Aidbox User Docs
Run Aidbox locallyRun Aidbox in SandboxTalk to us Ask community
  • Aidbox FHIR platform documentation
    • Features
    • Architecture
  • Getting Started
    • Run Aidbox in Sandbox
    • Run Aidbox locally
    • Run Aidbox on AWS
    • Upload Sample Data
  • Tutorials
    • CRUD, Search Tutorials
      • Delete data
      • Set up uniqueness in Resource
      • Search Tutorials
        • Custom SearchParameter tutorial
        • Create custom Aidbox Search resource
        • Multilingual search tutorial
        • Migrate from Aidbox SearchParameter to FHIR SearchParameter
        • Change sort order by locale collation
    • Bulk API Tutorials
      • 🎓Synthea by Bulk API
      • 🎓$dump-sql tutorial
    • Security & Access Control Tutorials
      • Allow patients to see their own data
      • Restrict operations on resource type
      • Relationship-based access control
      • Creating user & set up full user access
      • Restricting Access to Patient Data
      • Create and test access control
      • RBAC
        • Flexible RBAC built-in to Aidbox
        • RBAC with JWT containing role
        • RBAC with ACL
      • Set-up token introspection
      • Prohibit user to login
      • Debug access control
      • Managing Admin Access to the Aidbox UI Using Okta Groups
      • Run Multibox locally
      • How to enable labels-based access control
      • How to enable patient data access API
      • How to enable SMART on FHIR on Patient Access API
      • How to enable hierarchical access control
      • How to configure Audit Log
    • Terminology Tutorials
      • Load ICD-10 terminology into Aidbox
      • Uploading IG terminology content to external FHIR terminology server
    • Validation Tutorials
      • Upload FHIR Implementation Guide
        • Environment Variable
        • Aidbox UI
          • IG Package from Aidbox Registry
          • Public URL to IG Package
          • Local IG Package
        • Aidbox FHIR API
        • UploadFIG Tool
      • ISiK
      • Carin BB
      • US Core
      • Davinci Pdex
      • mCode
    • Integration Toolkit Tutorials
      • Postmark integration tutorial
      • Mailgun integration tutorial
    • Subscriptions Tutorials
      • AidboxTopicSubscription NATS tutorial
    • Other tutorials
      • Run Aidbox with FHIR R6
      • Migrate from Multibox to Aidbox
      • SDC with Custom Resources
      • How to create FHIR NPM package
      • Migrate from legacy licence portal to Aidbox portal
      • How to run Aidbox in GCP Cloud Run
  • Overview
    • Licensing and Support
    • Aidbox user portal
      • Projects
      • Licenses
      • Members
    • Aidbox UI
      • Aidbox Notebooks
      • REST Console
      • Database Console
      • Attrs stats
      • DB Tables
      • DB Queries
    • Versioning
    • Release Notes
    • Contact us
  • Configuration
    • Settings
    • Configure Aidbox and Multibox
    • Init Bundle
  • API
    • REST API
      • CRUD
        • Create
        • Read
        • Update
        • Patch
        • Delete
      • FHIR Search
        • SearchParameter
        • Include and Revinclude
        • Chaining
      • Aidbox Search
      • Bundle
      • History
      • $everything on Patient
      • Other
        • Aidbox & FHIR formats
        • Capability Statement
        • $document
        • Observation/$lastn
        • $validate
        • SQL endpoints
        • $matcho
        • $to-format
        • Aidbox version
        • Health check
    • Bulk API
      • Configure Access Policies for Bulk API
      • $dump
      • $dump-sql
      • $dump-csv
      • $export
      • $load & /fhir/$load
      • $import & /fhir/$import
      • aidbox.bulk data import
      • Bulk import from an S3 bucket
    • Batch/Transaction
    • GraphQL API
    • Other APIs
      • Plan API
        • Provider Directory API
          • Practitioner
          • PractitionerRole
          • Organization
          • OrganizationAffiliation
        • Plan API Overview
      • Archive/Restore API
        • create-archive
        • restore-archive
        • prune-archived-data
        • delete-archive
      • ETAG support
      • Cache
      • Changes API
      • RPC API
      • Sequence API
      • Encryption API
      • Batch Upsert
  • Modules
    • Profiling and validation
      • FHIR Schema Validator
        • Aidbox FHIR IGs Registry
        • Setup Aidbox with FHIR Schema validation engine
      • Skip validation of references in resource using request header
      • Asynchronous resource validation
    • Security & Access Control
      • Authentication Flows
        • Basic Auth
        • Client Credentials Grant
        • Resource Owner Grant
        • Authorization Code Grant
        • Implicit Grant
        • Two Factor Authentication
        • External OAuth 2.0 Providers
        • Token Exchange
      • External identity providers
        • Aidbox
        • Okta
        • Azure AD
        • Azure AD with certificate authentication
        • Keycloak
        • GitHub
        • Microsoft AD FS
        • Apple
      • Access Control
        • AccessPolicy
        • Evaluation engines
        • Role-Based Access Control (/RBAC)
        • Attribute-based Access Control (/ABAC)
        • Multitenancy
        • Access control lists (/ACL)
        • Access policy dev tool
        • AccessPolicy best practices
      • Audit
        • Audit Log
    • Observability
      • Getting started
        • Run Aidbox with OpenTelemetry locally
        • How to export telemetry to the OTEL collector
      • Logs
        • How-to guides
          • OpenTelemetry logs
          • Elastic Logs and Monitoring Integration
          • Datadog Log management integration
          • Loki Log management integration
        • Tutorials
          • Log analysis and visualization tutorial
          • Export logs to Datadog tutorial
        • Extending Aidbox Logs
        • Technical reference
          • Log appenders
          • Log transformations
          • Log Schema
          • OTEL logs exporter parameters
      • Metrics
        • How-to guides
          • How to export metrics to the OTEL collector
          • Use Aidbox Metrics Server
          • Set-up Grafana integration
        • Technical reference
          • OpenTelemetry Metrics
          • OTEL metrics exporter parameters
      • Traces
        • How to use tracing
        • OTEL traces exporter parameters
    • Subscriptions
      • Aidbox topic-based subscriptions
        • Kafka AidboxTopicDestination
        • Webhook AidboxTopicDestination
        • GCP Pub/Sub AidboxTopicDestination
        • Tutorial: produce QuestionnaireResponse to Kafka topic
      • Aidbox SubSubscriptions
    • Aidbox Forms
      • Getting started
      • Aidbox Forms Interface
      • Aidbox UI Builder
        • UI Builder Interface
        • Form creation
          • Form Settings
          • Widgets
          • Components
          • Versioning
          • Form customisation in Theme Editor
          • Form signature
          • How-to guides
            • How to: populate forms with data
            • How to extract data from forms
            • How to calculate form filling percentage
          • Multilingual forms
          • FHIRPath Editor
        • Import Questionnaire
        • Form sharing
        • Printing forms
          • Template-based PDF generation
        • FHIR versions
        • Offline forms
        • Embedding
          • Request Interception
        • Configuration
        • Forms multitenancy
        • Building reports using SQL on FHIR
        • Integration with external terminology servers
        • External FHIR servers as a data backend
        • Store attachments in S3-like storages
      • Access Control in Forms
      • Audit Logging in Forms
      • Aidbox Form Gallery
    • Define extensions
      • Extensions using StructureDefinition
      • Extensions using FHIRSchema
    • Custom Resources
      • Custom resources using FHIR Schema
      • Custom resources using StructureDefinition
      • Migrate to FHIR Schema
        • Migrate custom resources defined with Entity & Attributes to FHIR Schema
        • Migrate custom resources defined with Zen to FHIR Schema
    • Aidbox terminology module
      • Concept
        • $translate-concepts
        • Handling hierarchies using ancestors
      • ValueSet
        • ValueSet Expansion
        • ValueSet Code Validation
        • Create a ValueSet
      • CodeSystem
        • CodeSystem Concept Lookup
        • CodeSystem Subsumption testing
        • CodeSystem Code Composition
      • Import external terminologies
        • Import flat file (/CSV)
        • $import operation
        • Ready-to-use terminologies
      • $translate on ConceptMap
    • SQL on FHIR
      • Defining flat views with View Definitions
      • Query data from flat views
      • Reference
    • Integration toolkit
      • C-CDA / FHIR Converter
        • List of supported templates
          • Admission Diagnosis Section (/V3)
          • Advance Directives Section (/entries optional) (/V3)
          • Advance Directives Section (/entries required) (/V3)
          • Allergies and Intolerances Section (/entries optional) (/V3)
          • Allergies and Intolerances Section (/entries required) (/V3)
          • Assessment Section
          • Chief Complaint Section
          • Chief Complaint and Reason for Visit Section
          • Complications Section (/V3)
          • Course of Care Section
          • DICOM Object Catalog Section - DCM 121181
          • Default Section Rules
          • Discharge Diagnosis Section (/V3)
          • Document Header
          • Encounters Section (/entries optional) (/V3)
          • Encounters Section (/entries required) (/V3)
          • Family History Section (/V3)
          • Functional Status Section (/V2)
          • General Status Section
          • Goals Section
          • Health Concerns Section (/V2)
          • History of Present Illness Section
          • Hospital Consultations Section
          • Hospital Course Section
          • Hospital Discharge Instructions Section
          • Hospital Discharge Physical Section
          • Hospital Discharge Studies Summary Section
          • Immunizations Section (/entries optional) (/V3)
          • Immunizations Section (/entries required) (/V3)
          • Medical (/General) History Section
          • Medical Equipment Section (/V2)
          • Medications Administered Section (/V2)
          • Medications Section (/entries optional) (/V2)
          • Medications Section (/entries required) (/V2)
          • Mental Status Section (/V2)
          • Notes
          • Nutrition Section
          • Objective Section
          • Operative Note Fluids Section
          • Operative Note Surgical Procedure Section
          • Past Medical History (/V3)
          • Payers Section (/V3)
          • Plan of Treatment Section (/V2)
          • Postprocedure Diagnosis Section (/V3)
          • Preoperative Diagnosis Section (/V3)
          • Problem Section (/entries optional) (/V3)
          • Problem Section (/entries required) (/V3)
          • Procedure Description Section
          • Procedure Disposition Section
          • Procedure Estimated Blood Loss Section
          • Procedure Implants Section
          • Procedure Specimens Taken Section
          • Procedures Section (/entries optional) (/V2)
          • Procedures Section (/entries required) (/V2)
          • Reason for Visit Section
          • Results Section (/entries optional) (/V3)
          • Results Section (/entries required) (/V3)
          • Review of Systems Section
          • Social History Section (/V3)
          • Vital Signs Section (/entries optional) (/V3)
          • Vital Signs Section (/entries required) (/V3)
        • How to deploy the service
        • Producing C-CDA documents
        • How to customize conversion rules
      • HL7 v2 Integration
        • HL7 v2 integration with Aidbox Project
        • Mappings with lisp/mapping
      • X12 message converter
      • Analytics
        • Power BI
      • Mappings
      • Email Providers integration
        • Setup SMTP provider
    • SMARTbox | FHIR API for EHRs
      • Get started
        • Set up Smartbox locally
        • Deploy Smartbox with Kubernetes
      • (/g)(/10) Standardized API for patient and population services
      • The B11 Decision Support Interventions
        • Source attributes
        • Feedback Sections
      • How-to guides
        • Pass Inferno tests with Smartbox
        • Perform EHR launch
        • Pass Inferno Visual Inspection and Attestation
        • Revoke granted access
        • Set up EHR-level customization
        • Check email templates
        • Setup email provider
        • Register users
        • Set up SSO with Auth0
        • Publish Terms of Use link onto the documentation page
        • Find out what resources were exported during the $export operation
        • Find documentation endpoint
      • Background information
        • Considerations for Testing with Inferno ONC
        • Adding Clients for Inferno tests
        • Multitenancy approach
        • What is Tenant
        • Email templating
    • ePrescription
      • Getting started
      • Authentication with mTLS
      • Pharmacies synchronization
      • Prescribing
        • NewRx Message
        • CancelRx Message
        • How to test Callback
      • Directory
        • DirectoryDownload Message
        • GetProviderLocation Message
        • AddProviderLocation Message
        • UpdateProviderLocation Message
        • DisableProviderLocation Message
      • Medications
        • FDB
      • References
        • Environment Variables
      • Frequently Asked Questions
    • Other modules
      • MDM
        • Train model
        • Configure MDM module
        • Find duplicates: $match
        • Mathematical details
      • MCP
  • Database
    • Overview
    • Database schema
    • PostgreSQL Extensions
    • AidboxDB
      • HA AidboxDB
    • Tutorials
      • Migrate to AidboxDB 16
      • Working with pgAgent
  • File storage
    • AWS S3
    • GCP Cloud Storage
    • Azure Blob Storage
    • Oracle Cloud Storage
  • Deployment and maintenance
    • Deploy Aidbox
      • Run Aidbox on Kubernetes
        • Deploy Production-ready Aidbox to Kubernetes
        • Deploy Aidbox with Helm Charts
        • Highly Available Aidbox
        • Self-signed SSL certificates
      • Run Aidbox on managed PostgreSQL
      • How to inject env variables into Init Bundle
    • Backup and Restore
      • Crunchy Operator (/pgBackRest)
      • pg_dump
      • pg_basebackup
      • WAL-G
    • Indexes
      • Get suggested indexes
      • Create indexes manually
  • App development
    • Use Aidbox with React
    • Aidbox SDK
      • Aidbox JavaScript SDK
      • Apps
      • NodeJs SDK
      • Python SDK
    • Examples
  • Reference
    • FHIR Schema reference
    • Settings reference
      • General
      • FHIR
      • Security & Access Control
      • Modules
      • Database
      • Web Server
      • Observability
      • Zen Project
    • Environment variables
      • Aidbox required environment variables
      • Optional environment variables
      • AidboxDB environment variables
    • System resources reference
      • IAM Module Resources
      • SDC Module Resources
      • Base Module Resources
      • Bulk Module Resources
      • AWF Module Resources
      • Cloud Module Resources
      • HL7v2 Module Resources
      • SQL on FHIR Module Resources
    • Email Providers reference
      • Notification resource reference
      • Mailgun environment variables
      • Postmark environment variables
    • Aidbox Forms reference
      • FHIR SDC API
      • Aidbox SDC API
      • Generating Questionnaire from PDF API
    • Aidbox SQL functions
  • Deprecated
    • Deprecated
      • Zen-related
        • RPC reference
          • aidbox
            • mdm
              • aidbox.mdm/update-mdm-tables
              • aidbox.mdm/match
        • FTR
        • Aidbox configuration project
          • Run Aidbox locally using Aidbox Configuraiton project
          • Aidbox configuration project structure
          • Set up and use configuration projects
          • Enable IGs
          • Repository
          • Seed Import
          • Manage Indexes in Zen Project
          • Seed v2
          • 🎓Migrate to git Aidbox Configuration Projects
          • Aidbox Configuration project reference
            • Zen Configuration
            • Aidbox project RPC reference
            • aidbox.config/config
          • Custom resources using Aidbox Project
          • First-Class Extensions using Zen
          • Zen Indexes
        • US Core IG
          • US Core IG support reference
        • Workflow Engine
          • Task
            • Aidbox Built-in Tasks
            • Task Executor API
            • Task User API
          • Workflow
            • Workflow User API
          • Services
          • Monitoring
        • FHIR conformance Deprecated guides
          • Touchstone FHIR 4.0.1 basic server
          • Touchstone FHIR USCore ClinData
          • How to enable US Core IG
            • Start Aidbox locally with US Core IG enabled
            • Add US Core IG to a running Aidbox instance
          • HL7 FHIR Da Vinci PDex Plan Net IG
        • Terminology Deprecated Tutorials
          • Inferno Test-Suite US Core 3.1.1
        • API constructor (/beta)
        • zen-lang validator
          • Write a custom zen profile
          • Load zen profiles into Aidbox
        • FHIR topic-based subscriptions
          • Set up SubscriptionTopic
          • Tutorial: Subscribe to Topic (/R4B)
          • API Reference
            • Subscription API
        • 🏗️FHIR Terminology Repository
          • FTR Specification
          • Create an FTR instance
            • FTR from CSV
            • FTR from FHIR IG
            • FTR from FTR — Direct Dependency
            • FTR from FTR — Supplement
          • FTR Manifest
          • Load SNOMED CT into Aidbox
          • Load LOINC into Aidbox
          • Load ICD-10-CM into Aidbox
          • Load RxNorm into Aidbox
          • Load US VSAC Package to Aidbox
          • Import via FTR
        • Zen Search Parameters
      • Entity / Attribute
        • Entities & Attributes
        • First-Class Extensions using Attribute
        • Custom Resources using Entity
        • Working with Extensions
        • Aidbox Search Parameters
      • Forms
      • Other
        • Custom Search
        • SearchQuery
        • Subscribe to new Patient resource
        • App Development Deprecated Tutorials
          • Receive logs from your app
            • X-Audit header
          • Patient Encounter notification Application
        • Other Deprecated Tutorials
          • Resource generation with map-to-fhir-bundle-task and subscription triggers
          • APM Aidbox
          • Automatically archive AuditEvent resources in GCP storage guide
          • HL7 v2 pipeline with Patient mapping
          • How to migrate to Apline Linux
          • How to migrate transaction id to bigint
          • How to fix broken dates
          • Configure multi-tenancy
        • AidboxProfile
        • GCP Pub/Sub
Powered by GitBook
On this page
  • Demonstration Scenario
  • Debugging Extraction
  • Advanced substitution rules examples
  • Create SDC resource
  • Make it work on resource save

Was this helpful?

Edit on GitHub
  1. Tutorials
  2. Other tutorials

SDC with Custom Resources

Structured Data Capturing with Aidbox Custom Resources

PreviousMigrate from Multibox to AidboxNextHow to create FHIR NPM package

Last updated 8 months ago

Was this helpful?

Sometimes FHIR granularity is too small to collect patient data from user interfaces. For example, when a physician or a nurse records vital signs in terms of FHIR, they produce a bundle of observations. How to save this data to a FHIR server? How to keep track that this data was collected on the Vitals Form?

One option is to build a transaction bundle with a provenance on the client side and send it to the transaction endpoint. But with this approach it is rather problematic to track data back; update or delete it as a whole.

There is a (SDC IG) which describes how to collect data using Questionnaire and QuestionnaireResponse resources. It is a good idea and a work in progress. One problem we see with it is that the QuestionnaireResponse table is stuffed with all sorts of things and managing this table, doing searches and updates is problematic. Another problem is that Questionnaire/QuestionnaireResponse is too generic and verbose which makes working with them inconvenient.

Aidbox supports Custom Resources, which cover all Questionnaire functionality and flexibility while providing many more features - validation, separate storage, search, references to other FHIR resources, etc. We applied key ideas from the to Custom Resources to give you the best of both worlds.

Demonstration Scenario

The first step is to define your custom resource. We recommend using sugar App API. As an example we are defining resource Vitals with temperature, heart_rate, and patient reference:

custom-resource.yaml
POST /App

resourceType: App
id: Vitals
apiVersion: 1
type: app
entities:
  Vitals:
    attrs:
      temperature: {type: number}
      heart_rate: {type: number}
      ts: {type: dateTime}
      patient:
        type: Reference
        refers: [Patient]

Now we can check that Vitals work properly.

Create a new vitals record:

patient
PUT /Patient/pt-1

name: 
- family: Jackson
  given: ['John']
create-vitals
POST /Vitals

resourceType: Vitals
temperature: 36.6
heart_rate: 102
patient: {id: 'pt-1', resourceType: 'Patient'}
ts: '2019-04-09T12:00:00Z'

Get all vitals records for the patient pt-1:

get-vitals
GET /Vitals?.patient.id=pt-1

Debugging Extraction

Now we want to transform Vitals to a set of FHIR Observations. We are using template extraction. You can play and debug extraction using /AlphaSDC/$debug

debug.yaml
POST /AlphaSDC/$debug

source:
 id: src-1
 temp: 36.6
template:
  Observation:
     temp: 
       value: { $path!: [temp] }
response.yaml
source: {id: src-1, temp: 36.6}
template:
  Observation:
    temp:
      value:
        $path!: [temp]
extracted:
  Observation:
    temp:
      value: 36.6
      id: temp-src-1
      meta: {sourceId: src-1}

template it structured as { [resourceType] : { [id-prefix] : <resource-template> }}, for example to generate Observation with prefix tmp you write {Observation: {tmp: <resource-template>}}

<resource-template> is a template/prototype of a resulting FHIR resource, where some attributes contain substitution rules like { $path!: ["attr", "attr"]}. These rules will be replaced with values from Custom resource, indicated by this path.

Advanced substitution rules examples

resource.yaml
resourceType: QuestionnaireResponse
id: qr1
questionnaire: Questionnaire/q1|1
item:
- text: What is your height in feet.inches?
  answer:
  - valueDecimal: 5.2
  linkId: ht
- text: What is your weight in pounds?
  answer:
  - valueDecimal: 122
  linkId: wt

Let's suppose you want to extract the height of a respondent, for this purpose you can use this $path expression ["item, {"linkId": ht"}, "answer", 0, "valueDecimal"]

{"linkId": ht"} - this object is used for filtering, you can declare the objects with as many keys as you need to match item in the specified collection.

Create SDC resource

Now let's define how FHIR Observations will be extracted from Vitals. We have to create AlphaSDC resource for that:

PUT /AlphaSDC/Vitals

template:
  Observation:
    temp:
      subject:
        $path!: [patient]
      category:
      - coding:
        - {system: 'http://terminology.hl7.org/CodeSystem/observation-category', code: vital-signs, display: Vital Signs}
      status: final
      code:
        coding:
        - {system: 'http://loinc.org', code: 8310-5, display: Body temperature}
      effective:
        dateTime:
          $path!: [ts]
      value:
        Quantity:
          value:
            $path!: [temperature]
          unit: degrees C
          system: http://unitsofmeasure.org
          code: Cel
    hr:
      subject:
        $path!: [patient]
      category:
      - coding:
        - {system: 'http://terminology.hl7.org/CodeSystem/observation-category',
          code: vital-signs, display: Vital Signs}
      status: final
      code:
        coding:
        - {system: 'http://loinc.org', code: 8867-4, display: Heart rate}
      effective:
        dateTime:
          $path!: [ts]
      value:
        Quantity:
          value:
            $path!: [heart_rate]
          unit: beats/minute
          system: http://unitsofmeasure.org
          code: /min

.id of AlphaSDC resource should be exactly the same as the name of Custom Resource - i.e., Vitals

.template is a template described in the section above.

Now you can test how data is extracted using POST /AlphaSDC/<id>/$extract endpoint:

request
POST /AlphaSDC/Vitals/$extract

resourceType: Vitals
temperature: 36.6
heart_rate: 102
patient: {id: 'pt-1', resourceType: 'Patient'}
ts: '2019-04-09T12:00:00Z'

You should see the following response:

source: <original resource>
template: <template>
extracted: <result-of-extraction>

Make it work on resource save

To make this extraction work on Vitals save, we have to override its Create Operation

PUT /Operation/vitals-create

request: [post, Vitals]
action: sdc/create

sdc/create action will do extraction and save original custom resource and extracted FHIR resources:

create-vitals
POST /Vitals

resourceType: Vitals
id: v-2
temperature: 36.6
heart_rate: 102
patient: {id: 'pt-1', resourceType: 'Patient'}
ts: '2019-04-09T12:00:00Z'

Now we can see the Observations that have been created:

get-observations
GET /Observation?.subject.id=pt-1
# or
GET /Vitals?.patient.id=pt-1

Please provide your feedback and use cases for SDC using

Structured Data Capture Implementation Guide
SDC IG
github