Kai Kewley 

ECL 2.2 - published

Has anyone implemented this?

• New "Top" and "Bottom" operators
  • Ontoserver latest has this
    
    
• Alternate Identifiers (for LOINC initially)
  • None yet
  • Kai Kewley get these items scheduled at least with SI

All

ECL Lite

Review draft specification updates:

• 5.1.1 ECL Lite - Brief Syntax
• Appendix F - ECL Lite, Quick Reference
• 6.2 Refinements (label example)

Previous 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) }}, <!!, !!>
• Dot 
• Maybe? {{ C active }}
• Not included:
  • filters
  • cardinality
  • groups
• Declare profile using block/set of language capabilities
• Survey capabilities in existing implementations - any existing capability groups?
• There are parallels in ECL builder and education scopes

Feedback:

• Concrete string matching:
  • Remove?
  • Simplify - only whole string matching - vote passed - However, we want ECL Lite to be a true subset of ECL so need to keep the behaviour aligned.. Simplification of full ECL concrete string matching has been proposed.
    
    
• Removal description filters limits the ability to define a set of concepts by language and dialect
  • Publish this recommendation to mitigate the ECL functionality loss?
    • We recommend that FHIR servers use the displayTerm or Accept Language header to drive term matching, as well as selecting the display term returned.
      
      
• Spec Labels - Use positive labels rather than exclusions
• Appendix - make explict that ECL Lite syntax must work with servers with full - intension is true subset.

Previous 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) }}, <!!, !!>
• Dot - 
• Maybe? {{ C active }}
• Not included:
  • filters
  • cardinality
  • groups
• Declare profile using block/set of language capabilities
• Survey capabilities in existing implementations - any existing capability groups?
• There are parallels in ECL builder and education scopes

See comment here: Re: Discussions (2)

Use cases:

• Exploration for data analytics
• System design - finding existing relevant sets
  • Would require a set of concepts that are all included within a refset
• Browsing

Syntax options:

• ^[refsetId] * {{ M referencedComponentId = 404684003 }}
• @404684003
  • Overlaps with template language
• ? 404684003
  • A bit vague? 
• ^? 404684003
  • Looks intuitive - does not allow filtering which refsets match
  • ^? (<404684003)
  • Behaviour - refsets returned match any concepts in the nested expression.
• ^R 404684003

Michael Lawley 

Simplify concrete string matching.

See comment here: Re: Discussions (2)

We plan to add a "Maintenance Recommendations" page to the ECL guide.

Jeremy Rogers has drafted some content on this topic.

Kai Kewley to share document open for comments + B2i expo video.

Sections to consider adding:

• What does best practice ECL look like - what are the benefits
• ECL comments to record intent
• Existing tooling and features

There is a growing desire to enable access to the SNOMED CT Machine Readable Concept Model via FHIR Terminology Servers.

Use cases:

• To support the creation and validation of Expression Constraint Language queries
• Creation and validation of Postcoordinated expressions using Compositional Grammar

How could this work?

• An extension of the CodeSystem definition?
  • Kai Kewley  TODO: Draft a JSON format to represent the required parts of the MRCM to support this use case.

Other option was considered but rejected because of demand of TS implementation complexity

• 1. Focus concept(s) -> MRCM Domain → set of domain - attributes
  • ConceptMap? - translate focus concept to set of attributes
    • A map would support returning additional information like grouping
• 2. Attribute → Search within attribute range
  • ValueSet - expand URI with attribute ID, filter using text?
  • ValueSet/$expand?url=http://snomed.info/mrcm-attribute/X&filter=append

New implicit URIs?

Consider supporting a reverse lookup - given a focus concept, which attributes can this be used within.

Alejandro Lopez Osornio 

Very little feedback received so far.

An education module could be a way to expose more people to the caveats and best practises.

All

- Aim to round off the guidance - make expression repositories feasible -

An expression repository uses a specific edition and version of SNOMED CT - how can expressions be migrated to a new version?

Use cases of expressions:

• Classifying expressions to discover closest existing precoordinated concept - no requirement for maintenance because expression not recorded in patient record
• Expression is recorded in patient record - need the ability to find relevant patients. This may not work well over time as SNOMED changes.

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:
  • Capture user input (close to user form or template slot inputs) so that templates or transformations can be reapplied.
  • Transform input again against the new substrate:
    • Types of template based authoring / transformation
      • Level 1 postcoordinated transformations. 
      • Implementation defined template - input to template captured and stored outside for the terminology server.
      • Precoordinated template pairs - used by International Authoring teams
  • 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
  • Kai Kewley  What techniques from precoordinated authoring could be reused? How do 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?

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.

Michael Lawley 

Requirement

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. Author/modeller chooses a drug and wants to refine the selection using modification-of substances. 

• Alternate use case: Clinician chooses a drug and wants to refine the selection using modification-of substances
  • The product may not exist - it could be made up.
  • B2i have solved this problem using a real-time recursive search

Background

The modification-of attribute is a transitive property in OWL. Transitive properties have a similar characteristic to an is-a relationships but without stating a subtype relationship.

In SNOMED CT an OWL property chains are used to help organise the hierarchy, allowing products with modified substance to be subsumed into concept groupers defined using the base substance. However in this case the base substance should not be inherited into the product with the modified substance. The base (not modified) version of the substance is found as redundant and removed during NNF calculation. See OWL Guide: 2.5. Generating Necessary Normal Form Relationships from the OWL Refsets

Example property chain: "|Has active ingredient|o |Is modification of|" is a sub-property of  "|Has active ingredient|".

Example hierarchy:

Parent

Child

Because

And Property Chain:

SubObjectPropertyOf(
	ObjectPropertyChain(
		:127489000 |Has active ingredient (attribute)|
		:738774007 |Is modification of (attribute)|
	)
	:127489000 |Has active ingredient (attribute)|
)

.. which results in OWL seeing the non modified ingredient as a property of the concept for the purpose of subsumption.

Finally

TransitiveObjectProperty(:738774007 |Is modification of (attribute)|)

This could be used by the ECL engines.

Solution Options:

• ECL Solution: << 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 Solution: 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 Solution: 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.
  • Pseudo-code: Kai Kewley 
    • In an ECL engine, when building the ECL index:
       
      • Identify which properties are transitive: 

        Set<String> transitiveProperties = owlOntology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY).stream()
               .map(axiom -> axiom.getProperty().getNamedProperty().getIRI().getShortForm())
               .collect(Collectors.toSet());

      • Build up a set of transitive property ancestors:
      • Concept:

        Map<String, Set<String>> transitiveTypeParentMap;
        addRelationship(source, destination, type) {
          if (transitiveProperties.contains(type)) {
            transitiveTypeAncestorMap.get(type).add(destination);
          }
        }
        

• • • • Include transitive property ancestors in ECL index:
        • conceptId: 351000220100 |Minocycline hydrochloride dihydrate (substance)|
        • ancestors: (usual is-a ancestors)
        • 738774007_ancestors: (52886009 |Minocycline hydrochloride (substance)|, 372653009 |Minocycline (substance)|)
        • 738774007_parents: (52886009)

        • 733930001_ancestors: ()
          

        • further fields generated depending on the substrate.
          
          
    • ECL Language could allow something like: 
      • << [+738774007 |Is modification of|] meaning use modification of transitive hierarchy in addition to is-a hierarchy.
      • or << [+*] meaning use all available transitive hierarchies
      • Examples:
        • < |Product| : << |Has active ingredient| = << [+738774007 |Is modification of|] |Amoxicillin|
        • < |Product| : << |Has active ingredient| = << [+*] |Amoxicillin|
          
          
    • JR: At what point do we stop keeping everything stateless and use a reasoner. Should we check our approach / policy?
    • ML: We need a solution that works with all property chains, not just transitive properties... we have that during NNF calculation, we are currently removing it. Perhaps those could be put into the NNF or another file to enable ECL implementations.
    • Kai Kewley and Ale to catchup with Jim and Yong on this.
    • DK: concerned that complexity of ECL would increase and usefulness may decrease? Maybe other architectures are needed to support another way to run snomed queries?
    • JR: Suggests a hybrid ECL engine that can use a reasoner when needed, if the user needs to run a query that requires one and needs the complete answer.
      
    • ALO: Perhaps SI could pre-compute the ECL index in a standard format for use in any ECL engine. A way to reduce the complexity for implementers and also standardise the solution. This could be a file in the release and also an open source tool.
      
      
• New Type of SNOMED Query Engine including an OWL Reasoner (an idea from Jeremy)
  • Alternative approach to pre-computing the ECL index - see row below.

• Content Change Solution: 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.
    
    
  • Current content in numbers:
    • 2,297 Substances have the modification-of attribute
      • Two hop Example: 351000220100 |Minocycline hydrochloride dihydrate (substance)|
    • 89 Substance groupers exist with naming: "Substance-X and/or substance-X derivative"
      • Example: 412053006 |Urea and/or urea derivative (substance)|
    • 37 Product groupers exist with naming: "Product containing substance-X and/or substance-X derivative"

Jeremy and all

• New Type of SNOMED Query Engine including an OWL Reasoner (an idea from Jeremy)
  • Alternative approach to pre-computing the ECL index. The engine would detect when OWL reasoning is required and use OWL to execute specific types of query.. for example queries involving property chains where the NNF is not sufficient.
  • How is this different from postcoordination.
  • What is the gap between ECL and Postcoordination:
    • ECL things not available in PCE engines:
      • ECL filters
      • Refset membership and other fields
      • Cardinality constraints
  • Use Cases:
    • Clinical use case: Refining the selection of a drug (using property chains)
    • Back office / QA use case: Find all concepts with only one parent.
      • B2i support this by extending the spec and allowing cardinality on the is-a relationship.
    • Maybe in the future other attributes will be transitive: caused-by, due-to.