SNOMED CT Languages Project Group

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Date & Time

20:00 UTC Wednesday 29th January 2020

Location

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

Goals

  • To finalize any feedback on updates to SCG, ECL, URIs, Templates
  • To progress
    • Query language (accessing reference sets)

Attendees 

Apologies

Agenda and Meeting Notes

Description
Owner
Notes

Welcome and agenda

Linda Bird

Please note that the SLPG will be meeting in London on Sunday 4th April (9am to 12:30pm) - see schedule

Concrete valuesLinda Bird

Boolean added to draft SCG, ECL, STS and ETL specifications

PLEASE REVIEW BEFORE NEXT MEETING!

  • Draft SCG (v2.4) - Compositional Grammar - Specification and Guide
      • 1. Introduction → History
      • 3.2 Representation of clinical Meanings → Requirement M4
      • 4. Logical Model
      • 4.1 Details
      • 5.1 Normative Specification
      • 5.2 Informative Comments
      • 6.6 Examples → Expressions with Concrete Values
  • Draft ECL (v1.4) - Expression Constraint Language - Specification and Guide
      • 1. Introduction → History
      • 3.2 Expression Constraint and Query Requirements
      • 3.3 Concept Model Requirements
      • 4. Logical Model
      • 4.1 Details
      • 5.1 Brief Syntax (Normative)
      • 5.2 Long Syntax (Informative)
      • 5.3 Informative Comments
      • 6.2 Refinements
  • Draft STS/ETL (v1.1) - Template Syntax Specification
      • 1. Introduction → History
      • 4. Logical Model
      • 4.1 UML Class Diagram
      • 5.1 Normative Specification (boolean changes in blue / other proposed changes in red)
      • 5.2 Informative Comments (only boolean changes made)
      • 6.1 Expression Template Language
      • 8.2 Typed Replacement Slots → Concrete Values
      • 8.3 Constrained Replacement Slots → Value List Constraints? (currently unchanged)
URIs

Peter G. Williams & Linda Bird

PLEASE REVIEW BEFORE NEXT MEETING!

Draft URI standard for review - URI Standard

  • 2.1 URIs for Editions and Versions (formatting and examples only)
  • 2.2 URIs for Components and Reference Set Members (formatting and examples only)
  • 2.3 Version-Relative Component URIs (formatting and examples only)
  • 2.4 URIs for Modules (formatting and examples only)
  • 2.5 URIs for Properties (formatting and examples only)
  • 2.6 URIs for Language Syntaxes
  • 2.7 URIs for Language Instances
  • 2.8 URIs for Modelling Resources
  • 3.1 Resolving SNOMED CT URIs
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
Expression Constraint Language

Linda Bird

STILL TO DO:

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

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

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”, 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 - version 1.5
Reverse Member ofAll

Returning attributesMichael Lawley


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 29th January 2020 at 20:00 UT. Please enjoy your holidays everyone!

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3 Comments

  1. Daniel Karlsson

    Dear All,

    as mentioned during the discussion at the meeting, one of the largest contribution of ECL is the facilitation of working with transitive relationships, Is a in particular, and attributes, which requires effort from developers to get right in the same way. Thus, there is clear benefit in standardizing the current set of ECL features (as has been done).

    Another such source of complexity in using SNOMED CT in information systems is its linguistic features, i.e. finding and displaying terms in languages and language reference sets. Also here there would be benefit if the SNOMED languages could support the linguistic features in a simplified, standardized manner.

    /Daniel

    1. Linda Bird

      Hi Daniel,

      Understood and noted. Let's discuss this further at our meeting this week - particularly in terms of whether we should reconsider including the language refset in the planned ECL term searching .

      Kind regards,
      Linda.

  2. Ed Cheetham

    On the query language topic...

    I remain uncomfortable with the idea that SI really needs its own 'query language' for a single product, but am aware of several requirements that seem to be best met by fragments of such an approach.

    Digging around a bit, I see that there are relatively recent moves to extend SQL to include a graph query language:

    The candidate GQL language is richly described in the scope and features document here (BNF page 54).

    I'm not suggesting that this is a ready-made language for SNOMED queries, but would be curious to see whether it is possible/desirable to take advantage of this ongoing work, and investigate what else would be needed to synthesise the basic MATCH/WHERE/RETURN elements of GQL with the ECL and features of the published data. I know our group has already talked about representing (as metadata concepts) the schemas of the essential tables as well as the RefSets, and it may be that the 'query language challenge' needs both a query language AND a rethinking of how SNOMED CT's 'schema' is published (in order to make all aspects of the data - nodes, edges, descriptions and refsets easily accessible from an ECL/graph perspective).

    The Nebraska team have already shared their Neo4j implementation which might be useful background, although I confess I haven't investigated the model they settled on to see how well it could be used to specify atypical RETURN sets (such as Michael's request for attributes), or specify data features/filters that are only available 'in the tables'.

    Kind regards

    Ed