2019-05-22 - SLPG Meeting

2019-05-22 - SLPG Meeting

Date & Time

20:00 UTC Wednesday 22nd May 2019

Teleconference Details

To join the meeting please go to https://snomed.zoom.us/j/471420169

Further information can be found at SLPG meeting information

Goals

  • Review schedule for October business meeting

  • Review actions from last meeting

  • Proposed enhancements to expression constraint language

    • Term searching

  • Proposed new language features for mapping

Attendees 

  • Chair: @Former user (Deleted)

  • Project Group: @michael lawley@Daniel Karlsson@Ed Cheetham@Anne Randorff Højen@Former user (Deleted)

Apologies

  •  

Agenda and Meeting Notes

Description

Owner

Notes

Description

Owner

Notes

Welcome and apologies

@Former user (Deleted)

  • Question - Are there any conflicts in the current meeting schedule for October business meeting?

Actions from last week

@Former user (Deleted)

  • Actions from last week:

    • Additional use cases for term searching in ECL?

    • Search types? Include regex? Does anyone have a regex ABNF?

    • Language features required in ECL?

Introducing term searching to ECL

@Former user (Deleted)

Syntax

{{ term  =  [ termSearchType : ] "String"  }}

Term Search Type

  1. Wild Card Match (collation) - e.g.

    • {{  term = wild:"*heart*“ }}

    • {{  term = wild (sv):"*hjärta*“ }}

  2. ??? Perl Regex - e.g.

    • {{ term = regex:".*heart.*” }}

    • Question: Does the query suddenly become order dependent? Yes

  3. *** Word Prefix Any Order - e.g.

    • {{ term = match:“hear att” }}

  4. 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| ( {{ term = “heart” AND term = “hjärta"}}

  • (<< 64572001 |Disease|: |Associated morphology| = *) {{ term = “heart”, languageCode = "en", }} {{ term = “hjärta", languageCode = "sv"}}




  • (<< 64572001 |Disease| {{ term = “*cardio*” }}) MINUS (<< 64572001 |Disease| {{ term != “*heart*” }})

  • ?? << 64572001 |Disease| {{ term = “*cardio*” }} MINUS << 64572001 |Disease| {{ term != “*heart*” }}

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| }}

  • Do we include 'type' - e.g. << 64572001 |Disease| {{ D.term = “*heart*”, D.type synonym }}

  • Do we include 'languageCode' - e.g. << 64572001 |Disease| {{ D.term = “*heart*”, D.type synonym, D.languageCode = “en” }}

  • Do we include 'caseSignificanceId' - e.g. << 64572001 |Disease| {{ D.term = “*Heart*”, D.caseSignificanceId = 900000000000017005 |case sensitive|}}

  • Do we include 'caseSignificance' - e.g. << 64572001 |Disease| {{ D.term = “*Heart*”, D.caseSignificance = sensitive }}

  • Do we include 'language' and 'version' - e.g. << 64572001 |Disease| {{ term = “*heart*” }} VERSION = http://…, LANGUAGE = (999001881000000108|Gastro LRS|, |GB English|)

  • 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

  • Do we use/require the "D" at the start of "term"?

  • How does this relate to description templates? How does this relate to SNOSTORM implementation.

  • Packaging - Do we (over time) extend ECL with all the new Query Language features, and define a set of example ECL profiles - e.g. "Basic ECL", "ECL with basic term searching", "ECL with filters".

Executing maps

@Former user (Deleted)

Proposed extension to ECL to support the execution of maps

  • 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|)

      • mapSource (|Anatomy structure and part association refset|, << |Liver part|)

    • 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 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| 

  •  

    • 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|)

URI Standard

@Former user (Deleted)

  • Finalize and publish language and language instance URIs

Query Language
- Summary from previous meetings







@Former user (Deleted)

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|

Other topics

@Former user (Deleted)

  • Any other topics?

Confirm next meeting date/time

@Former user (Deleted)

The next SLPG meeting will be held in 2 weeks at 20:00 UTC on Wednesday 5th June.

  File Modified

Microsoft Excel Spreadsheet RegexCheat.xlsx

2019-May-20 by Former user



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