2020-04-01 - 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)

UPDATES NOW PUBLISHED - see http://snomed.org/uri

Expression Constraint Language

@Former user (Deleted)

WIP ECL Specification

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

  • New examples to be added

• TERM SEARCH FILTERS - Syntax currently being drafted

  • Examples

    • < 404684003 |Clinical finding (finding)| {{ term = "heart att"}}

    • < 404684003 |Clinical finding (finding)| {{ term != "heart att"}} – A concept for which there exists a description that does not match – E.g. Find all the descendants of |Fracture| that have a description that doesn't contain the word |Fracture|

    • < 404684003 |Clinical finding (finding)| MINUS * {{ term = "heart att"}} – A concept which does not have any descriptions matching the term

    • < 404684003 |Clinical finding (finding)| {{ term = match: "heart att" }} – match is word (separated by white space) prefix any order; Words in substrate are ....; Search term delimiters are any mws

    • < 404684003 |Clinical finding (finding)| {{ term = wild: "heart* *ack" }}

    • < 404684003 |Clinical finding (finding)| {{ term = ("heart" "att") }}
      
      

    • < 404684003 |Clinical finding (finding)| {{ term != ("heart" "att") }} – matches concepts with a description that doesn't match "heart" or "att"
      
      

    • < 404684003 |Clinical finding (finding)| {{ TERM = (MATCH:"heart" WILD:"*ack") }}

    • < 404684003 |Clinical finding (finding)| {{ term = "myo", term = wild:"*ack" }} — Exists one term that matches both "myo" and "*ack"

    • < 404684003 |Clinical finding (finding)| {{ term = "myo" }} {{ term = wild:"*ack" }} -– Exists one term that matches "myo", and exists a term that matches "*ack" (filters may match on either same term, or different terms)
      
      

    • < 404684003 |Clinical finding (finding)| {{ term = "hjärta", language = se }}

    • < 404684003 |Clinical finding (finding)| {{ term = "hjärta", language = SE, typeId = 900000000000013009 |synonym| }}

    • < 404684003 |Clinical finding (finding)| {{ term = "hjärta", language = SE, typeId = (900000000000013009 |synonym| 900000000000003001 |fully specified name|)}}
      
      

    • < 404684003 |Clinical finding (finding)| {{ term = "hjärta", language = SE, typeId != 900000000000550004 |Definition|}}

    • < 404684003 |Clinical finding (finding)| {{ term = "hjärta", language = SE, type = syn }}
      
      

    • < 404684003 |Clinical finding (finding)| {{ term = "hjärta", language = SE, type != def }}

    • < 404684003 |Clinical finding (finding)| {{ term = "hjärta", language = SE, type = (syn fsn) }}

    • < 404684003 |Clinical finding (finding)| {{ term = "hjärta", language = SE, type != (syn fsn) }}

    • < 404684003 |Clinical finding (finding)| {{ term = "cardio", dialectId = 900000000000508004 |GB English| }}

    • < 404684003 |Clinical finding (finding)| {{ term = "card", dialectId = ( 999001261000000100 |National Health Service realm language reference set (clinical part)|
      999000691000001104 |National Health Service realm language reference set (pharmacy part)| ) }}
      
      

    • < 404684003 |Clinical finding (finding)| {{ term = "card", dialect = en-gb }}

    • < 404684003 |Clinical finding (finding)| {{ dialect != en-gb }}
      
      

    • < 404684003 |Clinical finding (finding)| {{ term = "card", dialect = ( en-nhs-clinical en-nhs-pharmacy ) }}

    • < 404684003 |Clinical finding (finding)| {{ term = "card", dialect = en-nhs-clinical, acceptabilityId = 900000000000548007 |Preferred| }}
      
      

    • < 404684003 |Clinical finding (finding)| {{ term = "card", dialect = en-nhs-clinical, acceptability = prefer }}
      
      

    • < 404684003 |Clinical finding (finding)| {{ term = "card", dialect = en-nhs-clinical, acceptability != prefer }}
      
      

    • < 404684003 |Clinical finding (finding)| {{ term = "card", dialect = en-nhs-clinical, acceptability = (prefer accept) }}
      
      

    • < 404684003 |Clinical finding (finding)| {{ term = "card", dialect = en-nhs-clinical, acceptability = (prefer accept) }}
      
      

    • < 404684003 |Clinical finding| MINUS * {{ dialect = en-nhs-clinical}}

    • < 73211009 |diabetes|  MINUS * {{ dialect = en-nz-patient }}
      
      

    • < 73211009 |diabetes|  MINUS < 73211009 |diabetes|   {{ dialect = en-nz-patient }}
      
      

    • < 73211009 |diabetes|  {{ term = "type" }}  MINUS < 73211009 |diabetes|   {{ dialect = en-nz-patient }}
      
      

    • (< 404684003 |Clinical finding|:363698007|Finding site| = 80891009 |Heart structure|)  {{ term = "card" }}  MINUS < (404684003 |Clinical finding|:363698007|Finding site| = 80891009 |Heart structure|)   {{ dialect = en-nz-patient }}
      
      

    • < 73211009 |Diabetes|  {{ term = "type" }}  OR < 49601007 |Disorder of cardiovascular system (disorder)|  {{ dialect = en-nz-patient }}
      
      

  • Questions

    • Wild Term Filter - Is the search term everything inside the quotation marks? (note: Match term is tokenized, but wild search is not)

    • Would it be best to only allow each type of filter once within a filterConstraint. This would allow me to make acceptabilityFilter dependent on the dialectFilter. E.g.

      • NOT ALLOWED: * {{ term = "card", dialect = en-nhs-clinical, dialect = en-gb, acceptability = prefer, acceptability = accept }}

      • NOT ALLOWED: * {{ term = "card", acceptability = prefer }}

      • ALLOWED: * {{ term = "card", dialect = en-nhs-clinical, acceptability = prefer }}

    • Should we also introduce version filter? For example:

      • << 64572001 |Disease| {{ term = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131

      • or

      • << 64572001 |Disease| {{ term = "*heart*" , version = http://snomed.info/sct/900000000000207008/version/20180131 }}

    • Case/accent folding + Uni-code collation

  • Next steps

    • Answer above questions, and update brief syntax accordingly

    • Test brief syntax parser

    • Update long syntax and informative comments to match

    • Test long syntax parser

    • Add examples to specification

    • Clarify execution semantics for consistency

    • Document execution semantics in specification

    • SLPG review / Community review

    • Any required updates

    • Publish with PDF

•  

  • 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

• Potential Use cases - Note some of these will be out of scope for the simple ECL filters

  • Find concepts with a term which matches "car" that is preferred in one language refset and not acceptable in another

  • 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

  • Returning the set of concepts, for which there exists a description that matches the filter

•  

  • 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

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://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:

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 Templates

@Kai 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

@Former user (Deleted)

FUTURE WORK

Examples: version and dialect

•  

  • << 64572001 |Disease| {{ term = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131

  • << 64572001 |Disease| {{ synonym = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131

  • << 64572001 |Disease| {{ FSN = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131

  • << 64572001 |Disease| {{ FSN = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131, DIALECT W

  • << 64572001 |Disease| {{ preferredTerm = “*heart*”}}   VERSION http://snomed.info/sct/900000000000207008/version/20180131, DIALECT Y

  • << 64572001 |Disease| {{ acceptableTerm = “*heart*”}}   VERSION http://snomed.info/sct/900000000000207008/version/20180131, DIALECT Y

  • (* {{ term = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131, DIALECT Z) MINUS
    (* {{ term = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20170731, DIALECT W)

  • X MINUS Y WHERE X = * , Y = (* {{ term = "*heart*" }}) VERSION http://snomed.info/sct/900000000000207008/version/20180131, DIALECT W

Notes

•  

  • Allow nested where, version, language

  • Scope of variables is inner query

Confirm next meeting date/time

@Former user (Deleted)

Next meeting is scheduled for Wednesday 22nd April 2020 at 20:00 UTC.