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
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!