toward an ontology for general medical science
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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.
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