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Welcome and apologies

• Actions from last week:
  • Consider new syntax to support proposed map expression template use case
  • Consider new syntax to support proposed expression template map use case

Use cases: New concept development, querying based on template matching, and template-based modeling transformation

New requirements

1. Constrain values across 2 or more replacement slots
   • 2 replacement slots must have the same

1. • value, different values, subsumed values, or not subsumed values.
   • Example A - A clinical finding, with 2 role groups with the same morphology, and finding sites that not subsume each other

1. • • Template

       • [[ +id ]]:
         { 116676008 |Associated morphology| = [[ +id @morphology ]],
         363698007 |finding site| = [[ +id

1. • • • (<< |Body structurel MINUS << $findingSite2 ) @findingSite1 ]] },
          

1. • • • { 116676008 |Associated morphology| = [[ +id @morphology ]],
         363698007 |finding site| = [[ +id

1. • • • (* MINUS << $findingSite1) @findingSite2 ]] }

1. • • Valid Expression (Definition of 16027391000119109 |Bone cyst of bilateral tibias (disorder)|)
       • 64572001 |Disease|:
                     { 116676008 |Associated morphology|=

1. • • • 66954000 |Bone cyst|,
                       363698007 |Finding site|=

1. • • • 719491009 |Bone structure of right tibia|}
                     { 116676008 |Associated morphology|= 66954000 |Bone cyst|,
                       363698007 |Finding site|=

1. • • • 719492002 |Bone structure

1. • • • of left tibia|}
         
   • Example B - A clinical finding, with one or more role groups in which the morphology is always the same, and no 2 finding sites subsume each other.
     • Template - 3 role groups with 3 sites: site[1], site[2], site [3] /// site [1,2]
       
       •  [[+id]]:
         [[1..*] @group1] { |Finding site| = [[ +id (* MINUS $site[! SELF ] ) @site constraint ( [n] != << $site [!n] ]],
         |Associated morphology| = [[ +id ($morphology [! SELF] ) @morphology constraint ( [n] = $morphology [!n] ]] }
     • Valid Expression (Definition of208510002 |Multiple fracture of clavicle, scapula and humerus (disorder)| )
       • • 64572001 |Disease|:
                       { 363698007 |Finding site|= 85050009 |Bone structure of humerus|,
                         116676008 |Associated morphology|= 5468008 |Fracture of multiple sites of bone|}
                       { 363698007 |Finding site|= 51299004 |Bone structure of clavicle|,
                         116676008 |Associated morphology|= 5468008 |Fracture of multiple sites of bone|}
                       { 363698007 |Finding site|= 79601000 |Bone structure of scapula|,
                         116676008 |Associated morphology|= 5468008 |Fracture of multiple sites of bone|}
                       { 363698007 |Finding site|= 773134001 |Bone structure of multiple body regions|,
                         116676008 |Associated morphology|= 771485007 |Fracture of multiple bones|}
2. Default value for replacement slot
   
   • Default value for authoring and template-driven modelling transformations
   • Example A - Default finding site of 72673000 |Bone structure|
     
     • Template
       
       • [[ + id ]] :
         { |Finding site| = [[ +id (<< 72673000|Bone structure|) @site default (72673000 |Bone structure (body structure)|) ]]
3. Definition status of a replacement slot
   • Specifying whether the value used in a replacement slot must be primitive or defined
   • Example A - When proximal primitive modelling, the focus concept must be a primitive concept
     
     • Template - Requires use of more expressive query language with filters
       • [[ + id (<< 64572001 |Disease| {{ c.definitionStatus = primitive }}) ]]
     • Valid Expression
       
       • 195967001 |Asthma (disorder)|
4. Definition status of a templated expression
   • Specifying the definition status of a templated expression
   • Template
     
     • [[ +tok ("===" "<<<") ]] [[ +id ]] : { |Finding site| = [[+id]] }
     • Valid Expression
       
       • === 128272009 |Disorder of lower respiratory system|: 363698007 |Finding site|= 39607008 |Lung structure|
       • <<< 128272009 |Disorder of lower respiratory system|: 363698007 |Finding site|= 39607008 |Lung structure|
         
5. Attributes used in repeating role groups
   • Constraining the set of attributes that appear in a repeating role group
   • Example A - The same set of attributes must appear in each instance of a repeating role group (with optional attributes)
     
     • Template - using allOrNone
       • [[+id]]: [[1..* @group1 allOrNone ($site, $occurrence)]]
         { [[1..1]] |Associated morphology| = [[ +id @morphology ]],
         [[0..1 ]] |Finding site| = [[ +id @site]],
         [[0..1 ]] |Occurrence| = [[ +id @occurrence ]] }
       • Valid Expression - Injury of head, neck and chest
         
         • [[ |Disease| ]]: 
           { |Associated morphology| = |Injury|, |Finding site| = |Head structure| } 
           { |Associated morphology| = |Injury|,  |Finding site| = |Neck structure| }
           { |Associated morphology| = |Injury|,  |Finding site| = |Chest structure| }
       • Valid Expression - Congenital malformation of head and neck 
         • [[ |Disease| ]]: 
           { |Associated morphology| = |malformation|, |Finding site| = |Head structure|, |Occurrence| = |Gongenital| } 
           { |Associated morphology| = |malformation|,  |Finding site| = |Neck structure|, |Occurrence| = |Gongenital| }
   • Example B - Some of the optional attributes must either always or never appear in each instance of a repeating role groupTemplate - using "allOrNone"

1. • • • [[+id]]: [[1..* @group1 allOrNone($morph) ]]
         { [[

Proposed extension to ECL to support the execution of maps (focusing on the resolution of historical refsets)

• Example use cases
  • Mapping from international substance concepts to AMT substance concepts
  • Anatomy structure and part association reference set - e.g. find the anatomical parts of a given structure
• Potential syntax to consider
  • Functional
    • mapTarget (|Anatomy structure and part association refset|, << |Upper abdomen structure|)
    • mapSource (|Anatomy structure and part association refset|, << |Liver part|)
  • Dot notation
    • ( |Anatomy structure and part association refset|: |ReferencedComponent| = << |Upper abdomen structure ) . |mapTarget|
    • ( |Anatomy structure and part association refset|: |mapTarget| = << |Upper abdomen structure ) . |referencedComponent|
      
  • Filters
    
    • ( |Anatomy structure and part association refset| {{ |referencedComponent| = << |Upper abdomen structure| }} ). |mapTarget|
      
    • ( |Anatomy structure and part association refset| {{ mapTarget = << |Upper abdomen structure| }} ) . |referencedComponent|
      
      • ^ ( |Anatomy structure and part association refset| {{ mapTarget = << |Upper abdomen structure|
  The specific use-case here comes initially from Jeremy and relates to being able to work with inactive concepts via the historical association maps. For example, given an ECL expression that identifies a set of concepts 'c' to be used for retrieving patient records, you probably also want to retrieve records for sameAs (c) and replacedWith (c)
  • Example:
    • (< 72704001 |Fracture| AND ^ 900000000000527005 |SAME AS association reference set|) . 900000000000533001 |Association target component|
    • (900000000000527005 |SAME AS association reference set| . 900000000000533001 |Association target component| ): |Referenced component| = < |Fracture|
      
    • Michael's existing approach: mapsTo(|SAME AS|, < |Fracture|)
Or mappedTo(…)
mappedFrom(|SAME AS|, |inactive concept|)
mappedFrom(|REPLACED BY|, |inactive concept|)

      
    • Alternative suggestion: Use the substrate to include historical snapshots.
      • E.g. Historical and current concepts that are fractures and have an associated morphology, but not historical morphologies
      • ( < |Fracture of bone| {{ substrate >= http://snomed.info/sct/900000000000207008/version/20140131 }}) AND (* : |Associated morphology| = *)
    • Alternative use case - Substance (int) to substance (AMT) map (SNOMED-to-SNOMED)
      • ^ (711112009|ICNP diagnoses simple map reference set| {{ M.mapTarget= “R-FF2E9” }} )
        

Proposal from Michael:

• Currently ECL expressions can match (return) concepts that are either the source or the target of a relationship triple (target is accessed via the 'reverse' notation or 'dot notation', but not the relationship type (ie attribute name) itself. 

For example, I can write: 

<< 404684003|Clinical finding| : 363698007|Finding site| = <<66019005|Limb structure| 

<< 404684003|Clinical finding| . 363698007|Finding site| 

But I can't get all the attribute names that are used by << 404684003|Clinical finding| 

• • Perhaps something like:
    • ?? R.type ?? (<< 404684003 |Clinical finding|)
  • This could be extended to, for example, return different values - e.g.
    • ?? |Simple map refset|.|maptarget| ?? (^|Simple map refset| AND < |Fracture|)

• Finalize and publish language and language instance URIs

Examples: version and language

• • << 64572001 |Disease| {{ term = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131

  • << 64572001 |Disease| {{ synonym = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131

  • << 64572001 |Disease| {{ FSN = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131

  • << 64572001 |Disease| {{ FSN = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131, LANGUAGE W

  • << 64572001 |Disease| {{ preferredTerm = “*heart*”}}   VERSION http://snomed.info/sct/900000000000207008/version/20180131, LANGUAGE Y

  • << 64572001 |Disease| {{ acceptableTerm = “*heart*”}}   VERSION http://snomed.info/sct/900000000000207008/version/20180131, LANGUAGE Y

  • (* {{ term = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131, LANGUAGE Z) MINUS
    (* {{ term = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20170731, LANGUAGE W)

  • X MINUS Y WHERE X = * , Y = (* {{ term = "*heart*" }}) VERSION http://snomed.info/sct/900000000000207008/version/20180131, LANGUAGE W

Notes

• • Allow nested where, version, language
  • Scope of variables is inner query

Examples: where

• • X MINUS >! X WHERE X = (<< 1234 : 5678 = << 6547)

  • X MINUS >! X WHERE X = (<< 1234 : 5678 = << 6547) VERSION http://snomed.info/sct/900000000000207008/version/20180131

  • X MINUS >! Y WHERE X = (<< 1234 : 5678 = << 6547), Y = (<< 1456) VERSION http://snomed.info/sct/900000000000207008/version/20180131
  • X MINUS >! X WHERE X = (<< 1234 : 5678 = << 6547) VERSION http://snomed.info/sct/900000000000207008/version/20180131 , LANGUAGE 900000000000508004 |GB English|
  • X MINUS >! X WHERE X = (<< 1234 : 5678 = << 6547) VERSION http://snomed.info/sct/900000000000207008/version/20180131, LANGUAGE 999001881000000108|GB clinical extension LRS|, 900000000000508004 |GB English|
    
  • X minus >! X WHERE X = ( < M WHERE M = (< 1234))) VERSION http://snomed.info/sct/900000000000207008/version/20180131, LANGUAGE 999001881000000108|GB clinical extension LRS|, 900000000000508004 |GB English|

Notes

• • • Allow nested variable definitions, but recommend that people don't due to readability
    • Scope of variables is the inner query
    • No recursion e.g X WHERE X = 1234 MINUS X
      • ie can't use a variable in its own definition
      • ie X is only known on the left of the corresponding WHERE, and not on the right of the WHERE

Keywords for Term-based searching:

• D.term
  • D.term = "*heart*"
  • D.term = wild:"*heart*"
  • D.term = regex:".*heart.*"
  • D.term = match:"hear att"
  • D.term = (sv) wild: "*heart*"
• D.languageCode
  • D.languageCode = "en"
  • D.languageCode = "es"
• D.caseSignificanceId
  • D.caseSignificanceId = 900000000000448009 |entire term case insensitive|
  • D.caseSignificanceId = 900000000000017005 |entire term case sensitive|
  • D.caseSignificanceId = 900000000000020002 |only initial character case insensitive|
    
• D.caseSignificance
  • D.caseSignificance = "insensitive"
  • D.caseSignificance = "sensitive"
  • D.caseSignificance = "initialCharInsensitive"
• D.typeId
  • D.typeId = 900000000000003001 |fully specified name|
  • D.typeId = 900000000000013009 |synonym|
  • D.typeId = 900000000000550004 |definition|
• D.type
  • D.type = "FSN"
  • D.type = "fullySpecifiedName"
  • D.type = "synonym"
  • D.type = "textDefinition"
• D.acceptabilityId
  
  • D.acceptabilityId = 900000000000549004 |acceptable|
  • D.acceptabilityId = 900000000000548007 |preferred|
• D.acceptability
  
  • D.acceptability = "acceptable"
  • D.acceptability = "preferred"

Additional Syntactic Sugar

• FSN
  
  • FSN = "*heart"
    • D.term = "*heart", D.type = "FSN"
    • D.term = "*heart", D.typeId = 900000000000003001 |fully specified name|
  • FSN = "*heart" LANGUAGE X
    • D.term = "*heart", D.type = "FSN", D.acceptability = * LANGUAGE X
      
    • D.term = "*heart", D.typeId = 900000000000003001 |fully specified name|, acceptabilityId = * LANGUAGE X
• synonym
  
  • synonym = "*heart"
    • D.term = "*heart", D.type = "synonym"
      
    • D.term = "*heart", D.typeId = 900000000000013009 |synonym|
      
  • synonym = "*heart" LANGUAGE X
    • D.term = "*heart", D.type = "synonym", D.acceptability = * LANGUAGE X
      
    • D.term = "*heart", D.typeId = 900000000000013009 |synonym|, (D.acceptabilityId = 900000000000549004 |acceptable| OR D.acceptabilityId = 900000000000548007 |preferred|) LANGUAGE X
• synonymOrFSN
  • synonymOrFSN = "*heart"
    • synonym = "*heart" OR FSN = "*heart"
    • D.term = "*heart", (D.type = "synonym" OR D.type = "fullySpecifiedName")
  • synonymOrFSN = "*heart" LANGUAGE X
    • synonym = "*heart" OR FSN = "*heart" LANGUAGE X
    • D.term = "*heart", (D.type = "synonym" OR D.type = "fullySpecifiedName"), D.acceptability = * LANGUAGE X
      
• textDefinition
  
  • textDefinition = "*heart"
    • D.term = "*heart", D.type = "definition"
      
    • D.term = "*heart", D.typeId = 900000000000550004 |definition|
  • textDefinition = "*heart" LANGUAGE X
    • D.term = "*heart", D.type = "definition", D.acceptability = * LANGUAGE X
      
    • D.term = "*heart", D.typeId = 900000000000550004 |definition|, D.acceptabilityId = * LANGUAGE X
• Unacceptable Terms
  • (D.term = "*heart") MINUS (D.term = "*heart", D.acceptability = * LANGUAGE X)

Language preferences using multiple language reference sets

• LRSs that use the same Language tend to use 'Addition' - i.e. child LRS only includes additional acceptable terms, but can override the preferred term

  • E.g. Regional LRS that adds local dialect to a National LRS

  • E.g. Specialty-specific LRS

  • E.g. Irish LRS that adds local preferences to the en-GB LRS

    • 99999900 |Irish language reference set| PLUS |GB English reference set|

• LRSs that define a translation to a different language tend to use 'Replacement' - i.e. child LRS replaces set of acceptable and preferred terms for any associated concept

  • E.g. Danish LRS that does a partial translation of the International Release

    • 999999 |Danish language reference set| ELSE |GB English reference set|

• Any other topics?

The next SLPG meeting will be held in 2 weeks at 20:00 UTC on Wednesday 27th March.