2019-02-27 - SLPG Meeting

Welcome and apologies

Former user (Deleted)

Actions from last week

Former user (Deleted)

• Actions from last week:

  • Update ABNF with additional UTF characters - please refer to:

    • https://github.com/shexSpec/grammar/blob/master/ShExDoc.g4

    • https://github.com/hsolbrig/FormalExpressionSpec/blob/master/grammar/ECL.g4

    • https://www.fileformat.info/info/unicode/char/d7/index.htm

    • OUTCOME: No update to ABNF required; ANTLR representation must support full UTF-8 character sets

  • SLPG members to bring back a use case for historical associations in queries

    • OUTCOME: ??

Executing maps

Former user (Deleted)

Proposed extension to ECL to support the execution of maps (focusing on the resolution of historical refsets)

• The specific use-case here comes initially from Jeremy and relates to being able to work with inactive concepts via the historical association maps. For example, given an ECL expression that identifies a set of concepts 'c' to be used for retrieving patient records, you probably also want to retrieve records for sameAs (c) and replacedWith (c)

  • Example:

    • (< 72704001 |Fracture| AND ^ 900000000000527005 |SAME AS association reference set|) . 900000000000533001 |Association target component|

    • (900000000000527005 |SAME AS association reference set| . 900000000000533001 |Association target component| ): |Referenced component| = < |Fracture|

    • Michael's existing approach: mapsTo(|SAME AS|, < |Fracture|)
Or mappedTo(…)
mappedFrom(|SAME AS|, |inactive concept|)
mappedFrom(|REPLACED BY|, |inactive concept|)


    • Alternative suggestion: Use the substrate to include historical snapshots.

      • E.g. Historical and current concepts that are fractures and have an associated morphology, but not historical morphologies

      • ( < |Fracture of bone| {{ substrate >= http://snomed.info/sct/900000000000207008/version/20140131 }}) AND (* : |Associated morphology| = *)

    • Alternative use case - Substance (int) to substance (AMT) map (SNOMED-to-SNOMED)

      • ^ (711112009 |ICNP diagnoses simple map reference set| {{ M.mapTarget = “R-FF2E9” }} )

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| 

Template Syntax

Former user (Deleted)

New requirements

• 2 replacement slots must have the same/different or subsumed/not-subsumed values - for example, same morphology, finding sites not subsume each other (within a row of input data):

  • [[ +id ]]: { 116676008 |Associated morphology| = [[ +id @morphology ]], 363698007 |finding site| = [[ +id @findingSite1
    constraint ( != << $findingSite2) ]]},
                     { 116676008 |Associated morphology| = [[ +id @morphology ]], 363698007 |finding site| = [[ +id @findingSite2
    constraint (!= << $findingSite1) ]]}

  •  [[+id]]: [[1..*]]{ |Associated morphology| = [[ +id @morphology ]], |Finding site| = [[ +id @site constraint ($site[n] != <<$site[!n] ]]}

  • Example - 208510002 |Multiple fracture of clavicle, scapula and humerus (disorder)|

• Default value for slots - for example:

  • [[ + id ]]: { |Finding site| = [[ +id (<< 72673000|Bone structure|) @site default = 72673000 |Bone structure (body structure)| ]]

• Specifying the definition status of a slot - for example (proximal primitive modelling):

  • [[ + << 64572001 |Disease| {{ c.definitionStatus = primitive }} ]]

• Specifying the definition status of an expression - for example

  • [[ +tok ]][[ +id ]]: { |Finding site| = [[+id]]}

  • [[ +tok ("===" "<<<") ]][[ +id ]]: { |Finding site| = [[+id]]}

  • [[ +tok (< |Definition status|) ]][[ +id ]]: { |Finding site| = [[+id]]}

• Repeating role groups must have the same set of attributes (with respect to optional attributes) - for example (using #same or #allOrNone):

  • [[+id]]: [[1..* @group1]]
    { [[0..1 #same in group1]]|finding site| = [[+id]],
    [[0..1 #same in group1]]|associated morphology| = [[+id]],
    [[0..1]]|pathological process| = [[+id]]}

  •   [[+id]]: [[1..* @group1]]
    { [[1..1]]|Associated morphology| = [[ +id @morphology ]],
    [[0..1 #allOrNone in group1]]|Finding site| = [[ +id @site]],
    [[0..1 #allOrNone in gropu1]]|Occurrence| = [[ +id @occurrence ]]}

    Instance 1: Injury of head, neck and chest

    [[ |Disease| ]]: 
    [ @rolegroup[1] ] { |Associated morphology| = |Injury|, |Finding site| = |Head structure| } 
    [ @rolegroup[2] ] { |Associated morphology| = |Injury|,  |Finding site| = |Neck structure| }
    [ @rolegroup[3] ]{ |Associated morphology| = |Injury|,  |Finding site| = |Chest structure| }
    
    Instance 2: Congenital malformation of head and neck 
    [[ |Disease| ]]: 
    [ @rolegroup[1] ] { |Associated morphology| = |malformation|, |Finding site| = |Head structure|, |Occurrence| = |Gongenital| } 
    [ @rolegroup[2] ] { |Associated morphology| = |malformation|,  |Finding site| = |Neck structure|, |Occurrence| = |Gongenital| }

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

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|

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 6th February.