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OHDSI / Themis

Repository for OMOP CDM conventions as defined by THEMIS. These can be reference lists of concepts, pieces of standardized code for data generation or quality certification, and debates.
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Guidance needed in how to save the dose_ordered or dose_dispensed in the drug_exposure table #78

Open stephanieshong opened 1 year ago

stephanieshong commented 1 year ago

Issue Name: Be clear and concise. If it is an issue with a CDM table or field, then make sure the table name & field are part of the issue name. If it is an issue with source data, then the source data domain should be part of the issue name. Drug_exposure - Need further guidance in how to store the dose ordered or dispensed in the drug exposure. For example, if the injection is 2mg/mL but the patient got 80mL then quantity should be reported as 160. It would be helpful to have a field where we can save the dose ( 2mg, 10mg, etc.) Requesting a convention or guidance how to save the ingredient dose ordered or dispensed information for a given medication.

Issue Type: Usually the issue type is one of the following: Lack of an ETL convention for a CDM table and/or field, multiple standard concept_ids for an idea of interest, multiple ways to store source data in the OMOP CDM to represent an idea of interest. There is no place to save the dose ordered.

Description: Link to section of documentation which lacks or has unclear descriptions, description of idea of interest and the multiple standard concept_ids to represent this idea, or description of idea of interest and the different ways these data can be ETL’d into the CDM with standard concept_ids. https://ohdsi.github.io/CommonDataModel/cdm53.html#DRUG_EXPOSURE https://www.ohdsi.org/web/wiki/lib/exe/fetch.php?media=resources:doseform-poster-v04.pdf https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:dose_era

In PCORnet CDM, in the dispensing table, there’s DISPENSE_SUP (days supply), DISPENSE_AMT (number of units), and DISPENSE_DOSE_DISP (dose given). In the prescribing table, there’s a RX_DOSE_ORDERED, RX_QUANTITY, RX_REFILLS, and RX_DAYS_SUPPLY that would be relevant here. The med_admin table also contains some what less relevant information for this topic, but wondering how these three tables's dose ordered or dispensed information can be harmonized into the drug_exposure table as there is no dose_ordered or dose_dispensed field in the drug exposure. In N3C, we harmonize medication information coming in from the multiple CDM medication table and would like to have a clear guidance on how to save the dose ordered/dispensed information in the drug_exposure table.

Related forum post: If there is an OHDSI forum post related to this topic, please post all relevant links here. https://forums.ohdsi.org/t/estimating-daily-dose-in-various-drug-forms-routes-in-omop-cdm/18289/7

Reported By: Stephanie Hong

MaximMoinat commented 1 year ago

@stephanieshong This page contains some examples how to calculate dose from the existing OMOP fields: https://ohdsi.github.io/CommonDataModel/drug_dose.html.

As far as I know, it has been a design choice to NOT store dose in the OMOP CDM, but the components of the daily dose (quantity, days_supply, ingredient strength). This does lead to the situation that you calculation back and forth. For example the source data contains 'Paracetamol 500 mg, 2 times a day for 14 days'. Then, in OMOP you calculate the quantity as 2*14=28 pills and days_supply=14. Then, if at analysis you need dose, then you will do the reverse calculation 18/14=2 pills per day.

For 'Quantified drugs', we also have to take into account that we are dealing with a pack size. The quantity refers to the number of packs, not individual pills. e.g. '60 ACTUAT Salbutamol 0.500mg, 4 times a day for 30 days' would give a quantity of 4*30/60=2 packs.

My proposal: add a drug dose convention page from an ETL perspective. Similar to the page above, give a few examples based on different types of source medication data. As an additional ETL aid, we should also consider adding DQD checks to flag unrealistic dose values.

Also related to #76.

tiozab commented 1 year ago

@MaximMoinat is dose estimated during DQD?

MaximMoinat commented 1 year ago

It is not at the moment, but would be an interesting new check to implement. However, as given above, it is not trivial to calculate the drug dose in a generic way and we need to define acceptable ranges for each drug concept / ingredient.

tiozab commented 1 year ago

@MaximMoinat acceptable ranges are depicted by the WHO ATC DDD https://www.whocc.no/atc_ddd_index/ we use this to compare our dose estimates from the dose formulas we implemented in our drug utilisation package, agree that it is not trivial to estimate drug dosing in a generic way, but it would give an insight at ETL stage what the data mapper was up to (by looking at a specific set of ingredients that covers various drug strength patterns, you may get a good idea). We use drug strength patterns. https://www.ohdsi.org/2023showcase-502 about to be shown at the upcoming OHDSI US conference this weekend. Still needs expansion and wider proofing, but I think we are on the right track to get closer to estimating dose more generically :-)