Transcript Vortragstitel - Med Uni Graz

Catalina
MartínezCosta
Stefan
Schulz
Ontology-based
reinterpretation
of the SNOMED CT
context model
Medical University
of Graz (Austria)
ICBO 2013
Montreal
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
Semantic Interoperability requires distinction
between vocabularies and perspectives
"… integrating resources that were developed using
different vocabularies and different perspectives on the
data. To achieve semantic interoperability, systems must
be able to exchange data in such a way that the precise
meaning of the data is readily accessible and the data
itself can be translated by any system into a form that it
understands."
Jeff Heflin and James Hendler (2000) Semantic Interoperability on the Web
http://www.cs.umd.edu/projects/plus/SHOE/pubs/extreme2000.pdf
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
Semantic Interoperability requires distinction
between vocabularies and perspectives
"… integrating resources that were developed using
different vocabularies and different perspectives on the
openEHR
HL7 RIM
EN 13606,
data. To achieve
semantic
interoperability,
systems
must
proprietary
 Information
Terminologies /
be able toOntologies:
exchange data in suchmodels
a way that the preciseinformation
models
meaning of
the data
is readily accessible
and the
 Provide structure
and data
Provide
codes that
contextinto
for data
denote
entity typesby any system
itself can be
translated
a form that it
understands."
SNOMED
CT,
ICD,
…
Ontology
Epistemology
Jeff Heflin and James Hendler (2000) Semantic Interoperability on the Web
http://www.cs.umd.edu/projects/plus/SHOE/pubs/extreme2000.pdf
"Heart failure, suspected"
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
Epistemic Intrusion is common in
biomedical vocabularies
Bodenreider O, Smith B, Burgun A. The ontology-epistemology divide: A case study in medical terminology. Proceedings of
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
the Third International Conference on Formal Ontology in Information Systems (FOIS 2004): IOS Press; 2004. p. 185-195.
Epistemic Intrusion is common in
biomedical vocabularies
"… integrating resources that were developed using
different vocabularies and different on the data. To
achievesemantic
interoperability, systems must be able
Terminologies /
to exchange
data in such a way that the precise meaning
Ontologies:
of the data
is readily
accessible and the data itself can be
 Provide
codes that
entity
types into a form that it understands."
translateddenote
by any
system
Jeff Heflin and James Hendler (2000) Semantic Interoperability on the Web
Ontology
http://www.cs.umd.edu/projects/plus/SHOE/pubs/extreme2000.pdf
SNOMED CT: 394887005:
"Heart failure, suspected"
Bodenreider O, Smith B, Burgun A. The ontology-epistemology divide: A case study in medical terminology. Proceedings of
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
the Third International Conference on Formal Ontology in Information Systems (FOIS 2004): IOS Press; 2004. p. 185-195.
Most epistemic-laden SNOMED CT concepts are in
the hierarchy "Situation with explicit context (CM)"
•
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•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Body structure (body structure)
Clinical finding (finding)
Environment or geographical location (environment / location)
Event (event)
Linkage concept (linkage concept)
Observable entity (observable entity)
Organism (organism)
Pharmaceutical / biologic product (product)
Physical force (physical force)
Physical object (physical object)
Procedure (procedure)
Qualifier value (qualifier value)
Record artifact (record artifact)
"CM"
Situation with explicit context (situation)
Social context (social concept)
Special concept (special concept)
Specimen (specimen)
Staging and scales (staging scale)
Substance (substance)
SNOMED CT:
~ 300,000
concepts
• ~ 3,000
precoordinated
concepts
• patterns for
postcoordination
• information
model inside
SNOMED CT
CM concepts express absence, presence, history,
uncertainty, …
COMPLEX CLINICAL SITUATIONS
AND EPISTEMIC STATES
heart failure excluded
alexia and agraphia present
history of cat allergy
suspected neoplasm of brain
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
Example: SNOMED CT CM concept
"Heart failure excluded"
 Hierarchy:
 "Heart failure excluded (situation)" isA "No cardiac failure (situation)" isA
"Heart disease excluded (situation)" isA "Disorder excluded (situation)"
 Full definition:
"Heart failure excluded (situation)"
isA "No Cardiac Failure (situation)"
Group1
Associated finding: Heart failure (disorder)
Finding context: Known absent (qualifier value)
Temporal context: Current or specified time (qualifier value)
Subject relationship context: Subject of record (person)
 OWL EL++: (according to transformation script)
'Heart failure excluded (situation) ' subclassOf RoleGroup some
(('associated finding' some 'Heart failure') and
('finding context' some 'Known absent') and
('temporal context' some 'Current of specified') and
('subject relationship context' some 'Subject of record'))
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
Example: SNOMED CT CM concept
"Heart failure excluded"
 Hierarchy:
 "Heart failure excluded (situation)" isA "No cardiac failure (situation)" isA
"Heart disease excluded (situation)" isA "Disorder excluded (situation)"
 Full definition:
"Heart failure excluded (situation)"
isA "No Cardiac Failure (situation)"
Group1
Associated finding: Heart failure (disorder)
Finding context: Known absent (qualifier value)
Temporal context: Current or specified time (qualifier value)
Subject relationship context: Subject of record (person)
 OWL EL++: (according to transformation script)
'Heart failure excluded (situation) ' subclassOf RoleGroup some
(('associated finding' some 'Heart failure') and
('finding context' some 'Known absent') and
('temporal context' some 'Current of specified') and
('subject relationship context' some 'Subject of record'))
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
Problems of current interpretation of
SNOMED CT CM concepts
 Ontological homogeneity of CM ?
 Do they represent clinical situations or information about
situations?
 What is the difference between X (finding) and X present
(situation)?
 Current frame-like CM ontologically inappropriate if
transformed to EL++
 negations (absence of)
 value restrictions
 expression of uncertainty
 Computational consequences if using OWL DL?
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
Problems of current interpretation of
SNOMED CT CM concepts
 Ontological homogeneity of CM ?
 Do they represent clinical situations or information about
situations?
 What is the difference between X (finding) and X present
(situation)?
 Current frame-like CM ontologically inappropriate if
transformed to EL++
 negations (absence of)
 value restrictions
 expression of uncertainty
 Computational consequences if using OWL DL?
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
Methodology
 Ontological clarification of relevant toplevel categories
 Identification of modelling patterns in the CM
 Re-engineering of selected pattern using OWL DL and
considering basic principles of formal ontologies
 Peer-review and discussion of patterns, identification
of controversial design decisions
 Creating SNOMED CT modules using the re-engineered
portions
 Benchmarking classification time with description logics
reasoners
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
Methodology
 Ontological clarification of relevant toplevel categories
 Identification of modelling patterns in the CM
 Re-engineering of selected pattern using OWL DL and
considering basic principles of formal ontologies
 Peer-review and discussion of patterns, identification
of controversial design decisions
 Creating SNOMED CT modules using the re-engineered
portions
 Benchmarking classification time with description logics
reasoners
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model
Reinterpretation of Clinical Situation as part of life
when certain condition(s) present / absent
EHR
Clinical finding
present:
DOCTOR
Suspected:
Past history
of:
Cat allergy
situation
Alexia and agraphia situation
Brain neoplasm situation
t
PATIENT
Schulz
S, Rector
A, Rodrigues
JM, Spackman
K. Competing reinterpretation
interpretations of
codesCT
in SNOMED
CT and
Catalina
Martínez-Costa,
Stefan
Schulz: Ontology-based
ofdisorder
the SNOMED
context model
ICD. AMIA Annu Symp Proc. 2012;2012:819-27.
BioTopLite:
Particular
Process
Information object
Clinical Situation
Material object
Biological Life
EHR
Clinical finding
present:
DOCTOR
Suspected:
Past history
of:
Cat allergy
situation
Alexia and agraphia situation
Brain neoplasm situation
t
PATIENT
Schulz
S, Rector
A, Rodrigues
JM, Spackman
K. Competing reinterpretation
interpretations of
codesCT
in SNOMED
CT and
Catalina
Martínez-Costa,
Stefan
Schulz: Ontology-based
ofdisorder
the SNOMED
context model
ICD. AMIA Annu Symp Proc. 2012;2012:819-27.
Ontology Patterns for reinterpretation SNOMED CT
CM concepts
 "P": Clinical Finding present (situation):
'Alexia and agraphia present (situation)' equivalentTo
'Alexia (finding)' and 'Agraphia (finding)'
 "A": Clinical finding absent (situation):
'Heart failure excluded (situation)' equivalentTo
ClinicalSituation and
not (hasProcesualPart some 'Heart failure (finding)')
CM concepts
interpreted as
clinical
situations
(conjunctions or
complements)
 "N": No past history of clinical finding in subject:
'History of cat allergy (situation)' equivalentTo
InformationItem and isAboutSituation only
(BiologicalLife and
not (hasProcesualPart some 'Cat allergy (finding)'))
 "S": Suspected clinical finding:
'Suspected brain neoplasm (situation)' InformationItem and
isAboutSituation only 'Neoplasm of brain (finding)') and
hasInformationObjectAttribute some Suspected
CM concepts
are interpreted
as information
entities about
clinical
situations
Review of proposed ontology design patterns
EHR
Clinical finding
present:
Suspected:
Past history
of:
Controversy about representing "ontology binding" in OWL:
- Full OWL with puns
- Reference to ontology codes as literals that encode
queries (e.g. SNOMED CT query syntax)
- Using universal restriction operator ("only"), currently
preferred working solution
isAboutSituation only
Alexia and agraphia situation
Brain neoplasm situation
Benchmarking of SNOMED CT CM module
(Classification time)
•
•
•
•
10,773 classes
48 object properties
5,381 subclass axioms
5,391 equivalence axioms
Conclusions
 SNOMED CT context model (CM): important patterns of combing clinical
terms with epistemic information
 Current OWL-EL representation of the CM flawed
 Redesign patterns controversial regarding
 interpretation of all SNOMED CT findings / disorders as clinical situations
 the linkage between information entities and clinical situation classes
 Bipartition of current CM: parts of CM concepts re-interpreted as clinical
situations, parts as information entities
 "Friendly" computational behaviour of implemented OWL-DL redesign
patterns
 Future work: identification of all pattern in the current CM, consensus
process regarding redesign within SemanticHealthNet, scripting for producing
OWL models for complete CM
 Identification of epistemic-laden content in other parts of SNOMED CT
Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model