disease ontology: where we are kent a. spackman, md phd scientific director, snomed workshop on...

Disease Ontology:Where We Are

Kent A. Spackman, MD PhDScientific Director, SNOMED

Workshop on Disease OntologyBaltimore, MarylandNovember 6, 2006

Where we are from a SNOMED perspective

• The SNOMED terminology itself:

– SNOMED contains 62,697 active “disorder” codes (and another 12,087 “limited status” codes related to ICD)

– The terminology is freely available in the US, UK, Australia, and Denmark, and soon Canada, New Zealand, and other countries

– It is designated as the terminology for diseases by several US federal agencies (NCVHS, CHI, FDA – drug product labels)

– There is an open working group structure that invites your participation

– Formation of a new international SDO with transfer of intellectual property from the CAP is expected to result in even more openness, particularly in research

Potential formation of new SDO

Potential result of successful negotiation

International Health Terminology SDO

CAP

SNOMED CT IP & IPR

CAP Support Service

SDO Managed Support Services

Own Manage & Support the NON- SNOMED CT portfolio

Supply a Support Service

Open Market Derivative Products

New Technical Infrastructure

Is SNOMED an ontology?

• Depends on the definition of ontology• Prefer “controlled terminology” • Purpose:

– Recording statements about individual patients in electronic records, to be used for patient care (including documentation and decision support), health care administrative purposes, and research

• The content should be informed and shaped by formal ontological principles, but not limited only to the scope of a formal ontology

Defining “disease” is hard

• No consensus definition exists• No clear path to achieving such a

consensus is available to us– Medical community is fragmented and,

frankly, not that interested

• Probably best not to argue about the label, but instead define several (potentially overlapping) understandable, reproducible and useful categories

Codes, concepts and meanings

• One meaning per code– Concepts themselves are in people’s heads.– And the things (entities) that the concepts reference

via their meaning are in the real world.

• In talking about the terminology, we sometimes are sloppy in saying “concept” when we mean “code” or “meaning of a code”

Meaning, not language

• fundus• pyogenic granuloma• tumor• psoriasis• appendectomy• angiography• leg• anemia

URU criteria

1. Definitions should be Understandable by average clinicians, given brief explanations

2. We assess understandability by examining Reproducibility

3. We can ignore distinctions for which there is no Use in health care

What is a disease?

• Multiple definitions given on the workshop web site, some emphasizing:– Abnormality– Dysfunction– Etiology– Adverse consequences / risk– Treatment

Are these diseases?

• alcoholism• obesity• gambling addiction• menopause• jet lag• unhappiness• cellulite• hangover• anxiety about penis size• penis envy• pregnancy• childbirth• road rage• ignorance

• low IQ• bigotry• loneliness• ageing• overwork• boredom• bags under eyes• baldness• wrinkles• freckles• big ears• grey hair• ugliness

In search of "non-disease“. BMJ 2002;324:883-885

• BMJ 2002;324:883-885 ( 13 April )• In search of "non-disease"

• Richard Smith, editor.

• The BMJ recently ran a vote on bmj.com to identify the "top 10 non-diseases." Some critics thought it an absurd exercise, but our primary aim was to illustrate the slipperiness of the notion of disease. We wanted to prompt a debate on what is and what is not a disease and draw attention to the increasing tendency to classify people's problems as diseases.

These don’t work as a definition

• Anything coded by ICD

• Any abnormal clinical finding

• Any “disorder”

• Anything fitting the field “diagnosis”

Diagnosis

• Can be either a label or a process

• What is a valid result of the process, or a valid target of the label, varies widely with context

• NOT synonymous with disease

Diagnosis

• The meaning of “diagnosis” is highly variable and depends on context– “Diagnosis as a label (which really is its common usage in

clinical records) is a very different animal from the process. It is typically qualified by adjectival form such as "initial", "primary", "admission", "discharge", "differential", "working", "secondary", etc. According to the adjective it gains qualities which relate to administrative purposes (e.g. billing for "discharge diagnosis") or prompts a course of investigative action in others (e.g. "differential diagnosis" or "working diagnosis"). These uses have very different semantics from one another. They are not actions but are parts of the context surrounding the recording of a finding. … My view of this is that ‘diagnosis’ in all its flavours is an observation about another observation.” from an email by David Markwell on the HL7 vocab list.

What relationships define disease?

• An early attempt: the “axes” of the Systematized Nomenclature of Pathology, 1965– Topography– Morphology– Etiology– Function

Finding site

Causative agent

Associated morphology

Interprets

Acquired body structure, Anatomical concepts

Organism, Substance, Physical object, Physical force

Morphologically abnormal structure

Laboratory procedure, Observable entity, Patient evaluation procedure

Clinical finding attributesSNOMED CT, 2006

Due to

After Clinical finding, Procedure, event

Clinical finding, Event

Has interpretation Findings values, Result comments

Associated withClinical finding, Substance, Physical object, Physical force, Events, Organisms, Pharmacological / Biological product, Procedure

Clinical finding

Clinical finding attributes cont.

Has definitional manifestation

Occurrence

Pathological process

Clinical finding

Periods of life

Onset

Course

Episodicity

Sudden, Gradual

Courses

First episode, New episode, Ongoing episode

Severity

Finding method

Pathological process

Mild, Moderate, Severe

Clinical finding

Finding informer

Procedure

Performer of method, Subject of recordProvider of history other than subject,Subject of record or other provider of history

Diseases vs their manifestations

• 1) Should we always distinguish a disease from its manifestation? • 2) is the manifestation also a disease?

– Epilepsy, seizure.– Migraine headache disorder, migraine headache– Thrombotic disorder, thrombosis– Hypertensive disorder, hypertension– Anemia, low hemoglobin

– Laceration of forearm– Fracture of navicular bone of wrist– Cataract– Cogwheel rigidity– Spastic gait

“Disorders” vs “observations”

• Typically thought of as diseases and their manifestations• Observations are sometimes called findings, and sometimes

findings are separated from symptoms and/or signs– Important to realize the word “finding” is used in SNOMED to mean

things that can be observed or asserted to be present or absent, NOT assertions that they have in fact been observed or are present

• CTV3 (1993-97) separated disorders from observations/findings• SNOMED RT (2000-2001) had merged them due to lack of

reproducible criteria for separating them• SNOMED CT (2002- ) initially attempted to keep them separate,

then gave up and merged them• We have been unable to come up with a reproducible clean

distinction between findings and disorders

Findings & DisordersContinuants & Occurrents: Some Exploratory Ideas

CMWG October 2006

Current advice

• “Disorders are findings that are abnormal”

• Difficult to get reproducibility– Consensus of what is abnormal and what is not– Strong sense that an abnormal finding is not

necessarily a disorder– Words “finding” and “disorder” carry connotations that

are different depending on the context or individual

Findings & Disorders

• The finding/disorder distinction is not reproducible

• We should probably think about a different set of distinctions within the “clinical findings” hierarchy that helps us decide– One code or two?– Same or different?

• Examples: – anemia – low hemoglobin– Migraine (headache) disorder – migraine headache– Epilepsy – seizure

Some tentative categories:

Occ) occurrents (things that happen: exposures, accidents, events)

C0) continuants that may exist even when their defining characteristic(s) is/are not present (many disorders go here)

C1) continuants whose defining characteristics must always exist, i.e. it is possible for them to be observed/detected (by some method)

Some test cases (1)

• bleeding

• rash

• pharyngitis

• spasm


C0) continuants that may exist even when their defining characteristic(s) is/are not present

C1) continuants whose defining characteristics must always exist

Some test cases (1) – agree?

• bleeding = either Occ or C1, depending on what is meant (do you mean the process of bleeding, or the presence of blood that has escaped from the vascular system?)

• rash = C1 • pharyngitis = C1 • spasm = either Occ or C0, depending on what

is meant (the spasm occurrence, or the tendency to have repeated spasms)

Some test cases (2)

• deformities• abuse• victim of abuse

(status) • adhesions• hypothermia• anemia• low hemoglobin





• deformities = C1

• abuse = Occ

• victim of abuse (status) = C0

• adhesions = C1

• hypothermia = C1

• anemia = C0 (if you mean the category that includes aplastic anemia, etc)

• low hemoglobin = C1

Some test cases (3)

• thrombosis• tic• hemifacial spasm • anxiety• anxiety disorder





• thrombosis = C1

• tic = either Occ or C0, depending on whether you mean the occurrence of the tic, or the tendency for the tic to occur.

• hemifacial spasm = Occ or C0

• anxiety = C1

• anxiety disorder = C0

Some test cases (4)

• difficulty hearing• hearing disorder• vasovagal syncope• autoimmune

thrombocytopenia• low platelet count• low platelet count due

to autoimmune destruction





• difficulty hearing = C1 • hearing disorder = C0 • vasovagal syncope = Occ or C0, again depending on

whether you mean the event of fainting, or the tendency to faint

• autoimmune thrombocytopenia = C0. You can have autoimmune thrombocytopenia but have a transfused platelet level that is normal.

• low platelet count = C1 • low platelet count due to autoimmune destruction = C1

Some test cases (5)

• apnea in the newborn• secretory diarrhea• difficulty hearing due to

conductive hearing loss • lung cancer• malignant lung tumor





• apnea in the newborn = Occ or C0 • secretory diarrhea = C0, possibly Occ, depending on

what you mean. • conductive hearing loss due to disorder of external ear =

C0 (you still have it even if you put in a hearing aid that allows you to hear normally)

• difficulty hearing due to conductive hearing loss = C1 • lung cancer = C0 • malignant lung tumor = C1

Some test cases (6)

• loss of voice• sense of smell

altered• edema• calcified cataract• quadriplegia• pain• pain syndrome





• loss of voice = C1

• sense of smell altered = C1

• edema = C1

• calcified cataract = C1

• quadriplegia = C1

• pain = C1

• pain syndrome = C0

What to do about the “disorder” tag?

• Keep it – no change

• Revert to “finding” (the tag of the clinical finding hierarchy)

• Change it to a tag (or tags) with reproducible meaning

What is a disease?

Stedman's Concise Medical Dictionary for the Health Professions, 3rd Edition 1997. Williams and Wilkins:

1. An interruption, cessation, or disorder of body functions, systems, or organs.

Synonym: illness, morbus, sickness. 2. A morbid entity characterized usually by at least two of these criteria:

recognized etiologic agent(s), identifiable group of signs and symptoms, or consistent anatomical alterations.

See also: syndrome. 3. Literally, dis-ease, the opposite of ease, when something is wrong

with a bodily function

What is a disease?

• Wikipedia:– A disease is any abnormal condition of the body or mind that causes

discomfort, dysfunction, or distress to the person affected or those in contact with the person. Sometimes the term is used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function, while in other contexts these may be considered distinguishable categories

• So which are included and which aren’t?– Injuries: Paper cut? Skull fracture?

– Discomfort: ingrown hair? Psychogenic pain?

– Distress to those in contact with the person: bigotry, ignorance, low IQ?

What is a disease?

CanadaPharma.org• Any abnormality of bodily structure or function,

other than those arising directly from injury

Oregon State University, anthropology glossary:• a pathological condition that is cross-culturally

defined and recognized– excludes Karoshi, Gwarosa

disease ontology: where we are kent a. spackman, md phd scientific director, snomed workshop on...

Documents