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AIDAVA Reference Ontology
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Procedure status #23

Closed Wenjie225 closed 4 months ago

Wenjie225 commented 5 months ago

In UM's DTS, there is data about chemotherapies with variables such as "BR_CHEMO" (Yes/no/unknown), and "BR_CHEMO_START_DATE" (date time), etc. They mean whether the patient had a certain type of chemotherapy and the start date time.

How to map the status of chemotherapy based on SPHN? There seems to be no appropriate class for this.

Option 1: We can only map the chemotherapy that the patient received. But in this case, will it miss some information?

Option 2: We can add classes in the AIDAVA ontology called "chemotherapy" & "radiotherapy" to include the treatment status and information related to the drug administration.

KateSerafimova commented 4 months ago

In SPHN there is RadiotherapyProcedure, which is available. For Chemotherapy we need to discuss, maybe the general procedure can be used?

As for the Yes/No observations - that is another common thing, missing from SPHN. Are these always related to a therapy or treatment?

Wenjie225 commented 4 months ago

Yes, Chemotherapy can be mapped by using Procedure. In UM's DTS and local EHR system, Yes/No observations can be related to a treatment or some information about medical history such as comorbidities, toxicity after therapy, regional recurrence, etc. Maybe we could find more cases from other sites when using Boolean values to describe certain observations or conditions.

KateSerafimova commented 4 months ago

We will have to include Status, if we want to be able to provide output in FHIR IPS. There it is required many concepts, here are a few examples with the value sets:

The status can be a literal, but in that case the values may not be matched to a FHIR valueset. Second option will be to introduce aidava:Status, that can have a text field and a code. This class can be equivalent to SNOMED's 288529006 | Context values (qualifier value), which includes:

Option for Observation may be 419891008 | Record artifact (record artifact) | , or to just leave it as a default value "Final" - TBD

KateSerafimova commented 4 months ago

Deprecate RadiotherapyProcedure and use Procedure for therapies.

We will add Status and define it based on SNOMED codes mapped to the FHIR valueset.

not-done |   | 385660001 |Not done (qualifier value)| on-hold |   | 385655000 |Suspended (qualifier value)| completed | x | 385656004 |Ended (qualifier value)|410513005 |In the past (qualifier value)| entered-in-error |   | 723510000 |Entered in error (qualifier value)| stopped |   | 410545000 |Stopped before completion (qualifier value)| unknown |   | 410537005 |Action status unknown (qualifier value)|

What is the exact meaning of Yes and No in the data? @Wenjie225

Wenjie225 commented 4 months ago

"Yes" means that the patient has received certain type of chemotherapy, "No" means this chemotherapy was not used.

KateSerafimova commented 4 months ago

Thanks!

Status will be equivalent to the general SNOMED class 362981000 | Qualifier value (qualifier value), but it will be restricted accordingly for the Concept that it is related to. This way it will also be useful for Problem Condition and other concepts.

KateSerafimova commented 4 months ago

The subclasses of Procedure will be deprecated in a following issue. The changes to the RO here are regarding the Status for Procedure. There seems to be a property sphn:hasStatusCode and it will be added to Procedure with the restrictions listed as follows: 

('has status code' some 
(385651009 or 385655000 or 385656004 or 385660001 or 410513005 or 410537005 or 410545000 or 723510000)) and ('has status code' min 1 owl:Thing) and ('has status code' max 1 owl:Thing)