catalina martínez-costa, stefan schulz: ontology-based reinterpretation of the snomed ct context...

Catalina Martínez-Costa, Stefan Schulz: Ontology-based reinterpretation of the SNOMED CT context model

Ontology-based reinterpretation

of the SNOMED CT context model

CatalinaMartínez-Costa

Stefan Schulz

Medical University of Graz (Austria)

ICBO 2013Montreal


"… 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 Webhttp://www.cs.umd.edu/projects/plus/SHOE/pubs/extreme2000.pdf

Semantic Interoperability requires distinction between vocabularies and perspectives

http://www.cs.umd.edu/projects/plus/SHOE/pubs/extreme2000.pdf


"… 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."


Semantic Interoperability requires distinction between vocabularies and perspectives

Terminologies / Ontologies:

Provide codes that denote entity types

Information models

Provide structure and context for data

Ontology Epistemology

SNOMED CT,ICD,…

openEHRHL7 RIMEN 13606,proprietary information models

"Heart failure, suspected"


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 the Third International Conference on Formal Ontology in Information Systems (FOIS 2004) : IOS Press; 2004. p. 185-195.


"… integrating resources that were developed using different vocabularies and different 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."


Epistemic Intrusion is common in biomedical vocabularies

Terminologies / Ontologies:

Provide codes that denote entity types

Ontology

"Heart failure, suspected"

Bodenreider O, Smith B, Burgun A. The ontology-epistemology divide: A case study in medical terminology. Proceedings of the Third International Conference on Formal Ontology in Information Systems (FOIS 2004) : IOS Press; 2004. p. 185-195.

SNOMED CT: 394887005:

Most epistemic-laden SNOMED CT concepts are in the hierarchy "Situation with explicit context (CM)"

• 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)• Situation with explicit context (situation)• Social context (social concept)• Special concept (special concept)• Specimen (specimen)• Staging and scales (staging scale)• Substance (substance)

• ~ 3,000 precoordinated concepts

• patterns for postcoordination

• information model inside SNOMED CT

SNOMED CT:

~ 300,000 concepts

"CM"


CM concepts express absence, presence, history, uncertainty, …

alexia and agraphia present

COMPLEX CLINICAL SITUATIONS AND EPISTEMIC STATES

heart failure excluded

suspected neoplasm of brain

history of cat allergy

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)"

Group1Associated 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'))

Example: SNOMED CT CM concept "Heart failure excluded"


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?

Problems of current interpretation of SNOMED CT CM concepts


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

Methodology


Reinterpretation of Clinical Situation as part of life when certain condition(s) present / absent

PATIENT

tBrain neoplasm situation

Alexia and agraphia situationCat allergysituation

Clinical finding present:

Suspected:

Past history of:

EHR

DOCTOR

Schulz S, Rector A, Rodrigues JM, Spackman K. Competing interpretations of disorder codes in SNOMED CT and ICD. AMIA Annu Symp Proc. 2012;2012:819-27.


PATIENT

tBrain neoplasm situation

Alexia and agraphia situationCat allergysituation


Suspected:

Past history of:

EHR

DOCTOR

Schulz S, Rector A, Rodrigues JM, Spackman K. Competing interpretations of disorder codes in SNOMED CT and ICD. AMIA Annu Symp Proc. 2012;2012:819-27.

Particular

Information object Process Material object

Clinical Situation Biological Life

BioTopLite:

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)') "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 conceptsinterpreted as clinical situations(conjunctions or complements)

CM concepts are interpreted as information entities about clinical situations

Review of proposed ontology design patterns

Brain neoplasm situation

Alexia and agraphia situation


Suspected:

Past history of:

EHR

isAboutSituation only

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

Benchmarking of SNOMED CT CM module(Classification time)

• 10,773 classes• 48 object properties• 5,381 subclass axioms• 5,391 equivalence axioms


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

Conclusions

catalina martínez-costa, stefan schulz: ontology-based reinterpretation of the snomed ct context...

Documents

semantic interoperability

different vocabularies

catalina martnezcosta

formal ontology

different perspectives

ontologyepistemology

suspected slide

web http