Operator and Value concept Id - Measurement Table in CDM

SELVA_MUTHU_KUMARAN · April 22, 2019, 4:12am

Hello Everyone,

I am currently mapping the raw data of lab test results from the hospital to CDM format. I would like to know whether my interpretation of the field (Operator_concept_id and Value_concept_id) is correct. Can you please confirm my understanding?

Thanks
Selva

DTorok · April 22, 2019, 12:59pm

You should not be filling in value_concept_id based on the source data you proived. The operator concept is correct and the value as number should hold the values in the raw file. But the value as concept id should be either zero or NULL. The value of concept id is used when the source data provides a qualitative values such as high/low/abnormal … Otherwise the value as concept is should not be populated.

SELVA_MUTHU_KUMARAN · April 22, 2019, 2:09pm

Thank you @DTorok for the clarification. Much appreciated

ericaVoss · April 11, 2024, 7:23pm

For the April Olympians Check In I visited this topic. Hoping to get it documented as a Themis rule, however I think I’m disagreeing with @DTorok above. I think if the raw data has the value and a category in its output you document that in the CDM. Follow-along here:

github.com/OHDSI/Themis

How to populate MEASUREMENT.VALUE_AS_NUMBER

opened 06:33PM - 11 Apr 24 UTC

ericaVoss

# How to populate MEASUREMENT.VALUE_AS_NUMBER ## CDM or THEMIS convention? THEM…IS ## Table or Field level? Field ## Is this a general convention? No ## Summary of issues - VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID, do they need to be mutually exclusive? [[REF](https://forums.ohdsi.org/t/measurement-table-are-value-as-concept-id-and-value-as-number-mutually-exclusive/10975)] ## Summary of answer If the raw data provides categorial results as well as continuous results for measurements, it is a valid ETL choice to preserve both values. Thus, VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are not mutually exclusive. The continuous value should go in the VALUE_AS_NUMBER field and the categorical value should be mapped to a standard concept in the ‘Meas Value’ domain and put in the VALUE_AS_CONCEPT_ID field. If there is no categorial result in a source data, set VALUE_AS_CONCEPT_ID to NULL, if there is a categorial result in a source data but without mapping, set VALUE_AS_CONCEPT_ID to 0. For example, it would be feasible to receive a measurement for a LOINC `8867-4-heart rate` from a source system that both indicates that a patient experienced a heart rate of `60 beats per minute` and this measurement was considered `normal`. The 200 can be stored in VALUE_AS_NUMBER, the beats per minute in UNIT_CONCEPT_ID (`8541-per minute`), and finally the "normal" in VALUE_AS_CONCEPT_ID (`4069590-Normal`). ## Related links - https://ohdsi.github.io/CommonDataModel/cdm54.html#measurement - https://forums.ohdsi.org/t/measurement-table-are-value-as-concept-id-and-value-as-number-mutually-exclusive/10975 - [Operator and Value concept Id - Measurement Table in CDM](https://forums.ohdsi.org/t/operator-and-value-concept-id-measurement-table-in-cdm/6662) ## Other comments/notes - @MelaniePhilofsky - This wasn't ratified though. It looks like there might have been a discussion (see the forum thread below) but I don't see the entry. However, if I were to assert what to do here is we take the values the data give us. I think our DQD checks have shown us how difficult it is holistically to assert when things are "high" or "low" using the data. We may get there one day, but I don't think we are there yet. This is in the CDM documentation though: _If the raw data provides categorial results as well as continuous results for measurements, it is a valid ETL choice to preserve both values. The continuous value should go in the VALUE_AS_NUMBER field and the categorical value should be mapped to a standard concept in the ‘Meas Value’ domain and put in the VALUE_AS_CONCEPT_ID field. This is also the destination for the ‘Maps to value’ relationship. If there’s no categorial result in a source_data, set value_as_concept_id to NULL, if there is a categorial result in a source_data but without mapping, set value_as_concept_id to 0._