vials collected.
Explore Specimen Data
- Click the Specimen Data tab.
- Notice that now that some specimen data is available, there are many more options.
- In the Specimens web part, expand the Specimen Reports item by clicking the (plus) icon.
- Click View Available Reports.
- From this page you can view a variety of reports.
- For example, next to Type Summary Report, click View.
- Notice that here you see the number of specimens of each type collected in each time point.
- You can view by cohort as well as select different ways to view the specimen data.
- Clicking any link in the Summary table will itemize the specimen vials that make up that total count.
Usage Scenario
On the
Clinical and Assay Data tab, click
Lab Results to open the dataset. Notice that participant "101" had a visit on May 17, 2008 where blood was collected and a few values measured. If we are especially interested in that participant, or even in that specific sample, how can we learn more?
- Click Specimen Data.
- In the Vial Search web part, select "101" from the Participant pulldown menu.
- Click Search.
- You will see all specimens present for that participant.
- Click the heading for the Timepoint column and select Filter....
- In the popup, click the label for "Month 1" (scroll down to find it) to select only that box.
- Click OK.
- The grid now shows all the vials (and only those vials) collected for that participant in that month, which is only that single visit on May 17, 2008. You can see that some vials were treated with different derivatives and additives, which could support different types of further investigation.
Related Topics
Next Steps
This tutorial has given you a quick tour of LabKey Server's data integration features. There are many features that we haven't looked at, including:
- Custom participant groups. You can create groups that are independent of the cohorts and compare these groups against one another. For example, it would be natural to compare those receiving ARV treatment against those not receiving ARV treatment. For details see Participant Groups.
- Assay data. We have yet to add any assay data to our study. For details on adding assay data to a study, see Tutorial: Design a General Purpose Assay Type (GPAT). You can treat this assay tutorial as a continuation of this tutorial: simply use the same study repository and continue on to the assay tutorial.
- R reports. You can build R reports directly on top of the integrated study data. For details see R Reports. For an example see our online demo study.
