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 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 -> Descriptions
233604007 D2-0007F Pneumonia (disorder)
2Synonym In Local Extension233604007xxxyyyyyyy11x
2Synonym in US Extension233604007xxxx100012411x
2Synonym in International Release233604007xxxxxx01x
1Pneumonia233604007621810017
3Pneumonia (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.
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
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
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
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
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/
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