Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add DEATH table fields #646

Open
1 task done
jbnuh opened this issue Mar 1, 2024 · 4 comments · May be fixed by #900
Open
1 task done

Add DEATH table fields #646

jbnuh opened this issue Mar 1, 2024 · 4 comments · May be fixed by #900
Assignees
@AndrewThien
Labels
omop Related to omop mapping
Milestone
3.0.0

Comments

@jbnuh
Copy link

jbnuh commented Mar 1, 2024

Is there an existing issue for this?

  • I have searched the existing issues

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.
@jbnuh jbnuh changed the title Add DEATH table fields💡 <title> Add DEATH table fields Mar 1, 2024
@AndyRae
Copy link
Member

AndyRae commented May 15, 2024

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
Copy link
Member

AndyRae commented Jun 26, 2024

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.

@AndyRae AndyRae mentioned this issue Jul 31, 2024
Open
15 tasks
@AndyRae AndyRae added the omop Related to omop mapping label Aug 3, 2024
@AndyRae AndyRae moved this to Todo in Carrot Roadmap Aug 3, 2024
@AndrewThien
Copy link
Contributor

AndrewThien commented Sep 11, 2024 •
edited
Loading

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.

@AndrewThien AndrewThien self-assigned this Oct 4, 2024
@AndyRae AndyRae mentioned this issue Oct 4, 2024
Closed
@AndyRae
Copy link
Member

AndyRae commented Oct 7, 2024 •
edited
Loading

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.

@AndyRae AndyRae added this to the 2.4.0 milestone Oct 17, 2024
@AndrewThien AndrewThien linked a pull request Oct 17, 2024 that will close this issue
Open
@AndyRae AndyRae modified the milestones: 2.4.0, 2.5.0 Nov 4, 2024
@AndyRae AndyRae modified the milestones: 2.5.0, 3.0.0 Dec 19, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@AndrewThien AndrewThien

Labels
omop Related to omop mapping
Projects
Carrot Roadmap
Status: Todo
Milestone
3.0.0
Development

Successfully merging a pull request may close this issue.

Add support for adding concepts to DEATH table Health-Informatics-UoN/carrot-mapper
4 participants
@AndyRae @spco @AndrewThien @jbnuh