2020-02-26 - SLPG Meeting

Welcome and agenda

@Former user (Deleted)

Please note that the SLPG will be meeting in London on Sunday 5th April (9am to 12:30pm) - see schedule

Concrete values

@Former user (Deleted)

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

URIs

@Peter Williams & @Former user (Deleted)

Please review updates to the URI specification, and raise any comments in the next 2 weeks.

Draft URI standard for review - URI Standard

• 2.6 URIs for Language Syntaxes

• 2.7 URIs for Language Instances

• 2.8 URIs for Modelling Resources

• 3.1 Resolving SNOMED CT URIs

Expression Constraint Language

@Former user (Deleted)

NEXT STEP FOR ECL:

• 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 }}

• Question - Do we want to reconsider including optional parameters for 'type', 'dialect' and 'acceptability'

  • typeId = 900000000000013009 ; type = <synonym | fsn>

  • dialectId = 900000000000508004 ; dialect = <en-GB | en-AU | en-Patient | de-CardioSpecialist>

    • dialectId = 900000000000508004 + 900000000000509007 ; dialect = en-GB + en-US

  • acceptabilityId = 900000000000549004 ; acceptability = <acceptable | preferred >

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|

    • ? (<|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 Attributes

@michael 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 Of

@michael 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 Williams

• ON HOLD WAITING FROM IMPLEMENTATION FEEDBACK FROM INTERNAL TECH TEAM

• WIP version - https://snomed.atlassian.net/wiki/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:

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)