1. Ontology for General Medical Science Overview and OBO Foundry Criteria Albert Goldfain Blue Highway / University at Buffalo albertgoldfain@gmail.com ICBO 2011 July 28, 2011

2. OGMS OVERVIEW

3. Overview An OBO Foundry Candidate Ontology – Importing from BFO, IAO, OBI Provides a general theory of disease, disorder, and diagnosis. Mid-level ontology – ~100 terms – Imported by specific disease ontologies (e.g., IDO) – Terms referenced for specific applications (e.g., AEO/AERO)

4. Current OGMS Applications Sleep Domain Infectious Disease: – IDO-Core, Flu, Staph, Malaria, Brucellosis Medically Relevant Social Entities Vital Signs Mental Diseases Biospecimen Representation and Pathological Anatomy Hemorrhoids Newborn Screening and Translational Research Diabetes Hypertension Hypersensitivity Referent-Tracking enabled EHR Glucose Metabolism Disorders Medical Devices Adverse Events

5. Core Terms Disorder =def A disorder is a material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. Disease =def A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. – Diseases, like all dispositions, need not be realized Disease Course =def The totality of all processes through which a given disease instance is realized.

6. The ‘clincially abnormal’ primitive in OGMS Qualities of an organism or processes the organism participates in that are causally linked to an elevated risk of pain or other feelings of illness, to dysfunction, or to enhanced morbidity, and which (unlike pregnancy or menopause) are not such as to belong to the life plan for an organism of the relevant type.

7. Clinically abnormal relative to what? Clinical Medicine and Human Universals We are already approaching the age of data- driven, personalized medicine Nevertheless, clinical medicine relies on many boring/obvious universals of human anatomy and physiology – Donald E. Brown Human Universals – Wiliam D Gairdner The Book of Absolutes

8. OGMS Entities through Time

9. Extending from OGMS Material Entity Disposition Processual Entity Disorder Disease Disease Course Infection Infectious Disease Infectious Disease Course

10. Why OBO needs OGMS OBO = Open BioMEDICAL Ontologies – Current OBO Foundry: More ‘bio’ then ‘medical’ OGMS = Ontology of GENERAL Medical Science – Formal template almost any clinical application ontology – Debates in the OGMS community are constructive – OGMS reveals term usage difficulties and conflations in different domains.

11. OGMS AND THE OBO FOUNDRY CRITERIA

12. Open Content License: Creative Commons 3.0 BY License http://code.google.com/p/ogms/

13. Common Format OBO Format OWL (RDF/XML)

14. URIs Prefix: OGMS Numeric Local ID

15. Versioning Successive releases given unique version numbers – Unique PURL created for each historic release – Main PURL for latest stable release Changelog for successive versions

16. Delineated Content NL def of all core terms – Very few terms without NL def Cross-products OGMS – A clinical perspective on disease, disorder Grows organically – Survey of what is general across various clinical domains (the G of OGMS)

17. Textual Definitions For almost all terms Textual elucidations for primitive undefined terms. Concise Aristotelian form OWL-DL logical axioms – for several core terms – VSO, MDO OGMS extensions

18. Relations OGMS extensions use RO and RO_Proposed relations has_material_basis_in linking a disease (disposition) and a disorder (material entity) – Built from RO and RO_Proposed relations

19. Documented Original papers: – Toward an Ontological Treatment of Disease and Diagnosis (Scheuermann, Ceusters & Smith, 2009) – On Carcinomas and Other Pathological Entities (Smith, Kumar, Ceuster, & Rosse, 2005) Code Tracker and Issues List: http://code.google.com/p/ogms/issues/list http://code.google.com/p/ogms/issues/list Metadata Comments and usage examples for most terms

20. Users A steadily growing set of users...from different domains – SMEs of all sorts, ontologists, clinicians Efforts to reach out to other groups/resources – openEHR – DO – BioTop – CPR We always welcome new users!

21. Collaboration Monthly Skype Call ogms-discuss group – Documented answers, debates, use cases... Google Code Wiki pages

22. Locus of Authority http://ogms.googlecode.com

23. Naming Conventions Follow best practices of the OBO Foundry – Singulars – Positivity Principle Consider usage in the field, but don’t bend to it...we are creating an ontology, not a dictionary.

24. Maintenance Stable core Several incremental releases per year

25. THANKS! http://code.google.com/p/ogms/