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Health-Informatics-UoN / carrot-mapper

Convenient and Reusable Rapid Omop Transformer.
https://carrot.ac.uk
MIT License
14 stars 4 forks source link

Add DEATH table fields #646

Open jbnuh opened 9 months ago

jbnuh commented 9 months ago

Is there an existing issue for this?

Is your proposal related to a problem or functionality gap?

The SDE programme has defined a minimum OMOP data model for Cohort Discovery. Death-related data is included as it is relevant to research in the domain. It would be great if the following fields were included in the capability of CaRROT-Mapper.

Describe your proposal

Please could you add the following fields from the DEATH table? person_id (key) death_date (Records the date of death for mortality-related cohorts and survival analysis.) death_type_concept_id (Identifies the type of death (e.g., natural, accidental) for cohort definition and research on specific death causes.) cause_concept_id (Identifies the underlying cause of death for mortality analysis and research on disease burden and risk factors.

Describe alternatives you've considered

No response

I'm part of a Project Team

No response

Anything else?

No response

Are you willing to contribute to developing this feature?

🎨 Yes, I'm keen to be involved in design discussions.

AndyRae commented 6 months ago

We need to confirm in the CDM, is this 121 or a 12 many. There could be multiple causes of death, possible creating multiple entries.

AndyRae commented 5 months ago

This is not just a config change, adding "death" to the tables list.

death_type_concept_id will not be used.

But cause_concept_id - this will likely look up a "condition / observation" , so therefore we "might" need to intervene. When adding a Concept we rely on using the domain of the concept to identify it for the rule, we would need to conditional checking if this is the death table, and override it accordingly.

AndrewThien commented 2 months ago

We may need a separate workflow or page to let users notice and add the concept to this table. Maybe we can ask users about this in the "Edit Table"/"Edit Field" page or something like that.

AndyRae commented 1 month ago

Because we need to mark whether a specific ScanReportTable is a death table - we could add a boolean to the model, and allow users to select this when they set the PersonId and DateEvent for the table.