© 2015 hl7 ® international. licensed under creative commons. hl7 & health level seven are...

FHIR for Specifiers

Michel Rutten

Hilversum, 12 november 2015

Who am I?

Name: Michel Rutten Company: Furore, Amsterdam Background:

Professional software developer since 1998 Microsoft .NET; Healthcare industries Technical Specialist at Furore since May 2014 Member of the Furore FHIR development team Tool Smith - Lead developer of Forge

Contents of this tutorial

FHIR 1.0 DSTU 2 Introduction to FHIR Conformance Layer Principal components FHIR Conformance Resources Implementation Guides ValueSet StructureDefinition Registry

FHIR 1.0 DSTU2Overview of changes

DSTU 2 Version History

Version Name Publication date

1.0.0 DSTU 2 QA Preview Aug 31 2015

1.0.1 DSTU 2 Sept 23 2015

1.0.2 Technical Correction 1 Oct 24 2015

Maturity Framework

Level Description

0 Published on current build

1 Produces no warnings during the build processSubstantially complete and ready for implementation

2 Successfully exchanged between 3+ systems at a connectathonResults reported to the FHIR Management Group

3 Meets DSTU Quality Guidelines Subject to a round of formal balloting; 10+ implementer comments drawn from 3+ organizations resulting in 1+ substantive changes.

4 Tested across its scopePublished in a formal publication (e.g. DSTU)Implemented in multiple prototype projects.Sufficiently stable to require implementer consensus for subsequent non-backward compatible changes.

5 Published in two formal publication release cycles at FMM1+ (i.e. DSTU level)Implemented in 5+ independent production systems in >1 country

RESTful API

Add batch Several clarifications around versioning &

transactional integrity Changed Bundle URL resolution rules

Search

Changed the way <> etc. works Added _list parameter Changed rules around contained and

included resources

Data Types

New data types Markdown Annotation

Changed data types Coding Quantity Signature Timing Address ContactPoint

Data Types

Changes to ElementDefinition Add base

Specifies path & cardinality of base element Make type.profile repeat

Target resource must conform to all profiles Remove constraint.name and replace with

constraint.requirements Remove binding.name Add minValue[x] and maxValue[x]

Resources

New Account ImplementationGuide TestScript

Removed Supply

Resources

Renamed resources Contraindication -> DetectedIssue MedicationPrescription -> MedicationOrder QuestionnaireAnswers -> QuestionnaireResponse

Resources

Changed Almost all resources Too many to list (1317 tasks worth of changes) Add, remove elements Change types, references, definitions & value sets Re-order elements Provide much more documentation and new

examples

Implementation Guides

Move Argonaut content out http://argonautwiki.hl7.org/index.php?title=Main_Page

Changes of significance during the QA process: Remove the Clinical Quality Improvement

Framework (CQIF) from this published version Made fixes to generated schematrons Updated generated comformance resources

(StructureDefinitions and SearchParameters) so they were consistent with the specification

Many spelling / grammar / broken link fixes

Series of technical corrections to the specification following extensive review: Corrections to Extension cardinalities in

implementation guides Corrections in the conformance resources that

support the specifications Correct several erroneous invariants Various typos, broken links, and fixes in examples For a comprehensive list of corrections, see the

Task list for FHIR DSTU2 Technical Correction 116

PRINCIPAL COMPONENTSFHIR CONFORMANCE LAYER

Conformance Resources

Terminology

Naming System

Value Set

Concept Map

Content

Structure Definition

Data Element

Operations

Conformance

Operation Definition

Search Parameter

Implementation Guide

Test Script

Conformance

Conformance Resources

“Profile”

StructureDefinition

SearchParamDefinition

ValueSet

ConceptMap

NamingSystem OperationDefinition

ExcelImplementation

TestScript

Terminology

• Define which terminologies to use in which elements

ValueSet

• Define namespaces with unique symbols

NamingSystem

• Define mappings between terms from different systems

ConceptMap

Content

• Define data structures• Define restrictions and/or extensions

StructureDefinition

• Define data elements (ISO 11179)

DataElement

Operations

• Define server capabilities• Define supported API methods

Conformance

• Define additional (custom) operations

OperationDefinition

• Define additional (custom) searches

SearchParameter

Miscellaneous

• Author and publish an implementation guide

ImplementationGuide

• Define compliance tests against a FHIR server

TestScript

OVERVIEWFHIR CONFORMANCE RESOURCES

ImplementationGuide

• Define scope of usage• Describes requirements for an implementation

ImplementationGuide

Usage: Allow authors to publish an implementation

guide Allow tools to validate conformance Computable!

StructureDefinition

Defines datastructures• Core resources & datatypes (see validation.zip)• Constraints on resources & datatypes• Extensions

StructureDefinition

Share/publish to repository / registry Compare Validate resource Use to drive

Code generation Report generation UI generation (e.g. ClinFhir ResourceBuilder)

Computable!

NamingSystem

Describes “logical” numbering systems in use• What’s the name?• What are equivalent uri/uuid/oids

Represents a "System" used within the Identifier and Coding data types.

ValueSet

Define codes

ValueSet

Code System Defines a set of codes with meanings (also

known as enumeration, terminology, classification, and/or ontology)

Value Set Selects a set of codes from those defined by

one or more code systems

ConceptMap

Define mappingFrom one set of concepts to one or more other concept(s)

OperationDefinition

• Extend/restrict the API• Defines interactions

OperationDefinition

Describes additional operations over and above the RESTful interactions defined in the specification What is the name? Input/output parameters What does it do? Works on which resources?

SearchParameter

Extend/restrict searchesDescribes additional searches to filter resources• What is the name?• Elements filtered• Resource the search works on

Conformance

A set of capabilities of a FHIR Server

Binds all conformance resources together

Conformance

Describes how a client or server uses or should use the FHIR API Which wire formats supported? Which resources? Which operations supported? Which profiles supported? Is this a test server? What’s the name of the software?

For implementer convenience, the specification itself publishes its base definitions using these same resources!

Used in the core spec

For implementer convenience, the specification itself publishes its base definitions using these same resources!

Used in the core spec

Define FHIR “Profiling”?

General term: The process of creating an implementation

guide The process of creating a conformance

package The process of creating a conformance

resource

IMPLEMENTATION GUIDES

Examples

fhir.hl7.org Implementation > Implementation Guides

Argonaut DAF QICore SDC USLab

Different Kinds

Strategy•National scope guide•e.g. infrastructure, security

Principles•Overarching principles•e.g. basic components

Subject•Subject with multiple usecases•e.g. medication process

Usecase•Single usecase•e.g. prescription

Typical Content

Title Table of contents Document information Introduction to the guide Principles & background Functional requirements and high-level use cases Design considerations Package contents (= use case?) Privacy and security guidance Testing and certification Appendix List of all artifacts used in this guide

ImplementationGuide

New resource type introduced in DSTU2 1.0

Defines: Conformance Packages Documentation Pages Global Profiles Dependencies

Conformance Package

Defines a set of conceptually related conformance resources

Provides example resources Allows conformance validation of resources

Documentation Pages

Provides detailed description of the included conformance resources

E.g. HTML, Markdown Binaries: css, js, img, …

Global Profiles

A set of profiles that all resources covered by this implementation guide must conform to

Note: A resource can conform to the default profile by conforming to any profile derived from it

Dependencies

Other ImplementationGuide resources this guide depends on

Type Reference (hyperlink) Inclusion (embed)

Publish!

Test & Verify

Publish

Author & Store

Implementhttp://simplifier.nethttp://registry.fhir.org

Forge - Lipid

VALUE SETS

Coded types

Codes are defined in code systems

In a Profile, we may want to limit the codes that can possibly be used in coded elements in the Resources

“Code System”

CodeSystem vs. ValueSet

“Dante’s deadly sins”

PrideEnvyWrathSloth

AvariceGluttony

“ValueSet”

Takes concepts from…

An enumeration of terms

Definition of terms

Example: SNOMED-CT Example: “Childhood diseases”

“Special” cases

“All words under B”

“All words in theMerriam-Webster dictionary”

No need to write them all down!

“Words for ‘nerd’”

BookwormGeekGrind

WeenieWonk

Dink (slang)Dork (slang)Swot (slang)

Can take concepts from multipe codingsystems!

Identification of CodeSystems

If you refer to CodeSystems, you use a URL (instead of OID in v2 and v3): http://snomed.info/sct http://loinc.org http://hl7.org/fhir/sid/icd-10

We have introduced them for v2 and v3: http://hl7.org/fhir/v2/0078 http://hl7.org/fhir/v3/ActClass

Coded types (again)

The uri of the system

ValueSets

This models what we have been discussing so far:

• A ValueSet has metadata (much like Profile: identifier, version, name, etc)

• A ValueSet is built by inclusion of terms from CodeSystems

• A ValueSet can exclude specific codes from other valuesets

• A ValueSet can import codes from other ValueSets

Metadata

Include/Exclude Concepts

ValueSets

But it can also enumerate (and so indirectly define) all concepts for a new codesystem

• A ValueSet has metadata (much like Profile: identifier, version, name, etc)• A ValueSet is built by defining terms from and for a new CodeSystem• These new concepts have a display label and a definition • …and may be hierarchically organized

Bindings

When used in a Resource, the modelers include Bindings

Bindings specify which codes can be used

Profiling bindings

Depending on “core” spec, you can: “required”: not specify a different binding “extensible”: specify a different binding if needed “preferred”: specify a different binding if desired “example”: very likely specify a different binding

Change the bindings as specified in core: Define a new ValueSet

Allow additional codes, Restrict to a subset Specify whether implementers of your profile can

deviate from your valueset.

This is not too hard…

ValueSet Editor

Grahame Apolon …

ValueSet Editor

STRUCTUREDEFINITION

Profiling a resource

“Must use only the Dutch national patient identifier”

“Need to register an administrative race code for a Patient in the US”

“Patient Discharge documents must at least contain section “Discharge Medication” and section “Discharge Diagnosis”

“In our Patient registration system, we use these maritalStatus codes beyond those provided by HL7…”

“Our patient registration system, only supports having one single name per Patient”

Profiling a resource

Demand that the identifier uses your national patient identifier

Limit names to just 1 (instead of 0..*)

Limit maritalStatus to another set of codes that extends the one from HL7 international

Add an extension to support “RaceCode”

Note: hardly any mandatory elements in the core spec!

Uses for profiles

Server & client may publish and check their conformance to a profile

Validating instances, messages

Implement "FHIR spec-like" website from Profiles as part of an Implementation Guide

In v3 CDA…”text-based”

Write by hand…? Forge!

Publish!

http://simplifier.nethttp://registry.fhir.org

Find & maintain

Retrieve & use

Who publishes?

http://www.hl7.org/Profile/iso-21090

http://www.hl7.nl/Profile/patient-nl

http://www.health4all.nl/h4all-vitals

http://www.fit4all.nl/f4all-vitals

http://www.data4all.nl/d4all-obs

Layered profiles

HL7 Norge adapts Patient for Norway

Helse Nord/Vest/… introduces regional differences

Use-case specific constraints

Constrain

(Distributed) validation

DIPS’s server

Norway national validation server

Validate NO

Profile HNIKT, DIPS

Profile NO

nload &

Validate

StoreProfile

Profile

Examples…

Let’s look at DAF Profiles

http://fhir.hl7.org Implementation

Implementation Guides• DAF

METADATA AND VERSIONS

What’s in a profile?

Metadata “Lipid Profile” v1.0.0 Drafturn:acme.org:lipid-profile:v1Author: e.kramer@furore.com

Structure “LipidProfile”Element Definitions …

StructureDefinition for DiagnosticReport

Extension “calculated”

StructureObservation“Triglyceride”

StructureObservation“LDLCholesterol”

DiagnosticReportinstances (via Tag)

Referring to a profile

ObservationCholesterol

6.3 mmol/LHigh(recommended 4.5)

Metadata “Lipid Profile” v1.0.0 Drafturn:acme.org:lipid-profile:v1Author: e.kramer@furore.com

Structure “cholesterol”

http://acme.org/

http://acme.org/StructureDefinition/LDLCholesterol

I’m conforming to

http://acme.org/StructureDefinition/LDLCholesterol

Versioning…

A “version” – author assigned So what if you change something after

publishing? Just a typo? Change of definition? Make something optional that wasn’t? Make something mandatory that was optional? Add an extension?

“Non-breaking change”?

If old data can still be:

1. Validated against the new profile

2. Correctly interpreted against the new profile This can only be determined by the profile’s

authors (and even depends on the way it is used) A breaking change means you are

producing a new profile The profile’s author-assigned identifier changes A new Profile on the server, with a new REST utl

Authoring a Profile

Let’s do this in Forge Click “New Profile” Select base resource, e.g. Observation Edit metadata on tab page “Properties”

Name URL

STRUCTURES

Conformance Package: Lipid Report

Extension“calculated”

StructureObservation“Triglyceride”

StructureObservation“LDLCholesterol”

Structure Diagnostic Report“Lipid Profile”

StructureObservation“HDLCholesterol”

StructureObservation“Cholesterol”

DiagnosticReportinstances (via Tag)

Metadata “Lipid Profile” v1.0.0 Drafturn:acme.org:lipid-profile:v1Author: john.smith@furore.com

Structure “LipidProfile”Element Definitions …

StructureDefinition: DiagnosticReport

Structure DefinitionExtension“calculated”

Structure DefinitionObservation“Triglyceride”

Structure DefinitionObservation“LDLCholesterol”

Resource Reference

Structure Definitions

Profiles contain “Structure Definitions” Base definition of a core Resource or Datatype A set of constraints on (nested) elements of a

Resource or Datatype An extension definition

Observation resource

Let’s start constraining

= ‘ok’

“if no value…”

1..1 Subject 0..1? Why not 1..1 in spec?

Must support?

Authors: SHALL be capable of providing a value for the element and resource

Consumers: SHALL be capable of extracting and doing something useful with the data element.

"Something useful" is context dependent. The Profile SHALL describe what it means for applications to “support” the element

FORMAL CONSTRAINTS

Formal constraints

…beyond cardinalities and bindings, there are a lot of other conditions you might want to formulate: “If a Cholesterol value result is not available, use

the comments field” “A patient’s birthdate must be on or before today’s

date” These may concern a single element, or

cover multiple elements.

Formal constraints

Uses free text (human) + xpath (executable) Constraints should be declared on lowest

element in the hierarchy that is common to all nodes referenced by the constraint.

Identified by (local) ‘Key’, involved elements refer to that id

Specify severity (“error” or “warning”)

Context of the constraint

• This constraint is on the elements “valueQuantity” and “comments”

• We would have to formulate this constraint on the Observation, this is the context of the constraint

• We assign the constraint a “key” value that’s unique within the Observations’ constraints

• We refer from both “value[x]” and “comments” to this “key”. This means: if my value changes -> revalidate the constraint

“If a Cholesterol value result is not available, use the comments field”

Example xpath

Keep in mind: the condition is satisfied when the XPath expression evaluates to “true”

“If a Cholesterol value result is not available, use the comments field”

Note: to use both is ok! Otherwise said: not both empty In Xpath: exists(f:valueQuantity) or exists(f:comment) That’s a logical or, so not exclusive!

More xpath

“Either a valueQuantity or a comment is permitted” not( exists(f:valueQuantity) and exists(f:comment) )

“Can only have normal range if there is a valueQuantity” exists(f:valueQuantity) or not(exists(f:normalRange))

Steal from the spec (e.g. from Profile)

EXTENSIONS

Extension Context

An extension has a context type Resource, Datatype, Extension, Mapping

And a context path (Resource) Observation

“The observation was calculated” (Resource) Observation.value

“The observation’s ‘value’ was calculated” (Datatype) Quantity

“This quantity was calculated” (any Quantity used in any resource!)

Extension Definition

Note: multiplecontexts!

Extending a name

Key = location of formal definition

Value = value according to definition

Extensions

Let’s find a representative extension for Practitioner

Add it to the Practitioner (and show it’s both a reference & a definition)

The “Basic” resource

Now, what if you have the need for a completely “new” resource?

…then add extensions for each element

FHIR REGISTRYSimplifier

Collaborate

Manage projects Authorize team members Collaborate on profiles Github integration

Publish

Publish your conformance resources User-friendly structure rendering Detailed descriptions for elements Download as XML, JSON Related example resources

Find existing conformance resources Constraints & Extensions (StructureDefinitions) Value Sets Concept Maps Naming Systems Search Parameters Operation Definitions Conformance Packages Implementation Guides

Resolve

Resolve conformance resources by canonical Url Globally unique identifier SHOULD be the URL at which it is published Example:

http://example.org/fhir/StructureDefinition/MyPatient.xml

Alternative: Resolve from a global registry

Simplifier.net

Search

Constraint

ValueSet

Project

Versioning strategy

FHIR Normative no breaking changes => OK! Published resources will always remain available

and functional

FHIR Draft (current phase) FHIR spec may introduce breaking changes How should registry handle breaking changes?

Versioning strategy

Registry is based on a specific version of the .NET FHIR API

Uploaded resources are tagged with current API version at time of upload

Registry displays a warning if current system API version differs from saved resource API version => Author should update the resource

Security

Under development…

https OAuth2 OpenID.Connect

Base url claims

Under development… Proposal:

User can issue a claim for a specific base url E.g. http://example.org/fhir/

Granted claim provides exclusive permission to publish conformance resources on this base url

Delegation; grant claim permissions to other users Conflicting claim requests => prove domain

ownership

Forge Integration

Under development…

Configure your simplifier credentials & project(s) in Forge

Publish resources Publish ImplementationGuide packages Integrate simplifier resource rendering

139139

International HL7 FHIR Developer DaysNovember 18-20, 2015 in Amsterdam

Education 34 tutorials/presentations

pick & choose

Connectathon Meet fellow developers Put FHIR to the test

Networking FHIR experts and authors on hand

http://fhir.furore.com/devdays

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