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If you have never seen an ontology before, you may find John Sowa's top-level categories interesting - this is a well-known example of an upper ontology. Needless to say, this is regarded as by no means the best or most relevant in the biomedical sphere, but it is a useful reference point.
Do Ontologies make sense for Information?
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Ontologies of the first kind are therefore just as important. In our opinion, it is not yet clear how they inter-relate.... top
Some History
At the moment we are not trying to provide a comprehensive summary of the work done in the area of health information ontologies, but it is worth mentioning some of the work of ontological significance that has occurred over the years:
- Theoretical approaches
o 1968: Weed's POMR defined a problem/SOAP model of clinical information ref
o 1978: Elstein described a hypothetico-deductive model of clinical reasoning (mainly diagnosis) ref
o 1992: Rector, Nowlan and Kay described an approach in which EHR information included (paraphrasing) 'what can be said, thought and done for the patient' ref
o 1994: GEHR (Good European Health Record) an EU-funded project that developed requirements for an EHR and an information model ref
o 2003: Tange et al proposed a synthesis of the POMR, Elstein and 'conversation for action;' theory ref - Practical approaches:
o 1998- : the Danish G-EPJ ('EPJ' = 'EHR'), which described a cycle very similar to the one used in openEHR ref
o 2001-3: the Australian GeHR (Good electronic Health Record) project, an approach that introduced formal 'archetypes' ref
o 2005- : the Swedish Samba project distinguished 3 kinds of interlinked process: clinical, management and communication ref - Act-based approaches:
o 1992: RICHE consortium devised a method of representing health information in terms of acts carried out in the care delivery process ref
o 1993- : The HL7v3 RIM (reference information model) is a current approach that attempts to represent health information as acts. ref - Medical terminologies: all medical terminologies with any structure whatever are ontologies of some kind, whether they think they are or not, including:
o MeSH
o ICDx
o Read codes
o SNOMED CT
o LOINC
o and many others
Success Criteria
If we are to take an ontological analysis of openEHR seriously, we need to establish success criteria. These might include:
- defining tests to run on an openEHR repository that would prove correctness or show errors in the underlying ontological approach of the reference model or the archteypes.
- defining design-time tests to be run on archetypes that would show up problems; this might be done using an OWL / protege environment.
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Biomedical Ontologies
Relevant biomedical ontology resources to be investigated with respect to the openEHR appears to include the following.
- The NCBO (National Centre for Biomedical Ontology) OCI - the ontology of clinical investigation home page; visual schematic;
- The OBO - Open Biomedical Ontologies home page; the OBO Foundry (where the actual ontologies are); most of these appear to be 'ontologies of reality', although the following ones seem to be about information:
o Ontology for biomedical investigations (OBI)
o Evidence codes - The Basic Formal Ontology (BFO) home page (an ontology of reality), incorporating:
o SNAP, an ontology of substantial entities, tropes (their qualities and functions) and spatial regions
o SPAN, an ontology of process, temporal and spatio-temporal regions
o The paper "Biodynamic Ontology: Applying BFO in the Biomedical Domain" by Grenon, Smith and Goldberg is a good introduction to BFO in the biomedical domain. ref
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What parts of openEHR have Ontological Relevance?
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Of the biomedical ontologies mentioned above, the OBI and the OCI appear to be closest in purpose. No proper study of these has yet been made with respect to openEHR.
The openEHR Archetypes
In the openEHR approach, most description of the contents of recorded health information is left to archetypes (openEHR FAQ). An archetype can be thought of as a model of some clinical content (e.g. what is recorded in a urinalysis, or an ante-natal visit), expressed in a constraint formalism known as ADL (which has some similarities to OWL). Over 200 archetypes have been defined during NHS projects, Australian GP projects, and openEHR activities (openEHR archetypes page). To go straight to the point, an ontological way of looking at the archetypes that exist is the mindmap view. The structure of each archetype can be viewed by clicking on a node in this view. Another way to view archetypes is with the ADL workbench tool, and with various archetype editors. Example archetypes: Microbial lab observations; Adverse reaction; Examination of named body part.
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Of the work mentioned above, the BFO / SNAP / SPAN ontologies may be a good starting point.
Terminologies and openEHR
To be continued
References
- Rector A L, Nowlan W A, Kay S. Foundations for an Electronic Medical Record. Methods of Information in Medicine, 1991, 30:179-186. citeseer
- Austin JL. How to Do Things With Words. Cambridge (Mass.) 1962 - Paperback: Harvard University Press, 2nd edition, 2005. amazon
- HL7 International. Reference Information Model (RIM). See http://www.hl7.org.
- Weed LL. Medical Records, Medical Education and Patient Care. The Problem Oriented Medical Record as a Basic Tool. Cleveland: Case Western Reserve University press, 1968. google scholar amazon
- Elstein AS, Shulman LS, Sprafka SA. Medical problem solving: an analysis of clinical reasoning. Cambridge, MA: Harvard University Press 1978. amazon
- Tange HJ, Dietz JLG, Hasman A, de Vries Robbé PF. A Generic Model of Clinical Practice - A Common View of Individual and Collaborative Care. Methods of Information in Medicine 3/2003. Schattauer GmbH. complete article
- Bruun-Rasmussen M, Bernstein K, Vingtoft S, Nøhr C, Andersen SK. Quality labelling and certification of Electronic Health Record Systems. Studies in Health Technology and Informatics 2005; 116: p47-52. pubmed
- Areblad M, Fogelberg M, Karlsson D, Åhlfeldt H. SAMBA - Structured Architecture for Medical Business Activities. In: Engelbrecht R, et al. (editors) Connecting Medical Informatics and Bio-Informatics. MIE 2005: Proceedings of Medical Informatics Europe; 2005 Aug 28-31; Geneva, Switzerland. p. 1225-30.
- Beale T, Heard S. The GEHR Object Model - Technical Requirements. 2000. complete document.
- RICHE Consortium. RICHE ESPRIT Project. Final Report. Nov 30 1992.
- Ingram D, Lloyd D, Kalra D, Beale T, Heard S, Grubb, P, Dixon R, Camplin D, Ellis J, Maskens A. Deliverable 19,20,24: GEHR Architecture. GEHR Project 30/6/1995. complete document.
- Pierre GRENON, Barry SMITH and Louis GOLDBERG. Biodynamic Ontology: Applying BFO in the Biomedical Domain. From D. M. Pisanelli (ed.), Ontologies in Medicine, Amsterdam: IOS Press, 2004, 20-38. complete article
- Thomas Beale, Sam Heard. An Ontology-based Model of Clinical Information. Proceedings MedInfo 2007 (TBA)
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