Welcome and agenda | All |
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ECL Design:
Enable support for LOINC codes and other alternate identifiers in ECL | | - We have been asked to consider how LOINC codes (and other alternate identifiers) could be used in ECL to support the Regenstrief collaboration.
- How can LOINC codes be used in the SNOMED ECL language to select these concepts?
- LOINC concepts with LOINC codes are being created in a new LOINC SNOMED-CT extension.
The LOINC codes will be stored in the redesigned Alternate Identifier file. The concepts will also have a SNOMED CT concept identifier. - Example LOINC codes are available in the LOINC FHIR concept map - https://fhir.loinc.org/ConceptMap/?url=http://loinc.org/cm/loinc-parts-to-snomed-ct
- Discuss:
- Example Identifier Scheme:
- Concept Id: 705114005 |LOINC Code System (qualifier value)|
- URI: "http://loinc.org/"
- Second URI annotation with a resolvable URL?
- Alias: "LOINC"
- Whatever alias is used it should included as an annotation on the concept that represents the code system
- Considering seeding aliases with existing UMLS short codes
- ML: May not be unambiguous
- US based system.
- Chosen syntax:
- "LOINC#LP838383" |Glucose level|
- C1: "LOINC#*"
- This could match anything in the substrate that has an identifier in the LOINC scheme.
- Aliases can not have spaces. This seems okay, use a dash instead where needed.
- Allow these alternate identifiers in any place that a concept id can be used
- Examples:
- << "LOINC#LP838383" |Glucose level|
- Could quoting be optional? Only when necessary?
- Should we be able to request a preference for the identifier scheme used in the response?
- We reviewed the ABNF changes and tested in the ANTRL web based sandbox http://lab.antlr.org/
- Concerns about the semantics of LOINC:
- We need to understand the semantics of the LOINC SNOMED CT Edition so that we can provide advice about how these LOINC alternate identifiers in ECL should be used. Kai Kewley to contact Jim more information. Should LOINC attributes be used?
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ECL v2.2 Proposal Support translation of data into a subset like GPS | All | - Support the conversion of codes between Full SNOMED and GPS (highest and lowest match). Syntactic sugar to make it easy?
Find the leaves of a set of concepts - example use case (find the proximal set in the international core / or in the IPS) - example: - Example use cases
- Proximal ancestors in a specific module: ( >> |concept| {{ C moduleId = 1234 }} ) MINUS ( > (>> |concept| {{ moduleId = 1234 }}) )
- X = "> |concept| {{ C moduleId = 1234 }}"
- Leaf nodes: < |concept| MINUS (> (< |concept|))
- Removing any redundant concepts (ie subsumes another concept) from a set of concepts
- ^ |ref set| MINUS (> (^ |ref set|)
Find the root concepts of a set of concepts - example use case (find the proximal set in the international core / or in the IPS) - example: - Example use cases for
- Root nodes of an extension module: (< |concept| {{ module = X}}) MINUS (< (< |concept| {{ module = X}}))
- Only the 'root' concepts from a set of concepts
- ^ |ref set| MINUS (< (^ |ref set|)
- X MINUS (> X)
- Chosen syntax:
- !!< (bottom)
- !!> (top)
- Pros: Easy to type. Familiar syntax. Different enough from <! and >!
- Cons: None that we can think of
- Examples needed
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| The items below are currently on hold |
| URIs for language instances | | ON HOLD |
| ECL v2.1 - Requirement proposals (to be archived) | All | ON HOLD - Potential requirements for ECL v2.1 - Discussion and brainstorming - Daniel's comments
- Context supplements - e.g.
- << 56265001 |Heart disease| {{ + CONTEXT }} – This syntax is too general, as there is a risk of including absent finding, not-done procedure and family history
- << 56265001 |Heart disease| {{ + CONTEXT-DEFAULT }} ? – What would this mean?
- Brief form:
- [[@ecl_query]] {{ + Context (Temporal = [[ @temporal_value]] }}
- Expanded form:
- [[ @ecl_query ]] OR (< 243796009 |Situation with explicit context|:
{ ( 246090004 |Associated finding| = ( [[ @ecl_query ]] )
OR |Associated procedure| = ( [[ @ecl_query ]] )
( |Procedure context| = |Done| OR |Finding context| = |Known present|),
|Subject relationship context| = |Subject of record|,
|Temporal context| = [[ @temporal_value ]] } )
- Example 1: << |Heart procedure| {{ + Context (Temporal = *) }}
- << |Heart procedure| OR (< 243796009 |Situation with explicit context|:
{ 246090004 |Associated finding| = << 56265001 |Heart disease|,
|Procedure context| = |Done|,
|Subject relationship context| = |Subject of record|,
|Temporal context| = * } ) - Example 2: (<< |Heart disease| OR << |Heart procedure| ) {{ + Context (Temporal = *) }}
- << |Heart procedure| OR (< 243796009 |Situation with explicit context|:
{ ( 246090004 |Associated finding| = (<< |Heart disease| OR << |Heart procedure| )
OR |Associated procedure| = ( << |Heart disease| OR << |Heart procedure| ) )
( |Procedure context| = |Done| OR |Finding context| = |Known present|),
|Subject relationship context| = |Subject of record|,
|Temporal context| = * } )
- << 56265001 |Heart disease| {{ + Context (Temporal = *, FindingContext=<<|Known present| }}
- Will return all types of heart disease, plus concepts like 394886001 |Suspected heart disease (situation)|, and 429007001 |History of cardiac arrest (situation)|
- Expands to:
- However, you may want to exclude (or include) specific contexts - for example:
- To ensure that the finding was about the subject of the record (and not a family history, e.g. to exclude 429959009 |Family history of heart failure (situation)|), you could say:
- << 56265001 |Heart disease| {{ + CONTEXT (relationship = 410604004 |Subject of record| }}
- To ensure that the finding was 'Known present' (e.g. to exclude 394926003 |Heart disease excluded (situation)|), you could say:
- << 56265001 |Heart disease| {{ + CONTEXT (finding_context = << 410515003 |Known present| }}
- To ensure that the finding was about the subject of the record AND known present, you could say:
- << 56265001 |Heart disease| {{ + CONTEXT (relationship = 410604004 |Subject of record|,
finding_context = << 410515003 |Known present| }}
- ?? Is there any use case for restricting adding temporal context? (e.g. temporal != << 410513005 |In the past|)
- Is any more syntactic sugar required? E.g.
- {{ + CONTEXT (relationship = self, finding context = present, temporal != past) }}
- {{ + CONTEXT (self, present, ! past) }}
- Other ideas? Common profiles?
- --------------------------
- Ability to return attribute types (see proposal below)
- [ attributes ] << 125605004 |Fracture of bone (disorder)|
- << 125605004 |Fracture of bone (disorder)| . Attributes
- << 125605004 |Fracture of bone (disorder)| . (<< 125605004 |Fracture of bone (disorder)| . Attributes )
- [ attribute, value] << 125605004 |Fracture of bone (disorder)|
- -------------------------
- Reverse membership (see below)
- Which reference sets "contain" the given concept(s) - e.g. 421235005 |Structure of femur|?
- 421235005 |Structure of femur| . Refsets
- 421235005 |Structure of femur|. Refsets [ referencedComponentId ]
- 421235005 |Structure of femur| . Refsets [ targetComponentId ]
- --------------------------
- Other?
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| Returning Attributes | Michael Lawley | ON HOLD - - 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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| Reverse Member Of | Michael Lawley | ON HOLD - 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
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| Dynamic Templates |
| - ON HOLD -
- Continue discussion on dynamic templates
- Inter-attribute dependencies
- Acute/Chronic and Inflammation - Adding a clinical course requires specializing the inflammation morphology
 - E.g. |Pyelonephritis| : |Clinical course| = |Chronic|
should be
|Pyelonephritis| : |Clinical course| = |Chronic|, |Associated morphology| = |Chronic inflammation| - E.g. |Pyelonephritis| : |Clinical course| = |Sudden onset AND/OR short duration|
should be
|Pyelonephritis| : {|Clinical course| = |Sudden onset AND/OR short duration||, |Associated morphology| = |Acute inflammation|
- Infectious Causative Agents - Adding a |causative agent| = |Domain Bacteria| or |Virus| requires adding a |Pathological process| = |Infectious process|
- E.g. |Nephritis|: |Causative agent| = |Domain bacteria|
should be
|Nephritis|: |Causative agent| = |Domain bacteria|, |Pathological process| = |Infectious process|
- Congenital and Acquired - Adding an |Occurrence| of |Congenital| to a focus concept with an abnormal morphology, requires adding a |Pathological process| of |Pathological development process|
- E.g. |Koilonychia|: |Occurrence| = |Congenital|
should be
|Koilonychia|: |Occurrence| = |Congenital|, |Pathological process| = |Pathological developmental process|
- Situations with Explicit Context
- if the procedure context = |Planned|, then the temporal context should be << |Current of specified time|
- If the procedure context = |In progress|, then the temporal context should be << |Current|
- If the procedure context = |Performed| or |Done|, then the temporal context should be << |Current or past (actual)|
- Note: for this use case (of |Procedure with explicit context|) perhaps we just recommend (or require) that the full role group is spelled out.
- Next steps
- Representation of the content rules
- Who creates the complete list of rules and how?
- What formalism?
- Determine which are mandatory and which are optional
- Implementation of content rules - e.g.
- Guided data entry by pre-populating role groups in expression template based on definition of focus concepts (for design-time use, such as mapping)
- Mandatory content rules could be added to transform process
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| URIs for Extended Editions |
| ON HOLD - How to refer to an 'extended edition' using a URI - e.g. "International Edition plus the following 2 nursing modules: 733983009 |IHTSDO Nursing Health Issues module|and 733984003 |IHTSDO Nursing Activities module| Use Case - Need to execute an ECL, that refers to "^ 733991000 | Nursing Health Issues Reference Set (foundation metadata concept) |" and/or "^ 733990004 | Nursing Activities Reference Set (foundation metadata concept) |", where the substrate includes the international edition, plus the modules that include these reference sets July 2020 International Edition URI: http://snomed.info/sct/900000000000207008/version/20200731 July 2020 International Edition + nursing modules URI ?? - For example: |