How can we store the PFT data in CDM?

[Chungsoo_Kim]

Hi, I’m currently working on using the PFT (Pulmonary function test) data of our medical center. but I have a problem storing it to CDM v5. we just stored FEV(%) and FVC/FEV(%) data only in the measurement table regardless of the type of detailed test before. however, I think it is needed to store whole PFT data.

PFT data consists of various measurements related to lung status and function. For example, there are FEV1 (Forced Expiratory Volume in 1 second), FVC (forced vital capacity) which measured when pre- and post-bronchodilator applied. here is an example result.

Also to diagnose asthmatics in more detail, there are bronchial provocation tests like oral provocation test, methacholine challenge test, lys-asp broncho-provocation test, and so on. especially these data recorded the pulmonary functions by the concentration of a substance or by the time from when applied the substance to 3 min, 5 min, 10min, 20 min, and 1 hour. also I attached one example.

how can we store this PFT data with detailed information in CDM 5.3.1? it seemed that it could be stored in the measurement table, but I realized that detailed information would be lost. Should we store this in the observation table? Or should we use the fact_relationship table like bacterial culture and antibiotics susceptibility data?

Is there any prior discussion or anyone who has experience related to storing the PFT data to CDM? If you can share your experiences, that would be wonderful.

Thanks
Chungsoo Kim

[JayGee (Jay Greenfield)]

Isn’t the PFT as a whole and each of its components described in LOINC beginning at https://loinc.org/81458-2/. LOINC in turn is a standard vocabulary in OMOP so it ought to be possible to look up in Athena all the concept IDs that correspond to each LOINC concept code and create for each one that your PFT measures a MEASUREMENT record. You get fact relationships for nothing because of LOINC and the way the PFT panel and its components are represented in the standard vocabularies. Something may get lost in translation but you don’t need to start from scratch.

[Christian_Reich]

@Chungsoo_Kim:

LOINC has a lot, but not all. You have pre and post bronchodilation, you have the various methacholine concentrations, You don’t have the other substances and you don’t have the timing after challenge. I would start with what is there. When a use case comes up and somebody actually needs to study the data we would figure out how to deal with the detail.

Thoughts?

[Chungsoo_Kim]

Thanks @JayGee and @Christian_Reich. It was really helpful for me.

LOINC in turn is a standard vocabulary in OMOP so it ought to be possible to look up in Athena all the concept IDs that correspond to each LOINC concept code and create for each one that your PFT measures a MEASUREMENT record.

Yes, I agree. I also think that LOINC is great for mapping the PFT concepts

You don’t have the other substances and you don’t have the timing after challenge. I would start with what is there.

I have started to first identify which concepts of our PFT data can be mapped using our standard vocabulary and which concepts cannot. First of all, I would collect more opinions from other researchers. Of course, you can see it too in here.

When a use case comes up and somebody actually needs to study the data we would figure out how to deal with the detail.

Yes, Progress on demands is more efficient. I’m working with some allergists, so I can think of research related. Thanks for the comments again.