Ontology for General Medical Science Overview and OBO Foundry Criteria Albert Goldfain Blue Highway...
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Transcript of Ontology for General Medical Science Overview and OBO Foundry Criteria Albert Goldfain Blue Highway...
Ontology for General Medical Science Overview and OBO Foundry Criteria
Albert GoldfainBlue Highway / University at Buffalo
ICBO 2011July 28, 2011
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 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
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.
Open
• Content License: Creative Commons 3.0 BY License
• http://code.google.com/p/ogms/
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
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.