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The Scientific & Technical Foundations of SNOMED Clinical Terms. Kent A. Spackman, MD PhD Scientific Director, SNOMED. October 2, 2006. The Scientific & Technical Foundations of SNOMED Clinical Terms Overview. Codes and classifications Basic principles of design for a clinical terminology

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the scientific technical foundations of snomed clinical terms

The Scientific & Technical Foundations of SNOMED Clinical Terms

Kent A. Spackman, MD PhD

Scientific Director, SNOMED

October 2, 2006

the scientific technical foundations of snomed clinical terms overview
The Scientific & Technical Foundations of SNOMED Clinical TermsOverview
  • Codes and classifications
  • Basic principles of design for a clinical terminology
    • evolution & convergence
  • Clinical statements & information models
  • Language, meaning, and ontology
  • Description logic & terminology models
  • Curation & change management
  • Technical standardization for
    • distribution, interchange & reference
the scientific technical foundations of snomed clinical terms overview1
The Scientific & Technical Foundations of SNOMED Clinical TermsOverview
  • Codes and classifications
  • Basic principles of design for a clinical terminology
    • evolution & convergence
  • Clinical statements & information models
  • Language, meaning, and ontology
  • Description logic & terminology models
  • Curation & change management
  • Technical standardization for
    • distribution, interchange & reference
codes
Codes
  • Most people have experience with coding systems where:
    • The primary purposes of coding are reimbursement and epidemiology
    • Coding is done using a pre-existing record
    • It follows rules designed to help you choose the one right code that best expresses the main diagnosis, or the main procedure done.
  • Double counting - for epidemiology or reimbursement - is a bad thing
codes for electronic health records
Codes for electronic health records
  • Coding is done without a pre-existing record, but rather to express statements about the patient, in order to create a coded record
  • Double counting is a good thing whenever the statement has fidelity to the clinical situation

Roger Côté

the scientific technical foundations of snomed clinical terms overview2
The Scientific & Technical Foundations of SNOMED Clinical TermsOverview
  • Codes and classifications
  • Basic principles of design for a clinical terminology
    • evolution & convergence
  • Clinical statements & information models
  • Language, meaning, and ontology
  • Description logic & terminology models
  • Curation & change management
  • Technical standardization for
    • distribution, interchange & reference
snomed s approach
SNOMED’s approach
  • Evolutionary design
  • Convergence
    • Authoritative sources should be integrated, not left scattered and incompatible
  • Clinicians determine meaning
  • URU understandable, reproducible, usable
  • Terminology model must interact with information models and knowledge bases
evolutionary design
Evolutionary design
  • Campbell, K, Cohn, S, Chute, C, Rennels, G, and Shortliffe, E. Gálapagos: Computer-based support for evolution of a convergent medical terminology. in AMIA Fall Symposium. 1996, pp. 269-273.
  • Campbell, K, Scalable methodologies for distributed development of logic-based convergent medical terminology. Methods of Information in Medicine, 37:426-439,1998.

Keith Campbell

evolutionary design 1
Evolutionary Design (1)
  • Evolution without pre-ordained design
  • Accumulation of desirable features
    • Evidence-based assessment
      • All of the scientific and technical foundations are subject to revision based on best evidence
    • Graceful evolution
      • “graceful” implies the preservation of the value of encoded data
  • Heterogeneity of perspectives
evolutionary design 2
Evolutionary Design (2)
  • Dealing with Scale
    • Participatory consensus-based approach
      • Experts must be involved
    • Semantics-based concurrency control
      • Description logic underpinnings
    • Configuration management tools
      • Exemplified by the “Galapagos” tool set
uru criteria for evolutionary changes
URU criteria for evolutionary changes
  • Definitions should be Understandable by average clinicians, given brief explanations
  • We assess understandability by examining Reproducibility
  • We can ignore distinctions for which there is no Use in health care
slide13

`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

clinicians determine meaning
Clinicians Determine Meaning
  • SNOMED is not the language police
  • We are not trying to tell people which words they should or should not use that’s up to the clinical professions
    • E.g. Should dermatologists still use the term “pyogenic granuloma” for the small blood vessel tumor that is neither pyogenic nor a granuloma?
  • We also are not trying to tell clinicians how to operationally apply meanings to specific cases again, that is up to the clinical professions
    • E.g. What systolic and diastolic limits should be used for determining whether a patient has hypertension 140/90 ?
integration of terminologies
Integration of Terminologies
  • SNOMED is also not duplicating the work of established official consensus groups
  • Instead, it is providing an integrated resource where the various terminologies are available for electronic interoperability applications. Examples:
    • The International Society for Blood Transfusion ISBT provides a set of codes and names for red cell antigens and their antibodies
    • The WHO periodically revises numerous classifications of malignant neoplasms
the scientific technical foundations of snomed clinical terms overview3
The Scientific & Technical Foundations of SNOMED Clinical TermsOverview
  • Codes and classifications
  • Basic principles of design for a clinical terminology
    • evolution & convergence
  • Clinical statements & information models
  • Language, meaning, and ontology
  • Description logic & terminology models
  • Curation & change management
  • Technical standardization for
    • distribution, interchange & reference
statements as the foundation of epr
Statements as the foundation of EPR
  • The electronic patient record is fundamentally about what is said (statements).
      • Rector AL, Nowlan WA, Kay S. Foundations for an Electronic Medical Record. Meth Inform Med 30:179-86, 1991.
      • Rector AL, Nowlan WA, Kay S, Goble CA, Howkins TJ. A framework for modelling the Electronic Medical Record. Meth Inform Med 32:109-19, 1993.
slide18

Clinical Decision Support Model

+ Inference Rules

Interface

Interface

Interface

Information Model

+ Patient Data Structures

Terminology Model

+ Compositional Expressions

Diagram based on Figure 1 in Rector AL et al. “Interface of Inference Models with Concept and Medical Record Models” AIME 2001: 314-323

slide19

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

+ Expressions

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

hl7 clinical statement model extract
HL7 Clinical statement model extract

ActRelationship

Informant

Observation

Patient

id

Performer

Substance

Administration

Author

RelatedEntity

DataEnterer

Supply

AssignedEntity

Verifier

Procedure

Encounter

RecordTarget

Patient

id

Act

RelatedEntity

Organizer

Subject

Specimen

ActReference

the scientific technical foundations of snomed clinical terms overview4
The Scientific & Technical Foundations of SNOMED Clinical TermsOverview
  • Codes and classifications
  • Basic principles of design for a clinical terminology
    • evolution & convergence
  • Clinical statements & information models
  • Language, meaning, and ontology
  • Description logic & terminology models
  • Curation & change management
  • Technical standardization for
    • distribution, interchange & reference
cimino s desiderata 1998
Cimino’s “desiderata” 1998
  • Cimino, J, Desiderata for controlled medical vocabularies in the twenty-first century. Methods of Information in Medicine, 37:394-403,1998.
  • Requirements that are a consequence of assuming the terminology is multi-purpose

Jim Cimino

codes concepts and meanings
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.
  • No duplicates
  • No ambiguous meanings
    • But the meaning of a code may be at a very broad level of generality
  • In talking about the terminology, we sometimes are sloppy in saying “concept” when we mean “code” or “meaning of a code”
formal ontological analysis
Formal ontological analysis
  • Rector AL, Rogers J, “Patterns, Properties and Minimizing Commitment: Reconstruction of the GALEN Upper Ontology in OWL",  Core Ontologies Workshop, EKAW 2004.
  • Smith B, Ceusters W, Kumar A, Rosse C, “On Carcinomas and Other Pathological Entities”, Comparative and Functional Genomics 6 (7-8): 379 - 387, 2005.
  • Rosse, C, et al, “A Strategy for Improving and Integrating Biomedical Ontologies”, Proceedings of AMIA Symposium 2005, Washington DC, 639–643.
formal ontological analysis1
Formal ontological analysis
  • Benefit:
    • Better definitions
    • More reproducibility
  • Possible danger:
    • Introduction of non-useful distinctions
    • Proliferation of codes
some ontological distinctions of value for refining snomed ct
Some ontological distinctionsof value for refining SNOMED CT
  • Continuant vs occurrent
  • Discrete vs mass
  • Individual vs collection/group
  • others
the scientific technical foundations of snomed clinical terms overview5
The Scientific & Technical Foundations of SNOMED Clinical TermsOverview
  • Codes and classifications
  • Basic principles of design for a clinical terminology
    • evolution & convergence
  • Clinical statements & information models
  • Language, meaning, and ontology
  • Description logic & terminology models
  • Curation & change management
  • Technical standardization for
    • distribution, interchange & reference
logic based definitions and the terminology model
Logic-based definitionsand the terminology model
  • Conceptual graphs
    • K. E. Campbell, A. K. Das, & M. A. Musen. A Logical Foundation for Representation of Clinical Data. Journal of the American Medical Informatics Association 13:218-232, 1994.
  • Description logic
    • Spackman KA, Campbell KE, and Côté RA, SNOMED-RT: A reference Terminology for Health Care. Journal of the American Medical Informatics Association Symposium special issue: pp. 640-644, 1997.
  • Read code semantic definitions
    • Price C, O’Neil M, Bentley TE, Brown PJB. Exploring the ontology of surgical procedures in the Read Thesaurus. Meth Inform Med 37:420-425, 1998.
    • Brown PJB, O’Neil M, Price C. Semantic definition of disorders in Version 3 of the Read Codes. Meth Inform Med 37:415-419, 1998.
description logic foundation in a nutshell
Description Logic FoundationIn a Nutshell:
  • SNOMED CT’s formal concept definitions are based on a description logic with the following features:
    • Conjunction
    • Existential restrictions
    • Role hierarchies
  • Plus “role groups”
  • Plus role composition “transfers-thru” or “right identity” or “restricted role-value maps”
    • Currently:
      • direct-substance o has-active-ingredient
dl basics
DL Basics
  • Concepts are given formal definitions
    • e.g. “Red car” is a kind of “Car”, and has color “Red”
    • e.g. “Lung disorder” is a kind of disorder, and has site “Lung”
  • Definitions are expressed in description logic
    • conjunction logical “and” п
    • existentially quantified role restrictions R.C
      • red_car = car п  color.red
      • lung_disorder = disorder п  site.lung
evolution of snomed s dl
Evolution of SNOMED’s DL

Notation follows Donini in Ch.3 Description Logic Handbook

Except here omeans restricted role-value maps

need for role groups
Need for Role Groups
  • When a single concept may have more than one value for a particular attribute
    • for example, “bone fusion with tendon transfer”
      • method = fusion, site = bone, and
      • method = transfer, site = tendon
  • And, one attribute-value pair needs to be associated with another.
    • How can we specify that the fusion is done to the bone and not to the tendon? and that the transfer is done to the tendon and not to the bone?
role grouping logical form a nested existential restriction
Role Grouping Logical Form: A Nested Existential Restriction
  • 9RG:(9R1:C1⊓ 9R2:C2) ⊓ 9RG:(9R3:C3)
  • Distributed as rows in relationships table:

CR3C3 0

CR1C1 1

CR2C2 1

right identity
Right Identity

Other names:

“restricted role-value maps”

“propagates via”

“transfers-thru”

“role composition”

R S⊑ R

xRy ⋀ySz →xRz

  • femurFracture site femur
  • headOfFemurFracture site headOfFemur
  • headOfFemur part-of Femur
  • Allows the automated inference that:
    • headOfFemurFracture is-a FemurFracture
description logic for anatomy
Description logic for anatomy

Avoiding right identity by using SEP triples

Liver Structure

XM0Ps Liver structure

T-62000 Liver

is-a

is-a

part-of

Liver Part

Entire liver

T-D0535 Liver part

7N330 Liver

is-a

Schulz, Romacker and Hahn: “Part-whole reasoning in medical ontologies revisited: Introducing SEP triplets into classification-based description logics”, Proc. AMIA Fall 1998.

Lobe of liver

example liver
SNOMED RT

T-62000 Liver

T-D0535 Liver part

CTV3

XM0Ps Liver structure

7N330 Liver

Example: Liver
  • How is T-62000 used in pathology?
    • The site of tumors and other morphologies
  • Does it necessarily mean the entire liver?
    • No
  • In what sense is 7N330 Liver a subtype of XM0Ps Liver structure?
    • XM0Ps means “the entire liver OR some part of the liver”
    • 7N330 means “entire liver”..
role hierarchies
Role Hierarchies
  • Equipment
    • Direct-device
    • Indirect-device
    • Using
    • Access-instrument
what dl classifiers can we use
What DL classifiers can we use ?
  • 1996: Kaiser Convergent Medical Terminology Project together with College of American Pathologists CAP
    • Kaiser Colorado used K-REP description logic classifier from IBM
  • 1999-present: UK NHS and CAP
    • K-REP developers moved on to Apelon Corp., developed Ontylog classifier
  • Recent successful experiments with other classifiers
    • 2005: Cel+
    • 2006: Fact++
    • ?others
snomed s concept model
SNOMED’s Concept Model
  • Top-level categories & FSN suffixes
  • Attributes
suffixes
Suffixes

Top Level Suffixes

administrative concept

body structure

situation

environment / location

event

finding

linkage concept

observable entity

organism

physical force

physical object

procedure

product

qualifier value

record artifact

social concept

special concept

specimen

staging scale

substance

suffix subtypes
Suffix subtypes

Parent SuffixChild Suffix

body structure cell structure

body structure cell

body structure morphologic abnormality

cell structure cell

environment / location environment

environment / location geographic location

finding disorder

linkage concept attribute

linkage concept link assertion

morphologic abnormality cell

person occupation

physical object product

procedure regime/therapy

qualifier value administrative concept

social concept ethnic group

social concept life style

social concept occupation

social concept person

social concept racial group

social concept religion/philosophy

special concept inactive concept

special concept namespace concept

special concept navigational concept

staging scale assessment scale

staging scale tumor staging

Suffix subtypes
clinical finding attributes
Clinical finding attributes

Acquired body structure, Anatomical concepts

Finding site

Associated morphology

Morphologically abnormal structure

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

Associated with

Clinical finding

After

Clinical finding, Procedure, event

Due to

Clinical finding, Event

Organism, Substance,

Physical object, Physical force

Causative agent

Has interpretation

Findings values, Result comments

Laboratory procedure, Observable entity, Patient evaluation procedure

Interprets

clinical finding attributes cont
Clinical finding attributes cont.

First episode, New episode, Ongoing episode

Episodicity

Pathological process

Pathological process

Sudden, Gradual

Onset

Course

Courses

Clinical finding

Has definitional manifestation

Clinical finding

Occurrence

Periods of life

Mild, Moderate, Severe

Severity

Procedure

Finding method

Performer of method, Subject of record

Provider of history other than subject,

Subject of record or other provider of history

Finding informer

examples of procedure attributes
Examples of procedure attributes
  • Procedure site
    • Specifies the site affected by a procedure
    • Relates “Procedure” and “Body structure”

Aortic aneurysm repair procedure

Procedure-site: Aortic structure body structure

examples of procedure attributes1
Examples of procedure attributes
  • Method
    • Specifies the action being performed to accomplish the procedure

Incision of ureter procedure

Method: Incision - action qualifier value

procedure attributes
Procedure attributes

Procedure site

Acquired body structure, Anatomical concepts

Procedure site - direct

Acquired body structure, Anatomical concepts

Procedure site - indirect

Procedure Morphology

Morphologically abnormal structure

Indirect morphology

Direct morphology

Procedure device

Device, Physical force

Procedure

Direct device

Device

Indirect device

Device

Using

Device, Physical force

Access instrument

Endoscope and subtypes

Method

Action

Direct substance

Substance, Pharmaceutical / biologic product

procedure attributes proposed 2007
Procedure attributes proposed 2007

Procedure site

Acquired body structure, Anatomical concepts

Procedure site - direct

Acquired body structure, Anatomical concepts

Procedure site - indirect

Procedure Morphology

Morphologically abnormal structure

Indirect morphology

Direct morphology

Procedure device

Procedure

Device

Direct device

Indirect device

Using device

Endoscope and subtypes

Using access device

Method

Action

Direct substance

Substance, Pharmaceutical / biologic product

slide51

Procedure

Procedure attributes cont.

Access

Surgical access values

Procedural approach

Approach

Priority

Priorities

Has focus

Clinical finding, Procedures

Has intent

Intents

Recipient category

Person, Family, Community, Donor

Route of administration value

Route of administration

Revision-value, Part of multistage procedure, Primary operation

Revision status

Has specimen

Specimen

Substance, Observable entity,

Cell structure

Component

slide52

Procedure

Procedure attributes cont.Proposed revisions for 2007

Using substance

Substances

Using energy

Physical forces

Surgical approaches

Surgical approach

Priority

Priorities

Has focus

Clinical finding, Procedures

Has intent

Intents

Recipient category

Person, Family, Community, Donor

Route of administration value

Route of administration

Revision-value, Part of multistage procedure, Primary operation

Revision status

Has specimen

Specimen

Substance, Observable entity,

Cell structure

Component

the scientific technical foundations of snomed clinical terms overview6
The Scientific & Technical Foundations of SNOMED Clinical TermsOverview
  • Codes and classifications
  • Basic principles of design for a clinical terminology
    • evolution & convergence
  • Clinical statements & information models
  • Language, meaning, and ontology
  • Description logic & terminology models
  • Curation & change management
  • Technical standardization for
    • distribution, interchange & reference
examples of commons based peer production efforts
Examples of commons-based peer production efforts
  • GNU free software foundation
  • LINUX
  • Wikipedia
  • NASA Clickworkers
success of commons based peer production depends on
Success of commons-based peer production depends on
  • modularity
  • granularity
  • cost of integration
commons based peer production
Commons-based peer production
  • Supplies criteria to assess
    • Processes, tools
  • Does not necessarily imply
    • Anarchy
    • Lack of defined processes
    • Poor quality
    • Disorganization
the scientific technical foundations of snomed clinical terms overview7
The Scientific & Technical Foundations of SNOMED Clinical TermsOverview
  • Codes and classifications
  • Basic principles of design for a clinical terminology
    • evolution & convergence
  • Clinical statements & information models
  • Language, meaning, and ontology
  • Description logic & terminology models
  • Curation & change management
  • Technical standardization for
    • distribution, interchange & reference
standardization of structures
Standardization of structures
  • Distribution format
    • ANSI standard
    • Includes specs for SNOMED CT Identifier:
      • Extension namespaces
  • XML schema for interchange
    • SNOMED Interchange Format SIF
  • Reference Set RefSet mechanism
distribution file structure standard
Distribution file structure standard
  • Initially finalized for 2002 release
  • Changes coming in 2007-2008
interchange format spec
Interchange format spec
  • Designed for communication between different development tools and a central configuration management environment
refsets
RefSets
  • Replaces old “subset” mechanism
  • Improved ability to handle internationalization
  • Improved navigational reference sets
  • Normalized data structures
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