2016-10-12 - SLPG Meeting

Welcome, introductions and apologies

Relevant Modelling Advisory Group (MAG) meeting topics -

• Machine Readable Concept Model (MRCM) - released for community review
• SNOMED CT bindings to FHIR resources
• Extending SNOMED CT URI standard to support computable languages
  • For example (syntax):
    • • http://snomed.info/syntax/scg
      • http://snomed.info/syntax/scg/version/1.1
      • http://snomed.info/syntax/ecl
      • http://snomed.info/syntax/ecl/version/1.1
      • http://snomed.info/syntax/qry
      • http://snomed.info/syntax/qry/version/1.0
      • http://snomed.info/syntax/etl
      • http://snomed.info/syntax/etl/version/1.0
      • http://snomed.org/syntax/ect
      • http://snomed.org/syntax/ect/version/1.0
      • http://snomed.org/syntax/qrt
      • http://snomed.org/syntax/qrt/version/1.0
  • For example (instance):
    
    • • http://snomed.info/id
      • http://snomed.info/id/404684003
      • http://snomed.info/scg/404684003%3A47429007%3D2670138008 (where %3A is ":" and %3D is "=")
      • http://snomed.info/ecl/%3C404684003%3A%3C%3C47429007%3D%3C%3C267038008   (where %3C is "<")
  • Do we allow language instances to have a version
  • How should we refer to the version of a syntax? (e.g. "20160131" or "1.1")
  • Which characters must be replaced with hexidecimal? For example:
    • • Reserved characters

        • • ":" --> %3A

          • "/" --> %2F

          • "?" --> %3F

          • "#" --> %23

          • "[" --> %5B

          • "]" --> %5D

          • "@" --> %40

          • "!" --> %21

          • "$" --> %24

          • "&" --> %26

          • "'" --> %27

          • "(" --> %28

          • ")" --> %29

          • "*" --> %2A

          • "+" --> %2B

          • "," --> %2C

          • ";" --> %3B

          • "=" --> %3D

      • Other (?)

        • • Space --> %20

          • "<" --> %3C

          • ">" --> %3E

          • " " " --> %22

          • "%" -->

• Discuss new updates to ECL in v1.1
  • Decomposition syntax - for example:
    • • 57617002 |Urine specimen collection (procedure)| . 363701004 |Direct substance|
        • • ... equivalent to ... < *: { R 363701004 |Direct substance| = 57617002 |Urine specimen collection (procedure)| }
      • ( << 17636008 | specimen collection| : 260686004 | method | = 129314006 | Biopsy - action | ) . 363701004 | direct substance|
        
        • • ... equivalent to .... << 105590001|substance| : R 363701004 | direct substance| = ( << 17636008 | specimen collection| : 260686004 | method | = 129314006 | Biopsy - action | )
      • (X . |associated with| AND < |organism|) . |cb|
  • Subexpression requirements

• Discuss draft Template Syntax v0.1

Example 1: CT of X

71388002 |Procedure| : [[~1..1 @roleGroup1]]

{ 260686004 |Method| = 312251004 |Computed tomography imaging action|,

  405813007 |Procedure site - Direct| = [[+id (<<442083009 |Anatomical or acquired body structure|)] @site] }

Example 2: Family history of disease X in family member Y

413350009 |Finding with explicit context| : [[~1..1]]

{ 246090004 |Associated finding| = [[+id (< 404684003 |Clinical finding)]],

  408732007 |Subject relationship context| = [[+id (<< 125676002 |Person (person)|)]],

  408729009 |Finding context| = 410515003 |Known present|,

  408731000 |Temporal context| = 410511007 |Current or past (actual)| }

• Topics raised by Ed
  • • Preference for option 1 syntax. That is, with 'remove slots' e.g.[[ ~ 0..1 @slot1]] and 'replace slots' e.g. [[ + id (< 12345 |term|) @slot2 ]]
      • Note: Rather than '+ cpt' for a concept replacement, I now prefer '+ id' (for consistency with the URI standard which uses "http://snomed.info/id/267038008" for the concept 267038008 |Edema|)
    • The fact that the "~" may not be necessary in a 'remove slot', as the absence of a "+" may be sufficient (for discussion with the SLPG)
    • The requirement to be able to replace other characters in an expression constraint template (such as comparison operators "=" and "!=")
    • If we all agree on this requirement, then we just need to select an appropriate abbreviation. I see in your example you've used "+char". Perhaps we could also consider "+str"?
    • The fact that a template processor would need to 'clean-up' any left over characters, such as ":". I suggest that we try to document the steps that a template processor should follow to turn a template into an expression, constraint etc.

Proposed Syntax Rules and Questions

• Constraints and names appearing before a brace apply to the whole relationship group
• Constraints and names appearing before an attribute apply to the whole Attribute Value pair
• A cardinality constraint:
  • Preceding a brace indicates the number of times the following relationship group is allowed in the final expression (default separator between repetitions is ",")
  • Preceding an attribute within a relationship group indicates the number of times the following attribute may appear with a distinct (non-redundant) value in each instance of the given relationship group (default separator between repetitions is ",")
  • Preceding an attribute that is not in a relationship group indicates the number of times the following attribute may appear with a distinct (non-redundant) value in the relevant expression (or subexpression) (default separator between repetitions is ",")
  • Within a slot that is a focus concept of an expression (or subexpression) indicates the number of times the slot can be filled in the focus (default separator between repetitions is "+")
  • Within a slot that is the attribute in an Attribute-Value pair indicates the number of distinct attribute concepts that can be used in this position in the expression (default separator between repetitions is ",")
  • Within a slot that is the value of an Attribute-Value pair (but which is NOT the focus concept of a subexpression) is not allowed ???
• Question 1 - How do we represent the cardinality of how many non-redundant values may appear in a given Attribute-Value pair across any relationship group. While this is currently always [0..*] in the MRCM, this may be more relevant in specialized authoring templates.
• Question 2 - Do we need to provide support to vary the default connector between repetitions. Note, I think this is probably more important for Expression Constraint Templates, as there are more options (e.g. ANDs and ORs)
• Question 3 - Do we introduce the ability for expression constraints in a slot to be replaced by a variable name (assigned using a SET-IN construct)? For example:
  • SET (severity_range = < |Severities|) IN [[ @finding ]]: |Severity| = [[+ecl ([[$severity_range]]) ]]

Next meeting to be held at 20:00 UTC on Wednesday 9 November (due to SNOMED Expo in New Zealand)