Atlas inconsistently supports partial matches of ICD source codes when defining cohorts

Chris_Knoll · August 29, 2024, 2:44pm

Hi @Agota_Meszaros :

I found the issue that describes the feature, you can find it here if you are interested:

github.com/OHDSI/WebAPI

Non-Standard Concepts mapped to Standard Concepts to be replaced by Standard Concepts by the "Optimize" functionality of a Concept Set

opened 11:30AM - 13 Feb 24 UTC

alex-odysseus

feature

### Business Requirements If a Concept Set contains all non-Standard Concepts… that are comprised of a Standard Concept they should be replaced with the Standard Concept as the result of Concept Set optimization routine ### Design Ideas and Functional Requirements An initial idea is: An additional flag to be added on the "Concept Set Optimization" screen which will extend the existing optimization business logic with a possibility to replace non-Standard Concepts being mapped to the Standard Concepts by the appropriate Standard Concepts Based on Anthony's comment the following solution design is proposed: - a new button "Resolve mappings" to be added in between the "Optimize" and the Delete buttons, it is enabled only if at least one non-standard Concept is present as a Concept Set Item ![image](https://github.com/OHDSI/WebAPI/assets/75131044/ec7519e2-5b40-44f4-812d-15d7b0fe38e4) - after clicking on the button there will be a popup window displayed with the title "Non-standard Concepts Mapping Resolution" which will contain three visually distinguished blocks ![image](https://github.com/OHDSI/WebAPI/assets/75131044/f62eec2c-28cb-49f3-b99b-cbab135d8755) - 'Concept Set with resolved mappings' will contain all Standard and Classification Concepts which were present before clicking on the 'Resolve mappings' button -- additionally it will contain Standard Concepts counterparts (without duplicates) for those non-Standard Concepts where the mapping is straightforward -- 'Remove Selected' will allow to remove some of the items which may not be needed - 'Non-standard Concepts with multiple Standard Concepts mappings' will be grouped in a way that Standard Concepts with 'Non-standard to Standard map (OMOP)' will be followed by non-standard Concepts for which the ambiguity is present -- a User will be able to select both Standard and non-Standard Concepts and add them to the 'Concept Set with resolved mappings' block after selecting the appropriate ones and clicking on "Add to Concept Set" button -- by means of the 'Preview...' button it will be possible to preview a Concept Set and how it will look like after adding the selected Concepts to 'Concept Set with resolved mappings' (additionally displaying 'Included Concepts' and 'Included Source Codes' listings) - 'Original Concept Set' displays the version of Concept Set Items before any mapping resolution and User's manipulations after - a button to be placed in the popup dialogue so that a User will be able to choose what to do with the 'Concept Set with resolved mappings' block after a task on the dialogue is finished ![image](https://github.com/OHDSI/WebAPI/assets/75131044/3d3a59f3-2d4a-476e-8e77-d19895f450c6) - it is possible that 'Non-standard Concepts with multiple Standard Concepts mappings' is empty as all non-Standard Concepts can be mapped to one Standard Concept and there is no ambiguity (we may think about leaving a possibility to display such resolved mappings as well so that a User will be able to add non-Standard Concepts to the 'Concept Set with resolved mappings') The updated version of the design it the following (based on discussions with Amanda, Brad, Chris and Anthony) to simplify the design above having a compromise not to see on one screen a list of non-standard Concepts which are mapped to particular standard Concept(s): - a list of Standard Concepts into which non-standard Concepts from the given Concept Set can be mapped (it can be empty if there are no non-stadnard Concepts) - and the state of the Concept Set before it is saved ![image](https://github.com/user-attachments/assets/7754b47f-9162-4122-b1c3-bc8d3eda52ad) - 'Resolve one-to-one mappings' button will allow to replace non-Standard Concepts from the initial Concept Set to their Standard Concepts counterparts if there were no multiple non-Standard to Standard mappings available - 'Reset to initial state' all the mappings being made so far will be reverted and the Concept Set will look like as before any changes performed - 'Preview...' button should display a Concept Set if it would be saved in the state on the screen - clicking on one of the figures in the 'Mapped non-Standard' should display a form of the following example with three visual blocks -- Standard Concept description ![image](https://github.com/user-attachments/assets/34e66ae8-b886-4b47-87aa-62da983a92b4) ![image](https://github.com/user-attachments/assets/4b52cf52-ee88-4fb3-9541-3a3ec12268e8) -- a list of non-standard Concepts which are mapped to this Standard Concept ![image](https://github.com/user-attachments/assets/67cc120d-6212-4b96-ab37-302286a1c529) ![image](https://github.com/user-attachments/assets/1975631d-3736-4f5d-8633-c3abb9640c56) -- a list of Included Source Codes for this Standard Concept ![image](https://github.com/user-attachments/assets/96d490a9-6fe3-4629-9518-338061aac774) ![image](https://github.com/user-attachments/assets/e3c3d225-67c2-4627-bb7a-06aaa1431250) -- clicking on 'Map all selected to given Standard' should add the Standard Concept to the Result Concept Set -- for each item where 'Keep non-standard' checkbox is selected an appropriate non-standard Concept will be added to the Result Concept Set as well -- clicking on the 'Resolve mapping' button will perform the same business logic for the particular non-standard Concept ### Open Questions N/A @mrechkem @Sathyaraos

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