SNOMED CT Anatomy
Redesign Project Evaluation
Subproject parts, dependencies, and criteria for evaluation
Date 20130603
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20130126
Kent Spackman
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20130603
Kent Spackman
Expansion for review by standing committees
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© International Health Terminology Standards Development Organisation 2013. All rights reserved.
SNOMED CT® was originally created by the College of American Pathologists.
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Table of Contents
1 Introduction............................................................................................................................ 4
2 Project Overall Description and Aims .................................................................................... 4
2.1 Problems to be solved ................................................................................................................. 4
2.1.1 Specifying site and laterality – too difficult ............................................................................................... 4
2.1.2 Errors, omissions and inconsistencies .................................................................................................... 4
2.1.3 Maintenance burden ................................................................................................................................ 4
2.1.4 Coordination with other anatomy terminologies ...................................................................................... 5
2.1.5 Inadequate adoption and use of tools ..................................................................................................... 5
3 Background – what is the current model? ............................................................................. 5
4 Project Parts .......................................................................................................................... 6
4.1 SEP Assignment ......................................................................................................................... 6
4.2 Laterality Assignment .................................................................................................................. 6
4.3 Assignment of Subtype and Subpart Relationships ..................................................................... 6
4.4 Creation of Sufficient DL Definitions for Entire (E) Codes ............................................................ 7
4.5 Systematic Naming ..................................................................................................................... 7
4.6 Coordination with FMA ................................................................................................................ 7
4.7 Revisions to SNOMED CT to Eliminate S Codes ........................................................................ 7
5 Items to be evaluated, and some suggested criteria ............................................................. 8
5.1 SEP Assignment ......................................................................................................................... 8
5.2 Laterality Assignment .................................................................................................................. 8
5.3 Is-a and part-of differentiation...................................................................................................... 9
5.4 Creating sufficient definitions for E concepts ............................................................................... 9
5.5 Systematic naming ...................................................................................................................... 9
5.6 Mapping to FMA ........................................................................................................................ 10
5.7 Revision of concept model to get rid of S nodes ........................................................................ 10
6 Appendix: Assigning type S or E to concepts ...................................................................... 11
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1 Introduction
This document is to be used by those planning and executing an evaluation of the SNOMED CT
Anatomy Redesign Project, listed as artf6206 at csfe.aceworkspace.net. The project is too large to
evaluate as a single unit. Each sub-project can be assessed for its value to end users and
stakeholders, its degree of completeness and consistency, and its potential disruptive impacts on
implementers; and this will enable the IHTSDO to make decisions that will deliver high-value lowimpact quality-assured parts while keeping the option of deferring, doing further development, or
scrapping other parts. In addition, each sub-part of the project deserves its own tailored specific
evaluation effort, each with specific goals, objectives, methodologies and outcomes. This document
identifies the sub-projects, their dependencies, and general criteria by which they should be judged.
2 Project Overall Description and Aims
Simple Title: “Anatomy”. Expanded Title (as reviewed by the project group in 2011): “Revising the
anatomy model to improve usability and correctness”.
2.1 Problems to be solved
2.1.1 Specifying site and laterality – too difficult
The site and laterality of a disorder or procedure should be easy to specify, whether via pre- or postcoordination. This is one of the most common requirements of users, but currently the anatomy names
are confusing (“structure of ...”, “entire ...”), and anatomy organization appears awkward and
duplicative, even when strictly correct.
2.1.2 Errors, omissions and inconsistencies
The hierarchies in clinical findings and procedures depend on the anatomy hierarchies to determine
their structure, but anatomy contains many errors, omissions and inconsistencies, leading to the kind
of error that has been characterized in journal articles as having the “foot in the pelvis”. These errors
tend to be systematic and require scaled-up solutions, not merely one-by-one minor tweaks.
2.1.3 Maintenance burden
Because of the complex design structure adopted in the merger between SNOMED RT and CTV3, the
anatomy section inherently requires the manual checking of multiple hierarchical relationships for each
change. All changes are laborious, time-consuming, error-prone, and fraught with traps and pitfalls.
Any error in anatomy propagates (or has the potential to propagate) to the rest of the terminology. It is
very difficult to explain the model and train editors to be able to properly edit it. These negative
characteristics are not necessary, and could (and should) be significantly simplified and automated.
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2.1.4 Coordination with other anatomy terminologies
It is unclear how to coordinate SNOMED CT with “outside” resources. Some specialties have created
their own special-purpose clinical anatomy terminologies. For example, Radlex has a significant
anatomy section that supports clinical imaging applications. It would be desirable to coordinate with
(map to, or provide other types of linkages to) Radlex and probably other clinical anatomy
terminologies.
Many of the bioinformatics and biomedical research organizations have adopted the Foundational
Model of Anatomy (FMA) for annotating research data, and it would be desirable for SNOMED CT and
clinical data based on SNOMED CT to be compatible with or mapped to FMA. Some people have
even suggested that IHTSDO should “outsource” its anatomy model to an established external
anatomical standard such as FMA. Evaluation of SNOMED CT anatomy, and the mapping to FMA,
should provide some clear evidence of the actual strengths and weaknesses of each. The evaluation
of the mapping would be expected to provide a clearer picture that can assist decision-making that
considers such proposals or related suggestions for improving the maintenance, correctness and
usability of the anatomy section of SNOMED CT.
2.1.5 Inadequate adoption and use of tools
IHTSDO has invested in a workbench and description logic (DL) classifier tools, but uses these in only
a limited way in the current anatomy. All anatomy codes are currently primitive, and therefore each
meaning is edited individually. Proper adoption and use of DL tools should permit many codes to be
sufficiently defined, which in turn should reduce the editing burden, increase quality assurance
checking capabilities, and improve overall consistency and reliability.
3 Background – what is the current model?
The anatomy concepts were merged from CTV3 and SNOMED RT. Both systems had in common the
use of codes to represent individual anatomical entities, organized in multi-parent hierarchies
according to logical subsumption criteria. The main difference was that SNOMED RT used a DL
object property called “Part Of”, but CTV3 instead used a hierarchical term that added the word
“structure” to each anatomy term to indicate all or part of the structure. For example, SNOMED RT
had a code for the liver, and a code for ‘liver part’. CTV3 instead had codes for ‘liver structure’ and
liver.
The adopted model brought the two systems together using ideas very similar to those subsequently
reported by Schulz & Hahn in a paper in 2005 called “Part-whole representation and reasoning in
formal biomedical ontologies.” This model is sometimes called the Structure-Entire-Part, or SEP
model. The application of the model to hand, finger and index finger is illustrated in the two diagrams
below (Figures 1 and 2):
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finger structure
hand structure
entire hand
part of hand
finger structure
entire finger
part of finger
entire finger
part of finger
structure of index finger
entire index finger
part of index finger
Figures 1 and 2: SEP model applied to hand, finger, and index finger.
The current situation is that all the codes are primitive, and each is-a link (black arrow in the diagram)
must be individually modeled.
Further description of the SEP model can be found in the SNOMED CT Editorial Guide.
4 Project Parts
4.1 SEP Assignment
This subproject assigns exactly one of the three types structure (S), entire (E), part (P), to each code
(concept) in the hierarchy under 91722005 | physical anatomical entity |. SNOMED CT relies on the
semantic differentiation of S, E, and P, but does not yet have an agreed assignment for each code,
and this creates problems in interpretation, naming and use.
4.2 Laterality Assignment
Each anatomy code is to be assigned a laterality (left, right, lateralizable, or not lateralizable), and
there must be a clear definition of the meaning of laterality. This is essential to delivering a key
requirement for SNOMED CT, which is the support of recording and retrieving data that includes
lateralized findings and procedures. The project also needs to propose a decision about whether to
pre-coordinate lateralized anatomy concepts, and provide a clear model for post-coordination of
laterality.
4.3 Assignment of Subtype and Subpart Relationships
For each “E” entity, this subproject assigns appropriate is-a (subtype-of) parents, and also assigns and
uses (via a capable DL classifier) semantically defining part-of relationships. This supports ease-ofuse requirements for reference set creation and maintenance; ease-of-curation requirements for
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quality assuring and maintaining the terminology itself; and requirements for integrating and
coordinating with external anatomical reference terminologies such as the Foundational Model of
Anatomy (FMA).
4.4 Creation of Sufficient DL Definitions for Entire (E) Codes
For ‘defined classes’ in the hierarchy of Entire (E) codes, this project works to create definitions that
are sufficient (defined instead of primitive) to allow the DL classifier to properly recognize all subtypes.
This greatly reduces the maintenance burden while at the same time greatly improves completeness
of the is-a hierarchy; and consequently supports confidence in the accuracy of the anatomy section
and all disease and procedure sections that are defined in terms of anatomical groupings.
4.5 Systematic Naming
This subproject proposes the adoption of a single, standard, predictable approach to naming the S, E
and P variations of an anatomical concept. Currently many concepts that are logically interpreted as
S-structure do not have a name that clearly identifies them as such, creating confusion.
4.6 Coordination with FMA
This project involves the identification of one-to-one correspondence between SNOMED CT codes
and FMA codes, along with any cases where names do not mean the same thing (e.g. finger), and
adoption of some of the FMA categories for the is-a hierarchy.
4.7 Revisions to SNOMED CT to Eliminate S Codes
This sub-project envisions the creation of a revised concept model that does not use “S” codes, and
permits their deprecation. There is considerable confusion among users of SNOMED CT regarding
“which code do I choose” when there are two codes (S and E) for every anatomical entity, with
inconsistent naming (See Systematic Naming), and synonyms that are sometimes identical for
different concepts. It is feasible to eliminate this confusion, but the changes would likely have an
unacceptably high cost to implementers who have already developed systems based on our current
model.
Figure 3 (below) illustrates the dependency relationships among the various subprojects:
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4.1
4.6
4.2
4.5
4.3
4.1: SEP Assignment
4.2: Laterality Assignment
4.3: is-a and part-of modeling
4.4: Sufficient Definitions
4.5: Systematic Naming
4.6: FMA Alignment
4.7: Options for eliminating “S”
Depends on
Facilitated by
4.4
4.7
Figure 3: Dependency Relationships Among Subprojects
5 Items to be evaluated, and some suggested criteria
5.1 SEP Assignment
The data to be evaluated is in the table called “sep-map.txt” posted as doc3132 on collabnet.
Evaluation should consider:
1. The need for assigning status of S, E, or P to every anatomy concept; harm/problems
encountered without it; impact of doing it (QA of hierarchies; implementer benefits)
2. Criteria for doing the assignment in (1), based on Read code, Name, Subtypes (S,E,P), and
usage. [See Appendix ]
3. The proposed assignments to S, E, P for accuracy, impact, consistency, correctness, and
compatibility with Read codes.
5.2 Laterality Assignment
The same table “sep-map.txt” contains assignments of midline laterality (Y, L, R, -) for each row.
Items to evaluate include:
1. Need for assigning a laterality to each SEP triple
2. Definitions of the meaning(s) of laterality
3. The proposed assignment of laterality to the SEP triples for correctness, consistency
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5.3 Is-a and part-of differentiation
The is-a and part-of relationships are provided in OWL format in file “SNOMED CT Anatomy Redesign
Alpha, OWL format” which is posted as doc2000 on Collabnet.
Items to be evaluated include:
1. Need for clear is-a hierarchy and separate part-of relationships, of the "E" concepts
2. Components of the proposed structure:
a. top-level of the is-a hierarchy, based on FMA
i. do we agree with the definitions (see revised text definitions in OWL file)
ii. are the assignments properly made, according to the definitions
iii. are the definitions URU (understandable, reproducible, useful)
b. is-a and part-of assignments of E concepts
i. are they properly made, according to the definitions
c. logic model (2 options) for assigning is-a to S and P automatically, based on the SEP
table and E stated rels
i. which model (OWL2 EL with reflexive rels, or OWL 2 DL with disjunction)
ii. technical criteria for the impact of adopting the model, for usability, release
format, extensibility, etc
5.4 Creating sufficient definitions for E concepts
This is an area of active development in the OWL version file (doc2000). Further development and
revision could occur after the model is adopted and brought into the main release of SNOMED CT.
See the accompanying slides in doc4529 Anatomy redesign background slides.
Evaluation should focus on:
1. Need/benefit of sufficient definitions, example from skin/subcut/surface concepts
2. The proposed sufficient definitions, according to:
a. expected curation benefit
b. required curation tooling/distribution format changes - requirements and costs [GCIs
required]
c. potential impact on implementers
5.5 Systematic naming
The field “basename” in file “sep-map.txt” contains a proposed name for each SEP triple.
Evaluation should examine:
1. The need for a 'base name' for each SEP triple
2. Criteria for (1), based on existing names.
3. The proposed base names: for correctness, absence of plurals, spelling, etc
4. Need for systematic naming of S, E, and P concepts
5. Criteria for (4) - and multiple options
6. Value of different naming options (would be different for options that keep SEP vs options that
eliminate S – see Part 4.7 and 5.7 below)
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5.6 Mapping to FMA
The proposed mapping is contained in field “FMAID” in file “sep-map.txt”.
Evaluation can review:
1. Benefits of one-to-one alignment with FMA
2. Criteria for accuracy and correctness of the mapping
3. The existing draft mapping itself: completeness (we know it is incomplete), and correctness of
existing maps
5.7 Revision of concept model to get rid of S nodes
No existing artifact contains the whole revised model(s). These would have to be built in order to
evaluate them. The evaluation should consider:
1. Benefits of having a simpler set of anatomy codes
2. Drawbacks of significantly more complicated disorder and procedure (and specimen) models
3. Possible classifier execution time impact (does the classifier take much longer to run with the
revised model?)
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6 Appendix: Assigning type S or E to concepts
1) Exclude concepts that have the word “part” (P), and also exclude concepts that refer to
a point, level, location, plane, “both”, “all” (A), or “branch”
2) Assess and code for each of these features:
a. Current name type: “U” means unassigned, (not S, E, P, or A)
b. Read code existed: R=Read code existed, N=no Read code). Codes starting in
“XU...” are assumed to be fake/pseudo-codes.
c. Existing dual (either S or E) exists: A=dual S exists, B=dual E exists, X=none
d. S-descendants: Y=has type “S” descendants, N=does not
e. Uses: 0=not used as a value, 1 = used at least once by finding/procedure/etc
3) Patterns:
Pattern Count Assignment
URXY1 1032
S
URXN0 2396
E
URXN1 1126
S
URA
15
E
UNXY1
129
S
UNXN0 1463
E
UNXN1
326
S
URB
2
S
UNB
1
S
Basic principle for the U-X patterns: if it has S-descendants and it is already in use,
then make it S. If it has no S-descendants and is not in use, make it E.
If it is used, but has no S-descendants, it should be reviewed, with the idea of
making URX become Es and UNX become Ss.
Review each of the URA, URB and UNB manually (there are only 18 of them).
URA -> Entire;
URB & UNB -> Structure.
If there is an S-descendant, it has to be S. (E’s are not allowed to have S
descendants).
If there is an E-ancestor, it has to be E. (S’s are not allowed to have E ancestors).
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