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SNOMED CT Languages Project Group

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Date & Time

20:00 to 22:00 UTC Wednesday 18th March 2020

Location

Zoom meeting: https://snomed.zoom.us/j/471420169

Goals

  • To finalize URI updates for publication
  • To finalize requirements for term searching in ECL

Attendees 

Meeting Recording

The meeting recording can be found here.

Agenda and Meeting Notes

Description
Owner
Notes

Welcome and agenda

Linda Bird

SNOMED International has announced the cancellation of the face to face April 2020 business meetings. Therefore, the SNOMED Languages meeting on Sunday 5th April is also cancelled.

Concrete valuesLinda Bird

ON HOLD: SCG, ECL, STS, ETL - Ready for publication, but on hold until after MAG meeting in April confirming requirement for Boolean datatype.

URIs

Linda Bird

TO CONFIRM: Agree on wording of '3.1 Resolving SNOMED CT URIs', and finalize publishing of updated URI specification.

DECISION: New URI format for Modelling Resources to be published. URI formats for Language syntaxes and language instances will not be published until compelling use case is found.

Draft URI standard for review - URI Standard

  • 2.6 URIs for Language Syntaxes - Not for publication
  • 2.7 URIs for Language Instances - Not for publication
  • 2.8 URIs for Modelling Resources * - To publish
  • 3.1 Resolving SNOMED CT URIs * - To publish (with revised wording)
Expression Constraint LanguageLinda Bird

FUTURE PLANS

  • TO BE ADDED - Child or self (<<!) and Parent or self (>>!)

  • Term Searching: Agreement in Malaysia - ECL will add the following term searching syntax (no regex - just wild card and word prefix any order):

{{ term  =  [ termSearchType : ] "String" , language = <langCode> }}

  • Example - {{ term = "heart att", language = es }}
  • Type
    • type = (syn fsn)
    • What other optional parameters should be included? - e.g. type, 'dialect', 'acceptability'
      • typeId = 900000000000013009 |synonym|
      • typeId = ( 900000000000013009 |synonym| 900000000000003001 |fully specified name| )
      • type = syn
      • type = fsn
      • type = def
      • type = (syn fsn)
        • syn = 900000000000013009 |synonym|
        • fsn = 900000000000003001 |fully specified name|
        • def = 900000000000550004 |definition|
  • Dialect
    • dialectId = 900000000000508004 |GB English|
    • dialectId = ( 900000000000508004 |GB English| ??? |US English| )
    • dialect = [ fr-lrs, en-GB ]
      • Find concepts with a term which matches "car" that is preferred in one language refset and not acceptable in another
      • Acceptable
    • dialect = en-nhsClinical
    • dialect = ( en-nhsClinical en-nhsPharmacy )
    • dialectId = ( 999001261000000100 |National Health Service realm language reference set (clinical part) (foundation metadata concept)|
      999000691000001104 |National Health Service realm language reference set (pharmacy part) (foundation metadata concept)| )
      • ; dialect = <en-GB | en-AU | nz-Patient | en-Patient | de-CardioSpecialist>
        • dialectId = 900000000000508004 + 900000000000509007 ; dialect = en-GB + en-US
    • TO DO - Send recommendation to MAG to consider the following
      1. Dialect Alias Refset
        • Alternative 1 - Annotation Refset
          • Dialect_Alias refset : alias + languageRefset-conceptId - e.g. "en-GB", 900000000000508004
          • Example row
            • referencedComponentId = 999001261000000100
            • dialectAlias = nhs-clinical
        • Alternative 2 - Add alias as a synonym to the language refset concept
          • Create a simple type refset that refers to the preferred alias for each language refset
        2. Constructing a Language Refset from other Language Refset
        • Allowing an intensional definition for a language refset
        • Includes order/precedence of language refsets being combined
    • Acceptability
      • acceptabilityId = 900000000000549004 |Acceptable (foundation metadata concept)|
      • acceptabilityId = 900000000000548007 | Preferred (foundation metadata concept) |
      • acceptability = acceptable (ie acceptable but not preferred)
      • acceptability = preferred
          • acceptable = 900000000000549004 |Acceptable (foundation metadata concept)|
          • preferred = 900000000000548007 | Preferred (foundation metadata concept) |
      • dialect = X, acceptability = ( acceptable preferred ) IS THE SAME AS dialect = X
      • Find diabetes concepts that do not have a term in nz-patient
        • < |diabetes|  MINUS * {{ dialect = nz-patient }}
      • acceptability = acceptableOrPreferred
  • Use cases - Note some of these will be out of scope for the simple ECL filters
    • Find the concepts that ..... have a PT = X in language refset = Y
    • Find the concepts that ..... have a Syn = X in language refset = Y
    • Find the concepts that ... have one matching description in one language, and another matching description in another language
    • Find the concepts that have a matching description that is in language refset X and not in language refset Y
    • Find the concepts that .... have a matching description that is either preferred in one language refset and/or acceptable in another language refset
      • {{ term = "car", dialect
    • Find the concepts that .... have a matching description that is either preferred in one language refset and not acceptable in another language refset
      • {{ term = "car",
    • Returning the set of concepts, for which there exists a description that matches the filter -
      • * {{ filter }} MINUS * {{ filter2 }}

Term Search Type

    1. Wild Card Match (collation) - e.g.
      • {{  term = wild:"*heart*“ }}
      • {{  term = wild (sv):"*hjärta*“ }}
    1. Word Prefix Any Order - e.g.
      • {{ term = match:“hear att” }}
    1. Default (word prefix any order) - e.g.
      • {{ term = "hear att" }}
      • {{ term = "*heart*“ }}

Potential Examples

    • << 64572001 |Disease| {{ term = “heart”}}
    • << 64572001 |Disease| {{ term = “heart”, language = "en"}}
    • << 64572001 |Disease| {{ term = “heart”, language = "en"}} AND << 64572001 |Disease| {{ term = “hjärta”, language = "sv"}}
    • << 64572001 |Disease| {{ term = “heart”, language = "en"}} {{ term = “hjärta”, language = "sv"}}
    • << 64572001 |Disease| {{ term = “heart”, language = "en"}} OR << 64572001 |Disease| {{ term = “hjärta", language = "sv"}}
    • << 64572001 |Disease| {{ (term = “heart”, language = "en") OR (term = “hjärta", language = "sv")}}
    • (<< 64572001 |Disease|: |Associated morphology| = *) {{ term = “heart”, language = "en", }} {{ term = “hjärta", language = "sv"}}
    • (<< 64572001 |Disease| {{ term = “*cardio*” }}) MINUS (<< 64572001 |Disease| {{ term != “*heart*” }})
    • Recommendation to be made on (based on investigation of grammar):
      • << 64572001 |Disease| {{ term = “heart”, language = "en"}} AND {{ term = “hjärta”, language = "sv"}}
      • << 64572001 |Disease| ( {{ term = “heart”, language = "en"}} OR {{ term = “hjärta”, language = "sv"}} )
      • << 64572001 |Disease| ( {{ term = “heart”, language = "en"}} MINUS {{ term = “hjärta”, language = "sv"}} )

Use Cases

    • Intentionally define a reference set for chronic disease. Starting point was ECL with modelling; This misses concepts modelled using the pattern you would expect. So important in building out that reference set.
    • Authors quality assuring names of concepts
    • Checking translations, retranslating. Queries for a concept that has one word in Swedish, another word in English
    • AU use case would have at most 3 or 4 words in match
    • Consistency of implementation in different terminology services
    • Authoring use cases currently supported by description templates
    • A set of the "*ectomy"s and "*itis"s

Questions

    • Do we include 'typeId' - e.g. << 64572001 |Disease| {{ D.term = “*heart*”, typeId =  900000000000013009 |Synonym| }}
      • NO
    • Do we include 'type' - e.g. << 64572001 |Disease| {{ D.term = “*heart*”, D.type =  synonym }}
      • NO
    • Do we include 'languageCode' - e.g. << 64572001 |Disease| {{ D.term = “*heart*”, D.type =  synonym, D.languageCode = “en” }}
      • YES
    • Do we include 'caseSignificanceId' - e.g. << 64572001 |Disease| {{ D.term = “*Heart*”, D.caseSignificanceId = 900000000000017005 |case sensitive|}}
      • NO
    • Do we include 'caseSignificance' - e.g. << 64572001 |Disease| {{ D.term = “*Heart*”, D.caseSignificance = sensitive }}
      • NO
    • Do we include 'language' and 'version' - e.g. << 64572001 |Disease| {{ term = “*heart*” }} VERSION = http://…, LANGUAGE = (999001881000000108|Gastro LRS|, |GB English|)
      • NO
    • Do we include syntactic sugar - e.g.
      • << 64572001 |Disease| {{ preferredTerm = “*heart*”, languageRefSet = en-gb}}
      • << 64572001 |Disease| {{ fullySpecifiedTerm = “*heart*”, languageRefSet=en-gb}}
      • << 64572001 |Disease| {{ acceptableTerm = “*heart*”, languageRefSet = en-gb}}
      • << 64572001 |Disease| {{ preferredTerm = “*heart*”}} FROM  version = X, language = Y
      • NO
    • Do we use/require the "D" at the start of "term"?
      • NO
    • Packaging - How do we package this extension to ECL
      • A new version of ECL - version 1.5
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





Examples: where

Notes

      • Allow nested variable definitions, but recommend that people don't due to readability
      • Scope of variables is the inner query
      • No recursion e.g X WHERE X = 1234 MINUS X
        • ie can't use a variable in its own definition
        • ie X is only known on the left of the corresponding WHERE, and not on the right of the WHERE

Keywords for Term-based searching:

  • D.term
    • D.term = "*heart*"
    • D.term = wild:"*heart*"
    • D.term = regex:".*heart.*"
    • D.term = match:"hear att"
    • D.term = (sv) wild: "*heart*"
  • D.languageCode
    • D.languageCode = "en"
    • D.languageCode = "es"
  • D.caseSignificanceId
    • D.caseSignificanceId = 900000000000448009 |entire term case insensitive|
    • D.caseSignificanceId = 900000000000017005 |entire term case sensitive|
    • D.caseSignificanceId = 900000000000020002 |only initial character case insensitive|
  • D.caseSignificance
    • D.caseSignificance = "insensitive"
    • D.caseSignificance = "sensitive"
    • D.caseSignificance = "initialCharInsensitive"
  • D.typeId
    • D.typeId = 900000000000003001 |fully specified name|
    • D.typeId = 900000000000013009 |synonym|
    • D.typeId = 900000000000550004 |definition|
  • D.type
    • D.type = "FSN"
    • D.type = "fullySpecifiedName"
    • D.type = "synonym"
    • D.type = "textDefinition"
  • D.acceptabilityId
    • D.acceptabilityId = 900000000000549004 |acceptable|
    • D.acceptabilityId = 900000000000548007 |preferred|
  • D.acceptability
    • D.acceptability = "acceptable"
    • D.acceptability = "preferred"

Additional Syntactic Sugar

  • FSN
    • FSN = "*heart"
      • D.term = "*heart", D.type = "FSN"
      • D.term = "*heart", D.typeId = 900000000000003001 |fully specified name|
    • FSN = "*heart" LANGUAGE X
      • D.term = "*heart", D.type = "FSN", D.acceptability = * LANGUAGE X
      • D.term = "*heart", D.typeId = 900000000000003001 |fully specified name|, acceptabilityId = * LANGUAGE X
  • synonym
    • synonym = "*heart"
      • D.term = "*heart", D.type = "synonym"
      • D.term = "*heart", D.typeId = 900000000000013009 |synonym|
    • synonym = "*heart" LANGUAGE X
      • D.term = "*heart", D.type = "synonym", D.acceptability = * LANGUAGE X
      • D.term = "*heart", D.typeId = 900000000000013009 |synonym|, (D.acceptabilityId = 900000000000549004 |acceptable| OR D.acceptabilityId = 900000000000548007 |preferred|) LANGUAGE X
  • synonymOrFSN
    • synonymOrFSN = "*heart"
      • synonym = "*heart" OR FSN = "*heart"
      • D.term = "*heart", (D.type = "synonym" OR D.type = "fullySpecifiedName")
    • synonymOrFSN = "*heart" LANGUAGE X
      • synonym = "*heart" OR FSN = "*heart" LANGUAGE X
      • D.term = "*heart", (D.type = "synonym" OR D.type = "fullySpecifiedName"), D.acceptability = * LANGUAGE X
  • textDefinition
    • textDefinition = "*heart"
      • D.term = "*heart", D.type = "definition"
      • D.term = "*heart", D.typeId = 900000000000550004 |definition|
    • textDefinition = "*heart" LANGUAGE X
      • D.term = "*heart", D.type = "definition", D.acceptability = * LANGUAGE X
      • D.term = "*heart", D.typeId = 900000000000550004 |definition|, D.acceptabilityId = * LANGUAGE X
  • Unacceptable Terms
    • (D.term = "*heart") MINUS (D.term = "*heart", D.acceptability = * LANGUAGE X)

Language preferences using multiple language reference sets

  • LRSs that use the same Language tend to use 'Addition' - i.e. child LRS only includes additional acceptable terms, but can override the preferred term

    • E.g. Regional LRS that adds local dialect to a National LRS

    • E.g. Specialty-specific LRS

    • E.g. Irish LRS that adds local preferences to the en-GB LRS

      • 99999900 |Irish language reference set| PLUS |GB English reference set|

  • LRSs that define a translation to a different language tend to use 'Replacement' - i.e. child LRS replaces set of acceptable and preferred terms for any associated concept

    • E.g. Danish LRS that does a partial translation of the International Release

      • 999999 |Danish language reference set| ELSE |GB English reference set|

Confirm next meeting date/time
Linda Bird

Next meeting is scheduled for Wednesday 11th March 2020 at 20:00 UTC.

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