Medical-Event-Data-Standard / Medical-Event-Data-Standard/MEDS-DEV
Unit conversion with the existing tasks
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- Dominant language
- Python
- Stars
- 43
- Forks
- 10
- PR merge metrics
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Description
Hi, @mmcdermott @gkondas
I am looking to fit the tasks in different datasets to the following tasks:
"abnormal_lab/vital/hypotension/first_24h"
"abnormal_lab/blood_chemistry/metabolic_acidosis/first_24h"
"abnormal_lab/blood_chemistry/hyponatremia/first_24h"
"abnormal_lab/blood_chemistry/elevated_creatinine/first_24h"
"abnormal_lab/cbc/leukocytosis/first_24h"
"abnormal_lab/cbc/thrombocytopenia/first_24h"
"abnormal_lab/cbc/anemia/first_24h"
The issue is that several datasets report mmol/L instead of g/dL. Firstly, this is non-trivial, as we need to know the molecular mass (although we can use common conversions, such as those for hemoglobin).
Second: currently, the thresholds are in both the predicates.yaml and the task.yaml: see https://github.com/Medical-Event-Data-Standard/MEDS-DEV/blob/main/src/MEDS_DEV/tasks/abnormal_lab/blood_chemistry/elevated_creatinine/first_24h.yaml. I would think the preferred place to put them is in the predicates only, such that the unit can be dataset-agnostic. Is this a bug? Why is this redundancy here?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with src/MEDS_DEV/tasks/abnormal_lab/blood_chemistry/elevated_creatinine/first_24h.yaml and compare its thresholds with the predicates.yaml and task.yaml files mentioned in the issue. Trace how the existing tasks map measurements and units across datasets, including the listed abnormal-lab tasks. Done means the required unit conversions and the intended threshold location are established clearly enough to support dataset-agnostic task definitions.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, yaml
- Domain
- data, machine-learning
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100