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Upcoming changes
Two major changes are expected in this release:
- First, according to the Committee decision, concepts representing evaluation findings (e.g. Neutropenia or Elevated PSA) have been reconsidered:
- All pre-coordinated SNOMED concepts falling into the hierarchy of Evaluation Findings will undergo a revision of their Domain assignment as either Condition or Measurement.
- The source concepts mapped to pre-coordinated SNOMED Condition concepts will assume the same Domain as per mapping rules.
- The source concepts that have equivalent pre-coordinated SNOMED Measurement concepts (carrying the semantics of both lab test and its result ) will be mapped to these and assume the same Domain as per mapping rules.
- In cases, when there are no pre-coordinated SNOMED Measurement concepts, the source concepts will be mapped to post-coordinated SNOMED Measurement (analyte) concepts and adequate value concepts (the result).
- After extensive discussion, the Committee came up with the decision to roll back the mapping of CPT4 and HCPCS procedure codes to the Visit domain. These concepts are standard and belong to the Procedure or Observation domain according to their semantics. A new relationship is implemented to link CPT4 and HCPCS concepts to the Visit domain. Therefore, it will still be possible to use relationships to Visits, but with the help of a different relationship_id (Has asso visit).
In partnership with the European Organisation for Research and Treatment of Cancer (EORTC), we introduce new vocabulary to support source-level analytics coming from EORTC Quality of life surveys. The content was sourced from the EORTC QLQ via the Item Library Website and was limited to clinically validated items.
- Concepts’ level overview:
- Source and Transformation: Names come directly from the source. Concept Codes are made up of multiple components, including the item library id, the acronym of the concept class, and the entity's position within its specific concept class.
- New concept_class_id’s, specific for EORTC QLQ instrumentary, such as EORTC QLQ C30, and disease-specific modules(e.g. EORTC QLQ CR29). They are added to the Measurement, Observation, and Meas Value domains.
- Most of the concepts are non-standard, and classificational entries serving as intra-vocabulary groupers are added as exceptions for Time, Symptom, and Response Scales as well as for Questions to ease the navigation within terminology.
- Relationships‘ level overview:
- Structured relationships within the vocabulary include hierarchical and associative types, e.g. “Is a/Subsumes” and “Scale of/Has Scale”.
- There are no relationships to other vocabularies
| Vocabulary | Vocabulary Module | Version |
| ATC | NA | 2024-12-27 |
| LOINC | NA | 2.78 Aug 2024 |
| SNOMED | SNOMED CT International | 2024-08-01 |
| SNOMED | SNOMED CT US Edition | 2024-09-01 |
| SNOMED | SNOMED CT UK Edition | 2024-10-01 |
| MedDRA | NA | 2024-12-19 |
| HCPCS | NA | January 2025 |
| CPT4 | NA | 2024AB UMLS |
| ICD10PCS | NA | 2025 |
| CVX | NA | 2024-09-05 |
| RxNorm | NA | 2024-12-02 |
| SNOMED Veterinary | NA | 2025-01-01 |
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- Six HCPCS codes (G9247, G2077, G9246, G2076, M1259, M1260) significantly changed their source long descriptions and are considered reused.
NB! According to our current policy, we do not update the names of the reused codes. The whole list can be found on the Known Issues page.
- One NUCC concept 246Q00000X was assigned with the source-asserted name: ‘Pathology Specialist/Technologist’ instead of ‘Pathology Technician’
- One UCUM concept name was corrected: ml/cm [H2O], milliliter per centimeter of water
- Domain assignment of SNOMED concepts related to ‘Evaluation Findings’ has been revised. These concepts have been assigned with the Condition or Measurement domain as per the Committee's decision.
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CPT4 - SNOMED hierarchy has been expanded. We embedded more than 2k CPT4 codes into the SNOMED hierarchy.
‘CPT4 - SNOMED cat’ relationships will continue to contribute to the hierarchy. After extensive testing, we concluded that their exclusion from the hierarchy leaves many standard procedure codes outside the concepts_ancestor. - ICD10PCS - SNOMED hierarchy has been improved in its preciseness. More than 8k erroneous ‘Is a’ links have been deprecated.
- LOINC-SNOMED hierarchy has been expanded.
- SNOMED:
- HCPCS and CPT4:
- ICD Family of vocabularies (ICD10, ICD10CM, ICD9CM, ICD10GM, ICD10CN, CIM10, and KCD7: existing mappings have been updated either due to community contribution or following the SNOMED update.
- Other vocabularies (CC): new mapping has been added as a part of the Community Contribution Initiative for ICD10PCS.
Mapping of SNOMED concepts representing ‘Evaluation Findings’ to post-coordinated measurement and value pairs has been deprecated.
Mapping of HCPCS and CPT4 concepts to the Visit domain has been deprecated. Instead, we introduce a new relationship ‘Has associated visit’ (relationship_id = ‘Has asso visit’) to link concepts with the semantics of visit, and the corresponding concepts in the Visit domain/ ETL may use these relationships if transformation logic requires such precision to create visits from procedure codes.
For more advanced users, we have created a more detailed, vocabulary-focused version of the upcoming changes. Please find it below:
Click here to expand
- The ATC vocabulary has been updated to the December 2024 version.
- New Additions: 92 new ATC codes have been added.
- We continue refining the drugs with multiple ATC codes. We reviewed all RxNorm/RxNorm Extension concepts associated with five or more ATC codes. Unnecessary and redundant mappings were removed, resulting in cleaner ATC - RxNorm relationships.
- All multivitamin preparations and combinations of different amino acids for parenteral nutrition were remapped to A11AA03 and B05BA10, respectively.
- New QA: Additional validation checks were implemented based on information retrieved from the UMLS API. We use ATC codes assigned by UMLS to check a drug's corresponding 4th level of ATC. In case of a mismatch, concepts are subjected to review.
- CVX vocabulary has been updated with its CVX 20240905 version.
- 6 new concepts have been added.
- CPT4 has been updated to the 2024AB UMLS version.
- 27 historical CPT4 concepts have been added following the Community request.
- One immunization code for the Chikungunya virus vaccine (90593) has been added but remains unmapped due to the absence of a proper CVX or RxNorm target.
- Mapping to Visit rollback: CPT4 concepts, previously mapped to Visit concepts, are back to being Standard concepts in the Procedure or Observation domains. The rollback of mapping should simplify the usage of CPT4 and HCPCS concepts.
- A new type of relationship has been created: ‘Has associated visit’ (relationship_id = ‘Has asso visit’) which connects CPT4 concepts with the semantics of visit and the corresponding concepts in the Visit domain:
CPT4 concept standard_concept relationship_id Visit concept 59850, Induced abortion, by 1 or more intra-amniotic injections (amniocentesis-injections), including hospital admission and visits, delivery of fetus and secundines S Has asso visit A0, Hospital 99504, Home visit for mechanical ventilation care S Has asso visit OMOP4822459, Home Visit This relationship can be used to construct Visit records from CPT4 and HCPCS concepts.
- HCPCS has been updated to the January 2025 version.
- Mapping to Visit rollback: HCPCS concepts, previously mapped to Visit concepts, are back to being Standard concepts in the Procedure or Observation domains. The rollback of mapping should simplify the usage of CPT4 and HCPCS concepts.
- A new type of relationship has been created: ‘Has associated visit’ (relationship_id = ‘Has asso visit’) which connects HCPCS concepts with the semantics of visit and the corresponding concepts in the Visit domain:
HCPCS concept standard_concept relationship_id Visit concept G9478, Services performed by other qualified therapist in the hospice setting, each 15 minutes S Has asso visit 34, Hospice S9109, Congestive heart failure telemonitoring, equipment rental, including telescale, computer system and software, telephone connections, and maintenance, per month S Has asso visit OMOP5556618, Telehealth This relationship can be used to construct Visit records from CPT4 and HCPCS concepts.
- ICD10PCS has been updated to the 2025 version of the source.
- Mappings of 22 ICD10PCS codes to Standard concepts in the Drug domain have been added.
- 8k imprecise ‘Is a’ relationships from ICD10PCD to SNOMED have been deprecated, resulting in a cleaner hierarchy in the Procedural domain.
We continue mapping harmonization across vocabularies by refactoring groups of concepts and adjusting grouping criteria in the Common Data Environment for the ICD family. Some previously integrated groups have been split to enhance the granularity of mappings. ICD family has been affected by the post-coordination rollback. A group of concepts representing the evaluation findings (eg. E78.41, Elevated Lipoprotein(a)) has been remapped to pre-coordinated standard concepts in SNOMED.
- ICD10CM: Existing mappings have been updated following:
- SNOMED update
- Community contribution integration
- ICD10: Existing mappings have been updated following the SNOMED update.
- ICD9CM: Existing mappings have been updated following the:
- SNOMED update
- Community contribution integration
- ICD10GM: Existing mappings have been updated following the SNOMED update.
- ICD10CN: Existing mappings have been updated following the SNOMED update.
- KCD7: Existing mappings have been updated following the SNOMED update.
- CIM10: Existing mappings have been updated following the SNOMED update.
- LOINC vocabulary has been updated with its 2.78 Aug 2024 version.
- We continue the expansion of the LOINC - SNOMED hierarchy. In this release, we added more links between LOINC and SNOMED in the Lab tests area.
- The LOINC Consumer Name file has been utilized in the concept_synonym table. As a result, common synonyms for the LOINC Lab tests are available in the concept_synonym table:
| concept code | concept name | concept synonym |
| 32318-8 | Glucose [Moles/volume] in Specimen | Glucose, Specimen |
| 5183-9 | Hepatitis A virus Ab [Units/volume] in Serum or Plasma by Immunoassay | Hepatitis A virus (HAV) antibody, Blood |
- MedDRA has been updated according to the source version 27.1, effective September 2024.
- The MedDRA-SNOMED / OMOP Extension hierarchy has been expanded.
- A total of 1050 PT concepts and 12 LLTs have been mapped to concepts in standard vocabularies, primarily SNOMED.
- MedDRA has been almost unaffected by the rollback of postcoordination. The reason is a clear distinction between the precoordinated Measurement results (eg. 10005760, Blood pressure systolic increased) and Conditions (eg. 10027905, Monocytopenia) in the vocabulary.
- About 300 previously existing MedDRA-SNOMED mappings were manually reviewed to select the best mapping candidate, considering new suggested candidates from various sources, particularly UMLS, and the deprecation of some old concepts.
- SNOMED has been updated according to the following versions of its modules:
- 2024-08-01 SNOMED CT International;
- 2024-09-01 SNOMED CT US Edition;
- 2024-10-01 SNOMED CT UK Edition.
- Following the Committee’s resolution, we extensively reviewed concepts representing Evaluation Findings. These concepts became standard and, depending on their semantics, were assigned the condition or measurement domain.
- Mapping of SNOMED Evaluation Findings to the respective measurements and their values has been deprecated.
- Concept synonyms in Spanish have been introduced per the Community request.
- Minor changes related to mapping improvement have been performed.
- The vocabularies have been updated to the December 2024 version.
- The vocabulary has been updated to the February 2024 version.
- One concept has been added as per the Community’s request: {RU}/mL, relative units per milliliter
- One concept name has been corrected: ml/cm [H2O], milliliter per centimeter of water
The following source vocabularies have been updated:
- CIEL
- ICD9Proc
- MeSH
- OPCS4
- UK Biobank
- CDISC
- EDI
- CO-CONNECT TWINS
- GRR
- OMOP Invest Drugs
All vocabularies have included mapping improvements.
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Hierarchy of Routes by Theresa Burkard
Two new concepts for the Implant and Injectable routes have been added to the OMOP Extension. The relationship ‘Has route of administration’ was leveraged to link Dose Forms to the Route concepts. These changes allow simplified calculation of DDD, based on the use of route information in the data.
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HemOnc update by Robert Miller, Jeremy Warner, and Alexander Davydov
The HemOnc vocabulary has been updated according to the source version of 2024-12-19. The release adds approximately 3500 new Regimens, 750 new Regimen classes, and more than 200k new relationships.
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SNOMED Veterinary update by Julie Green
SNOMED Veterinary has been updated according to the source version of 2025-01-01. This is the first update of Veterinary SNOMED since 2019!
- ICD Family of vocabularies (ICD10, ICD10CM, ICD9CM, ICD10GM, ICD10CN, CIM10, and KCD7: existing mappings have been updated due to Community Contribution.
- Other vocabularies: new mapping has been added as a part of the Community Contribution Initiative for ICD10PCS.
In this release, we have renamed relationship_id predicate values in the relationship metadata table to correspond with the SSSOM format and the output of USAGI:
| Previous relationship_id predicate value | New relationship_id predicate value |
| eq - equivalent | [exactMatch] |
| up - uphill | [broadMatch] |
| down - downhill | [narrowMatch] |
Pre-/Post-coordination migration
According to the discussion around the post-coordination of pre-coordinated SNOMED measurements, the Vocabulary Team does not perform any further post-coordination work.
Pack_content table, unavailable in Athena, will be available via the Vocabulary-v5.0 github repository.
We will deliver the SSSOM-compatible metadata for certain relationships. The metadata will mimic the one we collect during the community contribution process and will contain the following information:
-
Relationship metadata
- Relationship_id predicate (how precise the relationships are): equivalent [exactMatch], uphill [broadMatch], downhill [narrowMatch]
- Mapping tool (name of the tool or approach used to derive mappings if any)
- Mapping source (source of the mapping if relationships are coming from the curated sources such as UMLS)
- Confidence (how confident human reviewer is about the quality of the mapping)
- Mapper_id (identifier of the person who performed the mappings if any)
- Reviewer_id (identifier of the person who reviewed the mappings if any)
-
Concept metadata
NB! The structure of basic vocabulary tables (i.e. concept,concept_relationship) will not be changed and the first release of metadata will be stored in separate tables.
- In partnership with the Critical Path Institute, we introduce the CDISC (Clinical Data Interchange Standards Consortium) - a cornerstone terminology used in SDTM (data model for clinical trial data). We used 2023_11 version.
- Concepts’ level overview:
- We used NCI-metathesaurus as the source. We included the full list of CDISC values available.
- In some cases concept codes are represented as a complex construct from a unique source identifier and CDISC code values (where available) separated by ‘-’.
- The vocabulary is enriched with synonyms to facilitate the ETL process.
- All the CDISC concepts are non-standard.
- Relationships‘ level overview:
- Mappings are limited to those that can be either algorithmically derived from NCI-metathesaurus tables for clear 1:1 mappings, or curated manually for pre-selected, prioritized ones.
| Vocabulary | Vocabulary Module | Version |
| ATC | NA | January 2024 version |
| LOINC | NA | 2.77 Feb 2024 version |
| SNOMED | SNOMED CT International | 2024-02-01 |
| SNOMED | SNOMED CT US Edition | 2024-03-01 |
| SNOMED | SNOMED CT UK Edition | 2024-04-10 |
| MedDRA | NA | version 27.0, effective from March 2024 |
| HCPCS | NA | July 2024 |
| CPT4 | NA | 2024AA |
| CMS Place of Service vocabulary | NA | May 2, 2024 |
| ICD10CM | NA | FY2025, effective from October 01, 2024 |
| EDI | NA | July 2024 version |
| Visit | NA | August 2024 |
| OMOP Extension | NA | August 2024 |
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HCPCS:
- We improved the precision of validity dates of reused codes to ensure more accurate cohort building.
-
CMS Place of Service:
- Concept ‘27, Inpatient Long-term Care (Deprecated)’ has been deprecated by the source and its concept code was reused.
NB! According to our current policy, we do not update the names of the reused codes.
-
ATC:
- We corrected the names of ATC classes based on the refined assignment of routes of administration.
-
CMS Place of Service:
- We added a note ‘(Deprecated)’ to the names of the codes deprecated by the source concepts. These codes are maintained as Standard (unless they are mapped).
-
PPI:
- Concept name has been changed for some concepts as a part of the Community Contribution Initiative.
-
SNOMED:
- Concepts related to ‘Allergic reactions’ have been moved to the Condition domain.
- Concepts related to ‘Patient encounters’ have been moved to the Observation domain.
-
PPI:
- Concept class has been changed for some concepts as a part of the Community Contribution Initiative.
Click here to expand
Vertical (hierarchical) relationships:
- LOINC - SNOMED hierarchy has been expanded.
- MedDRA - SNOMED / OMOP Extension hierarchy has been expanded.
-
CPT4 - SNOMED hierarchy has been expanded. We embedded CPT4 anesthesia-related codes into the SNOMED hierarchy.
CPT4 - SNOMED cat’ relationships will continue to contribute to the hierarchy. After extensive testing, we concluded that their exclusion from the hierarchy leaves a large number of standard procedure codes outside the concepts_ancestor. - ATC-RxNorm Relationships hierarchy has been expanded and refined. We introduced a new source-based approach to derive relationships from existing drug vocabularies and greatly refined the relationships to improve accuracy and comprehensiveness. We constructed new relationships for the ATC codes introduced since the previous release. We cleaned up old relationships from ATC to RxNorm drugs.
Horizontal (non-hierarchical/ mappings) relationships:
-
SNOMED:
- SNOMED concepts in the Measurement domain mapped to LOINC during the previous release have become standard and their mappings to LOINC have been reverted. LOINC - SNOMED deduplication to be discussed in future Vocabulary WG sessions.
- Some of the SNOMED concepts were mapped over to their standard counterparts.
It includes both cases when SNOMED concepts were standard and cases when SNOMED concepts did not have mappings. Currently, these affect the following chapters:
- Vaccine and immunization codes in the procedure domain
- Units, providers and drugs
- Personal history and allergies
- Geography
Concepts ‘02, Telehealth Provided Other than in Patient’s Home’ and ‘10, Telehealth Provided in Patient’s Home’ have been destandardized and mapped to the Standard Telehealth concept in the Visit vocabulary, as well as other concepts, previously mapped to ‘02, Telehealth Provided Other than in Patient’s Home’ and ‘10, Telehealth Provided in Patient’s Home’
For more advanced users, we have created a more detailed, vocabulary-focused version of the upcoming changes. Please find it below:
Click here to expand
- Pack_content table, unavailable from the Athena, will be available via the Vocabulary-v5.0 GitHub repository.
- We will deliver the SSSOM-compatible metadata for certain relationships. The metadata will mimic the one we collect during the community contribution process and will contain the following information:
-
Relationship metadata
- Relationship_id predicate (how precise the relationships are): equivalent [exactMatch], uphill [broadMatch], downhill [narrowMatch]
- Mapping tool (name of the tool or approach used to derive mappings if any)
- Mapping source (source of the mapping if relationships are coming from curated sources such as UMLS)
- Confidence (how confident a human reviewer is about the quality of the mapping)
- Mapper_id (identifier of the person who performed the mappings if any)
- Reviewer_id (identifier of the person who reviewed the mappings if any)
-
Relationship metadata
-
Concept metadata
NB! The structure of basic vocabulary tables (i.e. concept, concept_relationship) will not be changed, and the first release of metadata will be stored in separate tables.
- ATC has been refreshed to the most recent January 2024 version.
- Concepts’ level overview:
- We corrected the names of ATC classes based on the refined assignment of routes of administration.
- Relationships’ level overview:
- We introduced a new source-based approach to derive relationships from existing drug vocabularies and greatly refined the relationships to improve accuracy and comprehensiveness.
- We constructed new relationships for the ATC codes introduced since the previous release.
- We cleaned up old relationships from ATC to RxNorm drugs and ingredients.
- LOINC vocabulary has been updated with its 2.77 Feb 2024 version.
- Relationships’ level overview:
- The LOINC-SNOMED hierarchy has been expanded.
- SNOMED concepts in the Measurement domain mapped to LOINC during the previous release have become standard and their mappings to LOINC have been reverted. LOINC - SNOMED deduplication to be discussed in future Vocabulary WG sessions.
- SNOMED has been updated according to the following versions of its modules:
- 2024-02-01 SNOMED CT International;
- 2024-03-01 SNOMED CT US Edition;
- 2024-04-10 SNOMED CT UK Edition.
- Concepts’ level overview:
- Allergic reactions have been moved to the Condition domain.
- Patient encounters have been moved to the Observation domain.
- Relationships’ level overview:
- SNOMED concepts in the Measurement domain mapped to LOINC during the previous release have become standard and their mappings to LOINC have been reverted. LOINC - SNOMED deduplication to be discussed in future Vocabulary WG sessions.
- Some of the SNOMED concepts were mapped over to their standard counterparts.
- Vaccine and immunization codes in the procedure domain
- Units, providers and drugs
- Personal history and allergies
- Geography
- According to the discussion around the post-coordination of pre-coordinated SNOMED measurements, we do not perform any further post-coordination.
It includes both cases when SNOMED concepts were standard and cases when SNOMED concepts did not have mappings. Currently, these affect the following chapters:
- MedDRA has been updated according to the source version 27.0, effective from March 2024.
- Relationships’ level overview:
- The MedDRA-SNOMED / OMOP Extension hierarchy has been expanded.
- Hierarchy mirroring (bugfix):
- Pre-coordinated MedDRA terms (Measurements) are currently positioned below general SNOMED in affected cases.
- HCPCS has been updated according to the July 2024 version.
- Concepts’ level overview:
- We improved the precision of validity dates of reused codes to ensure more accurate cohort building.
- Relationships’ level overview:
- We improved drug mapping (incl. community contribution).
- CPT4 has been updated according to the 2024AA version of UMLS Metathesaurus.
- Relationships’ level overview:
- Newly added immunization codes 90624 and 90695 have been mapped to Standard concepts in the Drug domain.
- We expanded the CPT4 - SNOMED hierarchy by embedding CPT4 anesthesia-related codes into the SNOMED hierarchy.
- ‘CPT4 - SNOMED cat’ relationships will continue to contribute to the hierarchy. After extensive testing, we concluded that their exclusion from the hierarchy leaves a large number of standard procedure codes outside the concepts_ancestor.
- CMS Place of Service vocabulary has been updated according to the May 2, 2024 version.
- Concepts’ level overview:
- We added a note ‘(Deprecated)’ to the names of the codes deprecated by the source concepts. These codes are maintained as Standard (unless they are mapped).
- Concept ‘27, Inpatient Long-term Care (Deprecated)’ has been deprecated by the source and its concept code was reused. According to our current policy, we do not update the names of the reused codes.
- Relationships’ level overview:
- Concepts ‘02, Telehealth Provided Other than in Patient’s Home’ and ‘10, Telehealth Provided in Patient’s Home’ have been destandardized and mapped to the Standard Telehealth concept in the Visit vocabulary, as well as other concepts, previously mapped to ‘02, Telehealth Provided Other than in Patient’s Home’ and ‘10, Telehealth Provided in Patient’s Home’
- Concepts’ level overview:
- A new OMOP-created concept has been added to the Visit vocabulary: OMOP5556618, Telehealth. This concept is intended to be a standard concept for all Telehealth visits, with CMS Place of Service codes 02 and 10 mapped to it.
- Relationships’ level overview:
- Missing ‘Maps to value’ relationships have been added (bugfix)
- In partnership with the Critical Path Institute, we introduce the CDISC (Clinical Data Interchange Standards Consortium) - a cornerstone terminology used in SDTM (data model for clinical trial data). We used the 2023_11 version.
- Concepts’ level overview:
- We used NCI-metathesaurus as the source. We included the full list of CDISC values available.
- In some cases concept codes are represented as a complex construct from a unique source identifier and CDISC code values (where available) separated by ‘-’.
- The vocabulary is enriched with synonyms to facilitate the ETL process.
- All the CDISC concepts are non-standard.
- Relationships‘ level overview:
- Mappings are limited to those that can be either algorithmically derived from NCI-metathesaurus tables for clear 1:1 mappings, or curated manually for pre-selected, prioritized ones.
- Overview:
- In this release, we incorporate external mapping sources, such as SNOMED - ICD mappings and UMLS into the ICD Family Common Data Environment.
- ICD10, ICD10CM, ICD9CM, ICD10GM, ICD10CN, CIM10 and KCD7 vocabularies have been updated to take into account new mapping candidates.
- With additional mapping sources integration, we continue mapping harmonization across vocabularies by refactoring groups of concepts and adjusting grouping criteria. Some previously integrated groups have been split to enhance the granularity of mappings.
-
ICD10CM:
- Has been updated to the latest version (FY2025), effective from October 01, 2024.
- Relationships’ level overview:
- Existing mappings have been updated following:
- SNOMED update
- Community contribution integration
- Existing mappings have been updated following:
-
ICD10:
- Relationships’ level overview:
- Existing mappings have been updated following the SNOMED update.
- Relationships’ level overview:
-
ICD9CM:
- Relationships’ level overview:
- Existing mappings have been updated following the:
- SNOMED update
- Community contribution integration
- Existing mappings have been updated following the:
- Relationships’ level overview:
-
ICD10GM:
- Relationships’ level overview:
- Existing mappings have been updated following the SNOMED update.
- Relationships’ level overview:
-
ICD10CN:
- Relationships’ level overview:
- Existing mappings have been updated following the SNOMED update.
- Relationships’ level overview:
-
KCD7:
- Relationships’ level overview:
- Existing mappings have been updated following the SNOMED update.
- Relationships’ level overview:
-
CIM10:
- Relationships’ level overview:
- Existing mappings have been updated following the SNOMED update.
- Relationships’ level overview:
-
PPI:
- Concepts’ level overview:
- Concept class and concept name have been changed for some concepts
- Concepts’ level overview:
-
HCPCS
- Relationships’ level overview:
- The mapping of one drug HCPCS code has been improved using the community contribution input.
- Relationships’ level overview:
-
ICD10PCS
- Relationships’ level overview:
- Mappings of some ICD10PCS codes to Standard concepts in the Drug domain have been added.
- Relationships’ level overview:
-
ICD10CM
- Relationships’ level overview:
- Mappings have been improved with the help of the community contribution input.
- Relationships’ level overview:
-
ICD9CM
- Relationships’ level overview:
- Mappings have been improved with the help of the community contribution input.
- Relationships’ level overview:
- EDI, the Korean Electronic Data Interchange code system was updated as a part of a community contribution initiative/pipeline.
- The vocabulary has been updated to the July 2024 version.
- Source data update was done by Seng Chan You and Yiju Park.
- The resulting content was integrated by the vocabulary team using the stage table transfer approach.
SNOMED UK Drug Extension Module has been excluded from SNOMED OMOP vocabularies. Concepts that belonged to this module have been deprecated and linked to their duplicates in dm+d vocabulary. Their concept codes and names have been replaced by placeholders to avoid misuse. UK Drug Extension concepts in the Route domain have been de-standardized and mapped to standard Routes that belong to other SNOMED Modules.
The concept class Clinical Finding has been split into two concept classes: Disorder and Clinical Finding, as assigned in the source by SNOMED. This decision will help us to assign domains more easily and more precisely.
Concepts that belong to Attribute, Location (except countries), Social Context (except concepts that carry the semantics of relatives, religion, occupation), Physical Force, and Physical Object (except concepts in the Device domain) concept classes have been de-standardized.
Domain assignment has been improved to achieve better accuracy. For example, concepts ‘Positive’, ‘Negative’, and ‘Malignant’ were moved from Spec Disease Status to the Meas Value domain, and countries were moved to the Geography domain.
Pre-coordinated concepts that represent the results of evaluation procedures have been split and mapped to Measurements and their value. Concepts that cannot be properly mapped remain standard concepts in the Measurement domain. Pre-coordinated concepts that represent allergies have been split and mapped to ‘Allergy to substance’ + causative agent in a post-coordinated way.
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 the SNOMED CT Core Module they remain standard with the duplicative Procedure concepts mapped to them. Deduplication in the Measurement domain included mapping concepts in the Observable Entity concept class to their duplicates in the Staging/Scales concept class.
Secondary neoplasm concepts have been mapped to the Cancer Modifier.
Concepts in the Race and Provider domains have been mapped to standard concepts in the respective domains.
MedDRA remains a classification vocabulary and can be used in two directions: to map source MedDRA codes to OMOP standard codes and to use MedDRA codes as classification concepts for concept set construction. Our efforts in this release have been focused on mapping Preferred Terms (PT), which means that the mapping of LLT terms stays without major changes. More detailed information can be found at the forum.
Using MedDRA concepts as classification will be available for mapped PT and LLT concepts. In this case, ‘Maps to’ links are used for hierarchy construction. PT and LLT concepts without corresponding ‘Maps to’ links will become non-standard.
Concepts that previously were assigned the Visit and Provider domains according to their mapping have been moved to the Observation domain according to the Community’s request..
All HCPCS concepts in the Drug domain have become non-standard as HCPCS is not a standard vocabulary for Drugs. All HCPCS concepts in the Drug domain are supposed to be mapped to standard concepts in the Drug domain. If concepts cannot be mapped due to lack of specificity, they are assigned with Procedure domain, embedded into the hierarchy of Procedures, and remain standard.
LOINC vocabulary has been updated with its 2.76 Sep 2023 version.
The LOINC-SNOMED hierarchy was significantly expanded. Specifically, we've leveraged the outcomes of LOINC-SNOMED collaboration, particularly the LOINC ontology, to enhance and refine the hierarchical relationships between SNOMED and LOINC Measurements.
In this release, we are refreshing VANDF and VA Class vocabularies - Veterans Health Administration National Drug File, one of RxNorm source vocabularies.
We are completely changing the logic of the domain assignment. Previously, all of the concepts within VANDF vocabulary were considered drugs, even though they did not qualify as drugs in OHDSI. Currently, we are using hierarchical relationships with VA Class vocabulary to assign domains correctly.
LOINC vocabulary will be updated with its 2.74 Feb 2023 version.
More COVID-2019-related lab tests will be included in the hierarchy of Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
We detected and will fix the problem of LOINC - SNOMED hierarchy during the upcoming release. Some LOINC concepts had multiple ancestors in SNOMED, which are ancestors and descendants of each other:
| concept_code | concept_name | relationship_id | concept_code | concept_name | |
| Before | 12849-6 | Protein [Mass/volume] in Peritoneal dialysis fluid --7th specimen | Is a | 74040009 | Protein measurement |
| 12849-6 | Protein [Mass/volume] in Peritoneal dialysis fluid --7th specimen | Is a | 166776003 | Serum/plasma protein test (descendant of Protein measurement) | |
| 12849-6 | Protein [Mass/volume] in Peritoneal dialysis fluid --7th specimen | Is a | 166809004 | Electrophoresis: paraprotein (descendant of Protein measurement) | |
| After | 12849-6 | Protein [Mass/volume] in Peritoneal dialysis fluid --7th specimen | Is a | 74040009 | Protein measurement |
In the course of the v20230116_major release, a bunch of CPT4 concepts that carry the semantics of visits were de-standardized and mapped to standard concepts in the Visit domain and changed their domain according to the mapping. These domain changes caused a lot of difficulties in the ETL processes because CPT4 codes are not routinely used for creating visit records.
The Vocabulary team considered the Community’s opinion (as per discussions on the OHDSI Forums and CDM WG), and are rolling back the domain changes in the upcoming August release. Also, we are preserving the mapping of these codes to the standard concepts in the Visit domain as they still carry the semantics of visits.
Equivalence relationships between CPT4 and SNOMED ( 'CPT4 - SNOMED cat' and 'CPT4 - SNOMED eq') are created using the inter-vocabulary synonymous and categorical relationships present in the UMLS source, respectively. In the scope of this release, 2163 such links are added. Upon adding a new target concept to the UMLS source we are deprecating the previous link of equivalence for the respective CPT4 concept.
This release enriches the NAACCR vocabulary with mappings built and provided by the community contributors. Around 1.5k of codes from 'NAACCR Value' concept class are de-Standardized and mapped over to the Cancer Modifier vocabulary. Related NAACCR Variables with their standard concept and validity parameters remained intact.
Make sure that your ETL is ready to implement the changes:
- Retrieve the mappings from non-standard NAACCR Values to Cancer Modifier Measurement concepts (relationship_id = ‘Maps to’).
- Populate the measurement_concept_id with concept_id from the standard Cancer Modifier counterparts.
- Do not populate the value_as_concept_id field (even though it may be stored as the value in the source data).
Concept_id for event fields should be selected depending on the mapping of NAACCR Value solely.
Different ETL scenarios are described in following table:
| Source data (NAACCR Variable-Value) | OMOP CDM target | |||||||
| Logical group | NAACCR Variable | NAACCR Value | concept code | concept name | ||||
| concept code | concept name | std concept | concept code | concept name | std concept | |||
| 1 | 2860 | CS Mets Eval | S | For cases when value is not mapped or not populated | 2860 | CS Mets Eval | ||
| 2860 | CS Mets Eval | S | larynx_supraglottic@2860@3 | Meets criteria for AJCC pathologic staging of distant metastasis:||Specimen from metastatic site microscopically positive WITHOUT pre-surgical systemic treatment or radiation |OR specimen from metastatic site microscopically positive, unknown if pre-surg | NULL | OMOP4998856 | Metastasis | |
| 2.1 | 774 | EOD Regional Nodes | S | For cases when value is not mapped or not populated | 774 | EOD Regional Nodes | ||
| 774 | EOD Regional Nodes | S | melanoma_choroid_ciliary_body@774@999 | Unknown; regional lymph node(s) not stated|Regional lymph node(s) cannot be assessed|Not documented in patient record||Death Certificate Only | NULL | NA | NA | |
| 2.2 | 774 | EOD Regional Nodes | S | For cases when value is not mapped or not populated | NA | NA | ||
| 774 | EOD Regional Nodes | S | net_jejunum_ileum@774@400 | Large mesenteric masses (greater than 2 cm)|Lymph node metastasis greater than 2 cm | NULL | OMOP4998946 | Regional spread to lymph node | |
| 2.3 | 774 | EOD Regional Nodes | S | For cases when value is not mapped or not populated | 774 | EOD Regional Nodes | ||
| liver@774@800 | Regional lymph node(s), NOS|Lymph node(s), NOS | S | liver@774@800 | Regional lymph node(s), NOS|Lymph node(s), NOS | ||||
| 3 | merkel_cell_penis@2870 | Size of Metastasis in Lymph Nodes | NULL | Irrespective of value | OMOP4998351 | Dimension of Lymph Node | ||
| merkel_cell_penis@2870@990 | Metastasis or tumor nests in regional lymph nodes, size cannot be assessed | NULL | OMOP4998946 | Regional spread to lymph node | ||||
*std - standard_concept
Our team continues remapping of smoking-related concepts to the OMOP Extension vocabulary. During our last major release, we created a set of OMOP Extension concepts to accompany the ETL Smoking convention. The progress can be tracked here on the OHDSI Forum.
During this release we will focus on remapping of SNOMED concepts: the smoking-related SNOMED terms will be mapped to new OMOP Extension concepts. These changes affect smoking-related concept sets and cohorts built on currently standard SNOMED concepts. The top concept of hierarchy is Findings of tobacco or its derivatives use or exposure. Tobacco users are now defined according to the type of the product they use (Smokeless, Electronic, Cigarettes, Cigars, etc.), while cigarette smokers are also classified according to the severity of smoking (Trivial, Light, Moderate, Heavy, Very heavy). Cigarette pack-years smoked during life concept is intended to capture the cumulative consumption of cigarettes.
Note 1: these changes do not concern the concepts that are adjacent to smoking (for example, Nicotine dependence). Identification of patients who smoke can be based on more broad terms (such as nicotine dependence or nicotine abuse), more granular terms (such as fact of smoking, number of pack-years, etc.) or combination of such. The hierarchy we created enables clean representation and retrieval of the granular concepts. Your concept set design should depend on code utilization in the data intended to be used and intended specificity/sensitivity of your phenotype.
Note 2: in some cases post-coordination in data modeling may be changed to pre-coordination and vice versa. These may significantly affect ETL process through the source_to_concept_map table.
| Source data (various vocabularies*) | OMOP CDM target (OMOP Extension) | ||||||
| source_concept_id | source_concept_name | source_value_concept_id | source_value_concept_name | event_concept_id | concept_name | value_as_concept_id | concept_name |
| 4310250 | Ex-smoker | NA | 1340204 | History of event | 903657 | Cigarette smoker | |
| 903651 | Currently doesn't use tobacco or its derivatives | NA | |||||
| 4203874 | Smoking monitoring status | For cases when value is not mapped or not populated | NA | NA | NA | NA | |
| 4298794 | Smoker | 903657 | Cigarette smoker | ||||
* - this might be relevant to custom mapping vocabularies also
Please make sure that upcoming changes will be addressed in your ETLs and studies.
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