SNOMED CT Languages Project Group

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Date & Time

20:00 to 21:00 UTC Wednesday 4th November 2020

Location

Zoom meeting link (password: 764978)

Goals

  • Start development of postcoordination guidance

Attendees 

Apologies

Daniel Karlsson , Ed Cheetham

Agenda and Meeting Notes

Description
Owner
Notes

Welcome and agenda

Linda Bird

NOTE: Next meeting to be held on Wednesday 18th November

Postcoordination Guidance

Linda Bird , Anne Randorff Højen , Kai Kewley

Practical Guide to Postcoordination

  • Discuss use cases for postcoordination
    • Mapping local codes to postcoordinated expressions
    • Natural language processing – e.g. ""
    • Semantic interoperability (e.g. between FHIR resource instances)
    • Comparing 2 clinical meanings for equivalence and subsumption
      • E.g. Extemporaneous drug formulations
  • Comments
    • Should there be a syntactic distinction between refinement and constructive addition (ie adding a new role group)
  • Agree on approach and next steps - potentially including:
    • Agree on list of expression forms that need defining - 3.4 Transforming Expressions
    • Discuss different types of transformations required
    • Explain transformation steps



Other Options for Future Progress
  1. Postcoordination and close-to-user transformations
  2. URIs for draft editions
  3. 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)
  4. Template extensions
URIs for Extended Editions

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 AttributesLinda Bird

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

  • Example use cases
    • Execution of maps from international substance concepts to AMT substance concepts
    • Find the anatomical parts of a given anatomy structure concept (in |Anatomy structure and part association reference set)
    • Find potential replacement concepts for an inactive concept in record
    • Find the order of a given concept in an Ordered component reference set
    • Find a concept with a given order in an Ordered component reference set
  • Potential syntax to consider (brainstorming ideas)
    • SELECT ??
      • SELECT 123 |referenced component|, 456 |target component|
        FROM 799 |Anatomy structure and part association refset|
        WHERE 123 |referenced component| = (< 888 |Upper abdomen structure| {{ term = "*heart*" }} )
      • SELECT id, moduleId
        FROM concept
        WHERE id IN (< |Clinical finding|)
        AND definitionStatus = |primitive|
      • SELECT id, moduleId
        FROM concept, ECL("< |Clinical finding") CF
        WHERE concept.id = CF.sctid
        AND definitionStatus = |primitive|
      • SELECT ??? |id|, ??? |moduleId|
        FROM concept ( < |Clinical finding| {{ term = "*heart*" }} {{ definitionStatus = |primitive| }} )
      • Question - Can we assume some table joins - e.g. Concept.id = Description.conceptId etc ??
      • Examples
        • Try to recast relationships table as a Refset table → + graph-based extension
        • Find primitive concepts in a hierarchy
    • ROW ... ?
      • ROWOF (|Anatomy structure and part association refset|) ? (|referenced component| , |target component|)
        • same as: ^ |Anatomy structure and part association refset|
      • ROWOF (|Anatomy structure and part association refset|) . |referenced component|
        • same as: ^ |Anatomy structure and part association refset|
      • ROWOF (|Anatomy structure and part association refset|) {{ |referenced component| = << |Upper abdomen structure|}} ? |targetComponentId|
      • ROWOF (< 900000000000496009|Simple map type reference set| {{ term = "*My hospital*"}}) {{ 449608002|Referenced component| = 80581009 |Upper abdomen structure|}} ? 900000000000505001 |Map target|
        • (ROW (< 900000000000496009|Simple map type reference set| {{ term = "*My hospital*"}}) : 449608002|Referenced component| = 80581009 |Upper abdomen structure| ).900000000000505001 |Map target|
    • # ... ?
      • # |Anatomy structure and part association refset| ? |referenced component\
      • # (|Anatomy struture and part association refset| {{|referenced component| = << |Upper abdomen structure|) ? |targetComponentid|
    • ? notation + Filter refinement
      • |Anatomy structure and part association refset| ? |targetComponentId|
      • |Anatomy structure and part association refset| ? |referencedComponent| (Same as ^ |Anatomy structure and part association refset|)
        (|Anatomy structure and part association refset| {{ |referencedComponent| = << |Upper abdomen structure}} )? |targetComponentId|
      • ( |Anatomy structure and part association refset| {{ |targetComponentId| = << |Upper abdomen structure}} ) ? |referencedComponent|
      • ( |My ordered component refset|: |Referenced component| = |Upper abdomen structure ) ? |priority order|
      • ? |My ordered component refset| {{ |Referenced component| = |Upper abdomen structure| }} . |priority order|
      • ? |My ordered component refset| . |referenced component|
        • equivalent to ^ |My ordered component refset|
      • ? (<|My ordered component refset|) {{ |Referenced component| = |Upper abdomen structure| }} . |priority order|
      • ? (<|My ordered component refset| {{ term = "*map"}} ) {{ |Referenced component| = |Upper abdomen structure| }} . |priority order|
      • REFSETROWS (<|My ordered component refset| {{ term = "*map"}} ) {{ |Referenced component| = |Upper abdomen structure| }} SELECT |priority order|
    • Specify value to be returned
      • ? 449608002 |Referenced component|?
        734139008 |Anatomy structure and part association refset|
      • ^ 734139008 |Anatomy structure and part association refset| (Same as previous)
      • ? 900000000000533001 |Association target component|?
        734139008 |Anatomy structure and part association refset|
      • ? 900000000000533001 |Association target component|?
        734139008 |Anatomy structure and part association refset| :
        449608002 |ReferencedComponent| = << |Upper abdomen structure|
      • ? 900000000000533001 |Association target component|?
        734139008 |Anatomy structure and part association refset|
        {{ 449608002 |referencedComponent| = << |Upper abdomen structure| }}
      • (? 900000000000533001 |Association target component|?
        734139008 |Anatomy structure and part association refset| :
        449608002 |ReferencedComponent| = (<< |Upper abdomen structure|) : |Finding site| = *)
Returning AttributesMichael Lawley

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| 

    • 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|)
Reverse Member OfMichael Lawley

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 G. Williams

  • ON HOLD WAITING FROM IMPLEMENTATION FEEDBACK FROM INTERNAL TECH TEAM
  • WIP version - https://confluence.ihtsdotools.org/display/WIPSTS/Template+Syntax+Specification
      • Added a 'default' constraint to each replacement slot - e.g. default (72673000 |Bone structure (body structure)|)
      • Enabling 'slot references' to be used within the value constraint of a replacement slot - e.g. [[ +id (<< 123037004 |Body structure| MINUS << $findingSite2) @findingSite1]]
      • Allowing repeating role groups to be referenced using an array - e.g. $rolegroup[1] or $rolegroup[!=SELF]
      • Allow reference to 'SELF' in role group arrays
      • Adding 'sameValue' and 'allOrNone' constraints to information slots - e.g. sameValue ($site), allOrNone ($occurrence)
      • See changes in red here: 5.1. Normative Specification

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:

 [[0..1]] { [[0..1]]   246075003 |Causative agent|  = [[+id (<   410607006 |Organism| ) @Organism]] }

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.

Road Forward for SI

  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 TemplatesKai Kewley
  • 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
Query Language
- Summary from previous meetings




Linda Bird

FUTURE WORK

Examples: version and dialect

Notes

    • Allow nested where, version, language
    • Scope of variables is inner query

  File Modified
File general dentistry diagnostic refset members.svg 2020-Nov-03 by Linda Bird
File odontogram refset members.svg 2020-Nov-03 by Linda Bird


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