2021-08-26 - SLPG Meeting

Welcome and agenda

@Former user (Deleted)

Welcome to new attendees

ECL v1.6 - Concept Filters

@Former user (Deleted) and @Daniel Karlsson (Unlicensed)

1. Feedback from Brandon and Guillermo, re querying unpublished content using effectiveTime filter

   • {{ effectiveTime = "20200731" }} or {{ effectiveTime = "" }}     (= and != for "" may return results) (< or > "" always returns 0 results)

2. Should we also add module, effectiveTime and active filters to Descriptions in v1.6?

   • If so, then should we also add 'caseSignificanceId' for completeness (as the only other attribute not covered, except id)

ECL v1.7 - Access to historical refsets

Under consideration (brainstorming)

To leverage the existing memberOf (^) function, which currently only brings back the 'referencedComponentId', rather than the whole 'member' (i.e. row) as you might expect a 'memberOf' function to do. If we defined an expanded form of the current 'memberOf' function, which explicitly shows that by default we're selecting attributeOrder = 0 from the member, then the following 2 ECL would be equivalent.

1. ^ 447562003 |ICD-10 complex map refset|

2. ^ [0] 447562003 |ICD-10 complex map refset|

This would allow us to select other columns  of the refset using the same memberOf function - e.g.

• ^ [5] 447562003 |ICD-10 complex map refset|

And we could then introduce a 'Member filter' with a similar attribute reference - e.g.

• ^ [0] 447562003 |ICD-10 complex map refset| {{ M [5] = "L56.2" }} 

Additional Examples

• Find all the inactive concepts associated by any historical association to a subtype of 195967001 | Asthma (disorder) |

  • ^ < 900000000000522004 | Historical association refset| {{ M [1] =  < 195967001 |Asthma| }}

• Find all the SNOMED CT concepts that map to ICD-10 code "L56.2"

  • ^ 447562003 |ICD-10 complex map refset| {{ M [1] = "L56.2" }}

  • ^ [0] 447562003 |ICD-10 complex map refset| {{ M [5] = "L56.2" }}

• Find the SNOMED CT concept that maps to ICD-10 code "L56.2" with a mapRule = 1 and mapGroup = 1

  • ^ [0] 447562003 |ICD-10 complex map refset| {{ M [1] = #1, [2] = #1, [5] = "L56.2" }}

• Find the reason that concept 67415000 |Hay asthma| was inactivated (answer: 900000000000482003 |Duplicate component|)

  • ^ [1] 900000000000489007 |Concept inactivation indicator attribute value refset| {{ M [0] = 67415000 |Hay asthma| }}

• Find the active concept that is the 'same as' inactivated concept 67415000 |Hay asthma|

  • ^ [1] 900000000000527005 |SAME AS association refset| {{ M [0] = 67415000 |Hay asthma| }}

Questions

• Should we allow more than one column in a refset to be selected? What should the rules be about using this inside a subExpressionConstraint? e.g.

  • ^ [*] 447562003 |ICD-10 complex map refset|

  • ^ [0,5] 447562003 |ICD-10 complex map refset|

• Should we allow the file name (from the respective RF2 file?) and/or the refset attribute concept to be used instead of the attributeOrder? e.g.

  • ^ < 900000000000522004 | Historical association refset| {{ M [1] =  < 195967001 |Asthma| }}

  • ^ < 900000000000522004 | Historical association refset| {{ M [targetComponentId] =  < 195967001 |Asthma| }}

  • ^ < 900000000000522004 | Historical association refset| {{ M [900000000000533001 |Association target component|] =  < 195967001 |Asthma| }}

• Should we allow a 'or self' operator, to make it more efficient to create historical subsets - e.g. the following expression constraint would return all the inactive concepts that were replaced by an equivalent subtype of |Asthma| PLUS all the subtypes of |Asthma| as well. This would be useful for finding all the matches that you may need to look for in a health record.

  • ^ [0] 900000000000527005 |SAME AS association refset| {{ [1] += < 195967001 |Asthma| }}

• Should we allow filters to be nested inside other filters? e.g.

  • ^ 434532547 {{ M [1] = (* {{ term:matches = "chronic" }}) }}

  • ^ [1] 434532547 {{ M [0] = (<< 4756478567 {{ C moduleId = 546576478 }}) }}

Suggestions from last meeting:

• ^ |Refset| {{ M mapTarget = "N.75 }}

• ? |mapTarget| ? 

• mapOrSelfOf {{ refset = 900000000000527005 }} (<< 197710000)

• mapOrSelfOf(sameAs, << 197710000)

• mapOrSelfOf {{ refset = 281000036105, match = #2, result=#0 }} (386938006 OR 100005 OR 70570002)

• mapOf {{ refset = 281000036105, match = #2, result=#0 }} (386938006 OR 100005 OR 70570002)

Reference set descriptor templates (for easy reference)

• 900000000000521006 |Association type reference set|

  • 0 - referencedComponentId (900000000000532006 |Association source component|)

  • 1 - targetComponentId (900000000000533001 |Association target component|)

• 900000000000523009 |POSSIBLY EQUIVALENT TO association reference set|

  • 0 - referencedComponentId (900000000000532006 |Association source component|)

  • 1 - targetComponentId (900000000000533001 |Association target component|)

• 900000000000480006 |Attribute value type reference set| - e.g. 

  • 0 - referencedComponentId (449608002 |Referenced component|)

  • 1 - valueId ( 900000000000491004 |Attribute value|)

• 900000000000489007 |Concept inactivation indicator attribute value reference set|

  • 0 - referencedComponentId (449608002 |Referenced component|)

  • 1 - valueId (900000000000481005 |Concept inactivation value|)

• 900000000000496009 |Simple map reference set|

  • 0 - referencedComponentId (900000000000500006 | Map source concept |)

  • 1 - mapTarget (900000000000499002 | Scheme value |)

• Proposed updates to simple maps:

  • 900000000000496009 |Simple map from SNOMED CT reference set|

    • 0 - referencedComponentId (900000000000500006 | Map source |)

    • 1 - mapTarget (900000000000505001 | Map target |)

  • |Simple map to SNOMED CT reference set|

    • 0 - referencedComponentId (900000000000505001 | Map target |)

    • 1 - mapSource (900000000000500006 | Map source |)

See discussion below "Querying Refset Attributes"

 onlyThe 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}