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. Why 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. Compar Func Genom. 2005;6(7-8):379-97.

5. Evidence of the Need for OGMS Haemodialysis Haemofiltration Peritoneal Dialysis Artificial ventilation Chest drain Pericardial drain Heat therapy Surgical debridement ECMO Trans-urtheral urinary catheter Suprapubic urinary catheter Naso-gastric tube Therapeutic lumbar puncture/lumbar drain Maggot therapy (apologies !) Oral Intravenous Intramuscular Per rectum Nasogastric tube Cutaneous Local Sublingual Intrathecal Intravitreol 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 NowSoonPrinciple Open and available to all without constraint Common, shared syntax Unique identifier space within Foundry Procedure for identifying distinct successive versions Clearly specified and clearly delineated content Textual definitions for all terms Uses relations from the Relation Ontology Well documented Plurality of independent users Developed collaboratively

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) Sivaram Arabandi (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) Sivaram Arabandi (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/ http://code.google.com/p/ogms/ Open under Creative Commons 3.0 license

12. Some of the Terms diseasedisease courseclinical manifestation diagnosisclinical historypreclinical manifestation signvital signclinical history taking symptomnormal valuephysical examination clinical findingpreclinical findinglaboratory finding disordergenetic disorderepigenetic disorder homeostasislaboratory testpathological anatomical structure abnormal homeostasis clinical phenotypepredisposition to disease of type X

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

19. 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

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

21. 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.