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Conventions on storing ventilation data

(Tatiana) #1

Hi all!

I am working with the ventilation data and was wondering if there are any established conventions on how it should be stored (which CDM tables should be populated and at which level).

In source data there is an information on the device, oxygen therapy, associated device parameters and etc. I am attaching below a simple data example to hear your feedback on populating CDM tables.


Record 1:
source value = O2 therapy Device nasal cannula
date = 2020-01-01 09:00:00

Record 2:
source_value = O2 oxygen therapy 3 L/min
date = 2020-01-01 09:00:00

Record 3:
source value = O2 therapy Device nasal cannula
date = 2020-01-01 10:00:00

Record 4:
source_value = O2 oxygen therapy 2 L/min
date = 2020-01-01 10:00:00

Record 5:
source value = O2 therapy Device nasal cannula
date = 2020-01-01 11:00:00

Record 6:
source_value = O2 oxygen therapy 2 L/min
date = 2020-01-01 11:00:00


Record 1:
procedure_concept_id = 4239130 (Oxygen Therapy)
procedure_datetime = 2020-01-01 09:00:00

Record 2:
procedure_concept_id = 4239130 (Oxygen Therapy)
procedure_date = 2020-01-01 10:00:00

And etc.


Record 1:
measurement_concept_id = 4141684 (Delivered oxygen flow rate) or 3005629 (Inhaled oxygen flow rate)
measurement_datetime = 2020-01-01 09:00:00
value_as_number = 3
unit_concept_id = 8698 (liter per minute)

Record 2:
measurement_concept_id = 4141684 (Delivered oxygen flow rate) or 3005629 (Inhaled oxygen flow rate)
measurement_datetime = 2020-01-01 10:00:00
value_as_number = 2
unit_concept_id = 8698 (liter per minute)

And etc.


Device_concept_id = 4224038 (Oxygen nasal cannula)
device_start_datetime = 2020-01-01 09:00:00
device_end_datetime = 2020-01-01 11:00:00


Drug_concept_id = 19025274 (Oxygen)
drug_exposure_start_datetime = 2020-01-01 09:00:00
drug_exposure_end_datetime = 2020-01-01 11:00:00
route_concept_id = 45956874 (inhalation)

Open questions:

  1. Would it be better to have individual Device and Drug exposure records instead of aggregated?
  2. If the approach above of populating CDM tables is correct?.
  3. Any other CDM tables/ fields to be populated?

I am tagging people who answered in other posts on ventilation data. Hope you don’t mind :slight_smile:
@cukarthik, @Christian_Reich, @MPhilofsky, @Dymshyts, @Vlad_Korsik, @Alexdavv
Any feedback is welcome!

ETL High-Level Ventilator, Dialysis, CVVH Data
(Melanie Philofsky) #2

For v5.3, I think this is the best and most correct way to store all the relevant facts for supplemental oxygen. I really like the addition of oxygen to the Drug Exposure table! This allows researchers to use the Drug Era table for supplemental oxygen use.

I’m not intimately involved in the N3C research for COVID. I wonder if they have modeled supplemental oxygen use for the CDM? Adding @krfeeney

(Kristin Kostka, MPH) #3

You know, I was really hoping if I sat still long enough someone else would tell me the answer so I didn’t have to write the mapping myself :wink:

We haven’t tackled this (yet) in N3C. We want to. We’re planning to host a panel around data elements that we want to bring in even though they’re hard to ETL.

My thinking is this: can you think of a clinical question that can be answered by going for an individual approach? Or are more of your researchers asking for the aggregate?

I don’t know the answer yet. People are pounding the table for vent data but no one seems to like to write fully specified protocols. :smiley:

(Christian Reich) #4


Oxygen is a drug. Not a procedure. Ventilation or intubation are procedures. Question is how to represent the 2 L/min. Sounds like we need to add RxNorm Extension for this.

(Stephanie Hong) #5

oxygen is a drug?

(Christian Reich) #6

Is it not? It’s a substance that is exerting a biomedical effect on the organism.

(Stephanie Hong) #8

Most CMDs are not reporting it in the Drug domain.

(Dmytry Dymshyts) #9

Despite this seems to be not obvious, I like this idea.
And we can look into patient data and see what is the min - max range and create concepts with dosage step of 0.1 L/min.

(Christian Reich) #10

What’s that?

(Stephanie Hong) #11

what I meant was if patient is receiving oxygen, it is not reported as a drug.

(Stephanie Hong) #12

I also have another question. If source data has immunization records with CVX code and manufacture information, where can I store the manufacture information in the Drug domain?

(Melanie Philofsky) #13

The Procedure part of oxygen deliver is implicit, correct? Similar to the injection is implicit to the vaccine. There isn’t a need to record the Procedure of continuous oxygen delivery. I like it. We should add it to the conventions.

Oxygen: drug_concept_id at the ingredient level. Oxygen is dosed in liters per minute and/or at a percentage. We can convert liters per minute to a percentage. Then put the numeric to the quantity and the % to the dose_unit_source_value. Probably should bring back the dose_unit_concept_id we keep talking about in the CDM WG.

Device used to deliver the oxygen will live in the Device table.

(Roger Carlson) #14

Doesn’t blood in a transfusion exert a biomedical effect on an organism? Yet blood is a device.

(Karthik) #15

@Christian_Reich, @roger.carlson makes a good point on that. The more I’ve looked at transfusions, the more I’m thinking it fits in the drug table based on the attributes (fields) the table captures