Vocab. SNOMED

SNOMED CT

Overview

The Systematized Nomenclature of Medicine, Clinical Terms (SNOMED-CT) is a systematically organized computer-processable collection of medical terms providing codes, terms, synonyms, and definitions used in clinical documentation and reporting. The primary purpose of SNOMED CT is to encode the meanings that are used in health information and to support the effective clinical recording of data to improve patient care. SNOMED CT provides the core general terminology for electronic health records. SNOMED CT comprehensive coverage includes clinical findings, symptoms, diagnoses, procedures, body structures, organisms and other etiologies, substances, pharmaceuticals, devices, and specimens.

Sources

SNOMED CT International Edition

The clinical terminology is owned and maintained by SNOMED International, a not-for-profit association. The U.S. National Library of Medicine (NLM) distributes the SNOMED CT International Edition and derivatives via the UMLS Terminology Services.

SNOMED CT United States Edition

The U.S. National Library of Medicine (NLM) produces and distributes the U.S. Edition of SNOMED CT and derivatives via the UMLS Terminology Services.

SNOMED CT UK Edition

The SNOMED UK National Release Centre is hosted by NHS England (Information Representation Services) and is responsible for the creation of, and delegated authority to license, the SNOMED CT UK Edition and derivatives as well as developing and maintaining UK-specific content released in the UK Clinical Extension and UK Drug Extension.

Retired modules

In 2024 SNOMED UK Drug Extension Module was excluded from SNOMED OMOP vocabularies. Concepts that belonged to this module have been deprecated and linked to their duplicates in the dm+d vocabulary. Their concept codes and names have been replaced by placeholders to avoid misuse.

SNOMED specifications and guides are available here.

UMLS Metathesaurus

We use UMLS source files to add synonyms for SNOMED concepts.

Transformation

The procedures for transforming Concepts from the source to the OMOP Standard Vocabularies can be found on the OHDSI GitHub.

Concept Names

Concept names are assigned according to the preferred terms provided by the source. As preferred terms may vary for different SNOMED modules we consider them in the following precedence: SNOMED International Edition, then US Edition, then UK Edition.

A fully specified name with its semantic tag is put into synonyms.

Concept Code

Concept codes are assigned according to the conceptid field provided by the source.

Standard Concepts

• By default all valid concepts in Condition, Device, Language, Meas Value, Meas Value Operator, Measurement, Observation, Procedure, Relationship, Route, Spec Anatomic Site, and Specimen are standard.
• By default all concepts in Drug, Gender, Metadata, Provider, Race, Type Concept, Unit, and Visit are non-standard as in OMOP there are other standard vocabularies for these domains.
• Concepts that belong to the Location concept class and carry the semantics of countries remain standard in the Geography domain. Other Location concepts are non-standard.
• Concepts that belong to the Social Context concept class and carry the semantics of relationships, religion, and occupation remain standard. Other Social Context concepts are non-standard.
• Concepts that belong to Attribute, Physical Force, and Physical Object (except concepts in the Device domain) are non-standard.
• Concepts that are mapped not to themselves become non-standard.

Domains

Domains of concepts are assigned according to the concept semantics.

A list of domains presented in SNOMED is following:

Domain

Condition

Device

Drug

Gender

Geography

Language

Measurement

Meas Value

Meas Value Operator

Metadata

Observation

Procedure

Provider

Race

Relationship

Route

Spec Anatomic Site

Specimen

Type Concept

Unit

Visit

Concept Classes

Concept classes are assigned according to the semantic tags provided by the source in the fully specified concept names.

A list of concept classes presented in SNOMED is presented below:

Concept class

Admin Concept

Attribute

Biological Function

Body Structure

Clinical Drug

Clinical Drug Form

Clinical Finding

Context-dependent

Disorder

Disposition

Dose Form

Event

Inactive Concept

Linkage Assertion

Linkage Concept

Location

Model Comp

Morph Abnormality

Namespace Concept

Navi Concept

Observable Entity

Organism

Patient Status

Pharma/Biol Product

Physical Force

Physical Object

Procedure

Qualifier Value

Record Artifact

Social Context

Special Concept

Specimen

Staging / Scales

Substance

Concept Relationships

Attribute relationships

This type of relationship is created in OMOP following SNOMED attributes. A combination of an attribute name and an attribute value is used to specify a defining characteristic of a concept. Depending on the nature of the concept, they may include etiology, topography, method, etc., e.g.:

source concept	relationship_id	target concept
80146002, Appendectomy	Has method	129304002, Excision - action
	Has direct procedure site	66754008, Appendix structure
	Occurs before	446324006, Dehiscence of appendicectomy wound

A full list of attribute relationships can be found in the concept_relationship table. Note that the SNOMED source provides attributes that are used to create direct relationships. Reverse relationships are OMOP-created.

Replacement relationships

According to the SNOMED logic of concept inactivation, the reason for inactivation must be mentioned in the source file. Whenever possible, the inactivated concept should be linked to another active concept using the following replacement relationships:

association type	relationship_id	description
Replaced by	Concept replaced by	This relationship is used for a single replacement concept that is semantically similar to or more general than the inactivated concept
Same as	Concept same_as to	The concept has been made inactive because it has the same meaning as another concept
Alternative	Concept alt_to	The concept has been inactivated due to changes in the Editorial policy, e.g. branded products were considered out of scope for SNOMED CT, an Alternative would be the generic product.
Was_a	Concept was_a to	A historical type of relationship that was used for “Limited” inactivation reason. No longer in use for new content inactivations as of the July 2018 release.
Possibly equivalent to	Concept poss_eq to	This type of relationship is assigned to the concepts with “Ambiguous” inactivation reason. Unlike other replacement relationships, ‘Concept poss_eq to’ may not lead to a single and unambiguously synonymous target concept. According to the SNOMED logic, “every effort should be made to identify all of the clinically useful "POSSIBLY_EQUIVALENT_TO" target concepts, which should be semantically as close as possible to the meaning of the inactivated concept.” Since 2022 ‘Concept poss_eq to’ is no longer considered a replacement relationship in OMOP.

Concepts with active replacement links are considered upgraded (invalid_reason = ‘U’).

Hierarchy

In OMOP we create the internal SNOMED hierarchy using ‘Is a’ attribute relationships provided by the source.

At the same time, as SNOMED is considered standard vocabulary for the Condition, Observation, Procedure, and Measurement domains, other vocabularies are embedded into the hierarchy of SNOMED using OMOP-created ‘Is a’ relationships.

Mapping

• Standard SNOMED concepts map to themselves.
• Despite SNOMED being considered a standard vocabulary for the Measurement domain in case of a full semantic match mapping from SNOMED to LOINC is created.
• Concepts such as concepts with the semantics of allergies, personal history, and pre-coordinated measurement results are mapped to standard concept + value.
• Concepts that belong to the Race, Gender, Unit, and Provider domains are mapped to standard concepts in the respective domains.
• Concepts in the Drug domain are mapped to standard vocabularies for the Drug domain. In OMOP we use both UMLS sources for mapping from SNOMED to RxNorm, and manual mapping.
• Concepts that belong to the Observable Entity concept class are mapped to the concepts in the Staging/Scales concept class in case of a full semantic match.
• Concepts that carry the semantics of secondary neoplasms are mapped to Cancer Modifier vocabulary.
• Concepts that belong to Observable Entity and Procedure concept classes in most cases represented semantic duplicates in the Measurement domain. According to SNOMED official documentation, the deduplication of Measurements should be performed towards Observable Entities as these concepts are supposed to represent the result of the evaluation procedure. However, we noticed that currently, most measurements in the Observable Entity concept class belong to the UK Clinical Extension Module and their hierarchy is much less complete than the hierarchy of Procedures. In such cases, we have built ‘Maps to’ relationships in the opposite direction: from Observable Entities to Procedures. If Observable Entity concepts belong to SNOMED CT Core Module they remain standard with the duplicative Procedure concepts mapped to them.
• In OMOP, we create ‘Maps to’ relationships following the replacement relationships. Whether a concept has multiple replacement relationships with different target concepts, we consider the replacement relationship with the highest precedence: 'Concept replaced by' then ‘Concept same_as to' then 'Concept alt_to to' then 'Concept was_a to'.

Equivalent and categorical relationships

A range of relationships exist that provide semantic links from SNOMED to other vocabularies. Unlike ‘Maps to’, these relationships do not indicate a full semantic match and should be used only for reference:

relationship_id	relationship_name (source)
SNOMED - ATC eq	SNOMED to ATC equivalent (RxNorm)
SNOMED - CPT4 eq	SNOMED to CPT-4 equivalent (OMOP)
SNOMED cat - CPT4	SNOMED category to CPT-4 (OMOP)
SNOMED - HOI	SNOMED contained in HOI (OMOP)
SNOMED - MedDRA eq	SNOMED to MedDRA equivalent (OMOP)
SNOMED - NDFRT eq	SNOMED to NDF-RT equivalent (RxNorm)
SNOMED - RxNorm eq	SNOMED to RxNorm equivalent (RxNorm)
SNOMED - VA Class eq	SNOMED to VA Class equivalent (RxNorm)
SNOMED - ind/CI	SNOMED to Indication/Contra-indication