Why build a patient record ontology?

• Facilitate conversation & consensus around clinical content within the IG
• Lack of ontological commitment within existing clinical vocabularies
• Uniform record format is really the only outstanding medical record requirement
• Semantic Web vision is predicated on vocabulary consensus
• The pieces are mostly there already

Influential literature

• HL7 RIM: An Incoherent Standard
  • Highlights ontological inconsistencies within HL7 RIM between:
    • Act of documenting
    • The phenomena being documented
    • The corresponding record
  • Suggests a seperation between:
    • Reference Ontology of the Healthcare Domain
    • Model of Healthcare Information (HL7 RIM)
• Knowledge Representation for Relevance Ranking of Patient-Record Content in Primary-Care Situations
  • Emphasizes the use of POMR structure as a core framework
  • Proposes an alignment of
    • A process ontology
    • A formal (minimal) subsumption hierarchy for clinical care acts
    • A POMR-based information ontology
• A Strategy for Improving and Integrating Biomedical Ontologies
  • In depth analysis of the value of foundational ontologies for biomedicine
  • Proposes a minimal, comprehensive subsumption hierarchy of biomedical reality
  • Aligns with (FMA, BFO)
• Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain
  • Argues against the use of cognitive representations
  • Proposes a set of terms for referring (unambigously) to ontological terms

How can this ontology be used?

• To postcoordinate vocabulary terms for a Computer-based Patient Record (CPR)

• .. offer a set of pre-enumerated codes covering only a small fraction of all the things that might be said. But when a user can’t find what they want, they can create (postcoordinate) it on demand, defining what they need in terms of the pre-enumerated codes.

• As a bridge between healthcare information and biomedical ontologies
• As an interlingua for developing use cases which cover clinical content

Design Choices

• The use of expressive, freely available foundational ontologies
• Avoided the use of skos:Concept
• Support for a syntactic mapping to HL7 RIM (via GRDDL)
• Use of OWL time to model temporal logic
• Modeling the act of recording as a primary class
• Formal logic for (objective and subjective) interpretations and signs
• Use of FOAF for terminology related to people

Core classes

cpr:clinical-description

 inf:depiction AND rim:Act AND
(foaf:maker EXACTLY 1) AND (dol:has-quality SOME time:TemporalEntity) AND
(edns:realizes ONLY cpr:patient-record) AND (cpr:description-of min 1)         
    

cpr:screening

inf:information-realization AND cpr:diagnostic-act AND
(edns:realizes SOME cpr:medical-problem)  AND (dol:particpant SOME cpr:clinician)        
    

cpr:medical-problem

dol:linguistic-object AND (galen:hasSeverity MIN 1) AND (dol:has-quality SOME time:TemporalEntity)        
    

cpr:medical-sign

(edns:interpreted-by ONLY cpr:clinician) AND 
(cpr:interpretant-of ONLY cpr:disease) AND (cpr:interpretant-of MIN 1) 
    

cpr:symptom

((dol:interpreted-by ONLY cpr:patient) AND 
 (cpr:interpretant-of ONLY (cpr:disease OR physiological-state OR physiological-process))))
    

Ontologies used

• Clinical
  • General Architecture for Languages, Encyclopedias, and Nomenclatures in Medicine (GALEN)
  • Ontology of Biomedical Reality (OBR)
  • Laboratory for Applied Ontology (Clin-Act and Biologic-Functions theories)
• Non-clinical
  • Descriptive Ontology of Linguistics and Cognitive Engineering (DOLCE)
  • Friend of A Friend (FOAF)
  • OWL time

Best practices

• Mappings to foundational ontologies to facilitate ontological commitment
• Adoption of consient terminology for ontological constructs
• Avoidance of constructs which denote cognitive representations (skos:Concept)
• Careful use of partial and complete class axioms
• Clear seperation of temporal semantics
• Exhaustive disjointeness

Motivating usecases

Coronary Artery Bypass Graft (CABG) Indications

The POMR ontology was used to model guidelines for Coronary Artery Bypass Graft operations.

Modeling an Cardiac Catheterization

A clinical description entry in a patient record which describes a cardiac catheterization which shows an arterial stricture.

[ a cpr:clinical-description;
  dol:has-quality [ a time:Instant; time:inXSDDate "2006-12-06"^^xsd:date ]
  foaf:maker [];
  rdfs:label 'Cardiac Catheterization @ 2006-12-06';
  cpr:description-of
    [ a cpr:screening;
      edns:realizes
        [ a inf:diagrammatic-object,foaf:Image;
          edns:interpreted-by [ a cpr:clinician ];
          foaf:depicts 
            [ a galen:Stricture, cpr:pathological-structure; 
              galen:hasSeverity "50";
              galen:hasSpecificLocation galen:LeftAnteriorDescendingCoronaryArtery;           
            ]
        ]
    ]
]        
    

Mapping from HL7 CDA to POMR

The POMR ontology was used as the target vocabulary for a GRDDL transform written for HL7 CDA documents.

Namespace and resources

The cpr prefix is associated with the Namespace URI: http://purl.org/cpr/1.0/problem-oriented-medical-record.owl#

The /cpr PURL top-level domain has been registered as a home for this vocabulary

The Namespace URI resolves to a formal OWL ontology

Problems and Issues

• Expressing periodic time intervals with OWL Time
• No known URI-based naming convention (or OWL export) for SNOMED CT terms
• Lossy semantic transformation from HL7 to RDF
• No feasible means of reasoning over very large ontologies (GALEN, DOLCE, etc..)?