2021-04-08 - SLPG Meeting

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

  • 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| }

The items below are currently on hold

Other Options for Future Progress

1. URIs for draft editions

2. ECL extensions

   1. Primitive/Defined filters → concept filter

   2. Concept+Description filters (e.g. effectiveTime, module, active)

   3. Accessing Refset attributes → (e.g. historical association refsets) → historical ECL

   4. OR use full syntax to be able to query any table (e.g. Relationship table) - ie expand ECL into something more verbose (e.g. SNOMED query language)

3. Template extensions

URIs for Extended Editions

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)

Querying Refset Attributes

Former user (Deleted)

ON HOLD - Proposed syntax to support querying and return of alternative refset attributes (To be included in the SNOMED Query Language)

Returning Attributes

michael lawley

ON HOLD - Proposal (by Michael) for discussion

• 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| 

Reverse Member Of

michael lawley

ON HOLD - Proposal for discussion

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

Expression Templates

Peter Williams

Examples:

[[+id]]: [[1..*] @my_group sameValue(morphology)] { |Finding site| = [[ +id (<<123037004 |Body structure (body structure)| MINUS << $site[! SELF ] ) @site ]] , |Associated morphology| = [[ +id @my_morphology ]]}

• Implementation feedback on draft updates to Expression Template Language syntax

  • Use cases from the Quality Improvement Project:

    • Multiple instances of the same role group, with some attributes the same and others different. Eg same morphology, potentially different finding sites.

Note that QI Project is coming from a radically different use case. Instead of filling template slots, we're looking at existing content and asking "exactly how does this concept fail to comply to this template?"

For discussion:

Is it correct to say either one of the cardinality blocks is redundant? What are the implications of 1..1 on either side? This is less obvious for the self grouped case.

1. Generate the parser from the ABNF and implement in the Template Service

2. User Interface to a) allow users to specify template at runtime b) tabular (auto-completion) lookup → STL

3. Template Service to allow multiple templates to be specified for alignment check (aligns to none-off)

4. Output must clearly indicate exactly what feature of concept caused misalignment, and what condition was not met.

Additional note: QI project is no longer working in subhierarchies. Every 'set' of concepts is selected via ECL. In fact most reports should now move to this way of working since a subhierarchy is the trivial case. For a given template, we additionally specify the "domain" to which it should be applied via ECL. This is much more specific than using the focus concept which is usually the PPP eg Disease.

FYI Michael Chu

Description Templates

Kai Kewley

Query Language
- Summary from previous meetings

Former user (Deleted)

FUTURE WORK

Examples: version and dialect

Notes