Welcome and agenda

All

ECL 2.2 Publication

@Kai Kewley 

ECL 2.2 has been published

• In the ECL Guide: http://snomed.org/ecl

• and official GitHub repository: https://github.com/IHTSDO/snomed-expression-constraint-language

LOINC related things

All

Latest: Terminology Management Group on Saturday (pre-expo) - SNOMED International agreed to publish a URI to access alternate identifier maps via the FHIR API. 

Update on our suggestion "that a Map should be included in the LOINC extension, in addition to alt identifiers. This will enable terminology servers to translate back and forth between LOINC and SNOMED CT codes in the existing standard way."

Previously we added the following warning in the ECL guide in the alternate identifiers section:

• ECL is always evaluated against SNOMED CT concepts. When you run a query using alternate identifiers from another code system only concepts that are in the SNOMED CT representation of that other code system will be returned. For example the descendants of a concept in the SNOMED CT version of a code system is likely to be different from the code system of the alternate identifier.

Meds ECL Requirement

@michael lawley 

Requirement to select a substance or a modification of that substance .... use case: during authoring to prompt the user with all the active ingredient options. Clinician chooses a drug and wants to refine the selection using modification-of substances. 

Although modification-of is a transitive property in OWL, and used during subsumption, the NNF rules state that X relationships are redundant and must not be part of the output.

Options:

• ECL: << 372687004 |Amoxicillin (substance)| 
    OR ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = << 372687004 |Amoxicillin (substance)| )
    OR ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = << 372687004 |Amoxicillin (substance)| ) )
    OR ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = ( << 105590001 |Substance (substance)| : << 738774007 |Is modification of (attribute)| = << 372687004 |Amoxicillin (substance)| ) ) )
    )

  • Pros: Already works, if you know the maximum number of transitive hops

  • Cons: It's not pretty. It may work for modification-of but may not work for longer transitive chains like part-of (body structures)
    
    
    

• NNF change: Keep the modification-of relationships using a new characteristic type to support querying.
  
  

  • Pros: Do not need to increase number of concepts or complexity of ECL engines. 

  • Cons: Big change in the spec? Could be misinterpreted. Seems risky.

• ECL Engine and language change: Build a transitive closure for each transitive property, in the same way that we do for the is-a relationship. We would also need special ECL syntax for this.
  
  

  • Pros: No content change. No classification change.

  • Cons: Slightly more work in ECL engines.

  • Example: @Kai Kewley pseudo-code needed

• Content change: Create a grouper substance to include that substance and all single and multi-hop the modification substances.

  • Pros: Would work without other changes. This technique has precedent in the body structure hierarchy.

  • Cons: Approx. three times the number of substance concepts. May be hard for implementers who want a clean list. Because of the high number (around 2K) of substances with a modification relationship these groups would need to be generated.

Expression Repository Maintenance

All

Potential issues when upgrading the substrate of an expression repository

• Inactive concepts within the expression (focus concept, or attribute name or value)

• Concepts changing hierarchies (semantic tag) - e.g. procedure → observation

  • The has happened for promoted concepts

  • Is this a corner case / rare? Needs analysis. @Kai Kewley 

• Changes to concept model

  • MRCM Changes / Editorial Guide

  • Other modeling changes, perhaps driven by QI consistency efforts

• Will need to classify again to infer different ancestors and attributes

  • Maybe new equivalents 

• MC: This has a lot of overlap with ECL maintenance

• General approaches for identifying issues:

  • FHIR interface could validate the expression again to identify inactive concepts

  • Expand existing value sets to see if there is a radical change in size

  • Content unit tests - needs 

• Strategies to avoid these issues:

  • Types of template based authoring / transformation

    • Precoordinated template pairs - used by International Authoring teams

    • Level 1 postcoordinated transformations. 

  • Use the close to user form, level 1 transformations

    • Create expressions using a proximal parent with minimal modeling, lean on Level 1 transformations (see guide)

    • Expression repository should retransform existing close to user form expressions to classifiable expressions

  • What techniques from precoordinated authoring could be reused? How to international authors update PPP concepts, what automations?

  • Should expression repository be versioned before being upgraded, or should the repository be recreated against the new substrate.

• Strategies to fix content issues:

  • Use historical associations to replace inactive concepts used with an expression

    • What historical association types work, which do not?

    • Same As - Switch concept to target

    • Maybe (possibly equivalent to, possibly replaced by)

      • probably can't use both in an expression

      • need a strategy - may not be able to automate, need an author choice?

ECL EOF marker

Kai

Suggestion from Martin Gall (EMIS Health) https://github.com/IHTSDO/snomed-expression-constraint-language/issues/6

Answer - all known TS implementations call Antlr in a way that doesn't require EOF.

ECL Results - TS consistency

@Jeremy Rogers 

Testing consistency between Snowray (Snow Owl), Ontoserver, Snowstorm. Also using custom made NHS Subset maintenance tool, would like to migrate to a standardised solution.

Questions:

• Should inactive concepts be routinely suppressed from all results?

  • Answer: Inactive concepts should not be included when using hierarchy constraints, because they are not part of the hierarchy. They should be included when using wildcard. The default substrate includes inactive. Same in FHIR. All agree.

  • Action: Check the spec makes this clear. "Default substrate".

  • Known tooling issues: Snowstorm is not behaving well. e.g. ^ xxx AND YYY (where YYY is inactive). Check both native and FHIR API.
    
    
    

• Should inactive concepts be returned as active members of a simple refset?

  • Yes - they are active members - all agree

  • Snowstorm issues - seek example
    
    
    

• Are text definitions and FSNs routinely in scope of any description filters?

  • Text definitions should be left out?

    • Action: change the specification to exclude them by default

    • (FHIR should also exclude these when using "filter" parameter)

  • FSN 

    • KK: The FSN can be unique and help find relevant concepts, the PT should be presented

    • JR: The semantic tag can get in the way - 

    • We don't agree on this

    • Action: Let's add more examples around this.
      
      
      

• Do description filters run by default over inactive descriptions?

  • Inactive are excluded by default in the spec, however there is no way to search active and inactive at once

    • Action: Update ECL Spec to allow searching over active and inactive (apply everywhere, concept, description, members)

      • Suggested syntax update ECL 2.3: 

        ^  816080008 |International Patient Summary|  {{ D active = (true false) }}

      • .. TS should return error if no inactive descriptions loaded

  • Snow Owl searches active and inactive descriptions by default
    
    
    

• Is a “pending move (concept)” description active or inactive?

  • JR: Let's skip this for today. It means the concept is about to be moved to another Edition.
    
    
    

• Are the match and wild description filters case sensitive or not (or, in the case of Ontoserver, do they even work at all?)

  • Group recommends case insensitive matching for "match"

  • Action: Update the ECL guide with this recommendation.

  • Group does not agree about "wild" case sensitivity.

    • Action: Discuss option of adding a modifier to specify case sensitivity - make sure we include Daniel
      
      

  • Action: Consider adding ECL regex filter.
    
    
    

• There are also some interesting edge case differences in the ability of each server to process ECL match description filters if they contain various symbol characters, such as *^% and so on.

  • Action: Discuss updating the ECL spec to add escape character for matching double quotes.

  • MC: Implementation Note - ECL filters commonly include double quotes - when including these in FHIR ValueSet requests make sure they are escaped. Action: Add to ECL Guide and any Snomed FHIR IG.

  • Other characters are perhaps an edge case.

  • More testing needed against know TS.

ML: Some observations: it is interesting to see the number of examples that are querying against terms – the results are not surprising since 1., this is a relatively new part of the spec, and 2., it steps outside the original conception of ECL as a query language that only used defining aspects of concepts as supported by the Concept and Relationship tables.

Expanding the use of the ECL standard

All

Discussion:

How to make it easier to add an ECL capability to more tooling?

• SI already has open source implementations

• The specification is now very large. An ECL Lite profile would reduce the months of effort required to implement the whole specification when starting fresh.

ECL Lite - MVP Scope:

• *, <, <<, >, >>, <!, !>, ^, AND, OR, MINUS, (), {{ +HISTORY-(MIN,MOD,MAX) }}

• Maybe? {{ C active }}

Other Topics

All

• DK: Discussion of postcoordination transformations for Level 1+ or Level 2

  • use of template language?

  • Transformation choice interactive?

• JR: History supplements - Deprecate the WAS-A historic association? Causes implementation issues.

  • Bring in other groups? Editorial EAG

The items below are currently on hold