1. Revising the Anatomy Model to Improve Usability and Correctness

2. Some problems to solve
Post-coordination of site and laterality is one of the most common requirements of users
But anatomy names are confusing (“structure of…”, “entire …”)
And anatomy organization appears awkward and duplicative, even when strictly correct
The hierarchies in clinical findings and procedures depend on anatomy to determine their structure
But anatomy contains many errors and omissions and inconsistencies, leading to “foot in the pelvis” kinds of errors
Maintenance is difficult and error-prone and therefore costly
It is unclear how to coordinate with “outside” resources
Some specialties do their own clinical anatomy (cf Radlex)
Some people suggest IHTSDO should outsource its anatomy, e.g. FMA

3. The nodes are all primitive Therefore, each line is edited
SNOMED CT Concept
Body structure
Physical anatomical entity
The nodes are all primitive
Therefore, each line is edited
individually – and error-prone
Anatomical structure
Body region structure
Body part structure
Neck, chest, abdomen, and pelvis
Trunk structure
Body system structure
Neck, chest and abdomen
Chest, abdomen, and pelvis
Structure of subregion of trunk
Upper body structure
Cardiovascular structure
Chest and abdomen
Neck and chest
Upper trunk structure
Upper body part structure
Body space structure
Respiratory and/or intrathoracic structures
Thoracic structure
Body cavity structure
Regional cardiovascular structure
Body organ structure
Thoracic cavity structure
Cardiovascular structure of trunk
Lung and/or mediastinal structures
Structure of viscus
Intrathoracic cardiovascular structure
Mediastinal structure
Organ part
Structure of thoracic viscus
Heart AND pericardium structure
Developmental body structure
Cardiovascular organ part
Heart structure
Embryonic structure
Heart part
Embryonic cardiovascular structure
Cardiac internal structure
Anatomical spatial entity
Embryonic cardiac structure
Cardiac chamber structure
Anatomical junction
Primitive cardiac septal structure
Cardiac septum structure
Atrial structure
Anatomical orifice
Primitive atrial septal structure
Interatrial septum structure
Ostium
Septum primum structure
Structure of ostium secundum
Entire ostium secundum

4. A bit of background How did the anatomy section get to where it is?
What is the current model?

5. Merging Anatomy concepts from CTV3 and SNOMED RT
Features in common:
concepts, terms, hierarchies
logical subsumption
Main difference:
Part/whole representation
RT used “part-of x”
CTV3 used “x structure”

6. Example: Liver CTV3 SNOMED RT How is T-62000 used in coding?
T Liver
T-D0535 Liver part
CTV3
XM0Ps Liver structure
7N330 Liver
How is T used in coding?
The site of tumors and other morphologies
Does it necessarily mean the entire liver? No
In what sense is liver (7N330) a subtype of liver structure (XM0Ps)?
All instances of XM0Ps are either
instances of "Liver" or
they are related to some instance of liver via 'part-of' relations
7N330 means “entire liver”..

7. Where to put T-62000 “liver”? ? ? T-62000 Liver is-a is-a part-of is-a
Liver structure ?
T Liver
XM0Ps Liver structure ?
is-a
is-a
part-of
Liver part
Entire liver
T-D0535 Liver part
7N330 Liver
is-a
Lobe of liver

8. Solution Adopted: “SEP” model
Liver Structure
XM0Ps Liver structure
T Liver
is-a
is-a
part-of
LiPart
Entire liver
T-D0535 Liver part
7N330 Liver
Note: This structure corresponds closely to the structure described in the paper “Stefan Schulz, Udo Hahn: Part-whole representation and reasoning in formal biomedical ontologies. Artificial Intelligence in Medicine 34(3): (2005)

9. All of anatomy is primitive but it need not be
The meaning of “S” is
“PartOf <x> OR Entire <x>”
The meaning of “P” is
PartOf <x>
Therefore, both “S” and “P” can be sufficiently defined if we have the right DL (description logic) constructs

10. SEP diagram: E2 part of E1 S1 P1 E1 S2 E2 P2 Current situation:
Is-A
Current situation:
All nodes are primitive
All Is-A links must be individually modelled
P1 and P2 are seldom pre-coordinated in the terminology P1 E1 S2 E2 P2

11. SEP diagram: finger part of hand
hand structure
Is-A
Current situation:
All nodes are primitive
All Is-A links must be individually modelled
P1 and P2 are seldom pre-coordinated in the terminology
part of hand
entire hand
finger structure
entire finger
part of finger

12. SEP diagram: E2 part of E1 with no P1 and no P2 (typical in CTV3)
Is-A E1 S2 E2

13. SEP diagram: E2 part of E1 with no P1 and no P2 (typical in CTV3)
hand structure
Is-A
entire hand
Missing explicit representation that the finger is part of the hand
finger structure
entire finger

14. SEP diagram: E2 is-a E1 S1 Current situation: All nodes are primitive
All Is-A links must be individually modelled P1 E1 S2 E2 P2

15. SEP diagram: index finger is-a finger
finger structure
Is-A
Current situation:
All nodes are primitive
All Is-A links must be individually modelled
part of finger
entire finger
structure of index finger
entire index finger
part of index finger

16. SEP diagram: E2 is-a E1 S1
Is-A E1 S2 E2

17. SEP diagram: index finger is-a finger
structure of finger
Is-A
entire finger
Usual situation: no “part of” nodes and sometimes the E2->E1 links are missing or incorrect
structure of index finger
entire index finger

18. Start of solution: the SEP table
The SEP table provides a comprehensive classification of all SNOMED CT anatomy codes
Each single row giving:
A simple name for the anatomical entity (e.g. “hand”)
The code for the “S”, if pre-coordinated (else blank)
The code for the “E”, if pre-coordinated (else blank)
The code for the “P”, if pre-coordinated (else blank)

19. Inferred relationships from SEP table
part-of (inferred)
is-a (inferred) P1 E1
Benefit:
All three relationships derive automatically from a single row in the SEP table
Requirement
Maintenance burden of a valid SEP table (small burden)

20. Inferred relationships from SEP table
structure of hand
part-of (inferred)
is-a (inferred)
part of hand
entire hand
Benefit:
All three relationships derive automatically from a single row in the SEP table: labelled “hand”
Requirement
Maintenance burden of a valid SEP table (small burden)

21. E2 part-of E1 S1 P1 E1 S2 E2 P2 Requirements: SEP table classifier
part-of (inferred)
is-a (inferred)
Requirements:
SEP table
classifier
E2: part-of = E1 must be directly modeled
Benefit
“reified” relations all come automatically P1 E1 S2 E2 P2

22. finger part-of hand structure of hand part of hand entire hand
part-of (inferred)
is-a (inferred)
Requirements:
SEP table
classifier
E2: part-of = E1 must be directly modeled
Benefit
“reified” relations all come automatically
part of hand
entire hand
structure of finger
entire finger
part of finger

23. E2 isa E1 S1 P1 E1 S2 E2 P2 Requirements: 1. SEP table
part-of (inferred)
Is-A (inferred)
Requirements:
1. SEP table
2. Capable classifier
3. E2 is-a E1 must be directly modeled
Benefits
Dotted line relations are automatic and reliable P1 E1 S2 E2 P2

24. What I have to model S1 P1 E1 S2
Is-A E2 P2

25. What is inferred S1
part-of
Is-A P1 E1 S2 E2 P2

26. What I have to model S1 P1 E1
Part-of S2 E2 P2

27. What is inferred S1
part-of
Is-A P1 E1 S2 E2 P2

28. Even better: eliminate “S” and “P”
Migration path might maintain “S” and “P” algorithmically, for backwards compatibility
Curation effort, and naming, can be focused on the “E”
Drop the “entire” from the names
Potentially major improvement in post-coordination ability
Requires some systematic (automatic) substitution changes:
new attributes in the definitions of clinical findings, procedures, events, and specimens
Other steps:
impact assessment
revision of implementation advice

29. How do we model “finding-site” without “S” to refer to?
Current situation:
Entire limb -> is-a -> Limb structure (S)
One attribute: finding-site
Edema of extremity: finding-site = limb structure (S)
Edema of entire limb: finding-site = entire limb (E)
Proposed revision:
One target concept: limb
Two attributes: finding-site-entire (subrole of) finding-site
Right identity: finding-site o part-of -> finding-site
This means that findings with sites that are part of the limb will be inferred to have a site of limb
Edema of extremity: finding-site = limb
Edema of entire limb: finding-site-entire = limb

30. How does the right identity work?
Edema of calf == clinical finding and (rolegroup
(associated-morphology = edema)(finding-site = calf))
Calf := (part-of lower limb)
Lower limb := limb
Edema of limb == clinical finding and (rolegroup
(associated-morphology = edema)(finding-site = limb))
Right identity is invoked by the following pair of assertions:
(finding-site = calf) and calf := (part-of lower limb)
For edema of calf, this infers that (finding-site = lower limb), and therefore edema of calf is a kind of edema of lower limb, which is a kind of edema of limb.

31. How do we model “procedure-site” without “S” to refer to?
Current situation:
Entire lung-> is-a -> lung structure (S)
Lung excision: procedure-site-direct = lung structure (S)
Total pneumonectomy: procedure-site-direct = entire lung (E)
Proposed revision:
One target concept: lung
Two attributes: procedure-site-direct-entire (subrole of) procedure-site-direct
Right identity: procedure-site-direct o part-of -> procedure-site-direct
This means that procedures with sites that are part of the lung will be inferred to have a site of lung
Lung excision: procedure-site-direct = lung
Total pneumonectomy: procedure-site-direct-entire = lung

32. Additional improvements:
Consider how to fully define the “E” nodes also
Further increases correctness and reliability
Further reduces curation burden
Next section addresses how to fully define “skin” concepts
Using systematic patterns

33. Kent A. Spackman, MD PhD Sept. 2011
Content Definition Substitution Patterns: Examples from Skin & Integument
Kent A. Spackman, MD PhD
Sept. 2011
Presentation © 2008 Clinical Terminology Consulting Inc SNOMED Clinical Terms is a Copyright Work of the IHTSDO (

34. Substitution Patterns
Define a pattern for concepts of the same type, with one or more variables that are substituted into the pattern to define individual concepts
Examples in the past have typically come from the findings and situations hierarchies, but the technique can potentially be used anywhere

35. Example from situation hierarchy: Clinical finding absent + site
Associated
finding
<finding>
Group
Finding-site
<site>
Finding context
Known absent
Temporal context
Current or specified time
Subject relationship context
Subject of record
Clinical-finding-absent-with-site (<finding>,<site>)

36. Femoral bruit absent
Situation
Associated
finding
bruit
Group
Finding-site
Femoral artery
Finding context
Known absent
Temporal context
Current or specified time
Subject relationship context
Subject of record
Clinical-finding-absent-with-site (<finding>,<site>)

37. Applying the approach in anatomy
Requires a shift in thinking from the “Structure – Entire – Part” or “SEP” model
Allow anatomy entities to be fully defined
Manually curate only the “entire” entities
Allow “S” to be algorithmically and systematically defined as the disjunction “E or P”
Allow “P” to be algorithmically and systematically defined as simply “partOf E”

38. Consider user requirements
Take the anatomical parts of the skin as an example
There are multiple layers:
Surface
Integument
Skin
Epidermis
Dermis
Subcutaneous tissue (superficial fascia)
There is laterality
There are many regions and subregions of the body covered with skin

39. Using “skin” concepts: requirements (1)
Users should be able to select from a (relatively) small list of body regions that are covered with skin
Three questions suffice to specify the part intended:
What region? (e.g. “hand”)
What layer? (e.g. skin, skin and subcutaneous tissue, integument, epidermis, dermis, surface of skin)
What laterality? (none, left, or right)
Selection of the region should be from a small (ish) list of regions
In some cases, a default layer might be assumed (e.g. surface, or skin)
Selection of laterality should be prompted only when sensible (yes for ear or hand, no for mouth, nose)

40. Using “skin” concepts: requirements (2)
Inferences should be reliable and consistent (for both terminology curation and patient data retrieval)
Infer correct is-a relationships
Record “skin of index finger” and infer “skin of finger”
Infer correct part-of relationships
Record “skin of finger” and infer “part of skin of hand”, but
NOT subtype of “skin of hand”
Include inferences of sub-layers
Record “skin of finger” and infer “part of integument of finger”
And include inferences of laterality
Record “skin of finger of left hand” and infer “laterality = left”

41. Use capabilities of EL classifier (e.g. Snorocket)
Allow multiple fully-defined clauses
Gives the ability to infer partonomy in layers that are not mentioned or recorded
Allow transitive object properties
X part of Y, and Y part of Z, implies X part of Z
Allow role-chaining assertions (object property chaining)
Needed for handling laterality
part-of o laterality -> laterality
X part of Y, and Y laterality LR, implies X laterality LR.
So-called “left identity”

42. Adopt FMA’s partonomy properties
PartOf sub-properties:
Constitutional part of
The epidermis is a constitutional part of the skin
Regional part of
The skin of the finger is a regional part of the skin of the hand
Systemic part of
The thyroid gland is a systemic part of the endocrine system

43. Create common patterns for each layer:
Layers where we already have concepts pre-coordinated:
Surface
Skin
Skin and subcutaneous tissue (a.k.a. integument)
Subcutaneous tissue (a.k.a. superficial fascia)

44. Make a list of all regions of the body with skin, integument, surface, or superficial fascia
Develop a common list of regions and their pre-coordinated skin, subcutaneous tissue, and surface codes
Result: 419 regions. (some currently have no separate code for the region, but only a code for “skin of <region>”)
Total possible combinations: 419 regions x 3 (SEP) x 5 = 6285
Number of actually pre-coordinated codes: 1898 S E P
Region
223
200 19
Skin
375
241 75
Integument 40
Fascia
240
235
Surface 91
158 1

45. Curation burden
Curate arbitrary set of S, E, P, with no systematic approach (current situation):
1898 current codes, order of magnitude 10^4 possible is-a relationships
Potential for additional requests to approach expansion to 6,285 codes
Curate “E” only: 419 x 5 = 2,095
Still a large burden
Develop systematic pattern for each layer, applied algorithmically (no curation required, all inferences automatic)
Curation burden: define the “part-of” relationships of 419 regions
Small enough to make this a consensus-based community effort

46. One more wrinkle: laterality
Some regions are lateral (ear, arm, leg)
Some regions are not lateral (nose, occipital scalp)
Non-systematic curation:
Laterality doubles the number of codes to be curated
Systemic approach:
No increase in manually curated codes.
Requires that the 419 regions be classed as lateralizable (yes, no)
This is already required to support post-coordination in the first place

47. Skin of <region>≡
region of skin
constitutional part of
<region> ≡
region of skin
constitutional part of
zone of integument
constitutional part of
<region>

48. Skin of <region>, <side>≡
region of skin
constitutional part of
<region>
laterality
<side> ≡
region of skin
constitutional part of
zone of integument
constitutional part of
<region>
laterality
<side>
part of ◦ laterality → laterality

49. surface of <region>≡
subdivision of surface of body
constitutional part of
<region> ≡
subdivision of surface of body
constitutional part of
zone of integument
constitutional part of
<region>

50. surface of <region>, <side>≡
subdivision of surface of body
constitutional part of
<region>
laterality
<side> ≡
subdivision of surface of body
constitutional part of
zone of integument
constitutional part of
<region>
laterality
<side>
part of ◦ laterality → laterality

51. subcutaneous tissue of <region>≡
zone of superficial fascia
constitutional part of
<region> ≡
zone of superficial fascia
constitutional part of
zone of integument
constitutional part of
<region>

52. subcutaneous tissue of <region>, <side>≡
zone of superficial fascia
constitutional part of
<region>
laterality
<side> ≡
zone of superficial fascia
constitutional part of
zone of integument
constitutional part of
<region>
laterality
<side>
part of ◦ laterality → laterality

53. skin of part of <region>≡
region of skin
regional part of
region of skin
constitutional part of
<region> ≡
region of skin
constitutional part of
regional part of
<region>

54. skin of part of <region>, <side>≡
region of skin
regional part of
region of skin
constitutional part of
<region>
laterality
<side> ≡
region of skin
constitutional part of
regional part of
<region>
laterality
<side>
part of ◦ laterality → laterality

55. Next steps Complete mapping to FMA, and compare is-a relationships
? Look at FMA-owl with enhanced object properties (Alan Ruttenberg is working on this)
Create a draft editorial guide for the object properties and patterns used for the alpha version
What is aligned with FMA, what is not?
Comparison of the hierarchies of the alpha and official anatomy
Look for additions and removals, assess correctness (? Sample)
Revise alpha version
? Iterate

56. Next steps (2)
Look at aligning object properties with RO (relation ontology)
Particularly in the area of location and part-whole relationships
Is there a need for has-part? Examine value and use case
Comparison of the effect of introducing alpha anatomy as a substitute for “official” anatomy
Impact analysis on:
Implementation guidance and approaches/strategies
Backwards compatibility
Post-coordination patterns and advice
Correctness of hierarchies
Increased reliance on classifier for subsumption testing (difficulty for entry level?)

57. Next steps (3): Tooling
Development of tooling strategy to accommodate:
Nested definitions
GCIs and multiple sufficient definitions
Role chaining (left and right identity)
User interface for defining the above
Patterns
Defining, setting domain for patterns
Revision of RF2 implementation to repurpose for:
Nested definitions, anonymous concepts?, distribution in relationships table vs refsets

58. Anatomy project group summary
Simplified representation of anatomy
Get rid of SEP
More intuitive, aligned with FMA, can be partially automatically curated with rules
More complexity on some attributes (site for findings and procedures)
More expressive with some additional computational complexity
Testing will be done to determine correctness and impact