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Toward an Ontology for General Medical Science

Toward an Ontology for General Medical Science. SSFW09 September 4, 2009 William Hogan, MD, MS Associate Professor of Biomedical Informatics University of Pittsburgh. Outline. What, Why, Who Progress to Date Proposals. Ontology for General Medical Science (OGMS).

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Toward an Ontology for General Medical Science

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  1. Toward an Ontology for General Medical Science SSFW09 September 4, 2009 William Hogan, MD, MS Associate Professor of Biomedical Informatics University of Pittsburgh

  2. Outline • What, Why, Who • Progress to Date • Proposals

  3. Ontology for General Medical Science (OGMS) A small, upper-level ontology for the domain of clinical medicine and research

  4. Define general terms in medicine Serve as anchor point for domain ontologies: medication, disease, laboratory test Serve as a common, upper-level ontology that bridges clinical medicine and basic science Continue the work begun—and give unique, machine-readable identifiers to the terms—in: Scheuermann et al. Towards an Ontological Treatment of Disease and Diagnosis. Proceedings, AMIA Translational Summit, 2009. Smith et al. On carcinomas and other pathological entities.ComparFuncGenom. 2005;6(7-8):379-97. Why

  5. Evidence of the Need for OGMS Requests for terms such as these requires an organized, logical approach to clinical medicine in the OBO Foundry. OGMS is the first step!

  6. OGMS Does… • Include definitions for high-level types such as • Disease • Disorder • Sign • Symptom • Finding • Follow the OBO Foundry principles • Use BFO/RO as starting point • Have Aristotelian text definitions for each term

  7. OBO Foundry Principles

  8. Who • Albert Goldfain: Coordinator/Owner • Alan Ruttenburg (Science Commons): Owner • Barry Smith • Werner Ceusters • Richard Scheuerman (University of Texas Southwestern Medical Center) • Lindsay Cowell (Duke) • SivaramArabandi (Case Western) • Myself • You!

  9. Who • Albert Goldfain: Coordinator/Owner • Alan Ruttenburg (Science Commons): Owner • Barry Smith • Werner Ceusters • Richard Scheuerman (University of Texas Southwestern Medical Center) • Lindsay Cowell (Duke) • SivaramArabandi (Case Western) • Myself • You! Close coordination with OBI and IDO to avoid violating orthogonality.

  10. We are NOT • Creating a giant, ‘ontology of everything’ • Fighting a turf war for particular terms • Violating the principle of orthogonality

  11. Progress to Date • Aristotelian text definitions for 44 terms • Terms represented in OBO/OWL format • Ontology page on Google code: http://code.google.com/p/ogms/ • Open under Creative Commons 3.0 license

  12. Some of the Terms

  13. Definitions • Disorder: a causally relatively isolated combination of physical components that is (i) clinically abnormal and (ii) maximal, in the sense that it is not part of some larger combination. • Disease: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.

  14. Definitions • Disease course: the totality of all processes through which a given disease is realized. • Diagnosis: the conclusion of an interpretive process that has as input a clinical picture of a given patient and as output an assertion to the effect that the patient has a disease of such and such a type.

  15. Definitions • Sign: a bodily feature of a patient that is observed in physical examination and is deemed by the clinician to be of clinical significance. • Symptom: A bodily feature of a patient that is observed by a patient and is hypothesized by the patient to be a realization of a disease. One proposal is to modify symptom to be a subject experience of the patient

  16. Proposals • Avoid the terms genotype and clinical phenotype (is there a real distinction?) • Modify the definition of symptom to mention subjective experience of patient • New terms: • Drug/medication • Drug administration • Patient • Provider • Surgical procedure • Complication: predisposition to disease of type X because of disease of type Y • Pain • Encounter • Order

  17. Acknowledgements • All the attendees of the Dallas workshop • Werner Ceusters • Albert Goldfain • Alan Ruttenberg • Richard Scheuermann • Barry Smith

  18. Definitions • Sign: a bodily feature of a patient that is observed in physical examination and is deemed by the clinician to be of clinical significance. • Symptom: A bodily feature of a patient that is observed by a patient and is hypothesized by the patient to be a realization of a disease.

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