2019-11-06 - SLPG Meeting

Welcome and agenda

@Former user (Deleted)

• Boolean to be added to SCG, ECL, STS and ETL

  • SCG & ECL - See draft syntax

  • STS & ETL - Use abbreviation "bool"

URIs

@Peter Williams

Expression Templates

@Peter Williams

• Summary of discussions in Malaysia
  
  

  • Published version: https://snomed.atlassian.net/wiki/display/DOCSTS/Template+Syntax+Specification

  • Work in progress: https://snomed.atlassian.net/wiki/display/WIPSTS/Template+Syntax+Specification

    • Added a 'default' constraint to each replacement slot - e.g. default (72673000 |Bone structure (body structure)|)

    • Enabling 'slot references' to be used within the value constraint of a replacement slot - e.g. [[ +id (<< 123037004 |Body structure| MINUS << $findingSite2) @findingSite1]]

    • Allowing repeating role groups to be referenced using an array - e.g. $rolegroup[1] or $rolegroup[!=SELF]

    • Adding 'sameValue' and 'allOrNone' constraints to information slots - e.g. sameValue ($site), allOrNone ($occurrence)

    • Self

    • See changes in red here: 5.1. Normative Specification

  • Recap of discussions in Malaysia regarding exchange of templates

    • ReferencedComponentId

    • Name

    • Version

    • Domain of template - ECL where template should be applied

    • Template itself - ETL

    • Additional rules

    • Mandatory / optional

Examples:

[[+id]]: [[1..*] @my_group sameValue(morphology)] { |Finding site| = [[ +id (<<123037004 |Body structure (body structure)| MINUS << $site[! SELF ] ) @site ]] , |Associated morphology| = [[ +id @my_morphology ]]}

• Implementation feedback on draft updates to Expression Template Language syntax

  • Use cases from the Quality Improvement Project:

    • Multiple instances of the same role group, with some attributes the same and others different. Eg same morphology, potentially different finding sites.

Note that QI Project is coming from a radically different use case. Instead of filling template slots, we're looking at existing content and asking "exactly how does this concept fail to comply to this template?"

For discussion:

Is it correct to say either one of the cardinality blocks is redundant? What are the implications of 1..1 on either side? This is less obvious for the self grouped case.

Road Forward for SI

1. Generate the parser from the ABNF and implement in the Template Service

2. User Interface to a) allow users to specify template at runtime b) tabular (auto-completion) lookup → STL

3. Template Service to allow multiple templates to be specified for alignment check (aligns to none-off)

4. Output must clearly indicate exactly what feature of concept caused misalignment, and what condition was not met.

Additional note: QI project is no longer working in subhierarchies. Every 'set' of concepts is selected via ECL. In fact most reports should now move to this way of working since a subhierarchy is the trivial case. For a given template, we additionally specify the "domain" to which it should be applied via ECL. This is much more specific than using the focus concept which is usually the PPP eg Disease.

FYI @Michael Chu

Description Templates

@Kai Kewley

• Summary of discussions in Malaysia

  • Overview of current use

  • Review of General rules for generating descriptions

    • Removing tags, words

    • Conditional removal of words

    • Automatic case significance

    • Generating PTs from target PTs

    • Reordering terms

  • Mechanism for sharing general rules - inheritance? include?

  • Description Templates for translation

  • Status of planned specification

Expression Constraint Language

@Former user (Deleted)

• Agreement in Malaysia - ECL will add the following term searching syntax (no regex - just wild card and word prefix any order):

{{ term  =  [ termSearchType : ] "String", languageCode = [langCode] }}

Term Search Type

Potential Examples

Use Cases

Questions

Maps and History

@Former user (Deleted)

Recap discussions in Malaysia regarding querying historical patient records - e.g Find all patients with a respiratory disease in the last 10 years. Do we include patients whose records contain |Recurrent chest infection|? (an inactive concept)

Solutions suggested include:

1. Multiple queries - Either run multiple queries against successive releases of SNOMED CT and collate results OR look at the latest snapshot before the given concept was inactivated.

2. Use historical associations - Either create map from inactive to active concepts, OR update EHR to replace inactive concepts with active ones

3. Enhanced transitive closure table - Create an ETCT containing inactive concepts as their last known position

4. Augmented solution - Check the position of each replacement to determine concepts inactivated due to wrong placement

Proposed syntax to support execution of maps (Outstanding question: ECL or Query Language? Scope and packaging needs further discussion)

• 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

  • Checking replacement concept for inactive concept in record

• Potential syntax to consider

  • Functional (Note: Would need a different function for each refset attribute, so not so extensible)

    • mapTarget (|Anatomy structure and part association refset|, << |Upper abdomen structure|)

      • Return the map targets from the given map refset. where the referencedComponent matches the condition

    • mapSource (|Anatomy structure and part association refset|, << |Liver part|)

      • Return the referencedComponent from the given map refset, where the targetId matches the condition.

  • Dot notation + Attribute refinement (Note: Could be added to ECL)

    • |Anatomy structure and part association refset| . |targetComponentId|
      
      

    • |Anatomy structure and part association refset| . |referencedComponent| (Same as ^ |Anatomy structure and part association refset|)

    • ( |Anatomy structure and part association refset|: |referencedComponent| = << |Upper abdomen structure ) . |targetComponentId|

    • ( |Anatomy structure and part association refset|: |targetComponentId| = << |Upper abdomen structure ) . |referencedComponent|
      
      

  • Dot notation + Filters (Note: May be more appropriate in extended query language)
    
    

    • ( |Anatomy structure and part association refset| {{ |referencedComponent| = << |Upper abdomen structure| }} ). |targetComponentId|
      
      

    • ( |Anatomy structure and part association refset| {{ targetComponentId = << |Upper abdomen structure| }} ) . |referencedComponent|
      
      

      • ^ ( |Anatomy structure and part association refset| {{ targetComponentId = << |Upper abdomen structure| }} )
        
        

  • Specify value to be returned (Note: This solution enables the language to return non-concept values)

    • ? 449608002 |Referenced component|?
      734139008 |Anatomy structure and part association refset|
      
      

    • ^ 734139008 |Anatomy structure and part association refset|

    • ? 900000000000533001 |Association target component|?
      734139008 |Anatomy structure and part association refset|

    • ? 900000000000533001 |Association target component|?
      734139008 |Anatomy structure and part association refset|
      {{ 734139008.449608002 |referencedComponent| = << |Upper abdomen structure| }}

    • ? 900000000000533001 |Association target component|?
      734139008 |Anatomy structure and part association refset| :
      449608002 |ReferencedComponent| = << |Upper abdomen structure|

    • (? 900000000000533001 |Association target component|?
      734139008 |Anatomy structure and part association refset| :
      449608002 |ReferencedComponent| = << |Upper abdomen structure|) : |Finding site| = *
      
      

• Reverse memberOf function

  • What refsets is a concept a member of?

Returning attributes

@michael lawley

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| 

Query Language
- Summary from previous meetings

@Former user (Deleted)

Examples: version and dialect

Notes

Examples: where

Notes

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|

Next steps

@Former user (Deleted)

• Discuss and plan next steps

Confirm next meeting date/time

@Former user (Deleted)

Welcome and agenda

@Former user (Deleted)

URIs

@Peter Williams

Expression Templates

@Peter Williams

• Summary of discussions in Malaysia
  
  

  • Published version: https://snomed.atlassian.net/wiki/display/DOCSTS/Template+Syntax+Specification