Overview of SNOMED CT International Release, U. S Overview of SNOMED CT International Release, U.S. Extension of SNOMED CT and NLM SNOMED Resources Everything (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

Lists of words… Terminology Nomenclature Vocabulary Classification 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)

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)

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

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.

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.

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

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.

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).

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

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

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.

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.

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

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.

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.

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

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

SNOMED Data Structure

SNOMED Core Concepts Table Descriptions Table Relationships 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.

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)

Concepts -> Descriptions 233604007 D2-0007F Pneumonia (disorder) 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

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

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.

SNOMED CT Component ID The ComponentID does 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 ID avoids 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.

SNOMED CT ComponentID format SCTID for International release component.

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

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

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) Supercedes subsetting mechanism if RF1 Replaces all status codes with components (everything is a component) First production release July 2011 RF2 → RF1 conversion tool available

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/

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

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

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.

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.

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

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)

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

http://uts.nlm.nih.gov

SNOMED CT Resources

SNOMED CT at NLM

SNOMED CT International Release

SNOMED CT Browsers 15 Active browsers listed

NLM SNOMED CT/UMLS Browser

NLM SNOMED CT/UMLS Browser Why 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

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

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

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

US Extension to SNOMED CT

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

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

NLM SNOMED CT Content Request Submission (USCRS)

Rationale for USCRS IHTSDO requires submissions to the International release to go through the member National Release Center Existing request system being phased out No new accounts accepted Older users “grandfathered – in” Needed support for U.S. users who need to add content to SNOMEDCT Support users who need content with stable (maintained) identifiers before next release Must support functions defined by IHTSDO Triage and handling by NLM

USCRS Login Uses UTS Login

Main Screen

New request allows a number of request types Search allows you to search all current requests from any user

Dentistry 123445 Supernumerary second incisor of maxilla (disorder) Supernumerary second incisor of maxilla 95267007 Teeth which appear in addition to the regular number of teeth. Needed to support dental findings

Currently “Post-beta” General availability Fall 2011 Future phases USCRS Status Currently “Post-beta” General availability Fall 2011 Future phases Access to complete history of request changes Manager alerts (priority todo) Notes enhancements: links & attachments Enhanced reporting capabilities (e.g. report of submitter activity) Duplicate request identification and review Extended request types – ref sets, content areas, etc. Mobile app interface https://uscrs.nlm.nih.gov/

State diagram for requests

Questions? Jim Case casejt@mail.nih.gov