HCLS/POMROntology

From W3C Wiki
Jump to: navigation, search

Contents

A Problem-Oriented Medical Record Ontology

This is an attempt to demonstrate how a few best practices in ontology engineering can be applied to address the problem of the lack of a unified vocabulary for Computer-based Patient Records (CPR) [20]. This developed from an initial effort to develop a Patient Record ontology (in the absence of any), an initial presentation - during the 2006 F2F - on how a major Coronary Artery Bypass Graft (CABG) Procedure Guideline could be implemented using Notation 3 rules and OWL, a recent presentation [1] to the HCLSIG in ISWC on CPRs and how Semantic Web representation standards can be applied to CPR requirements, and the development of two use cases: 1) demonstrating how GRDDL can be applicable as a technology for enabling Clinical Content Management systems and 2) modeling an angiogram finding:


[ a cpr:clinical-description;
   dc:date "2006-12-06"^^xsd:date;
   foaf:maker [ 
                foaf:name "Chimezie Ogbuji";
                a cpr:person  ];
   rdfs:label 'Cardiac Catheterization @ 2006-12-06';
   cpr:description-of
    [ a ptrec:CardiacCatheterization, cpr:diagnostic-act;
      inf:realizes
       [ a inf:diagrammatic-object;
         edns:interpreted-by [ a cpr:clinician ];
         foaf:depicts 
             [ a galen:Stricture, cabg:ImportantStenosis,cpr:pathological-structure, cpr:medical-problem; 
               galen:hasSeverity "50";
               galen:hasSpecificLocation galen:CoronaryArtery;           
       ]
    ]
]


For the terms described the prefix cpr is associated with the namespace URL http://purl.org/cpr/1.0/problem-oriented-medical-record.owl#


HCLS$$POMROntology$CPR-Modeling.png

The goal is to define a minimal set of terms that connect representations from well defined healthcare information & process models (such as HL7 RIM) with more expressive foundational ontologies [3] through the use of the criteria outlined in the traditional Problem-oriented Medical Record (POMR) structure. This separation is necessary [4] in order to provide sound ontological commitment for heavily adopted models of health care information. The approach taken for building a vocabulary around the POMR structure takes after the recommendations outlined in Ontologies for Knowledge Representation in a Computer-Based Patient Record [6].

The Problem-Oriented Medical Record

From A Problem Oriented Approach to the Computerized Patient Record:

  • The fundamental motivation for the design and philosophy of the Problem-Oriented Medical Record (POMR) is the belief that the medical record is the central medium of communication and the first repository of knowledge in the practice of clinical medicine

The traditional structure / organization of the POMR is:

  • Screening Data (collected in order to discover problems)
  • Problem List
  • Initial Plans (organized by problem)
  • Progress Notes (outcomes and follow-up)

Foundational / Upper Ontologies

Wikipedia has a (mildly) useful description of upper / foundational ontologies - along with a list of a few. It probably can be said that foundational ontologies (such as BFO and DOLCE) are typically more rigorously oriented around philosophy and linguistics.

  • DOLCE [5]
  • OBR [3]
  • bio-zen [11]
  • Galen [7]
  • Laboratory for Applied Ontology (Clin-Act and Biologic-Functions theories) [13]

Grounding HL7 RIM Ontologically

The cpr:clinical-description class is an attempt to reconcile the ontological inconsistencies with the archetype of a recording of an act and the thing the recording describes (which could be either a continuant / endurant or an occurrant / perdurant).


The Classes

cpr:patient-record

A patient record is a universal [17].

cpr:person

The person whom the patient record is about. An anchor for associating (non-lingitudinal) demographic and genetic data with the patient. Also a bridge for other vocabularies which describe people and their related data (vCard and FOAF for instance). Galen has the notion of a role which is missing from FOAF but essential for medical record ontologies.

A person is a universal.

cpr:patient

A patient is a defined class [17].

cpr:clinician

Restricts the person class to only those that play clinical roles (from galen).

A clinician is a defined class.

cpr:clinical-description

Corresponds (at least syntactically) with the HL7 RIM Act Class, insofar as it is the class of clinical recordings (a REPRESENTATIONAL ARTIFACT [17]) of a natural phenomenon (cpr:medical-problems, cpr:clinical-acts, and anything else of relevance) by an individual (foaf:maker and dc:creator are used for this relation as a bridge to agent and provenance vocabularies - respectively). This recording manifests itself as the patient record. Note that it is crucial that the recording be associated with a point on a time scale in order to later facilitate temporal reasoning. Expressive, interoperable, and freely available knowledge representations [18] can be used or the natural unicode ordering of ISO 8601 can be leveraged intuitively [19] with rules. Towards this end, the instances of the cpr:clinical-description class can be associated with a TemporalEntity from the OWL-time vocabulary.

A clinical-description is a defined class.

This class is a partial attempt to resolve the ontological inconsistencies [4] of the HL7 RIM design intent (especially with regards to the act of recording or documenting).

Clinical descriptions can be directly associated with provenance data (via Dublin Core vocabulary terms such as dc:source, dc:date):

cpr:anatomical-structure

An anatomical-structure a universal.

cpr:immaterial-anatomical-entity

An immaterial-anatomical-entity a universal.

cpr:anatomical-space

cpr:anatomical-surface

cpr:anatomical-point

cpr:physiological-state

A physiological-state is a defined class.

cpr:physiological-role

A physiological-role is a defined class.

cpr:physiological-process

A physiological-process is a universal.

From OBR:

   The transformations of one physiological state into another are instances of physiological process,

cpr:medical-problem

  • ".. problems that clearly require the intervention of a health care professional. These include acute problems requiring hospitalization and chronic problems requiring long-term management."

A medical-problem is a defined class.

Whether or not a medical problem is active is an important distinction within the POMR model [2].

  This needs to be modeled as an attribute of the medical problem?

A medical problem is typically associated with a measureable severity (especially an objective problem - cpr:medical-sign), an onset modifier, and a time interval.

How subtle is the distinction between symptoms, findings, and diseases? See: http://en.wikipedia.org/wiki/Medical_sign#Signs_versus_symptoms

cpr:medical-sign

Wikipedia entry:

  an "objective" indication of some medical fact or quality that is detected by a physician during a physical examination of a patient.

See: http://en.wikipedia.org/wiki/Medical_sign#Signs_versus_symptoms

cpr:symptom

From Wordnet:

  • "(medicine) any sensation or change in bodily function that is experienced by a patient and is associated with a particular disease."

So a symptom is related to a cpr:disease by some relation. INTERPRETANT-OF is a relationship between a SIGN-OR-SYMPTOM and a cpr:disease. Typically interpreted by the cpr:patient.

cpr:disease

From Wordnet:

  • "..an impairment of health or a condition of abnormal functioning."

Corresponds directly with pathological universals [17] from OBR [3]: pathological entity, continuant, or process. Typically interpreted by a cpr:physician. This constraint corresponds well with OBJECTIVE-MEDICAL-SIGN (Clinical Act Theory [13]) which uses the relationship INTERPRETED-BY for this purpose.

cpr:immaterial-pathological-entity

cpr:pathological-space

cpr:pathological-surface

cpr:pathological-structure

From OBR:

  • "Since tumors or portions of pus do not exist in the domain of entities represented in canonical anatomy, pathological structure and portion of pathological body substance are not subordinated in OBR to the class material anatomical entity, but rather to its sibling class material pathological entity."
"In analogy with their normal anatomical counterparts, we recognize also pathological spaces and boundaries such as surfaces and lines. These immaterial anatomical and pathological entities are dependent continuants, since their existence depends on corresponding independent continuant entities."

cpr:pathological-process

From OBR:

" ..processes that transform a physiological into a pathological state, or one pathological state into another, are instances of pathological process."

cpr:pathological-process = galen:NAMEDPathologicalProcess or galen:PathologicalBodyProcess

cpr:pathological-state

Processes and states (conditions) (from DOLCE):

  • "Within stative occurrences, we distinguish between states and processes according to homeomericity: sitting is classified as a state but running is classified as a process, since there are (very short) temporal parts of a running that are not themselves runnings."

cpr:clinical-act

The root class for clinical acts described in a patient record. This hierarchy corresponds with Elisabeth Bayegan's CareActType class [6].

cpr:diagnostic-act

cpr:screening
  • ".. data collected with pre-defined and standardized screening questionnaires in order to discover problems."

Equivalent (syntactically) with rim:Observation

Corresponds well with a DIAGNOSTIC-PROCEDURE (Medical-procedures Theory [13]):

  • "A procedure, method, or technique used to determine the nature or identity of a disease or disorder. This excludes procedures which are primarily carried out on specimens in a laboratory."

cpr:history-screening

= cpr:family-history-screening =

= cpr:social-circumstance-screening =

cpr:clinical-examination

cpr:laboratory-test

cpr:therapeutic-act

cpr:physical-therapy

cpr:psychological-therapy

cpr:medical-therapy

cpr:substance-administration

From HL7 RIM:

  • "The act of introducing or otherwise applying a substance to the subject."

cpr:surgical-procedure

Corresponds well with GALEN's notion of SurgicalDeed and HL7 RIM's notion of a Procedure (defined below):

  • "An Act whose immediate and primary outcome (post-condition) is the alteration of the physical condition of the subject."

Finally, from the notion of a THERAPEUTIC-OR-PREVENTIVE-PROCEDURE:

  • "A procedure, method, or technique designed to prevent a disease or a disorder, or to improve physical function, or used in the process of treating a disease or injury."

cpr:medical-device

cpr:medication

Corresponds well with PHARMACOLOGIC-SUBSTANCE:

  • "A substance used in the treatment, diagnosis, prevention, or analysis of normal and abnormal body function. This includes substances that occur naturally in the body and are administered therapeutically."

Or from Wordnet:

  • "(medicine) something that treats or prevents or alleviates the symptoms of disease."

Related HL7 RIM ActCodes:

  • ActInvoiceDetailDrugProductCode
  • ActMedicationList
  • ActMedicationTherapyDurationWorkingListCode

The Roles/Properties

cpr:interpretant-of

Relates a medical sign with associated phenomena.

cpr:description-of

Relates a clinical description with the phenomena it describes

Functions v.s. Processes

   Functions are certain sorts of potentials of independent anatomical continuants for engagement and participation in one or more processes through which the potential becomes realized. Whereas processes unfold in time, the function (e.g., the potential of a cell to synthesize a particular protein) is a continuant, since it, too, endures through time and it exists even during those times when it is not being realized. The

A GRDDL Transform

An XSLT transformation can be written to extract RDF statements (which adhere to this ontology) from HL7 CDA documents as a means to seperate the structural nature of healthcare information from it's unambigious interpretation (to the extent that this is possible with a well-founded target ontology). See Health Care: Querying an XML-based clinical data using an standard ontology

For the details, see: POMROntology and GRDDL

Ontology files

You can load the ontology in SWOOP - using the nightly java webstart build.


Papers and References

  1. A Comprehensive Representation Methodology for CPRs
  2. A Problem Oriented Approach to the Computerized Patient Record
  3. A Strategy for Improving and Integrating Biomedical Ontologies
  4. HL7 RIM: An Incoherent Standard
  5. DOLCE: Descriptive Ontology of Linguistics and Cognitive Engineering
  6. Ontologies for Knowledge Representation in a Computer-Based Patient Record
  7. Open Galen OWL Ontology
  8. DOLCE OWL Ontology - full
  9. HL7 RIM OWL Ontology
  10. Manchester OWL Syntax
  11. bio-zen-plus.owl
  12. openEHR Archetypes
  13. Laboratory for Applied Ontology (LOA) - Medical Theories
  14. HL7 Reference Information Model
  15. Health Level Seven Releases Updated Clinical Document Architecture (CDA) Specification.
  16. Ontology: Philosophical and Computational
  17. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain
  18. Time Ontology in OWL
  19. Practical Temporal Reasoning with Notation 3
  20. National Institutute of Medicine, The Computer-Based Patient Record: An Essential Technology for Health Care - Revised Edition., 1998, ISBN: 0309055326.