Using the Case Series Analyzer

One of the most powerful tools in the MTools web application is the Case Series Analyzer (CSA).  The CSA lets you upload a file containing adverse event data and quickly breakdown cases at all levels of the MedDRA and SMQ hierarchies.  It even aggregates cases that meet the conditions of the most complex algorithmic SMQs.  Case filtering, demographic statistics and series subset creation are all supported.

Before explaining how to use the CSA, a caveat is needed.  At the time of this post, the CSA is a working prototype only.  It has a fixed input specification with a limited selection of fields and provides only a few statistical charts.  Our intention is to generalize the CSA if users find the prototype valuable.  This will include allowing users to create their own metadata descriptions so any kind of AE data can be uploaded, the ability to select appropriate charts and the ability to download and upload analyses at a minimum.  We need to hear from you about your requirements, though, before we get started on a production version.

Here is how to use the prototype:

Step 1: Create a CSA tool

Open the web application at and select "Case Series Analyzer" from the Tools menu.  A CSA tool will be created in a new tab

Case Series Analyzer screenshot

Step 2: Get some data

test javascript screenshotGo to the Tools > Clinical menu on our website (  At the bottom of the page in the "Reference Materials" section is a file named "case_series.json" containing case series analyzer test data.  Download the file to your PC.  It contains simulated test data in the standard Javascript Object Notation (JSON) format.  Each item contains an AER number, a list of randomly selected MedDRA LLTs representing events associated with the case, along with sex, age and country.  JSON files can be easily generated for cases series from most AE databases.

Step 3: Upload the data

Click the "Choose File" button in the Case Series Analyzer and upload the case_series.json file you just downloaded to your PC.  Please note that the data is only uploaded to your browser.  No identifying information is EVER sent to the Terminologix server.  Immediately, you will see the AE data displayed in a data grid along with statistical charts.  You can scroll through the data, sort it by clicking on a column header, or filter the series using the filter icon controls associated with the column labels.

MTools Chart

Step 4:  View MedDRA/SMQ analysis

When you click on the "MedDRA Analysis" tab, the event codes for each AE case and a unique identifier (not the AE number) are sent to the MTools server.  A complete hierarchical breakdown is returned and displayed graphically:

SMQ Analysis view

The chart shows the number of cases in the case series that have one or more event terms in each SOC.  The blue bars represent cases with at least one event that is on a primary path for the SOC, and the green bars represent cases that only have events that are on non-primary or secondary paths.  Hover over the bar to get an exact count.

Step 5:  Drill-down in the analysis

The MedDRA analysis chart is "live".  If you click on a bar in the chart, it will drill-down to the next level in the MedDRA hierarchy and show a similar chart for the selected subset of cases.  For example, if you click on the bar next to the "Gastrointestinal disorders" SOC, you will get a breakdown at the HLGT level for the 415 cases with one or more events in that SOC:

Drill-down analysis

You can continue to drill-down to the PT level.

Step 6:  View additional breakdowns

There is a drop-down menu at the upper left of the display showing additional breakdowns that were performed.  In addition to the full MedDRA hierarchy analysis, you can look at breakdowns by primary SOC only, the full SMQ hierarchy, or cases that meet all the criteria for the SMQ algorithms.  In the case of the SMQ analysis, the bars are segmented to indicate cases that have one or more narrowly defined terms vs cases with only broadly defined terms.

Additional Breakdown view

Step 7:  Create a sub-series

If you right-click on a bar in one of the hierarchical analyses, you will see a menu that allows you create a sub-series that only contains cases that have the indicated terms.  For example, if you go back to the MedDRA hierarchy analysis, right-click on the bar for the "Gastrointestinal disorders" SOC and select "New series (primary only)", a new tab will be created labelled "Sub-Series X" containing the 232 cases that have at least one event that is on a primary path in the "Gastrointestinal disorders" SOC.  You can do anything with the sub-series that you can with the full series including creating further sub-series as your analysis progresses.

instructions on how to create a sub-series

A sub-series can also be created containing filtered terms in the grid using the menu next to the case count.


Categories: Clinical