2008 Snomed Tutorial Krmed

KR-MED 2008
Representing and Sharing Knowledge

Using SNOMED
Kent
Spackman
International Healthcare
Terminology Standards
Development Organisation
(IHTSDO)
SNOMED CT:
Ontological, Terminological, and
Knowledge Representation
Aspects
Stefan
Schulz
Medical Informatics
Research Group
University Medical Center
Freiburg, Germany
May 31, 2008, Phoenix, Arizona, USA
Purpose of the Tutorial (I)

1: Theoretical underpinnings
Get aware of the enormous variety of biomedical
vocabularies and their diverging architectural
principles
Comprehend the current structure of SNOMED CT
as a result of its evolution
Understand the nature of terminologies in contrast to
classifications, nomenclatures, and ontologies
Understand the basic principles of formal ontology as
a foundation of modern vocabulary development
Envisage the limitations of terminological /
ontological knowledge representation related to the
representation of domain knowledge in a broader
sense
Purpose of the Tutorial (II)

2: The practice of SNOMED CT
Understand the description logics used for
representing SNOMED CT
Apply the description logics to special
requirements: partonomies, complex procedures
Understand Pre-coordination and the SNOMED
CT compositional syntax
Get insight into current redesign efforts (e.g.
substance redesign)
Discuss the SNOMED CT context model and the
terminology / information model interface
Preliminary remarks
Attendees:
Heterogeneous
Experts: please challenge our viewpoints
Novices: please ask if you dont understand a term
All: participate actively, feel free to interrupt us
We have enough time for (moderated)

discussions
1st half: Presenter: Stefan, Moderator: Kent
2nd half: Presenter: Kent, Moderator: Stefan
Download tutorial slides from:

http://www.kr-med.org/2008/tutorial/tutorial1.zip
Biomedical Vocabularies
Understanding / Semantic Interoperability
data
Consumers
data
Health
Care
data
Enables
understanding
between human
and computational
agents
Biomedical
Research
Public
Health
data
Common languages: Biomedical Vocabularies
Meta Terminological Issues

Biomedical
Vocabulary
Biomedical
Terminology
Biomedical
Ontology
SNOMED CT
Biomedical
Classification
- Real systems are not ideal

- Real systems are often hybrids
A cruise through the archipelago of biomedical

vocabularies
FBcv
MedDRA
MeSH
ChEBI
BRENDA
GO
MA
FMA
GENIA
TA
ICD
NCI
GALEN
SNOMED
WordNet
CLGRO
FAO
What biomedical vocabularies have in

common
Hierarchy
Node:
Code
Label
(Definition)
Semantics
B68
Taeniasis
B68.0
Taenia
solium
taeniasis
B68.1 Link
Taenia
saginata
taeniasis
B68.9
Taeniasis,
unspecified
MeSH: Medical Subject Headings
ICD
International Classification
of Diseases
CLASSIFICATION: ICD-10
Hierarchy of
Classes
Disjointness
(non-overlapping)
Exhaustiveness
Nodes represent:
Mutually disjoint classes of particular disease entities
Often Idiosyncratic classification criteria
I83 Varicose veins of lower extremities

Excludes: complicating: pregnancy ( O22.0 ), puerperium ( O87.8 )
Classification criteria mix inherent properties of entities with

epistemic information
A15.1
Tuberculosis of lung, confirmed by culture only
Labels: explanatory
Terms: quasi-synonymous entry terms in different languages
(alphabetical index)
Links:
Connect classes with superclasses (taxonomy)
Semantics:
Taxonomy: All particular entities that instantiate one class, also
instantiate all superclasses
MeSH
Medical Subject Headings
THESAURUS: Medical Subject Headings
Hierarchical principle:
broader term / narrower
term

Nodes:
Descriptors for content of biomedical publications
Labels: Common, Unambiguous Terms; Definitions (scope notes)
Terms: entry terms (synonyms, more specific terms) , translations
Links:
Polyhierarchical connections of broader with narrower terms
Semantics:
Documents
Descriptor 1
Descriptor 2 is broader than descriptor 1

Nodes:
Descriptors for content of biomedical publications
Labels: Common, Unabbiguous Terms, Definitions (scope notes)
Terms: entry terms (synonyms, more specific terms) , translations
Links:
Polyhierarchical connections of broader with narrower terms
Semantics:
Descriptor 2
broader
Documents
narrower
Descriptor 1
Descriptor 2 is broader than descriptor 1
TA
Terminologia Anatomica
NOMENCLATURE: Terminologia Anatomica
NOMENCLATURE: Terminologia Anatomica

Nodes:
Standardized Anatomical Terms (English / Latin)
Junctura Membris Inferioris- Joints of Lower Limb
Links:
Partonomic
Semantics:
A part of B: In an canonic instance of a human body the
anatomical structure denoted by A is included into the
anatomical structure denoted by B and vice versa
FMA
Foundational Model of
Anatomy
ONTOLOGY: Foundational Model of Anatomy
ONTOLOGY: Foundational Model of Anatomy

Nodes:
Classes of anatomical entities that constitute a canonic human
body
Labels: Exact anatomical terms, compatible with TA
Posterior ramus of third thoracic nerve
Terms: Synonyms and Translations
Links:
Taxonomic, Partonomic, Topological
Semantics:
Frame-based
A part-of B: In all canonic instances of a human body the
anatomical structure that instantiates A is included into the
anatomical structure that instantiates B
and vice versa
GO
Gene Ontology
ONTOLOGY: Gene Ontology

Part of
(partonomy)
Is a
(taxonomy)

Nodes stand for:
Originally: document/resource descriptors like MeSH, now:
classes of particular entities as delineated by the meaning of
the ontology labels
Labels: unambiguous, self-explaining noun phrases
low voltage-gated potassium channel auxiliary protein activity
Links:
Connect classes with superclasses
(taxonomy)
Connect parts with wholes
(partonomy)
Semantics:
A part of B: All particular entities that instantiate A are part of at
least one particular entity that instantiates B
openGALEN
ONTOLOGY: OpenGALEN
('SurgicalProcess' which
IsMainlyCharacterisedBy
{Performance
IsEnactmentOf ('SurgicalFixing' which
hasSpecificSubprocess ('SurgicalAccessing'
hasSurgicalOpenClosedness
(SurgicalOpenClosedness which hasAbsoluteState
surgicallyOpen))
actsSpeclflcallyOn (PathologlcalBodyStructure which <
Involves Bone
hasUniqueAssociatedProcess FracturingProcess
hasSpecificLocation (Collum whlch
IsSpecificSolidDivisionOf (Femur whlch
hasLeftRlghtSelectorleftSelect!on))>))))
ONTOLOGY: OpenGalen
Nodes:
Medical Concepts
Labels: Artificial, Self-Explaining:
SurgicalOpenClosedness
Links:
Taxonomic, partonomic, other relations
Semantics:
Description Logics T-Box (unary and binary predicates)

Non partonomic relations as existential restrictions
Sanctioning
Closed-world semantics
Better understanding SNOMED CT
SNOMED CT
SNOMED since 1965
Fusion with
CTV 3
Principles of
Formal
Ontology
Context
Model
Logic-based
descriptions
multiaxial
nomenclature of
medicine
Nomenclature /
Pathology
1965
SNOP
1970
SNOMED
Embryo
1975
SNOMED
im UMLS
1980
SNOMED II
Fetus
1985
1990
IHTSDO
1995
2000
2005
SNOMED 3.0 SNOMED 3.5 SNOMED RT SNOMED CT
Infant
Child
Adolescence
SNOMED CT
The current structure of SNOMED CT is a result

of its evolution
Represents several tendencies from decades of
nomenclature, terminology, ontology, and
classification system development
Nomenclature:
Multiaxial Structure
Formal Language
Benign neoplasm of heart =
Thesaurus
64572001|disease|:
{116676008|hasasociated morphology|
=3898006|neoplasm, benign|
,363698007|finding site|=80891009|heart
structure|}
SNOMED CT
Ontological
Principles
Sanctioning
Clinically relevant
classes
SNOMED CT

of its evolution
Identification of elements of
Terminology
Ontology
SNOMED CT
of its evolution
Terminology vs. Ontology
What biomedical vocabularies have in

common
Hierarchy
Node:
Code
Label
(Definition)
Semantics
B68
Taeniasis
B68.0
Taenia
solium
taeniasis
B68.1 Link
Taenia
saginata
taeniasis
B68.9
Taeniasis,
unspecified
Terminology vs. Ontology

Dictionaries of
Natural language Terms
Hierarchically ordered
Nodes and Links
Formal or informal
Definitions
bla bla bla

Benign neoplasm of heart
Benign tumor of heart
Benign tumour of heart
Benign cardiac neoplasm
Gutartiger Herzumor
Gutartige Neubildung am
Herzen
Gutartige Neubildung: Herz
Gutartige Neoplasie des
Herzens
Tumeur bnigne cardiaque
Tumeur bnigne du cur
Neoplasia cardaca benigna
Neoplasia benigna do corao
Neoplasia benigna del corazn
Tumor benigno do corazn
D18
Benign
Neoplasm
Terminology
Heart Neoplasms [MeSH]:

Tumors in any part of the heart.
They include primary cardiac
tumors and metastatic tumors to
the heart. Their interference with
normal cardiac functions can
cause a wide variety of
symptoms
Formal Ontology
D18.0
Benign
Neoplasm
of
Thymus
Set of terms
representing the system
of concepts of a
particular subject field.
(ISO 1087)
D18.1
Benign
Neoplasm
of
Heart

(disorder)
B68.9
[SNOMED CT]:
Taeniasis,
64572001|disease|:
unspecified
{116676008|associated morphology|
structure|}
Ontology is the study of what there is.

Formal ontologies are theories that
attempt to give precise mathematical
formulations of the properties and
relations of certain entities.
(Stanford Encyclopedia of Philosophy)
Terminology
Dictionaries of
Natural language Terms
Hierarchically ordered
Nodes and Links
Formal or informal
Definitions
bla bla bla

Benign tumor of heart
Benign tumour of heart
Benign cardiac neoplasm
Gutartiger Herzumor
Gutartige Neubildung am
Herzen
Gutartige Neubildung: Herz
Gutartige Neoplasie des
Herzens
Tumeur bnigne cardiaque
D18.0
Tumeur bnigne du cur
Benign
Neoplasia cardaca benigna
Neoplasm
of
Neoplasia benigna do corao
Thymus
Neoplasia benigna del corazn
benign neoplasm of heart
Tumor benigno do corazn
Entities of
Language
(Terms)
Heart Neoplasms [MeSH]:

Tumors in any part of the heart.
They include primary cardiac
tumors and metastatic tumors to
the heart. Their interference with
normal cardiac functions can
Shared /
cause a wide variety of
Meanings /
symptoms
D18
Benign
Neoplasm
D18.1
Benign
Neoplasm
of
Heart
Entities of
Benign neoplasm
of heart
Thought
(disorder)
B68.9
[SNOMED CT]:
Taeniasis,
64572001|disease|:
unspecified
{116676008|associated morphology|
structure|}
gutartige Neubildung des Herzmuskels

neoplasia cardaca benigna
(Concepts)
Example: UMLS (mrconso table)
Shared /
Meanings /
Entities of
Thought
Entities of
Language
(Terms)
C0153957|ENG|P|L0180790|PF|S1084242|Y|A1141630||||MTH|PN|U001287|benign neoplasm of heart|0|N||

C0153957|ENG|P|L0180790|VC|S0245316|N|A0270815||||ICD9CM|PT| 212.7|Benign neoplasm of heart|0|N||
C0153957|ENG|P|L0180790|VC|S0245316|N|A0270817||||RCD|SY|B727.| Benign neoplasm of heart|3|N||
C0153957|ENG|P|L0180790|VO|S1446737|Y|A1406658||||SNMI|PT|
D3-F0100|Benign neoplasm of heart, NOS|3|N||
C0153957|ENG|S|L0524277|PF|S0599118|N|A0654589||||RCDAE|PT|B727.|Benign tumor of heart|3|N||
C0153957|ENG|S|L0524277|VO|S0599510|N|A0654975||||RCD|PT|B727.| Benign tumour of heart|3|N||
C0153957|ENG|S|L0018787|PF|S0047194|Y|A0066366||||ICD10|PS|D15.1|Heart|3|Y||
C0153957|ENG|S|L0018787|VO|S0900815|Y|A0957792||||MTH|MM|U003158|Heart <3>|0|Y||
C0153957|ENG|S|L1371329|PF|S1624801|N|A1583056|||10004245|MDR|LT|10004245|Benign cardiac neoplasm|3|N||
C0153957|GER|P|L1258174|PF|S1500120|Y|A1450314||||DMDICD10|PT| D15.1|Gutartige Neubildung: Herz|1|N||
C0153957|SPA|P|L2354284|PF|S2790139|N|A2809706||||MDRSPA|LT| 10004245|Neoplasia cardiaca benigna|3|N||
Unified Medical Language System, Bethesda, MD: National Library of Medicine, 2007:
http://umlsinfo.nlm.nih.gov/
Example: UMLS (mrrel table)
Shared /
Meanings /
Entities of
Thought
Shared /
Meanings /
Entities of
Thought
C0153957|A0066366|AUI|PAR|C0348423|A0876682|AUI |
|R06101405||ICD10|ICD10|||N||
C0153957|A0066366|AUI|RQ |C0153957|A0270815|AUI |default_mapped_ from|R03575929||NCISEER|NCISEER|||N||
C0153957|A0066366|AUI|SY |C0153957|A0270815|AUI |uniquely_mapped_ to |R03581228||NCISEER|NCISEER|||N||
C0153957|A0270815|AUI|RQ |C0810249|A1739601|AUI |classifies
| R00860638||CCS|CCS|||N||
C0153957|A0270815|AUI|SIB|C0347243|A0654158|AUI |
|R06390094
|| ICD9CM|ICD9CM||N|N||
C0153957|A0270815|CODE|RN|C0685118|A3807697|SCUI |mapped_to
| R15864842||SNOMEDCT|SNOMEDCT||Y|N||
C0153957|A1406658|AUI|RL |C0153957|A0270815|AUI |mapped_from
| R04145423||SNMI|SNMI|||N||
C0153957|A1406658|AUI|RO |C0018787|A0357988|AUI |location_of
| R04309461||SNMI|SNMI|||N||
C0153957|A2891769|SCUI|CHD|C0151241|A2890143|SCUI|isa
|R19841220|47189027|SNOMEDCT|SNOMEDCT|0|Y|N||
Semantic relations
Example: UMLS
Shared /
Meanings /
Entities of
Thought
Shared /
Meanings /
Entities of
Thought
C0153957|A0066366|AUI|PAR|C0348423|A0876682|AUI |
|R06101405||ICD10|ICD10|||N||
C0153957|A0066366|AUI|RQ |C0153957|A0270815|AUI |default_mapped_ from|R03575929||NCISEER|NCISEER|||N||
C0153957|A0066366|AUI|SY |C0153957|A0270815|AUI |uniquely_mapped_ to |R03581228||NCISEER|NCISEER|||N||
C0153957|A0270815|AUI|RQ |C0810249|A1739601|AUI |classifies
| R00860638||CCS|CCS|||N||
C0153957|A0270815|AUI|SIB|C0347243|A0654158|AUI |
|R06390094
|| ICD9CM|ICD9CM||N|N||
C0153957|A0270815|CODE|RN|C0685118|A3807697|SCUI |mapped_to
| R15864842||SNOMEDCT|SNOMEDCT||Y|N||
C0153957|A1406658|AUI|RL |C0153957|A0270815|AUI |mapped_from
| R04145423||SNMI|SNMI|||N||
C0153957|A1406658|AUI|RO |C0018787|A0357988|AUI |location_of
| R04309461||SNMI|SNMI|||N||
C0153957|A2891769|SCUI|CHD|C0151241|A2890143|SCUI|isa
|R19841220|47189027|SNOMEDCT|SNOMEDCT|0|Y|N||
INFORMAL
Semantic relations
Formal Ontology represents the world

bla bla bla
Terminology
Set of terms
representing the system
of concepts of a
particular subject field.
(ISO 1087)
Formal
Ontology
Ontology is the study of what
there is (Quine).
Formal ontologies are theories
that attempt to give precise
mathematical formulations of the
properties and relations of
certain entities.
(Stanford Encyclopedia of Philosophy)
Formal Ontology
Organizing Entities
Entity Types
The type
benign
neoplasm of
heart
My benign
neoplasm of
heart
Entities of
the World
Organizing Entities
abstract
Entity Types
The type
benign
neoplasm of
heart
Universals, classes,
(Concepts)
Instance_of
concrete
Entities of
the World
Particulars,
instances
The benign
neoplasm of my
heart
Organizing Entities
abstract
represents
Entity Types
The type
benign
neoplasm of
heart
Universals, classes,
(Concepts)
Entities of
Language
Instance_of
Terms, names
represents
The string
benign neoplasm of heart
concrete
Entities of
the World
Particulars,
instances
The benign
neoplasm of my
heart
Organizing Entities
(the complication
of my)
benign heart tumor
(die
Komplikation
meines)
Gutartigen
Herztumors
represents
Organizing Entities
represents
(the)
benign heart tumor
(is congenital)
Terms, names
(die
Komplikation
meines)
Gutartigen
Herztumors
Entities of
Language
are represented by
terminologies
Databases systems represent

Entities of
the World
Entity Types
are organized in formal ontologies
Hierarchies, Types, Classes, Individuals
World
World

Type 1
World

Formal Ontology
Is_a
Subtype
1.1
World
Type 1
Is_a
Subtype
1.2
Is_a
Subtype
1.3

Formal Ontology
Inflammatory
Disease

Formal Ontology
Inflammatory
Disease
Is_a
Gastritis
Is_a
Hepatitis
Is_a
Pacreatitis

Formal Ontology
Inflammatory
Disease
Is_a
Gastritis
Is_a
Hepatitis
Is_a
Pacreatitis

Formal Ontology
Inflammatory
Disease
Is_a
Gastritis
Is_a
Hepatitis
Is_a
Pacreatitis
Relations and Definitions

Formal Ontology
Inflammatory
Disease
Is_a
Hepatitis
has
Location
Liver

Formal Ontology
Inflammatory
Disease
Is_a
Hepatitis
has
Location
Liver

Formal Ontology
Inflammatory
Disease
Is_a
Population
Is_a
Population of Virus
caused
by
Hepatitis
Viral Hepatitis
has
Location
Liver
Languages for formal ontologies

Natural Language
Every hepatitis is an inflammatory disease that is located in some liver
Every inflammatory disease that is located in some liver is an hepatitis
Logic
x: instanceOf(x, Hepatitis) instanceOf(x, Inflammation)

y: instanceOf(y, Liver) hasLocation(x,y)
Logic is computable: it supports

machine inferences but
it only scales up if it has a very
limited expressivity
SNOMED CT: Terminology and Ontology

aspects
bla bla bla
Fully Specified Name

Preferred Term
Synonyms
Same structure for other languages
Terminology
Taxonomic
Parents (isA)
Logical
Restrictions
Full-text definitions mostly missing
Formal Ontology
Terminologies vs. Formal Ontologies

Terminologies
Describe: Meaning of human
language units
Concepts: aggregate (quasi)synonymous terms
Relations: informal, elastic
Associations between Concepts
..
Description pattern:
Concept1 Relation Concept2
Formal Ontologies
Describe: entities of reality as
they generically are
independent of human
language
Types: represent the generic
properties of world entities
Relations: rigid, exactly
defined, quantified
relationships between
particulars
Description pattern:
for all instance of Type1 : there
is some
Example Hepatitis - Liver

Terminologies
Concept Hepatitis:
{Hepatitis (D), Leberentzndung (D),

hepatitis (E), hpatite (F)}
Concept Liver:
{Leber (D), liver (E), foie (F)}
Relations:
Hepatitis hasLocation Liver
Hepatitis isA - Inflammation
Formal Ontologies
Type: Hepatitis:
Description:
Every hepatitis is an inflammatory
disease that is located in some liver
Every inflammatory disease that is
located in some liver is an hepatitis
Example Hand - Thumb

Terminologies
Concept Hand:
{Hand (D), hand (E), main (F)}
Concept Thumb:
{Daumen (D), thumb (E), pouce (F)}
Relations:
Hand hasPart Thumb
Thumb partOf Hand
Formal Ontologies
Type: Thumb:
Description:
Every thumb is part of some hand
Every hand has some thumb as
part
Example Aspirin - Headache

Terminologies
Concept Aspirin:
{Aspirin (D,E), Acetylsalicylsure (D),

ASS (D), acetylsalicylic acid (E), Acide
actylsalicylique(F)}
Concept Headache:
{Kopfschmerz (D), headache (E),

cphale(F)}
Relation:
Formal Ontologies
Type: Aspirin:
Description:
For every portion of aspirin there is

some disposition for treating
headache
Aspirin treats Headache
fuzzy
complicated !
Strengths of Formal Ontologies
Exact, logic-based descriptions of entity types that

are instantiated by real-world objects, processes,
states
Representation of stable, context-independent
accounts of reality
Use of formal reasoning methods using tools and
approaches from the AI / Semantic Web
community
Formal Ontologies: Limitations (I)

Only suitable to represent shared, uncontroversial
meaning of a domain vocabulary
Supports universal statements about instances of
a type:
All Xs are Ys
For all Xs there is some Y
Properties of types are properties of all entities that
instantiate these types (strict inheritance)
Classification vs. Ontology
Classification systems vs. Ontologies
Classifications vs. Formal Ontologies

Classifications
Formal Ontologies
A
A1
A2
A3
A4
A
nec
A
nos
not
elsewhere
classified
not
otherwise
specified
A1
A2
A3
A4
Classifications vs. Formal Ontologies

Classifications
Diabetes
Mellitus
Diabetes
Mellitus
Formal Ontologies
Diabetes
Mellitus
Diabetes
Mellitus
In Pregnancy
SNOMED CT: Classification aspects
SNOMED CT and Classifications

Many classes in classification systems cannot be
adequately expressed in SNOMED
Problem:
SNOMED supports existential quantification and
conjunction, but not negation
Classifications contain classes defined by negation:
Viral hepatitis (B15-B19)
Excludes: cytomegaloviral hepatitis ( B25.1 )
herpesviral [herpes simplex] hepatitis ( B00.8 )
sequelae of viral hepatitis ( B94.2 )
B17 Other acute viral hepatitis
B17.0 Acute delta-(super)infection of hepatitis B carrier
B17.1 Acute hepatitis C
B17.2 Acute hepatitis E
B17.8 Other specified acute viral hepatitis Hepatitis non-A non-B (acute)(viral) NEC
Continuum of knowledge
Universally accepted
assertions
Consolidated but contextdependent facts
Hypotheses, beliefs,
statistical associations
Domain Knowledge
Formal Ontology !
Universally accepted
assertions
Consolidated but contextdependent facts
Hypotheses, beliefs,
statistical associations
Domain Knowledge
Instance-level Knowledge / Belief

Working Hypothesis
The patient was admitted with suspected appendicitis
Unknown facts
Allergies unknown
Ruled-out facts
No Pregnancy
Absent corneal reflex
Imprecise
Patient reports liver disease
Epistemic
The diabetes was recently diagnosed
Classification-related:
Cause of death: A09 - Diarrhoea and gastroenteritis of presumed infectious

origin
Diagnosis: B37.8 - Candidiasis of other sites
Domain Knowledge
Facts that are known to be true under certain circumstances:
Excessive alcohol consumption can cause gout
Context dependent facts:

Hg2Cl2 is a diuretic drug
Aspririn is an analgetic drug
Facts about populations:
Malaria is endemic in Mozambique
Recommendations / Guidelines:
Old patients with newly diagnosed Hypertension should be treated with

diuretics or Ca channel blockers
Basic scientific facts
Many urokinase-type plasminogen activators are expressed in the kidney
Results from clinical trials:
One-lung overventilation does not induce inflammation in the normally

ventilated contralateral lung.
Default / canonic knowledge

Adult humans have 32 teeth
Take home messages

Ontologies describe classes of domain entities
(ideally) by their inherent properties
Classifications classify entities according to welldefined criteria
Terminologies relate words and terms
SNOMED CT is a hybrid terminology / ontology
with elements of classifications
Knowledge representation extends terminology /
ontology by large
(Computable) Ontologies are restricted to make
universal statements of the type for all some
Practice of Good Ontology
Practice of Good Ontology
Learning good ontology practice from bad

ontologies
Dont mix up universals (Concepts, Classes) with

individuals (Instances)
Is_a = subclass_of:
subclass-of (Motor Neuron, Neuron)
(FMA, OpenGALEN)
Is_a (Motor Neuron, Neuron)
instance-of (Motor Neuron, Neuron) (FlyBase)
But:
instance-of (my Hand, Hand)
instance-of (this amount of insulin, Insulin)
instance-of (Germany, Country)
not: instance of (Heart, Organ)
not: instance of (Insulin, Protein)
Taxonomic
Subsumption
Instance_of
Class Membership
Dont use superclasses to express roles

Is_a (Fish, Animal)
Is_a (Fish, Food) ??
Is_a (Acetylsalicylic Acid, Salicylate)
Is_a (Acetylsalicylic Acid, Analgetic Drug) ??
Be aware of the rigidity of entity types
Partition the ontology by principled upper level

categories
Example: DOLCEs Upper Ontology

Endurant (Continuant)
Physical
Amount of matter
Physical object
Feature
Non-Physical
Mental object
Social object
Perdurant (Occurrent)
Static
State
Process
Dynamic
Achievement
Quality
Physical Qualities
Spatial location
Temporal Qualities
Temporal location
Abstract Qualities
Abstract
Quality region
Time region
Space region
Color
region
Source: S. Borgo ISTC-CNR
Limit to a parsimonious set of semantically

precise Basic Relations
Barry Smith, Werner Ceusters, Bert Klagges, Jacob Khler,

Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus,
Alan L Rector and Cornelius Rosse. Relations in biomedical ontologies.
Genome Biology, 6(5), 2005.
Avoid idiosyncratic categorization

Body structure (10)
Acquired body structure
Anatomical organizational pattern
()
Clinical finding (22)
Administrative statuses
Adverse incident outcome categories
()
Environment or geographical location
Environment
Geogr. and/or political region of the world
Event (19)
Abuse
Accidental event
Bioterrorism related event
()
Linkage concept
Attribute
Link assertion
Observable entity
Age AND/OR growth period
Body product observable
()
Clin. history / examination observable (21)
Device observable
Drug therapy observable
Feature of Entity
()
Organism (11)
Animal
Chromista
Infectious agent
()
Pharmaceutical / biologic product (58)
Alcohol products
Alopecia preparation
Alternative medicines
()
Physical force (21)
Altitude
Electricity
()
Physical object (8)

Device
Domestic, office and garden
Fastening
()
Procedure (23)
Administrative procedure
Community health procedure
()
Qualifier value (52)
Action
Additional dosage instructions
()
Record artifact
Record organizer
Record type
Situation with explicit
context (17)
A/N risk factors
Critical incident factors
()
Social context (10)
Community
Family
Group
()
Special concept
Namespace concept
Navigational concept
Non-current concept
Specimen (45)
Biopsy sample
Body substance sample
Cardiovascular sample
()
Staging and scales (6)
Assessment scales
Endometriosis classification of
American Fertility Society
()
Substance (11)
Allergen class
Biological substance
Body substance
()
artefact
The Celestial Emporium

of Benevolent Knowledge
Jorge Luis Borges
"On those remote pages

it is written that animals
are divided into:
a. those that belong to the
Emperor
b. embalmed ones
c. those that are trained
d. suckling pigs
e. mermaids
f. fabulous ones
g. stray dogs
h. those that are included
in this classification
i. those that tremble as if
they were mad
j. innumerable ones
k. those drawn with a
very fine camel's hair
brush
l. others
m. those that have just
broken a flower vase
n. those that resemble
flies from a distance"
Be aware of ambiguities
Institution may refer to

1. (abstract) institutional rules
2. (concrete) things instituted
3. act of instituting sth.
Tumor
1. evolution of a tumor as a disease process
2. having a tumor as a pathological state
3. tumor as a physical object
Gene
1. a (physical) sequence of nucleotides on a DNA
chain
2. a collection of (1)
3. A piece of information conveyed by (1)
Dont mix up ontology with epistemiology

Is_a (Infection of unknown origin, Infection)
Is_a (Newly diagnosed diabetes, Diabetes)
Is_a (Family history of diabetes, Diabetes)
what is
what sth.
knows about
Dont mix up Ontology IDs with Terms
Glycerin Kinase
Glycerokinase
GK
Glyzerinkinase
how it is expressed
in human language
what is
what sth.
knows about
Dont underestimate Ontology Maintenance

Formal Ontologies must always be maintained
consistent (free of logic contradiction): prerequisite for
machine reasoning
adequate (correctly describe the domain) prerequisite to
prevent erroneous deductions
Maintenance load is much higher than with

terminologies.
Ontology maintenance is mainly task of domain
experts. IT staff has supportive function
Typical design and maintenance errors
Aspects of Knowledge Representation

Terminological Knowledge: What is known about
the meaning of terms in a domain
neoplasm has a broader meaning as sarcoma
Ontological Knowledge: What is univocally

accepted as generic properties of types of entities
of a domain (often definitional or trivial):
every hepatitis is located in some liver
every cell has some cell membrane
Terminologies and Ontologies represent this kind

of Knowledge, but
Knowledge representation is more:
in Practice: SNOMED CT
Kent A. Spackman, MD, PhD
Chief Terminologist, IHTSDO
Clinical Professor, Oregon Health & Science University, Portland Oregon
USA
KR-MED 2008 Tutorial

Phoenix May 30, 2008
Tutorial 2nd Half Topics

Description logic basics
Concept model domains, ranges and attributes
Application of additional description logic features
to special requirements:
Right identities: partonomies (SEP)

Role groups: complex procedures, disorders, situations
Role hierarchies: direct and indirect objects; causal and associational
relationships
Composition and syntax

normal forms
SNOMED compositional syntax, KRSS, and OWL
Current redesign efforts

substances, observables, anatomy, events, conditions, organisms
The context model & negation

The terminology / information model interface
DESCRIPTION LOGIC
BASICS
What is description logic?

Mathematical viewpoint:
A family of logics characterized by
Formal set-theoretic semantics
Proofs of correctness and completeness of computation
Proofs of algorithmic complexity (PSpace, NP-complete,
NExpTime, etc)
Knowledge representation viewpoint:

A set of constructs for representing terminological
knowledge (that which is always true of a meaning)
Algorithms and their implementations for performing:
Subsumption (testing pairs of expressions to see
whether one is a subtype of the other & vice versa)
Classification (structuring a set of expressions
according to their subsumption relationships)
Constructs for a very simple DL: EL
Reading DL expressions
is the symbol for Boolean conjunction
Short name: and

Operands are placed on either side: C u D
Both operands C and D must be true in order for the
expression to be true
is the symbol for existential restriction
Short name: some

Operands follow the backwards E symbol: 9RC
R represents a role or relationship
C represents the value or target of the relationship
Requires that there be an instance of relationship named R to
some instance of the class named C in order for the expression
to be true
The logic of green frogs
How could you use EL to define a green frog?

First, some concept names (A in the EL notation table):
Frog
Green
GreenFrog
Then a role name (R in the EL notation table):
hasColor
Now introduce a definition of GreenFrog,

using Frog, Green, and hasColor, along with C u D and 9RC as follows
GreenFrog Frog u 9 hasColor.Green

How do we read these expressions?
Usual DL syntax
GreenFrog Frog u 9 hasColor.Green
KRSS syntax:
(defconcept GreenFrog (and Frog (some hasColor Green)))
Every instance of the class named GreenFrog
is an instance of the class named Frog which also
has a hasColor relationship to an instance
of the class named Green
And, every instance of the class named Frog which also
has a hasColor relationship to an instance
of the class named Green
is an instance of the class named GreenFrog.

Right hand side only:
Usual DL syntax
Frog u 9 hasColor.Green
KRSS syntax:
(and Frog (some hasColor Green))
SNOMED compositional syntax:
Frog: hasColor = Green
an instance of the class named Frog which also
has a hasColor relationship to an instance of the
class named Green
Exercise for the reader: how do you represent frogs that are
completely green?
A SNOMED example
Headache is-a ache: finding-site = head structure
(and headache is marked as defined in concepts table).
The class headache is sufficiently defined as the

set of instances of the class ache which also
have at least one finding-site relationship to an
instance of the class head structure.
And all instances of class ache with some
finding-site relationship to an instance of head
structure are instances of headache.
Now, is that what you mean when you say headache?
EXPRESSIONS &
COMPOSITION
SNOMED CT Expressions
SNOMED CT coded information consists of structured
(composed) collections of concept codes
These are called expressions
The meaning of an expression depends on the situation in which it is
used
Example
The SNOMED CT code for fracture of femur represents the
meaning of a break in a femur
Depending on where it is used in a patient record, the code may
mean
The
The
The
The
patient has a fractured femur

patients main diagnosis is a fracture of the femur
patient has a past history of fractured femur
patient is suspected of having a fractured femur . etc
In a query it may be one of several criteria for retrieving the records

of patients with particular types of injury
In an index to the clinical literature it might indicate a paper that is
relevant to this condition
Expressions can be pre-coordinated or postcoordinated

Pre-coordinated expression
Terminology producer provides a single ConceptId
for the meaning
31978002
means fracture of tibia
Post-coordinated expression
A user composes a combination of ConceptIds to
represent the meaning
31978002 : 272741003 = 7771000
(fracture of tibia : laterality = left)
In human readable form fracture of left tibia
Refinement and qualification:

Two common ways to derive post-coordinated
expressions
Refinement
Replacing value C with a more specific value C1
within an existing (defining) 9RC relationship in the
definition, giving 9RC1
Example
Fracture of femur
Defined as: finding-site = bone structure of femur
May be refined to: finding-site = structure of neck of
femur
Yielding the new meaning: Fracture of neck of

femur
Refinement and qualification:

Two common ways to derive post-coordinated
expressions
Qualification (also called subtype qualification)

Replacing value C with a more specific value C1 within a
qualifier 9RC relationship (found in the qualifying
relationships in the relationships table), giving 9RC1
Example
Bronchitis
Qualifier exists as: clinical-course = courses (any course value)

May be qualified to: clinical-course = acute (sudden onset
AND/OR short duration)
Yields the meaning: Acute bronchitis

End results of refinement or qualification are postcoordinated expressions with an identical logical structure
Compositional grammar (1)

Simplest expression is a single conceptid
For example
71620000
Optionally conceptId may be followed by a

term enclosed in pipe delimiters
For example
71620000|fracture of femur|
Concepts can be combined with a plus sign

that means logical and (conjunction)
For example
31978002|fracture of tibia| +75591007|fracture of
fibula|
Compositional grammar (2)

Refinements can be added after a colon
For example
125605004: 363698007=29627003
Refinements can be nested in parentheses

For example
53057004|hand pain|:
363698007|finding site| =(76505004|thumb structure|:
272741003|laterality| =7771000|left|)
Refinements can be grouped in braces

For example
71388002|procedure|:
{260686004|method| =129304002|excision - action|,
363704007|procedure site| =66754008|appendix
structure|}
Note: the comma also means logical and in this expression
Severe pain, left thumb

Pain
Finding site
Thumb structure
Laterality
Severity
Severe
22253000|pain|:
363698007|finding site|=
(76505004|thumb structure|:
272741003|laterality|=7771000|left|),
246112005|severity|=24484000|severe|
Left
Severe pain, left thumb

Hand Pain
Finding site
Thumb structure
Laterality
Severity
Severe
53057004|hand pain|:
363698007|finding site|=
(76505004|thumb structure|:
272741003|laterality|=7771000|left|),
246112005|severity|=24484000|severe|
Left
Subtype relationships
Every concept is a refined type of one
or more other concepts
For example
Pain in the leg is a type of pain
Pain in the leg is a type of lower
limb finding
SNOMED CT represents these defining
relationships with the relationship type
is a
Lower limb finding

Is
a
su
bt
yp
e
Pain
of
Pain in lower limb

Pain in calf
A pain in the calf is-a pain the lower limb, and
Pain in the lower limb is-a pain, and is-a lower limb finding
Lung disease
Is
su
b
typ
e
of
Infectious disease
Infectious pneumonia
Bacterial pneumonia
Bacterial pneumonia is-a infectious pneumonia, and

Infectious pneumonia is-a lung disease, and is-a Infectious
disease
Why have subtype relationships?

Because when you selectively retrieve
information you usually want to include
subtypes
For example
When searching for Deep Venous
Thrombosis you would usually want to
retrieve all kinds of DVT including
DVT of specific sites (e.g. lower limb)
DVT with particular causes (e.g. air travel related
DVT)
and others
Root
Subtype hierarchy
Clinical
finding
Looking from leaf to root

Finding by
site
Disorder
Disorder by
body site
Finding of
body region
Disorder of
body system
Disorder of
cardiovascular
system
Finding of
limb structure
Disorder of
extremity
Vascular
disease
Thrombotic
disorder
Disease of
vein
Peripheral
vascular disease
Vascular disorder
of lower
extremity
Thrombosis of
Deep venous
vein of lower
thrombosis
limb
Deep venous
thrombosis of lower
extremity
Deep vein thrombosis
of leg related to air
DVT
travel
Finding of
lower limb
Disorder of
lower
extremity
Venous
thrombosis
Leaf
leg assoc w air travel
Other defining relationships

The difference between two concepts
may be represented by other defining
relationships
Only relationships that are
necessarily true are defining
relationships
For example
Pain in calf has finding site calf
structure

Lower limb finding
Pain
Pain in lower limb
lower limb
structure
Calf structure
Pain in calf
A pain in the calf has finding site calf

Pain in the lower limb has finding site lower limb

Bacterial disease
Lung disease
Bacterial
pneumonia
Lung structure
RLL structure
RLL bacterial
pneumonia
Bacterial pneumonia has finding site lung structure
RLL bacterial pneumonia has finding site RLL
structure
Why have other defining

relationships?
Confirm and enhance the accuracy of the
subtype hierarchy
For example, all pain findings with a finding
site of lower limb (or a subtype of lower limb
structure) must be subtypes of lower limb pain
Enable concepts to be refined by increasing

the specificity of a defined relationship
For example, a pain in the foot could be refined
to specify a more precise finding site such as
the third toe of the left foot, even if SNOMED
CT did not include a specific concept for pain in a
such a specific location.
Allow recognition of equivalence between

different ways of expressing the same concept
Primitive & sufficiently-defined

concepts
A concept is sufficiently defined
if its definition is sufficient to
distinguish it from all its
supertype concepts
A concept is primitive
if it is not sufficiently defined
Primitive & sufficiently defined

concepts
Head injury
Is a = Disease
Associated morphology = Traumatic abnormality
Finding site = Head structure
Sufficiently Defined
Aching pain
Is a = Pain
Primitive
Headache
Is a = Aching pain
Finding site = Head structure
Sufficiently Defined
The value of sufficiently defining concepts

Allows auto-classification
Consistent hierarchy and definition
Allows computation of equivalence and

subsumption between
Different ways of expressing the same meaning
E.g.
open fracture of left femur
or
fracture of bone
site=femur: laterality=left
morphology=open fracture
Different views of relationships

Stated view
The view that SNOMED CT modelers edit
Includes only the defining relationships that an author
has explicitly stated to be true
(soon will be distributed in KRSS and/or OWL syntax)
Inferred view
The view distributed in the distribution file
Generated by auto-classification
Includes relationships inferred from the stated view
Excludes redundant relationships
Normalized view
The view best suited to comparing expressions
Reduces all values to their proximal primitive subtypes
Auto-classification
Many relationships are inferred by autoclassification rather than authored directly
Auto-classification
Takes definitions stated by SNOMED authors and
uses them to infer other relationships
Removes redundant (less specific) defining
relationships
Creates a logically consistent parsimonious set of
relationships
Review the results of classification

Although logically consistent it may not be correct
due to errors in stated definitions
Human errors that might otherwise be overlooked are
often highlighted by auto-classification
Auto-classification is repeated frequently during
authoring and the results are then rechecked
An example of a stated view
The diagram is a directed acyclic graph, or DAG, of the is-a relationships
pain
is a
is a
pain in lower limb
lower limb structure
is a
pain in calf
calf structure
Auto-classification can add

inferred relationships to the stated view
pain
is a
is a
pain in lower limb

Inferred
from other
relationships
is a
is a
calf structure
pain in calf
For the distributed inferred view less specific

subtype relationships are removed
In computer science terms this structure is called the transitive reduction
i.e. the distributed is-a relationships are the transitive reduction of the DAG
pain
Redundant after
adding inferred
relationship
is a
is a
pain in lower limb
is a
is a
calf structure
pain in calf
In another view all the possible

subtype relationships are stated
directly
This is transitive
closure view is
useful for
optimization
It can be
computed from
distributed data
SNOMED is likely
to release this
view later this
year
finding
is a
is a
is a
pain
is a
pain in lower limb
is a
is a
pain in calf
Description Logic Classifiers

Various DL Classifiers exist
SNOMED uses the Apelon TDE classifier
It has some limitations but performs well
on a large database
Some other classifiers testing in past failed or
became very slow with so many concepts
Others include
FaCT++ (Fast Classifier of Terminologies)

Pellet
CEL
RacerPro
Definition of Normal Forms

In original RT work, dual independent
modeling required exact agreement on stated
definition
Resulted in unresolved arguments about modeling
style
State most immediate parent concepts only, and only
those relationships that have changed, or
State proximal primitives only, and all defining
relationships
Defining a normal form allowed different

modeling styles for different purposes or
preferences
Spackman KA. Normal forms for description logic expression of clinical concepts in SNOMED RT.
Proceedings/AMIA Annual Symposium. :627-631, 2001.
Illustration of need for normal form:

basal cell carcinoma (BCC) of skin of
eyelid
Multiple different ways to postcoordinate:
Disorder, M=BCC, T=skin of eyelid

Malignant disorder, M=BCC, T=skin of eyelid
Skin disorder, M=BCC, T=skin of eyelid
Disorder of skin of eyelid, M=BCC
Malignant neoplastic disorder of skin eyelid,
M=BCC
Basal cell carcinoma (disorder), T=skin of
eyelid
...
D1
D3
D6
Basal cell
malignancy
D9
Neoplastic
disorder
Malignant
neoplasm
D7
D4
D2
Disorder
of skin
Neoplastic
disorder of skin
Malignant
neoplasm of skin
Basal cell
carcinoma of skin
D11
Disorder
D8
Disorder of skin
of eyelid
Neoplastic disorder
of skin of eyelid
D10 Malignant neoplasm

of skin of eyelid
Basal cell carcinoma

of skin of eyelid
D5
Neoplastic
Morphology
Malignant
Morphology
Disorder
Skin structure
M1
M2
T1
D1
Neoplastic
disorder
D2
Disorder
of skin
T2
M3 BCC
Morphology
D6
D3
Basal cell
malignancy
D9
Malignant
neoplasm
D7
D4
Malignant
neoplasm of skin
Basal cell
carcinoma of skin
D11
Neoplastic
disorder of skin
D8
Disorder of skin
of eyelid
Neoplastic disorder
of skin of eyelid

of skin of eyelid

of skin of eyelid
D5
Skin
structure
of eyelid
Neoplastic
Morphology
Malignant
Morphology
Disorder
Skin structure
M1
M2
T1
D1
Neoplastic
disorder
D2
Disorder
of skin
T2
M3 BCC
Morphology
D6
D3
Basal cell
malignancy
D9
Malignant
neoplasm
D7
D4
Neoplastic
disorder of skin
Malignant
neoplasm of skin
Basal cell
carcinoma of skin
D8
Disorder of skin
of eyelid
Neoplastic disorder
of skin of eyelid

of skin of eyelid
re
u
ct
id
u
l
r
e
y
st
e
D11
n
i
of skin of eyelid
of
sk
n
i
sk
D5
Skin
structure
of eyelid
Neoplastic
Morphology
Disorder
Skin structure
M1
Malignant
Morphology M2
T1
D1
Neoplastic
disorder
D2
Disorder
of skin
T2
M3 BCC
Morphology
D6
D3
Malignant
neoplasm
Basal cell
carcinoma
D7
D9
D4
Malignant
neoplasm of skin
Basal cell
carcinoma of skin
Basal cell carcinoma D11

of skin of eyelid
Neoplastic
disorder of skin
D5
Skin
structure
of eyelid
Disorder of skin
of eyelid
Neoplastic disorder
of skin of eyelid
N
o
m
N
or
eo
ph
pl
as
sp
t ic
ec
Malignant
neoplasm
D10
ifi
m
of skin of eyelid
ed
o
N
rp
eo
h
pl
M
as
al
M
ig
t ic
al
na
ig
BC
m
na
nt
or
C
nt
m
ph
or
m
ph
or
ph
D8
Neoplastic
Morphology
Disorder
Skin structure
M1
Malignant
Morphology M2
T1
D1
Neoplastic
disorder
D2
Disorder
of skin
T2
M3 BCC
Morphology
D6
D3
Basal cell
malignancy
D9
Malignant
neoplasm
D7
D4
Malignant
neoplasm of skin
Basal cell
carcinoma of skin
D11
Neoplastic
disorder of skin
D8
D5
Skin
structure
of eyelid
Disorder of skin
of eyelid
Neoplastic disorder
of skin of eyelid

of skin of eyelid

of skin of eyelid
Note that D1 through

D11 are all sufficiently
defined (nonprimitive)
Neoplastic
Morphology
Disorder
Skin structure
M1
Malignant
Morphology M2
T1
D1
Neoplastic
disorder
D2
D3
Malignant
neoplasm
D4
Basal cell
malignancy
Neoplastic
disorder of skin
M=M1
T=T1
M=M2
D6
D7
Malignant
neoplasm of skin
M=M2
T=T1
M=M3
D9
Basal cell
carcinoma of skin
M=M3
T=T1
D5
Skin
structure
of eyelid
Disorder of skin
of eyelid
T=T2
D8
Neoplastic disorder
of skin of eyelid
M=M1
T=T2
of skin of eyelid
M=M2
Attributes
T=T2

of skin of eyelid
M=M3 T=T2
D11
T2
T=T1
M=M1
M3 BCC
Morphology
Disorder
of skin
and
values are all
inherited
downwards
Neoplastic
Morphology
Malignant
Morphology
Disorder
Skin structure
M1
M2
T1
D1
Neoplastic
disorder
D2
Disorder
of skin
T2
M3 BCC
Morphology
D6
D3
Basal cell
malignancy
D9
Malignant
neoplasm
D7
D4
Neoplastic
disorder of skin
Malignant
neoplasm of skin
Basal cell
carcinoma of skin
D10
D8
D5
Skin
structure
of eyelid
Disorder of skin
of eyelid
Neoplastic disorder
of skin of eyelid
Malignant neoplasm
of skin of eyelid
Some valid forms for D11:

D9 and T=T2
D11

of skin of eyelid
D10 and M=M3

D6 and D5
Neoplastic
Morphology
Disorder
Skin structure
M1
Malignant
Morphology M2
T1
D1
Neoplastic
disorder
D2
Disorder
of skin
T2
M3 BCC
Morphology
D6
D3
Basal cell
malignancy
D9
Malignant
neoplasm
D7
D4
Neoplastic
disorder of skin
Malignant
neoplasm of skin
Basal cell
carcinoma of skin
D10
D8
D5
Skin
structure
of eyelid
Disorder of skin
of eyelid
Neoplastic disorder
of skin of eyelid
Malignant neoplasm
of skin of eyelid

D9 and T=T2
D11

of skin of eyelid
D10 and M=M3

D6 and D5
Neoplastic
Morphology
Disorder
Skin structure
M1
Malignant
Morphology M2
T1
D1
Neoplastic
disorder
D2
Disorder
of skin
T2
M3 BCC
Morphology
D6
D3
Basal cell
malignancy
D9
Malignant
neoplasm
D7
D4
Neoplastic
disorder of skin
Malignant
neoplasm of skin
Basal cell
carcinoma of skin
D10
D8
D5
Skin
structure
of eyelid
Disorder of skin
of eyelid
Neoplastic disorder
of skin of eyelid
Malignant neoplasm
of skin of eyelid

D9 and T=T2
D11

of skin of eyelid
D10 and M=M3

D6 and D5
Summary of BCC example:

Because of the many different valid forms, it
is useful to define a normal form to which
we can transform all expressions for
comparison
In this case, the normal form combines the
proximate primitive (disorder) with the nonredundant existential restrictions
disorder :
finding-site = skin of eyelid (body structure),
associated-morphology = basal cell carcinoma
(morphologic abnormality)
CONCEPT MODEL
Procedure concept model (1)

Procedure site
Procedure site - direct
Anatomical structure,
Procedure site - indirect
Procedure Morphology
Indirect morphology
Procedure
Morphologically
abnormal structure
Direct morphology
Procedure device
Direct device
Device
Indirect device
Using device
Using access device
Endoscope and subtypes
Method
Action
Direct substance
Substance, Pharmaceutical /
biologic product

Procedure site
Direct
Object
Anatomical structure,
Procedure site - indirect
Procedure Morphology
Indirect morphology
Procedure
Morphologically
abnormal structure
Direct morphology
Procedure device
Direct device
Device
Indirect device
Using device
Using access device
Endoscope and subtypes
Method
Action
Direct substance
Substance, Pharmaceutical /
biologic product
Procedure
Using substance
Substances
Using energy
Physical forces
Surgical Approach
Procedural approaches
Priority
Priorities
Has focus
Clinical findings, Procedures
Has intent
Intents
Recipient category
Person, Family, Community, Donor, Group
Route of administration
Route of administration value
Revision status
Revision-value, Part of multistage

procedure, Primary operation
Access
Open, closed, percutaneous

(surgical access values)
Attributes
Procedures (1)
Method
The action being performed to accomplish the procedure
Does not include access (e.g., percutaneous) or approach (e.g., translumbar)
Values are subtypes of action

Procedure site
Values are subtypes of anatomical concept
Procedure site direct
The site directly affected by the action
Procedure site indirect
A site that is acted on but is not the direct target of the action
appendectomy
G
method
excision - action
procedure site - direct
appendix structure
Attributes
Procedures (2)
Morphology
Values are subtypes of morphologically abnormal
structure
Direct morphology
The morphology to which the procedure is directed
Indirect morphology
A morphology that is acted upon, but is not the direct
target of the action being performed
Evacuation of intracerebral
hematoma
method
procedure site G
indirect
direct morphology
evacuation - action
cerebral structure
hematoma
Attributes
Procedures (3)
Device
Values are subtypes of device
Direct device
The device to which the procedure is directed.
Indirect device
A device that is acted upon, but which is not the direct

target of the action being performed
Replacement of electronic heart device

battery
direct device
pacemaker battery
indirect device
cardiac pacemaker
Attributes
Procedures (4)
Using device
Specifies the instrument utilized to perform the procedure
Value are subtypes of device
core needle biopsy of

larynx
Using device
core biopsy needle
Using access device
Specifies the instrument utilized to gain access to the

site
Value are subtypes of endoscope
Endoscopic biopsy
Using access device
endoscope
Attributes
Procedures (5)
Using energy
Specifies the energy utilized to perform the procedure
Value are subtypes of physical force
gamma ray therapy

Using energy
gamma radiation
Attributes
Procedures (6)
Access
Used to distinguish open, closed, endoscopic, and
percutaneous procedures
Only used if access is specified in the name of the
concept
Values are subtypes of surgical access values
open reduction of fracture

access
open approach
Surgical Approach
Specifies the directional, relational or spatial access
to the site of a surgical procedure.
Values are subtypes of surgical approach
transurethral laser prostatectomy
Surgical approach
transurethral approach
Measurement procedure concept

model
Component
Cell structure, organism,

substance, observable
Property
Property of
measurement
Time Aspect
Time frame
Scale Type
Nominal, narrative, ordinal,

Quantitative, qualitative,
Text, ordinal OR quantitative
Has Specimen
Specimen
Measurement method
Laboratory procedure
categorized by method
Measurement
Procedure
Attributes
Measurement procedures
Has specimen
Specifies the type of specimen on which a measurement
or observation is performed
Values are subtypes of specimen
Component
Specifies the substance or observable being observed or
measured by a procedure
Values are subtypes of substance, observable entity,
or cell structure
creatinine measurement, 24 hour urine

has specimen
24 hour urine sample
component
creatinine
Clinical finding concept model (1)

Finding site
Acquired body structure, Anatomical concepts
Associated morphology
Associated with
Clinical
finding
Morphologically abnormal structure
Clinical finding, Substance, Physical object, Physical force,

Events, Organisms, Pharmacological / Biological product,
Procedure
After
Clinical finding, Procedure
Due to
Clinical finding, Event
Causative agent
Organism, Substance,
Physical object, Physical force
Has interpretation
Findings values, Result comments
Interprets
Laboratory procedure, Observable entity, Patient

evaluation procedure
Clinical finding concept model (2)
Clinical
finding
Pathological process
Pathological process
Clinical Course
Courses
Has definitional manifestation
Clinical finding
Occurrence
Periods of life
Severity
Mild, Moderate, Severe
Episodicity
First episode, New episode,

Ongoing episode
Finding method
Procedure
Finding informer
Performer of method, Subject of record

Provider of history other than subject,
Subject of record or other provider of history
Attributes
Clinical Findings (1)

Associated morphology
Specifies morphologic change seen at tissue or cellular level

as a characteristic feature or the disease
Values are subtypes of morphologically abnormal
structure
Finding site
Specifies the body site affected by a condition

Values are subtypes of anatomical concept
open fracture of femur

associated morphology
fracture, open
finding site
bone structure of femur
Attributes

Causative agent
Specifies the direct causative agent of the disease
Does not include vectors (e.g. not mosquito for malaria)
Values are subtypes of organisms, substances,

physical objects or physical forces
bacterial pneumonia
causative agent
bacteria
Attributes

Due to
Used when one finding/disorder is a cause of another finding,

disorder or procedure. Differs from Causative agent in that the
cause is not an Organism, Substance, Physical Object, or Physical
agent
Values are subtypes of clinical findings
diabetic retinopathy
due to
diabetes mellitus
After
Specifies a temporal relationship between a Finding/Disorder

and a Finding, Disorder, or Procedure when there is not
necessarily a causal relationship
Values are subtypes of clinical findings or procedures
post-viral disorder
after
viral disease
Attributes
Clinical Course
Specifies the course of a condition.

Used for acute and chronic conditions.
Not used to refer to rapidity of onset or severity of a
condition.
Values are subtypes of courses
acute myocardial infarction
Clinical course
acute
Attributes

Episodicity
Specifies the particular episode of a finding that may recur
If an episode is not the initial episode and is not an ongoing
episode, it is considered a new episode
Values are first episode, new episode & ongoing episode
new onset angina
episodicity
new episode
Severity
Specifies the level of severity for a Disease concept.

Values are mild, moderate, and severe
severe vertigo
severity
severe
Attributes

Interprets
Specifies the observable entity or function being
evaluated or interpreted by a finding.
Values are subtypes of observable entity, biological
function or measurement procedure
Has interpretation
Specifies the judgement being made about an observable
or function (e.g., presence, absence, degree, normality, etc.)
Values are subtypes of findings values or result
comments
decreased cardiac output

has interpretation
decreased
interprets
cardiac output
Situation concept model

Associated finding
Associated procedure
Clinical finding; or
Observable / Observation with result
Procedure
Finding context value

Finding context
Situation with
explicit context
Present, absent, possible

Unknown
Goal, risk, etc
Context values for actions

Procedure context
Done, not done

Planned, requested
Temporal context value

Temporal context
Current
Past, etc
Subject relationship value

Subject relationship context
Subject of record
Family member, etc
Specimen concept model
Specimen
Specimen procedure
Procedure
Specimen source topography
Body structure
Specimen source morphology
Morphology
Specimen substance
Substance
Specimen source identity
Person, Family, Donor, Device,

Environment, Community
Pharmaceutical/Biologic Product
concept model
Pharmaceutical /
Biologic product
Has active ingredient

Has dose form
Substance (substance)
Type of drug preparation (product)
Body structure concept model
Body structure
Laterality
Left, Right, Right and left, (unilateral)
Part-of
Body structure
Note: use of unilateral implies one side and not the other.
This is a type of negation, and therefore unilateral procedures and unilateral findings
actually must be in the situation hierarchy.
RIGHT IDENTITIES
Right identity
(restricted role value maps)
R S R
x Ry y Sz x Rz
allergyToAspirin v 9 causativeAgent.aspirinSubstance
aspirinProduct v 9 hasActiveIngredient.aspirinSubstance
allergyToAspirinProduct v 9 causativeAgent.aspirinProduct
Allows the automated inference that:

allergyToAspirinProduct v allergyToAspirin
Right identity
(restricted role value maps)
R S R
x Ry y Sz x Rz
femurFracture v 9 site.femur
headOfFemurFracture v 9 site.headOfFemur
headOfFemur v 9 part-of.Femur
Allows the automated inference that:

headOfFemurFracture v FemurFracture
But this isnt the purpose for which we use right identity in the
current release !
Avoiding Right Identities by Using SEP

Triplets
ROLE GROUPS
Role Groups
Certain defining relationships may be
grouped to indicate the way they relate to
each other
For example:
Laparoscopy inspects the peritoneal cavity
Appendicectomy excises the appendix
Laparoscopic appendicectomy
inspects the peritoneal cavity
and
excises the appendix
but does not
Excise the peritoneal cavity
Grouping action and site avoids

misinterpretation
Role groups
Another example
Cholecystectomy and exploration of bile duct
Method: Excision
Procedure site: Gallbladder
Method: Exploration
Procedure site: Bile duct
Role group 1
Role group 2
Role Grouping as a Compromise

Implementers and modelers fear/loathe
nesting of expressions
Nesting violates simple flat frame-based model
Reality demands faithful representation

Role grouping attempted (with partial
success) to hide the complexity
But it was misunderstood by some in DL community
as being a proprietary hack
Spackman KA, Dionne R, Mays E, Weis J. Role grouping as an extension to the description logic of Ontylog
motivated by concept modeling in SNOMED. Proceedings/AMIA Annual Symposium. :712-716, 2002.
Need for Role Groups

When a single concept may have more than one value
for a particular attribute
for example, bone fusion with tendon transfer
method = fusion, site = bone, and
method = transfer, site = tendon
And, one attribute-value pair needs to be associated
with another.
How can we specify that the fusion is done to the
bone and not to the tendon? and that the transfer is
done to the tendon and not to the bone?
Role Groups as a Solution

Informally:
dont nest or create sub procedures
simply group the attribute-value pairs
Using curly braces as a syntactic marker:

{ site=bone, method=fusion},
{site=tendon, method=transfer}
Or, in tabular form, use a group column:
attr
value
group
site
bone
1
method
fusion
1
site
tendon 2
method
transfer
2
Role Grouping Logical Form:

A Nested Existential Restriction
C 9 RRG :(9R1:C1 9R2:C2) 9 RRG :(9R3:C3 )
Distributed as three 4-tuples in relationships
table:
C R 3 C3 0
C R1 C 1 1
C R 2 C2 1
Role group numbers are arbitrary integers, and not
designed to be stable across changes in the concept
definition
ROLE HIERARCHIES
Role (attribute) hierarchies

Selected SNOMED CT attributes have a
hierarchical relationship to one another
known as role hierarchies. In a role
hierarchy, one general attribute is the parent
of one or more specific subtypes of that
attribute. Concepts defined using the more
general attribute can inherit concepts
modeled with the more specific subtypes of
that attribute.
Role hierarchies procedures

PROCEDURE DEVICE
DIRECT DEVICE
INDIRECT DEVICE
USING DEVICE
USING ACCESS DEVICE
PROCEDURE MORPHOLOGY
DIRECT MORPHOLOGY
INDIRECT MORPHOLOGY
PROCEDURE SITE
PROCEDURE SITE - DIRECT
PROCEDURE SITE - INDIRECT
Role hierarchies clinical findings

ASSOCIATED WITH role hierarchy:
ASSOCIATED WITH
AFTER
DUE TO
CAUSATIVE AGENT
Summary of SNOMEDs use of DL

SNOMED
version
Concept & RoleRole

forming Operators axioms
Early work
(1996-1999)
(, 9R:C)( )
SNOMED RT
(2000-2001)
(, 9R:C)(+)
SNOMED CT (, 9R:C)()
(Jan02-Jan04)
SNOMED CT
(Jul04present)
(, 9R:C)(+)
R S
Notation mostly follows Donini in Ch.3 Description Logic Handbook

(+) means right identities were used
Language
Role
grouping
EL
No
EL+
No
EL
Yes
ELH+
Yes
CONTEXT MODEL
Common patterns
Caveat: these are intended for illustrative
purposes only, as examples of ways that
system builders might simplify postcoordination for their clinical experts
They are full logical models for which the
meaning can be represented in the interface
and in storage with more than one split
between the information model and
terminology model
Common patterns
Clinical finding present

Clinical finding absent
Clinical finding unknown
History of
No history of
Family history of
No family history of
Observable + value
Procedure done
Procedure not done
(Drug or procedure) contraindicated
Plus:
all the above with site, or site & laterality
Clinical finding present
Situation
Associated finding
Finding context
<finding>
Known present
Group
Temporal context
Subject relationship
context
Clinical-finding-present (<finding>)
Current
Current
or specified time
Subject of record
Abrasion of upper limb
Situation
Associated finding
Abrasion of upper limb
Finding context
Known present
Group
Temporal context
Current
Current
or specified time
context
Clinical-finding-present (abrasion of upper limb)
Subject of record
Clinical finding absent
Situation
Associated finding
Finding context
<finding>
Known absent
Group
Temporal context
context
Clinical-finding-absent (<finding>)
Current
Current
or specified time
Subject of record
No chest retractions
Situation
Associated finding
Finding context
Chest wall retraction

Known absent
Group
Temporal context
context
Clinical-finding-absent (chest wall retraction)
Current
Current
or specified time
Subject of record
Clinical finding unknown
Situation
Associated finding
Finding context
<finding>
Unknown
Group
Temporal context
context
Clinical-finding-unknown (<finding>)
Current
Current
or specified time
Subject of record
Splenomegaly: unknown
Situation
Associated finding
splenomegaly
Finding context
Unknown
Group
Temporal context
Current
Current
or specified time
context
Clinical-finding-unknown (splenomegaly)
Subject of record
History of <finding>
Situation
Associated finding
Finding context
<finding>
Known present
Group
Temporal context
context
History-of (<finding>)
Current
In the past
Subject of record
History of MI
Situation
Associated finding
Finding context
Myocardial
infarction
Known present
Group
Temporal context
context
History-of (myocardial infarction)
Current
In the past
Subject of record
No history of <finding>
Situation
Associated finding
Finding context
<finding>
Known absent
Group
Temporal context
context
No-history-of (<finding>)
Current
All times past
Subject of record
No history of seizure
Situation
Associated finding
Finding context
seizure (finding)
Known absent
Group
Temporal context
context
No-history-of (seizure (finding) )
Current
All times past
Subject of record
Family history of <finding>
Situation
Associated finding
Finding context
<finding>
Known present
Group
Temporal context
context
Family-history-of (<finding>)
Current
In the past
Family member
Family history of ischemic heart

disease
Situation
Associated finding
Finding context
Ischemic heart
disease
Known present
Group
Temporal context
context
Current
In the past
Family member
Family-history-of (ischemic heart disease)
No family history of <finding>
Situation
Associated finding
Finding context
<finding>
Known absent
Group
Temporal context
context
No-family-history-of (<finding>)
Current
All times past
Family member
No family history of dementia
Situation
Associated finding
Finding context
dementia
Known absent
Group
Temporal context
context
No-family-history-of (dementia)
Current
All times past
Family member
Switch to procedures
Slightly different:
Two attributes:
Associated-procedure
Procedure-context
Same:
Temporal context
Subject relationship context
Procedure done
Situation
Associated
procedure
Procedure
context
<procedure>
Done
Group
Temporal context
context
Procedure-done (<procedure>)
Current
Current
or specified time
Subject of record
Tetanus booster given
Situation
Associated
procedure
Procedure
context
Booster tetanus
vaccination (procedure)
Done
Group
Temporal context
context
Procedure-done (booster tetanus vaccination)
Current
Current
or specified time
Subject of record
Procedure not done
Situation
Associated
procedure
Procedure
context
<procedure>
Not done
Group
Temporal context
context
Procedure-not-done (<procedure>)
Current
Current
or specified time
Subject of record
Neurological examination not done
Situation
Associated
procedure
Neurological examination
(procedure)
Procedure
context
Not done
Group
Temporal context
context
Procedure-not-done (neurological examination)
Current
Current
or specified time
Subject of record
Drug contraindicated
Situation
Direct-substance
Procedure context
Administration
of medication
<substance>
Contraindicated
Group
Temporal context
context
Drug-contraindicated (<substance>)
Current or specified time
Subject of record
Warfarin contraindicated
Situation
Direct-substance
Procedure context
Administration
of medication
warfarin
Contraindicated
Group
Temporal context
context
Drug-contraindicated (warfarin)
Subject of record
Add site to previous patterns
Clinical
Clinical
Clinical
Clinical
finding
finding
finding
finding
present + site
present + site + laterality
absent + site
absent + site + laterality
Clinical finding present + site

Situation
Associated
finding
<finding>
Finding-site
<site>
Group
Finding context
Temporal context
context
Clinical-finding-present-with-site
Known present
Subject of record
Bleeding finger
Situation
Associated
finding
bleeding
Finding-site
Finger structure
Group
Finding context
Temporal context
context
Known present
Subject of record
Clinical-finding-present-with-site (bleeding, finger structure)
Bleeding index finger

Situation
Associated
finding
bleeding
Finding-site
Index finger
structure
Group
Finding context
Temporal context
context
Known present
Subject of record
Clinical-finding-present-with-site (bleeding,index finger structure)
Clinical finding absent + site

Situation
Associated
finding
<finding>
Finding-site
<site>
Group
Finding context
Temporal context
context
Clinical-finding-absent-with-site
Known absent
Subject of record
No right femoral bruit

Situation
Associated
finding
Femoral bruit
Finding-site
Right femoral
artery
Group
Finding context
Temporal context
context
Known absent
Subject of record
Clinical-finding-absent-with-site (femoral bruit,right femoral artery)

Situation
Associated
finding
bruit
Finding-site
Right femoral
artery
Group
Finding context
Temporal context
context
Known absent
Subject of record
Clinical-finding-absent-with-site (bruit,right femoral artery)
Clinical finding present + site + side

Situation
Associated
finding
<finding>
Finding-site
<site>
Laterality
Group
Finding context
Temporal context
context
<side>
Known present
Subject of record
Clinical-finding-present-with-site-and-side
Right femoral bruit present

Situation
Associated
finding
bruit
Finding-site
Femoral artery
Laterality
Group
Finding context
Temporal context
context
Right
Known present
Subject of record
Clinical-finding-present-with-site-and-side (bruit, femoral artery, right
Clinical finding present + site + side

Situation
Associated
finding
<finding>
Finding-site
<site>
Laterality
Group
Finding context
Temporal context
context
<side>
Known present
Subject of record
Bleeding of left index finger present

Situation
Associated
finding
bleeding
index finger
structure
Finding-site
Laterality
Group
Finding context
Temporal context
context
left
Known present
Subject of record
Clinical-finding-present-with-site-and-side (bleeding, index finger
Bleeding skin, left index finger

Situation
Associated
finding
bleeding
Finding-site
Skin of index finger

Laterality
Group
Finding context
Temporal context
context
Known present
Subject of record
(bleeding, skin of index finger, left)
left
Clinical finding absent + site + side

Situation
Associated
finding
<finding>
Finding-site
<site>
Laterality
Group
Finding context
Temporal context
context
<side>
Known absent
Subject of record
Clinical-finding-absent-with-site-and-side (<finding>,<site>,<side>

Situation
Associated
finding
bruit
Finding-site
Femoral artery
Laterality
Group
Finding context
Temporal context
context
right
Known absent
Subject of record
Clinical-finding-absent-with-site-and-side (bruit, femoral artery, right)
Using observables
Finding present + observable + value
Finding present, observable + value

Situation
Associated
finding
Clinical finding
Group
Has-interpretation
Interprets
<value>
<observable>
Group
Finding context
Known present
Temporal context
context

Subject of record
Finding-present-observable-value
Knee jerk reflex 2+ (out of 4)

Situation
Associated
finding
Clinical finding
Group
Has-interpretation
++
260348001
Interprets
Knee jerk reflex
Group
271714006
Finding context
Temporal context
context
Known present
Subject of record
Finding-present-observable-value (knee jerk reflex,++)
Finding present, observable + site + value

(assuming we approve a site attribute for observables)
Situation
Associated
finding
Clinical finding
Group
Has-interpretation
Interprets
<value>
<observable>
Group
obs-site
Finding context
Temporal context
context
<site>
Known present
Subject of record
Finding-present-obs-site-value (<observable>,<site>,<value>)
Left knee jerk reflex ++

(assuming we approve a site attribute for observables)
Situation
Associated
finding
Clinical finding
Group
Has-interpretation
Interprets
++
Knee jerk reflex
Group
obs-site
Finding context
Temporal context
context
Left knee
Known present
Subject of record
Finding-present-obs-site-value (knee jerk reflex, left knee,++)
Procedure patterns
Procedure done + method + site
Procedure done + method + site + laterality
Procedure done, method+site

Situation
Associated
procedure
procedure
Group
Method
Group
Procedure context
Temporal context
context
<site>
<method>
Done
Subject of record
Procedure-done-plus-method-site (<method>,<site>)
X-ray of wrist done

Situation
Associated
procedure
procedure
Group
Method
Group
Procedure context
Temporal context
context
Radiographic
imaging
Done
Subject of record
Procedure-done-plus-method-site (x-ray, wrist)
wrist
Procedure done, method+site+side

Situation
Associated
procedure
procedure
Group

Laterality
<site>
<side>
Group
Method
Procedure context
Temporal context
context
Procedure-done-method-site-side
(<method>,<site>,<side>)
<method>
Done
Subject of record
X-ray of left wrist done

Situation
Associated
procedure
procedure
Group

Laterality
Group
Method
Procedure context
Temporal context
context
Procedure-done-method-site-side
(radiographic imaging, wrist, left)
left
radiographic
imaging
Done
Subject of record
wrist
More specific patterns also possible

For example:
Suture of skin done + site + laterality
Suture of skin done, site + side

Situation
Associated
procedure
Closure of skin by suture

Group
Proceduresite-indirect
<site>
Laterality
Group
Proceduremorphology-direct
Method
Temporal context
context
Laceration
Closure by device
Using-device
Procedure context
<side>
Suture
Done
Subject of record
Suture of laceration of skin of left index

finger: done
Situation
Associated
procedure
Closure of skin by suture

Group
Proceduresite-indirect
Skin of index
finger
Laterality
Group
Proceduremorphology-direct
Method
Temporal context
context
Laceration
Closure by device
Using-device
Procedure context
left
Suture
Done
Subject of record
REDESIGN PROJECTS
Anatomy Redesign
Reintroduce part-of roles
Sufficiently define the S and P of the SEP triad
Align the E with the Foundational Model of
Anatomy (FMA)
Reflexive roles
Plan to introduce reflexive part-of as a way
of handling SEP model evolution
proper-part-of v part-of
v part-of
S 9 part-of . E
P 9 proper-part-of . E
Suntisrivaraporn B, Baader F, Schulz S, and Spackman K. Replacing SEP-Triplets in SNOMED CT using Tractable Description
Logic Operators. In Jim Hunter Riccardo Bellazzi, Ameen Abu-Hanna, editor, Proceedings of the 11th Conference on Artificial
Intelligence in Medicine (AIME'07), Lecture Notes in Computer Science. Springer-Verlag, 287-291, 2007.
Substance Redesign
Remove inappropriate is-a relationships
Add new attributes and values
Many difficult decisions remain
How to represent may be used as
Timolol may be used as an eye medicine for
glaucoma
Timolol may be used as a cardiac beta blocker
Are H2CO3 and HCO3- the same or different? Do we
represent the various anions of drugs also?
organism redesign
Major steps:
1.organize SNOMED's taxonomy into a
systematic and consistent Linnean
hierarchy
2.remove all non-taxonomic information
about living organisms from the taxonomic
hierarchy
3.represent such information, when
understandable, reproducible and useful,
elsewhere in the terminology
Current taxonomy includes:

Linnean taxonomic terms (Canis
familiaris)
Common names for organisms (Dog)
Non-taxonomic information
Use and Circumstances
Laboratory fur-bearing animal
Pathogenicity
Parasite, pyogenic bacterium
Life cycle stage of organisms

Worm eggs
Common names in the FSN:

Some organisms have many common names
Butorides virescens = green heron, green-backed
heron, little green heron, crab-catcher, fly-up-thecreek, green bittern, poke, shitepoke, skeow,
skow, and swamp squaggin
May be impossible to verify what organism

is meant
Ex: Comte de Paris star frontlet (organism) ???
A single common name may refer to more

than one species:
Ex: Yellowhammer (organism) MAY BE A
Emberiza citrinella, MAY BE A Colaptes auratus
Non-taxonomic terms in a taxonomic

hierarchy:
a subtype is always and necessarily a "kind
of" its parent (this is what subsumption
means)
interpolation of non-taxonomic terms in a
taxonomic hierarchy violates this convention
these terms are often context-dependent rather
than defining.
An elephant may be a domestic animal in India
a dog may be a food animal in Korea
Is a canary a Wild bird--chordate or a

Domestic fowl?
Answer: Neither. It is Serinus canaria
Further enhancements of the model

Attributes & values to represent contextual
information about living organisms
Contexts of domesticity (domestic, feral, wild)
Contexts of use (food, laboratory, companion,
service, breeding, etc)
Contexts of life stage (oocyst, larva, spore,
trophozooite, etc)
Contexts of medical significance (parasite,
renotrophic organism, pathogen)???
Qualifiers for organisms?

An organism might be qualified by nontaxonomic attributes/values, just as a disease
might be qualified by severity, stage, episode,
degree of control, etc.
But:
Type 2 diabetes that is out of control is not really a
different type of disease; it is a different type of
situation in which type 2 diabetes (the disease) is
present.
Dairy cattle and beef cattle are not really different
types of organisms; they are different types of
contexts in which cattle (organisms) are used for
different purposes.
What about infectious agents?

The taxonomy of parasites, bacteria and other
potentially pathogenic microorganisms is also
a mixture of scientific names, common names,
and contextual information
Attempting to convey contexts of
pathogenicity creates errors in logic:
Ex: Helminth ISA Parasite?
Wrong. Most helminths are not parasitic
Ex: Fungus ISA Infectious agent?
Wrong. Most fungi are not infectious
Observable Redesign
Separate processes, functions, and qualities
Add attributes that define observables in
terms of:
Properties they observe

Timing
Scales or units
Techniques of observation
Add attributes that define qualities/properties

in terms of:
the independent continuant in which they inhere
DRAFT model of observables

Observable entity
COMPONENT
Substances, functions,
processes, activities,
organisms, cell structures
PROPERTY
Properties
SYSTEM /
OBSERVABLE
SITE
Specimens, Sites
TIME ASPECT
Time aspects
SCALE / UNITS
Scale types, units
TECHNIQUE
techniques
DRAFT alternative model of observables

Observable
entity
PROPERTY
INHERES IN
TOWARDS
properties
independent
continuant
Functions,
substances
TIME ASPECT
Time aspects
SCALE / UNITS
Scale types, units
TECHNIQUE
techniques
Events, conditions, episodes

Need to define what is an event, what is a
condition, what is an episode
Need criteria for deciding whether we need
one code or two
seizure, epilepsy: clearly different, so we need two
codes
tachycardia, tachyarrhythmia: same or different?
low hemoglobin, anemia: same or different?
rash of forearm: do we need both a disorder and a
finding?
Should we add more expressive DL

features?
General concept inclusion axioms

Transitive roles
Reflexive roles
Disjointness axioms
Value restrictions
Negation
Disjunction
Cyclic definitions
Number restrictions
General concept inclusion axioms

Extremely useful feature
Compatible with a polynomial-time structural
subsumption algorithm
Allows us to say what is true in addition to
what is sufficient
Gastric ulcer is located in the stomach, and in
addition it necessarily involves the gastric mucosa
Transitive roles
x Ry y Rz x Rz
Useful for causal/associational chains
Interaction with role hierarchy is interesting &
useful
Example: Associated-with-after
Varicella (chicken pox)
An infection with causative-agent = varicella virus
Herpes zoster
Also has causative-agent = varicella virus, and occurs after
varicella
Post-herpetic neuralgia
Occurs after herpes zoster (therefore occurs after
varicella), but is not an infection with causative-agent
varicella virus
Reflexive roles
Plan to introduce reflexive part-of as a way
of handling SEP model evolution
proper-part-of v part-of
v part-of
S 9 part-of . E
P 9 proper-part-of . E
Suntisrivaraporn B, Baader F, Schulz S, and Spackman K. Replacing SEP-Triplets in SNOMED CT using Tractable Description
Logic Operators. In Jim Hunter Riccardo Bellazzi, Ameen Abu-Hanna, editor, Proceedings of the 11th Conference on Artificial
Intelligence in Medicine (AIME'07), Lecture Notes in Computer Science. Springer-Verlag, 287-291, 2007.
Value restriction 8R:C

Not an intuitive construct
person u 8hasCar:Jaguar
Includes people who have no car, but if they had one
it would have to be a Jaguar . . . . Do we encounter
this kind of concept in common-sense thinking?
Creates pernicious interactions with disjunction and
negation that tend to make structural subsumption
algorithms incomplete
But it was included in ALC and FL, so languages
including it were studied extensively.
Negation :C
Head injury without loss of consciousness

headInjury u : lossOfConsciousness
situation u
9 includes.headinjury u
: 9 includes.lossOfConsciousness
Disjunction C t D
Some high-level aggregators are naturally
disjunctive
We can address this need partially by using
navigation hierarchies
Cyclic definitions, number

restrictions
? No significant need for these at present
INFORMATION MODEL
INTERACTIONS
Interaction between Terminology and Information Models

Clinical Decision Support Model
+ Inference Rules
I nt e
rfac
rfa
e
t
n
I
ce
Interface
Terminology Model
+ Compositional Expressions
Information Model
+ Patient Data Structures
Diagram based on Figure 1 in Rector AL et al. Interface of Inference Models with

Concept and Medical Record Models AIME 2001: 314-323
Terminology vs Information model

Whats the issue?
Information model:
Determines and organizes the kinds of entities
which carry values in a record
Loosely referred to as slots, facets, fields,
questions
Terminology model:
Determines and organizes the kinds of entities
which are the values
Variously referred to as the terminology or
ontology or value sets
Extremes (reductio ad absurdum)

Put all meaning in the terminology
A code (or terminology expression) for every

meaning that needs to be expressed
Only one field in the record
What about dates, numeric values, names,
places, and relationships between them?
Put all meaning in the information model

Two values: yes and no
A question for every meaning that needs to
be expressed, and a field for every question
What about combinatorial explosion of
subtypes of things in the real world?
Representing the semantics of clinical

data
For any given application
There needs to be a boundary between
information model and terminology
without gaps or overlaps
There are several different choices for

where to draw the boundary between
No single choice of boundary is globally
the best
How can we achieve standardization for
interoperability?
Terminology information model

interaction:
broad tasks required
Identify gaps and overlaps
Design a strategy to
Fill the gaps
Manage the overlaps
Demonstrate implementability
TermInfo Specific advice
Act.code & Observation.value

HL7 theory
(1)
code nature of observation

value value of the observation
Practical implementation
Simple for numeric observations
Reasonable for observations with coded results
Hemoglobin level (code) = 14g/dL (value)

Visual acuity (code) = Can count fingers (value)
Tricky for observations where the distinction

between the nature and value is arbitrary
Blood group AB could be
1. ABO Blood grouping (code) Blood group AB

(value)
2. Blood group A antigen (code) Present (value)
and Blood group B antigen (code) Present
(value)
3. Blood group AB (code)
Act.code & Observation.value

(2)
The code-value split is even more
arbitrary for general clinical
observations
For example
Finding of abdominal tenderness

1. Examination (code) abdomen tender (value)
2. Abdominal examination (code) abdomen tender
(value)
3. Abdominal palpation (code) abdomen tender
(value)
4. Abdominal tenderness (code) present (value)
5. Abdomen tender (code)
Code and Value guidance

HL7 code and value distinction should be used for
Numeric and non-numeric results of measurement
procedures
A single coded attribute should express the full
semantics
If there is no non-arbitrary reproducible distinction
Recommended Implementation
Act.Code = ASSERTION
Observation.Value = Coded SNOMED expression
Rationale
SNOMED CT clinical findings are
not just the value of a particular type of
observation
equivalent to an observable or observation type
with a value
Code-value discussion
Not unique to HL7
Suggests terminology-information model
standardization efforts may benefit from each
other

2008 Snomed Tutorial Krmed

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KR-MED 2008

Representing and Sharing Knowledge

May 31, 2008, Phoenix, Arizona, USA

Purpose of the Tutorial (I)

Purpose of the Tutorial (II)

We have enough time for (moderated)

Download tutorial slides from:

Understanding / Semantic Interoperability

Common languages: Biomedical Vocabularies

Meta Terminological Issues

- Real systems are not ideal

A cruise through the archipelago of biomedical

What biomedical vocabularies have in

MeSH: Medical Subject Headings

I83 Varicose veins of lower extremities

Classification criteria mix inherent properties of entities with

Tuberculosis of lung, confirmed by culture only

MeSH: Medical Subject Headings

THESAURUS: Medical Subject Headings

THESAURUS: Medical Subject Headings

THESAURUS: Medical Subject Headings

THESAURUS: Medical Subject Headings

THESAURUS: Medical Subject Headings

Descriptor 2 is broader than descriptor 1

THESAURUS: Medical Subject Headings

Descriptor 2 is broader than descriptor 1

MeSH: Medical Subject Headings

NOMENCLATURE: Terminologia Anatomica

NOMENCLATURE: Terminologia Anatomica

MeSH: Medical Subject Headings

ONTOLOGY: Foundational Model of Anatomy

ONTOLOGY: Foundational Model of Anatomy

Terms: Synonyms and Translations

MeSH: Medical Subject Headings

ONTOLOGY: Gene Ontology

ONTOLOGY: Gene Ontology

ONTOLOGY: Gene Ontology

ONTOLOGY: Gene Ontology

MeSH: Medical Subject Headings

Description Logics T-Box (unary and binary predicates)

Better understanding SNOMED CT

MeSH: Medical Subject Headings

SNOMED since 1965

SNOMED 3.0 SNOMED 3.5 SNOMED RT SNOMED CT

The current structure of SNOMED CT is a result

The current structure of SNOMED CT is a result

Terminology vs. Ontology

What biomedical vocabularies have in

Terminology vs. Ontology

bla bla bla

Heart Neoplasms [MeSH]:

Benign neoplasm of heart

Ontology is the study of what there is.

bla bla bla

Heart Neoplasms [MeSH]:

gutartige Neubildung des Herzmuskels

Example: UMLS (mrconso table)

C0153957|ENG|P|L0180790|PF|S1084242|Y|A1141630||||MTH|PN|U001287|benign neoplasm of heart|0|N||

Example: UMLS (mrrel table)

Formal Ontology represents the world

Databases systems represent

are organized in formal ontologies