Medication updates

[alexmbennett2]

An update to the medication resources in FHIR needs to be done. The following updates to each resource:

• Medication- MedicationMix

  • [x] Update so only generating distinct medication mixes (currently generating one for every prescription). Look into using product_decription/product_code. Currently with prescriptions we get ~23,000 medication resources, but only 10,625 are straight medication resources and only ~2,000 prescriptions are needed for multiple drugs. The rest of the prescriptions are just one drug (so should be mapped to medication resource instead of making a medication mix).
  • [x] Debate UUID source text, should it be product_code or some concatenation of values. Currently pharmacy_id which won't work after distinct medication mixes are made
  • [x] Add medication-drug binding to mimic-medication profile (not bound right now until the medication/medication mix sorted)

• MedicationAdministration

  • [x] Set provenance for administration (icu vs hosp). But also think of better provenance groupings than icu/hosp
  • Do we set this as the EventHistory provenance or add an extension for the info?
  • [x] Reference the medication mixes via product_description (found in emar_detail for hosp, not in inputevents or d_items). ICU medadmin should be fine without medication mixes as they are a subset of about ~400 meds just for ICU
  • [x] Add in SIG to the text field (or see if there is a good spot for it, SIG may go in MedicationRequest actually)
  • [x] dosage.dose.value must be numeric but the source column emar.dose_due does provides some text and some numeric values. Need to either decide on some logic how to deal with this, or have multiple medication admin for the dose_given?
  • Multiple admin for each dose given (but still text in dose_given... so need to strip that out)
  • Potentially have a parent med admin with dose_due information (kinda like a Dispense resource, but no way to connect Medication Dispense resource into Medication Administration resource

• MedicationRequest

  • [x] Add medication requests not in pharmacy. Pull from prescriptions table
  • [x] Add fhir_etl table for status element for mapping of MIMIC-IV status value to FHIR standard value. status element is bound in MedicationRequest as a code, so no codesystem can be supplied like in a CodeableConcept. Need this updated so that profiles will validate in anneal.
  • [x] Add additional info to dosageInstructions. Look into prescriptions and pharmacy columns for anything on dose, rate, duration etc. Document in MIMIC-IV to FHIR mappings file
  • [x] Reference medication mixes via the updated medication-codes

• MedicationDispense

  • [x] Investigate the use in adding MedicationDispense. Can link to MedicationAdministrations

Misc To Do

• [x] Delete fhir_etl.map_drug_id. NDC mapping to be done later so all drugs pulled into Medication resource
• [x] Map out medication landscape for MIMIC (jupyter notebook)
  • Example code from MIMIC-IV playing with medications: https://colab.research.google.com/drive/1REu-ofzNzqsTT1cxLHIegPB0nGmwKaM0?usp=sharing
  • Look into emar, emar_detail, and inputevents
  • Look at specific cases for common medication types
  • Pills - ranitidine/acetominophin
  • Infusion - heparin/noepinephrine. Heparin will have varying dose_due from the titration.
  • Antibiotic - vancamycin. See how it is administered (ie IV)
  • Saline - good example of med admin with NULL medication
  • [ ] Medication-site codesystem needs to be cleaned up
  • Looks like a lot of free text in here... so mapping some of that?

[alexmbennett2]

Medication Mix Notes

• Medication mix updated id from pharmacy_id to the aggregated drug name. This removes duplicate medications orders from prescriptions.
• Final format for the drug name if multiple drugs prescribed in one order: MAIN_BASE_ADDITIVE_ADDITIVE (where additive may or may not be present)

[alexmbennett2]

Medication Administration

• There are some product_description/product_code that are set to NULL. I don't think we can use this as the medication code. I'll be sticking with just the drug name for now
  • Also not all medication mix prescriptions are used in emar, so can't rely on the product_descriptions

[alexmbennett2]

Medication Administration dose_given troubleshooting

• Total non null dose_given: 26.2 million
• Total numeric values: 26,131,112
• Total non-numeric values: 71,198
  • Units present still (~47,000) -> set dosage.dose null, and store free text value under dosage.text
  • value is N/INI, with information in the formulary dose (~24,000) -> grab formulary dose