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Achilles - proposal for new Observation/Measurement value visualisation

(Maxim Moinat) #1

Achilles gives great visualisations for the measurement values in the measurement concept detail panel. Both for the actual values (per unit) as the ranges. I could not find a good example on the public Achilles, so here is a screenshot of the details I am referring to:

image.png1864x1055 93.7 KB

However, there is no distribution of value_as_concept_id . Besides for measurements, this would also be very insightful for observations (at least to check that the value_as_concept_id is indeed an affirmative ‘yes’).

My proposal is to create a pie chart for the distribution of value_as_concept_id. First, the Achilles R package needs to be extended with functionality to create these aggregates (counts). Then the json export and/or webapi need to be adapted. Lastly, the user interface needs to display this data in a chart.

Are there people with similar ideas or have even started with such an integration?
And is AchillesWeb still maintained, or do all new integrations have to be in Atlas/Data sources?
Is there potentially a use case to integrate this with new Achilles Heel checks?

Comments and feedback are greatly appreciated!

(Karthik) #2

It think this would be useful. The other place where it might be useful is in the observation table. I know this would be useful for surveys that get into OMOP.

It would be nice if some if data types can select and visualized in a dashboard. For example, if one is interested in cultures, the user could select it and then get a histogram of sensitivity for a particular type of test.

(Taha Abdul-Basser) #3

  • I agree that this is a welcome idea.

  • I am not aware of any one else working on this.

  • If you would like to move forward on this please feel free to open a proposal at the Achilles GitHub repo.

  • New features on the analysis and visualization side should be added to the Achilles-DB-WebAPI-Atlas Data Sources pathway and not to the exportToJSON-AchillesWeb pathway, which is essentially frozen with regard to new features.

  • What type of Achilles Heel checks did you have in mind?

(Maxim Moinat) #4

Will surveys be stored in a separate table? Or will they go into the observation table? I remember there is some kind of proposal for this. Would be great to also provide support for the new survey structure.

@t_abdul_basser
Thanks for your feedback. I did not have any specific Achilles Heel checks in mind, but most Achilles rules have some Heel check associated with it. That was why I was asking :slight_smile:
Will go for the WebAPI/Data Sources pathway. Although we still use exportToJSON internally to share Achilles results. We might need to explore a different way to share results without giving access to the data.

(Maxim Moinat) #5

Short update. The code to create the new Data Source visualisations is currently under review. Links to the pull requests to Atlas and WebAPI for reference:


(Peter Rijnbeek) #6

@Maxim: have a chat with @mvspeybr on sharing Achilles outputs without using the JSON format. It means you have to share the tables from the results schema (so no data) and his team has been working on this recently. Correct me if I am wrong Michel.

(Maxim Moinat) #7

@mvspeybr Any update on this sharing of Achilles results?
Or should we putting more development effort in the Achilles Shiny apps as recently developed for Achilles Heel?

t