Goals
- Consider the processes required for data entry, display, query and exchange of a postcoordinated expression
Attendees
- Chair: Linda Bird
- Project Group: Daniel Karlsson, Rob Hausam, Ed Cheetham, Michael Lawley, Kai Kewley, Anne Randorff Højen
Apologies
Agenda and Meeting Notes
Description Owner Notes Welcome and agenda Postcoordinated expression processes 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 Expression Processes All 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)
8 Comments
Ed Cheetham
Linda, all
You asked for a few examples of inter-attribute dependencies:
The one I originally mentioned is acute/chronic and inflammation:
Addition of 263502005 | Clinical course | = 424124008 | Sudden onset AND/OR short duration | or 263502005 | Clinical course | = 90734009 | Chronic | seems to be accompanied by specialisation of neighbouring 116676008 | Associated morphology | = 409774005 | Inflammatory morphology | role(s):
(In the combined focus diagrams I'm use a private convention that's omitting extraneous supertypes (for ease of reading) and colouring the equivalent/subset of character blue to indicate that something's missing from each definition). The aim is to show how refinement of the 'pyelonephritis' focus requires >1 change to its role definition).
Anyway, the implication here is that clinical course refinement of '-itis' to 'acute -itis' or 'chronic -itis' requires changes to associated morphology values too during transformation.
A couple of other examples - after a quick squint at the editorial guide are:
Addition of infectious causative agents:
Superficially it would seem reasonable to refine 'nephritis' to 'bacterial nephritis' but just adding 246075003 | Causative agent | = 409822003 | Domain Bacteria | as a refinement. However, this isn't sufficient; a 370135005 | Pathological process | = 441862004 | Infectious process | role needs adding too:
Specifying congenital and acquired variants:
Superficially it would seem reasonable to specify these variants with 246454002 | Occurrence | = 255399007 | Congenital | or 246454002 | Occurrence | = 767023003 | Period of life between birth and death |. In the case of 'congenital' more is needed, as congenital variants also carry a 370135005 | Pathological process | = 308490002 | Pathological developmental process | role:
There are no doubt many similar rules (and other patterns) that would need to be included in the transformation, but perhaps this is a useful taster.
In addition, and picking up on Anna's point about the importance of terms, term preservation and term generation, two of these examples have significant differences between the terms for 'selection' and those that would really be thought or intended:
Neither of these are unreasonable conceptual variants to want to produce, but it would currently appear to be impossible to produce idiomatic clinical terms based on the available SNOMED CT term 'ingredients'.
Ed
Ed Cheetham
Another thought...
For the 'lateralisation use case', if the laterality value 51440002 |Right and left (qualifier value)| is available for selection then there is a need to ensure that the stored/CTU form is eventually expanded to be comparable with the reference data (where separate 'right' and 'left' groups are used). I'll leave it to Kai's expertise as to how this is achieved, but suspect that the process would be helped by making 51440002 |Right and left (qualifier value)| sufficiently defined to allow the classifier to take on some of the work.
For example, at some point the single RG of CT Hip would need to become two when transforming a CTU of 241571002 | CT of hip |: 272741003 | Laterality | = 51440002 |Right and left |:
Ronald Cornet
Hi Ed Cheetham, all,
Being a lurker on SLPG, I do enjoy discussions like these.
Please ignore if my comment is off-topic given the context in which this discussion is held.
Ed states rightfully that: "clinical course refinement of '-itis' to 'acute -itis' or 'chronic -itis' requires changes to associated morphology values"
Shouldn't this be addressed by an OWL-expression? I was trying to find it, but didn't.
I would expect a GCI stating (sorry for sloppy formulation)
SubClassOf( (SOME Associated Morphology . Inflammatory morphology AND SOME Clinical Course . Chronic) (SOME Associated Morphology . Chronic Inflammation) )
And similar for acute. Happy to hear thoughts on this.
Ronald
Ed Cheetham
Thanks Ronald.
I'll leave it to others to decide how/where the business rules are represented - my motivation was to point out that there are plenty of rules that currently sit in the narrative of the editorial guide that will need to be machine-processable before many, if not all, post-coordination use cases are to be supported. A DL representation of a modelling/DL-relevant rule certainly seems attractive. The Galen work identified several varieties of transformation rule to get from their 'intermediate representation' (sort of 'close-to-user') to a classifiable form, and SI seems to be tackling something very similar now. Some rules will be best represented in OWL, others will, I imagine, benefit from other formalisms. Whatever's used will need to satisfy a bunch of desirable characteristics such as maintainability, availability and explainability, as well as traceability back to the original editorial guide text they represent.
Ed
Ronald Cornet
Ed, I fully agree that "rules that currently sit in the narrative of the editorial guide ... will need to be machine-processable before many, if not all, post-coordination use cases are to be supported. "
This is what Daniel and I addressed in 2013 in:
Cornet R, Nyström M, Karlsson D. User-Directed Coordination in SNOMED CT. In: Proceedings of Medinfo 2013, Copenhagen (2013), Studies in Health Technology & Informatics; 2013;192:72-6.
It is important, though, to realize that being machine-processable is only relevant if machine processing is actually done:
Machine-processing does need to be done, by EHR/terminology services, to establish / realize the inferences.
Machine-processing will likely need to be performed not only at concept-level, but also at instance-level. This is something that seems to be challenging now. SnoRocket doesn't support instance reasoning. It might be that RDFox can do this, I know it has been used on previous versions of SNOMED CT, but I'm not sure if all "new" features in SNOMED CT, including concrete domains / numbers, are addressed. And it strikes me that there is currently seemingly little activity in further development of reasoners. I hope I'm wrong, as it is crucial that there is sufficient reasoning support provided for SNOMED CT, and the more expressive direction in which it is developing.
Ed Cheetham
Thanks Ronald - this is really useful.
Things are unarguably moving in the directions your paper proposes (not least the stabilisation of the MRCM and emergence of an ECL/template formalism in recent years), but there's still a lot to do. This quote stands out to me:
"...The 2010 release of the GALEN meta-model consists of about 280 grammatical sanctions and about 23,000 sensible sanctions..."
To my maths the current set of MRCM Domain-Attribute-Range constraints resolve to the roughly same order of magnitude as GALEN's grammatical sanctions (and as your paper says, they essentially perform the same function). The scale and challenge of sensible sanctioning (as a prerequisite for workable post-coordination) should therefore not be underestimated...
Ed
Ed Cheetham
A quick, peripherally-related question...
I'm curious about the attribute 762951001 |Has ingredient |. It is the only attribute with a contentType setting in the 723604009 |MRCM attribute domain reference set| of 723595009 |All postcoordinated SNOMED CT content|. There is little documented about it - I can find mention of it being a 'grouper', and here I am told it is "...not used in the international edition...". Its entry here confirms the contentType setting. I'm sure there used to be a section in the pharmacy editorial guidance, but I cannot find that today.
Whatever, here are my questions:
Thanks. Ed
Linda Bird
Thanks very much Ed and Ronald for the very interesting discussion.
Ed - I really appreciate the examples of inter-attribute dependencies and the subsequent discussion. Let's talk this through at this week's SLPG meeting.
Ronald - Thanks for the paper reference and discussion. We tried the GCI that you suggested, but it didn't quite have the desired effect (ie it grouped the example under |Chronic inflammatory disease|, but because it didn't specialise the morphology of the existing role groups, it still didn't classify the example in the right spot). We're currently wondering whether before+after expression templates may work ... but are very open to suggestions.
Thank you both! Kind regards, Linda.