Date & Time

10:30am (local time) Tuesday 29th October 2019

Location

Grand Residence 103, Grand Hyatt Hotel Kuala Lumpur, Malaysia

Goals

  • To review current priorities and plan future work based on these priorities
  • To progress work on
    • URIs
    • Templates
    • ECL
    • Query language

Attendees 

Apologies

Agenda and Meeting Notes


Description
Owner
Notes

Welcome and agenda

Linda Bird


PrioritiesLinda Bird
  • Discuss current priorities and new requirements
    • Add 'boolean' to Compositional Grammar, ECL and Templates
    • Use abbreviation "bool".
URIs

Peter G. Williams

Expression Templates

Peter G. Williams

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
  • 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
Expression Constraint Language

Linda Bird

  • Review scope and syntax of previous internal implementation (Kai Kewley )
  • Recap where we were up to with adding term-searches to ECL (see below)

Previous discussions

Syntax

{{ term  =  [ termSearchType : ] "String", languageCode = [langCode] }}

Term Search Type

    1. Wild Card Match (collation) - e.g.
      • {{  term = wild:"*heart*“ }}
      • {{  term = wild (sv):"*hjärta*“ }}
    1. Regex - e.g.
      • {{ term = regex:".*heart.*” }}
    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”, languageCode = "en"}}
    • << 64572001 |Disease| {{ term = “heart”, languageCode = "en"}} AND << 64572001 |Disease| {{ term = “hjärta”, languageCode = "sv"}}
    • << 64572001 |Disease| {{ term = “heart”, languageCode = "en"}} {{ term = “hjärta”, languageCode = "sv"}}
    • << 64572001 |Disease| {{ term = “heart”, languageCode = "en"}} OR << 64572001 |Disease| {{ term = “hjärta", languageCode = "sv"}}
    • << 64572001 |Disease| {{ (term = “heart”, languageCode = "en") OR (term = “hjärta", languageCode = "sv")}}
    • (<< 64572001 |Disease|: |Associated morphology| = *) {{ term = “heart”, languageCode = "en", }} {{ term = “hjärta", languageCode = "sv"}}
    • (<< 64572001 |Disease| {{ term = “*cardio*” }}) MINUS (<< 64572001 |Disease| {{ term != “*heart*” }})
    • Recommendation to be made on (based on investigation of grammar):
      • << 64572001 |Disease| {{ term = “heart”, languageCode = "en"}} AND {{ term = “hjärta”, languageCode = "sv"}}
      • << 64572001 |Disease| ( {{ term = “heart”, languageCode = "en"}} OR {{ term = “hjärta”, languageCode = "sv"}} )
      • << 64572001 |Disease| ( {{ term = “heart”, languageCode = "en"}} MINUS {{ term = “hjärta”, languageCode = "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 - e.g. 2.0 (or 1.4?) → same specification document
      • An optional extension to ECL for SNOMED authors/content developers - e.g. ECL++ / ECLv1.3++ → An appendix on the ECL document? (with Filter Language)
      • A subset/profile of the Query Language → A separate document that defines SNOMED filters, which can be added to any version of ECL
      • Filter Language
Executing maps

Linda Bird

Reverse memberOf function

  • What refsets is a concept a member of?

Proposed syntax to support execution of maps (Outstanding question: ECL or Query Language? Scope and packaging needs further discussion)

  • Example use cases
    • Mapping from international substance concepts to AMT substance concepts
    • Anatomy structure and part association reference set - e.g. find the anatomical parts of a given structure
  • Potential syntax to consider
    • Functional
      • mapTarget (|Anatomy structure and part association refset|, << |Upper abdomen structure|)
        • Return the map targets from the given map refset. where the referencedComponent matches the condition
      • mapSource (|Anatomy structure and part association refset|, << |Liver part|)
        • Return the referencedComponent from the given map refset, where the targetId matches the condition.
    • Dot notation + Attribute refinement
      • |Anatomy structure and part association refset| . |mapTarget|
      • |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 ) . |mapTarget|
      • ( |Anatomy structure and part association refset|: |mapTarget| = << |Upper abdomen structure ) . |referencedComponent|
    • Dot notation + Filters
      • ( |Anatomy structure and part association refset| {{ |referencedComponent| = << |Upper abdomen structure| }} ). |mapTarget|
      • ( |Anatomy structure and part association refset| {{ mapTarget = << |Upper abdomen structure| }} ) . |referencedComponent|
        • ^ ( |Anatomy structure and part association refset| {{ mapTarget = << |Upper abdomen structure| }} )
    • Specify value to be returned
      • ?|mapTarget|? |Anatomy structure and part association refset|
      • ?|mapTarget|? |Anatomy structure and part association refset| {{ |referencedComponent| = << |Upper abdomen structure| }}
      • ?|mapTarget|? |Anatomy structure and part association refset| : |referencedComponent| = << |Upper abdomen structure|
Returning attributesMichael Lawley

Proposal from Michael:

  • 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|)
Query Language
- Summary from previous meetings




Linda Bird

Examples: version and language

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|

Next steps

Linda Bird

  • Discuss and plan next steps
Confirm next meeting date/time
Linda Bird