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mimic-profiles's Introduction

mimic-profiles

FHIR profiles for MIMIC-IV. The MIMIC-IV and MIMIC-IV-ED databases have been modelled as FHIR resources. The process to generate the full implementation guide with resources is:

  1. Set up FSH and SUSHI - SUSHI Setup Guide
  • Install Node.js (needed for SUSHI): https://nodejs.org/en/
    • Check node.js is properly set up: node --version or npm --version
  • Install SUSHI: npm install -g fsh-sushi
  1. Generate FHIR resources from FSH
  • In the main directory of the repo run sushi .
  • This command will generate the FHIR resources from the FSH files
  1. Set up the IG Publisher
  • Install Jekyll (need for the IG html output)
  • Run ./_updatePublisher.sh from the top of the repository to get the latest IG Publisher
    • If _updatePublisher.sh does not work you can manually download the IG publisher
  1. Generate the mimic-fhir implementation guide
  • Run ./_genonce.shfrom the top of the repository to generate the mimic-fhir IG

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mimic-profiles's Issues

Identifiers in MIMIC example instances

The demo data still contains identifiers for every resource. I didn't remove those.

To do: check for which resources the identifier can be removed (no business identifier in MIMIC) and for which it should stay.

Fix FSH errors (due to new instances) so Publisher runs

Based on the demo data, I found:

  • The profile MimicObservationDatetimeevents only allows Quantity for value[x], but the demo data contains a dateTime. Should value[x] here also allow dateTime?
    If so, change * value[x] only Quantity to * value[x] only Quantity or dateTime in SD_MimicObservationDatetimeevents.fsh

  • The profile MimicProcedureICU only allows dateTime for performed[x], but the demo data contains a Period range. Should performed[x] also allow Period?
    If so, change * performed[x] only dateTime to * performed[x] only dateTime or Period in SD_MimicProcedureICU.fsh

What did we do with pain?

Pain code is still in the MimicObservationTypeED value set, it needs to be in MimicObservationTypeVital instead. Maybe I forgot to move it.. or did we eventually decide to not move pain to MimicObservationVitalSigns? We went back and forth on this and now I don’t remember!

Joint profiles: what to do with 1..1 elements in either ED or MIMIC-IV

Example: Patient.birthDate is (always?) present in MIMIC-IV but is not in MIMIC-ED. When creating the ED Patient example instance I changed the cardinality of Patient.birthDate to 0..1 instead of 1..1. But after some thought I figured that maybe it's better to keep 1..1 cardinalities whenever an element is always present in either of the databases, and then add a dataAbsentReason extension with code 'unsupported' (http://hl7.org/fhir/R4B/valueset-data-absent-reason.html) if needed.

If we do that for every element that should be 1..1 in ED or IV (joint profiles Procedure, Patient, Encounter, Condition) validation won't be broken.

What do you think?

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