Download Clinical Finding - Buffalo Ontology Site

Problems with Current
Approaches to Clinical Data
William R. Hogan, MD
Associate Professor of Biomedical Informatics
University of Pittsburgh
Director, Medical Vocabulary/Ontology Services
UPMC
UPMC Overview
• Facilities
–
–
–
–
–
20 Hospitals
400 Ambulatory sites with 2300 physicians
16 Long-term care facilities
43 Academic/community cancer centers
International ventures in Italy, Ireland, Britain
• Information technology
– 200 clinical applications from 120 vendors
– 610 system interfaces
– $1B investment over 5 years
But One Key Element was Missing
• Interoperability
– 3 inpatient Electronic Medical Records (EMRs)
– 3 outpatient EMRs
– Ancillary systems (lab, radiology, registration, etc)
– Commercial laboratories (e.g., Quest)
• dbMotion, Inc.
– Interoperability solution based on HL7 v3
reference information model
– Facilitating data exchange for over 70% of Israel
Problem 1: A Finding is Many Things…
• The term “finding” does little to discriminate among:
– Entities and their qualities
– Surmises, hypotheses, beliefs, degrees of belief, and
statements about entities and their qualities
– Observations/methods of finding entities/qualities
• Thus, we get:
–
–
–
–
–
Type 2 diabetes mellitus (disorder)
Uncertain viability of pregnancy (finding)
On examination - equivocally anemic (disorder)
Admitted to a children's home (finding)
On examination - dead - unattended death (finding)
Problem 2: …but Not Everything
• Situation: used in SNOMED-CT for conditions/
procedures:
– That are absent or have not occurred
– Pertain to someone other than subject of medical
record
– That occurred or were present in the past
• Findings, by contrast, have a “default context”:
– Present
– Subject of medical record
– Current or some specified time
Thus, we get:
• No family history of cardiovascular accident or stroke
(situation)
• Absence of signs and symptoms of physical injury
(situation)
• Electrocardiogam improved compared to prior study
(situation)
• Pathology examination findings absent (situation)
• Past myocardial infarction diagnosed on ECG
AND/OR other special investigation, but currently
presenting no symptoms (disorder)
DOES IT MATTER?
Past history of colon cancer
increases one’s risk. Thus, to
determine “average risk”,
you need to know if this risk
factor is present.
The following could also be problematic…
•
•
•
•
Body mass index 20-24 - normal (finding)
Erythrocyte sedimentation rate (ESR) abnormal (finding)
C-reactive protein abnormal (finding)
Lupus hepatitis (disorder) is a Systemic lupus
erythematosus (disorder)
• On examination - equivocally anemic (disorder) is a
Anemia (disorder)
• Chronic hypertension complicating AND/OR reason for
care during childbirth is a Pregnancy-induced
hypertension
Epistemological Basis of “Finding”
• According to SNOMED-CT User Guide (p. 42):
Concepts in [the Clinical Finding] hierarchy represent
the result of a clinical observation, assessment,
or judgment, and include both normal and
abnormal clinical states.
• SNOMED is not alone:
– RadLex: Cardiovascular disease is a Imaging
observation
– NCI Thesaurus: Death is a Finding
Proposed Definition
• Clinical Finding =def.
• A representation of a bodily feature of a patient that
is recorded by a clinician because the feature is
hypothesized to be of clinical significance.
Emphasis is mine.
• Caution:
– Be careful to distinguish the feature itself from…
– The method, timing, certainty, etc. related to how
we found it
– And the record of all the above
Ontology vs. Epistemology
• Ontology*
The science of what is, of the kinds and structures of
objects, properties, events, processes and relations
in every area of reality
• Epistemology†
– The study of how cognitive subjects come to know
the truth about given phenomena in reality
– …it encompasses the ways in which physicians
come to know about the existence of given
diseases in given patients
*Smith B. Ontology. In: Floridi L, ed. The Blackwell Guide to Philosophy of Computing and Information: Blackwell Publishing 2003.
†Bodenreider O, Smith B, Burgun A. The ontology-epistemology divide: A case study in medical terminology. In: Varzi A, Vieu L,
editors. Proceedings of the Formal Ontology in Information Science Conference (FOIS 2004); 2004; Turin; 2004.
Per SNOMED-CT
• Disease is a Clinical Finding
• Also, per the User Guide:
IS_A relationships are also known as “SupertypeSubtype relationships”
• Thus, a disease is a subtype of …result of a
clinical observation, assessment, or judgment…
• And so is a Drug action, Edema, Deformity, and
Administrative statuses
But,
• Diseases, signs, symptoms, etc. all exist
regardless of whether a clinician finds them
• Failure to “find” (i.e., diagnose) cancer is a
leading cause of malpractice claims
Problems with Epistemological Criteria
• Cannot differentiate true subtype from what is
known:
– Presbyterian vs. Unknown religion
– Chronic hypertension complicating AND/OR reason
for care during childbirth vs. Chronic hypertension
• Whatever we say is true of all instances of the
type Religion, the computer will assume to be
true of the Unknown religion, too
PubMed as Barometer of Scientific Terms
Search string
Total
Hits on
Hits
Title Only
“chronic hypertension”
1573
314
“chronic hypertension” reason care
3
0
“chronic hypertension” complicating
14
1
“chronic hypertension” childbirth
6
0
We gave Chronic hypertension
complicating AND/OR reason for care
during childbirth every chance. It’s
just not a subtype of chronic
hypertension.
Epistemology and Combinatorial Explosion
• Rash
– Cutaneous eruption (morphologic abnormality), with
synonym Rash
– Eruption of skin (disorder), with synonym Rash
– Complaining of a rash (finding)
– On examination - a rash (finding)
Will we eventually need:
– On examination - rash present (situation)
On digital photograph
• Fever
transmitted by a
– Fever - 386661006
– On exam – fever - 271897009telemedicine device – a
rash (finding)?
– Fever symptoms - 248427009
– Feeling feverish - 103001002
Epistemology and Time
• Today, I document the problem list:
– History of - myocardial infarction in last year
– Recent weight gain
– New onset angina
We also need a coherent,
– Hepatitis A - current infectionshared representation of
disease vs. course of
– Newly diagnosed diabetes
disease
• The patient returns to the office for the first
time two years from now.
Epistemology and Negation
• If the EMR says:
NOT Colitis presumed infectious
• Does that mean:
NOT Colitis
• Or
NOT presumed infectious
(and then, is it certainly not infectious or certainly infectious,
or have we just stopped presuming altogether and chosen
instead to remain agnostic about whether the colitis is of
infectious origin?)
Logical Conjunction as Set Membership
• Contradiction!
• Someone forgot to tell the computer :
– About complications
– When complications are present vs. absent
• But the real issue is more subtle…
Neither is a Subtype of Diabetes Mellitus
• There are no instances (and there never has been) of
the disease Type II diabetes mellitus with neuropathy
• Nothing is both elevated blood glucose and nerve
damage at the same
• However, there are millions of instances of human with:
The disease Type II diabetes mellitus,
Thus and
this term represents
two
in a set,
the disease Neuropathy, where
thediagnoses
former caused
thethat
latter.
are erroneously conjoined
• Similarly, for Hypertensive heart
and renal disease with
with AND.
both (congestive) heart failure and renal failure
(disorder)
To which diagnosis/disease in the set
do the following apply?
•
•
•
•
•
•
•
Onset date
Method of diagnosis
Date diagnosis made
Uncertainty
Course (acute, chronic, etc.)
Negation
Treatment
Conclusions/Recommendations
• Avoid finding and its younger sibling situation as catchas-catch-cans
– Distinguish carefully and always between what was found,
the finding process, and the record of the finding
– A disease is not a finding***
• No epistemological criteria for ontology terms
– More work on course of disease vs. disease
– Does a different course imply a different subtype?
• Avoid logical conjunction/disjunction of terms,
especially diseases and their complications
A DAY IN THE LIFE OF A DIRECTOR
OF MEDICAL VOCABULARY/
ONTOLOGY…
From: Fiorillo, Anthony MD
Sent: Monday, August 13, 2007 10:20 AM
To: Hogan, William R
Subject:
Bill FYI the limits of both ICD and SnowMed; I was unable to
find a dx specific to this patients new dx. Submucosal colonic
Leiomyoma. Here is a snap shot of the search:
Note that ICD9 assumes Leiomyoma occur only in the uterus
when they can occur any where there is smooth muscle!
A problem that the “finer
granularity” of ICD-10-CM does not
address, incidentally.
53 results in ICD-9-CM
and SNOMED-CT
combined. Mixture of
“Body structure” and
“Clinical Finding”.
Trying to be helpful, I conduct the
search also, and respond…
Although SNOMED does have Leiomyoma of stomach and
Leiomyoma of esophagus, it does not have even leiomyoma
of colon let alone a submucosal one.
…
Looks like the best you could do in either case is “Benign
tumor of the colon”, which isn’t terribly helpful.
The Final Outcome?
He is asymptomatic; found on screening colonoscopy. I used
an annotated SnowMed code 74391019
74391019 is Leiomyoma (body
structure)
It was 52nd of 53 search results.
The Issue(s)?
• Clinician reproducibility
– Some will choose body structure
– Some might choose clinical finding
– Few will care about the distinction, let alone try to
understand, or even succeed if they do
– Vendors obviously don’t care, either
• This user
– Cared about ontology (what the leiomyoma was)
– Didn’t care about epistemology (the fact that someone
found it on colonoscopy)