MAJOR ISSUE: Epic not using standard system, instead using EPIC proprietary

[comorbidity]

Epic doesn’t always the FHIR standard system, instead Epic uses custom system=urn:oid:EPIC PROPRIATARY.
This is why we now see that counts are “None” for Encounter type, serviceType, or priority.
Probably also impacts Laboratory, Condition, and other FHIR resource types when system is expected to be standard.

SEE ALSO
#82
#31

IMPACT:
Coding.system may not be used reliably in Epic EHR, which instead provides custom OID with no known public documentation.
Consequently any programatic use that requires a standard "system" may not work in Epic sites.

DEVIATION FROM STANDARD

Encounter.type.system
Expected
http://hl7.org/fhir/us/core/STU4/ValueSet-us-core-encounter-type.html

Actual
[{coding=[{code=2, display=Emergency, system=urn:oid:1.2.840.114350.1.13.93.2.7.10.698084.10110}], text=Emergency, id=null}, {coding=[{code=3, display=Hospital Encounter, system=urn:oid:1.2.840.114350.1.13.93.2.7.10.698084.30}], text=Hospital Encounter, id=null}, {coding=[{code=1, display=Emergency Admission, system=urn:oid:1.2.840.114350.1.13.93.2.7.10.698084.18875}], text=Emergency Admission, id=null}]

[comorbidity]

Encounter.serviceType.system

Expected
http://hl7.org/fhir/R4/valueset-service-type.html

Actual
system=urn:oid:1.2.840.114350.1.13.93.2.7.10.698084.18886

[comorbidity]

Encounter.priority.system

Expected
Field is optional, if field is provided system should be:
https://terminology.hl7.org/1.0.0//ValueSet-v3-ActPriority.html

Actual
system=urn:oid:1.2.840.114350.1.13.93.2.7.10.698084.410

[comorbidity]

Observation Code (category=Laboratory)
Expected: LOINC required
Actual: LOINC is usually provided but sometimes only Epic OID is provided instead
system=urn:oid:1.2.840.114350.1.13.93.2.7.5.737384.113 and possibly also
system=urn:oid:1.2.840.114350.1.13.93.2.7.2.768282

[comorbidity]

Condition.code
Expected: SNOMED-CT and/or ICD10
Actual: frequent use of custom Epic OID for "reason for visit" effectively a text that looks like patient "chief complaint"
Impact: minimal, appears to only be related to free text fields.
system=urn:oid:1.2.840.114350.1.13.93.2.7.2.768282

[comorbidity]

Encounter.diagnosis
Expected: encounter-diagnosis not problem-list-item
http://hl7.org/fhir/us/core/STU4/StructureDefinition-us-core-encounter.html

Actual: problem list was found to be linked from Encounter.diagnosis to a condition

[comorbidity]

POSSIBLE WORKAROUNDS:

1. Do NOT filter patient cohorts using
   select * from fhir_resource where system=.....

2. Allow EPIC root OID http://oidref.com/1.2.840.114350
   select * from fhir_resource where system like urn:oid:1.2.840.114350%

[dogversioning]

confirmed the the root OID seems to be present across multiple implementations.

[dogversioning]

So, with the changes in #178, anyplace that we are looking at the value of system explictly, we are now looking for the observed EPIC OIDs. Between this and the symptom extractor, we've got the spirit of this covered - we just know that, if we're looking for code systems, we will have to include some set of observed OIDs.

This will be a work in progress, but we've got the bones covered, so I'm going to close this issue as resolved.