Ontology for General Medical Science Overview and OBO Foundry Criteria

Albert GoldfainBlue Highway / University at Buffalo

albertgoldfain@gmail.com

ICBO 2011July 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 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

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

THANKS!

http://code.google.com/p/ogms/