Toward an Ontology for General Medical Science

SSFW09

September 4, 2009

William Hogan, MD, MSAssociate Professor of Biomedical Informatics

University of Pittsburgh

Outline

• What, Why, Who• Progress to Date• Proposals

Ontology for General Medical Science (OGMS)

A small, upper-level ontology for the domain of clinical medicine and research

Why

• Define general terms in medicine• Serve as anchor point for domain ontologies:

medication, disease, laboratory test• Serve as a common, upper-level ontology that

bridges clinical medicine and basic science• Continue the work begun—and give unique,

machine-readable identifiers to the terms—in:– Scheuermann et al. Towards an Ontological Treatment of Disease and

Diagnosis. Proceedings, AMIA Translational Summit, 2009.– Smith et al. On carcinomas and other pathological entities. Compar Func

Genom. 2005;6(7-8):379-97.

Evidence of the Need for OGMSHaemodialysisHaemofiltrationPeritoneal DialysisArtificial ventilationChest drainPericardial drainHeat therapySurgical debridementECMOTrans-urtheral urinary catheterSuprapubic urinary catheterNaso-gastric tubeTherapeutic lumbar puncture/lumbar drainMaggot therapy (apologies !)

OralIntravenousIntramuscularPer rectumNasogastric tubeCutaneous LocalSublingualIntrathecalIntravitreol

Requests for terms such as these requires an organized, logical approach to clinical

medicine in the OBO Foundry.

OGMS is the first step!

OGMS Does…

• Include definitions for high-level types such as – Disease– Disorder– Sign– Symptom– Finding

• Follow the OBO Foundry principles• Use BFO/RO as starting point• Have Aristotelian text definitions for each term

OBO Foundry PrinciplesNow Soon Principle Open and available to all without constraint

Common, shared syntax

Unique identifier space within Foundry

Procedure for identifying distinct successive versions

Clearly specified and clearly delineated content

Textual definitions for all terms

Uses relations from the Relation Ontology

Well documented

Plurality of independent users

Developed collaboratively

Who• Albert Goldfain: Coordinator/Owner• Alan Ruttenburg (Science Commons): Owner• Barry Smith• Werner Ceusters• Richard Scheuerman (University of Texas Southwestern

Medical Center)• Lindsay Cowell (Duke)• Sivaram Arabandi (Case Western)• Myself• You!

Who• Albert Goldfain: Coordinator/Owner• Alan Ruttenburg (Science Commons): Owner• Barry Smith• Werner Ceusters• Richard Scheuerman (University of Texas Southwestern

Medical Center)• Lindsay Cowell (Duke)• Sivaram Arabandi (Case Western)• Myself• You!

Close coordination with OBI and IDO to avoid violating

orthogonality.

We are NOT

• Creating a giant, ‘ontology of everything’• Fighting a turf war for particular terms• Violating the principle of orthogonality

Progress to Date

• Aristotelian text definitions for 44 terms• Terms represented in OBO/OWL format• Ontology page on Google code:

http://code.google.com/p/ogms/• Open under Creative Commons 3.0 license

Some of the Termsdisease disease course clinical manifestation

diagnosis clinical history preclinical manifestation

sign vital sign clinical history taking

symptom normal value physical examination

clinical finding preclinical finding laboratory finding

disorder genetic disorder epigenetic disorder

homeostasis laboratory test pathological anatomical structure

abnormal homeostasis

clinical phenotype predisposition to disease of type X

Definitions

• Disorder: a causally relatively isolated combination of physical components that is (i) clinically abnormal and (ii) maximal, in the sense that it is not part of some larger combination.

• Disease: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.

Definitions

• Disease course: the totality of all processes through which a given disease is realized.

• Diagnosis: the conclusion of an interpretive process that has as input a clinical picture of a given patient and as output an assertion to the effect that the patient has a disease of such and such a type.

Definitions

• Sign: a bodily feature of a patient that is observed in physical examination and is deemed by the clinician to be of clinical significance.

• Symptom: A bodily feature of a patient that is observed by a patient and is hypothesized by the patient to be a realization of a disease.

One proposal is to modify symptom to

be a subject experience of the

patient

Proposals• Avoid the terms genotype and clinical phenotype (is there a real

distinction?)• Modify the definition of symptom to mention subjective experience

of patient• New terms:

– Drug/medication– Drug administration– Patient– Provider– Surgical procedure– Complication: predisposition to disease of type X because of disease of type Y– Pain– Encounter– Order

Acknowledgements

• All the attendees of the Dallas workshop• Werner Ceusters• Albert Goldfain• Alan Ruttenberg• Richard Scheuermann• Barry Smith

Definitions

• Sign: a bodily feature of a patient that is observed in physical examination and is deemed by the clinician to be of clinical significance.

• Symptom: A bodily feature of a patient that is observed by a patient and is hypothesized by the patient to be a realization of a disease.