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Profiling FHIR
Profiling FHIR

Profiling FHIR - PowerPoint Presentation

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Profiling FHIR - Description

Ewout Kramer San Antonio TX January 2015 Updated for FHIR DSTU2 httpwwwslidesharenetewoutkramerfhirprofilingtutorial Who am I Name Ewout Kramer Company Furore ID: 541724 Download Presentation

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Presentation on theme: "Profiling FHIR"— Presentation transcript

Slide1

Profiling FHIR

Ewout KramerSan Antonio, TX – January 2015

Updated for FHIR DSTU2!

http://www.slideshare.net/ewoutkramer/fhir-profiling-tutorialSlide2

Who am I?

Name: Ewout

KramerCompany: Furore, AmsterdamBackground:FHIR core team, RIMBAASoftware developer & healthcare architectContact:e.kramer@furore.comwww.thefhirplace.comSlide3

Introduce ourselves

Who has looked at Profiling FHIR in the spec for more than 5 minutes?Who has near-future needs for authoring profiles?Slide4

Contents of this tutorial

Introduction to profiling

MetadataRestricting resources

Bindings

Formal constraints

Extensions

SlicingSlide5

Introduction

to profilingSlide6

The need for

profiling FHIRMany different contexts in

healthcare, but a single set of operations and ResourcesNeed to be able to describe restrictions based on use and contextAllow for these usage statements to be:Authored in a structured mannerPublished in a repositoryUsed as the basis for validation, code, report and UI generation.Slide7

Uses for profile packages

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

Validating instances, messagesImplement "FHIR spec-like" website from Profiles as part of an Implementation GuideSlide8

In v3 CDA…”text-based”Slide9

openEHR ADL

…computable!Slide10

Conformance package

- normal resources

CompositionExtension DefinitionProfile

ValueSet

Search

Parameter

…computable!

Operation

Definition

Naming

SystemSlide11

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”++Slide12

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 internationalAdd an extension to support “RaceCode”Note: hardly any mandatory elements in the core spec!Slide13

Extend/restrict the API

Add operations to turn a FHIR server into a Terminology serverAdd operations for merging patientsSlide14

Compliance

Publication

Guidance

Implementation

Find

& maintain

Retrieve & use

RepositorySlide15

Who publishes?

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

http://www.hl7.nl/Profile/patient-nlhttp://www.health4all.nl/h4all-vitals

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

http://www.data4all.nl/d4all-obsSlide16

Declaring conformance

Patient

MRN 22234“Ewout Kramer”30-11-1972Amsterdam

I’m

a

Patient

conforming

to

the

Norwegian

Profile –

see

http://hl7.no/

Profiles

/

patient

-no

I’m

a

Patient

conforming

to

the

ContosoHIS

Profile –

see

http://contoso.no/

Profiles

/

patient”

in

Patient.meta.profileSlide17

(Distributed) validation

ContosoHIS’s

serverNorway national validation serverValidate NO

Profile Contoso

Profile NO

Download & Validate

Store

Profile NO

Profile

ContosoSlide18

Write by hand? Forge!Slide19

Running example…

We are taking the “Lipid Profile” example from the spec from now on.This is a DiagnosticReport

, containing 4 results:1x Cholesterol1x Triglyceride1x HDL Cholesterol0/1x LDL CholesterolAnd package it up in a messageSlide20

Preparing the Conformance Package

Let’s do this in ForgeChoose: “File

 New”Click “Edit Package Properties” on the left of the screenUnder “Meta Properties” enter values for the mandatory fields& SaveSlide21

Metadata and versionsSlide22

Conformance

Package - Bundle

What’s in a profile?Composition“Lipid Profile” by e.kramer@furore.comProfile“LipidProfile

ExtensionDefinition

“calculated

Profile

“Triglyceride”

Profile

LDLCholesterol

DiagnosticReport

instance (via

meta

)

DiagnosticReport

instance (via meta)

DiagnosticReport

instance

(via meta)

SectionSlide23

Metadata

Profile

ExtensionDefinitionSearchParameterOperationDefinitionValueSetNamingSystemurlurlurlidentifieridentifier identifieridentifierversion versionversion

name

name

name

title

name

name

publisher

publisher

publisher

publisher

publisher

telecom

telecom

telecom

telecom

telecom

description

description

description

description

description

description

copyright

status

status

status

status

status

experimental

experimental

experimental

experimental

date

date

date

datecodecodeSlide24

Referring to a profile

http://acme.org/Profile/lipids-v1

1. Where?DiagnosticReportLipid Report

Wile E. COYOTE

2009-03-03

14:26

Cholesterol 6.3

mmol

/L

Triglyceride 1.3

mmol

/L

HDL

Chol

. 1.3

mmol

/L

LDL

Chol

. 4.2

mmol

/L

Dr. Pete Pathologist,

Acme Labs

DiagnosticReport.meta.profile

http://acme.org/Profile/lipids-v1

http://

acme.org/Profile/

87408b94

( or

any

valid technical FHIR id, not

necessarily “comprehensible

)

orSlide25

Identifiers

So, Profile has a REST id on a server

Might not be under your control, server assignedBut also:A “url” – A canonical url that identifies the profileA “name” – human readable, e.g. “Lipid Profile”An “identifier” – author-assigned, globally uniqueOID (2.16.840.1.113883.10.20.2.1)UUID (09bd961e-c629-11e3-8841-1a514932ac01)URN (urn:openEHR.org:EHR-ACTION.medication.v1)Slide26

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? Slide27

“Non-breaking change”?

If old data can still be:Validated against the new profile

Correctly interpreted against the new profileThis 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 profileThe profile’s author-assigned identifier changesA new Profile on the server, with a new REST utlSlide28

Versioning schema

We used semantic versioningUses “<major>.<minor>.<patch>”

See semver.orgMajor version number is increased on breaking changesMajor version number is part of author-assigned identifier AND REST urlBoth versions may co-exist on server, they have different URLs and namesSlide29

Example

Url

http://acme.org/Profile/patient.v1Idurn:acme.org:profile:patient:v1Version1.0.0Urlhttp://acme.org/Profile/patient.v1Idurn:acme.org:profile:patient:v1Version1.0.1…after a small typo, clarification or correction (“bugfix”) becomes……after a bigger non-breaking change, like an addition, becomes…Url

http://acme.org/Profile/patient.v1

Id

urn:acme.org:profile:patient:v1

Version

1.1.0

Url

http://acme.org/Profile/patient.v2

Id

urn:acme.org:profile:patient:v2

Version

2.0.0

…after a breaking change (like cardinality) becomes…Slide30

Authoring a Resource Profile

Let’s do this in ForgeIn the middle under Profiles click “Add” and choose “

DiagnosticReport”Edit the Profile Properties on the left of the screen& SaveSlide31

31Slide32

Restricting resourcesSlide33

Profile –a normal resource

…computable!Slide34

Profile –a normal resource

ElementDefinition

Path: Patient.nameType: HumanNameCardinality: 0..*EtceteraSlide35

Profiles

A set of constraints on (nested) elements of a Resource or DatatypeSort of a “subclass” of a Resource, with specific limits on its elements

CardinalityValue domainsInvariantsSlide36

Observation resourceSlide37

Example

“Cholesterol observation” is an Observation :

That has a fixed LOINC code 35200-5 (Cholesterol) as its nameHas a quantity as value that’s expressed in mmol/L (a UCUM unit) (without a ‘comparator’) OR ELSE there’s a commentAn interpretation limited to LL,L,N,H,HHA “recommended” high reference range of 4.5 (no low) mmol/L, independent of age (no age)Is an independent observation (no related)Slide38

Let’s start constraining

0

..1

= ‘ok’

“if no value…”

1..1

1..1

Subject 0..1? Why not 1..1 in spec?Slide39

Constraining a Resource

Let’s do this in ForgeIn the middle, under “Profiles” press “Add”

Name the Profile “Cholesterol” using the property panel on the leftStart setting the cardinalities for each element, by clicking on them in the middle and using the property panelSlide40

40Slide41

Referring to a profile

http://acme.org/Profile/lipid-cholesterol

ObservationCholesterol6.3 mmol

/L

High

(recommended 4.5)

Observation.meta.profile

http://acme.org/Profile/lipid-cholesterolSlide42

Reusable constraints

We have multiple components within the “Lipid Profile” package with QuantityAll

with the same constraints Units are mmol/Lin UCUM (http://unitsofmeasure.org) no comparatorLet us first make a reusable “lipid quantity” constraint on the Quantity datatype!Slide43

bindingsSlide44

Coded types

Codes are defined in

code systemsWe may want to limit the codes that can possibly be used in coded elements in the ResourcesSlide45

“Code System”

CodeSystem

vs. ValueSet“Dante’s deadly sins”PrideEnvyWrathSlothAvariceGluttonyLust“ValueSet”Takes

concepts

from…

An enumeration of terms

Defintion

of terms

Example: SNOMED-CT

Example: “Childhood diseases”Slide46

“Special” cases

“All words under B”

“All words in theMerriam-Webster dictionary”Takes concepts from…

No need to write them all down!

Takes

concepts

from…

Takes

concepts

from…

“Words for ‘nerd’”

Bookworm

Geek

Grind

Weenie

Wonk

Dink (slang)

Dork (slang)

Swot

(slang)

Can take concepts from

multipe

codingsystems

!Slide47

Identification of CodeSystems

If you refer to CodeSystems, you use a URL (instead of OID in v2 and v3):

http://snomed.info/scthttp://loinc.orghttp://hl7.org/fhir/sid/icd-10We have introduced them for v2 and v3:http://hl7.org/fhir/v2/0078http://hl7.org/fhir/v3/ActClassSlide48

Coded types (again)

The

url of the systemMay aid interpretationSlide49
Slide50

50

MetadataIn/exclude conceptsThis 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

ValueSetsSlide51

51

But it can also enumerate (and so indirectly

define) all concepts for a new codesystemA ValueSet is built by defining terms from and for a new CodeSystemThese new concepts have a display label and a definition …and may be hierarchically organizedSlide52

Bindings

When used in a Resource, the modelers include BindingsBindings specify which codes can be usedSlide53

Profiling bindings

Depending on “core” spec, you can:“fixed”: not specify a different binding

“incomplete”: specify a different binding if needed“example”: very likely specify a different bindingChange the bindings as specified in core:Define a new ValueSet Allow additional codes, Restrict to a subsetSpecify whether implementers of your profile can deviate from your valueset.Slide54

ValueSets

In order of precision:A “true” FHIR

ValueSet resource (may be version specific)A general reference to some web content that defines a set of codes (e.g. mime types). A textual description of the possible codes Slide55

Interpretation Binding

Let us limit http://hl7.org/fhir/vs/observation-interpretation

Let’s Define a new ValueSet using codes from the existing Code systemhttp://hl7.org/fhir/v2/0078Slide56

This is not too hard…Slide57

Conformance levels

IsExtensible

“N”IsExtensible “Y”Required “SHALL”Validation error, non-conformantAdditional codes allowedPreferred “SHOULD”“Guidance”Validation warning, discouragedSupplemental codes likelyAlternatives allowedExample “MAY”Just a suggestion, no preferenceIf implementers of your profile provide a different code than you have in your profile….Slide58

Must support?

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

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 elementSlide59

Refer to ValueSet

And now…make the Profile point to the newly created ValueSet using ForgeSlide60

Formal constraintsSlide61

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.Slide62

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 idSpecify severity (“error” or “warning”)Slide63

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 constraintWe assign the constraint a “key” value that’s unique within the Observations’ constraintsWe 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” Slide64

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 emptyIn Xpath: exists(f:valueQuantity) or exists(f:comment)That’s a logical or, so not exclusive!Slide65

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)Slide66

Add constraint

Let’s do this in ForgeClick the Cholesterol Observation (that’s the context, remember!), add under the “Constraints” in the property panel

Give it key “chol-01”Click both “value[x]” and “comment” and set their condition to “chol-1”.Slide67

extensionsSlide68

Extensions

Add the fact that: “an LDL Cholesterol value is calculated”

There’s no such indication on Observation (or Observation.value) -> Extension!!Note!! - You’re not extending a resource per se, but you specify where an extension applies. This may be multiple places. So “haircolor” may be applied to “Patient” and “Practitioner”Slide69

ExtensionDefinition

–a normal resource

ElementDefinitionPath: Patient.nameType: HumanNameCardinality: 0..*EtceteraSlide70

Extension Context

An extension has a context typeResource,

Datatype, Extension, MappingAnd 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!)Slide71

Extension definition

Note: multiple

contexts!Slide72

Extending

a name

Key = location of formal definitionValue = value according to definitionSlide73

Complex extensionsSlide74

Complex extensionsSlide75

The “Basic” resource

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

…then add extensions for each elementSlide76

Authoring an extension

Let’s do this in ForgeOpen the “Extensions” tab in the middle of the screenPress “Add”

Give it a name, context and datatypeSlide77

slicingSlide78

Where are we?

Cholesterol

Observationname: loinc.org#35200-5TriglycerideObservationname: loinc.org#35217-9

HDL Cholesterol

Observation

name: loinc.org#2085-9

LDL Cholesterol

Observation

name: loinc.org#

13457-7

Quantity (

lipidQuantity

)

use

ValueSet

(

lipidInterpretation

)

bind

Extension

(calculated)

boolean

applies

to

TODO:

DiagnosticReport

containing

4

results:

1x Cholesterol

1x Triglyceride

1x

HDL

Cholesterol

0/1

LDL CholesterolSlide79

The Diagnostic Report

Cholesterol

TriglycerideHDL Cholesterol

LDL Cholesterol

= loinc.org#57698-3

(Lipid

panel with direct

LDL)

1

1

1

0/1Slide80

Slicing!

Reference(Observation)

Result: Reference(Observation)Reference(Observation)Reference(Observation)

ResourceReference

(Observation)

Reference(Observation)

ResourceReference

(Observation)

Cholesterol

Observation

name: loinc.org#35200-5

Triglyceride

Observation

name: loinc.org#35217-9

HDL Cholesterol

Observation

name: loinc.org#2085-9

LDL Cholesterol

Observation

name: loinc.org#

13457-7

0..*

3

..4

Reference(Observation)

Discriminator

1..

1

1..

1

1..

1

0

..

1

"There MUST be

exactly one

Observation

with

LOINC 35200-5

. And if you find it, it

must conform to our

"Cholesterol" StructureSlide81

Properties of slices

Each slicing group indicates a discriminator

here, that is Observation.nameEach slicing group indicates a cardinalityhere, that was 3..4Each slice indicates its own cardinality within the slicehere 1..1 for chol,trig,hdlc, 0..1 for ldlcEach slice indicates additional constraintshere "must conform to Cholesterol profile" etc. Slide82

Authoring slices

Let’s do this in ForgeClick "result" and then "Slice" above property panel

Indicate the discriminator and the cardinality for the whole sliceClick "Add slice" (4x), and name each slice, give it the cardinality, tie Reference to "cholesterol", "triglyceride" etc.Slide83

One step further!

Cholesterol

TriglycerideHDL Cholesterol

LDL Cholesterol

DiagnosticReport

data: Reference(

DiagnosticReport-lipidPanel

) 1..1

Package the

DiagnosticReport

in a "

LipidResultMessage

"Slide84

FHIR server @ hospitalA.org

Practitioner Bernard

FHIR server @ lab.hospitalA.orgMessageHeader

Diagnostic

Report A

data

In REST: Possibly distributed…

FHIR server @ pat.registry.org

Patient Joe

subject

performer

FHIR server @

lab2.hospitalA.org

HDL

Obs

34

Triglyceride

Obs

78

Cholesterol

Obs

1

resultSlide85

Aggregation

Aggregation: for each ResourceReference choose one to all of these options:

CodeDefinitioncontainedReference to a contained resource.referencedReference to a resource that has to be resolved externally..bundledReference points to will be found in the same

bundle

read:

Message,

DocumentSlide86

Authoring aggregation

Let’s do this in ForgePick any of the

ResourceReferences in the model.Notice none of the checkboxes next to a ResourceReference is checked: all aggregation types are allowedNow select those checkboxes to changeSlide87

Finally…

“Conformance Package” tab on each Resource, e.g.:http

://hl7.org/implement/standards/FHIR-Develop/patient-packages.htmlForge downloadhttp://fhir.furore.com/forge/http://fhir.furore.com/Tooling/ProfileEditorFind this presentation on SlideShareSlide88

Questions?