Profiling with clin fhir

Dr. David Hay | Orion Health Product Strategist | Chair Emeritus HL7 NZ
Profiling with clinFHIR
Devdays | November 2017

Plan for the sessions
‣ Yesterday
‣ Review overall process
‣ Review key FHIR elements
‣ ‘Clinical’ Models
‣ Information, Resources, References
‣ Today
‣ Structured and Coded data
‣ Profiling: create/view FHIR artifacts
‣ ValueSet
‣ Extension Definition
‣ Profile
‣ Implementation Guide

The road to FHIR (aka the process)
Clinical
Problem
Information
Model
Resources
Model
References
Graph
Clinician / Business Analyst
FHIR Expert / Terminology
FHIR
artifacts

Adapting FHIR to your needs: Profiling
‣ Many different contexts in healthcare, but want a single set of Resources
‣ Need to be able to describe ‘usage of FHIR’ based on context
‣ Allow for these usage statements to:
- Authored in a structured manner
- Published in a registry & Discoverable
- Used as the basis for validation, code, report and UI generation.
‣ 3 main aspects:
- Constraining a resource - remove element, change multiplicity fix values
- Change coded element binding
- Adding a new element (an extension)
‣ Profiling adapts FHIR for specific scenarios
‣ A statement of use

For example…
Limit names to
just 1 (instead
of 0..*)
Change
maritalStatus to
another set of
codes that
extends the one
from HL7
international
Require that the
identifier uses the NHI
number – and is
required
Don’t support
photo
Add an
extension
to support
ethnicity

This talk:
‣ 3 Main aspects
‣ Coded data (and identifiers)
‣ Binding to a ValueSet
‣ Extensions
‣ The Profile
‣ Implementation Guide

Why have structured / coded data
▸ Structured vs Coded
▸ Coded:
▸ Greatly improves quality of exchange
▸ ‘semantic’ interoperability
▸ Secondary uses
▸ Decision Support
▸ Analytics
▸ Population Health
▸ Reporting

Resource type structure in the spec

Datatypes
‣ Datatypes in resource type definition
- Backbone element
- ‘choice’ data types
- Eg deceased[x]
‣ Identifiers
‣ Review coded data
- ValueSet binding

Data types: Primitive
Based on w3c schema and ISO data types
▸ Stick to the “80% rule” – only expose what most will use
– Simplified
instant
Value : xs : dataTime 0..1
time
Value : xs : Time 0..1
date
Value : xs:gYear [xs:gYearMonth | Time 0..1
dateTime
Value : xs:gYear [xs:gYearMonth | xs:date | Time 0..1
decimal
Value : xs : decimal 0..1
integer
Value : xs : int 0..1
Element
Extension : Extension 0..*
boolean
value : xs:boolean 0..1
string
Value : xs :string 0..1
uri
Value : xs :anyURI 0..1
base64Binary
Value : xs : base64Binary 0..1
unsignedint positiveInt code id oid

Ratio
numerator: Quality [0..1]
denominator: Quantity [0..1]
Quantity
value: decimal [0..1]
comparator: code [0..1] QuantityComparator!
units: string [0...1]
system: uri [0..1]
code: code [0..1]
Range
low: Quantity(SimpleQuantity) [0..1]
high: Quantity(SimpleQuantity) [0..1]
HumanName
use: code [0..1] NameUse!
text: String [0..1]
family: String [0..*]
given: String [0..*]
prefix: String [0..*]
suffix: String [0..*]
period: Period [0..1]
Identifier
use: code [0..1] IdentifierUse!
type: CodeableConcept [0..1] IdentifierType+
system: uri [0..1]
value: String [0..1]
assigner: Reference [0..1] Organization
Address
use: code [0..1] AddressUse!
type: code [0..1] AddressType!
text: string [0..1]
line: string [0..*]
city: string [0..1]
district: string [0..1]
state: string [0..1]
postalCode: string [0..1]
country: string [0..1]
period: Period 0...1
Coding
system: uri [0..1]
version: string [0..1]
code: code [0..1]
display: String [0..1]
userSelected: boolean [0..1]
Element
extension:
Extension 0..*
Timing
event: dataTime [0..*]
code: CodeableConcept [0..1] TimingAbbreviation?
Repeat
bounds[x]: Type [0..1] Duration|Range|Period
dount: Integer [0..1]
dountMax: integer [0..1]
duration: decimal [0..1]
durationMax: decimal [0..1]
durationUnit: code [0..1] UnitsOfTime!
frequency: integer [0..1]
frequencyMax: integer [0..1]
period: decimal [0..1]
periodMax: [0..1]
periodUnit: code [0..1] UnitsOfTime
dayOfWeek: code [0..*] DaysOfWeek!
timeOfDay: time [0..*]
when: Code [0..*] EventTiming!
offset: unsginedInt [0..1]
ContactPoint
system: Code [0..1] ContactPointSystem!
value: String [0..1]
use: Code [0..1] ContactPointUse!
rank: PositiveInt [0...1]
CodeableConcept
coding: Coding [0..*]
text: String [0..1]
Attachment
contentType: Code [0..1] MimeType!
language: Code [0..1] CommonLanguages+
data: base64Binary [0..1]
url: uri [0..1]
size: unsignedInt [0..1]
hash: base64binary [0..1]
title: string [0..1]
creation: dateTime [0..1]
Period
start: dateTime [0..1]
end: dateTime [0..1]
SampledData
origin: Quantity(SimpleQuantity) [1..1]
period: Decimal [1..1]
factor: Decimal [0..1]
lowerLimit: Decimal [0..1]
upperLimit: Decial [0..1]
dimensions: Positivelnt [1..1]
data: String [1..1]
Data types: Complex
Signature
type:Coding [1..*] Signature Type?
when: Instant [1..1]
who[x]: Type [1..1] uri |
Reference(Practitioner|Related
person|PatientDevice|Organization)
onBehalfOf[x]: Type [0..1]
uri|Reference(Practitioner|RelatedPers
on|Pateint|Device|Organization)
contentType: code [0..1] MimeType!
blob: base64Binary [0..1]
Annotation
author[x]: Type [0..1]
Reference(Practitioner|Patient|
RelatedPerson)|string
Time: dateTime [0..1]
Text: string [1..1]
repeat
[0..1]

Identifiers
‣ Identifies an object (Person) within a given system
‣ Eg National Identifier (NHI), Drivers License, HPI
‣ Main sub components:
‣ System – what ‘sort’ of identifier
‣ Value – unique within the system
‣ NamingSystem resource

Coded datatypes
• code: "status" : "confirmed"
• Coding: {
"system": "http://www.nlm.nih.gov/research/umls/rxnorm",
"code": "C3214954",
"display": "cashew nut allergenic extract Injectable"
}
• CodeableConcept: {
"coding": [{
"system": "http://snomed.info/sct",
"code": "39579001",
"display": "Anaphylactic reaction“
}],
"text" : "Anaphylaxis"
}

ValueSet
{
"resourceType": "ValueSet",
"compose": {
"include": [
{
"system": http://snomed.info/sct",
"filter": [
{
"property": "concept",
"op": "is-a",
"value": "404684003"
}
]
}
]
}
}
‣ A context specific subset of one or more
Code Systems
‣ Bound to an element
‣ Promotes consistency between
applications
‣ Key component of Terminology
- Also CodeSystem
‣ Start thinking about in Information model
‣ Used by a number of services
- $expand

Terminology Sub-system
Code System:
Defines a set of
concepts with a
coherent meaning
Code
Display
Definition
‣ SNOMED CT / LOINC / RxNORM
‣ ICPC, MIMS + 100s more
‣ ICD-X+
‣ A drug formulary
‣ Custom

Code System:
Defines a set of
concepts with a
coherent meaning
Code
Display
Definition
Value Set:
A selection of a set
of codes for use in a
particular context
Selects

Code System:
Defines a set of
concepts with a
coherent meaning
Code
Display
Definition
Value Set:
particular context
Element Definition:
Type and Value set
reference
Selects Binds
▸ Binding:
– Connection between element and ValueSet
– Strength determines if can change

Code System:
Defines a set of
concepts with a
coherent meaning
Code
Display
Definition
Value Set:
particular context
Element:
code/
Coding/
CodeableConcept
Element Definition:
Type and Value set
reference
Selects Binds
Refers to
Conforms

Code System:
Defines a set of
concepts with a
coherent meaning
Code
Display
Definition
Value Set:
particular context
Element:
code/
Coding/
CodeableConcept
Element Definition:
Type and Value set
reference
Selects Binds
Refers to
Conforms
Define
Instance

Demo
‣ Adding structures and coded data to
the scenario

Demo
‣ Viewing/Building a ValueSet in
clinFHIR

Extension Definitions
‣ Also a StructureDefinition
• Defines the content of a single extension
‣ Simple or Complex
‣ Complex has children
‣ Definition:
• Available on the web
• Canonical Url – Globally unique identifier
- Resolvable or Registry
‣ In resource instance:
• Reference to Canonical Url
• Recipiant can always find out definition
• Extension or ModifierExtension

Demo
‣ Create an Extension Definition

The ‘profile’
‣ On a single resource type
‣ Defined by StructureDefinition resource
- Same as used for core resources
‣ Defines each element
- Path, name, dataType, binding, multiplicity. mapping & much more
- Including allowable extension points
‣ Can use Forge tooling to build
- clinFHIR (and others) for learning/viewing
‣ US Core (was DAF)
- http://hl7.org/fhir/us/core/index.html

clinFHIR: Profiling support
‣ Build from Logical Model
‣ On single resource
‣ Main options
‣ Remove elements
‣ Add extensions
‣ Change Bindings
‣ This is not Forge!

Implementation Guide
‣ Brings all the artifacts together
‣ Clinical & FHIR
‣ Demo of guide
‣ CareConnect (UK)

Main Conformance artifacts
‣ StructureDefinition
‣ Profile and Extension Definitions
‣ In resources model
‣ ValueSet
‣ From Information model
‣ CodeSystem
‣ ConceptMap
‣ NamingSystem
‣ ImplementationGuide

Exercises
1. Choose resource to profile
2. Build Logical model (single resource)
3. Edit model
1. Constrain
2. Extend
3. Re-bind
4. Create profile
• Getting started
• Set servers (hapi-3)
• Create user account
• Use initials for model name
• Remember to save models
Notes Process

clinFHIR help on the FHIR Chat
https://chat.fhir.org/#narrow/stream/clinFHIR

More information
From HL7
‣ http://hl7.org/fhir/index.html
‣ wiki.hl7.org/index.php?title=FHIR
‣ http://www.fhir.org/
Community
‣ https://chat.fhir.org/
‣ List server (fhir@lists.hl7.org )
‣ Stack Overflow (tag FHIR)
Blogs
‣ www.healthintersections.com.au/
‣ https://fhirblog.com/
‣ https://thefhirplace.com/
‣ https://brianpos.com
Libraries
‣ Java (http://hapifhir.io/)
‣ C# (NuGet HL7.FHIR)Tooling
‣ Forge (http://fhir.furore.com/Forge)
‣ http://clinfhir.com/
Tooling
‣ Forge (http://fhir.furore.com/Forge)
‣ http://clinfhir.com/
Test servers
‣ http://wiki.hl7.org/index.php?title=Publi
cly_Available_FHIR_Servers_for_testi
ng
‣ https://fhirblog.com/2016/10/19/setting
-up-your-own-fhir-server-for-profiling/

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