Welcome and agenda

All

Review Feedback for: Postcoordination Guide (Phase 1)

@Anne Randorff Højen 

Socialise feedback received so far. Talk through any new/outstanding issues raised.

A big thank you for the feedback so far!

• Need for a more thorough introduction to expressions

• Upgrade and maintenance is out of scope for the first version

  • Multiple classifiable forms. (one-to-many cardinality between a CTU and CF)

• Definition status of postcoordinated expressions (vs. correlation between a term and an expression)

Postcoordination Implementation Previews

@Kai Kewley 

A slot to share information about any complete or ongoing postcoordination implementations.

• Kai will show a preview of the work going on in the SnowstormX project.

• Anyone else is welcome to show what they have.

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|

    • Congenital and Acquired - Adding an |Occurrence| of |Congenital| to a focus concept with an abnormal morphology, requires adding a |Pathological process| of |Pathological development process|

      • E.g. |Koilonychia|: |Occurrence| = |Congenital|
        should be
        |Koilonychia|: |Occurrence| = |Congenital|, |Pathological process| = |Pathological developmental process|

    • Situations with Explicit Context 

    1. if the procedure context = |Planned|, then the temporal context should be << |Current of specified time|

       1. If the procedure context = |In progress|, then the temporal context should be << |Current|

       2. If the procedure context = |Performed| or |Done|, then the temporal context should be << |Current or past (actual)|

    • Note: for this use case (of |Procedure with explicit context|) perhaps we just recommend (or require) that the full role group is spelled out.

    • Next steps

      • Representation of the content rules

        • Who creates the complete list of rules and how?

          • What formalism?

          • Determine which are mandatory and which are optional

        • Implementation of content rules - e.g.

          • Guided data entry by pre-populating role groups in expression template based on definition of focus concepts (for design-time use, such as mapping)

          • Mandatory content rules could be added to transform process

Postcoordination Use Case Examples

All

Example 1 - Dentistry / Odontogram

• Requires an expression template to create expressions.

• Resulting expression still requires a transformation to make it classifiable

Example 2 - Terminology binding

• Uses a fixed expression template to combine codes entered into separate fields

• The procedure+laterality example still requires a transformation to make it classifiable

Example 3 - Mapping

• Design-time activity

• Map targets may not be able to be fully represented using concept model attributes

• In many cases, an extension (with primitive concepts) should be recommended where there are gaps in the mapping

• There may be some cases in which postcoordination is helpful (e.g. LOINC to SNOMED CT map)

Example 4 - Natural Language Processing

• Usually run-time activity.

• May require manual confirmation of coding suggestions (unless low clinical risk, eg for suggesting relevant patient records for manual review)

Postcoordination Guidance

@Anne Randorff Højen , @Kai Kewley

Practical Guide to Postcoordination

• Proposal - Use syntax (i.e. braces) to distinguish refinement vs new role group

  • There should be a syntactic distinction between refinement and constructive addition (ie adding a new role group). That is:

    1. 83152002 |Oophorectomy| :  405815000 |Procedure device|  =  122456005 |Laser device|

       • is classified as (i.e. the refinement is added to the role groups in the definition of the focus concept(s)):

         • 83152002 |Oophorectomy| :  
           { 260686004 |Method| = 129304002 |Excision - action|,
              405813007 |Procedure site - Direct| = 15497006 |Ovarian structure|,
              405815000 |Procedure device|  =  122456005 |Laser device| }