Welcome and agenda

• Meeting room in Portugal has been booked - Sunday 25th September 5pm-6:30pm (followed by group dinner?)
• ECL v2.0 is now available in the SNOMED International browser - https://browser.ihtsdotools.org 
• ECL v2.1 is in draft, and will be published this week if no further comments are received.
• URIs for edition plus derivates will be published if no further comments are received
• URIS for language syntax and language instances will be published if no further comments are received.

Proposal - Add the ability to find concepts for a given description id, e.g.

• * {{ D id = 426422019 }}

Please review the following pages:

• http://snomed.org/-ecl 
• 1. Introduction
• 3.2 Expression Constraint and Query Requirements (added "identifier" to filter methods of 'Description filter')
• 4. Logical Model (description identifier filter added to text and diagram)
• 4.1 Details 
• 5.1 Brief Syntax (Normative) - updates in red (including description Id filter, memberFilter reordering, and rule renaming match → matchKeyword)
• 5.2 Long Syntax (Informative) - updates in red (same)
• 5.3 Informative Comments
• 6.8 Description Filters (new Description Id Filter section)

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| "
• X MINUS (> X)
• HOMEWORK - Suggest some syntax for this.
  • ML: leaves(X) or roots(X)

Homework from last week:

• Consider new URI format
  • http://snomed.info/sct/900000000000207008;module/733983009;module/715152001
  • http://snomed.info/sct/900000000000207008/version/20220228;module/733983009/time/20191031;module/715152001/time/20191031
• Review draft: 2.5 URIs for Editions plus Derivatives

Reminder of Problem We're Solving

• SNOMED CT user, who needs to use an edition with one or more derivative packages that are not included in the MDRS for that edition
• For example, how do they specify a substrate for this ECL in a shareable way?
  • ECL: < 404684003 |Clinical finding| AND ^ 733991000 |Nursing| Health Issues Reference Set AND ^ 450970008 |General and family practice reference set| 
• Possible use case: Implicit value sets defined using ECL
• Constraint: Only concepts
• metadata (e.g. module concept with no defining attributes) in package - does not require classification

Solutions considered:

1. Require everyone (e.g. every country) to create their own module and module dependencies to define which derivatives are to be used
   1. Action: Make this process super easy (Q: is that possible? Everyone will need a namespace identifier)
2. International modules created for each (popular) derivative combinations with associated module dependencies
3. A 'flexible' derivative extension module created by SI, with locally defined module dependencies
4. URI format to include edition plus derivate composition, e.g.
   1. http://snomed.info/sct/900000000000207008/version/20220228;module/733983009/time/20191031;module/715152001/time/20191031
5. Terminology services endpoints to check (a) what modules are required to execute a given ECL, and (b) what modules are currently loaded

Proposal

• Publish format of URIs for language instances
  • 2.9 URIs for Language Syntaxes
  • 2.10 URIs for Language Instances
  • 2.11 Comparing URIs for Equality of Reference
• Implement resolution of URIs for ECL instances → SNOMED International browser
• Update ECL specification, to create clickable ECL execution

• 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|)

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

• 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

• 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

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)

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| }
    2. 83152002 |Oophorectomy| :  { 405815000 |Procedure device|  =  122456005 |Laser device| }
       • is classified as:
         • 83152002 |Oophorectomy| :  
           { 260686004 |Method|= 129304002 |Excision - action|,
              405813007 |Procedure site - Direct|= 15497006 |Ovarian structure|},
           {  405815000 |Procedure device|  =  122456005 |Laser device| }
  • However, for attributes which are always self-grouped - i.e. Priority, Due to, After, Before, During, Clinical course, Temporally related to, and all Observable entity attributes (see Relationship Group), these must always be put into their own role group:
  • 1. 125605004 | Fracture of bone |: 42752001 | Due to (attribute) | = 1912002 | Fall |
       
       •  is classified as:
         • 125605004 | Fracture of bone |: { 42752001 | Due to (attribute) | = 1912002 | Fall | }
         • or
         • 125605004 | Fracture of bone |: 
           { 363698007 |Finding site|= 272673000 |Bone structure|,
             116676008 |Associated morphology |= 72704001 |Fracture|}
           { 42752001 | Due to (attribute) | = 1912002 | Fall | }
• Proposal: Expression forms needed for this (see 3.4 Transforming Expressions)
  • Close to user form - e.g. 83152002 |Oophorectomy| :  405815000 |Procedure device|  =  122456005 |Laser device|
  • Canonical close to user form - e.g. 83152002:405815000=122456005
  • Classifiable form (SCG) - e.g. 83152002:{260686004=129304002,405813007=15497006,405815000=122456005}
    • PLUS Classifiable form (OWL) - e.g.  
      • EquivalentClasses(:123063
           ObjectIntersectionOf (:71388002
               ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf( ObjectSomeValuesFrom(:260686004 :129304002)
               ObjectSomeValuesFrom(:405813007 :15497006))))
  • Necessary normal form - e.g. 83152002+416376001:{260686004=129304002,405813007=15497006,405815000=122456005}
    • PLUS Necessary normal form (tables)
      • Relationships:
        • (123063 116680003 83152002) - 0
        • (123063 260686004 129304002) - 0 
        • (123063 405813007 15497006) - 1
        • (123063 405815000 122456005) - 1
  • Primitive expressions - "<<<" (only useful in a mapping context) → .... relies on the assigned identifier (which are necessarily semantically unique).

• Proposed Transformation Rules - Refinements (in valid domain of focus concepts)
  Close-to-user-form - IF the grouping of the refinement is not concept model valid THEN
            If there is a single (non-self-grouped) role group in the definition of the focus concept, then any ungrouped (but groupable) refinements are merged with this role group
            If there is more than one (non-self-grouped) role group in the definition then flag as ambiguous and require refinement
                         NEED TO FIND a realistic clinical example where this may occur // Prevent failing cases from coming up // use template
                         ALTERNATIVE: Refinement is applied to all (non-self-grouped) role groups in the definition
            Self-grouped attributes in the refinement are grouped on their own - i.e. Priority, Due to, After, Before, During, Clinical course, Temporally related to, and all Observable entity attributes (see Relationship Group)
           Self-grouped attributes in the definition of the focus concept(s) are left unchanged
• 1. Single refinement
     83152002 |Oophorectomy| :  405815000 |Procedure device|  =  122456005 |Laser device|
     • →  83152002 |Oophorectomy| :
              { 260686004 |Method|  =  129304002 |Excision - action| ,
                405813007 |Procedure site - direct|  =  15497006 |Ovarian structure|,
                405815000 |Procedure device|  =  122456005 |Laser device|  }
  2. Two groupable refinements
     83152002 |Oophorectomy| :  405815000 |Procedure device|  =  122456005 |Laser device|, 363700003 |Direct morphology| = 367643001 |Cyst |
     • →  83152002 |Oophorectomy| :
     •        { 260686004 |Method|  =  129304002 |Excision - action| ,
                405813007 |Procedure site - direct|  =  15497006 |Ovarian structure|,
                405815000 |Procedure device|  =  122456005 |Laser device| ,
                363700003 |Direct morphology| = 367643001 |Cyst | }
  3. One groupable refinement with one self-grouped refinement
     83152002 |Oophorectomy| :  405815000 |Procedure device|  =  122456005 |Laser device|, 260870009 |Priority| = 394849002 |High priority|
     
     • →  83152002 |Oophorectomy| :
     •        { 260686004 |Method|  =  129304002 |Excision - action| ,
                405813007 |Procedure site - direct|  =  15497006 |Ovarian structure|,
                405815000 |Procedure device|  =  122456005 |Laser device| }
              { 260870009 |Priority (attribute)| = 394849002 |High priority| }
  4. Refinement attribute matches (or subsumed by) attribute in focus concept's definition
     83152002 |Oophorectomy| : 260686004 |Method|  = 277261002 |Excision biopsy (qualifier value)|
     • → 83152002 |Oophorectomy| :
     •        { 260686004 |Method|  =  129304002 |Excision - action| ,
     •          260686004 |Method|  =  277261002 |Excision biopsy (qualifier value)| ,
     •          405813007 |Procedure site - direct|  =  15497006 |Ovarian structure| }
  5. Refinement explicitly in role group
     83152002 |Oophorectomy| :  { 260686004 |Method|  =  281615006 | Exploration - action | , 405813007 |Procedure site - direct|  =  367643001 |Cyst | }
     • →  83152002 |Oophorectomy| :
     •        { 260686004 |Method|  =  129304002 |Excision - action| ,
                405813007 |Procedure site - direct|  =  15497006 |Ovarian structure| },
              {  260686004 |Method|  =  281615006 | Exploration - action | , 
                405813007 |Procedure site - direct|  =  367643001 |Cyst |}

• Proposed Transformation Rules - Refinements (NOT in valid domain of focus concepts)
  Close-to-user-form - IF the refinement's attribute is not valid for the domain of the focus concept THEN
            If there is a single role group in the definition of the focus concept, which has an attribute value in the domain of the refinement's attribute THEN nest the relevant attribute value with the refinement added to the attribute value
                   (Note: It doesn't matter if the role group is self-grouped or not (see example 1 below)
          If there is more than one role group in the definition of the focus concept, which has an attribute value in the domain of the refinement's attribute THEN  (non-self-grouped) role group in the definition then flag as ambiguous and require refinement

• 1. Left aural temperature
     • 415974002 |Aural temperature|: 272741003 |Laterality| = 7771000 |Left|
     • → 415974002 |Aural temperature|: {704327008 |Direct site| = (42859004 |Ear drum|: 272741003 |Laterality| = 7771000 |Left|)}
  2. Malignant tumor of right ovary
     

     • 363443007 |Malignant tumor of ovary|: 272741003 |Laterality| = 24028007 |Right|

     • → 363443007 |Malignant tumor of ovary|: 
     •      { 116676008 |Associated morphology| = 367651003 |Malignant neoplasm of primary, secondary or uncertain origin|,
               363698007 |Finding site| = ( 15497008 |Ovarian structure| :  272741003 |Laterality| = 24028007 |Right| ) }
• Other Example - Emergency excision of appendix
  1.     80146002 | Excision of appendix | :
            260870009 |Priority|  =  25876001 |Emergency|
• Other Example - Fracture of bone
• 1. 125605004 |Fracture of bone|: 363698007 |finding site| = 84167007 |Foot bone|
  2. 125605004 |Fracture of bone|: {363698007 |finding site| = 84167007 |Foot bone| }
  3. 125605004 |Fracture of bone|: {116676008 |Associated morphology| = 72704001 |Fracture|,
                                                             363698007 |finding site| = 84167007 |Foot bone| }
  4. 64572001 |Disease|: {116676008 |Associated morphology| = 72704001 |Fracture|,
                                                             363698007 |finding site| = 84167007 |Foot bone| }

ON HOLD - How to refer to an 'extended edition' using a URI - e.g. "International Edition plus the following 2 nursing modules: 733983009  |IHTSDO Nursing Health Issues module|and 733984003 |IHTSDO Nursing Activities module|

Use Case - Need to execute an ECL, that refers to "^ 733991000 | Nursing Health Issues Reference Set (foundation metadata concept) |" and/or "^ 733990004 | Nursing Activities Reference Set (foundation metadata concept) |", where the substrate includes the international edition, plus the modules that include these reference sets

July 2020 International Edition URI: http://snomed.info/sct/900000000000207008/version/20200731

July 2020 International Edition + nursing modules URI ?? - For example:

• http://snomed.info/sct/900000000000207008/version/20200731/module/733983009/time/20200131/module/733984003/time/20200131
  
• http://snomed.info/sct/900000000000207008/version/20200731/modules/733983009:733984003
  
• http://snomed.info/sct/900000000000207008:733983009:733984003/version/20200731:20190731:20200131
  
• Canonical order? Or order doesn't matter?
• Constraints on what can go in the additional packages (only refsets and their metadata)

Expression Templates

• ON HOLD
• Previous discussion (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