Follow up: Total Fraction Metabolized => Define pie chart plot showing fraction contributions

[msevestre]

Once #1171 is implemented, we could add another type of plot to a simulation (name to be defined), something like a "Fraction metabolization contribution" chart.

This could be a pie chart showing all contributions, taking all enzymes defined in the system

FYI: @teutonicod. Please feel free to enhance if you have some examples of such charts

[msevestre]

@TWendl, @Aedginto: Your feedback and suggestion is welcome here

[teutonicod]

Hi @msevestre, @TWendl, @Aedginto
Yes, I was thinking to something like a pie chart to visualize the relative contribution of the different eliminations (feces, urine, and the different enzymes). The example below is taken from a publication on Vilaprisan, we could immagin something similar with the different enzymes included in the model and the other elimination pathways

More in general, what I think it is important is to discribe/visualize the different components of the mass balance that we have for, the drug, as recommended in the last EMA guideline. With the information we get from the model we should be able to build the following picture.

I think that most of the components of this picture could also be get with some observers.

[msevestre]

@teutonicod I think chart 1 could be somehow done (however it would be a contribution based on all pathways and maybe other fractions such as to urine and feces.. you would not be able to group contributions together)

The second one is much more complicated. We do not calculate a fraction of dose when active metabolites are in place for example. It might be possible with observers...but I would not know how :)

[Aedginto]

This is a very important addition. During model building, I often use this type of information and it would be much easier to have it readily available.
I am in full support of including this in a future version.
Andrea

[regulus92]

Glad that you do this. Great job!

[teutonicod]

Hi guys,
Will part of this implemented in the next release? I am thinking to something like an observer that defines the total fraction metabolized from a specific enzyme? I am just asking to know if it is worth it to work on an R script to calculate it (did not manage to do it in MoBi).
Thanks
Donato

[msevestre]

observer that defines the total fraction metabolized from a specific enzyme

Yes this will be part of v8. The visual stuff not

You can try it anytime btw by using the latest version (pk-sim.portable.open-systems-pharmacology.org)
Download the zip file, unzip it and enjoy

[teutonicod]

Thanks a lot @msevestre !
I will have a look then already in the portable version and let you know if there is any issue.
Don't hesitate to contact me if you need some help with the visual stuff!

Donato

[teutonicod]

Hi @msevestre,
I checked the portable version but I did not found the observer. I only found the observers located in the different organs describing the fraction metabolized in each compartment but not the global one defining the total fraction metabolized by an enzyme. I used the PK-Sim portable located here

https://ci.appveyor.com/project/open-systems-pharmacology-ci/pk-sim/build/artifacts

Donato

[Yuri05]

@teutonicod
You will find it in the newly created simulations under „Total fraction of Dose-XXX“ (XXX is a Compound)

[nina-nauwelaerts]

Hi, I was wondering if there is also a way to see the fractions for the last dose only, when simulating multiple doses (steady state).
If I use the "total fraction of dose", I see the cumulative fraction metabolized via each enzyme (from all doses). In literature, I have the fractions metabolized via each enzyme at a certain time point for a 'single' dose given at steady-state. However, in this study, there is also a fraction of the parent medicine (i.e. not metabolized); and there is auto-induction for some enzymes, thus I cannot compare to the 'total' fraction metabolized over all doses.

[Yuri05]

@nina-nauwelaerts Please post your question in the forum and I will answer there :)