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0 An Introduction To Snomed Ct1

Abbas Shojaee MD, CHDA, profile picture
Abbas Shojaee MD, CHDA

SNOMED CT is a clinical terminology used for coding, retrieving, and analyzing health care data. It consists of codes, terms, and relationships that can precisely record and represent clinical information across health care. SNOMED CT concepts are organized into hierarchies and linked through relationships. It aims to enable automated clinical decision support and research by structuring information in a semantically meaningful way.

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SNOMED CT & HL7 Terminology BindingDr. Abbas Shojaee – BUMS, June 2010This presentation uses works of:Tim BensonIan HorrocksKent A. Spackman
VocabularySyntactic: شکليSemantic:معنايي Lexical: واژه شناسي، وابسته به واژه Homonym: اشاره يک واژه به چند معناSynonym:هم معنايي، اشاره چند واژه به يک معني
PresentationWhat is interoperability?What is SNOMED CT?Uses of SNOMED CTSNOMED Standard Development Organisation (SSDO)- Why the change/why join?- What is the current situation?The role of WHOConclusions
Definition
SNOMED CT5The Systematized Nomenclature of Medicine – Clinical Terms
6SNOMED CT“SNOMED Clinical Terms (SNOMED CT) is a dynamic, scientifically validated clinical health care terminology and infrastructure that makes health care knowledge more usable and accessible. The SNOMED CT Core terminology provides a common language that enables a consistent way of capturing, sharing and aggregating health data across specialties and sites of care. Among the applications for SNOMED CT are electronic medical records, ICU monitoring, clinical decision support, medical research studies, clinical trials, computerized physician order entry, disease surveillance, image indexing and consumer health information services.”http://www.snomed.org/snomedct/index.html
Motivation
Why SNOMED CT might be of my interest?Archimedes: “Give me a place to stand and a lever long enough and I will move the world”This lever to mathematicians is Numbers, they try to percept and move the world through numbers.This lever to medical knowledge and information workers, is going to appear in SNOMED CT or its successors.
ORIGIN and HISTORYSNOMED CT
SNOMEDSNOMED® International:The division of the College of American Pathologists responsible for maintenance and release of SNOMED CTSNOMED CTReleases twice yearly (January & July) of the terminology commonly called SNOMED
Development of terminologiesSNOMED CT2000SNOMEDRTREAD 3 (CTV3)1990READ 2SNOMED 3Read 4 byte1980SNOMED 21970SNOP
SNOMED Clinical TermsSNOMED – CTV3 Timelines SNOMED Read CodesSNOMED 21979 - 19821983 Read Codes (v1) 1984 1985 1986 1987 1988 Professional Endorsement 1989 1990 Purchased by NHS 1991 1992 Clinical Terms ProjectsSNOMED 31993 , “ 1994 “ 1995 CTV3 (Clinical Terms version 3) 1996 UK Gov’t Inquiries into Read Codes CAP business plan 1997 “ 1998 “NHS Agreement1999 CAP AgreementSNOMED RT 2000 2001 2002Formation of the SNOMED International Division of the C.A.P.
SNOMED HistorySNOP – 1965 – basis for ICD-O SNOMED – 1974 SNOMED II – 1979 SNOMED Version 3.0 – 1993 SNOMED Version 3.5 – 1998 SNOMED RT – 2000 (Merge with UK NHS)SNOMED CT (SNOMED RT + CTV3) – 2002 SNOMED CT Spanish Edition – April 2002 SNOMED CT German Edition - April 2003 Free in USA - Agreement with NLM – June 2003SNOMED SDO Proposal 2006
User distribution - SNOMED CT Users
What is SNOMED CTEssence
What is it?A reference terminologyA clinical terminology with reference and interface properties A CD containing a set of tablesA set of codes with namesA set of definitions “per genus et differentiam”A clinical terminology standardA 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 principlesIncludes terms and non-ontological assertions / ideasI 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
What is an Ontology?
What is an Ontology?A model of (some aspect of) the world
What is an Ontology?A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:Anatomy
What is an Ontology?A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:AnatomyCellular biology
What is an Ontology?A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:AnatomyCellular biologyAerospace
What is an Ontology?A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:AnatomyCellular biologyAerospaceDogs
What is an Ontology?A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:AnatomyCellular biologyAerospaceDogsHotdogs…
What is a Clinical Terminology?Ordinarily:A finite enumerated set of terms intended to convey information unambiguouslySNOMED is more than thisTerms plus codes plus the ability to put them together in meaningful ways
What is SNOMED CT?A work of clinical terminology for coding, retrieving and analyzing data about health and health careComprised of codes, terms and relationships, for use in precisely recording and representing clinical information across the scope of health careConcept-based: Each code represents a single meaning and can have multiple descriptions (terms)
What is notSNOMED is not the language policeClinicians determine what words mean by how they use them. SNOMED reflects those meanings.SNOMED is not an independent source of scientific/professional practice standardsScientists and professional groups define their standards. We try to follow those standards.SNOMED is not a comprehensive knowledge base for healthcareThis is out of scope. SNOMED’s goal is terminological knowledge: that which is always necessarily true of a term.
What does it do?SNOMED CT is a terminological resource that can be implemented in software applications to represent clinically relevant informationIn 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 individualsIn a way that permits retrieval according to the meaning of the statements, rather than just the words usedRetrieving individual cases and groups of casesTo enable more automated and sophisticated decision support, epidemiology, and research
Pictures can also be presented more dramatically in widescreen.Desiderata for a global terminology
Desiderata for a global terminologyComprehensiveness:Coverage for all aspects of health careAdequacy:Is it fit or purpose – multiple purposes?Does it have a good information model and ontological basis?Multilingual applicabilitylanguage independent formal concept representationRepresentation in multiple languages – more than translationUtility:Is it beneficial for: Care providers : decision making, outcome evaluation Consumers : participation – ownership – evaluation – risk reductionPolicy/Decision Makers : informed decision making on costs, benefits, efficiencyReliability:does it give the same results in different usersSource: T. Ustun, WHO, SNOMED Semantic Mining Conference, Copenhagen, Oct. 2006
Desiderata for a global terminology Validity:Does it indicate the right things – and does the indication make senseComparabilityDoes the data in different context have same properties to be comparedInteroperabilityTechnical: Can information systems exchange information and use it? Semantic: Can information systems interpret the data with the same meaning? Quality AssuranceProduct: Annotation and ContentProcess: Use and UsabilitySustainabilitySecured maintenance: commitment to stability with earlier versions Openness to address emerging technical issuesSource: T. Ustun, WHO, SNOMED Semantic Mining Conference, Copenhagen, Oct. 2006
SNOMED CT StructureHierarchiesParent child relationshipsVertical structureConcepts may have multiple parentsRelationships between conceptsUsing attributes, concepts may be linked to each otherHorizontal relationships
Healthcare systems includedICD9-CMICD-V2-OncologyLOINCOphthalmology-related termsSystematized Nomenclature of DentistrySM of Vet Med NANDA Taxonomy IINursing Interventions ClassificationNursing Outcomes ClassificationPeri-operative Nursing Data SetThe Omaha SystemThe Georgetown Home Health Care Classification
SNOMED CT Structural componentsSNOMED CT is composed of components, which include concepts, relationships, descriptions, subsets, and cross maps, Each of which is identified by a SNOMED CT Identifier (SCTID) and has a validity status.
Components of SNOMED CT ConceptsThe basic units of SNOMED CTDescriptionsThese relate terms that name the concepts to the concepts themselves. Each concept has at least two Descriptions.HierarchiesConcepts are organized into twenty SNOMED CT hierarchies (in UK extension). Each hierarchy has sub-hierarchies within it.RelationshipsRelationships are the connections between concepts in SNOMED CT.+ mappingsMany-to-many mappings to terms in ICD and OPCS+ Inclusion of Dictionary of Medicines and Devices
SNOMED Clinical Terms Identifier (SCTID)The SCTID is a 64 bit integer- between 6 and 18 digits long.All components are identified using a special SCTID.
Validity StatusAn important principle of SNOMED CT is that of permanence. Once a component such as a concept or description has been created it is never deletedStatus codes:Active: Current (0), Limited (6), Pending move (11)Inactive: Retired (1), Duplicate (2), Obsolete (3), Ambiguous (4), Erroneous (5),Inappropriate (7), Inactive concept (8), Implied (9), Moved elsewhere (10)
ConceptsSNOMED CT is concept-orientedA concept is just a clinical idea to which a unique ConceptID that is a SCTIDConcepts are formally defined in terms of their relationships with other concepts:Subtype relationship: Concept Z IS_A concept YAttribute relationship
Content of SNOMED CT: Organized in 19 different hierarchiesThese are indeed high level concepts SNOMED CT : Root conceptClinical FindingProcedureObservable entityBody structureOrganismSubstancePharmaceutical/biology productSpecimenPhysical objectPhysical forceEventsEnvironments/Geographical locationsSocial ContextContext-dependent categoriesStaging and scalesAttributeQualifier valueSpecial concept
Concept ExampleGastric ulcer(SCTID397825006)Terms:Gastric ulcer (disorder)Gastric ulcerStomach ulcerGU – Gastric ulcerGastric ulcerationRelationships:Is_a Disease of stomachIs_aGastrointestinal ulcer Associated morphology  Ulcer Finding site  Stomach
DescriptionsEach description has a DescriptionIDwhich is a SCTIDEach description links a human-readable term with a concept.Every concept has at least two descriptions: Fully specified name (FSN) : is a phrase that names a concept in a way that is both unique and unambiguousPreferred term:the common phrase or word used by clinicians to name a conceptEach concept may have several other descriptions: e.g. synonyms, translations
RelationshipsRelationships are at the heart of SNOMED.More than 1.3 millionEach relationship is defined as an object-attribute-value triple. The object is the source concept (the one that has the relationship) (ConceptID1). The attribute specified the type of relationship and is also a SNOMED CT concept. The value is the target.Concept: attribute = value (e.g. Gastric ulcer(SCTID397825006)Is_a Disease of stomach)SNOMED CT Components
SNOMED Clinical Terms Identifier (SCTID)A 64 bit integer - between 6 and 18 digits long.
SNOMED CT Hierarchies
Lets bypass the rest of SNOMED CT structures
SNOMED CT ExpressionsClinical records are created for the purpose of providing information about events or states of affairs.A SNOMED CT expression is a collection of references to one or more concepts used to express an instance of a clinical idea. pre-coordinateda single concept identifier is used to represent a clinical ideaPost-coordination representation of a clinical meaning using a combination of two or more codes
SNOMED CT expression
SNOMED CT Expressions: Sample|50043002 | disorder of respiratorysystem |+ 87628006 | bacterial infectious disease |:246075003 | causative agent | = 9861002 | streptococcus pneumoniae|, 363698007 | finding site | = (45653009 | structure of upper lobe of lung | : 272741003 | laterality | = 7771000 | left |)
Documentation
SNOMED CT Documentation: User GuideExplains the content and the principles used to model the terminology.Intend: To explain SNOMED CT’s capabilities and uses from a content perspective.Audience: clinical personnel, business directors, software product managers, and project leaders; information technology experience, though not necessary, can be helpful.
SNOMED CT Documentation: Technical Reference Guide (TRG)Contains reference material related to the current release of SNOMED CT and includes file layouts, field sizes, required values and their meanings, and high-level data diagrams.Audience: for SNOMED CT implementers, such as software developers. assumes an information technology background , clinical knowledge is not a prerequisite.
SNOMED CT Documentation: Technical Implementation Guide (TIG)Contains guidelines and advice about the design of applications, terminology services, entering and storing information, and migration of legacy information.Audience: for SNOMED CT implementers, such as software designers. assumes information technology and software development experience. Clinical knowledge is not required, although some background is helpful to understand the application context and needs
CLINI ClueBROWSER
Pulmonary Tuberculosiskind of pneumonitiskind of tuberculosiscaused by Mycobacterium tuberculosis complexkind of Pulmonary disease due to Mycobacteriafound in lung structure
Employing SNOMED CT
What about clinical decision support?IF Two blood cultures, drawn throughan antibiotic removal device, more than 30 minutes apart, grow no organism,THEN discontinue antibiotic.
proceduresIFTwoblood cultures, drawn throughan antibiotic removal device, more than 30 minutes apart, growno organism,THENdiscontinueantibiotic.findingdevice
Clinical Decision Support Model + Inference RulesInterfaceInterfaceInterfaceInformation Model+ Patient Data StructuresTerminology Model+ Coded DataDiagram 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 RulesIFTwoblood cultures, drawn throughAntibiotic removal device, more than 30 minutes apart, grows no organism,THENdiscontinueantibiotic.InterfaceInterfaceInterfaceHL7 RIMSNOMED CTInformation Model+ Patient Data StructuresTerminology Model+ Coded DataWhat 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 device264868006 No growth281789004 antibiotic therapy223438000 advice to discontinue a procedureDiagram based on Figure 1 in Rector AL et al. “Interface of Inference Models with Concept and Medical Record Models” AIME 2001: 314-323
Using SNOMED CT and HL7 togetherwe cannot separate the issues of information structure from those of terminology.We cannot slot any terminology into any data structure and expect it to work.SNOMED CT was designed to be syntax-neutral, so it could work with any syntax.HL7 RIM and set out to be terminology-neutral.
Benefits of
InteroperabilityIn the context of e-health, interoperability is the way in which reliable data is provided and communicated in a secure, accurate and efficient way. It has to surmount the barriers of national policies, culture, language and systems of medical knowledge representation and use of ICT’s.Towards Interoperable eHealth for Europe. Telemedicine Alliance. BR255, November 2005
Classifying and Coding, which is more important?Coding means understanding?Assigning codes to concepts.Identifying the concepts.Clarifying them.Dealing with homonyms, synonyms and overlapsEnables us to identify and document interrelationshipsThis is indeed
SNOMED CT is the most comprehensive, multilingual clinical healthcare terminology in the world.The value of SNOMED CT can only be realized when it is built into software and systems that are designed around itKent Spackman:The first rule of data quality is that the quality of data collected is directly proportional to the care with which options are presented to the user. The first rule of coding is that yesterday’s data should be usable today.Heterogeneity of healthcareHealtcare data need to be permanent
SNOMED CT at 2009SNOMED Reference Terminology ® Clinical Terms Version 3®310,000 health care concepts990,000 synonyms and English descriptions1.38 million semantic relationshipsICD 10 contains 10760 concepts coming in three large volumes
Content, Content, Content
Standardized Healthcare LanguagesNeed for a normalized healthcare vocabulary. Across settings, applications, datasets. SNOMED CT, UMLS.
Problems of SNOMED CT
Percentage of SNOMED CT concept codes that are “fully defined”Eventually should reach ~70% or more of disorders, findings & procedures
7202.10.2006Gergely Héja - SMCS2006Error types - 1Misplacing concepts in the hierarchy
smoker (an agent) is subsumed by tobacco smoking behaviour – finding (a role)
severe asthma is not a kind of asthma, but a kind of asthma finding.
Mixing the subsumption relation with other roles (typically part of)
haemoglobin subsumes haemin (instead of constitutional part)
exacerbation of asthma attack is subsumed by asthma (instead of temporal part)7302.10.2006Gergely Héja - SMCS2006Error types - 2Hierarchy violating medical thinking and biomedical knowledge
Disease, observation and finding are subsumed by clinical finding
acute on chronic, which is both subsumed by acute and chronic
polycarbonate is a polymer (instead of synthetic polymer)7402.10.2006Gergely Héja - SMCS2006Error types - 3Contracting disjoint entities into one concept
Smoker (an agent) and smoker (finding) (a description of a situation)
additional pathologic finding in tumor specimen (observable entity) and additional pathologic finding
Function is classified as an observable entityOntological definition: ability of an object to play a certain role in a certain kind of activityfunctions (e.g. gene function,adaptation) measures (quality) that evaluate the realisation of a function (e.g. respiratory rhythm, excretory rate)Inflammation (morphological abnormality) (a physical object) and inflammatory reaction (perdurant)7502.10.2006Gergely Héja - SMCS2006Additional problems - 1Categories taken form classification systemspneumonia in other diseases classified elsewhere (marked as “ConceptStatus Limited”) The danger of taking over concepts from other conceptual systems: the context of the concept is lost. What is meant by “other diseases classified elsewhere”? relations (such as part of) are represented also as conceptsIt prohibits the direct conversion to any formalism based on first order logic, thus to any DL formalism
7602.10.2006Gergely Héja - SMCS2006Additional problems - 2Underspecification:roles are not quantified (existential / universal)criteria are not specified (necessary / sufficient)conversion to DL: do we have to decide in each particular case, or can it be done universally?Multiple hierarchyalcoholic beverage (through its parent ingestible alcohol) is subsumed by central depressant, ethyl alcohol and psychoactive substance of abuse – non-pharmaceutical. Alcoholic drinks contain ethyl alcohol, which plays a role of depressant and substance of abuse (with respect to human beings)Is this a general phenomenon in SNOMED?Which relations are asserted and which are inferred?
7702.10.2006Gergely Héja - SMCS2006Discussion - 1The intended meaning of the categories is not always clear: possible translation errorsIs it reasonable to import categories from medical classifications? SizeArtificial conceptsConsistency errors
7802.10.2006Gergely Héja - SMCS2006Discussion - 2Real world entities listed heterogeneouslyMars bar and Kit Kat (chocolate candy would suffice)UFO is subsumed by transport vehicletendon pulley reconstruction is represented, but tendon pulley not
Solutions02.10.2006Gergely Héja - SMCS200679Use SNOMED as a plain or loosely structured list of terms (with extending the coverage). Not appropriate for intelligent services.
Restructure SNOMED into a high-quality ontology.
Build a new medical ontology from scratch (partial reuse of the existing ones), and to restrict the use of SNOMED for interoperability by mapping concepts to it. Restructuring SNOMED02.10.2006Gergely Héja - SMCS200680A formal top level ontology (e.g. DOLCE).A high level core reference ontology of general medical knowledge (e.g. anatomy, physiology, pathology, medical procedures).Logic-based formalismSingle hierarchies with formal definitions(sub)domain ontologies of specialitiesCompound entities (e.g. tonsillitis)Manual assertion (e.g. autism)
Future Researches
Some Research ChallengesExtend saturation-based techniques to non-Horn fragmentsSNOMED users want negation and/or disjunctionNon infectious PneumoniaInfectious or Malignant disorder of lungBurn injury of face neck or scalpExtend reasoning supportModularityExplanation...
Some (more) Research ChallengesOpen questions w.r.t. query rewritingFO rewritability (AC0) only for very weak ontology languagesEven for AC0 languages, queries can get very large (order ), and existing RDBMSs may behave poorlyLarger fragments require (at least) Datalog engines and/or extension to technique (e.g., partial materialisation)Integrating DL/DB researchOntologies -v- dependenciesOpen world -v- closed world
Widescreen Test Pattern (16:9)Aspect Ratio Test(Should appear circular)4x316x9
85SNOMED CT hierarchy
Why Care About Semantics?Herasy!Herasy!Herasy!

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0 An Introduction To Snomed Ct1

  • 1. SNOMED CT & HL7 Terminology BindingDr. Abbas Shojaee – BUMS, June 2010This presentation uses works of:Tim BensonIan HorrocksKent A. Spackman
  • 2. VocabularySyntactic: شکليSemantic:معنايي Lexical: واژه شناسي، وابسته به واژه Homonym: اشاره يک واژه به چند معناSynonym:هم معنايي، اشاره چند واژه به يک معني
  • 3. PresentationWhat is interoperability?What is SNOMED CT?Uses of SNOMED CTSNOMED Standard Development Organisation (SSDO)- Why the change/why join?- What is the current situation?The role of WHOConclusions
  • 5. SNOMED CT5The Systematized Nomenclature of Medicine – Clinical Terms
  • 6. 6SNOMED CT“SNOMED Clinical Terms (SNOMED CT) is a dynamic, scientifically validated clinical health care terminology and infrastructure that makes health care knowledge more usable and accessible. The SNOMED CT Core terminology provides a common language that enables a consistent way of capturing, sharing and aggregating health data across specialties and sites of care. Among the applications for SNOMED CT are electronic medical records, ICU monitoring, clinical decision support, medical research studies, clinical trials, computerized physician order entry, disease surveillance, image indexing and consumer health information services.”http://www.snomed.org/snomedct/index.html
  • 8. Why SNOMED CT might be of my interest?Archimedes: “Give me a place to stand and a lever long enough and I will move the world”This lever to mathematicians is Numbers, they try to percept and move the world through numbers.This lever to medical knowledge and information workers, is going to appear in SNOMED CT or its successors.
  • 10. SNOMEDSNOMED® International:The division of the College of American Pathologists responsible for maintenance and release of SNOMED CTSNOMED CTReleases twice yearly (January & July) of the terminology commonly called SNOMED
  • 11. Development of terminologiesSNOMED CT2000SNOMEDRTREAD 3 (CTV3)1990READ 2SNOMED 3Read 4 byte1980SNOMED 21970SNOP
  • 12. SNOMED Clinical TermsSNOMED – CTV3 Timelines SNOMED Read CodesSNOMED 21979 - 19821983 Read Codes (v1) 1984 1985 1986 1987 1988 Professional Endorsement 1989 1990 Purchased by NHS 1991 1992 Clinical Terms ProjectsSNOMED 31993 , “ 1994 “ 1995 CTV3 (Clinical Terms version 3) 1996 UK Gov’t Inquiries into Read Codes CAP business plan 1997 “ 1998 “NHS Agreement1999 CAP AgreementSNOMED RT 2000 2001 2002Formation of the SNOMED International Division of the C.A.P.
  • 13. SNOMED HistorySNOP – 1965 – basis for ICD-O SNOMED – 1974 SNOMED II – 1979 SNOMED Version 3.0 – 1993 SNOMED Version 3.5 – 1998 SNOMED RT – 2000 (Merge with UK NHS)SNOMED CT (SNOMED RT + CTV3) – 2002 SNOMED CT Spanish Edition – April 2002 SNOMED CT German Edition - April 2003 Free in USA - Agreement with NLM – June 2003SNOMED SDO Proposal 2006
  • 14. User distribution - SNOMED CT Users
  • 15. What is SNOMED CTEssence
  • 16. What is it?A reference terminologyA clinical terminology with reference and interface properties A CD containing a set of tablesA set of codes with namesA set of definitions “per genus et differentiam”A clinical terminology standardA knowledge base?A dictionary?An ontology?An application ontology?
  • 17. 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 principlesIncludes terms and non-ontological assertions / ideasI 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
  • 18. What is an Ontology?
  • 19. What is an Ontology?A model of (some aspect of) the world
  • 20. What is an Ontology?A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:Anatomy
  • 21. What is an Ontology?A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:AnatomyCellular biology
  • 22. What is an Ontology?A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:AnatomyCellular biologyAerospace
  • 23. What is an Ontology?A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:AnatomyCellular biologyAerospaceDogs
  • 24. What is an Ontology?A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:AnatomyCellular biologyAerospaceDogsHotdogs…
  • 25. What is a Clinical Terminology?Ordinarily:A finite enumerated set of terms intended to convey information unambiguouslySNOMED is more than thisTerms plus codes plus the ability to put them together in meaningful ways
  • 26. What is SNOMED CT?A work of clinical terminology for coding, retrieving and analyzing data about health and health careComprised of codes, terms and relationships, for use in precisely recording and representing clinical information across the scope of health careConcept-based: Each code represents a single meaning and can have multiple descriptions (terms)
  • 27. What is notSNOMED is not the language policeClinicians determine what words mean by how they use them. SNOMED reflects those meanings.SNOMED is not an independent source of scientific/professional practice standardsScientists and professional groups define their standards. We try to follow those standards.SNOMED is not a comprehensive knowledge base for healthcareThis is out of scope. SNOMED’s goal is terminological knowledge: that which is always necessarily true of a term.
  • 28. What does it do?SNOMED CT is a terminological resource that can be implemented in software applications to represent clinically relevant informationIn a “semantically structured” form that can be used by automated applications
  • 29. What is it for?It is for building applications capable of:Recording statements about the health and health care of individualsIn a way that permits retrieval according to the meaning of the statements, rather than just the words usedRetrieving individual cases and groups of casesTo enable more automated and sophisticated decision support, epidemiology, and research
  • 30. Pictures can also be presented more dramatically in widescreen.Desiderata for a global terminology
  • 31. Desiderata for a global terminologyComprehensiveness:Coverage for all aspects of health careAdequacy:Is it fit or purpose – multiple purposes?Does it have a good information model and ontological basis?Multilingual applicabilitylanguage independent formal concept representationRepresentation in multiple languages – more than translationUtility:Is it beneficial for: Care providers : decision making, outcome evaluation Consumers : participation – ownership – evaluation – risk reductionPolicy/Decision Makers : informed decision making on costs, benefits, efficiencyReliability:does it give the same results in different usersSource: T. Ustun, WHO, SNOMED Semantic Mining Conference, Copenhagen, Oct. 2006
  • 32. Desiderata for a global terminology Validity:Does it indicate the right things – and does the indication make senseComparabilityDoes the data in different context have same properties to be comparedInteroperabilityTechnical: Can information systems exchange information and use it? Semantic: Can information systems interpret the data with the same meaning? Quality AssuranceProduct: Annotation and ContentProcess: Use and UsabilitySustainabilitySecured maintenance: commitment to stability with earlier versions Openness to address emerging technical issuesSource: T. Ustun, WHO, SNOMED Semantic Mining Conference, Copenhagen, Oct. 2006
  • 33. SNOMED CT StructureHierarchiesParent child relationshipsVertical structureConcepts may have multiple parentsRelationships between conceptsUsing attributes, concepts may be linked to each otherHorizontal relationships
  • 34. Healthcare systems includedICD9-CMICD-V2-OncologyLOINCOphthalmology-related termsSystematized Nomenclature of DentistrySM of Vet Med NANDA Taxonomy IINursing Interventions ClassificationNursing Outcomes ClassificationPeri-operative Nursing Data SetThe Omaha SystemThe Georgetown Home Health Care Classification
  • 35. SNOMED CT Structural componentsSNOMED CT is composed of components, which include concepts, relationships, descriptions, subsets, and cross maps, Each of which is identified by a SNOMED CT Identifier (SCTID) and has a validity status.
  • 36. Components of SNOMED CT ConceptsThe basic units of SNOMED CTDescriptionsThese relate terms that name the concepts to the concepts themselves. Each concept has at least two Descriptions.HierarchiesConcepts are organized into twenty SNOMED CT hierarchies (in UK extension). Each hierarchy has sub-hierarchies within it.RelationshipsRelationships are the connections between concepts in SNOMED CT.+ mappingsMany-to-many mappings to terms in ICD and OPCS+ Inclusion of Dictionary of Medicines and Devices
  • 37. SNOMED Clinical Terms Identifier (SCTID)The SCTID is a 64 bit integer- between 6 and 18 digits long.All components are identified using a special SCTID.
  • 38. Validity StatusAn important principle of SNOMED CT is that of permanence. Once a component such as a concept or description has been created it is never deletedStatus codes:Active: Current (0), Limited (6), Pending move (11)Inactive: Retired (1), Duplicate (2), Obsolete (3), Ambiguous (4), Erroneous (5),Inappropriate (7), Inactive concept (8), Implied (9), Moved elsewhere (10)
  • 39. ConceptsSNOMED CT is concept-orientedA concept is just a clinical idea to which a unique ConceptID that is a SCTIDConcepts are formally defined in terms of their relationships with other concepts:Subtype relationship: Concept Z IS_A concept YAttribute relationship
  • 40. Content of SNOMED CT: Organized in 19 different hierarchiesThese are indeed high level concepts SNOMED CT : Root conceptClinical FindingProcedureObservable entityBody structureOrganismSubstancePharmaceutical/biology productSpecimenPhysical objectPhysical forceEventsEnvironments/Geographical locationsSocial ContextContext-dependent categoriesStaging and scalesAttributeQualifier valueSpecial concept
  • 41. Concept ExampleGastric ulcer(SCTID397825006)Terms:Gastric ulcer (disorder)Gastric ulcerStomach ulcerGU – Gastric ulcerGastric ulcerationRelationships:Is_a Disease of stomachIs_aGastrointestinal ulcer Associated morphology  Ulcer Finding site  Stomach
  • 42. DescriptionsEach description has a DescriptionIDwhich is a SCTIDEach description links a human-readable term with a concept.Every concept has at least two descriptions: Fully specified name (FSN) : is a phrase that names a concept in a way that is both unique and unambiguousPreferred term:the common phrase or word used by clinicians to name a conceptEach concept may have several other descriptions: e.g. synonyms, translations
  • 43. RelationshipsRelationships are at the heart of SNOMED.More than 1.3 millionEach relationship is defined as an object-attribute-value triple. The object is the source concept (the one that has the relationship) (ConceptID1). The attribute specified the type of relationship and is also a SNOMED CT concept. The value is the target.Concept: attribute = value (e.g. Gastric ulcer(SCTID397825006)Is_a Disease of stomach)SNOMED CT Components
  • 44. SNOMED Clinical Terms Identifier (SCTID)A 64 bit integer - between 6 and 18 digits long.
  • 46. Lets bypass the rest of SNOMED CT structures
  • 47. SNOMED CT ExpressionsClinical records are created for the purpose of providing information about events or states of affairs.A SNOMED CT expression is a collection of references to one or more concepts used to express an instance of a clinical idea. pre-coordinateda single concept identifier is used to represent a clinical ideaPost-coordination representation of a clinical meaning using a combination of two or more codes
  • 49. SNOMED CT Expressions: Sample|50043002 | disorder of respiratorysystem |+ 87628006 | bacterial infectious disease |:246075003 | causative agent | = 9861002 | streptococcus pneumoniae|, 363698007 | finding site | = (45653009 | structure of upper lobe of lung | : 272741003 | laterality | = 7771000 | left |)
  • 51. SNOMED CT Documentation: User GuideExplains the content and the principles used to model the terminology.Intend: To explain SNOMED CT’s capabilities and uses from a content perspective.Audience: clinical personnel, business directors, software product managers, and project leaders; information technology experience, though not necessary, can be helpful.
  • 52. SNOMED CT Documentation: Technical Reference Guide (TRG)Contains reference material related to the current release of SNOMED CT and includes file layouts, field sizes, required values and their meanings, and high-level data diagrams.Audience: for SNOMED CT implementers, such as software developers. assumes an information technology background , clinical knowledge is not a prerequisite.
  • 53. SNOMED CT Documentation: Technical Implementation Guide (TIG)Contains guidelines and advice about the design of applications, terminology services, entering and storing information, and migration of legacy information.Audience: for SNOMED CT implementers, such as software designers. assumes information technology and software development experience. Clinical knowledge is not required, although some background is helpful to understand the application context and needs
  • 55. Pulmonary Tuberculosiskind of pneumonitiskind of tuberculosiscaused by Mycobacterium tuberculosis complexkind of Pulmonary disease due to Mycobacteriafound in lung structure
  • 57. What about clinical decision support?IF Two blood cultures, drawn throughan antibiotic removal device, more than 30 minutes apart, grow no organism,THEN discontinue antibiotic.
  • 58. proceduresIFTwoblood cultures, drawn throughan antibiotic removal device, more than 30 minutes apart, growno organism,THENdiscontinueantibiotic.findingdevice
  • 59. Clinical Decision Support Model + Inference RulesInterfaceInterfaceInterfaceInformation Model+ Patient Data StructuresTerminology Model+ Coded DataDiagram based on Figure 1 in Rector AL et al. “Interface of Inference Models with Concept and Medical Record Models” AIME 2001: 314-323
  • 60. Clinical Decision Support Model + Inference RulesIFTwoblood cultures, drawn throughAntibiotic removal device, more than 30 minutes apart, grows no organism,THENdiscontinueantibiotic.InterfaceInterfaceInterfaceHL7 RIMSNOMED CTInformation Model+ Patient Data StructuresTerminology Model+ Coded DataWhat 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 device264868006 No growth281789004 antibiotic therapy223438000 advice to discontinue a procedureDiagram based on Figure 1 in Rector AL et al. “Interface of Inference Models with Concept and Medical Record Models” AIME 2001: 314-323
  • 61. Using SNOMED CT and HL7 togetherwe cannot separate the issues of information structure from those of terminology.We cannot slot any terminology into any data structure and expect it to work.SNOMED CT was designed to be syntax-neutral, so it could work with any syntax.HL7 RIM and set out to be terminology-neutral.
  • 63. InteroperabilityIn the context of e-health, interoperability is the way in which reliable data is provided and communicated in a secure, accurate and efficient way. It has to surmount the barriers of national policies, culture, language and systems of medical knowledge representation and use of ICT’s.Towards Interoperable eHealth for Europe. Telemedicine Alliance. BR255, November 2005
  • 64. Classifying and Coding, which is more important?Coding means understanding?Assigning codes to concepts.Identifying the concepts.Clarifying them.Dealing with homonyms, synonyms and overlapsEnables us to identify and document interrelationshipsThis is indeed
  • 65. SNOMED CT is the most comprehensive, multilingual clinical healthcare terminology in the world.The value of SNOMED CT can only be realized when it is built into software and systems that are designed around itKent Spackman:The first rule of data quality is that the quality of data collected is directly proportional to the care with which options are presented to the user. The first rule of coding is that yesterday’s data should be usable today.Heterogeneity of healthcareHealtcare data need to be permanent
  • 66. SNOMED CT at 2009SNOMED Reference Terminology ® Clinical Terms Version 3®310,000 health care concepts990,000 synonyms and English descriptions1.38 million semantic relationshipsICD 10 contains 10760 concepts coming in three large volumes
  • 68. Standardized Healthcare LanguagesNeed for a normalized healthcare vocabulary. Across settings, applications, datasets. SNOMED CT, UMLS.
  • 70. Percentage of SNOMED CT concept codes that are “fully defined”Eventually should reach ~70% or more of disorders, findings & procedures
  • 71. 7202.10.2006Gergely Héja - SMCS2006Error types - 1Misplacing concepts in the hierarchy
  • 72. smoker (an agent) is subsumed by tobacco smoking behaviour – finding (a role)
  • 73. severe asthma is not a kind of asthma, but a kind of asthma finding.
  • 74. Mixing the subsumption relation with other roles (typically part of)
  • 75. haemoglobin subsumes haemin (instead of constitutional part)
  • 76. exacerbation of asthma attack is subsumed by asthma (instead of temporal part)7302.10.2006Gergely Héja - SMCS2006Error types - 2Hierarchy violating medical thinking and biomedical knowledge
  • 77. Disease, observation and finding are subsumed by clinical finding
  • 78. acute on chronic, which is both subsumed by acute and chronic
  • 79. polycarbonate is a polymer (instead of synthetic polymer)7402.10.2006Gergely Héja - SMCS2006Error types - 3Contracting disjoint entities into one concept
  • 80. Smoker (an agent) and smoker (finding) (a description of a situation)
  • 81. additional pathologic finding in tumor specimen (observable entity) and additional pathologic finding
  • 82. Function is classified as an observable entityOntological definition: ability of an object to play a certain role in a certain kind of activityfunctions (e.g. gene function,adaptation) measures (quality) that evaluate the realisation of a function (e.g. respiratory rhythm, excretory rate)Inflammation (morphological abnormality) (a physical object) and inflammatory reaction (perdurant)7502.10.2006Gergely Héja - SMCS2006Additional problems - 1Categories taken form classification systemspneumonia in other diseases classified elsewhere (marked as “ConceptStatus Limited”) The danger of taking over concepts from other conceptual systems: the context of the concept is lost. What is meant by “other diseases classified elsewhere”? relations (such as part of) are represented also as conceptsIt prohibits the direct conversion to any formalism based on first order logic, thus to any DL formalism
  • 83. 7602.10.2006Gergely Héja - SMCS2006Additional problems - 2Underspecification:roles are not quantified (existential / universal)criteria are not specified (necessary / sufficient)conversion to DL: do we have to decide in each particular case, or can it be done universally?Multiple hierarchyalcoholic beverage (through its parent ingestible alcohol) is subsumed by central depressant, ethyl alcohol and psychoactive substance of abuse – non-pharmaceutical. Alcoholic drinks contain ethyl alcohol, which plays a role of depressant and substance of abuse (with respect to human beings)Is this a general phenomenon in SNOMED?Which relations are asserted and which are inferred?
  • 84. 7702.10.2006Gergely Héja - SMCS2006Discussion - 1The intended meaning of the categories is not always clear: possible translation errorsIs it reasonable to import categories from medical classifications? SizeArtificial conceptsConsistency errors
  • 85. 7802.10.2006Gergely Héja - SMCS2006Discussion - 2Real world entities listed heterogeneouslyMars bar and Kit Kat (chocolate candy would suffice)UFO is subsumed by transport vehicletendon pulley reconstruction is represented, but tendon pulley not
  • 86. Solutions02.10.2006Gergely Héja - SMCS200679Use SNOMED as a plain or loosely structured list of terms (with extending the coverage). Not appropriate for intelligent services.
  • 87. Restructure SNOMED into a high-quality ontology.
  • 88. Build a new medical ontology from scratch (partial reuse of the existing ones), and to restrict the use of SNOMED for interoperability by mapping concepts to it. Restructuring SNOMED02.10.2006Gergely Héja - SMCS200680A formal top level ontology (e.g. DOLCE).A high level core reference ontology of general medical knowledge (e.g. anatomy, physiology, pathology, medical procedures).Logic-based formalismSingle hierarchies with formal definitions(sub)domain ontologies of specialitiesCompound entities (e.g. tonsillitis)Manual assertion (e.g. autism)
  • 90. Some Research ChallengesExtend saturation-based techniques to non-Horn fragmentsSNOMED users want negation and/or disjunctionNon infectious PneumoniaInfectious or Malignant disorder of lungBurn injury of face neck or scalpExtend reasoning supportModularityExplanation...
  • 91. Some (more) Research ChallengesOpen questions w.r.t. query rewritingFO rewritability (AC0) only for very weak ontology languagesEven for AC0 languages, queries can get very large (order ), and existing RDBMSs may behave poorlyLarger fragments require (at least) Datalog engines and/or extension to technique (e.g., partial materialisation)Integrating DL/DB researchOntologies -v- dependenciesOpen world -v- closed world
  • 92. Widescreen Test Pattern (16:9)Aspect Ratio Test(Should appear circular)4x316x9
  • 94. Why Care About Semantics?Herasy!Herasy!Herasy!
  • 95. Why Care About Semantics?Why should I care about semantics?
  • 96. Why Care About Semantics?Why should I care about semantics?
  • 97. Why Care About Semantics?Why should I care about semantics?Well, from a philosophical POV, we need to specify the relationship between statements in the logic and the existential phenomena they describe.
  • 98. Why Care About Semantics?Why should I care about semantics?Well, from a philosophical POV, we need to specify the relationship between statements in the logic and the existential phenomena they describe.That’s OK, but I don’t get paid for philosophy.
  • 99. Why Care About Semantics?Why should I care about semantics?Well, from a philosophical POV, we need to specify the relationship between statements in the logic and the existential phenomena they describe.That’s OK, but I don’t get paid for philosophy.From a practical POV, in order to specify and test ontology-based information systems we need to precisely define their intended behaviour
  • 100. In FOL we define the semantics in terms of models (a model theory). A model is supposed to be an analogue of (part of) the world being modeled. FOL uses a very simple kind of model, in which “objects” in the world (not necessarily physical objects) are modeled as elements of a set, and relationships between objects are modeled as sets of tuples.Why Care About Semantics?
  • 101. Why Care About Semantics?In FOL we define the semantics in terms of models (a model theory). A model is supposed to be an analogue of (part of) the world being modeled. FOL uses a very simple kind of model, in which “objects” in the world (not necessarily physical objects) are modeled as elements of a set, and relationships between objects are modeled as sets of tuples.This is exactly the same kind of model as used in a database: objects in the world are modeled as values (elements) and relationships as tables (sets of tuples).

Editor's Notes

  • #13: SNOMED was born from SNOP, the Systematized Nomenclature of Pathology, and has been part of the College of American Pathologists ever since. In the mid 70’s, SNOMED was extended to cover all of clinical medicine. Two recent milestones, which have profoundly affected SNOMED’s current content, are the merger with National Health Service Read Codes (also know as CTV3) and the agreement with the National Library of Medicine for the United States in 2003.