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Ontology for General Medical Science Overview and OBO Foundry Criteria Albert Goldfain Blue Highway / University at Buffalo [email protected] ICBO 2011 July 28, 2011 OGMS OVERVIEW 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) 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 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. 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. Clinically abnormal relative to what? • Clinical Medicine and Human Universals • We are already approaching the age of datadriven, 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 OGMS Entities through Time Extending from OGMS • Material Entity • Disposition • Processual Entity • Disorder • Disease • Disease Course • Infection • Infectious Disease • Infectious Disease Course 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. OGMS AND THE OBO FOUNDRY CRITERIA Open • Content License: Creative Commons 3.0 BY License • http://code.google.com/p/ogms/ Common Format • OBO Format • OWL (RDF/XML) URIs • Prefix: OGMS • Numeric Local ID Versioning • Successive releases given unique version numbers – Unique PURL created for each historic release – Main PURL for latest stable release • Changelog for successive versions 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) 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 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 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 • Metadata Comments and usage examples for most terms 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! Collaboration • Monthly Skype Call • ogms-discuss group – Documented answers, debates, use cases... • Google Code Wiki pages Locus of Authority • http://ogms.googlecode.com 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. Maintenance • Stable core • Several incremental releases per year http://code.google.com/p/ogms/ THANKS!