The readme in the examples folder says there is a ConstructDDITest.csv file. This isn't there.

The results given for Identify Sequential DDIs seem incorrect. I would have thought that there would also be DDIs (2,3) (2,4) (3,4) in SEQ1, if there are DDIs between all of the drugs.

These DDIs would depend on the missing csv file. Could we get a csv file to clear it up?

There are a few issues with some of the proposed iteration 2 features that we can hopefully iron out.

Issues With DINTO

DDI Timing Information

The features in the Timing Analysis Section assume that DINTO contains information about the timing of DDIs. Unfortunately, there is no such information in the current version(s) of DINTO.

Providing suggestions to users about altering pathway timings, without any idea about DDI time frames, would be irresponsible. Without accurate timing information, the only reasonable suggestion the system can make is that the pathway is unsafe and should be investigated by medical professionals.

DDI Classification

There is an even more fundamental problem with DINTO. While it is possible to identify a DDI between two drugs, there is no way of knowing whether the interaction would be beneficial to the patient, or if it would be harmful.

There are classes for potentially harmful and potentially beneficial, but there are no members of these classes. Furthermore, there is no reasonable approach to populating these classes without the assistance of the creators of DINTO. We reached out to the DINTO maintainers several weeks ago about populating these classes, but they have not responded.

Again, it would be irresponsible to assume that any DDI is beneficial. As such - without these updates to DINTO - the system must assume that all DDIs are harmful and report them as such to the users.

Discussion

These issues affect some of the timing analysis features. Without updates to DINTO, these features in their current form would be unsafe to implement.

I'm opening this issue so there is a central place for discussing these problems - so we can get your input and input from other groups as we work to resolve them.