MIE 2006 Tutorial Standards and Ontology Part 3: SNOMED - CT Sunday August 27th, 2006

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MIE 2006 TutorialStandards and OntologyPart 3
SNOMED - CT Sunday August 27th, 2006

• Werner Ceusters, MD
• Ontology Research Group
• Center of Excellence in Bioinformatics Life
  Sciences
• SUNY at Buffalo, NY

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Objectives

• Use the history of the development of SNOMED-CT
  to show the differences between a terminological
  and an ontological approach
• Look at some problematic features of
  concept-based thinking and how they are addressed
  in SNOMED-CT
• Make you think ontologically
• 
  ?

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The real MIE2006 SNOMED-CT Tutorial

• logical definitions
• integrated broad content
• table structures
• interaction between the relational model (three
  core tables) and the concept model used to
  represent medical content (hierarchies and
  relationship types linking the hierarchies)
• related mappings
• support for data recording, retrieval and
  analysis
• quality assurance processes
• highlights of the SNOMED CT January 2006 release.

Kent A Spackman Sunday, 27 August 2006 09.30
12.30 http//www.mie2006.org/documents/ TutorialSp
ackman.pdf
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Presentation outline

• Ontology versus Terminology
• Terminological thinking in SNOMED
• From SNOP to SNOMED-CT
• Mistakes in SNOMED-CT due to terminological
  thinking
• How to make SNOMED-CT better using real ontology

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Terminology
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Terminology has two meanings

• The discipline of terminology management
• synonymous with terminology work (used in ISO
  704)
• The set of designations used in the special
  language of a subject field, such as the
  terminology of medicine
• Used in in both the singular and plural
• Used with an article in the singular a
  terminology

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Terminology is VERY standardised

• ISO 704 2000 Terminology work Principles
  and methods
• ISO 860 1996 Terminology work
  Harmonization of concepts and terms
• ISO 1087-1 2000 Terminology work Vocabulary
  Part 1 Theory and application
• ISO 15188 2001 Project management guidelines for
  terminology standardization
• ISO 1087-22000 Terminology work Vocabulary
  Part 2 Computer applications
• ISO 12620 1999 Computer applications in
  terminology Data categories
• ISO 16642 2003 Computer applications in
  terminology Terminological markup framework
• ISO 2788 1986 Documentation Guidelines for
  the establishment and development of monolingual
  thesauri

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ISO Standards in Terminology building blocks

• Objects
• perceived or conceived, concrete or abstract
• abstracted or conceptualized into concepts
• Concepts
• depict or correspond to a set of objects based on
  a defined set of characteristics
• represented or expressed in language by
  designations or by definitions
• organized into concept systems
• Designations
• represented as terms, names (appellations) or
  symbols
• designate or represent a concept
• attributed to a concept by consensus within a
  special language community

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Fundamental Activities of Terminology Work

• Identifying concepts and concept relations
• Analyzing and modeling concept systems on the
  basis of identified concepts and concept
  relations
• Establishing representations of concept systems
  through concept diagrams
• Crafting concept-oriented definitions
• Attributing designations (predominantly terms) to
  each concept in one or more languages and,
• Recording and presenting terminological data,
  principally in terminological entries stored in
  print and electronic media (terminography).

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Origin Peirce, Ogden Richards, Wüster
Unit of Thinking (Concept)
(Unit of Thought, Unit of Knowledge)
Referent (Concrete Object, Real Thing, Conceived
Object)
Designation (Symbol, Sign, Term, Formula etc.)
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cancer in SNOMED-CT
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Cancer as disease versus morphology
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Why terminologies ?

• As such ?
• Fixing/stabilizing the language within a domain
  and a linguistic community
• Unambiguous communication.
• In Healthcare Information Technology ?
• Semantic Indexing
• Information exchange and linking between
  heterogeneous systems
• Terminologies as basis for documentation through
  coding and classification

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Coding versus classification

• Coding
• Annotate terms in the EHR with codes from a
  coding system
• ? synonyms, translations, hierarchies
• Classification
• Assign patients exhibiting certain features to a
  predefined class
• ? purpose oriented, culture dependent
• Frequently mixed up !

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Fracturednose Fractureofnose
?
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Coding / classification confusion

• patient with fractured nose
• patient with fracture of nose
• But therefor not
• fractured nose
• fracture of nose !

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Ontology
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Ontology

• Ontology the science of what things exist and
  how they relate to each other
• An ontology is a representation of some
  pre-existing domain of reality which
• (1) reflects the properties of the objects within
  its domain in such a way that there obtains
  a systematic correlation between reality and the
  representation itself,
• (2) is intelligible to a domain expert
• (3) is formalized in a way that allows it to
  support automatic information processing

OWL (DLs) does only this bit !
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A division of labour

• Terminology
• Communication amongst humans
• Communication between human and machine
• Ontology
• Representation of reality inside a machine
• Communication amongst machines
• Interpretation by machines

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• SNOMED-CT

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SNOMED-CT

• SNOMED CT is a comprehensive and precise clinical
  reference terminology that makes healthcare
  information accessible and useable, whenever and
  wherever it is needed. Global in scope, yet
  adaptable for national purposes, SNOMED CT
  provides a common language of unsurpassed depth
  that enables a consistent way of capturing,
  sharing and aggregating health data across
  clinical specialties and sites of care.

http//www.snomed.org/news/pdfs/CTbrochure0902.pdf
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SNOMED International
www.snomed.org
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Milestones in the development of SNOMED

• SNOP 1965
• SNOMED 1974
• SNOMED II 1979
• SNOMED Version 3.0 1993
• LOINC codes integrated into SNOMED 1997
• SNOMED Version 3.5 1998
• SNOMED RT 2000
• SNOMED CT (SNOMED RT CTV3) First release
  January 2002
• SNOMED CT Spanish Edition April 2002
• SNOMED CT German Edition - April 2003
• Last version SNOMED-CT English July 2006

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Systematized Nomenclature of Pathology (1965)

• Author
• CAP Committee on Nomenclature and Classification
  of Disease
• 4 coding axes
• Topography (physical/natural features),
• Morphology (structure/form),
• Etiology (causes), and
• Function

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4 Hierarchies of SNOP

• Topography T-terms
• names of body sites
• Morphology M-terms
• names of structural changes that occur in tissues
  as a result of disease
• Etiology E-terms
• causative agents of disease (chemicals,
  bacteria, viruses)
• Function F-terms
• names of the physiological manifestations
  associated with disease (also symptoms and some
  viral diseases)

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Standard SNOP statement

• In TMEF-form
• The body site T has undergone morphological
  change M due to the causative agent E resulting
  in physiological manifestations F.
• Or more accurate
• Morphology
• in Topography
• caused by Etiology
• leads to Function

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SNOP example statement

• M inflammation
• in T lung
• caused by E Influenza virus
• leads to F hypoxia

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SNOMED International (1995, V3.1)

• T Topography 12,385
• M Morphology 4,991
• F Function 16,352
• L Living Organisms 24,265
• C Drugs Biological Products 14,075
• A Physical Agents, Forces and Activities 1,355
• D Disease/ Diagnosis 28,623
• P Procedures 27,033
• S Social Context 433
• J Occupations 1,886
• G General Modifiers 1,176
• TOTAL RECORDS 132,641

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Merriam-Webster On-Line Dictionary on diagnosis

• 1a the art or act of identifying a disease from
  its signs and symptoms
• 1b the decision reached by diagnosis
• 2 a concise technical description of a taxon
• 3a investigation or analysis of the cause or
  nature of a condition, situation, or problem
• 3b a statement or conclusion from such an
  analysis.

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Hierarchical structure of Snomed International
posterior anatomic
leaflet mitral cardiac
valve cardiovascular
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SNOMED Internationals Hierarchical
organization an example

• Bone
• Long Bone
• Periosteum
• Shaft

Isa Part or adjacency ? Part of
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SNOMED InternationalMultiple ways for
expressing the same entities
D5-46210 Acute appendicitis, NOS D5-46100 App
endicitis, NOS G-A231 Acute M-41000 Acute
inflammation, NOS G-C006 In T-59200 Appendix,
NOS G-A231 Acute M-40000 Inflammation,
NOS G-C006 In T-59200 Appendix, NOS
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SNOMED-RT first attempt to make relationships
explicit
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D5-30150 Postoperative esophagitis

• In SNOMED III
• Parent term in the hierarchy D5-30100
  Esophagitis, NOS
• Cross-reference field (T-56000)(M-40000)(F-06030
  )
• where T-56000 Esophagus
• M-40000 Inflammation
• F-06030 Post-operative state
• In SNOMED-RT (in KRSS syntax)
• (defconcept D5-30150
• (and D5-30100
• (some assoc-topography T-56000)
• (some assoc-morphology M-40000)
• (some assoc-etiology F-06030)))

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Spackman KA, Campbell KE, Cote RA. SNOMED RT a
reference terminology for health care. Proc AMIA
Annu Fall Symp. 1997640-4.
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KRSS an old description logics

• Description logics
• A decidable fragment of FOL
• A propositional modal logic
• A classes and properties (concepts and roles)
  oriented KR language
• Subsumption and satisfiability (consistency) are
  the key inferences
• Most DLs are supersets of ALC
• Boolean operators on concepts
• Existential and Universal quantifiers
• OWL-DL is a large superset (SHOIN)
• Property hierarchies Transitive roles (SH)
• Inverse (I)
• Nominals (O) (hasValue and one of)
• Number restrictions (counting quantifiers)

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2002 SNOMED-CT

• A merger between
• SNOMED-RT, and
• the England and Wales National Health Service's
  Clinical Terms (previously known as the Read
  Codes).
• SNOMED CT is considered to be the first
  international terminology.

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SNOMED-CT hierarchies

• Body structure
• Clinical finding
• Context-dependent category
• Environments and geographical locations
• Event
• Linkage concept
• Observable entity
• Organism
• Pharmaceutical / biologic product

• Physical force
• Physical object
• Procedure
• Qualifier value
• Record artifact
• Social context
• Special concept
• Specimen
• Staging and scales
• Substance

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Clinical Finding hierarchy

• Administrative statuses
• Adverse incident outcome categories
• Clinical history and observation findings
• Clinical stage finding
• Deformity
• Disease (disorder)
• Drug action
• Edema
• Effect of exposure to physical force

• Finding by method
• Finding by site
• Finding of grade
• Finding related to physiologic substance
• Finding reported by subject or history provider
• General clinical state finding
• Neurological finding
• Prognosis/outlook finding
• Sequelae of external causes and disorders
• Wound finding

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SNOMED-CT evolution
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Description of Algorithms
Ceusters W, Smith B, Kumar A, Dhaen C. Mistakes
in Medical Ontologies Where Do They Come From
and How Can They Be Detected? in Pisanelli DM
(ed) IOS Press, Studies in Health Technology and
Informatics, vol 102, 2004.
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ExploitingLexical, semantic and conceptual
relations
urine
bladder
gallbladder inflammation
gall bladder
urinary bladder
gall
biliary cystitis
urine
inflammation
gall
cystitis
urinary bladder
inflammation
gallbladder
gallbladder inflammation
urinary bladder inflammation
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Find the mistakes
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Undetected synonymy
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Undetected synonymy
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Inadequate homonymy
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Mistakes dueto inappropriatelexical mapping
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Total / partial inconsistencies
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Wrongmanually created subsumption
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Wrongmanually created subsumption
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Wrong computed subsumption
SNOMED-RT (2000)
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Missed subsumption
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Mereologicalerrors
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Improper negation handling
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Take off of ontology in biomedical informatics

• Concept/terminology-based systems make implicit
  knowledge explicit
• Ontologies aim to push explicitness further
• reasoning by machines
• Classification
• Prediction
• Triggering of alerts

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Conclusion

• Concept-based terminology (and standardisation
  thereof) is there as a mechanism to improve
  understanding of messages by humans.
• It is NOT the right device
• to explain why reality is what it is, how it is
  organised, etc., (although it is needed to allow
  communication),
• to reason about reality,
• to make machines understand what is real,
• to integrate across different views, languages,
  conceptualisations, ...

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Why not ?

• Because there is no valid benchmark !

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Why not ?

• Does not take care of universals and particulars
  appropriately
• Concepts not necessarily correspond to something
  that (will) exist(ed)
• Sorcerer, unicorn, leprechaun, ...
• Definitions set the conditions under which terms
  may be used, and may not be abused as conditions
  an entity must satisfy to be what it is
• Language can make strings of words look as if it
  were terms
• Middle lobe of left lung

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Todays biggest problem a confusion between
terminology and ontology

• The conditions to be agreed upon when to use a
  certain term to denote an entity, are often
  different than the conditions which make an
  entity what it is.
• Trees would still be different from rabbits if
  there were no humans to agree on how these things
  should be called.
• ontos means being. The link with reality
  tends to be forgotten one concentrates on the
  models instead of on the reality.

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For example some SNOMED definitions

• The SNOMED Glossary
• Concept A clinical idea to which a unique
  ConceptID has been assigned in SNOMED CT. Each
  Concept is represented by a row in the Concepts
  Table.
• The SNOMED-CT User Manual
• Concepts are unique units of thought .
• Disorders are concepts in which there is an
  explicit or implicit pathological process causing
  a state of disease which tends to exist for a
  significant length of time under ordinary
  circumstances.

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What to do about it ? (1)

• Research
• Revision of the appropriatness of concept-based
  terminology for specific purposes
• Relationship between models and that part of
  reality that the models want to represent
• Adequacy of current tools and languages for
  representation
• Boundaries between terminology and ontology and
  the place of each in semantic interoperability in
  healthcare

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What to do about it ? (2)

• Training and awareness
• Make people more critical wrt terminology and
  ontology promisses
• What is needed must be based on needs, not on the
  popularity of a new paradigm
• But in a system, its not just your own needs, it
  is each components needs !
• Towards an ontology of ontologies
• First description
• Then quality criteria

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Ontology based on Unqualified Realism

• Accepts the existence of
• a real world outside mind and language
• a structure in that world prior to mind and
  language (universals / particulars)
• Rejects nominalism, conceptualism, ontology as a
  matter of agreement on conceptualizations
• Uses reality as a benchmark for testing the
  quality of ontologies as artifacts by building
  appropriate logics with referential semantics
  (rather than model-theoretic)

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3 fundamentally different in levels

• the reality on the side of the patient
• the cognitive representations of this reality
  embodied in observations and interpretations on
  the part of clinicians and others
• the publicly accessible concretizations of such
  cognitive representations in representational
  artifacts of various sorts, of which ontologies
  and terminologies are examples.

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From concepts to universals
Universal ???
Unit of Thinking (Concept)
(Unit of Thought, Unit of Knowledge)
Referent (Concrete Object, Real Thing, Conceived
Object)
Designation (Symbol, Sign, Term, Formula etc.)
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Relevance for EHR Semantic Interoperability
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Relevance for EHR Semantic Interoperability
The realist approach
R E A L I T Y
L O G O L K A I S N S G
Ontology
EHR
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What should be done with SNOMED-CT concretely to
make it a good standard ?
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1. Adhere to a consistent upper ontology grounded
in realism (BFO)

• Differentiate between
• Particulars universals
• Thus not Belgium isa European Country isa WEU
  country
• Occurrents continuants
• Thus not vomiting isa disease
• Unless all diseases would be occurrents
• Dependents independents
• fracture of nasal bones - fractured nasal bones
• Build relationships that take these distinctions
  into account

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2. Distinguish what is ontological, from what is
epistemological, from what is pragmatic

• Thus not (in the ontology !)
• Notable event isa event
• Seriously reportable event isa event
• Disease of presumed infectious origin (disorder)
• Iatrogenic disease (disorder)

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3. Make a sound upper domain ontology

• Requires good description of what is
• Disease / disorder / illness
• Symptom / sign
• Normal / canonical / variant / pathological
• Observation
• Procedure / action

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4. Document reason for changes in SNOMED

• changes in the underlying reality
• does the appearance of an entry (in a new version
  of an ontology or in an EHR) relate to the
  appearance of an entity or a relationship among
  entities in reality ?
• changes in our (scientific) understanding
• reassessments of what is considered to be
  relevant for inclusion (notion of purpose), or
• encoding mistakes introduced during data entry or
  ontology development.