Transcript Toward an Ontology for General Medical Science

Toward an Ontology for General
Medical Science
SSFW09
September 4, 2009
William Hogan, MD, MS
Associate 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 OGMS
Haemodialysis
Haemofiltration
Peritoneal Dialysis
Artificial ventilation
Chest drain
Oral
Intravenous
Intramuscular
Per rectum
Requests
for terms
Nasogastric
tube such as
these
requires an organized,
Cutaneous
logical
Local approach to clinical
medicine
in the OBO Foundry.
Sublingual
Intrathecal
OGMS is the first step!
Intravitreol
Pericardial drain
Heat therapy
Surgical debridement
ECMO
Trans-urtheral urinary catheter
Suprapubic urinary catheter
Naso-gastric tube
Therapeutic lumbar puncture/lumbar
drain
Maggot therapy (apologies !)
OGMS Does…
• Include definitions for high-level types such as
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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 Principles
Now Soon Principle
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Clearly specified and clearly delineated content
Textual definitions for all terms
Uses relations from the Relation Ontology
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Open and available to all without constraint
Common, shared syntax
Unique identifier space within Foundry
Procedure for identifying distinct successive versions
Well documented
Plurality of independent users
Developed collaboratively
Who
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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
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Albert Goldfain: Coordinator/Owner
Alan Ruttenburg (Science Commons): Owner
Barry Smith
Close coordination with OBI
Werner Ceusters
and IDO
to avoid
violating
Richard Scheuerman (University
of Texas
Southwestern
orthogonality.
Medical Center)
Lindsay Cowell (Duke)
Sivaram Arabandi (Case Western)
Myself
You!
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 Terms
disease
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
One proposal is to
significance.
modify symptom to
be a subject
• Symptom: A bodily feature
of a patient that is
of the
observed by a patientexperience
and is hypothesized
by
patient
the patient to be a realization of a disease.
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:
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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
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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.