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First-Class Extensions

In Aidbox there are two ways to define first-class extensions:

First-class extension as Zen profile

While FHIR uses two different ways to define core elements and extensions, zen profiles provide unified framework to describe both. Zen FHIR format offers user-defined elements or "first-class extensions". In zen profiles, you can define new attributes (elements) for existing (FHIR) resources. The example below shows how to define extensions in zen profiles.

resourceType: Patient
id: sample-pt
extension:
- url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-race
  extension:
  - url: text
    valueString: Asian Indian
  - url: ombCategory
    valueCoding:
       system: urn:oid:2.16.840.1.113883.6.238
       code: 2028-9
       display: Asian
  - url: detailed
    valueCoding:
       system:
       code: 2029-7	
       display: Asian Indian

Note that extension elements have :confirms to a FHIR primitive or complex type specified. Previously these were specified in the base profile schema. These :confirms and the :fhir/extensionUri are needed to allow zen FHIR <-> FHIR format transformation.

Steps to define first-class extension as zen profile:

  1. Initialize zen project and add additional IGs if necessary.

  2. Define your custom first-class extension. For syntax and more examples refer to this page.

    {ns my-zen-project
 import #{zen.fhir
          hl7-fhir-r4-core.string
          hl7-fhir-r4-core.dateTime
          hl7-fhir-r4-core.uri}

 MyPatient
 {:zen/tags #{zen/schema zen.fhir/profile-schema}
  :zen/desc "Patient resource schema with first-class extension definition examples"
  :zen.fhir/version "0.5.20"
  :confirms #{zen.fhir/Resource}
  :zen.fhir/type "Patient"
  :zen.fhir/profileUri "urn:profile:MyPatientProfile"
  :type zen/map
  
  :keys {:meta {:type zen/map
                :keys {:tenant-id
                       {:confirms #{hl7-fhir-r4-core.string/schema}
                        :zen/desc "Patient.meta.tenant-id first-class extension"
                        :fhir/extensionUri "http://tenant-id-extension-url"}}}

         :form {:type zen/vector
                :zen/desc "Patient.form.[*] array first-class extension"
                :every {:confirms #{hl7-fhir-r4-core.uri/schema}
                        :fhir/extensionUri "http://patient-form-url"}}

         :info {:type zen/map
                :zen/desc "Patient.info nested first-class extension"
                :fhir/extensionUri "http://patient-info"
                
                :keys {:registration {:confirms #{hl7-fhir-r4-core.dateTime/schema}
                                      :zen/desc "Patient.info.registration 
                                                 extension.url deduced from key"}
                       
                       :referral {:confirms #{hl7-fhir-r4-core.uri/schema}
                                  :fhir/extensionUri "http://patient-info-referral"
                                  :zen/desc "Patient.info.referral
                                             extension.url is specified"}}}}}

  3. Fix :zen.fhir/version errors if needed

    In order to fix this error, provide IG bundle with the matching zen FHIR version.

    Error message example:

    Expected '0.5.8', got '0.4.9'
path: [:zen.fhir/version]

  4. Define :fhir/extensionUri property value. :fhir/extensionUri "http://tenant-id-extension-url" is an equivalent of the extensionUrl field of the Attribute resource and used to form FHIR extension.

  5. Replace plain zen type by FHIR type in your extensions. I.e. use :confirms #{hl7-fhir-r4-core.string/schema} instead of :type zen/string.

Define new extension with Attribute

In Aidbox, you can define first-class extensions using the custom resource Attribute.

Let's create an extension definition of type Reference in the REST Console of Aidbox:

Create new extension in the Aidbox format:
PUT /Attribute/ServiceRequest.requestedOrganizationDepartment

description: Department in the organization that made the service request
resource: {id: ServiceRequest, resourceType: Entity}
path: [requestedOrganizationDepartment]
type: {id: Reference, resourceType: Entity}
refers: 
  - Organization
extensionUrl: urn:extension:requestedOrganizationDepartment

  • description - string.

    Attribute text description

  • resource - required, Reference(Entity).

    Reference to a target resource type

  • path - required, array of strings.

    Path to a new attribute location in the target resource type

  • type - Reference(Entity).

    Type of data stored in this attribute. Can be any primitive or complex type.

    If omitted, treated as BackboneElement, i.e. a complex-type object with structure defined via other Attributes relying on this attribute in their path

  • isCollection - boolean.

    Whether the attribute is a collection, i.e. if true sets attribute cardinality to ..*

  • isRequired - boolean.

    Whether the attribute is required, i.e. if true sets attribute cardinality to 1..

  • isUnique - boolean. Sets unique restriction on the attribute.

  • refers - Reference(Entity).

    Only for type=Reference. Specifies to which resourceTypes this reference can refer to

  • extensionUrl - string.

    URL which will be used to create extension element in FHIR format. If omitted, Attribute won't be transformed in FHIR format

Note: you can not use Attributes and zen profiles on the same resource at the same time

Use your extension

Now, you can create the ServiceRequest resource using the new attribute requestedOrganizationDepartment in the root of the resource:

Create resource in the Aidbox format:
PUT /ServiceRequest/servicerequest-with-aidbox-native-extensions

requestedOrganizationDepartment:
  resourceType: Organization
  display: City Hospital Neurology Department
  identifier: {system: 'urn:oid:1.2.3.4.5.6.7.8', value: '456'}
category:
- coding:
  - {code: '183829003', 
    system: 'http://snomed.info/sct', 
    display: "Refer for imaging"}
authoredOn: '2020-01-18T15:08:00'
resourceType: ServiceRequest
requester:
  resourceType: PractitionerRole
  display: Din Morgan
  identifier: {value: "1760", system: 'urn:oid:1.2.3.4.5.6.7.6'}
priority: routine
status: active
intent: original-order
performer:
- resourceType: Organization
  display: Aga Khan University Hospital Laboratory
  identifier: {value: "1514", system: 'urn:oid:1.2.3.4.5.6.7.8'}
subject:
  resourceType: Patient
  display: Jack Black, 10.12.1941
  identifier: {value: '2155800871000065', system: 'urn:oid:1.2.3.4.5.6.7.9'}

FHIR Format

You can get the resource in the FHIR format where our new attribute is rendered as the extension element:

Note that the URL is different:GET /fhir/ServiceRequest/

Get the resource in the FHIR format:
GET /fhir/ServiceRequest/servicerequest-with-aidbox-native-extensions

Other extension examples

Let's create an extension of type Reference and list allowed resource types (Organization in that case) in the refers property.

managingOrganization
PUT /Attribute/ServiceRequest.managingOrganization

resourceType: Attribute
description: Organization that made the service request
resource: {id: ServiceRequest, resourceType: Entity}
path: [managingOrganization]
id: ServiceRequest.managingOrganization
type: {id: Reference, resourceType: Entity}
refers: 
  - Organization
extensionUrl: urn:extension:requestedOrganization

Extension of type Coding:

paymentType
PUT /Attribute/ServiceRequest.paymentType

resourceType: Attribute
description: Payment type for the service request, e.g. government health insurance
id: ServiceRequest.paymentType
resource:
  id: ServiceRequest
  resourceType: Entity
path:
- paymentType
type:
  id: Coding
  resourceType: Entity
extensionUrl: urn:extension:paymentType
Create resource using these extensions:
PUT /ServiceRequest/servicerequest-with-aidbox-native-extensions

managingOrganization:
  resourceType: Organization
  display: City Hospital
  identifier: {value: "123", system: 'urn:oid:1.2.3.4.5.6.7.8'}
requestedOrganizationDepartment:
  resourceType: Organization
  display: City Hospital Neurology Department
  identifier: {system: 'urn:oid:1.2.3.4.5.6.7.8', value: '456'}
paymentType: {system: 'urn:CodeSystem:paymentType', 
              code: "1", 
              display: "Government Health Insurance"}
resourceType: ServiceRequest
status: active
intent: original-order
subject:
  resourceType: Patient
  display: Jack Black, 10.12.1941
  identifier: {value: '2155800871000065', system: 'urn:oid:1.2.3.4.5.6.7.9'}
Get resource in the FHIR format:
GET /fhir/ServiceRequest/servicerequest-with-aidbox-native-extensions

Nested extensions

Let's create a structure of nested attributes:

performerInfo
PUT /Attribute/ServiceRequest.performerInfo

resourceType: Attribute
description: Information filled in by performer
resource: {id: ServiceRequest, resourceType: Entity}
path: [performerInfo]
id: ServiceRequest.performerInfo
extensionUrl: urn:extension:performerInfo
performerInfo.performedBy
PUT /Attribute/ServiceRequest.performerInfo.performedBy

resourceType: Attribute
description: 'Information filled in by performer: performed by ["Practitioner" "PractitionerRole" "Organization" "CareTeam" "HealthcareService" "Patient" "Device" "RelatedPerson"]'
resource: {id: ServiceRequest, resourceType: Entity}
path: [performerInfo, performedBy]
id: ServiceRequest.performerInfo.performedBy
type: {id: Reference, resourceType: Entity}
isCollection: true
refers: 
  - Practitioner
  - PractitionerRole
  - Organization
  - CareTeam
  - HealthcareService
  - Patient
  - Device
  - RelatedPerson
extensionUrl: urn:extension:performerInfo.performedBy
performerInfo.actualLocationReference
PUT /Attribute/ServiceRequest.performerInfo.actualLocationReference

resourceType: Attribute
description: 'Information filled in by performer: actual location reference'
resource: {id: ServiceRequest, resourceType: Entity}
path: [performerInfo, actualLocationReference]
id: ServiceRequest.performerInfo.actualLocationReference
type: {id: Reference, resourceType: Entity}
isCollection: true
refers: 
  - Location
extensionUrl: urn:extension:performerInfo.actualLocationReference
performerInfo.requestStatus
PUT /Attribute/ServiceRequest.performerInfo.requestStatus

resourceType: Attribute
description: 'Information filled in by performer: request status'
resource: {id: ServiceRequest, resourceType: Entity}
path: [performerInfo, requestStatus]
id: ServiceRequest.performerInfo.requestStatus
type: {id: code, resourceType: Entity}
enum:
  - draft
  - new
  - in-progress
  - suspended
  - expanded
  - completed
  - archive
  - cancelled
extensionUrl: urn:extension:performerInfo.requestStatus
performerInfo.requestActionHistory
PUT /Attribute/ServiceRequest.performerInfo.requestActionHistory

resourceType: Attribute
description: 'Information filled in by performer: request action history'
resource: {id: ServiceRequest, resourceType: Entity}
path: [performerInfo, requestActionHistory]
id: ServiceRequest.performerInfo.requestActionHistory
isCollection: true
extensionUrl: urn:extension:performerInfo.requestActionHistory
performerInfo.requestActionHistory.action
PUT /Attribute/ServiceRequest.performerInfo.requestActionHistory.action

resourceType: Attribute
description: 'Information filled in by performer: request action history - action'
resource: {id: ServiceRequest, resourceType: Entity}
path: [performerInfo, requestActionHistory, action]
id: ServiceRequest.performerInfo.requestActionHistory.action
type: {id: string, resourceType: Entity}
extensionUrl: urn:extension:performerInfo.requestActionHistory.action
performerInfo.requestActionHistory.date
PUT /Attribute/ServiceRequest.performerInfo.requestActionHistory.date

resourceType: Attribute
description: 'Information filled in by performer: request action history - date'
resource: {id: ServiceRequest, resourceType: Entity}
path: [performerInfo, requestActionHistory, date]
id: ServiceRequest.performerInfo.requestActionHistory.date
type: {id: dateTime, resourceType: Entity}
extensionUrl: urn:extension:performerInfo.requestActionHistory.date
performerInfo.requestActionHistory.subject
PUT /Attribute/ServiceRequest.performerInfo.requestActionHistory.subject

resourceType: Attribute
description: 'Information filled in by performer: request action history - subject'
resource: {id: ServiceRequest, resourceType: Entity}
path: [performerInfo, requestActionHistory, subject]
id: ServiceRequest.performerInfo.requestActionHistory.subject
type: {id: Reference, resourceType: Entity}
extensionUrl: urn:extension:performerInfo.requestActionHistory.subject
performerInfo.requestActionHistory.note
PUT /Attribute/ServiceRequest.performerInfo.requestActionHistory.note

resourceType: Attribute
description: 'Information filled in by performer: request action history - note'
resource: {id: ServiceRequest, resourceType: Entity}
path: [performerInfo, requestActionHistory, note]
id: ServiceRequest.performerInfo.requestActionHistory.note
type: {id: string, resourceType: Entity}
extensionUrl: urn:extension:performerInfo.requestActionHistory.note
performerInfo.requestActionHistory.author
PUT /Attribute/ServiceRequest.performerInfo.requestActionHistory.author

resourceType: Attribute
description: 'Information filled in by performer: request action history - author'
resource: {id: ServiceRequest, resourceType: Entity}
path: [performerInfo, requestActionHistory, author]
id: ServiceRequest.performerInfo.requestActionHistory.author
type: {id: Reference, resourceType: Entity}
extensionUrl: urn:extension:performerInfo.requestActionHistory.author

Let's add a resource using created extensions:

Create resource in the Aidbox format:
PUT /ServiceRequest/servicerequest-with-aidbox-native-extensions

resourceType: ServiceRequest
performerInfo:
  performedBy:
  - resourceType: Organization
    display: City Hospital
  - resourceType: PractitionerRole
    display: Mark Sloan
  requestStatus: completed
  requestActionHistory:
  - date: '2020-01-14T12:15:22'
    action: new
    author: {display: Meredith Grey (Psychiatrist-narcologist), resourceType: PractitionerRole}
  - date: '2020-01-14T12:15:36'
    action: in-progress
    author: {display: Derek Shepherd (General practitioner), resourceType: PractitionerRole}
  - date: '2020-01-14T12:19:00'
    action: in-progress
    author: {display: Derek Shepherd (General practitioner), resourceType: PractitionerRole}
    subject: {display: Mark Sloan (Dental surgeon), resourceType: PractitionerRole}
    note: Referred to Dr. Mark Sloan (Dental surgeon)
  - date: '2020-01-14T15:05:20'
    action: meeting
    author: {display: Mark Sloan (Dental surgeon), resourceType: PractitionerRole}
  - date: '2020-01-14T15:22:46'
    action: completed
    author: {display: Mark Sloan (Dental surgeon), resourceType: PractitionerRole}    
status: completed
intent: original-order
category:
- text: Telemedicine consultation referral
  coding:
  - {code: "TMC", system: 'urn:CodeSystem:servicerequest-category', display: "Telemedicine consultation"}
subject:
  resourceType: Patient
  display: Jack Black, 10.12.1941
  identifier: {value: '2155800871000065', system: 'urn:oid:1.2.3.4.5.6.7.9'}
Get resource in the FHIR format:
GET /fhir/ServiceRequest/servicerequest-with-aidbox-native-extensions

Using FHIR extensions

FHIR extensions defined in the specification can be found in the registry http://hl7.org/fhir/extensibility-registry.html.

Let's create an attribute for the servicerequest-precondition extension:

PUT /Attribute/ServiceRequest.precondition

resourceType: Attribute
description: "The condition or state of the patient, prior or during 
the diagnostic procedure or test, for example, fasting, at-rest, 
or post-operative. This captures circumstances that may influence 
the measured value and have bearing on the interpretation of the result."
resource: {id: ServiceRequest, resourceType: Entity}
path: [precondition]
id: ServiceRequest.precondition
type: {id: CodeableConcept, resourceType: Entity}
isCollection: true
extensionUrl: "http://hl7.org/fhir/StructureDefinition/servicerequest-precondition"

Let's create a resource in the FHIR format:

Create resource in the FHIR format:
PUT /fhir/ServiceRequest/servicerequest-with-aidbox-native-extensions

resourceType: ServiceRequest
status: active
intent: original-order
subject:
  type: Patient
  display: Jack Black, 10.12.1941
extension:
  - url: http://hl7.org/fhir/StructureDefinition/servicerequest-precondition
    valueCodeableConcept:
      text: After calorie fasting
      coding:
        - code: "726055006"
          system: http://snomed.info/sct
          display: After calorie fasting
  - url: http://hl7.org/fhir/StructureDefinition/servicerequest-precondition
    valueCodeableConcept:
      text: At rest
      coding:
        - code: "263678003"
          system: http://snomed.info/sct
          display: At rest

Let's get the resource in the Aidbox format:

Get resource in the Aidbox format:
GET /ServiceRequest/servicerequest-with-aidbox-native-extensions

Create FHIR primitive type extension

FHIR primitive named fieldName can be extended with _fieldName field. Aidbox treats fieldName as independent from fieldName. Aidbox do not validate fields with names started with underscore.

Suppose we need to extend Patient.gender attribute with primitive type. It means, that we need to create Patient._gender attribute.

PUT /Attribute/Patient._gender

path:
  - _gender
resource:
  id: Patient
  resourceType: Entity
id: Patient._gender
resourceType: Attribute

Now we can add extension attribute into _gender attribute.

PUT /Attribute/Patient._gender.extension

path:
  - _gender
  - extension
resource:
  id: Patient
  resourceType: Entity
id: Patient._gender.extension
isCollection: true
type:
  id: Extension
  resourceType: Entity
resourceType: Attribute

Finally, add Patient with extended gender.

PUT /Patient/p-gender

gender: male
_gender: 
  extension:
    - valueCodeableConcept: 
        coding:
          - code: code-male
            system: system-gender
      url: https://example.com
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