Fhir dev days_advanced_fhir_terminology_services

Advanced FHIR Terminology Services,
incl. SNOMED CT
AUSTRALIAN E-HEALTH RESEARCH CENTRE, HEALTH & BIOSECURITY
Michael Lawley, PhD | Research Group Leader
16 November 2017
FHIR® is the registered trademark of HL7 and is used with the permission of HL7. The Flame Design mark is the registered trademark of HL7 and is used with the permission of HL7.

Who am I?
• Australian eHealth Research Centre, CSIRO
• SNOMED involvement since late 2000s
• Technical Committee 2010-2015
• Modelling Advisory Group 2015-present
• SNOMED Languages Project Group
• SNOMED Logic Profile Working Group
• SNOMED CT URI specification
• Expression Constraint Language
• Ontoserver, Shrimp, Snapper, Snorocket
• Australia’s National Clinical Terminology Service

Shrimp
- for browsing
http://ontoserver.csiro.au/shrimp

Snapper
:Author
(also :Map)
work-in-
progress

ValueSet
Explorer
- compare
performance
and behaviour
http://ontoserver.csiro.au/vstool/

Getting to know each other
• Jim’s Practical Terminology Services this morning?
• Used Terminology services?
• Implemented any part of the Terminology subsystem?
• SNOMED CT knowledge?
• Other code system knowledge?

FHIR Terminology - big picture
Concept Map
Defines a set of
concepts with a
coherent meaning
src rel tgt
Code System
Defines a set of
concepts with a
coherent meaning
url, version, name, …
Filters, Properties
Concepts
• Code
• Display
• Definition
Code System
Defines a set of
concepts with a
coherent meaning
url, version, name, …
Filters, Properties
Concepts
• Code
• Display
• Definition
Value Set
A selection of a
set of codes for
use in a
particular
context
Value Set
A selection of a
set of codes for
use in a
particular
context

Terminology in FHIR Search
• A lot of search parameters in FHIR are of type ‘token’
• These can leverage terminology services
• :above/:below
• E.g.: /Condition?body-site:below=http://snomed.info/sct|272673000 (all
Conditions where the finding site is a descendent of Bone Structure
• :in/:not-in
• E.g.:
/ProcedureRequest?code:in=http://snomed.info/sct?fhir_vs=refset/3257036
1000036108 (all ProcedureRequests in the Imagine Procedure refset
Basic Terminology Services | Jim Steel8 |

Externally defined code systems

SNOMED CT
• 19 hierarchies
• ~ 400K Concepts
• ~ 1M Descriptions
• 3 types
• Fully Specified Name
• Preferred term
• Synonyms
• ~ 65 Attributes
• Combined in triplets forming ~ 1.5M relationships
• ~ 125 relationship patterns

Practical tips
1. Beware out-of-order responses
2. Minimise latency
– Batch multiple operations for single round-trip
– Also avoids need for client-side synchronisation
3. Minimise bandwidth
– count for $expand
– includeDefinition, includeDesignations on $expand
– property for $lookup
– _count, _elements for search / read operations
– Accept-Encoding: gzip
4. GET can be cached (HTTP level), POST cannot
Warning: A lot of these can be server-dependent. They’re not proprietary, but you should
check support for them by your terminology server.

Implicit ValueSets
Defined for specific code systems
SNOMED CT, LOINC, …
http://snomed.info/sct?fhir_vs
http://snomed.info/sct?fhir_vs=isa/{sctid}
http://snomed.info/sct?fhir_vs=refset
http://snomed.info/sct?fhir_vs=refset/{sctid}

Typeahead controls
https://plnkr.co/edit/wOjWbt
<input
uib-typeahead="suggestion for suggestion in concepts($viewValue,
'http://snomed.info/sct?fhir_vs=isa/138875005')” />
$scope.concepts = function(term, valueSet) {
return $http.get(
‘https://ontoserver.csiro.au/stu3-latest/ValueSet/$expand', {
params: {
identifier: valueSet,
filter: term,
count: 15,
'_format': 'json’
},
responseType: 'json’
}).then(function(response) {
return response.data.expansion.contains || [{ display: term }];
});

Typeahead controls
https://plnkr.co/edit/wOjWbt
<input
uib-typeahead="suggestion for suggestion in concepts($viewValue,
'http://snomed.info/sct?fhir_vs=isa/73211009')” />
$scope.concepts = function(term, valueSet) {
return $http.get(
‘https://ontoserver.csiro.au/stu3-latest/ValueSet/$expand', {
params: {
identifier: valueSet,
filter: term,
count: 5,
'_format': 'json’
},
responseType: 'json’
}).then(function(response) {
return response.data.expansion.contains || [{ display: term }];
});

SNOMED CT Versioning
• International release (6 monthly)
• National releases (1-6 monthly)
• Other releases
Version is an Edition + Effective Time
http://snomed.info/sct/{module}/version/{date}

Branching version structure
No single “latest” version
INT
US
AU
X
Y
Z
time
dependency

Implicit ValueSets
http://snomed.info/sct/{module}

Implicit ValueSets
http://snomed.info/sct/{module}/version/{date}

ValueSets and CodeSystem versions
{

“Complex” ValueSets
Cycles with ValueSet inclusion / exclusion
Mixing codes from multiple code systems (don’t)
Multiple versions of the same code system

“Complex” ValueSets
“compose”: {
“include”: [{
“valueSet”:
“http://snomed.info/sct/32506021000036107/version/
20171031?fhir_vs=isa/138875005”
}],
“exclude”: [{
“valueSet”:
“http://snomed.info/sct/32506021000036107/version/
20170930?fhir_vs=isa/138875005”
}],

Expression Constraint Language (ECL)
http://snomed.org/ecl
Based on post coordination syntax
Wildcard, descendants, ancestors, reference set members, cardinality
constraints
http://ontoserver.csiro.au/shrimp/ecl_help.html
filter:[{property:’constraint’, op:’=‘, value: ‘…’ }]

ECL brief summary
Category Syntax Example
Basic sctId, *, ^ sctId ^ 723264001 |lateralizable
body structure|
Hierarchy << sctId, < sctId, <! sctId,
>> sctId, > sctId, >! sctId
<< 404684003 |clinical finding|
Composition x AND y, x OR y, x MINUS y
Relationships a : b = c, a : { b = c, d = e},
a.b
<< 404684003 :
363698007 |finding site| =
^ 723264001
Cardinality a : [low..high] b = c << 404684003 :
[1..1] 363698007 = *

SNOMED CT Post coordination
http://snomed.org/scg
71620000|Fracture of femur|:
272741003|Laterality| = 7771000|Left|
74400008|Appendicitis|:
116676008|Associated morphology|= 4532008|Acute inflammation|
64572001|Disease|:
{
116676008|Associated morphology|= 4532008|Acute inflammation|,
363698007|Finding site| = 66754008|Appendix structure|
}

CodeSystem operations
$subsumes?codeA= &codeB=
• equivalent, subsumes, subsumed-by, and not-subsumed
• terminology server handles post coordination semantics
$compose
• “Given a set of properties, return one or more possible matching
codes”
Presentation title | Presenter name31 |

http://hl7.org/fhir/terminology-service.html#closure
Why? stateful??
Consider implementing search:
[base]/Condition?code:below=126851005
[base]/Condition?code:in=http://snomed.info/sct%3Ffhir_vs
%3Disa/126851005
join
ConceptMap$closure
TerminologyClinical Data

$closure – usage flow
• init
• add set of codes
• ConceptMap of hierarchy &
equivalence [transitively closed]
• add more codes
• ConceptMap of additional
hierarchy & equivalence
• …
• resynchronisation
• {}
• 0: {}
• {a, c}
• 1: {a subsumes c}
• {b, d}
• 2: {a subsumes b, b subsumes c,
a subsumes d}

code:below
• Use $closure to maintain local edge-table of parent-child
relationships
• code:below=123
SELECT C.*
FROM Condition C, Edges E
WHERE C.code = 123
OR (E.parent = 123 AND C.code = E.child);

Code Mnemonic Code Mnemonic
equivalent wider
equal subsumes
inexact narrower
unmatched specializes
disjoint relatedto
ConceptMap - equivalence relationships
TS
TS
S T
S T
TS
S
TS
TS
S=T
TS

• Shrimp
– search & browse SNOMED CT, LOINC, ...
– http://ontoserver.csiro.au/shrimp
• Ontoserver
– powerful features, simple to deploy & use
– ECL queries
– http://ontoserver.csiro.au/shrimp/ecl.html
e.g., concepts with finding site of appendix structure
• Snapper:Author
– Author (simple) FHIR Terminology Resources
• Snorocket
– Description Logic reasoning engine
Tooling summary

Fhir dev days_advanced_fhir_terminology_services

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