2019-12-04 - SLPG Meeting

Welcome and agenda

@Former user (Deleted)

Concrete values

@Former user (Deleted)

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

PLEASE REVIEW BEFORE NEXT MEETING!

URIs

@Peter Williams & @Former user (Deleted)

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

Expression Templates

@Peter 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:

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

Expression Constraint Language

@Former user (Deleted)

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

Potential Examples

Use Cases

Questions

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)

Reverse Member of

All

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

Returning attributes

@michael 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| 

Query Language
- Summary from previous meetings

@Former user (Deleted)

Examples: version and dialect

Notes

Examples: where

Notes

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

@Former user (Deleted)

• Discuss and plan next steps

Confirm next meeting date/time

@Former user (Deleted)

Welcome and agenda

@Former user (Deleted)

URIs

@Peter Williams

Expression Templates

@Peter Williams

• Summary of discussions in Malaysia

  • Published version: https://snomed.atlassian.net/wiki/display/DOCSTS/Template+Syntax+Specification

  • Work in progress: 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]

    • Adding 'sameValue' and 'allOrNone' constraints to information slots - e.g. sameValue ($site), allOrNone ($occurrence)

    • Self

    • See changes in red here: 5.1. Normative Specification

  • Recap of discussions in Malaysia regarding exchange of templates

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

• Summary of discussions 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

@Former user (Deleted)

• 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

Potential Examples

Use Cases

Questions

Maps and History

@Former user (Deleted)

Recap discussions in Malaysia regarding querying historical patient records - e.g Find all patients with a respiratory disease in the last 10 years. Do we include patients whose records contain |Recurrent chest infection|? (an inactive concept)

Solutions suggested include:

1. Multiple queries

   Reverse memberOf function

   • What refsets is a concept a member of?

2. Use historical associations - either create map from inactive to active concepts, or update EHR to replace inactive concepts with active ones

3. Look at the latest snapshot before the concept is inactivated

4. Multiple queries run against successive releases of SNOMED CT with results collated

5. Update the EHRs to the latest concept using historical associations

6. Create an enhanced transitive closure table containing inactive concepts as their last known position

7. Augmented solution checks the position of replacement to determine concepts inacctivated due to wrong placement

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|)