What concepts are represented for OMOP.CDM.VISIT_DETAIL care_site_type_concept_id in your OMOP ETL?

[Chesterguan]

How locations are represented in your site OMOPalization?

Please upload your ideas for your organization!

@del42 @tompollard @qqndrew

[del42]

Am I wrong to think that we only care about care_site_type_concept_id = (9202: Inpatient Hospital).
There was a discussion in Tooling meeting to have distinct hospital IDs, as model can perform better/worse due to hospital.
I am following this discussion... @Chesterguan

[Chesterguan]

Hi Del, the question is actually prompted by Gilles, seems different sites have different mapping methods.
We had this care_site_type_concept_id to indicate such as ICU/WARD/OR room and etc. I will follow the others' answers as well.

[clermontg]

My understanding is that the visit_detail_type_concept_id conveys the provenance of the information (some ADT system). It would be EHR most of the time, or some non-EHR administrative source (we can choose among 80 in "Accepted concepts"). But the visit_detail_concept_id is the actual place of service. I was planning to use among the 51 choices from the "CMS place of service" vocab. There there is ER, Critical Care Inpatient and Cardiac critical care, and Inpatient, which I would map to ED, ICU, CCU and Ward. There is no concept of type of ICU there, or step-down unit. What have people done. I realize this is really a Standards mapping issue.

[qqndrew]

@Chesterguan I don't believe there is a "care_site_type_concept_id" column in VISIT_DETAIL for any OMOP CDM version I am aware of (at least for 5.x/6.x -- from https://ohdsi.github.io/CommonDataModel/cdm53.html#VISIT_DETAIL)? Can you point me to the relevant definition for this column?
Unless you are talking about "care_site_id", which would (to my understanding) be a direct FK to entries in your CARE_SITE table. The granularity for that varies by implementation but historically I just did campus->dept->building by increasing granularity as necessary.

[heschmidt04]

Thanks qqndrew for that information on how you did campus -> dept -> building.
For our data warehouse that houses the Clarity data in a view - I think we can access Epic.Reference.Department and fill in a mailing address for address, and look up the county, etc.
My question to folks here is what is the concept id for surgery to fill in table CARE_SITE column place_of_service_concept_id?
I found Athena id 32037 for Intensive care for the concept id.
When I search in Athena I don't find a generic hospital "surgery" https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=surgery&boosts

Thanks
Heidi

[heschmidt04]

And it looks like we have the street address info in Epic.Reference.DepartmentAddress. The zip, county, and state will either have to be extrapolated by hand or the Enterprise Data Warehouse architects consulted. WIP.

[clermontg]

Heidi, this is in the NUCC vocab. I believe we should settle on a single VOCAB. Which field are you trying to populate here? As a note to @Chesterguan, we should make sure everybody refers to https://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_DETAIL , the 5.4 version.
I will try to go the Standards example ETL to see what is suggested there.

[heschmidt04]

Updating here on the thread. In August I had access to SQL Server version of data warehouse. By October 1st 2023 I have access to Snowflake data warehouse where the same data is laid out differently.
I looked at https://ohdsi.github.io/ETL-LambdaBuilder/JMDC/JMDC_Visit_Occurrence.html to help give me ideas and then made the following decisions based on our data.

When speaking with Eric about locations in December 2023. He had the impression we'd put patient locations too for future tie into SDOH.
My first go at this in November 2023 I put only the Departments information into LOCATION and CARE_SITE because I don't want to source huge tables in order to create the person data for the PERSON table.
I hope this information is helpful.

For visit_occurrence I am using the following CASE statement to walk through our patient data -

    , CASE
        WHEN DEPARTMENT_DSC LIKE '%EMERGENCY%' THEN 262 -- https://athena.ohdsi.org/search-terms/terms/262   ER then Inpatient
        WHEN DEPARTMENT_DSC LIKE '%ICU%' THEN 32037     -- https://athena.ohdsi.org/search-terms/terms/32037 Intensive Care
        WHEN DEPARTMENT_DSC LIKE '%NEURO%' THEN 32037   -- https://athena.ohdsi.org/search-terms/terms/32037 Intensive Care
        WHEN DEPARTMENT_DSC LIKE '%CCU%' THEN 32037     -- https://athena.ohdsi.org/search-terms/terms/32037 Intensive Care
        WHEN DEPARTMENT_DSC LIKE '%CATH%' THEN 581383   -- https://athena.ohdsi.org/search-terms/terms/581383 Inpatient Cardiac Facility
        WHEN DEPARTMENT_DSC LIKE '%CPC%' THEN 32037     -- https://athena.ohdsi.org/search-terms/terms/32037 Intensive Care (Nothing for Surgery)
        WHEN DEPARTMENT_DSC LIKE '%RACU%' THEN 32037    -- https://athena.ohdsi.org/search-terms/terms/32037 Intensive Care (Nothing for Respiratory Acute Care)
        ELSE 0 -- a catch all in case the logic doesn't catch new departments
      END AS VISIT_CONCEPT_ID -- Jansen is using 9201 for inpatient as visit_concept_id but we have ICU which implies in patient