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
DTorok
April 22, 2019, 12:59pm
2
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.
1 Like
Thank you @DTorok for the clarification. Much appreciated
ericaVoss
April 11, 2024, 7:23pm
4
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:
opened 06:33PM - 11 Apr 24 UTC
closed 04:57PM - 18 Apr 24 UTC
# MEASUREMENT.VALUE_AS_NUMBER/VALUE_AS_CONCEPT_ID/UNIT_CONCEPT_ID/MEASUREMENT_CO… NCEPT_ID THEMIS Rules
## CDM or THEMIS convention?
THEMIS
## 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
- Only records where the source value maps to a CONCEPT_ID in the 'Measurement' domain should be included in this table.
- For some MEASUREMENT concepts the result is included in the test. For example, ICD10 CONCEPT_ID [45548980](https://athena.ohdsi.org/search-terms/terms/45548980) ‘Abnormal level of unspecified serum enzyme’ indicates a Measurement and the result (abnormal). In those situations, the CONCEPT_RELATIONSHIP table in addition to the ‘Maps to’ record contains a second record with the RELATIONSHIP_ID set to ‘Maps to value’. In this example, the ‘Maps to’ relationship directs to [4046263](https://athena.ohdsi.org/search-terms/terms/4046263) ‘Enzyme measurement’ as well as a ‘Maps to value’ record to [4135493](https://athena.ohdsi.org/search-terms/terms/4135493) ‘Abnormal’.
- 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 and put in the VALUE_AS_CONCEPT_ID field. 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`).
- It is also not mandatory to have one or both VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID as it is possible for the result to not be given in the source data. When the result is not known, the MEASUREMENT record represents just the fact that the corresponding measurement was carried out, which in itself is already useful information for some use cases.
Technically this part of a ratified THEMIS concept:
[CONCEPT_ID (to NULL or not to NULL) #11](https://github.com/OHDSI/Themis/issues/11)
## 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)
- [CONCEPT_ID (to NULL or not to NULL) #11](https://github.com/OHDSI/Themis/issues/11)
## 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._
