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2021-04-21 - SLPG Meeting

2021-04-21 - SLPG Meeting

2025-Sep-05

Date & Time

20:00 to 21:00 UTC Wednesday 21st April 2021

Location

To join, please register for the April 2021 SNOMED Business Meetings, and login to the event's virtual platform to join the "SNOMED Computable Languages Project Group" meeting

Goals

  • A brief summary of postcoordination discussions so far

  • Explore further examples of transform a close-to-user form expression to classifiable form

  • Consider how a dynamic template-guided approach could work

  • Identify errors and warnings in the transformation processes

Attendees 

  • Chair: @Former user (Deleted)

  • Project Group: @Kai Kewley, @Anne Randorff Højen, @michael lawley, @Ed Cheetham, @Feikje Hielkema (Unlicensed), @Peter Jordan (Unlicensed), @Rob Hausam, @Daniel Karlsson (Unlicensed)

  • Observers: @Former user (Deleted), @Ian Spiers, @Dion McMurtrie, @Márk Czotter , @Andrew Perry (Unlicensed), Roger Jane, @Mikael Nyström, @Patrick McLaughlin, @Former user (Deleted), @Alejandro Lopez Osornio, @Jeff Pierson (Unlicensed) , @David Op De Beeck , @Gábor Nagy , @Former user (Deleted) , @VScoutellas (Unlicensed) , @ines otegui , @Guillermo Reynoso , Shahidah Adilah, @Lea Miharsa , @Renate Schmidt (Unlicensed) , @Libby Antoun (Unlicensed)

  • Staff: @Ian Spiers, @Jon Zammit, @Michael Chu, @Steve Archbold, @Former user (Deleted)

Presentation

How to Process Postcoordinated Expressions - Topics for Discussion

Recording

Computable Languages Project Group - 21st April 2021

Agenda and Meeting Notes

Description

Owner

Notes

Description

Owner

Notes

Welcome and agenda

@Former user (Deleted)

 

Postcoordinated Expression Transformations

 

  • National Cancer Registry use case in the Netherlands

  • Brief recap of transformation process

  • Examples of expression transformation

  • 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|

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

      3. 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 Expression Processes

All

Postcoordinated expression processes

  • Generic

  • Use case specific

    • Mapping (from an interface term)

    • Terminology binding (using an expression template)

    • Natural Language processing

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

  • 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).

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