Vocab. SNOMED - OHDSI/Vocabulary-v5.0 GitHub Wiki
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.
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.
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.
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.
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 Their concept codes and names have been replaced by placeholders (Retired SNOMED UK Drug extension concept, do not use, use concept indicated by the CONCEPT_RELATIONSHIP table, if any) to avoid misuse.
SNOMED specifications and guides are available here.
We use UMLS source files to add synonyms for SNOMED concepts.
The procedures for transforming Concepts from the source to the OMOP Standard Vocabularies can be found on the OHDSI GitHub.
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 codes are assigned according to the conceptid field provided by the source.
- 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 of concepts are assigned according to the following algorithm:
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 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 |
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.
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’).
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 rules are subject to change constantly, please follow the discussions on the OHDSI Forum and OHDSI Vocabulary working group (a subgroup of the CDM WG) for the most recent information.
- 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'.
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 |