Activities in Clinical Trials, part 2

This post is a sequel to one I recently posted about Activities in Clinical Trials. As I mentioned in that post, clinical trials are fundamentally a group of many Activities and the rules that describe when they are performed, grouped, and analyzed. The recently launched PhUSE SDTM Data in RDF project is developing a mini Study Ontology to represent clinical data using RDF in a way that will make it easier, we think, to generate high quality SDTM-compliant datasets. Our Study Ontology   recognizes that all Activities have Outcomes. In the case of an Observation, it is the result. We examine results of Observation today in detail. The ontology needs to represent Observations and their Outcomes in a highly consistent and semantically precise manner, yet it should be flexible enough to accommodate all Observations.

So we have the basic premise in the Ontology that:

:Activity :hasOutcome :ActivityOutcome.

What does that look like for various Observations? When we look at results of Observations, we basically see two types: categorical results and numeric results. The categorical results can be controlled terminology, The numeric results have a value and often, but not always, a unit.  There may also be a free text description of the results, but that's easy to add and we won't consider it further today. So now we have:

:ActivityOutcome :hasValue "<number>"
:ActivityOutcome hasUnit :Unit .
:ActivityOutcome :hasCodedTerm :ActivityOutcomeCode .

Also let's acknowledge that Observations may have components, or SubActivities:
:Activity :hasSubActivity :Activity .

The ontology looks like this:

Here are some simple examples. The first is Age. (a more detailed model would link to the method for obtaining the age. Is it collected by asking the subject his/her age, or is it derived from the birthdate).

The next example is a lab test, RPR test for syphilis.

The next one is BP, the most complex, as it has two sub activities: SBP and DBP. 

The big question is will this work for the vast majority of observations out there? I'm not sure but it is worth testing. I'm optimistic that it will handle most. I'm intentionally leaving out important details like data types, methods, provenance information. I think these can all be addressed relatively easily.

It is worth noting that many "tests" contain both observations and and assessment of those observations by a qualified professional. Histopathology and Radiology tests are the most common. The report is divided into two sections as a result. The first describes the findings, and the second section describes the Assessment (i.e. interpretation) of those findings, often resulting in a diagnosis and/or further characterization of an existing medical condition. Representation of Assessment information in the ontology is a discussion left for another day. 

In an upcoming blog, I discuss Rules that determine when Activities are conducted. These include Eligibility Criteria. 

Thank you for your comments. 

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