drug_concept_id - "... ETL to provide as much information as possible from the data" - where to cut off validity?

Open
  • Is something wrong?
#785 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
35/100
Issue type
Documentation
Clarity
Needs clarification
Activity status
Quiet
Tech stack
html
Domain
databases, documentation

Research direction

Start with the CDM 5.4 drug_exposure documentation linked in the issue, focusing on drug_concept_id and the guidance to use as much information as possible. Review the SICdb paper for the validity examples, then determine what cutoff and wording the documentation should provide; done means an agreed, documented recommendation for handling unreliable drug detail.

Written by the indexing model from the issue text.

Description

I am an ICU dataset developer and publisher, with a research focus on data bias in routinely collected clinical data. When transforming the dataset to the OMOP CDM, I encountered the following issue.

Documentation notes, ETL should use "as much information as possible from the data" [1]. Nevertheless, it gives no guidance on data validity levels, although data that is not used in clinical practice is often highly invalid.

An example is the granularity of drug_concept_id.

Validity Estimation: (absolute numbers represent Salzburg University Hospital ICU Data (SICdb[2]) 2013-2021)

Ingredient: 3.8 % invalid entries (outliers etc.), (MAR estimated ~1%, MNAR probably insigificant)
Clinical Drug Component: Estimated 5-10% invalid data
Branded X: Estimated >50-80% invalid data

Example for invalidity Ingredient: 1 kg of paracetamole documented (wrong unit)
Example for Clinical Drug Component: 1.5 Units of Enoxaparin 40 mg applied (when changing dosage, product is not updated)

For Branded Drugs, as long as no closed-loop documentation is established, it is actually quite unlikely the exact product is applied. At least in Austria almost every branded drug changes regularily, different brands in same drawer. Without closed-loop it is not possible to document this.

At least at my units, the product information in templates is (almost at the point of setting up) outdated.

So, guidance would be needed. "...as much information as possible from the data" or "...as much reliable information as possible from the data", and where to cut of?

This may appliy to other topics too, but drug_concept_id is a good example.

  1. https://ohdsi.github.io/CommonDataModel/cdm54.html#drug_exposure
  2. https://doi.org/10.1038/s41597-024-03164-9
Dominant language
HTML
Stars
1.1k
Forks
513
Avg merge
8d 3h
Merged PRs (30d)
4

Getting set up

This project ships no dev container, Dockerfile or contributing guide, so setting up is up to you: start from its README, and see our first-contribution guide for the general steps.

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from OHDSI/CommonDataModel

All issues in OHDSI/CommonDataModel

Similar issues

More Databases issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.