2020-03-18 - SLPG Meeting

Welcome and agenda

@Former user (Deleted)

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 values

@Former user (Deleted)

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

URIs

@Former user (Deleted)

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 URI formats for Language syntaxes and language instances will not be published until compelling use case is found.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• 2.6 URIs for Language Syntaxes - Not for publication

• 2.7 URIs for Language Instances - Not for publication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 Language

@Former user (Deleted)

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.  

   1. Wild Card Match (collation) - e.g.

2.  

   •  

     • {{  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 Attributes

@Former user (Deleted)

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|