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Blood culture result in measurement or observation table and vocabulary to be used

CDM Builders
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#1

Hello,

I am relatively new to the OMOP CDM and am currently designing the ETL process for our data at the moment. I would like to transform our blood culture results. However, I am not quite sure about the CDM table that the results should be added to.

The problem I have is as follows:
As I understand it, the microbiology results (if there is an organism present and if so, which one) should be part of the measurement table as the observation table user guide states the following: “If the generation clinical facts requires a standardized testing such as lab testing or imaging and leads to a standardized result, the data item is recorded in the MEASUREMENT table.” I would then store the organism in value_as_concept_id or the concept 9190 (Not detected) if no organism was detected.
However, my problem is that less than 20% of the organisms present in our data can be mapped to the Meas Value domain. The rest didn’t have a match in this domain but in the observation domain instead. And it would also be possible to map all the organisms that I mapped to the Meas Value domain to the Observation domain. In other words, the vocabulary used for the Meas Value domain (LOINC) is not complete at all, but the vocabulary used for the Observation domain (SNOMED) is almost complete.
Having the data mapped to two different vocabularies does not seem appropriate when I could just map everything to SNOMED which is in the observation domain.

Now I am wondering what is the preferred way to handle this situation.

  • Using the measurement table, mapping everything to the observation domain
  • Using the observation table, mapping everything to the observation domain
  • Using the measurement table, mapping as much as possible to the Meas Value domain and the rest to the observation domain and having mixed terminologies for the organisms
  • Split the data in the measurement and observation tables based on the domain to which the data can be mapped

Thank you very much for your help and opinion on this topic!

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#2

Hello! I am having the same issue, did you decide how to handle this?

#3

At the moment, I am using the following approach. However, this is not a convention that has already been decided on.

measurement_concept_id → microorganism (SNOMED, observation domain, organism class)
value_as_concept_id → Detected/Not detected (SNOMED, Meas Value domain, Qualifier Value class)
measurement_event_id → link to corresponding specimen
meas_event_field_concept_id → 1147049 specimen.specimen_id

What are your findings and thoughts on this?

#4

Hi @HeideNei @rosiehamilton

The problem in general (microorganisms detection and susceptibility) is not solved in OMOP mostly because there are many ways to represent this, and none of them have a ready-to-use vocabulary that would cover the entire semantic space. So any solution requires significant vocabulary effort.

This looks a bit desperate. OMOP CDM doesn’t work the way there’s an “OBSERVATION” of the organism with a negative or positive result. The concept should mean something, something that is observed or measured. Concepts like that are not self-sufficient events, probably they should live in the Meas Value domain.

Why don’t you use the LOINC concepts?
Bacteria identified in Blood by Culture
Bacteria identified in Blood by Aerobe culture
Bacteria identified in Blood by Anaerobe culture

They also explicitly tell you what the table should be.

I would not even try mapping them to LOINC (Meas Value, Answers) because there are not a lot of them and they’re question-specific.
SNOMED provides a full option to map them to Organisms but as you correctly noted, conventions expect the Meas Value values here. This is exactly the case where we should change the convention or Domain of these concepts.

#5

A related question regarding choice of vocabulary was posted in June of ’22.

We, too, are wrestling with this situation.

Culture result organisms are supposed to go into Measurement but the only Standard Taxonomy of organism names not cluttered with extraneous information that we’ve found is SNOMED, in the Observation domain.

My take on addressing this problem:

  1. Changing the domain of SNOMED Organism Concepts to Measurement could be problematic because these concepts may already be widely used in their current domain.
  2. While we have found concepts in LOINC that initially seem useful, they are Classification concepts, not Standard concepts. Therefore, using them would violate the “Standard Concepts Only” rule.
  3. The least problematic solution might be to revise the convention to allow the use of SNOMED Observation/Organism concepts for transformations into the Measurement tables.

Is there a current consensus or best practice for handling the issue of choosing vocabulary for culture-result organisms within the context of OMOP 5.4 standards?

If not, perhaps we could come to one now.

#6

Because in this post @Christian_Reich told me to put the organism in the measurement_concept_id. However, there is no vocabulary yet stating “{organism} in blood culture” that’s why I used the existing organism concepts from SNOMED so far.

Would it be possible to add them to both domains?

Agree

Not that I am aware of. That’s where all these problems are coming from.

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