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openEHR-AdverseReactionRisk-to-FHIR-AllergyIntolerance-STU3-mappings.adoc

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openEHR AdverseReactionRisk to FHIR allergyIntolerance STU3 mappings

Ian McNicoll <[email protected]> v1.1.2, 12-Feb-2018

FHIR resource operation Requirements

Operation : read

  1. Expose any active allergy records held in the underlying openEHR CDR 'Adverse reaction list' as a bundle of FHIR AllergyIntolerance resources, profiled to meet NHS Care-Connect Profile STU3.

  2. Deleted records, those entered in error, inactive, refuted or resolved allergies should not be sent.

  3. Individual allergy negations, handled in openEHR as Specific Exclusions such as 'No history of penicillin allergy' should not be exposed.

  4. Support the read, search and conformance FHIR resource operations.

  5. The following FHIR AllergyIntolerance data elements should be exposed where corresponding openEHR data is available

    • id (logical resource identifier)

    • text (This will be generated narrative from concatenated structured data below)

    • clinicalStatus

    • verificationStatus

    • type

    • category

    • criticality

    • code - Mandatory

    • patient.reference - Mandatory

    • patient.identifier- Mandatory

    • assertedDate - Mandatory

    • onset.onsetDateTime

    • asserter

    • lastOccurence

    • note

    • reaction.manifestation

    • reaction.description

    • reaction.onset

    • reaction.exposureRoute

Operation: search

The following Search criteria must be supported

  • date (including date ranges)

  • patient.id (via logicalID)

  • patient.identifier (via NHS Number)

  • verificationStatus (To be Confirmed after review by Care-Connect)

  • category

  • $current-allergies - see Named Queries in HAPI-FHIR

  • $current-drug—​allergies

Implementation will require appropriate AQL construction and or AQL resultSet filtering, for which guidance will be provided.

Operation: conformance

The AllergyIntolerance profile should emit a conformance statement on request via the /metadata resource - it is expected that the default handling provided by the HAPI-FHIR stack should be sufficient for this purpose.

FHIR node: Ignored FHIR Care-connect extension nodes

  • allergyIntolerance.encounter

  • allergyIntolerance.evidence

  • reaction.note

  • reaction.certainty

FHIR node: Approach

  1. Retrieve candidate openEHR Allergies data via a an openEHR /query POST call, using AQL.

  2. Where the openEHR data is held as DV_TEXT/DV_CODED_TEXT ELEMENT, return the whole ELEMENT value as an object.

  3. Create a generic DV_TEXT/DV_CODED_TEXT to a FHIR CodeableConcept / Coding equivalent mapping library.

  4. Create handlers for Excluded/Absent information items when Care-Connect guidance emerges. Assume making use of FHIR List resource for now.

FHIR node: Full AQL (includes search parameters and dv_coded_text objects)

select
    e/ehr_id/value as ehrId,
    e/ehr_status/subject/external_ref/id/value as subjectId,
    e/ehr_status/subject/external_ref/namespace as subjectNamespace,
    a/uid/value as compositionId,
    a/composer/name as composerName,
    a/composer/external_ref/id/value as composerIdentifier,
    a/composer/external_ref/namespace as composerNamespace,
    a/context/start_time/value as compositionStartTime,
    b_a/uid/value as entryId,
    b_a/data[at0001]/items[at0002]/value as Causative_agent,
    b_a/data[at0001]/items[at0063]/value/defining_code/code_string as Status_code,
    b_a/data[at0001]/items[at0101]/value/defining_code/code_string as Criticality_code,
    b_a/data[at0001]/items[at0120]/value/defining_code/code_string as Category_code,
    b_a/data[at0001]/items[at0117]/value/value as Onset_of_last_reaction,
    b_a/data[at0001]/items[at0058]/value/defining_code/code_string as Reaction_mechanism_code,
    b_a/data[at0001]/items[at0006]/value/value as Comment,
    b_a/protocol[at0042]/items[at0062]/value/value as Adverse_reaction_risk_Last_updated,
    b_a/data[at0001]/items[at0009]/items[at0010]/value as Specific_substance,
    b_a/data[at0001]/items[at0009]/items[at0021]/value/defining_code/code_string as Certainty_code,
    b_a/data[at0001]/items[at0009]/items[at0011]/value as Manifestation,
    b_a/data[at0001]/items[at0009]/items[at0012]/value/value as Reaction_description,
    b_a/data[at0001]/items[at0009]/items[at0027]/value/value as Onset_of_reaction,
    b_a/data[at0001]/items[at0009]/items[at0089]/value/defining_code/code_string as Severity_code,
    b_a/data[at0001]/items[at0009]/items[at0106]/value as Route_of_exposure,
    b_a/data[at0001]/items[at0009]/items[at0032]/value/value as Adverse_reaction_risk_Comment
from EHR e

contains COMPOSITION a[openEHR-EHR-COMPOSITION.adverse_reaction_list.v1]
contains EVALUATION b_a[openEHR-EHR-EVALUATION.adverse_reaction_risk.v1]

where a/name/value='Adverse reaction list'
-- Optional parameters, depending on FHIR search criteria
and e/ehr_id/value = '{{fhir.patient.id_param}}'
and e/ehr_status/subject/external_ref/id/value = '{{fhir.patient.identifier.value.param}}'
and e/ehr_status/subject/external_ref/namespace =  '{{fhir.patient.identifier.system.param}}'
and b_a/data[at0001]/items[at0120]/value/defining_code_string = '{{fhir_category_params}}'
and b_a/protocol[at0042]/items[at0062]/value/value >= '{{fhir_date_param_min}}'
and b_a/protocol[at0042]/items[at0062]/value/value <= '{{fhir_date_param_max}}'

Node mappings

FHIR node:: allergyIntolerance.id

openEHR AQL node

compositionId+ '_' + entryId

Valueset mappings

None

ℹ️
 The FHIR id is constructed by a concatenation of the openEHR compositionId and entryId as above. If entryID is null, simply send the compositionID. entryID is currently not supported by Ethercis.

FHIR node:: allergyIntolerance.clinicalStatus

openEHR AQL node

  • Status_code_string ⇒ allergyIntolerance.clinicalStatus

Datatype Mapping style

DV_CODED_TEXT ⇒ Code

Valueset mappings

  • always map to ⇒ active

==== FHIR node

allergyIntolerance.verificationStatus

openEHR AQL node

  • Status ⇒ allergyIntolerance.verificationStatus

Datatype Mapping style

DV_CODED_TEXT ⇒ Code

Valueset mappings

  • at0127::Suspected ⇒ unconfirmed (default)

  • at0065::Confirmed ⇒ confirmed

ℹ️
 If the openEHR node is unpopulated default to unconfirmed

FHIR node:: allergyIntolerance.type

openEHR AQL node

  • Reaction_mechanism_code ⇒ allergyIntolerance.type

Datatype Mapping style

DV_CODED_TEXT ⇒ Code

Valueset mappings

  • at0059::Immune mediated ⇒ allergy

  • at0060::Non-immune mediated ⇒ intolerance

  • at0126::Indeterminate ⇒ DO NOT PERSIST

ℹ️
 If the openEHR value is at0126::Indeterminate then this node should not be persisted in FHIR.

FHIR node:: allergyIntolerance.category

openEHR AQL node

  • Category_code ⇒ allergyIntolerance.category

Datatype Mapping

DV_CODED_TEXT ⇒ Code

Valueset mappings

  • at0121::Food ⇒ food

  • at0122::Medication ⇒ medication

  • at0123::Other ⇒ environment

  • at0122::Medication ⇒ biologic

==== FHIR node

allergyIntolerance.criticality

openEHR AQL node

  • Criticality ⇒ allergyIntolerance.criticality

Datatype Mapping

DV_CODED_TEXT ⇒ Code

Valueset mappings

  • at0102::Low ⇒ low

  • at0103::High ⇒ high

  • at0124::Indeterminate ⇒ unable-to-assess

FHIR node: allergyIntolerance.code

openEHR AQL node

  • Causative_agent ⇒ allergyIntolerance.code

Datatype mapping

DV_TEXT ⇒ CodeableConcept
see Datatype mapping guidance

FHIR node: allergyIntolerance.patient

openEHR AQL node

ehrId ⇒ allergyIntolerance.patient.reference subjectId ⇒ allergyIntolerance.patient.identifier.value subjectNamespace ⇒ allergyIntolerance.patient.identifier.system

Valueset mappings

  1. For subjectNamespace ⇒ allergyIntolerance.patient.identifier.system

    1. uk.nhs.nhs_number ⇒ https://fhir.nhs.uk/Id/nhs-number

ℹ️
 We are using the patient’s openEHR ehrId as the id of the FHIR patient resource, and using the patient’s NHS Number, carried in the openEHR 'ehr' object as subjectId as the patient identifier. If the subjectNamespace is not uk.nhs.nhs_number, it should not be mapped to https://fhir.nhs.uk/Id/nhs-number but simply passed through unchanged.

allergyIntolerance.lastOccurence

openEHR AQL node

Onset_of_last_reaction ⇒ allergyIntolerance.lastOccurence

Valueset mappings

None

FHIR node: allergyIntolerance.assertedDate

openEHR AQL node

Adverse_reaction_risk_Last_updated ⇒ allergyIntolerance.assertedDate

if Adverse_reaction_risk_Last_updated is null compositionStartTime ⇒ allergyIntolerance.assertedDate

ℹ️
 Where the last Updated date is null the start_time attribute of the parent composition is a safe proxy.
Datatype mapping

DV_DATE_TIME ⇒ dateTime

Valueset mappings

None

FHIR node: allergyIntolerance.note

openEHR AQL node

Comment ⇒ allergyIntolerance.note.text

Datatype mapping

DV_TEXT ⇒ Annotation.

Valueset mappings

None

FHIR node: allergyIntolerance.reaction.substance

openEHR AQL node

Specific_substance_value ⇒ allergyIntolerance.reaction.substance.text

Valueset mappings

Specific_substance_terminology_id ⇒ allergyIntolerance.reaction.substance.coding.system

Datatype mapping

DV_TEXT ⇒ CodeableConcept
see Datatype mapping guidance

FHIR node: allergyIntolerance.reaction.manifestation

openEHR AQL node

Manifestation_value ⇒ allergyIntolerance.reaction.manifestation.text

Datatype mapping

DV_TEXT ⇒ CodeableConcept

Valueset mappings

Specific_substance_terminology_id ⇒ allergyIntolerance.reaction.substance.coding.system

Datatype mapping

DV_TEXT ⇒ CodeableConcept
see Datatype mapping guidance

FHIR node: allergyIntolerance.reaction.description

FHIR Description

- Description of the event as a whole.

openEHR AQL node

Reaction_description ⇒ allergyIntolerance.reaction.description

Datatype mapping

DV_TEXT ⇒ String

Valueset mappings

None

FHIR node: allergyIntolerance.reaction.onset

openEHR AQL node

Onset_of_reaction ⇒ allergyIntolerance.reaction.onset

Valueset mappings

None

FHIR node: allergyIntolerance.reaction.severity

openEHR AQL node

Severity ⇒ allergyIntolerance.reaction.severity

Datatype mapping

DV_CODED_TEXT ⇒ Code

Valueset mappings

local::at0093| Mild ⇒ mild local::at0092| Moderate ⇒`moderate` local::at0090| Severe ⇒ severe

FHIR node: allergyIntolerance.reaction.exposureRoute

FHIR Description

- How the subject was exposed to the substance.

openEHR AQL node

Route_of_exposure_value ⇒ allergyIntolerance.reaction.exposureRoute

Datatype mapping

DV_TEXT ⇒ CodeableConcept
see Datatype mapping guidance

FHIR node: allergyIntolerance.reaction.note

FHIR Description

- Date(/time) when manifestations showed.

openEHR AQL node

Adverse_reaction_risk_Comment ⇒ allergyIntolerance.note.text

Datatype mapping

DV_TEXT ⇒ Annotation

Valueset mappings

None

FHIR node: allergyIntolerance.asserter.name

FHIR Description

- The name of the person asserting the allergy.

openEHR AQL node

composerName ⇒ allergyIntolerance.asserter.name

Datatype mapping

DV_TEXT ⇒ string

Valueset mappings

None

FHIR node: allergyIntolerance.asserter.identifier.value

FHIR Description

- The identifier of the person asserting the allergy.

openEHR AQL node

composerIdentifier ⇒ allergyIntolerance.asserter.identifier.value composerNamespace ⇒ allergyIntolerance.asserter.identifier.system

Datatype mapping

DV_TEXT ⇒ String

Valueset mappings

None

Alternative FLAT AQL

This flattened form of the AQL avoids use of DV_CODED_TEXT objects.

select
    e/ehr_id/value as ehrId,
    e/ehr_status/subject/external_ref/id/value as subjectId,
    e/ehr_status/subject/external_ref/namespace as subjectNamespace,
    a/composer/name as composerName,
    a/composer/external_ref/id/value as composerId,
    a/composer/external_ref/namespace as composerNamespace,
    a/uid/value as compositionId,
    a/context/start_time/value as compositionStartTime,
    b_a/uid/value as entryId,
    b_a/data[at0001]/items[at0002]/value/value as Causative_agent_value,
    b_a/data[at0001]/items[at0002]/value/defining_code/code_string as Causative_agent_code,
    b_a/data[at0001]/items[at0002]/value/defining_code/terminology_id/value as Causative_agent_terminology,
    b_a/data[at0001]/items[at0063]/value/defining_code/code_string as Status_code,
    b_a/data[at0001]/items[at0101]/value/defining_code/code_string as Criticality_code,
    b_a/data[at0001]/items[at0120]/value/defining_code/code_string as Category_code,
    b_a/data[at0001]/items[at0117]/value/value as Onset_of_last_reaction,
    b_a/data[at0001]/items[at0058]/value/defining_code/code_string as Reaction_mechanism_code,
    b_a/data[at0001]/items[at0006]/value/value as Comment,
    b_a/protocol[at0042]/items[at0062]/value/value as Adverse_reaction_risk_Last_updated,
    b_a/data[at0001]/items[at0009]/items[at0010]/value/value as Specific_substance_value,
    b_a/data[at0001]/items[at0009]/items[at0010]/value/defining_code/code_string as Specific_substance_code,
    b_a/data[at0001]/items[at0009]/items[at0010]/value/defining_code/terminology_id/value as Specific_substance_terminology,
    b_a/data[at0001]/items[at0009]/items[at0021]/value/defining_code/code_string as Certainty_code,
    b_a/data[at0001]/items[at0009]/items[at0011]/value/value as Manifestation_value,
    b_a/data[at0001]/items[at0009]/items[at0011]/value/defining_code/code_string as Manifestation_code,
    b_a/data[at0001]/items[at0009]/items[at0011]/value/defining_code/terminology_id/value as Manifestation_terminology,
    b_a/data[at0001]/items[at0009]/items[at0012]/value/value as Reaction_description,
    b_a/data[at0001]/items[at0009]/items[at0027]/value/value as Onset_of_reaction,
    b_a/data[at0001]/items[at0009]/items[at0089]/value/defining_code/code_string as Severity_code,
    b_a/data[at0001]/items[at0009]/items[at0106]/value/value as Route_of_exposure_value,
      b_a/data[at0001]/items[at0009]/items[at0106]/value/defining_code/code_string as Route_of_exposure_code,
        b_a/data[at0001]/items[at0009]/items[at0106]/value/defining_code/terminology_id/value as Route_of_exposure_terminology,
    b_a/data[at0001]/items[at0009]/items[at0032]/value/value as Adverse_reaction_risk_Comment
from EHR e

contains COMPOSITION a[openEHR-EHR-COMPOSITION.adverse_reaction_list.v1]
contains EVALUATION b_a[openEHR-EHR-EVALUATION.adverse_reaction_risk.v1]

where a/name/value='Adverse reaction list'
-- Optional parameters, depending on FHIR search criteria
and e/ehr_id/value = '{{fhir.patient.id_param}}'
and e/ehr_status/subject/external_ref/id/value = '{{fhir.patient.identifier.value.param}}'
and e/ehr_status/subject/external_ref/namespace =  '{{fhir.patient.identifier.system.param}}'
and b_a/data[at0001]/items[at0120]/value/defining_code_string = '{{fhir_category_params}}'
and b_a/protocol[at0042]/items[at0062]/value/value >= '{{fhir_date_param_min}}'
and b_a/protocol[at0042]/items[at0062]/value/value <= '{{fhir_date_param_max}}'

FHIR Narrative block

This is optional in Care-Connect but is good practice.

NOTE

TBD