SNOMED CT Languages Project Group

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Date & Time

Wednesday 22nd June 2016, 20:00 UTC

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Goals

  • To progress the SNOMED CT Template Syntax

Attendees 

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Observers

Agenda and Meeting Notes

ItemDescriptionOwnerNotesAction

1

Welcome, introductions and apologiesLinda Bird

SLPG meetings will be recorded and recordings will be accessible to SLPG members.

 

2Agenda reviewLinda Bird

Review agenda for today's meeting

  • Template Syntax - HL7 FHIR Examples
      • SNOMED CT Expression Templates and corresponding FHIR Structured Definitions
      • FHIR Mapping Example
  • Template Syntax - Details
      • Optionality (slots and relationship groups)
      • Naming (slots and relationship groups)
      • References

 

3Template Syntax - FHIR Example TemplatesLinda Bird

STEP 1 - Convert SNOMED CT Expression Template into FHIR Structure Definition (for use as Target of Mapping)

CONDITION RESOURCE

  • SNOMED CT Expression Template

[[ [1..1] @findingWithExplicitContext ]]:

#[1..2] @RGa { 246090004 |Associated finding| = ([[ [0..1] @associatedFinding ]]:

#[0..1] @RGb { 246112005 |Severity| = [[ [0..1] @severity]],

363698007 |Finding site| = [[ [0..1] @findingSite]] })

408732007 |Subject relationship context| = 410604004 |Subject of record|,

408731000 |Temporal context| = [[ [1..1] @temporalContext ]],

408729009 |Finding context| = [[ [1..1] @findingContext ]] }

  • FHIR Structure Definition

SCT_ConditionTemplate: SNOMEDCTExpressionTemplate

findingWithExplicitContext [1]: CodeableConcept

RGa [1..2]: RelationshipGroupElement

associatedFinding [1]: CodeableConcept

RGb [0..1]: RelationshipGroupElement

severity [0..1]: CodeableConcept

findingSite [0..1]: CodeableConcept

subjectRelationship [1]: CodeableConcept = 410604004 |Subject of record|

temporalContext [1]: CodeableConcept

findingContext [1]: CodeableConcept

ALLERGYINTOLERANCE RESOURCE

  •  SNOMED CT Expression Template

[[ [1..1] @findingWithExplicitContext ]]:

#[0..2] @RGa { 246090004 |Associated finding| = ([[ [1..1] @associatedFinding ]]:

370135005  |Pathological process| = [[ [0..1] @pathologicalProcess ]],

#[0..1] @RGb { 255234002 |After| = [[ [0..1] @after ]],

246075003 |Causative agent| = [[ [1..1] @causativeAgent ]] })

408732007 |Subject relationship context| = 410604004 |Subject of record|,

408731000 |Temporal context| = [[ [1..1] @temporalContext ]],

408729009 |Finding context| = [[ [1..1] @findingContext ]] }

  • FHIR Structure Definition 

SCT_AllergyIntoleranceTemplate: SNOMEDCTExpressionTemplate 

findingWithExplicitContext [1]: CodeableConcept

RGa [1..2]: RelationshipGroupElement

associatedFinding [1]: CodeableConcept

pathologicalProcess [0..1]: CodeableConcept

RGb [0..1]: RelationshipGroupElement

after [0..1]: CodeableConcept

causativeAgent [1]: CodeableConcept

subjectRelationship [1]: CodeableConcept = 410604004 |Subject of record|

temporalContext [1]: CodeableConcept

findingContext [1]: CodeableConcept

PROCEDURE RESOURCE

  • SNOMED CT Expression Template

129125009 |Procedure with explicit context|: 

#[1..1] @RGa { 363589002 |Associated procedure| = ([[ [1..1] @associatedProcedure ]] :

#[0..1] @RGb { 363704007 |Procedure site| = [[ [0..1] @procedureSite ]],

363699004 |Direct device| =  [[ [0..1] @directDevice ]],

424361007 |Using substance| = [[ [0..1] < 105590001 |Substance| @usingSubstance ]],

424226004 |Using device| = [[ [0..1] < 49062001 |Device|) @usingDevice]] }),

408732007 |Subject relationship context| =  410604004 |Subject of record|,

408731000 |Temporal context| =  410512000 |Current or specified time|,

408730004 |Procedure context| = [[ [0..1] @procedureContext ]] }

  • FHIR Structure Definition

SCT_ProcedureTemplate: SNOMEDCTExpressionTemplate

findingWithExplicitContext [1]: CodeableConcept

RGa [1..2]: RelationshipGroupElement

associatedFinding [1]: CodeableConcept

RGb [0..1]: RelationshipGroupElement

severity [0..1]: CodeableConcept

findingSite [0..1]: CodeableConcept

subjectRelationship [1]: CodeableConcept = 410604004 |Subject of record|

temporalContext [1]: CodeableConcept

findingContext [1]: CodeableConcept

 

4Template Syntax - FHIR Mapping Example 

STEP 2 - Define Mapping Rules from Source Structure (FHIR Resource) to Target Structure (SNOMED CT Expression Template)

SOURCE STRUCTURE

Condition: Resource

code [1]: CodeableConcept (coding [1..*] - system, version, code, display, userSelected [0..1] - text [0..1])

category [0..1]: CodeableConcept (values: complaint | symptom | finding | diagnosis)

clinicalStatus [0..1]: code (values: active | relapse | remission | resolved)

verificationStatus [1]: code (values: provisional | differential | confirmed | refuted | entered-in-error | unknown)

severity [0..1]: CodeableConcept

bodySite [0..*]: CodeableConcept

TARGET STRUCTURE

SCT_ConditionTemplate: SNOMEDCTExpressionTemplate

findingWithExplicitContext [1]: CodeableConcept

RGa [1..2]: RelationshipGroupElement

associatedFinding [1]: CodeableConcept

RGaa [0..1]: RelationshipGroupElement

severity [0..1]: CodeableConcept

findingSite [0..1]: CodeableConcept

subjectRelationship [1]: CodeableConcept = 410604004 |Subject of record|

temporalContext [1]: CodeableConcept

findingContext [1]: CodeableConcept

RULES

rule_1: for  source.code as code where verificationStatus != "entered-in-error" then {

rule_1a: for code where code in descendantsOf (404684003 |Clinical finding|) make target.findingWithExplicitContext = 413350009 |Finding with explicit context|, target.RGa as rga then {

rule_1aa: for code make rga.associatedFinding = code

rule_1ab: for code where severity in descendantsOf (272141005 | Severities|) OR findingSite in descendantsOf (123037004 |Body structure|) make rga.RGb as rgb then {

rule_1aba: for source.severity as sev where severity in descendantsOf (272141005 | Severities|) make rgb.severity = sev

rule_1abb: for source.bodySite as bs where findingSite in descendantsOf (123037004 |Body structure|) make rgb.findingSite = bs }

rule_1ac: for code make rga.subjectRelationship = 410604004 |Subject of record|

rule_1ad: for code make rga.temporalContext = 410512000 |Current or specified time|

rule_1ae: for source.clinicalStatus as cs, source.verificationStatus as vs  make rga.findingContext as fc then {

rule_1aea: for vs make fc.coding as coding then {

rule_1aeaa: for vs make coding.code = translate ((clinicalStatus,verificationStatus), 'status-to-findingContext-map', code)

rule_1aeab: for vs make code.system = "http://snomed.info/"

rule_1aeac: for vs make code.display = preferredTerm (en-us, coding.code) }

} }

  rule_1b: for code where code in descendantsOf (413350009 |Finding with explicit context|) make target.findingWithExplicitContext = code then {

rule_1ba:

} }

 
5Template Syntax - DetailsLinda Bird
  • Optionality
    • Optional refinements
    • Optional groups
  • Names
    • Naming refinements
    • Naming groups
  • References
    • References to location of values

Condition

[[ [1..1] @findingWithExplicitContext ]]:

#[1..2] @RGa { 246090004 |Associated finding| = ([[ [0..1] @associatedFinding ]]:

#[0..1] @RGb { 246112005 |Severity| = [[ [0..1] @severity]],

363698007 |Finding site| = [[ [0..1] @findingSite]] })

408732007 |Subject relationship context| = 410604004 |Subject of record|,

408731000 |Temporal context| = [[ [1..1] @temporalContext ]],

408729009 |Finding context| = [[ [1..1] @findingContext ]] }

AllergyIntolerance

[[ [1..1] @findingWithExplicitContext ]]:

#[0..2] @RGa { 246090004 |Associated finding| = ([[ [1..1] @associatedFinding ]]:

370135005  |Pathological process| = [[ [0..1] @pathologicalProcess ]], 

#[0..1] @RGb { 255234002 |After| = [[ [0..1] @after ]], 

246075003 |Causative agent| = [[ [1..1] @causativeAgent ]] }) 

408732007 |Subject relationship context| = 410604004 |Subject of record|, 

408731000 |Temporal context| = [[ [1..1] @temporalContext ]], 

408729009 |Finding context| = [[ [1..1] @findingContext ]] }

Procedure

129125009 |Procedure with explicit context|: 

#[1..1] @RGa { 363589002 |Associated procedure| = ([[ [1..1] @associatedProcedure ]] :

#[0..1] @RGb { 363704007 |Procedure site| = [[ [0..1] @procedureSite ]],

363699004 |Direct device| =  [[ [0..1] @directDevice ]],

424361007 |Using substance| = [[ [0..1] < 105590001 |Substance| @usingSubstance ]],

424226004 |Using device| = [[ [0..1] < 49062001 |Device|) @usingDevice]] }),

408732007 |Subject relationship context| =  410604004 |Subject of record|,

408731000 |Temporal context| =  410512000 |Current or specified time|,

408730004 |Procedure context| = [[ [0..1] @procedureContext ]] }

 
6Confirm next meeting date/timeLinda Bird

 

Confirm date and time of next SLPG meeting - Wednesday 6th July, 20:00 UTC

 

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1 Comment

  1. Linda Bird

    As promised - here are some questions relating to 'SNOMED CT Expression Templates' to think about (and respond to) prior to our next meeting ....

    1. Do we need to support naming of SNOMED CT Relationship Groups within the SNOMED CT Expression Template syntax? For example: [[ .... ]]: @RelationshipGroupName { .......}
      1. Note: This requirement comes from the need for a stable name for each relationshipgroup, in the FHIR Structure Definition used to represent the SNOMED Expression Template that is the target of a mapping (examples above).
      • A possible alternative would be to not include relationship group names in the template, and instead rely on a reproducible approach to automatically generating these names (e.g. RG1, RG1.1, RG1.2, RG2, RG2.1). However, because these names are used in the mapping code, we would need to ensure that they are absolutely stable - so given this, is this approach appropriate?
    2. What syntax should we use to define cardinality constraints?
      1. On a focus concept, an attribute or an attribute value - e.g. in the relevant slot [[ [1..*] < 123456 @slotName ]]
      2. On a relationship group - e.g. 123456 |concept|: #[1..*] { .......}
        1. Note: I would like the syntax to clearly indicate that the cardinality on a relationship group does not appear in the concrete expression that is generated when the expression template is populated. This is needed to distinguish an Expression Template (with relationship group cardinalities) from an Expression Constraint Template (for which the relationship group cardinalities do appear in the populated version of the template). In this example syntax, the "#" is being used to say "The following constraint needs to be removed when the template is populated."
    3. What is the expected behaviour when a cardinality constraint in an Expression Template is not met?
    4. Are there any other template requirements that we haven't yet considered for other use cases (e.g. for concept authoring)

    If you have any additional questions (or answers), please post these as well.

    Thanks! Next meeting is Wednesday 6th July.

    Linda.