Vocab. SNOMED_Veterinary

SNOMED CT Veterinary Extension

Overview

SNOMED CT Veterinary Extension is an extension to SNOMED CT that provides content of veterinary importance and terms veterinarians use.

Sources

SNOMED CT Veterinary Extension is maintained by the Veterinary Terminology Services Laboratory (VTSL) at Virginia-Maryland College of Veterinary Medicine.

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.

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, Measurement, Observation, Procedure, Spec Anatomic Site, and Specimen domains are Standard.
• By default all valid concepts that belong to the Metadata and Drug domains are non-Standard.

Domains

Domains of concepts are assigned according to the concept semantics. A list of domains presented in SNOMED Veterinary is following:

Condition

Device

Drug

Measurement

Metadata

Observation

Procedure

Spec Anatomic Site

Specimen

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:

Attribute

Body Structure

Clinical Finding

Event

Life circumstance

Location

Model Comp

Morph Abnormality

Navi Concept

Observable Entity

Organism

Physical Object

Procedure

Qualifier Value

Social Context

Specimen

Substance

Concept Relationships

A wide spectrum of relationships links concepts within the SNOMED CT Veterinary Extension and between SNOMED Veterinary and SNOMED CT. Below we describe the main groups of the 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
42600140, Adenoma of bronchus	Has associated morphology	4266171, Benign adenomatous neoplasm - category
	Has finding site	4317407, Bronchial structure

A full list of attribute relationships can be found in the concept_relationship table. Note that the SNOMED Veterinary source provides attributes 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

SNOMED CT Veterinary Extension is embedded in the SNOMED CT hierarchy using ‘Is a’ attribute relationships provided by the source.