Saturday, December 2, 2017

An e-Protocol Annotation Tool

As part of my professorship in medical informatics at the Institute of e-Health at the University of Applied Sciences FH Joanneum, I also have a little bit of time to do some more "basic" research. This research is often not funded, as "applied sciences" universities in Austria only get money from the state for teaching activities.

In the last days, I started working on a clinical research protocol tool.
It is still extremely primitive, but I want to share my first results with you anywhere.

The tool makes extreme usage of RESTful web services, for example the NLM RESTful web services, web services from HIPAA (require an account and token), UMLS RESTful web services, and of course, our own RESTful web services.

CDISC-SDTM annotation

Much of the information from the protocol finally goes in the SDTM submission to the FDA or PMDA. For example, there is a lot of information that goes in the SDTM "TS" (trial summary) dataset. The protocol can be annotated with the information about where the information needs to go into the TS dataset and with which parameter name.
The same info also goes into clinical trial registry submissions, ideally using the CDISC CTR-XML standard.
Here is a short demo about how the annotation works:

... and so on ...
As one can see, the user cannot only annotate the part where the code should be assigned to (yellow), but also the value of the code or parameter (green).
This one of course is a "easy pray" for an artificial intelligence program. So in my opinion, assigning and retrieving such "trial summary parameters" can easily be automated.

LOINC annotation

With this tool, annotating laboratory tests with their LOINC code becomes very easy. A simple demonstration is shown here:

SNOMED-CT annotation

For SNOMED-CT annotation, I used the UMLS RESTful web services API. Please remark that these require a UMLS account and API token, and possibly a (country) SNOMED-CT license. A short demo is shown here:

If you do not have a UMLS account and API token, you can of course always a "Google Search" which can be started from within the tool.

Other types of annotations that can currently be used are UMLS, ICD-10 (WHO) and the ATC (Anatomic, Therapeutic, Chemical) classification system for therapeutic drugs.

1 comment:

  1. Perhaps one day will will have protocol-XML and can state advanced data about the protocol.