SNOMED CT Languages Project Group

Space shortcuts

Page tree

Versions Compared

Old Version 2

changes.mady.by.user Linda Bird

Saved on

compared with

New Version Current

changes.mady.by.user Linda Bird

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

Date & Time

10:00 to 11:00 UTC Wednesday 18th May 2022

Location

Zoom meeting link (password: 764978)

Goals

  • URIs for edition+derivative combos
  • URIs for ECL
  • ECL implementation questions
  • ECL with description ids in filters
  • Reverse engineering ECL from a list of codes
  • Next meeting: Postcoordination guidance strategy

Attendees 


Agenda and Meeting Notes

Advanced Tables - Table Plus
border2
rowStylesbackground-color:#ccccff;font-weight:bold;,background-color:"#eeeeff";font-weight:normal;,background-color:#eeffff;font-weight:normal;
autoNumberSorttrue
autoNumbertrue
enableSortingfalse


Description

Owner

Notes

Welcome and agenda

All
  • Next meeting - Thursday 2nd June 2022
  • Should we book a meeting room in Portugal?
URIs for edition+derivative combosAllURIs for ECL

Linda Bird

Problem:

  • User of the international edition (without an extension) who needs to access one or more derivative packages
  • How do they specify a substrate for this ECL (in a shareable way)?
  • Constraint: Only metadata (e.g. module concept with no defining attributes) in package - does not require classification
  • Use case: Implicit value sets (ecl and reference set)

Potential solutions:

  1. Require everyone (e.g. every country) to create their own module and module dependencies to define which derivatives are to be used
    1. Action: Make this process super easy (Q: is that possible? Everyone will need a namespace identifier)
  2. International modules created for each (popular) derivative combinations with associated module dependencies
  3. A 'flexible' derivative extension module created by SI, with locally defined module dependencies
  4. URI format to include edition plus derivate composition, e.g.
    1. http://snomed.info/sct/900000000000207008/version/20220228;module/733983009/time/20191031;module/715152001/time/20191031
  5. Terminology services endpoints to check (a) what modules are required to execute a given ECL, and (b) what modules are currently loaded

Action: To consider 4a solution before next meeting.

URIs for ECL

Linda Bird

Proposal:

ECL implementation questionsKai Kewley

Topics to discuss include:

  1. Difference between "^ 700043003 |Example problem list concepts reference set|" and "^ [referencedComponentId] 700043003 |Example problem list concepts reference set|", in terms of removal of duplicate rows
  2. Rule order in memberFilter rule - suggestion:
    • memberFilter = memberFieldFilter / moduleFilter / effectiveTimeFilter / activeFilter
    • => 
    • memberFilter = moduleFilter / effectiveTimeFilter / activeFilter / memberFieldFilter
  3. Other?
ECL with description ids in filters

Jeremy Rogers

Proposal:

  • Add the ability to find concepts for a given description id, e.g.
    • * {{ D id = 426422019 }}
Reverse engineering ECL from a list of codesJeremy Rogers
  1. Should we ask for the opposite of a $expand operation?
  2. How can we make the operation more efficient
ECL implementation questionsKai KewleyReverse engineering ECL from a list of codesJeremy Rogers
The items below are currently on hold
ECL v2.1 - Requirement proposalsAll

Potential requirements for ECL v2.1 - Discussion and brainstorming

  • Daniel's comments
  • Context supplements - e.g.
    • << 56265001 |Heart disease|  {{ + CONTEXT }} – This syntax is too general, as there is a risk of including absent finding, not-done procedure and family history
    • << 56265001 |Heart disease| {{ + CONTEXT-DEFAULT }} ? – What would this mean?
      • Brief form:
        • [[@ecl_query]] {{ + Context (Temporal = [[ @temporal_value]] }}
      • Expanded form:
        • [[ @ecl_query ]] OR  (< 243796009 |Situation with explicit context|:
                  { ( 246090004 |Associated finding| = ( [[ @ecl_query ]] ) 
                         OR |Associated procedure| = ( [[ @ecl_query ]] )
                   ( |Procedure context| = |Done| OR |Finding context| = |Known present|),
                      |Subject relationship context| = |Subject of record|,
                       |Temporal context| = [[ @temporal_value ]] } )
      • Example 1: << |Heart procedure| {{ + Context (Temporal = *) }}
        • <<  |Heart procedure| OR  (< 243796009 |Situation with explicit context|:
                  { 246090004 |Associated finding| = << 56265001 |Heart disease|,
                      |Procedure context| = |Done|,
                      |Subject relationship context| = |Subject of record|,
                       |Temporal context| = * } )
        • Example 2: (<< |Heart disease| OR << |Heart procedure| ) {{ + Context (Temporal = *) }}
          • <<  |Heart procedure| OR  (< 243796009 |Situation with explicit context|:
                    { ( 246090004 |Associated finding| = (<< |Heart disease| OR << |Heart procedure| ) 
                           OR |Associated procedure| = ( << |Heart disease| OR << |Heart procedure| ) )
                        ( |Procedure context| = |Done| OR |Finding context| = |Known present|),
                        |Subject relationship context| = |Subject of record|,
                         |Temporal context| = * } )
      • << 56265001 |Heart disease| {{ + Context (Temporal = *, FindingContext=<<|Known present| }}
        • Will return all types of heart disease, plus concepts like 394886001 |Suspected heart disease (situation)|, and 429007001 |History of cardiac arrest (situation)|
        • Expands to: 

          • << 56265001 |Heart disease| OR
              (< 243796009 |Situation with explicit context|:
                    { 246090004 |Associated finding| = << 56265001 |Heart disease| } )


    • However, you may want to exclude (or include) specific contexts - for example:
      1. To ensure that the finding was about the subject of the record (and not a family history, e.g. to exclude 429959009 |Family history of heart failure (situation)|), you could say:
        • << 56265001 |Heart disease|  {{ + CONTEXT (relationship = 410604004 |Subject of record| }}
      2. To ensure that the finding was 'Known present' (e.g. to exclude 394926003 |Heart disease excluded (situation)|), you could say:
        • << 56265001 |Heart disease|  {{ + CONTEXT (finding_context = << 410515003 |Known present| }}
      3. To ensure that the finding was about the subject of the record AND known present, you could say:
        • << 56265001 |Heart disease|  {{ + CONTEXT (relationship = 410604004 |Subject of record|, 
                                                                                                    finding_context = << 410515003 |Known present| }}
      4. ?? Is there any use case for restricting adding temporal context? (e.g. temporal != << 410513005 |In the past|)
    • Is any more syntactic sugar required? E.g.
      • {{ + CONTEXT (relationship = self, finding context = present, temporal != past) }}
      • {{ + CONTEXT (self, present, ! past) }}
    • Other ideas? Common profiles?
  • --------------------------
  • Ability to return attribute types (see proposal below)
    • [ attributes ] << 125605004 |Fracture of bone (disorder)|
    • << 125605004 |Fracture of bone (disorder)| . Attributes
    • << 125605004 |Fracture of bone (disorder)| . (<< 125605004 |Fracture of bone (disorder)| . Attributes )
    • [ attribute, value] << 125605004 |Fracture of bone (disorder)|
  • -------------------------
  • Reverse membership (see below)
    • Which reference sets "contain" the given concept(s) - e.g. 421235005 |Structure of femur|?
      • 421235005 |Structure of femur| . Refsets
      • 421235005 |Structure of femur|. Refsets [ referencedComponentId ]
      • 421235005 |Structure of femur| . Refsets [ targetComponentId ]
  • --------------------------
  • Other?
Returning AttributesMichael Lawley
  • 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

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
Postcoordination Topics
  • Discuss feedback on transformation implementation
    • Resources
    • 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 (question)
        • 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 ExamplesAll

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

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).
The items below are currently on hold
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:

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:

Scg expression
 [[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



Attachments

...