Welcome and agenda

All

Update to URI for Subontologies

Alejandro

2.11 URIs for Subontologies (page is in draft at this time)

Postcoordination guidance

Implementation Team

Timeline for review

Postcoordination Profile Levels

Implementation Team

Continue discussion of transformations in Level 2 to agree recommended postcoordination profile for phase 1

• Level 1 - TS expects expressions to be fully MRCM compliant

• Level 2 - TS permits some non-MRCM compliant expressions for limited, predefined patterns

• Level 3 - TS uses generic transformations, but gives warning/errors if transformation is "risky" (note: requires MRCM compliance after transformation)

• Level 4 - TS uses generic transformations, but only gives warning/error if expression is not MRCM compliant after transformation

Discussion:

DK: Concern that once above level 1 transformation may happen without the user wanting it - because Close-to-User-Form and Classifiable-Form look the same.

Mitigation options:

• Request could ask for transformation? How would this fit in with FHIR?

• Syntax could include definition status (e.g. “===”) explicitly when transformation not wanted? Would fit with FHIR. 

  • The group like this option

• Something in the response to detail any transformation?

• Separate endpoint.

Expression communication - which form to send for interoperability?

• Send classifiable form? (After transformation)

  • Receiving system wouldn’t have to support the same level of transformation

• Send close to user form?

  • More robust against modeling change

  • Could be interpreted manually

• Must send the code system version that the expression repository is dependent on

Transformation documentation

• How should we express the agreed transformations?

  • Pairs of templates?

    • Limits of capability not known

  • How else?

    • English and pseudocode

      • Group preferred this option

• How do we categorize a transformation as level 2?

  • Only transformations that can never go wrong (an undesired transformation without an error)

  • If the associated precondition are not all true then there is an error and the transformation fails

Transformations for Phase 1, based on Level 2:

• 1. Procedure + Laterality

•  

  •  

    • Precondition: Procedure must have exactly one? attribute with a body structure. The body structure must be lateralisable (this part of the validation could happen before or after transformation).

      • Could we allow lateralization of multiple body structures?

        • Perhaps direct sites if they are the same body structure?

        • Will this classify badly?

        • Concern that the indirect site should not be lateralized

        • TODO: find cases where applying to direct and indirect would be wrong

• 2. Findings + Laterality

•  

  •  

    • Precondition: Same as above

• 3. Finding + context attribute? (More discussion needed)

• 4. Disorder + severity / course?

  • TODO: Analysis of common sets needed - @Anne Randorff Højen 

• 5 Procedure + priority / intent?

  • TODO: Analysis of common sets needed

• 6. Any concept + specialisation of one existing attribute

•  

  • Precondition: The attribute must already exist with:

    • the same or ancestor attribute type

    • The same or supertype of the specialisation. The attribute may or may not be grouped.

  • Allow specialisation of attribute type? Drugs model? E.g. “Active ingredient” > “Precise active ingredient”. Procedure site > direct site

  • Considering allowing refining multiple existing attributes, using one attribute refinement?

    • should there be no descendant concepts that have refined a subset of the existing attributes? Too complex?

    • TODO find any cases where this is a bad idea

    • Maybe Level 3

• More to follow...

The items below are currently on hold

URIs for language instances

ECL v2.2 Proposal

Find the leaves of a set of concepts - example use case (find the proximal set in the international core / or in the IPS) - example:

• Example use cases

  • Proximal ancestors in a specific module: (  > |concept|  {{ C moduleId = 1234 }} ) MINUS ( > (> |concept| {{ moduleId = 1234 }}) )

    • X =   "> |concept| {{ C moduleId = 1234 }}"

  • Leaf nodes:   < |concept| MINUS (> (< |concept|))

    • X =  " < |concept| "

  • Removing any redundant concepts (ie subsumes another concept) from a set of concepts

    • ^ |ref set| MINUS (> (^ |ref set|)

      • X = " ^ |ref set| "

Find the root concepts of a set of concepts - example use case (find the proximal set in the international core / or in the IPS) - example:

•  

  • Example use cases for 

    • Root nodes of an extension module:   (< |concept| {{ module = X}}) MINUS (< (< |concept| {{ module = X}}))

      • X =  " < |concept| "

    • Only the 'root' concepts from a set of concepts

      • ^ |ref set| MINUS (< (^ |ref set|)

        • X = " ^ |ref set| "

• X MINUS (> X)

• HOMEWORK - Suggest some syntax for this.

  • leaves(X) - eg

    • leaves (> |concept| {{ C moduleId = 1234 }} )

    • leaves (< |concept|)

    • leaves (^ |refset|)

    • Pros: Easy to read

    • Cons: More consistent with the long form of ECL rather than the short form

  • L(X)    - eg

    • L (> |concept| {{ C moduleId = 1234 }} )

    • L (< |concept|)

    • L (^ |refset|)

    • Pros: Easy to type

    • Cons: L could mean anything? English specific.

  • _ (X)   - eg

    • _ (> |concept| {{ C moduleId = 1234 }} )

    • _ ( < |concept|)

    • _ (^ |refset|)

  • !_

    • Pros: Looks like lowest / floor

    • Cons: No equivalent highest / top symbol

  • !<

    • Pros: Easy to type. Familiar looking syntax.

    • Cons: May be too similar to children of - confusing?

  • !!< (bottom) !!> (top)

    • Pros: Easy to type. Familiar syntax. Different enough from <! and >!

    • Cons: None that I can think of

  • ⌊ X ⌋  (bottom),  ⌈ X ⌉  (top)

    • Pros: Matches existing mathematical syntax for the Floor and Ceiling functions, which have similar meaning.

    • Cons: Could be challenging for some people to type on the keyboard

  • <!!  (bottom),  >!!  (top)

    • Pros: Easy to type. Familiar looking syntax. Won't be mistaken for children of. Both top and bottom can be represented clearly.

    • Cons: Too long? (Makes operators three characters rather than two).

ECL v2.1 - Requirement proposals (to be archived)

All

Potential requirements for ECL v2.1 - Discussion and brainstorming

• Daniel's comments

  • An explanation of the results of this ECL: <<385540001 |Olmesartan containing drug| MINUS (<<763158003 |Medicinal product (product)|: { <<127489000 |Active ingredient| = <<412259001 |Olmesartan| })

  • Cardinality of focus concepts is not supported (Example use case: which concepts have 2 or more stated IsAs)

  • (Related) Using 116680003 |Is a (attribute)| in refinement/dotted expressions, e.g. 395026007.116680003, 395026007:[2..*]116680003=*
    Snowstorm and Ontoserver give different results for dotted expressions.
    https://snowstorm-alpha.ihtsdotools.org/snowstorm/snomed-ct/fhir/ValueSet/$expand?_format=json&count=10&url=http:%2F%2Fsnomed.info%2Fsct%3Ffhir_vs%3Decl%2F395026007.116680003
    https://r4.ontoserver.csiro.au/fhir/ValueSet/$expand?_format=json&count=10&url=http:%2F%2Fsnomed.info%2Fsct%3Ffhir_vs%3Decl%2F395026007.116680003

  • We've done history for concepts but not for any other components...

    Realizing the information on inactive concepts is different and more extensive from other components, {{ + HISTORY... }} is (just) sugar and maybe just maybe there might be reasons to sprinkle other components with this sweetness (or not).

    Examples: previously active refset members (and their fields), previously active descriptions (e.g. Refers to association refset), ...

• Context supplements - e.g.

  • << 56265001 |Heart disease|  {{ + CONTEXT }} – This syntax is too general, as there is a risk of including absent finding, not-done procedure and family history

  • << 56265001 |Heart disease| {{ + CONTEXT-DEFAULT }} ? – What would this mean?

    • Brief form:

      • [[@ecl_query]] {{ + Context (Temporal = [[ @temporal_value]]}}

    • Expanded form:

      • [[ @ecl_query ]] OR  (< 243796009 |Situation with explicit context|:
                { ( 246090004 |Associated finding| = ( [[ @ecl_query ]] ) 
                       OR |Associated procedure| = ( [[ @ecl_query ]] )
                 ( |Procedure context| = |Done| OR |Finding context| = |Known present|),
                    |Subject relationship context| = |Subject of record|,
                     |Temporal context| = [[ @temporal_value ]] } )

    • Example 1: << |Heart procedure| {{ + Context (Temporal = *) }}

      • <<  |Heart procedure| OR  (< 243796009 |Situation with explicit context|:
                { 246090004 |Associated finding| = << 56265001 |Heart disease|,
                    |Procedure context| = |Done|,
                    |Subject relationship context| = |Subject of record|,
                     |Temporal context| = * } )

      • Example 2: (<< |Heart disease| OR << |Heart procedure| ) {{ + Context (Temporal = *) }}

        • <<  |Heart procedure| OR  (< 243796009 |Situation with explicit context|:
                  { ( 246090004 |Associated finding| = (<< |Heart disease| OR << |Heart procedure| ) 
                         OR |Associated procedure| = ( << |Heart disease| OR << |Heart procedure| ) )
                      ( |Procedure context| = |Done| OR |Finding context| = |Known present|),
                      |Subject relationship context| = |Subject of record|,
                       |Temporal context| = * } )

    • << 56265001 |Heart disease| {{ + Context (Temporal = *, FindingContext=<<|Known present| }}

      • Will return all types of heart disease, plus concepts like 394886001 |Suspected heart disease (situation)|, and 429007001 |History of cardiac arrest (situation)|

      • Expands to: 

        • << 56265001 |Heart disease| OR
            (< 243796009 |Situation with explicit context|:
                  { 246090004 |Associated finding| = << 56265001 |Heart disease| } )

  • However, you may want to exclude (or include) specific contexts - for example:

    1. To ensure that the finding was about the subject of the record (and not a family history, e.g. to exclude 429959009 |Family history of heart failure (situation)|), you could say:

       • << 56265001 |Heart disease|  {{ + CONTEXT (relationship = 410604004 |Subject of record| }}

    2. To ensure that the finding was 'Known present' (e.g. to exclude 394926003 |Heart disease excluded (situation)|), you could say:

       • << 56265001 |Heart disease|  {{ + CONTEXT (finding_context = << 410515003 |Known present| }}

    3. To ensure that the finding was about the subject of the record AND known present, you could say:

       • << 56265001 |Heart disease|  {{ + CONTEXT (relationship = 410604004 |Subject of record|, 
                                                                                                   finding_context = << 410515003 |Known present| }}

    4. ?? Is there any use case for restricting adding temporal context? (e.g. temporal != << 410513005 |In the past|)

  • Is any more syntactic sugar required? E.g.

    • {{ + CONTEXT (relationship = self, finding context = present, temporal != past) }}

    • {{ + CONTEXT (self, present, ! past) }}

  • Other ideas? Common profiles?

• --------------------------

• Ability to return attribute types (see proposal below)

  • [ attributes ] << 125605004 |Fracture of bone (disorder)|

  • << 125605004 |Fracture of bone (disorder)| . Attributes

  • << 125605004 |Fracture of bone (disorder)| . (<< 125605004 |Fracture of bone (disorder)| . Attributes )

  • [ attribute, value] << 125605004 |Fracture of bone (disorder)|

• -------------------------

• Reverse membership (see below)

  • Which reference sets "contain" the given concept(s) - e.g. 421235005 |Structure of femur|?

    • 421235005 |Structure of femur| . Refsets

    • 421235005 |Structure of femur|. Refsets [ referencedComponentId ]

    • 421235005 |Structure of femur| . Refsets [ targetComponentId ]

• --------------------------

• Other?

Returning Attributes

@michael lawley

• 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|)

Reverse Member Of

@michael lawley

What refsets is a given concept (e.g. 421235005 |Structure of femur|) a member of?

• Possible new notation for this:

  • ^ . 421235005 |Structure of femur|

  • ? X ? 421235005 |Structure of femur| = ^ X

Postcoordination Topics

• Discuss feedback on transformation implementation

  • Resources

    • Expression transformation service generates the classifiable form and the necessary normal form from a close to user form expression

    • Contribute your expression examples and write your feedback for consideration and discussion

  • Recap of SNOMED on FHIR discussions

    • What is the functionality scope of a terminology server that supports postcoordination? For example, does it include:

      • Classifying multiple expressions in a single substrate? What are the use cases for this?

      • Assigning (local) identifiers to expressions? What are the use cases for this?

      • Autogenerating or assigning a term to an expression? What are the use cases for this?

    • Does a terminology server that supports postcoordination, include all the functions of an expression repository?

    • What is the relationship between a terminology server that supports postcoordination, and an expression repository?

  • Outstanding questions

    • What are the pros and cons of extending SCG to allow an expression as the focus of a postcoordinated expression?

      • Note: This was raised in context of a NNF generated over a postcoordinated substrate, where the proximal parent is an expression

    • Example of using expressions in focus concept

      • ( 125605004 |Fracture of bone|:363698007 |finding site| = 84167007 |Foot bone| ) : 
        272741003 |Laterality| = 7771000 |Left|

      • 125605004 |Fracture of bone|:363698007 |finding site| = 84167007 |Foot bone| , 
        272741003 |Laterality| = 7771000 |Left|

    • What is the expected NNF when classifying an expression that is equivalent to a precoordinated concept? For example:

      • Expression that is equivalent to 111273006 |Acute respiratory disease|

      • 64572001 | Disease (disorder) | :
        {263502005 |Clinical course (attribute)| = 424124008 |Sudden onset AND/OR short duration (qualifier value)|}
        {363698007 |Finding site (attribute)| = 89187006 |Airway structure (body structure)|}

      • Options:

        1. 111273006 |Acute respiratory disease| :
           {263502005 |Clinical course| = 424124008 |Sudden onset AND/OR short duration|}
           {363698007 |Finding site| = 89187006 |Airway structure|}

        2. 50043002 |Disorder of respiratory system (disorder)| +
           2704003 |Acute disease (disorder)| :
           {263502005 |Clinical course| = 424124008 |Sudden onset AND/OR short duration|}
           {363698007 |Finding site| = 89187006 |Airway structure|}

        3. Other?

  • Recap of internal discussions with Content Team

    • Inter-attribute dependencies

    • Grouping rules

Dynamic Templates

• Continue discussion on dynamic templates

  • Inter-attribute dependencies

    • Acute/Chronic and Inflammation - Adding a clinical course requires specializing the inflammation morphology 

      • E.g. |Pyelonephritis| : |Clinical course| = |Chronic|
        should be
        |Pyelonephritis| : |Clinical course| = |Chronic|, |Associated morphology| = |Chronic inflammation|

      • E.g. |Pyelonephritis| : |Clinical course| = |Sudden onset AND/OR short duration|
        should be
        |Pyelonephritis| : {|Clinical course| = |Sudden onset AND/OR short duration||, |Associated morphology| = |Acute inflammation|

    • Infectious Causative Agents - Adding a |causative agent| = |Domain Bacteria| or |Virus| requires adding a |Pathological process| = |Infectious process|

      • E.g. |Nephritis|: |Causative agent| = |Domain bacteria|
        should be
        |Nephritis|: |Causative agent| = |Domain bacteria|, |Pathological process| = |Infectious process|