James T. Case MS, DVM, PhD

1. Overview of SNOMED CT International Release, U.S. Extension of SNOMED CT and NLM SNOMED ResourcesEverything (more than) you wanted to know about SNOMED CT James T. Case MS, DVM, PhD Health Program Specialist – SNOMED CT National Library of Medicine Bethesda, MD

2. Lists of words… • Terminology • The body of specialized words relating to a particular subject • Nomenclature • The system or set of names for things, etc., commonly employed by a person or community (ICD-9, CPT, HL7 Tables, SNOMED CT) • Vocabulary • A collection or list of words with explanations of their meanings (HL7 Tables, SNOMED CT) • Classification • The result of classifying; a systematic distribution, allocation, or arrangement, in a class or classes; esp. of things which form the subject-matter of a science or of a methodic inquiry. (ICD-9)

3. When do you need a controlled nomenclature? • Aggregation of text-based content from multiple sources • Multiple individuals • Multiple institutions • Any time you rely on a computer to manipulate language and “meaning” is critical. • Test lists (for comparability)

4. Why did “we” pick SNOMED CT? • A shared nomenclature must be maintained. • SNOMED is the ONLY actively maintained reference nomenclature that addresses public health content. • NLM/CDC has a long-term investment • Public Health CANNOT afford: • To build it’s own competent nomenclature • To continue to live without a competent nomenclature

5. Characteristics of a controlled vocabulary / nomenclature. Cimino, JJ. Desiderata for Controlled Medical Vocabularies in the Twenty-First Century Methods of Information in Medicine. 1998 Nov, 37(4-5): 394-403 • THE Review of ideal characteristics of a controlled medical vocabulary / nomenclature. • Perhaps the best READING review of medical vocabulary / nomenclature available.

6. Content, content, content • First criticism of ANY nomenclature (by users) is lack of content • At least 3 approaches: • Enumerate all possible concepts (both simple and complex) • Provide all necessary “atoms”; create effective syntax; “teach” the syntax to users (or systems); hope for the best. • Drastically limit the scope of the nomenclature. • Restricting a nomenclature may actually improve usability of the nomenclature for a limited purpose, however: • It restricts expressivity • The next project and the next interaction require development of a new nomenclature • Connections between projects require “mapping”. • Users will not be happy. Might be easier to build and use a large single nomenclature.

7. Concept Orientation • Concept – an embodiment of a particular meaning • Characteristics: • Non-vagueness - Concepts must correspond to at least one meaning • Non-ambiguity - Concepts must correspond to no more than one meaning • Non-redundancy - Meanings correspond to no more than one concept

8. Concept permanence • Once created, the meaning of a concept is inviolable. • Any “meaningful” change requires retirement and reassignment of ID. • Concept identifiers can NEVER be reused. • Used to provide the history of concept status. • Contributes to stability of legacy information.

9. Non-semantic identifier • Unique name • Using the name as identifier inhibits (prohibits?) improvements in a concept’s “name” • Harder to cope with synonymy. • Hierarchical designators (codes with meaning) inhibit classification • Monohierarchies provide inadequate classification capability for retrieval purposes. • Polyhierarchies cannot be supported. • (A concept can’t be in its multiple logical locations).

10. Polyhierarchies • Medical concepts are often classified in multiple ways • By site • By pathology • By function • Etc… • E.g. Acute bacterial pneumonia • It is a bacterial (infectious) disease • It is a pulmonary disease • It is an inflammatory condition • It is an acute condition

11. Formal definitions • A collection of relationships to other concepts in the vocabulary • Acute Bacterial pneumonia • Causative agent = bacteria • Has location = lung • Has morphology = inflammation • Has course = acute

12. Evolve Gracefully • A nomenclature must have a strategy for coping with new content. • The bane of home grown nomenclatures • Who’s looking after your list of concepts? • Nomenclature maintenance is not everyone’s cup of tea. • A controlled nomenclature serves as an “arbiter” of sorts. • A nomenclature used by more than one organization (PH lab) must have update and distribution mechanisms in place.

13. Recognize redundancy • Redundancy must be avoided in the concept list • Redundancy must be provided for using a synonym mechanism. • Personal preference and dispersed training insures that there exist multiple ways to say almost anything. • They’re still talkin’ about the same thing.

14. SNOMED CT Top-level Hierarchies • Body structure • Clinical finding • Environment or geographical location • Event • Linkage concept • Observable entity • Organism • Pharmaceutical / biologic product • Physical force • Physical object • Procedure • Qualifier value • Record artifact • Situation with explicit context • SNOMED CT Model Component • Social context • Special concept • Specimen • Staging and scales • Substance

15. Complaints about SNOMED CT • It’s too… • Big • Complicated • Expensive • Yes but… • We can make it smaller (sort of), and use smaller pieces (for most purposes). • We can use it in simple and straightforward ways • Yeah, while the terminology is free, it’s a bit expensive to make it work.

16. Is the effort/expense worth it? • IF the long-range goal is useful… • The selected standards adhere to design specifications that have developed through hard experience in the medical profession. • Essential / desirable features have been documented. • The selected standards represent extraordinary functionality, produced and maintained at great cost to the medical profession.

17. Reportable condition reporting • Demographics - Race and ethnicity • Occupation and social context concepts • List of reportable diseases • Lab tests that support disease lists • Result values for non-numeric tests • Place to put the concepts in the message structures • Lab to Lab • Lab to network

18. P.H. Reportable P.H. disorders Specialty practice General practice Subsets of standards SNOMED-CT, HL-7, LOINC

19. SNOMED Data Structure

20. SNOMED Core Concepts Table • Each row in this table represents a concept relevant to the health domain. Descriptions Table • Each row in this table specifies a term that can be applied to describe a single clinical concept. Relationships Table • Each row in this table specifies a relationship between two clinical concepts. The nature of each relationship is represented using a special kind of clinical concept.

21. Terminology of Terminology • Concept • embodiment of a particular meaning • Really a “virtual” element in the system • The string in the concepts table is a member of the related list of descriptions (for RF1). • Description • Any string used to represent a concept • Relationship • (in SNOMED) an object – attribute – value triple connecting two concepts through an attribute • Relationships in SNOMED are “stated” (explicitly modeled) or “inferred” (based on a classifier)

22. Concepts -> Descriptions 350049016 233604007 Pneumonia (disorder) 3 621810017 233604007 Pneumonia 1 xxxxxx01x 233604007 Synonym in International Release 2 xxxx100012411x 233604007 Synonym in US Extension 2 xxxyyyyyyy11x 233604007 Synonym In Local Extension 2 1 = “preferred” description (term) – preferred by SNOMED, perhaps not your users 2 = synonym (alternate) 3 = fully specified name

23. Concepts Table SCT ID SNOMED ID Concept Name 71620000 DD-13100 Fracture of Femur (disorder) 116676008 G-C504 Associated Morphology (attribute) 72704001 M-12000 Fracture (morphologic abnormality) Relationship Table Concept ID Relationship ID Concept ID 71620000 116676008 72704001 Concept -> Relationship

24. SNOMED CT Component ID • The ComponentID data type is a 64-bit integer, which is subject to the following constraints: • Only positive integer values are permitted. • The minimum permitted value is 100,000 (6 digits) • The maximum permitted value is 999,999,999,999,999,999 (18-digits). • As result of rules for the partition-identifier and check-digit, many integers within this range are not valid SCTIDs.

25. SNOMED CT Component ID • The ComponentIDdoes not contain semantic information related to the meaning of a concept or term • It does have a structure that is designed to allow different types of terminological components to be recognized. • The nature of a component can be derived from the table in which a component is distributed. • Partitioning the IDavoids reuse of the same identifier for a different type of component – thus avoiding both ambiguity and duplication. • This also allows the nature of the identifier to be recognized when stored in a record or transferred in a message.

26. SNOMED CT ComponentID format SCTID for International release component.

27. SNOMED CT Extension ID Format SCTID for a component in an extension.

28. A Word about SNOMED IDs (legacy codes) • Currently still assigned by IHTSDO for each release • Do NOT support differentiation among description types • Are discouraged/deprecated by IHTSDO • May not be “legally” assigned by SNOMED extension managers • Thus no way to link extension terms to core using legacy codes • Will be eliminated in the future

29. SNOMED CT Release Format 2 (RF2) • Addresses shortcomings of RF1 • Provides a comprehensive history mechanism of all components • New attribute for “ownership” (moduleID) • Extended mechanism for creation of Reference Sets (refsets) • Supercedessubsetting mechanism if RF1 • Replaces all status codes with components (everything is a component) • First production release July 2011 • RF2 → RF1 conversion tool available

30. Accessing SNOMED Documentation • User’s Guide • A terminology user’s intro to SNOMED CT • Editorial Guide • Describes how to model SNOMED CT content • For content developers • Technical Implementation Guide • Aimed at technical implementers (developers) • Updates on the web version are ongoing • http://ihtsdo.org/fileadmin/user_upload/doc/

31. Additional introductory material • CAP STS offers free Introductory webinars • http://www.cap.org/ • Introductory you tube videos by Dr. Kent Spackman, IHTSDO Chief terminologist • http://www.youtube.com/watch?v=ISfoMR4aygc

32. SNOMED CT Post-coordination • What is post-coordination? • Create a new concept by adding specificity to an existing SNOMED concept. • Discussion for another time

33. SNOMED Extensions • Enable authorized organizations to add Concepts, Descriptions, Relationships and Subsets to complement those that are centrally maintained as the International release content of SNOMED CT. • specialized terminology needs of an organization. • Extensions maintain unique identification across organizations for data transmission and sharing.

34. SNOMED Extensions • Distinguishable from the main body of SNOMED CT • in the thesaurus • when stored in a patient record, query or decision support protocol. • Distinguishable from other Extensions, in the same way as they are distinguishable from the main body of SNOMED CT. • Able to be distributed and processed in the same way as equivalent components from the main body of SNOMED CT without requiring specific adaptations of SNOMED-enabled applications.

35. NLM’s Role Relating to Interoperability • Central coordinating body for clinical terminology standards within the U.S. Department of Health and Human Services • Coordinate efforts with the Office of the National Coordinator for Health Information Technology (ONC) • Distributor (within the UMLS) of: • HIPAA classifications & code sets AND • Terminologies required for EHR certification • Support for development and maintenance of standard terminologies

36. NLM’s Relationship to IHTSDO • Charter member on behalf of US/HHS • US distributor of SNOMED CT (via UMLS) • US licensor of IHTSDO Affiliates (via UMLS) • Serve on IHTSDO: • General Assembly (US Representative and Chair) • Member Forum (US Representatives and Vice-Chair)

37. UMLS Terminology Services (UTS) • Access to UMLS domain objects • Web site to browse, search, display, download • Metathesaurus and SNOMED CT browser • Authenticated, secure access to data requiring a UMLS license • One-stop access to terminology resources and applications at the NLM • Web services for programmatic access

38. http://uts.nlm.nih.gov

39. SNOMED CT Resources

40. SNOMED CT at NLM

41. SNOMED CT International Release

42. SNOMED CT Browsers 15 Active browsers listed

43. NLM SNOMED CT/UMLS Browser

44. NLM SNOMED CT/UMLS BrowserWhy yet another SCT browser? • Leverages the UMLS to find SCT concepts • Allows location of SNOMED CT concepts using UMLS descriptions • As part of UTS, will link directly to other UTS services

45. Restrict to a specific top level concept Can limit to active concepts only Full information about concept available Results pared down with additional search terms

46. No SNOMED CT Description? Informs you whether there is a UMLS concept matching your search term

47. UMLS Concept Concept exists in ICD9; ICD10CM and MEDCIN

48. US Extension to SNOMED CT

49. U.S. Extension of SNOMED CT • NLM-maintained SNOMED CT components for U.S. use cases • Concepts jurisdictionally or domain specific • Rapid access to identifiers for implementers • Interim concept IDs pending IHTSDO approval • Regulatory or legislatively mandated terms • Domains out of scope for international release • Specific inclusion and exclusion criteria

50. US Extension of SNOMED CT… • Identifiers in NLM namespace: 1000124 • First release in March 2011 • Latest release scheduled for March 1, 2012 • Harmonized with the latest International release • Future releases approx. one month after International release • Future releases may come more frequently