Goals
- Discuss feedback and examples on transformation implementation
- Discuss the scope of postcoordination functionality in the terminology server
- Continue discussion on dynamic templates
Attendees
- Chair: Linda Bird
- Project Group: Ed Cheetham, Michael Lawley, Kai Kewley, Daniel Karlsson, Peter Jordan, Rob Hausam
Goals
- Discuss feedback and examples on transformation implementation
- Discuss the scope of postcoordination functionality in the terminology server
- Continue discussion on dynamic templates
Attendees
- Chair: Linda Bird
- Project Group:
Agenda and Meeting Notes
Description Owner Notes Welcome and agenda Example 1 - Dentistry / Odontogram Example 2 - Terminology binding Example 3 - Mapping Example 4 - Natural Language Processing Practical Guide to Postcoordination Proposed Transformation Rules - Refinements (NOT in valid domain of focus concepts) 363443007 |Malignant tumor of ovary|: 272741003 |Laterality| = 24028007 |Right| 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: ON HOLD - Proposed syntax to support querying and return of alternative refset attributes (To be included in the SNOMED Query Language) ON HOLD - Proposal (by Michael) for discussion 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| ON HOLD - Proposal for discussion What refsets is a given concept (e.g. 421235005 |Structure of femur|) a member of? Expression Templates Examples: [[+id]]: [[1..*] @my_group sameValue(morphology)] { |Finding site| = [[ +id (<<123037004 |Body structure (body structure)| MINUS << $site[! SELF ] ) @site ]] , |Associated morphology| = [[ +id @my_morphology ]] } 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: 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. 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 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| {{ 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 NotesPostcoordination Transformations
{
263502005 |Clinical course (attribute)| = 424124008 |Sudden onset AND/OR short duration (qualifier value)|
}{
363698007 |Finding site (attribute)| = 89187006 |Airway structure (body structure)|
}
{
263502005 |Clinical course| = 424124008 |Sudden onset AND/OR short duration|
}{
363698007 |Finding site| = 89187006 |Airway structure|
}
2704003 |Acute disease (disorder)| :
{
263502005 |Clinical course| = 424124008 |Sudden onset AND/OR short duration|
}{
363698007 |Finding site| = 89187006 |Airway structure|
}Dynamic Templates
should be
|Pyelonephritis| : |Clinical course| = |Chronic|, |Associated morphology| = |Chronic inflammation|
should be
|Pyelonephritis| : {|Clinical course| = |Sudden onset AND/OR short duration||, |Associated morphology| = |Acute inflammation|
should be
|Nephritis|: |Causative agent| = |Domain bacteria|, |Pathological process| = |Infectious process|
should be
|Koilonychia|: |Occurrence| = |Congenital|, |Pathological process| = |Pathological developmental process|Postcoordination Use Case Examples All Postcoordination Guidance
{ 260686004 |Method| = 129304002 |Excision - action|,
405813007 |Procedure site - Direct| = 15497006 |Ovarian structure|,
405815000 |Procedure device| = 122456005 |Laser device| }
{ 260686004 |Method| = 129304002 |Excision - action|,
405813007 |Procedure site - Direct| = 15497006 |Ovarian structure|},
{ 405815000 |Procedure device| = 122456005 |Laser device| }
{ 363698007 |Finding site| = 272673000 |Bone structure|,
116676008 |Associated morphology | = 72704001 |Fracture| }
{ 42752001 | Due to (attribute) | = 1912002 | Fall | }
ObjectIntersectionOf (:71388002
ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf( ObjectSomeValuesFrom(:260686004 :129304002)
ObjectSomeValuesFrom(:405813007 :15497006))))
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
83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device|
83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device|, 363700003 |Direct morphology| = 367643001 |Cyst |
405813007 |Procedure site - direct| = 15497006 |Ovarian structure|,
405815000 |Procedure device| = 122456005 |Laser device| ,
363700003 |Direct morphology| = 367643001 |Cyst | }
83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device|, 260870009 |Priority| = 394849002 |High priority|
405813007 |Procedure site - direct| = 15497006 |Ovarian structure|,
405815000 |Procedure device| = 122456005 |Laser device| }
{ 260870009 |Priority (attribute)| = 394849002 |High priority| }
83152002 |Oophorectomy| : 260686004 |Method| = 277261002 |Excision biopsy (qualifier value)|
83152002 |Oophorectomy| : { 260686004 |Method| = 281615006 | Exploration - action | , 405813007 |Procedure site - direct| = 367643001 |Cyst | }
405813007 |Procedure site - direct| = 15497006 |Ovarian structure| },
{ 260686004 |Method| = 281615006 | Exploration - action | ,
405813007 |Procedure site - direct| = 367643001 |Cyst |}
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
363698007 |Finding site| = ( 15497008 |Ovarian structure| : 272741003 |Laterality| = 24028007 |Right| ) }
260870009 |Priority| = 25876001 |Emergency|
363698007 |finding site| = 84167007 |Foot bone| }
363698007 |finding site| = 84167007 |Foot bone| }The items below are currently on hold Other Options for Future Progress URIs for Extended Editions Querying Refset Attributes Linda Bird
FROM 799 |Anatomy structure and part association refset|
WHERE 123 |referenced component| = (< 888 |Upper abdomen structure| {{ term = "*heart*" }} )
FROM concept
WHERE id IN (< |Clinical finding|)
AND definitionStatus = |primitive|
FROM concept, ECL("< |Clinical finding") CF
WHERE concept.id = CF.sctid
AND definitionStatus = |primitive|
FROM concept ( < |Clinical finding| {{ term = "*heart*" }} {{ definitionStatus = |primitive| }} )
(|Anatomy structure and part association refset| {{ |referencedComponent| = << |Upper abdomen structure}} )? |targetComponentId|
734139008 |Anatomy structure and part association refset|
734139008 |Anatomy structure and part association refset|
734139008 |Anatomy structure and part association refset| :
449608002 |ReferencedComponent| = << |Upper abdomen structure|
734139008 |Anatomy structure and part association refset|
{{ 449608002 |referencedComponent| = << |Upper abdomen structure| }}
734139008 |Anatomy structure and part association refset| :
449608002 |ReferencedComponent| = (<< |Upper abdomen structure|) : |Finding site| = *)Returning Attributes Michael Lawley Reverse Member Of Michael Lawley Road Forward for SI
Description Templates Kai Kewley Query Language
- Summary from previous meetings
(* {{ term = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20170731, DIALECT W)
Agenda and Meeting Notes
Description Owner Notes Welcome and agenda Example 1 - Dentistry / Odontogram Example 2 - Terminology binding Example 3 - Mapping Example 4 - Natural Language Processing Practical Guide to Postcoordination Proposed Transformation Rules - Refinements (NOT in valid domain of focus concepts) 363443007 |Malignant tumor of ovary|: 272741003 |Laterality| = 24028007 |Right| 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: ON HOLD - Proposed syntax to support querying and return of alternative refset attributes (To be included in the SNOMED Query Language) ON HOLD - Proposal (by Michael) for discussion 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| ON HOLD - Proposal for discussion What refsets is a given concept (e.g. 421235005 |Structure of femur|) a member of? Expression Templates Examples: [[+id]]: [[1..*] @my_group sameValue(morphology)] { |Finding site| = [[ +id (<<123037004 |Body structure (body structure)| MINUS << $site[! SELF ] ) @site ]] , |Associated morphology| = [[ +id @my_morphology ]] } 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: 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. 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 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| {{ 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 NotesPostcoordination Transformations
{
263502005 |Clinical course (attribute)| = 424124008 |Sudden onset AND/OR short duration (qualifier value)|
}{
363698007 |Finding site (attribute)| = 89187006 |Airway structure (body structure)|
}
{
263502005 |Clinical course| = 424124008 |Sudden onset AND/OR short duration|
}{
363698007 |Finding site| = 89187006 |Airway structure|
}
2704003 |Acute disease (disorder)| :
{
263502005 |Clinical course| = 424124008 |Sudden onset AND/OR short duration|
}{
363698007 |Finding site| = 89187006 |Airway structure|
}Dynamic Templates
should be
|Pyelonephritis| : |Clinical course| = |Chronic|, |Associated morphology| = |Chronic inflammation|
should be
|Pyelonephritis| : {|Clinical course| = |Sudden onset AND/OR short duration||, |Associated morphology| = |Acute inflammation|
should be
|Nephritis|: |Causative agent| = |Domain bacteria|, |Pathological process| = |Infectious process|
should be
|Koilonychia|: |Occurrence| = |Congenital|, |Pathological process| = |Pathological developmental process|Postcoordination Use Case Examples All Postcoordination Guidance
{ 260686004 |Method| = 129304002 |Excision - action|,
405813007 |Procedure site - Direct| = 15497006 |Ovarian structure|,
405815000 |Procedure device| = 122456005 |Laser device| }
{ 260686004 |Method| = 129304002 |Excision - action|,
405813007 |Procedure site - Direct| = 15497006 |Ovarian structure|},
{ 405815000 |Procedure device| = 122456005 |Laser device| }
{ 363698007 |Finding site| = 272673000 |Bone structure|,
116676008 |Associated morphology | = 72704001 |Fracture| }
{ 42752001 | Due to (attribute) | = 1912002 | Fall | }
ObjectIntersectionOf (:71388002
ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf( ObjectSomeValuesFrom(:260686004 :129304002)
ObjectSomeValuesFrom(:405813007 :15497006))))
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
83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device|
83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device|, 363700003 |Direct morphology| = 367643001 |Cyst |
405813007 |Procedure site - direct| = 15497006 |Ovarian structure|,
405815000 |Procedure device| = 122456005 |Laser device| ,
363700003 |Direct morphology| = 367643001 |Cyst | }
83152002 |Oophorectomy| : 405815000 |Procedure device| = 122456005 |Laser device|, 260870009 |Priority| = 394849002 |High priority|
405813007 |Procedure site - direct| = 15497006 |Ovarian structure|,
405815000 |Procedure device| = 122456005 |Laser device| }
{ 260870009 |Priority (attribute)| = 394849002 |High priority| }
83152002 |Oophorectomy| : 260686004 |Method| = 277261002 |Excision biopsy (qualifier value)|
83152002 |Oophorectomy| : { 260686004 |Method| = 281615006 | Exploration - action | , 405813007 |Procedure site - direct| = 367643001 |Cyst | }
405813007 |Procedure site - direct| = 15497006 |Ovarian structure| },
{ 260686004 |Method| = 281615006 | Exploration - action | ,
405813007 |Procedure site - direct| = 367643001 |Cyst |}
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
363698007 |Finding site| = ( 15497008 |Ovarian structure| : 272741003 |Laterality| = 24028007 |Right| ) }
260870009 |Priority| = 25876001 |Emergency|
363698007 |finding site| = 84167007 |Foot bone| }
363698007 |finding site| = 84167007 |Foot bone| }The items below are currently on hold Other Options for Future Progress URIs for Extended Editions Querying Refset Attributes Linda Bird
FROM 799 |Anatomy structure and part association refset|
WHERE 123 |referenced component| = (< 888 |Upper abdomen structure| {{ term = "*heart*" }} )
FROM concept
WHERE id IN (< |Clinical finding|)
AND definitionStatus = |primitive|
FROM concept, ECL("< |Clinical finding") CF
WHERE concept.id = CF.sctid
AND definitionStatus = |primitive|
FROM concept ( < |Clinical finding| {{ term = "*heart*" }} {{ definitionStatus = |primitive| }} )
(|Anatomy structure and part association refset| {{ |referencedComponent| = << |Upper abdomen structure}} )? |targetComponentId|
734139008 |Anatomy structure and part association refset|
734139008 |Anatomy structure and part association refset|
734139008 |Anatomy structure and part association refset| :
449608002 |ReferencedComponent| = << |Upper abdomen structure|
734139008 |Anatomy structure and part association refset|
{{ 449608002 |referencedComponent| = << |Upper abdomen structure| }}
734139008 |Anatomy structure and part association refset| :
449608002 |ReferencedComponent| = (<< |Upper abdomen structure|) : |Finding site| = *)Returning Attributes Michael Lawley Reverse Member Of Michael Lawley Road Forward for SI
Description Templates Kai Kewley Query Language
- Summary from previous meetings
(* {{ term = "*heart*" }} VERSION http://snomed.info/sct/900000000000207008/version/20170731, DIALECT W)