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Welcome and apologies | |
| | Actions from last week | | - Actions from last week:
- Consider new syntax to support proposed map expression template use case
- Consider new syntax to support proposed expression template map use case
| | Template Syntax | Linda Bird | New requirements - Constrain values across 2 or more replacement slots
- 2 replacement slots must have the same
/different or subsumed/not-subsumed values - for example, - 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
(within a row of input data):
116676008
[[+id]]: [[1..*]] { - Valid Expression (Definition of 16027391000119109 |Bone cyst of bilateral tibias (disorder)|)
- 64572001 |Disease|:
{ 116676008 |Associated morphology|=
[[ +id @morphology ]], Example - 208510002 |Multiple fracture of clavicle, scapula and humerus (disorder)|Default value for slots - for example:[[ + id ]] : { - 66954000 |Bone cyst|,
363698007 |Finding site|=
[[ +id @site constraint ($site[n] != <<$site[!n] ]] }- 719491009 |Bone structure of right tibia|}
{ 116676008 |Associated morphology|= 66954000 |Bone cyst|,
363698007 |Finding site|=
[[ +id (<< 72673000- 719492002 |Bone structure
|) @site default = 72673000 |Bone structure (body structure)| ]]Specifying the definition status of a slot - for example (proximal primitive modelling):- 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
- [[+id]]:
[[1..*]] { |Finding site| = [[ +id @site constraint ( [n] != << $site [!n] ]],
|Associated morphology| = [[ +id @morphology constraint ( [n] = $morphology [!n] ]] }
- Valid Expression (Definition of208510002 |Multiple fracture of clavicle, scapula and humerus (disorder)| )
- 64572001 |Disease|:
{ 363698007 |Finding site|= 85050009 |Bone structure of humerus|,
116676008 |Associated morphology|= 5468008 |Fracture of multiple sites of bone|}
{ 363698007 |Finding site|= 51299004 |Bone structure of clavicle|,
116676008 |Associated morphology|= 5468008 |Fracture of multiple sites of bone|}
{ 363698007 |Finding site|= 79601000 |Bone structure of scapula|,
116676008 |Associated morphology|= 5468008 |Fracture of multiple sites of bone|}
{ 363698007 |Finding site|= 773134001 |Bone structure of multiple body regions|,
116676008 |Associated morphology|= 771485007 |Fracture of multiple bones|}
- 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
[[ + - << 64572001 |Disease| {{ c.definitionStatus = primitive }}
]]- Valid Expression
- 195967001 |Asthma (disorder)|
- Definition status of a templated expression
- Specifying the definition status of
an expression - for example- a templated expression
- Template
- [[ +tok ("===" "<<<") ]] [[ +id ]] : { |Finding site| = [[+id]] }
[[ +tok ("===" "<<<") ]] [[ +id ]] : { - Valid Expression
- === 128272009 |Disorder of lower respiratory system|: 363698007 |Finding site|=
[[+id]] }- 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
[[ +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| }
| | Executing maps | | 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| - 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 27th March. |
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