Welcome and agenda | | Welcome to new attendees |
| ECL v1.7 - Access to historical refsets | All | Proposal To leverage the existing memberOf (^) function, which currently only brings back the 'referencedComponentId', rather than the whole 'member' (i.e. row) as you might expect a 'memberOf' function to do. If we defined an expanded form of the current 'memberOf' function, which explicitly shows that by default we're selecting attributeOrder = 0 from the member, then the following 2 ECL would be equivalent. - ^ 447562003 |ICD-10 complex map refset|
- ^ [referencedComponentId] 447562003 |ICD-10 complex map refset|
This would allow us to select other columns of the refset using the same memberOf function - e.g. - ^ [mapTarget] 447562003 |ICD-10 complex map refset|
And we could then introduce a 'Member filter' with a similar attribute reference - e.g. - ^ [referencedComponentId] 447562003 |ICD-10 complex map refset| {{ M mapTarget = "L56.2" }}
Additional Examples - Find all the inactive concepts associated by any historical association to a subtype of 195967001 | Asthma (disorder) |
- ^ < 900000000000522004 | Historical association refset| {{ M targetComponentId = < 195967001 |Asthma| }}
- Find all the SNOMED CT concepts that map to ICD-10 code "L56.2"
- ^ 447562003 |ICD-10 complex map refset| {{ M mapTarget = "L56.2" }}
- ^ [referencedComponentId] 447562003 |ICD-10 complex map refset| {{ M mapTarget = "L56.2" }}
- Find the SNOMED CT concept that maps to ICD-10 code "L56.2" with a mapRule = 1 and mapGroup = 1
- ^ [referencedComponentId] 447562003 |ICD-10 complex map refset| {{ M mapGroup = #1, mapPriority = #1, mapTarget = "L56.2" }}
- Find the reason that concept 67415000 |Hay asthma| was inactivated (answer: 900000000000482003 |Duplicate component|)
- ^ [valueId] 900000000000489007 |Concept inactivation indicator attribute value refset| {{ M referencedComponentId = 67415000 |Hay asthma| }}
- Find the active concept that is the 'same as' inactivated concept 67415000 |Hay asthma|
- ^ [targetComponentId] 900000000000527005 |SAME AS association refset| {{ M referencedComponentId = 67415000 |Hay asthma| }}
Questions - Should we allow the column headers (ie fields) from the file name and/or the refset attribute concept to be used and/or the attributeOrder?
ANSWER: OPTION 2 only
- OPTION 2: ^ < 900000000000522004 | Historical association refset| {{ M targetComponentId = < 195967001 |Asthma| }}
- ^ [referencedComponentId] < 900000000000522004 | Historical association refset| {{ M targetComponentId = < 195967001 |Asthma| }
- Should we allow a 'or self' operator, to make it more efficient to create historical subsets - e.g. the following expression constraint would return all the inactive concepts that were replaced by an equivalent subtype of |Asthma| PLUS all the subtypes of |Asthma| as well. This would be useful for finding all the matches that you may need to look for in a health record.
- FULL: < 195967001 |Asthma| OR ^ 900000000000527005 |SAME AS association refset| {{ M targetComponentId = < 195967001 |Asthma| }}
- << 195967001|asthma| {{ +HISTORY-STRICT }} – or HISTORY-SAME
- NEW editorial rules - SAME_AS
- Example use cases requiring very high confidence – e.g. Clinical decision support
- << 195967001|asthma| {{ +HISTORY-DEFAULT }} – or HISTORY-BASIC, HISTORY-GENERAL, HISTORY-BROAD
/* Adds inactive referencedComponents with matching targetComponentId for ALL historical association refsets */- NEW editorial rules - HISTORY-SAME + REPLACED_BY (and WAS_A), PARTIALLY_EQUIVALENT_TO (only for conjunction - includes the parts) – e.g. Clinical research, Clinical audit
- << 195967001|asthma| {{ +HISTORY-ANY }} – or HISTORY-ALL, HISTORY-FULL
- NEW editorial rules - HISTORY-DEFAULT + ALTERNATIVE, POSSIBLY_EQUIVALENT_TO (includes disjunction with ambiguity), POSSIBLY_REPLACED_BY
- e.g. to identify patients for review of notes
- e.g. potential clinical trial candidates (to be manually reviewed before selection)
- EXAMPLES (based on use cases defined by MAG) Example list
- QUESTIONS for EAG subgroup
- How are the changes to the historical association rules being managed?
- Will existing historical associations be updated to match the new editorial policy?
- How will transitive dependencies be managed moving forward?
- GOOD NEWS! Inactive concepts will always point towards an active target (except for a few exceptions in the distant past)
- OTHER
- << 195967001|asthma| {{ +HISTORY (< 900000000000522004 | Historical association refset|) }}
- << 195967001|asthma| {{ +HISTORY (90000000527005 |SAME AS association reference set| 900000000000523009 |POSSIBLY EQUIVALENT TO association reference set|) }} /* uses only the identified historical association refsets */
- << 195967001|asthma| {{ +HISTORY (SAME_AS POSSIBLY_EQUIVALENT_TO)
- Should we allow more than one column in a refset to be selected? What should the rules be about using this inside a subExpressionConstraint? e.g.
- ^ [*] 447562003 |ICD-10 complex map refset|
- ^ [referencedComponentId, mapTarget] 447562003 |ICD-10 complex map refset|
- Should we allow filters to be nested inside other filters? e.g.
Reference set descriptor templates (for easy reference) See discussion below "Querying Refset Attributes" |
| onlyThe items below are currently on hold |
| Postcoordination Topics |
| - Discuss feedback on transformation implementation
- Resources
- Recap of SNOMED on FHIR discussions
- What is the functionality scope of a terminology server that supports postcoordination? For example, does it include:
- Classifying multiple expressions in a single substrate? What are the use cases for this?
- Assigning (local) identifiers to expressions? What are the use cases for this?
- Autogenerating or assigning a term to an expression? What are the use cases for this?
- Does a terminology server that supports postcoordination, include all the functions of an expression repository?
- What is the relationship between a terminology server that supports postcoordination, and an expression repository?
- Outstanding questions
- What are the pros and cons of extending SCG to allow an expression as the focus of a postcoordinated expression?
- Note: This was raised in context of a NNF generated over a postcoordinated substrate, where the proximal parent is an expression
- Example of using expressions in focus concept
- ( 125605004 |Fracture of bone|:363698007 |finding site| = 84167007 |Foot bone| ) :
272741003 |Laterality| = 7771000 |Left| - 125605004 |Fracture of bone|:363698007 |finding site| = 84167007 |Foot bone| ,
272741003 |Laterality| = 7771000 |Left|
- What is the expected NNF when classifying an expression that is equivalent to a precoordinated concept? For example:
- Expression that is equivalent to 111273006 |Acute respiratory disease|
- 64572001 | Disease (disorder) | :
{263502005 |Clinical course (attribute)| = 424124008 |Sudden onset AND/OR short duration (qualifier value)|}
{363698007 |Finding site (attribute)| = 89187006 |Airway structure (body structure)|} - Options:
- 111273006 |Acute respiratory disease| :
{263502005 |Clinical course| = 424124008 |Sudden onset AND/OR short duration|}
{363698007 |Finding site| = 89187006 |Airway structure|} - 50043002 |Disorder of respiratory system (disorder)| +
2704003 |Acute disease (disorder)| :
{263502005 |Clinical course| = 424124008 |Sudden onset AND/OR short duration|}
{363698007 |Finding site| = 89187006 |Airway structure|} - Other?
- Recap of internal discussions with Content Team
- Inter-attribute dependencies
- Grouping rules
|
| Dynamic Templates |
| - 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
|
| Postcoordination Use Case Examples | All | Example 1 - Dentistry / Odontogram - Requires an expression template to create expressions.
- Resulting expression still requires a transformation to make it classifiable
Example 2 - Terminology binding - Uses a fixed expression template to combine codes entered into separate fields
- The procedure+laterality example still requires a transformation to make it classifiable
Example 3 - Mapping - Design-time activity
- Map targets may not be able to be fully represented using concept model attributes
- In many cases, an extension (with primitive concepts) should be recommended where there are gaps in the mapping
- There may be some cases in which postcoordination is helpful (e.g. LOINC to SNOMED CT map)
Example 4 - Natural Language Processing - Usually run-time activity.
- May require manual confirmation of coding suggestions (unless low clinical risk, eg for suggesting relevant patient records for manual review)
|
| Postcoordination Guidance | | Practical Guide to Postcoordination - Proposal - Use syntax (i.e. braces) to distinguish refinement vs new role group
- There should be a syntactic distinction between refinement and constructive addition (ie adding a new role group). That is:
- 83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device|
- is classified as (i.e. the refinement is added to the role groups in the definition of the focus concept(s)):
- 83152002 |Oophorectomy| : { 405815000 |Procedure device| = 122456005 |Laser device| }
- However, for attributes which are always self-grouped - i.e. Priority, Due to, After, Before, During, Clinical course, Temporally related to, and all Observable entity attributes (see Relationship Group), these must always be put into their own role group:
- 125605004 | Fracture of bone |: 42752001 | Due to (attribute) | = 1912002 | Fall |
- is classified as:
- 125605004 | Fracture of bone |: { 42752001 | Due to (attribute) | = 1912002 | Fall | }
- or
- 125605004 | Fracture of bone |:
{ 363698007 |Finding site| = 272673000 |Bone structure|,
116676008 |Associated morphology | = 72704001 |Fracture| }
{ 42752001 | Due to (attribute) | = 1912002 | Fall | }
- Proposal: Expression forms needed for this (see 3.4 Transforming Expressions)
- Close to user form - e.g. 83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device|
- Canonical close to user form - e.g. 83152002:405815000=122456005
- Classifiable form (SCG) - e.g. 83152002:{260686004=129304002,405813007=15497006,405815000=122456005}
- PLUS Classifiable form (OWL) - e.g.
- EquivalentClasses(:123063
ObjectIntersectionOf (:71388002
ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf( ObjectSomeValuesFrom(:260686004 :129304002)
ObjectSomeValuesFrom(:405813007 :15497006))))
- Necessary normal form - e.g. 83152002+416376001:{260686004=129304002,405813007=15497006,405815000=122456005}
- PLUS Necessary normal form (tables)
- Relationships:
- (123063 116680003 83152002) - 0
- (123063 260686004 129304002) - 0
- (123063 405813007 15497006) - 1
- (123063 405815000 122456005) - 1
- Primitive expressions - "<<<" (only useful in a mapping context) → .... relies on the assigned identifier (which are necessarily semantically unique).
- Proposed Transformation Rules - Refinements (in valid domain of focus concepts)
Close-to-user-form - IF the grouping of the refinement is not concept model valid THEN
If there is a single (non-self-grouped) role group in the definition of the focus concept, then any ungrouped (but groupable) refinements are merged with this role group
If there is more than one (non-self-grouped) role group in the definition then flag as ambiguous and require refinement
NEED TO FIND a realistic clinical example where this may occur // Prevent failing cases from coming up // use template
ALTERNATIVE: Refinement is applied to all (non-self-grouped) role groups in the definition
Self-grouped attributes in the refinement are grouped on their own - i.e. Priority, Due to, After, Before, During, Clinical course, Temporally related to, and all Observable entity attributes (see Relationship Group)
Self-grouped attributes in the definition of the focus concept(s) are left unchanged - Single refinement
83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device| - Two groupable refinements
83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device|, 363700003 |Direct morphology| = 367643001 |Cyst | - One groupable refinement with one self-grouped refinement
83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device|, 260870009 |Priority| = 394849002 |High priority|
- Refinement attribute matches (or subsumed by) attribute in focus concept's definition
83152002 |Oophorectomy| : 260686004 |Method| = 277261002 |Excision biopsy (qualifier value)| - Refinement explicitly in role group
83152002 |Oophorectomy| : { 260686004 |Method| = 281615006 | Exploration - action | , 405813007 |Procedure site - direct| = 367643001 |Cyst | }
Proposed Transformation Rules - Refinements (NOT in valid domain of focus concepts)
Close-to-user-form - IF the refinement's attribute is not valid for the domain of the focus concept THEN
If there is a single role group in the definition of the focus concept, which has an attribute value in the domain of the refinement's attribute THEN nest the relevant attribute value with the refinement added to the attribute value
(Note: It doesn't matter if the role group is self-grouped or not (see example 1 below)
If there is more than one role group in the definition of the focus concept, which has an attribute value in the domain of the refinement's attribute THEN (non-self-grouped) role group in the definition then flag as ambiguous and require refinement - Left aural temperature
- 415974002 |Aural temperature|: 272741003 |Laterality| = 7771000 |Left|
- → 415974002 |Aural temperature|: {704327008 |Direct site| = (42859004 |Ear drum|: 272741003 |Laterality| = 7771000 |Left|)}
- Malignant tumor of right ovary
- Other Example - Emergency excision of appendix
- 80146002 | Excision of appendix | :
260870009 |Priority| = 25876001 |Emergency|
- Other Example - Fracture of bone
- 125605004 |Fracture of bone|: 363698007 |finding site| = 84167007 |Foot bone|
- 125605004 |Fracture of bone|: {363698007 |finding site| = 84167007 |Foot bone| }
- 125605004 |Fracture of bone|: {116676008 |Associated morphology| = 72704001 |Fracture|,
363698007 |finding site| = 84167007 |Foot bone| } - 64572001 |Disease|: {116676008 |Associated morphology| = 72704001 |Fracture|,
363698007 |finding site| = 84167007 |Foot bone| }
|
| The items below are currently on hold |
| Other Options for Future Progress |
| - URIs for draft editions
- ECL extensions
- Primitive/Defined filters → concept filter
- Concept+Description filters (e.g. effectiveTime, module, active)
- Accessing Refset attributes → (e.g. historical association refsets) → historical ECL
- OR use full syntax to be able to query any table (e.g. Relationship table) - ie expand ECL into something more verbose (e.g. SNOMED query language)
- Template extensions
|
| 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: |
| Querying Refset Attributes | Linda Bird | ON HOLD - 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 | ON HOLD - 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 | ON HOLD - 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 | | - 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
| | FUTURE WORK Examples: version and dialect Notes
- Allow nested where, version, language
- Scope of variables is inner query
|
1 Comment
Jeremy Rogers
Linda asked me to dig a little more in the MOVED_TO | MOVED_FROM stuff, and provide examples:
Over the years to Jan 2021, the International Core has "gifted" a cumulative total of 17,590 codes to a select band of exactly five other loci of editorial control as recipients, with each such transfer being signalled by 2 elements:
This MOVED_TO manoevre is ongoing today:
2002
14
2003
883
2004
7
2005
77
2006
107
2007
47
2008
366
2009
12890
2010
46
2011
6
2014
2423
2015
67
2016
88
2017
16
2018
190
2019
77
2020
181
2021
105
The lucky recipients of this traffic have so far been limited to just these five namespaces:
12062 codes to 370137002 Extension Namespace 1000000
415 codes to 370138007 Extension Namespace 1000001
167 codes to 384597007 Extension Namespace 1000002
4931 codes to 416516009 Extension Namespace 1000009
15 codes to 442502009 Extension Namespace 1000124
...which we can (rather painfully) decode using the not-very-machine-readable Namespace Identifier Registry at https://cis.ihtsdotools.org/info/index.html?home=namespaces to be actually:
12062 codes to 370137002 Extension Namespace 1000000 → UK Clinical Extension
415 codes to 370138007 Extension Namespace 1000001 → UK Drug Extension
167 codes to 384597007 Extension Namespace 1000002 → SNOMED International (huh?)
4931 codes to 416516009 Extension Namespace 1000009 → Veterinary Terminology Service Laboratory, USA (Veterinary Extension)
15 codes to 442502009 Extension Namespace 1000124 → National Library of Medicine (US Drug Extension)
Note that there has also been some quantity of traffic in the reverse direction.
For example, the UK Extensions record that they've historically MOVED a total of 764 conceptIds to the International Core:
Regardless of who is giving what to whom, however, from the point of view of any effort to repair data involving inactive codes, the MOVED_TO association is of course utterly useless.
What you really need are the MOVED_FROM relationships that the MOVED_TOs live in hope of eventually matching up with: each MOVED_FROM relationship will state a 1:1 bidirectional equivalent relationship that holds eternally between the original inactive identifier and an entirely different and new identifier that was created by the recipient NRC in a different namespace, after editorial control of the underlying idea MOVED_TO it.
As an example of such pairing, in the UK we have the following pair of lines in the union of all der2_cRefset_AssociationSnapshot files in our current release:
or, in more human readable form:
20180731 (CORE) 412785001 Women's refuge (qualifier value) MOVED_TO 370137002 Extension Namespace 1000000 (namespace concept)
20181001 (UK CLINICAL) 725291000000102 Women's refuge (qualifier value) MOVED_FROM 412785001 Women's refuge (qualifier value)
NB how MOVED_FROM is encoded here, with the referencedComponentId being the new active code!
Other examples from the UK Extension content of the same phenomenon include:
effectiveTime
effectiveTime
20080131
294861006
Acset allergy (disorder)
20080401
338451000000103
Acset allergy (disorder)
20090131
213576007
[X]Traumatic amputation of other parts of foot (disorder)
20090401
470771000000109
[X]Traumatic amputation of other parts of foot (disorder)
20090131
274590004
[EDTA] Diabetes Type II (non-insulin-dependent) associated with renal failure (disorder)
20090401
453171000000101
Diabetes Type II (non-insulin-dependent) associated with renal failure - European Dialysis and Transplant Association (disorder)
20100731
183652002
Mental therapy follow-up (administrative concept)
20101001
749201000000109
Mental health therapy follow-up (record artifact)
20140731
270611000
Patient died in part 4 accommodation (finding)
20141001
929161000000107
Patient died in Part IV accommodation (finding)
20140731
185376003
Referred by NHS Direct (finding)
20141001
929141000000106
Referred by NHS Direct (finding)
20160731
303209007
Unfit to plead Criminal Procedure (Insanity & Unfitness to Plead) Act 1991 (finding)
20161001
1052741000000105
Unfit to plead under Criminal Procedure (Insanity and Unfitness to Plead) Act 1991 (finding)
20160731
414386002
Health visitor accident and emergency attendance follow up visit (procedure)
20161001
1052861000000102
Accident and emergency attendance follow-up visit by health visitor (procedure)
20180131
288831009
Care Program Approach assessment (procedure)
20180401
1092341000000101
Care Programme Approach assessment (procedure)
20180731
311129002
Technician - Royal Army Medical Corps (occupation)
20181001
1100841000000100
Technician - Royal Army Medical Corps (occupation)
20180731
310945005
Technician - Royal Electrical and Mechanical Engineers (occupation)
20181001
1100391000000103
Technician - Royal Electrical and Mechanical Engineers (occupation)
20180731
311090006
Telecommunications operator - Royal Signals (occupation)
20181001
1100761000000108
Telecommunications operator - Royal Signals (occupation)
20180731
311087000
Telecommunications technician - Royal Signals (occupation)
20181001
1100751000000105
Telecommunications technician - Royal Signals (occupation)
20180731
225927009
Utilities (qualifier value)
20181001
1099991000000104
Utilities (qualifier value)
We might reasonably suppose that, as other recent and continuing recipients of concepts that have been MOVED_TO them, both the Veterinary and US Extensions may also have MOVED_FROM associations.
For example, here are some very recent MOVED_TOs where content has been sent to the 1000009 namespace of the Veterinary Extension:
20180131 428593008|Abortion due to Brucella canis (disorder)|
20180131 6176008|Mycotic abortion (disorder)|
20180731 726858007|Entire infraorbital sinus (body structure)|
20180731 727198003|Entire palatine sinus (body structure)|
20180731 727411004|Entire subiliac lymph node (body structure)|
20180731 727146000|Entire supramammary lymph node (body structure)|
20180731 95642002|Granulomatous meningoencephalitis (disorder)|
20180731 10079006|Infection caused by Cysticercus cellulosae (disorder)|
20180731 1858000|Infection caused by Stilezia globipunctata (disorder)|
20180731 13218000|Infraorbital sinus (body structure)|
20180731 62248006|Juvenile pyoderma (disorder)|
20180731 471379007|Necrotizing mycotic dermatitis (disorder)|
20180731 71214009|Palatine sinus (body structure)|
20180731 113338001|Subiliac lymph node (body structure)|
20180731 127165003|Subiliac lymphadenopathy (disorder)|
20180731 62630005|Supramammary lymph node (body structure)|
20180731 127108004|Supramammary lymphadenopathy (disorder)|
20190131 82816005|Application of Kirschner-Ehmer splint (procedure)|
20190131 26484003|Bordetellosis (disorder)|
20190131 15477001|Coligranuloma (disorder)|
20190131 727055004|Entire prefemoral lymph node (body structure)|
20190131 292715003|Episioplasty (procedure)|
20190131 35047007|Infection caused by Histomonas (disorder)|
20190131 3660008|Lethal glossopharyngeal defect (disorder)|
20190131 48193007|Prefemoral lymph node (body structure)|
20190131 127201003|Prefemoral lymphadenopathy (disorder)|
20190131 9480005|Viral papular dermatitis (disorder)|
20190731 37649008|Acute metritis (disorder)|
20190731 196111003|Bacterial hemorrhagic septicemia (disorder)|
20190731 111908007|Branchiomycosis (disorder)|
20190731 370470002|Diskospondylitis (disorder)|
20190731 9772004|Hemorrhagic septicemia due to Pasteurella multocida (disorder)|
20190731 32701000|Infectious pustular vulvovaginitis (disorder)|
20190731 409935006|Juvenile pubic symphysiodesis (procedure)|
20190731 417293005|Laryngeal tie-forward (procedure)|
20190731 64230001|Mastitis-metritis-agalactia syndrome (disorder)|
20190731 15363000|Metritis (disorder)|
20190731 398048002|Placental lactogen measurement (procedure)|
20200131 6501005|Atrophic myositis (disorder)|
20200131 449238002|Canine coronavirus vaccine (substance)|
20200131 398758009|Chlamydophila psittaci vaccine (substance)|
20200131 399283001|Everted laryngeal saccules (disorder)|
20200131 195284000|Hemorrhagic septicemia barbone (disorder)|
20200131 198462004|Hemorrhagic septicemia caused by Pasteurella multocida (disorder)|
20200131 398976007|Parvovirus vaccine (substance)|
20200731 398856000|Bordetella vaccine (substance)|
20200731 7230005|Brucella vaccine (product)|
20200731 396421002|Brucella vaccine (substance)|
20200731 7141001|Brucellosis vaccination (procedure)|
20200731 64546005|Carpal hygroma (disorder)|
20200731 424548006|Elbow hygroma (disorder)|
20200731 730496001|Entire posterior medullary spinothalamic tract (body structure)|
20200731 370525007|Exudative diathesis (disorder)|
20200731 8605003|Immunization for bordetella (procedure)|
20200731 4118000|Multilobular chondroma and osteoma (morphologic abnormality)|
20200731 41039001|Omphalophlebitis (disorder)|
20200731 95731004|Pigmentary keratitis (disorder)|
20200731 449332004|Porphyromonas denticanis + porphyromonas gulae + porphyromonas salivosa vaccine (substance)|
20200731 361556005|Posterior medullary spinothalamic tract (body structure)|
20200731 399134006|Primary seborrhea (disorder)|
20200731 111355005|Pyogranulomatous serositis (disorder)|
20200731 398776002|Reovirus vaccine (substance)|
20200731 81970008|Swine influenza virus vaccine (product)|
20200731 428771000|Swine influenza virus vaccine (substance)|
20200731 38719000|Toxicoinfectious botulism (disorder)|
20200731 75211007|Trefoil dermatitis (disorder)|
20200731 370459009|West Nile virus vaccine (product)|
20200731 398775003|West Nile virus vaccine (substance)|
20210131 31437008|Lymphocytic-plasmacytic colitis (disorder)|
20210131 7024001|Lymphocytic-plasmacytic enteritis (disorder)|