Welcome and apologies | | - Question - Are there any conflicts in the current meeting schedule for October business meeting?
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| Actions from last week | | - 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?
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| Introducing term searching to ECL | Linda Bird | Syntax {{ term = [ termSearchType : ] "String" }} Term Search Type - Wild Card Match (collation) - e.g.
- {{ term = wild:"*heart*“ }}
- {{ term = wild (sv):"*hjärta*“ }}
- ??? Perl Regex - e.g.
- {{ term = regex:".*heart.*” }}
- Question: Does the query suddenly become order dependent? Yes
- *** Word Prefix Any Order - e.g.
- {{ term = match:“hear att” }}
- 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".
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| 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|
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| 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|)
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| URI Standard | | - Finalize and publish language and language instance URIs
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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
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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)
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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
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| Other topics | | |
| Confirm next meeting date/time | | The next SLPG meeting will be held in 2 weeks at 20:00 UTC on Wednesday 5th June. |
2 Comments
Ed Cheetham
Linda
Just a quick observation re. 'Does anyone have a regex ABNF?' The nearest thing I can find is at the end of section 9 here (http://pubs.opengroup.org/onlinepubs/9699919799/), divided into BRE and ERE sections.
Regarding the homework from last call, I'm struggling to see what the language-independent defaults (for all the variables in section 9 of the agenda) should be for a lightweight 'ECL with basic term searching', not to mention other unstated assumptions related to Daniel's comments about collation and character normalisation/accent handling. Default substrate is currently defined as:
"the set of active components from the snapshot release (in distribution normal form) of the SNOMED CT versioned edition currently loaded into the given tool"
I'd assume that this necessarily includes the loading of at least one LRS, and as section 10 indicates, the logic for combining multiple LRSs is highly configurable. Whatever, there needs to be agreement on defaults for specifying the LRS, D.type and D.acceptability (via the LRS(s)) and a default D.languageCode (presumably *). However even for 'basic term searching' (given the use cases listed) it should be possible to over-ride/modify all of these, and the syntax needs to handle it. Once we've got through all this metadata, we'd then need to declare how characters in terms are actually indexed. If so, then there isn't much that won't be required in 'basic term searching' left over for any later iteration!
Ed
Linda Bird
Thanks Ed! Very helpful as always!
Kind regards,
Linda.