James T. Case MS, DVM, PhDHealth Program Specialist – SNOMED CT

National Library of MedicineBethesda, MD

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

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)

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:

1. Enumerate all possible concepts (both simple and complex)2. Provide all necessary “atoms”; create effective syntax;

“teach” the syntax to users (or systems); hope for the best.3. 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

SNOMED-CT, HL-7,LOINC

General practice

Subsets of standards

Specialty practice

P.H. disorders

P.H. Reportable

SNOMED Data Structure

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.

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 -> Descriptions233604007 D2-0007F Pneumonia (disorder)

2Synonym In Local Extension233604007xxxyyyyyyy11x

2Synonym in US Extension233604007xxxx100012411x2Synonym in International Release233604007xxxxxx01x

1Pneumonia2336040076218100173Pneumonia (disorder)233604007350049016

1 = “preferred” description (term) – preferred by SNOMED, perhaps not your users2 = synonym (alternate)3 = fully specified name

Concept -> Relationship

7270400111667600871620000

Concept IDRelationship IDConcept ID

Relationship Table

Fracture (morphologic abnormality)M-1200072704001

Associated Morphology (attribute)G-C504116676008

Fracture of Femur (disorder)DD-1310071620000

Concept NameSNOMED IDSCT ID

Concepts 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

15 Active browsers listed

SNOMED CT Browsers

NLM SNOMED CT/UMLS Browser

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

Can limit to active concepts only

Restrict to a specific top level concept

Results pared down with additional search terms

Full information about concept available

No SNOMED CT Description?

Informs you whether there is a UMLS concept matching your search term

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

Uses UTS Login

USCRS Login

Main Screen

New request allows a number of request

types

Search allows you to search all current

requests from any user

Dentistry

123445Supernumerary second incisor of maxilla (disorder)

Supernumerary second incisor of maxilla

95267007

Needed to support dental findings

Teeth which appear in addition to the regular number of teeth.

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