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Welcome and apologies | | - Question - Should we hold a SLPG meeting in October (in Malaysia)?
| | Actions from last week | | - Actions from last week:
- Update template syntax with new features
- Consider new syntax to support proposed map use case
| | Template Syntax | Linda Bird | 2 new proposals to meet SNOMED International's use cases - Require slotnames to be unique
- Why? To avoid having 2 ways to do the same thing, and to clarify the meaning through value restrictions.
- Template
[[ +id ]]:
{ 116676008 |Associated morphology| = [[ +id @morphology ]],
363698007 |finding site| = [[ +id @findingSite ]] },
{ 116676008 |Associated morphology| = [[ +id ($morphology) ]],
363698007 |finding site| = [[ +id (* MINUS << $findingSite) ]] }
- Valid Expression (Definition of 16027391000119109 |Bone cyst of bilateral tibias (disorder)|)
- 64572001 |Disease|:
{ 116676008 |Associated morphology|= 66954000 |Bone cyst|,
363698007 |Finding site|= 719491009 |Bone structure of right tibia|}
{ 116676008 |Associated morphology|= 66954000 |Bone cyst|,
363698007 |Finding site|= 719492002 |Bone structure of left tibia|}
- Introduce a sameValue constraint (similar to the allOrNone constraint)
- Template
- [[+id]]: [[1..*] @group sameValue (morphology$morphology)]
{ |Finding site| = [[ +id ]],
|Associated morphology| = [[ +id @morphology ]] }
- Valid Expression (Definition of 31580001000004106 |Bilateral sacral insufficiency fracture (disorder)| )
- 702561005 |Insufficiency fracture (disorder)|:
{ 363698007 |Finding site (attribute)|= 736830008 |Bone structure of left half of sacrum (body structure)|,
116676008 |Associated morphology (attribute)|= 22640007 |Pathologic fracture (morphologic abnormality)|}
{ 363698007 |Finding site (attribute)|= 736831007 |Bone structure of right half of sacrum (body structure)|,
116676008 |Associated morphology (attribute)|= 22640007 |Pathologic fracture (morphologic abnormality)|}
Use cases: New concept development, querying based on template matching, and template-based modeling transformation Other requirements - Constrain values across 2 or more replacement slots
- 2 replacement slots must have the same value, different values, subsumed values, or not subsumed values.
- Example A - A clinical finding, with 2 role groups with the same morphology, and finding sites that not subsume each other
Template
[[ +id ]]:
{ 116676008 |Associated morphology| = [[ +id @morphology ]],
363698007 |finding site| = [[ +id (<< |Body structurel MINUS << $findingSite2 ) @findingSite1 ]] },
{ 116676008 |Associated morphology| = [[ +id @morphology ]],
363698007 |finding site| = [[ +id (* MINUS << $findingSite1) @findingSite2 ]] }
Valid Expression (Definition of 16027391000119109 |Bone cyst of bilateral tibias (disorder)|)64572001 |Disease|:
{ 116676008 |Associated morphology|= 66954000 |Bone cyst|,
363698007 |Finding site|= 719491009 |Bone structure of right tibia|}
{ 116676008 |Associated morphology|= 66954000 |Bone cyst|,
363698007 |Finding site|= 719492002 |Bone structure of left tibia|}
- Example B - A clinical finding, with one or more role groups in which the morphology is always the same, and no 2 finding sites subsume each other.
Template - 3 role groups with 3 sites: site[1], site[2], site [3] /// site [1,2]
[[+id]]:
[[1..*] @group1] { |Finding site| = [[ +id (* MINUS << $site[! SELF ] ) @site ]],
|Associated morphology| = [[ +id ($morphology [! SELF] ) @morphology ]] }
Valid Expression (Definition of 31580001000004106 |Bilateral sacral insufficiency fracture (disorder)| )702561005 |Insufficiency fracture (disorder)|:
{ 363698007 |Finding site (attribute)|= 736830008 |Bone structure of left half of sacrum (body structure)|,
116676008 |Associated morphology (attribute)|= 22640007 |Pathologic fracture (morphologic abnormality)|}
{ 363698007 |Finding site (attribute)|= 736831007 |Bone structure of right half of sacrum (body structure)|,
116676008 |Associated morphology (attribute)|= 22640007 |Pathologic fracture (morphologic abnormality)|}
- Default value for replacement slot
- Default value for authoring and template-driven modelling transformations
- Example A - Default finding site of 72673000 |Bone structure|
- Template
- [[ + id ]] :
{ |Finding site| = [[ +id (<< 72673000|Bone structure|) @site default (72673000 |Bone structure (body structure)|) ]]
- Definition status of a replacement slot
- Specifying whether the value used in a replacement slot must be primitive or defined
- Example A - When proximal primitive modelling, the focus concept must be a primitive concept
- Template - Requires use of more expressive query language with filters
- [[ + id (<< 64572001 |Disease| {{ c.definitionStatus = primitive }}) ]]
- Valid Expression
- 195967001 |Asthma (disorder)|
- Definition status of a templated expression
- Specifying the definition status of a templated expression
- Template
- [[ +tok ("===" "<<<") ]] [[ +id ]] : { |Finding site| = [[+id]] }
- Valid Expression
- === 128272009 |Disorder of lower respiratory system|: 363698007 |Finding site|= 39607008 |Lung structure|
- <<< 128272009 |Disorder of lower respiratory system|: 363698007 |Finding site|= 39607008 |Lung structure|
- Attributes used in repeating role groups
- Constraining the set of attributes that appear in a repeating role group
- Example 1 - In a given matching expression, either all the role groups include the attribute |site|, or none of the role groups include the attribute |site|. Similarly, either all role groups include |Occurrence|, or none of the role groups do.
- Template - using allOrNone
- [[+id]]: [[1..* @group1 allOrNone (site$site), allOrNone(occurrence$occurrence)]]
{ [[1..1]] |Associated morphology| = [[ +id @morphology ]],
[[0..1 @site]] |Finding site| = [[ +id ]],
[[0..1 @occurrence]] |Occurrence| = [[ +id ]] } - Valid Expression - Injury of head, neck and chest
- [[ |Disease| ]]:
{ |Associated morphology| = |Injury|, |Finding site| = |Head structure| }
{ |Associated morphology| = |Injury|, |Finding site| = |Neck structure| }
{ |Associated morphology| = |Injury|, |Finding site| = |Chest structure| }
- Valid Expression - Congenital malformation of head and neck
- [[ |Disease| ]]:
{ |Associated morphology| = |malformation|, |Finding site| = |Head structure|, |Occurrence| = |Congenital| }
{ |Associated morphology| = |malformation|, |Finding site| = |Neck structure|, |Occurrence| = |Congenital| }
- Example 2 - Some of the optional attributes must either always or never appear in each instance of a repeating role group
- [[+id]]: [[1..* allOrNone(morph$morph) ]]
{ [[ 1..1 ]] |Method| = [[+id]],
[[ 0..1 @morph ]] |Direct morphology| = [[+id ]],
[[ 0..1 ]] |Procedure site - Direct| = [[+id]],
[[ 0..1]] |Using device| = [[+id]] ,
[[ 0..1]] |Has intent| = [[+id]] }
- Valid Expression - Closure of skin by suture
- |Procedure|:
{ |Method| = |Closure - action|, |Procedure site - Direct| = |Skin structure| , |Using device| = |Surgical suture, device|}
- Valid Expression - Core needle biopsy of skin using ultasonographic guidance
- |Procedure|:
{ |Method| = |Ultrasound imaging - action|, |Procedure site - Direct| = |Skin structure| , |Has intent| = |Guidance intent|}
{ |Method| = |Biopsy - action|, |Procedure site - Direct| = |Skin structure| , |Using device| = |Core biopsy needle, device|}
- Valid Expression - Toilet and suture of wound
- |Procedure|:
{ |Method| = |Surgical toilet - action|, |Direct morphology| = |Wound| }
{ |Method| = |Closure - action|, |Direct morphology| = |Wound|,
|Procedure site - Direct| = |Skin structure|, |Using device| = |Surgical suture, device| }
- Example 3 - Some of the optional attributes must either always or never appear in each instance of an inner-nested, repeating role group
- |Finding with explicit context|: [[1..2]]
{ [[ 1..1 ]] |Finding context| = [[+id]],
[[ 1..1 ]] |Temporal context| = [[+id ]],
[[ 1..1 ]] |Subject relationship context| = [[+id]],
[[ 1..1]] |Associated finding| = ( [[+id]] : [[1..* allOrNone(site$site) allOrNone(Occurrence$Occurrence) ]]
{ [[1..1]] |Associated morphology| = [[ +id @morphology ]],
[[0..1 @site]] |Finding site| = [[ +id ]],
[[0..1 @occurrence]] |Occurrence| = [[ +id ]] } ) }
- Valid Expression - History of Injury of head, neck and chest, and of congenital malformation of head and neck
- |Finding with explicit context|:
{ |Finding context| = |Done|,
|Temporal context| = |In the past|
|Associated finding| = ( |Disease| :
{ |Associated morphology| = |Injury|, |Finding site| = |Head structure| }
{ |Associated morphology| = |Injury|, |Finding site| = |Neck structure| }
{ |Associated morphology| = |Injury|, |Finding site| = |Chest structure| } ) }
{ |Finding context| = |Done|,
|Temporal context| = |In the past|,
|Associated finding| = ( |Disease| :
{ |Associated morphology| = |malformation|, |Finding site| = |Head structure|, |Occurrence| = |Gongenital| }
{ |Associated morphology| = |malformation|, |Finding site| = |Neck structure|, |Occurrence| = |Gongenital| } ) }
- Example 4 - Some of the optional attributes must either always or never appear in each instance of an outer-nested, repeating role group
- |Finding with explicit context|: [[1..2 allOrNone (site$site), allOrNone(occurrence$occurrence), allOrNone(relationship$relationship) ]]
{ [[ 1..1 ]] |Finding context| = [[+id]],
[[ 1..1 ]] |Temporal context| = [[+id ]],
[[ 0..1 @relationship]] |Subject relationship context| = [[+id ]],
[[ 1..1]] |Associated finding| = ( [[+id]] : [[1..* ]]
{ [[1..1]] |Associated morphology| = [[ +id ]],
[[0..1 @site]] |Finding site| = [[ +id ]],
[[0..1 @occurrence]] |Occurrence| = [[ +id ]] }
- Valid Expression - History of Injury of head, neck and chest, and of malformation of head and neck
- |Finding with explicit context|:
{ |Finding context| = |Done|,
|Temporal context| = |In the past|,
|Subject relationship context| = |Subject of record|,
|Associated finding| = ( |Disease| :
{ |Associated morphology| = |Injury|, |Finding site| = |Head structure| }
{ |Associated morphology| = |Injury|, |Finding site| = |Neck structure| }
{ |Associated morphology| = |Injury|, |Finding site| = |Chest structure| } ) }
{ |Finding context| = |Done|,
|Temporal context| = |In the past|,
|Subject relationship context| = |Subject of record|,
|Associated finding| = ( |Disease| :
{ |Associated morphology| = |malformation|, |Finding site| = |Head structure| }
{ |Associated morphology| = |malformation|, |Finding site| = |Neck structure| }
| | Introducing term searching to ECL | Linda Bird | Syntax term = [lexicalSearchType ":"] String Lexical Search Type - Wild Card Match (collation) - e.g.
- {{ term = wild (sv):"*heart*“ }}
- Perl Regex - e.g.
- {{ term = regex:".*heart.*” }}
- Word Prefix Any Order - e.g.
- {{ term = match:“hear att” }}
- Default (wild card match) - e.g.
Examples - << 64572001|Disease| {{ term= “*heart*” }}
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' - e.g. << 64572001|Disease| {{ term = “*heart*” }}FROM 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"?
- 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 | | 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 | | - Finalize and publish language and language instance URIs
| Query Language
- Summary from previous meetings
| | Examples: version and language Notes
- Allow nested where, version, language
- Scope of variables is inner query
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| 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
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
| | Other topics | | | | Confirm next meeting date/time | | The next SLPG meeting will be held in 2 weeks at 20:00 UTC on Wednesday 22nd May. |
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