2020-04-22 - SLPG Meeting

Date & Time

20:00 to 22:00 UTC Wednesday 25th March 2020

Location

Zoom meeting: https://snomed.zoom.us/j/471420169

Goals

To finalize syntax for term searching in ECL

Attendees

Chair: Linda Bird
Project Group:

Apologies

Agenda and Meeting Notes

Description	Owner	Notes
Welcome and agenda	Linda Bird
Concrete values	Linda Bird	ON HOLD: SCG, ECL, STS, ETL - Ready for publication, but on hold until after MAG meeting in April confirming requirement for Boolean datatype.
Expression Constraint Language	Linda Bird	WIP ECL Specification ADDED TO DRAFT SYNTAX - Child or self (<<!) and Parent or self (>>!) New examples to be added TERM SEARCH FILTERS - Syntax currently being drafted Examples < 404684003 \|Clinical finding (finding)\| {{ term = "heart att"}} < 404684003 \|Clinical finding (finding)\| {{ term != "heart att"}} – A concept for which there exists a description that does not match – E.g. Find all the descendants of \|Fracture\| that have a description that doesn't contain the word \|Fracture\| < 404684003 \|Clinical finding (finding)\| MINUS * {{ term = "heart att"}} – A concept which does not have any descriptions matching the term < 404684003 \|Clinical finding (finding)\| {{ term = match: "heart att" }} – match is word (separated by white space) prefix any order; Words in substrate are ....; Search term delimiters are any mws < 404684003 \|Clinical finding (finding)\| {{ term = wild: "heart* ack" }} < 404684003 \|Clinical finding (finding)\| {{ term = ("heart" "att") }} < 404684003 \|Clinical finding (finding)\| {{ term != ("heart" "att") }} – matches concepts with a description that doesn't match "heart" or "att" < 404684003 \|Clinical finding (finding)\| {{ TERM = (MATCH:"heart" WILD:"ack") }} < 404684003 \|Clinical finding (finding)\| {{ term = "myo", term = wild:"ack" }} — Exists one term that matches both "myo" and "ack" < 404684003 \|Clinical finding (finding)\| {{ term = "myo" }} {{ term = wild:"ack" }} -– Exists one term that matches "myo", and exists a term that matches "ack" (filters may match on either same term, or different terms) < 404684003 \|Clinical finding (finding)\| {{ term = "hjärta", language = se }} < 404684003 \|Clinical finding (finding)\| {{ term = "hjärta", language = SE, typeId = 900000000000013009 \|synonym\| }} < 404684003 \|Clinical finding (finding)\| {{ term = "hjärta", language = SE, typeId = (900000000000013009 \|synonym\| 900000000000003001 \|fully specified name\|)}} < 404684003 \|Clinical finding (finding)\| {{ term = "hjärta", language = SE, typeId != 900000000000550004 \|Definition\|}} < 404684003 \|Clinical finding (finding)\| {{ term = "hjärta", language = SE, type = syn }} < 404684003 \|Clinical finding (finding)\| {{ term = "hjärta", language = SE, type != def }} < 404684003 \|Clinical finding (finding)\| {{ term = "hjärta", language = SE, type = (syn fsn) }} < 404684003 \|Clinical finding (finding)\| {{ term = "hjärta", language = SE, type != (syn fsn) }} < 404684003 \|Clinical finding (finding)\| {{ term = "cardio", dialectId = 900000000000508004 \|GB English\| }} < 404684003 \|Clinical finding (finding)\| {{ term = "card", dialectId = ( 999001261000000100 \|National Health Service realm language reference set (clinical part)\| 999000691000001104 \|National Health Service realm language reference set (pharmacy part)\| ) }} < 404684003 \|Clinical finding (finding)\| {{ term = "card", dialect = en-gb }} < 404684003 \|Clinical finding (finding)\| {{ dialect != en-gb }} < 404684003 \|Clinical finding (finding)\| {{ term = "card", dialect = ( en-nhs-clinical en-nhs-pharmacy ) }} < 404684003 \|Clinical finding (finding)\| {{ term = "card", dialect = en-nhs-clinical, acceptabilityId = 900000000000548007 \|Preferred\| }} < 404684003 \|Clinical finding (finding)\| {{ term = "card", dialect = en-nhs-clinical, acceptability = prefer }} < 404684003 \|Clinical finding (finding)\| {{ term = "card", dialect = en-nhs-clinical, acceptability != prefer }} < 404684003 \|Clinical finding (finding)\| {{ term = "card", dialect = en-nhs-clinical, acceptability = (prefer accept) }} < 404684003 \|Clinical finding (finding)\| {{ term = "card", dialect = en-nhs-clinical, acceptability = (prefer accept) }} < 404684003 \|Clinical finding\| MINUS * {{ dialect = en-nhs-clinical}} < 73211009 \|diabetes\| MINUS * {{ dialect = en-nz-patient }} < 73211009 \|diabetes\| MINUS < 73211009 \|diabetes\| {{ dialect = en-nz-patient }} < 73211009 \|diabetes\| {{ term = "type" }} MINUS < 73211009 \|diabetes\| {{ dialect = en-nz-patient }} (< 404684003 \|Clinical finding\|:363698007\|Finding site\| = 80891009 \|Heart structure\|) {{ term = "card" }} MINUS < (404684003 \|Clinical finding\|:363698007\|Finding site\| = 80891009 \|Heart structure\|) {{ dialect = en-nz-patient }} < 73211009 \|Diabetes\| {{ term = "type" }} OR < 49601007 \|Disorder of cardiovascular system (disorder)\| {{ dialect = en-nz-patient }} Questions Wild Term Filter - Is the search term everything inside the quotation marks? (note: Match term is tokenized, but wild search is not) In a Wildcard search, is the search term everything inside the quotation marks (including leading and trailing spaces)? I assume so, but since this is different to the Word-prefix-any-order/Match search, I wanted to check. Note: I think we agreed at last week's meeting to tokenize the words within a WPAO/match search, but to leave the search term for the Wildcard search in tact as a single search string. Does everyone still agree? Would it be best to only allow each type of filter once within a filterConstraint. This would allow me to make acceptabilityFilter dependent on the dialectFilter. E.g. NOT ALLOWED: * {{ term = "card", term = "itis" dialect = en-nhs-clinical, dialect = en-gb, acceptability = prefer, acceptability = accept }} ALLOWED: * {{ term = "card", dialect = en-nhs-clinical (accept prefer), dialect = en-gb (prefer) }} ALLOWED: * {{ term = "card", dialect = en-nhs-clinical, dialect != en-nhs-clinical (accept), dialect = en-gb (900000000000548007 \|Preferred\| 545) }} NOT ALLOWED: * {{ term = "card", acceptability = prefer }} ALLOWED: * {{ term = "card", dialect = en-nhs-clinical, acceptability = prefer }} Discussion: We're currently allowing each type of filter to appear more than once within a filterConstraint (in any order). Does it make sense for the same type of filter to be repeated (I've included some examples of 2 dialect filters below, for discussion)? If so, then I can't find a way in the ABNF of restricting the acceptabilityFilter such that it can only be used when a dialect is specified (as discussed last week). If we were to limit each type of filter to appearing only once, then I think this may also impose a required order on the filter types (e.g. term, then type, then language, then dialect, then acceptability), which is not really user-friendly. Here are some examples: * {{ term = "card", dialect = en-nhs-clinical, dialect = en-gb, acceptability = prefer }} This includes 2 dialect filters and 1 acceptability filters. If the comma means "and", then this probably means - "Concepts which have a description that contains a word starting with "card" that is in both the en-nhs-clinical LRS and the en-gb LRS and it has an acceptability of \|Preferred\| in [both or at least one?] LRSs. * {{ term = "card", dialect = en-nhs-clinical, dialect = en-gb, acceptability = prefer, acceptability = accept }} This includes 2 dialect filters and 2 acceptability filters. Would this return any concepts, and what would this mean? Would it, for example, return concepts that have a matching description that is in both the en-nhs-clinical LRS and the en-gb LRS, where that description is \|preferred\| in one LRS and \|acceptable\| in the other LRS? ... or is this just too confusing to be useful? Thoughts? Use cases? * {{ term = "card", acceptability = prefer }} -- Note: This has an acceptability without a dialect. We discussed that this should be illegal ... just need to work out how to constrain this in the ANBF. Deferred for now - Should we consider introducing the 'version' filter into ECL when we add search terms? We had previously discussed this. A possible example could be: (<< 64572001 \|Disease\| VERSION http://snomed.info/sct/900000000000207008/version/20190131) MINUS (<< 64572001 \|Disease\| VERSION http://snomed.info/sct/900000000000207008/version/20180131) Note: I don't think it makes sense to include 'version' inside the filter, as this is different in nature to restricting the matching descriptions of a concept (which the filters are currently doing). i.e. NOT << 64572001 \|Disease\| {{ term = "heart" , version = http://snomed.info/sct/900000000000207008/version/20180131 }} Concept Filters: Deferred for now. Case/accent folding + uni-code collation - What advice should we be giving in the specification? Daniel - Profolding Tokenizing the substrate - What advice should we be giving in the specification? Next steps Answer above questions, and update brief syntax accordingly Test updated brief syntax parser Update long syntax and informative comments to match Test updated long syntax parser Add examples to specification Clarify execution semantics for consistency Document execution semantics in specification SLPG review / Community review Any required updates Publish with PDF DONE - Send recommendation to MAG to consider the following Dialect Alias Refset Alternative 1 - Annotation Refset Dialect_Alias refset : alias + languageRefset-conceptId - e.g. "en-GB", 900000000000508004 Example row referencedComponentId = 999001261000000100 dialectAlias = nhs-clinical Alternative 2 - Add alias as a synonym to the language refset concept Create a simple type refset that refers to the preferred alias for each language refset 2. Constructing a Language Refset from other Language Refset Allowing an intensional definition for a language refset Includes order/precedence of language refsets being combined Potential Use cases - Note some of these will be out of scope for the simple ECL filters Find concepts with a term which matches "car" that is preferred in one language refset and not acceptable in another Find the concepts that ..... have a PT = X in language refset = Y Find the concepts that ..... have a Syn = X in language refset = Y Find the concepts that ... have one matching description in one language, and another matching description in another language Find the concepts that have a matching description that is in language refset X and not in language refset Y Find the concepts that .... have a matching description that is either preferred in one language refset and/or acceptable in another language refset Returning the set of concepts, for which there exists a description that matches the filter 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
Querying Refset Attributes	Linda Bird	Proposed syntax to support querying and return of alternative refset attributes (To be included in the SNOMED Query Language) Example use cases Execution of maps from international substance concepts to AMT substance concepts Find the anatomical parts of a given anatomy structure concept (in \|Anatomy structure and part association reference set) Find potential replacement concepts for an inactive concept in record Find the order of a given concept in an Ordered component reference set Find a concept with a given order in an Ordered component reference set Potential syntax to consider (brainstorming ideas) SELECT ?? SELECT 123 \|referenced component\|, 456 \|target component\| FROM 799 \|Anatomy structure and part association refset\| WHERE 123 \|referenced component\| = (< 888 \|Upper abdomen structure\| {{ term = "heart" }} ) SELECT id, moduleId FROM concept WHERE id IN (< \|Clinical finding\|) AND definitionStatus = \|primitive\| SELECT id, moduleId FROM concept, ECL("< \|Clinical finding") CF WHERE concept.id = CF.sctid AND definitionStatus = \|primitive\| SELECT ??? \|id\|, ??? \|moduleId\| FROM concept ( < \|Clinical finding\| {{ term = "heart" }} {{ definitionStatus = \|primitive\| }} ) Question - Can we assume some table joins - e.g. Concept.id = Description.conceptId etc ?? Examples Try to recast relationships table as a Refset table → + graph-based extension Find primitive concepts in a hierarchy ROW ... ? ROWOF (\|Anatomy structure and part association refset\|) ? (\|referenced component\| , \|target component\|) same as: ^ \|Anatomy structure and part association refset\| ROWOF (\|Anatomy structure and part association refset\|) . \|referenced component\| same as: ^ \|Anatomy structure and part association refset\| ROWOF (\|Anatomy structure and part association refset\|) {{ \|referenced component\| = << \|Upper abdomen structure\|}} ? \|targetComponentId\| ROWOF (< 900000000000496009\|Simple map type reference set\| {{ term = "My hospital"}}) {{ 449608002\|Referenced component\| = 80581009 \|Upper abdomen structure\|}} ? 900000000000505001 \|Map target\| (ROW (< 900000000000496009\|Simple map type reference set\| {{ term = "My hospital"}}) : 449608002\|Referenced component\| = 80581009 \|Upper abdomen structure\| ).900000000000505001 \|Map target\| # ... ? # \|Anatomy structure and part association refset\| ? \|referenced component\ # (\|Anatomy struture and part association refset\| {{\|referenced component\| = << \|Upper abdomen structure\|) ? \|targetComponentid\| ? notation + Filter refinement \|Anatomy structure and part association refset\| ? \|targetComponentId\| \|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}} )? \|targetComponentId\| ( \|Anatomy structure and part association refset\| {{ \|targetComponentId\| = << \|Upper abdomen structure}} ) ? \|referencedComponent\| ( \|My ordered component refset\|: \|Referenced component\| = \|Upper abdomen structure ) ? \|priority order\| ? \|My ordered component refset\| {{ \|Referenced component\| = \|Upper abdomen structure\| }} . \|priority order\| ? \|My ordered component refset\| . \|referenced component\| equivalent to ^ \|My ordered component refset\| ? (<\|My ordered component refset\|) {{ \|Referenced component\| = \|Upper abdomen structure\| }} . \|priority order\| *? (<\|My ordered component refset\| {{ term = "map"}} ) {{ \|Referenced component\| = \|Upper abdomen structure\| }} . \|priority order\| REFSETROWS (<\|My ordered component refset\| {{ term = "map"}} ) {{ \|Referenced component\| = \|Upper abdomen structure\| }} SELECT \|priority order\|* Specify value to be returned ? 449608002 \|Referenced component\|? 734139008 \|Anatomy structure and part association refset\| ^ 734139008 \|Anatomy structure and part association refset\| (Same as previous) ? 900000000000533001 \|Association target component\|? 734139008 \|Anatomy structure and part association refset\| ? 900000000000533001 \|Association target component\|? 734139008 \|Anatomy structure and part association refset\| : 449608002 \|ReferencedComponent\| = << \|Upper abdomen structure\| ? 900000000000533001 \|Association target component\|? 734139008 \|Anatomy structure and part association refset\| {{ 449608002 \|referencedComponent\| = << \|Upper abdomen structure\| }} (? 900000000000533001 \|Association target component\|? 734139008 \|Anatomy structure and part association refset\| : 449608002 \|ReferencedComponent\| = (<< \|Upper abdomen structure\|) : \|Finding site\| = *)
Returning Attributes	Michael Lawley	Proposal (by Michael) for discussion 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\|)
Reverse Member Of	Michael Lawley	Proposal for discussion 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
Expression Templates	Peter G. Williams	ON HOLD WAITING FROM IMPLEMENTATION FEEDBACK FROM INTERNAL TECH TEAM WIP version - https://confluence.ihtsdotools.org/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 $rolegroup[!=SELF] Allow reference to 'SELF' in role group arrays Adding 'sameValue' and 'allOrNone' constraints to information slots - e.g. sameValue ($site), allOrNone ($occurrence) See changes in red here: 5.1. Normative Specification 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: [[0..1]] { [[0..1]] 246075003 \|Causative agent\| = [[+id (< 410607006 \|Organism\| ) @Organism]] } 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 Generate the parser from the ABNF and implement in the Template Service User Interface to a) allow users to specify template at runtime b) tabular (auto-completion) lookup → STL Template Service to allow multiple templates to be specified for alignment check (aligns to none-off) 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	ON HOLD Previous discussion (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
Query Language - Summary from previous meetings	Linda Bird	FUTURE WORK Examples: version and dialect << 64572001 \|Disease\| {{ term = "heart" }} VERSION http://snomed.info/sct/900000000000207008/version/20180131 << 64572001 \|Disease\| {{ synonym = "heart" }} VERSION http://snomed.info/sct/900000000000207008 /version /20180131 << 64572001 \|Disease\| {{ FSN = "heart" }} VERSION http://snomed.info/sct/900000000000207008 /version /20180131 << 64572001 \|Disease\| {{ FSN = "heart" }} VERSION http://snomed.info/sct/900000000000207008 /version /20180131, DIALECT W << 64572001 \|Disease\| {{ preferredTerm = “heart”}} VERSION http://snomed.info/sct/900000000000207008 /version /20180131, DIALECT Y << 64572001 \|Disease\| {{ acceptableTerm = “heart”}} VERSION http://snomed.info/sct/900000000000207008 /version /20180131, DIALECT Y (* {{ term = "heart" }} VERSION http://snomed.info/sct/900000000000207008 /version /20180131, DIALECT Z) MINUS (* {{ term = "heart" }} VERSION http://snomed.info/sct/900000000000207008 /version /20170731, DIALECT W) X MINUS Y WHERE X = * , Y = (* {{ term = "heart" }}) VERSION http://snomed.info/sct/900000000000207008 /version /20180131, DIALECT W Notes Allow nested where, version, language Scope of variables is inner query
Confirm next meeting date/time	Linda Bird	Next meeting is scheduled for Wednesday 22nd April 2020 at 20:00 UTC.

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