2021-07-29 - SLPG Meeting

Welcome and agenda

@Former user (Deleted)

Welcome to new attendees

URIs for unpublished content

2.8 URIs for Unpublished Content

2.3 Edition and Version-Relative Component URIs

Enhancements to Template Syntax

Enhancements include:

• Default values

• Slot references

• Interslot dependencies, including 'same value' and 'all or none' constraints

• Upgrade to ECL 1.5 (with description filters)

See

5.1 Normative Specification

7.4 Default Values for Replacement Slots

7.7 Interslot Dependencies

Outstanding features:

• Concept filters - e.g. ability to say that the focus concept of an expression must be primitive (for proximal primitive modelling)

ECL - Concept Filters

Concept Filters - draft updates for review:

• 3.2 Expression Constraint and Query Requirements

• 4. Logical Model

• 4.1 Details

• 5.1 Brief Syntax (Normative)

• 5.2 Long Syntax (Informative)

• 5.3 Informative Comments

• 6.9 Concept Filters

Concept Filters - examples

• definitionStatusId

  • {{ C definitionStatus = primitive }}

  • {{ C definitionStatus = defined }}

  • {{ C definitionStatusId = 900000000000074008 |Not sufficiently defined by necessary conditions definition status| }}

  • {{ C definitionStatusId = 900000000000073002 |Sufficiently defined by necessary conditions definition status| }}

• moduleId

  • {{ C moduleId = 900000000000207008 |SNOMED CT core module| }}

  • {{ C moduleId = 900000000000012004 |SNOMED CT model component module| }}

  • {{ C moduleId = 45991000052106 | SNOMED CT Sweden NRC maintained module| }}

• effectiveTime

  • {{ C effectiveTime = "20210131" }}

  • {{ C effectiveTime <= "20210131" }}

• active

  • {{ C active = 0 }}

  • {{ C active = 1 }}

  • {{ C active = yes }}

  • {{ C active = no }}

• Full example

  • < 404684003 |Clinical finding| {{ C definitionStatus = primitive, effectiveTime <= "20210131", module = (900000000000207008 45991000052106), active = 1 }} {{ D term = "cardio" }}

  • < 404684003 |Clinical finding| {{ C definitionStatusId = 900000000000074008 |Not sufficiently defined by necessary conditions definition status|, effectiveTime <= "20210131", moduleId = 900000000000207008 |SNOMED CT core module|, active = yes}} {{ D term = "cardio" }}

ECL - Access to historical refsets

See discussion below "Querying Refset Attributes"

The items below are currently on hold

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

@Former user (Deleted) , @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| }

    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|  }