SNOMED CT Languages Project Group

Space shortcuts

Page tree

Date & Time

20:00 to 21:00 UTC Wednesday 18th November 2020

Location

Zoom meeting link (password: 764978)

Goals

  • Develop postcoordination guidance

Attendees 

Apologies


Agenda and Meeting Notes

Description

Owner

Notes

Welcome and agenda

Linda Bird

NOTE

  • The last meeting for 2020 to be held on Wednesday 2nd December.
  • Meetings will resume in 2021 on Wednesday 27th January.
Postcoordination Guidance

Linda Bird , 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).



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

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:

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-18 by Linda Bird
File odontogram refset members.svg 2020-Nov-18 by Linda Bird


  • No labels

6 Comments

  1. Michael Lawley

    One issue I have with the "NLP use case", is that it doesn't actually involve post coordination.  At the least, following named-entity recognition on some free text you have an ordered list of SNOMED concepts.  You may even have a tree-structured collection of codes (using, for example, a parse-tree from the free text).  But you don't  have anything in post coordination syntax.

    In this context, the use case is "how do I take this list/tree of concepts and construct an MRCM-valid expression?"


  2. Daniel Karlsson

    Sorry, I was trying to be in two meetings at the same time, and I guess I failed at participating in any of them.

  3. Daniel Karlsson

    But, generally, I'm with Ed and Michael. A reason which might or might not have been mentioned at the call is that with current close-to-user form, we're trying to solve two incompatible problems with the same representation: 1. a compact but strict representation of SNOMED semantics and 2. a "light" accessible, less volatile SNOMED representation resulting in something that is neither. Unless you can specify that "this is CtU" and "this is strict" then it is not possible to determine the intended meaning. Separating the two problems out might be helpful, perferably with two syntaxes: SCG minus CtU for 1, SCG templates with slots for 2.

    Looking at how use cases map to SCG vs. templates, I think the dental case maps to a template solution, NLP I'm less sure, information model construction binding seems to map to templates as well.

    1. Dion McMurtrie

      In fact if you can come up with a compact but strict representation of SNOMED CT semantics that is "light" and accessible and also less volatile for change over time...then why wouldn't we author SNOMED CT that way?

      1. Ed Cheetham

        Which sort of brings us back (20 years!) to Galen's notion of an intermediate representation plus abstraction/transformation rules [e.g. 1, 2] . In principle this would be closer to Daniel's 'compact but strict' representation (I think), so may still not be enough. If such an approach can achieve the Galen project's goal of democratising the act of content creation ("...facilitating the involvement of many domain experts by deferring indefinitely any need for them to become familiar with GRAIL or the CRM..."), whether that be modelled content in the reference data or compositional expressions in records, then yes, I agree, why wouldn't we (and a growing number of user recruits, largely insulated from the complexity of the reference data) author SNOMED CT that way?

    2. Ed Cheetham

      Thanks all. I agree that the dental case(s) should yield to a template-based constraints. However it would be really good to work through them properly as part of this work to see how tricky things can get. For example:

      1. The odontogram set gives us procedures, body sites and action states. A CtU approach applied here might allow refinement of a procedure with both the procedure site=site value and the procedure context=action state value. If so then resolution rules need to be included that look further afield (both 'up' and 'down') from the focus to try and resolve these to a well-formed context-specific expression.

      2. Despite both of them expecting elements of expression creation/'post-coordination', neither of the dental refsets name the attributes that are expected to be used. Consistency of use (both between expressions and between expressions and reference data) will require these to be declared explicity (in particular where role hierarchies are involved).

      3. Not explicitly referred to in the dental sets, but quite easy to flush out based on the content available, are modelling rules that exist between attributes. These rules are followed in the creation of reference data, and will need to be 'available' to the creators of expressions if consistency and comparability are to be achieved. For example, we have 41565005 |Periodontitis| in the odontogram set, and several 'chronic' specialisations such as 715287007 |Localized severe chronic periodontitis| in the general dentistry set. An enthusiastic user of the odontogram set may wish to create a 'chronic' variant by adding their own 263502005 |Clinical course| = 90734009 |Chronic| refinement. However the reference data indicates that this is insufficient - the associated morphology value also needs refining to a 'chronic inflammation' subtype. It is unlikely that this extra refinement would be expected to happen at the time of expression creation, but would need to be included in the transformation rules.