SNOMED Clinical Terms:Concepts and Descriptions Kent A. Spackman, MD, PhD Oregon Health & Science University, Portland OR Chair, SNOMED International Editorial Board HL7 UK London – November 2004
Which concepts and which descriptions? • What is SNOMED CT? • What is it for? • How can it be used? • Relationship to information models, patient data • What is involved in developing & maintaining it? • Semantics • Design principles & logic foundation • Opportunities for having input
`I don't know what you mean by "glory,"' Alice said. Humpty Dumpty smiled contemptuously. `Of course you don't -- till I tell you. I meant "there's a nice knock-down argument for you!"' `But "glory" doesn't mean "a nice knock-down argument,"' Alice objected.`When I use a word,' Humpty Dumpty said in rather a scornful tone, `it means just what I choose it to mean -- neither more nor less.' `The question is,' said Alice, `whether you can make words mean so many different things.' `The question is,' said Humpty Dumpty, `which is to be master - - that's all.' From Through the Looking Glass, Lewis Carrol
What is it? • “The Systematized Nomenclature of Medicine”
What is it? • A reference terminology • A clinical terminology • with reference and interface properties • A CD containing a set of tables • A set of codes with names • A set of definitions “per genus et differentiam” • A clinical terminology standard • A knowledge base? • A dictionary? • An ontology? • An application ontology?
Formal Ontology? • SNOMED is not a formal ontology (but some parts of it are migrating in that direction) • It is a reference terminology that is progressively more well-supported by formal ontological principles • Includes terms and non-ontological assertions / ideas • I dislike the term “application ontology” – fish or fowl? • Many of SNOMED’s design decisions are supported by formal ontological principles. • But… • Many of SNOMED’s hierarchies are still “unprincipled” and incomplete. • Requires continued evolution and maturation
SNOMED Clinical Terms SNOMED Read Codes SNOMED 2 1979 1980 1981 1982 1983 Read Codes (v1) 1984 1985 1986 1987 1988 Professional Endorsement 1989 1990 Purchased by NHS 1991 1992 Clinical Terms Projects SNOMED 3 1993 “ 1994 “ 1995 CTV3 (Clinical Terms version 3) 1996 UK Gov’t Inquiries into Read Codes CAP business plan 1997 “ 1998 “ NHS Agreement1999 CAP Agreement SNOMED RT 2000 2001 2002 SNOMED – CTV3 Timelines Formation of the SNOMED International Division of the C.A.P.
SNOMED CT Releases 1st Jan 31, 2002 2nd July 31, 2002 3rd Jan 31, 2003 4th July 31, 2003 5th Jan 31, 2004 6th July 31, 2004 . . .
Emergence as a Standard:Recent Events • Government Actions – US and UK • US National License • ANSI – Terminology Distribution Structure Standard • US NCVHS – HIPAA recommendation • US Government CHI Initiative recommendation • UMLS release • UK NPfIT adoption
What does it do? • SNOMED CT is a terminological resource that can be implemented in software applications to represent clinically relevant information • In a “semantically structured” form that can be used by automated applications
What is it for? • It is for building applications capable of: • Recording statements about the health and health care of individuals • In a way that permits retrieval according to the meaning of the statements, rather than just the words used • Retrieving individual cases and groups of cases • To enable more automated and sophisticated decision support, epidemiology, and research
Successful use of SNOMED CT depends on: • Implementation in clinical records systems • Which in turn requires (at least) a patient data model (information model)
The simplest information model • Put all clinical data here ___________________ The simplest terminology model • Two values: • Yes • No Intermediate between these extremes there are many possible solutions!
IF Two blood cultures, drawn through an antibiotic removal device, more than 30 minutes apart, grow no organism, THEN discontinue antibiotic. What about clinical decision support?
IFTwoblood cultures, drawn through an antibiotic removal device, more than 30 minutes apart, growno organism, THENdiscontinueantibiotic. procedures finding device
Clinical Decision Support Model + Inference Rules Interface Interface Interface Information Model + Patient Data Structures Terminology Model + Coded Data Diagram based on Figure 1 in Rector AL et al. “Interface of Inference Models with Concept and Medical Record Models” AIME 2001: 314-323
Clinical Decision Support Model + Inference Rules IFTwoblood cultures, drawn through Antibiotic removal device, more than 30 minutes apart, grows no organism, THENdiscontinueantibiotic. Interface Interface Interface HL7 RIM SNOMED CT Information Model + Patient Data Structures Terminology Model + Coded Data What test was performed? How many were done? At what time? What device was used? What was the result of the test? 30088009 blood culture 55512120 antibiotic removal device 264868006 No growth 281789004 antibiotic therapy 223438000 advice to discontinue a procedure Diagram based on Figure 1 in Rector AL et al. “Interface of Inference Models with Concept and Medical Record Models” AIME 2001: 314-323
What is involved in creating and maintaining SNOMED CT? • Representation of meaning • Judgments of “same or different” • Representing clearly “what clinicians mean when they say …”
It is notoriously difficult to tell what people mean just by what they say • From “The Economist”, Charlemagne column, Sept 4, 2004 • “Decoding a Euro-diplomat takes more than a dictionary” • “Up to a point” means “I agree in part”? Wrong, it means: • “No, not in the slightest” • “I hear what you say” means “He accepts my point of view”? Wrong, it means: • “I disagree and do not want to discuss it any further” • “With the greatest respect” means • “I think you are wrong, or a fool” • “By the way” or “incidentally” means “This is not very important”? Wrong, it means • “The primary purpose of our discussion is …” • “I’ll bear it in mind” “I’ll do nothing about it” • “Correct me if I’m wrong” “I’m right, don’t contradict me”
Discerning and representing meaning of health terminology is difficult • What is juvenile rheumatoid arthritis? • Seropositive chronic idiopathic arthritis in child < 16 yrs ? • Any chronic arthritis in child < 16 yrs? • Is Adult-onset Still’s disease included? • Three different published terminology standards, all incompatible • JRA (juvenile rheumatoid arthritis) – US • JCA (juvenile chronic arthritis) – UK • JIA (juvenile idiopathic arthritis) – International
Words alone are insufficient • There are national, regional and local variations in meaning of words and phrases (even within the same language) • Multiple meanings with the same “preferred name” • Combining words gives something entirely different from the sum of the parts • Ambiguous shorthand and abbreviations are common • The same phrase means different things to different specialists • The same word or phrase means different things depending on what you are doing at the time • Significant differences in meaning are often obscured through use of the same word • Formal definitions are often at variance with common clinical usage • A general name takes on a more specific meaning • A manifestation is often used to name the disorder in which it occurs • Successful communication relies on making ontological distinctions that are ignored by common phrasing
What is “pudding”? • At dinner in Phoenix, Roger (from the UK) asked “Is anyone having pudding?” • To which I replied, “Do you mean dessert?” • And he said, “No, I mean pudding.” ? Within the same language there are significant national, regional and local variations
What is “scalp”? • scalp: the skin covering the cranium (Stedman’s) • scalp: the soft tissue envelope of the cranial vault, consists of 5 layers: the skin, connective tissue, epicranial aponeurosis + occipitofrontalis muscle, loose areolar tissue, and pericranium. (Gardner, Gray & O’Rahilly, anatomy text) • Epicranium (Stedman’s): the muscle, aponeurosis and skin covering the cranium It is quite clear SNOMED must have two different codes (two different Meanings) that bear the name “scalp” We say like Humpty Dumpty “When I use the word scalp, …”
What is a “pyogenic granuloma?” • Pyogenic = pus forming • Granuloma = a collection of inflammatory cells of a particular type • Pyogenic granuloma = a benign tumor of small blood vessels of the skin • It is neither pyogenic nor a granuloma. Combinations are frequently very different from the sum of their parts
What is “general paresis”? • General = affecting all skeletal muscles • Paresis = weakness • GPI = a form of tertiary neurosyphilis characterized by generalized weakness Shorthand and abbreviations are common
What is “acute inflammation”? • To the GP, it is inflammation with an acute onset, characterised by redness, heat, swelling and pain. • To the pathologist, it is inflammation in which polymorphonuclear leukocytes predominate, as opposed to chronic inflammation, in which “mononuclear cells” (lymphocytes, plasma cells, monocytes, histiocytes) predominate. The same phrase can mean different things to different specialists
What is the “fundus”? • When caring for a pregnant patient – • When examining the eyes – • When doing a gastroscopy – • When doing a cholecystectomy – What you are doing at the time changes the meaning of words
Is there an error in this hierarchy? Radiographic procedures Angiography procedures Magnetic resonance angiography procedures
Is there an error in this hierarchy? Radiographic procedures Angiography procedures Magnetic resonance angiography procedures It is common for a general name to acquire a more specific meaning
Is there an error in this hierarchy? psoriasis psoriasis with arthropathy juvenile psoriatic arthritis juvenile psoriatic arthritis without psoriasis
It is common for the disorder to be named by its manifestation Is there an error in this hierarchy? psoriasis psoriasis with arthropathy juvenile psoriatic arthritis juvenile psoriatic arthritis without psoriasis
What is a “laceration”? • Torn or jagged wound vs • Accidental cut wound • Perineal laceration during O-P delivery • vs • Laceration of thumb while using kitchen knife Subtle distinctions are often implicit
What is the “leg”? • 1) same as “lower limb” • 2) just the part from the knee to the ankle • Stedman’s “the segment of the inferior limb between the knee and the ankle” • Dorland’s “that section of the lower limb between the knee and ankle” Some formal definitions are in conflict with ordinary usage
What does “aspirin” mean? • Some aspirin – the chemical ASA • An aspirin – a tablet containing ASA Formal ontologists insist on a clean distinction between the individual and the matter or stuff of which it is made.
How does SNOMED address these issues? • Careful representation of meaning • Evolutionary design • Formal description logic foundation • Consensus process • URU criteria: understandable, reproducible, useful
Evolutionary Design • Evolution without pre-ordained design • Accumulation of desirable features • Heterogeneity of perspectives • Dealing with Scale • Participatory consensus-based approach • Involve the experts • Semantics-based concurrency control • Description logic underpinnings • Configuration management tools • Keith Campbell’s “Galapagos” tool set
Description Logic Foundation • SNOMED is based on the description logic known as ELH • Conjunction • Existential restrictions • Role hierarchies • Plus “role groups” (see 2002 AMIA paper) • Plus role composition • So far, only one: direct-substance o has-active-ingredient
How large is large? • With 800,000+ terms in SNOMED CT • if you spent 5 seconds looking at each one it would take you • 4 million seconds = 66,666 minutes = 1,111 hours • 138 work days if that’s all you did every day • 138/5 = almost 28 work weeks • At SNOMED we don’t just pretend to know about the problems of scale. • That’s not saying we think we’ve solved them.
Number of attributes (relationship types) in the SNOMED concept model
Percentage of SNOMED CT concept codes that are “fully defined” Eventually should reach ~70% or more of disorders, findings & procedures
How long will it take? • That depends on what you want: • It is ready for use now. • If you wait for perfection you wait forever. • But tell us what needs the most urgent attention.
SNOMED phases • 1975-1994 Roger Cote phase • 1995-1997 Kaiser CMT phase • 1997-1999 CAP phase – building SNOMED RT • 1999-2002 SNOMED – Read merge phase • 2002-2004 US/UK endorsement phase • 2004- adoption, use & maintenance phase • The hardest part is still ahead
There is opportunity to be involved • Open working group meetings + on-line discussion forums • Active working groups: • Concept model working group • Mapping working group • Content-area focused working groups • Primary care • Nursing • Genomics • Anesthesiology, pathology, dermatology, ophthalmology, … • Upcoming in-person meeting dates: • Feb 2, 2005, S. California • June 14-15, 2005, Chicago • Oct 5, 2005, London
Concept Model Working Group issues: • Context • Negation • Composition (“post-coordination”) • Interface between concept model & information model • Specifically interface between SNOMED & HL7 v3 • Proposed work item (or possible SIG) with HL7 vocab