Release notes v20230831
This guide can provide you more background on how to read the release notes.
What's New
1. CPT4
- The vocabulary was updated according to the 2023AA version of the UMLS source.
- 1612 CPT4 concepts in Procedure, Measurement and Observation domains were mapped to standard concepts in the respective domains, and 2761 concepts were embedded into the hierarchy of SNOMED.
- 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 were added. Upon addition a new target concept to the UMLS source we deprecate the previous link of equivalence for the respective CPT4 concept.
- Concepts whose domains had been changed to Visit in the course of v20230116_major release obtained their original domains (Observation, Procedure, Measurement) as per community request.
- In CPT4 concepts migrate between categories and obtain new concept_codes. This results in semantic duplicates within the vocabulary. 71 duplicative concepts were destandardized and mapped over to the newest CPT4 codes or the standard SNOMED concepts in the respective domain.
- 10 CPT4 Hierarchy concepts for COVID-19 vaccines were mapped to standard concepts in the Drug domain according to their semantics.
- Logic of concept class assignment to CPT4 Modifiers was fixed, so that deprecated by the source modifiers preserve their concept_class_id = ‘CPT4 Modifier’.
2. RxNorm
- The vocabulary has been updated to July 2023 version
3. NDC/SPL
- The vocabulary has been updated to August 2023 version, effective from 27th of August
4. LOINC
-
LOINC vocabulary has been updated with its 2.75 Aug 2023 version.
-
LOINC-SNOMED hierarchy was improved:
Some LOINC concepts had multiple ancestors in SNOMED, which were ancestors and descendants of each other. This resulted in loops of hierarchical relationships
-
COVID-2019-related lab tests were rolled up to the respective parent concept and were included in the hierarchy of Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
-
One-to-many mapping was fixed.
5. VANDF
- In this release, we refresh VANDF and VA Class vocabularies - Veterans Health Administration National Drug File, one of drug source vocabularies.
- We changed 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 use hierarchical relationships with VA Class vocabulary to assign Device domain correctly.
6. Co-connect
- Co-connect family of vocabularies are now distributed under the open-source license.
- Reference changed to authoring institution.
7. Smoking hierarchy (UK Biobank, HCPCS, ICD10CM)
- During this release we continued remapping Smoking related concepts in source vocabularies (UK Biobank, HCPCS, ICD10CM).
- Minor bugfixing included into the release of the affected vocabularies.
Find more information about the Smoking hierarchy convention here.
8. Read
- Enhanced and refined vaccines mapping.
- Successfully incorporated smoking mapping according to the Smoking Convention.
- Resolved improper one-to-many mappings, including instances where concepts were both ascendants and descendants of each other.
9. Community contribution
As a part of Vocabularies improvement initiative, August release was the first release in which we implemented community contribution as a transparent pathway for community to contribute their vocabularies and suggest changes to the existing.
We incorporated all submissions submitted and approved (if modification of content) by the end of June (2 months before the release).
These include:
- New vocabularies - NHS Ethnic category and NHS Place of Service (link)
- Remapping of ICD10CM terms to SNOMED (link)
- Addition of new RxNorm Extension terms to support analytics across data sources using Z index (link)
More details about the process can be found here and here.
10. Problems found during the release, but not yet fixed
-
Nearly 30% of VANDF mappings, related to solutions of all kinds (topical solution, injectable solution, etc.) are incorrect. These mappings are coming directly from the source data. VANDF and target RxNorm concepts differ in the amount of ingredients and concentration of the ingredients. We have found no differences in ingredients between VANDF and RxNorm concepts. Therefore, mappings may be used for the drug_exposure population, unless drug dosages are a prime question of the study. The examples of the mappings may be found at Known Issues page
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The CPT Editorial Panel approves new Vaccine and Immunization codes and releases them to the AMA website quarterly or sometimes even monthly. These changes often are not captured by our releases of CPT4 OMOP vocabulary, as we take UMLS as a source, and it’s updated bi-annually. Besides, the newly introduced stable cadence of bi-annual OHDSI Vocabulary releases limits our ability to add codes on requests. It may pose a problem for CDM users, who need these codes for their research.
The Vocabulary Team usually includes such concepts in the nearest scheduled CPT4 release (see Roadmap) on request. We recommend adding the necessary codes to the local CDMs in case of urgent need.
Domain changes
| vocabulary_id | old_domain_id | new_domain_id | count |
|---|---|---|---|
| CPT4 | Drug | Measurement | 1 |
| CPT4 | Measurement | Observation | 24 |
| CPT4 | Measurement | Procedure | 2 |
| CPT4 | Procedure | Measurement | 5 |
| CPT4 | Procedure | Observation | 17 |
| CPT4 | Provider | Observation | 9 |
| CPT4 | Visit | Measurement | 3 |
| CPT4 | Visit | Observation | 175 |
| CPT4 | Visit | Procedure | 8 |
| HCPCS | Visit | Observation | 16 |
| LOINC | Measurement | Observation | 2 |
| LOINC | Observation | Note | 1 |
| VANDF | Drug | Device | 11598 |
Newly added concepts grouped by Vocabulary_id and Domain
| vocabulary_id | domain_id | count |
|---|---|---|
| CPT4 | Drug | 1 |
| CPT4 | Measurement | 83 |
| CPT4 | Observation | 23 |
| CPT4 | Procedure | 142 |
| LOINC | Measurement | 2453 |
| LOINC | Meas Value | 215 |
| LOINC | Note | 114 |
| LOINC | Observation | 1217 |
| LOINC | Procedure | 402 |
| NDC | Device | 80 |
| NDC | Drug | 15352 |
| NHS Ethnic Category | Race | 15 |
| NHS Place of Service | Visit | 15 |
| RxNorm | Drug | 663 |
| RxNorm Extension | Drug | 2215 |
| SPL | Device | 3 |
| SPL | Drug | 15242 |
| VANDF | Device | 736 |
| VANDF | Drug | 813 |
Standard concept changes
| vocabulary_id | old_standard_concept | new_standard_concept | count |
|---|---|---|---|
| CPT4 | Standard | Non-standard with mapping | 1617 |
| CPT4 | Non-standard with mapping | Standard | 3 |
| LOINC | Standard | Non-standard with mapping | 1015 |
| LOINC | Classification without mapping | Non-standard without mapping | 59 |
| LOINC | Standard | Non-standard without mapping | 12 |
| LOINC | Non-standard with mapping | Standard | 1 |
| RxNorm | Standard | Non-standard without mapping | 49 |
| RxNorm | Standard | Non-standard with mapping | 7 |
| RxNorm | Classification without mapping | Non-standard without mapping | 2 |
| RxNorm Extension | Standard | Non-standard with mapping | 1410 |
| SPL | Classification without mapping | Non-standard without mapping | 3 |
| SPL | Classification without mapping | Non-standard with mapping | 1 |
| VANDF | Non-standard without mapping | Standard | 9565 |
| VANDF | Non-standard with mapping | Standard | 10 |
Newly added concepts and their standard concept status
| vocabulary_id | new_standard_concept | count |
|---|---|---|
| CPT4 | Classification with mapping | 6 |
| CPT4 | Non-standard with mapping | 9 |
| CPT4 | Classification without mapping | 40 |
| CPT4 | Standard | 194 |
| LOINC | Non-standard with mapping | 1 |
| LOINC | Classification without mapping | 620 |
| LOINC | Non-standard without mapping | 1033 |
| LOINC | Standard | 2747 |
| NDC | Standard | 80 |
| NDC | Non-standard with mapping | 7026 |
| NDC | Non-standard without mapping | 8326 |
| NHS Ethnic Category | Non-standard with mapping | 15 |
| NHS Place of Service | Non-standard with mapping | 15 |
| RxNorm | Non-standard with mapping | 28 |
| RxNorm | Non-standard without mapping | 33 |
| RxNorm | Classification without mapping | 82 |
| RxNorm | Standard | 520 |
| RxNorm Extension | Non-standard without mapping | 79 |
| RxNorm Extension | Standard | 2136 |
| SPL | Classification without mapping | 15245 |
| VANDF | Non-standard without mapping | 217 |
| VANDF | Non-standard with mapping | 617 |
| VANDF | Standard | 715 |
| Vocabulary | Non-standard without mapping | 2 |
Changes of concept mapping status grouped by target domain
| vocabulary_id | Old target Domain/Status | New target Domain/Status | count |
|---|---|---|---|
| AMT | Drug | No mapping | 1 |
| ATC | Drug | No mapping | 1 |
| ATC | No mapping | Drug | 2 |
| CPT4 | Drug/Procedure | Drug | 3 |
| CPT4 | Measurement | Procedure | 7 |
| CPT4 | New concept | Drug | 7 |
| CPT4 | New concept | Measurement | 78 |
| CPT4 | New concept | Observation | 9 |
| CPT4 | New concept | Procedure | 115 |
| CPT4 | No mapping | Drug | 4 |
| CPT4 | Observation | Condition | 5 |
| CPT4 | Observation | Measurement | 1 |
| CPT4 | Observation | Procedure | 1 |
| CPT4 | Procedure | Measurement | 16 |
| CPT4 | Procedure | Observation | 7 |
| CPT4 | Procedure | Observation/Procedure | 1 |
| CPT4 | Provider | Observation | 3 |
| CPT4 | Provider | Procedure | 6 |
| CPT4 | Visit | Observation | 1 |
| CTD | Drug | No mapping | 1 |
| DA_France | Drug | No mapping | 2 |
| dm+d | Drug | No mapping | 12 |
| GCN_SEQNO | Drug | No mapping | 2 |
| GPI | Drug | No mapping | 7 |
| GRR | Drug | No mapping | 2 |
| HCPCS | No mapping | Observation | 1 |
| HemOnc | Drug | No mapping | 1 |
| ICD10CM | Condition | Condition/Observation | 18 |
| ICD10CM | No mapping | Condition/Observation | 1 |
| ICD10CM | No mapping | Observation | 4 |
| JMDC | Drug | No mapping | 1 |
| LOINC | Measurement | Observation | 1 |
| LOINC | Meas Value | No mapping | 12 |
| LOINC | New concept | Measurement | 1950 |
| LOINC | New concept | Meas Value | 215 |
| LOINC | New concept | Note | 94 |
| LOINC | New concept | Observation | 172 |
| LOINC | New concept | Procedure | 317 |
| LOINC | Observation | Note | 1 |
| NCCD | Drug | No mapping | 1 |
| NCCD | No mapping | Drug | 1 |
| NDC | Drug | No mapping | 175 |
| NDC | New concept | Device | 80 |
| NDC | New concept | Drug | 7026 |
| NDC | No mapping | Drug | 1737 |
| NHS Ethnic Category | New concept | Race | 15 |
| NHS Place of Service | New concept | Visit | 15 |
| OMOP Invest Drug | Drug | No mapping | 21 |
| OPS | Procedure | No mapping | 4 |
| Read | Drug | Drug/Procedure | 126 |
| Read | Drug | No mapping | 4 |
| Read | Drug/Observation | Drug | 2 |
| Read | Drug/Procedure | Procedure | 2 |
| Read | No mapping | Condition | 1 |
| Read | No mapping | Drug | 6 |
| Read | No mapping | Drug/Procedure | 9 |
| Read | No mapping | Measurement | 1 |
| Read | No mapping | Observation | 69 |
| Read | Provider/Visit | Visit | 1 |
| Read | Race | No mapping | 3 |
| Read | Visit | No mapping | 1 |
| RxNorm | Drug | No mapping | 49 |
| RxNorm | New concept | Drug | 548 |
| RxNorm Extension | New concept | Drug | 2136 |
| SNOMED | No mapping | Drug | 6 |
| SNOMED | Observation | Drug/Observation | 1 |
| SPL | No mapping | Drug | 1 |
| UK Biobank | No mapping | Observation | 164 |
| UK Biobank | No mapping | Provider | 10 |
| VANDF | Drug | Device | 10 |
| VANDF | New concept | Device | 715 |
| VANDF | New concept | Drug | 617 |
| VANDF | No mapping | Device | 9565 |
| VANDF | No mapping | Drug | 86 |
New vocabularies added
| vocabulary_id |
|---|
| NHS Ethnic Category |
| NHS Place of Service |
New vocabulary dependencies
| source vocabulary_id | target vocabulary_id | count |
|---|---|---|
| NHS Ethnic Category | Race | 15 |
| NHS Place of Service | CMS Place of Service | 9 |
| NHS Place of Service | NUCC | 6 |
If you have any questions, please try to find the answers on http://forums.ohdsi.org. If you can't find it, please ask here: http://forums.ohdsi.org/t/vocabulary-release-questions/6650