Release notes v20230116_major
This guide can provide you more background on how to read the release notes.
What's New
This release was originally meant to come in late autumn, then it was designated the Christmas release, but finally we present the “New Year 2023” release with a fair deal of meaningful updates and additions, which is why we declare this release a major release.
1. CPT4.
- The vocabulary was updated with the version 2022AB from UMLS, finally bringing CPT4 up to the 2022 release, as this was not available before from UMLS.
- Visit, Provider, Measurement and a number of Procedure concepts (1164 in total) were deStandardized and mapped over to the Standard concepts in the respective domains.
- Mapping of Drugs was improved in its granularity and completeness.
- Domain assignment was improved.
- 628 concepts in Procedure, Measurement and other domains were included into the hierarchy of Standard concepts.
- 277 new concepts were added as Standard and embedded into the existing hierarchy of Standard concepts or created as non-Standard and mapped over to the respective Standard concepts
2. Oncology-Genomic package
The update provides a new source of genomic information to be used for development and validation of OMOP Genomic terminology and KOIOS tool. The Hematology-Oncology terminology update improves Regimens utilization, as well as it defines the representation of steroid drugs in the context of specific therapeutic regimen.
2.1 HemOnc
This update (based on November 2022) introduces a number of new concepts in almost every HemOnc domain: Regimen, Drug, Condition, Procedure (sequence ordered from highest number of new concepts added to lowest). Released HemOnc update separates current and historical indications for different age patients’ population as new relationships. New relationships are also added to reflect the steroid role for steroid-containing chemotherapy Regimens. Regimen synonyms are enhanced according to the provided data from the author.
2.2 COSMIC
A brand new genomic terminology was added providing an impressive number of concepts and their synonyms. The COSMIC (Catalog Of Somatic Mutations In Cancer) is a powerful repository of somatic alterations occurring in cancer cells. During the implementation effort, the Vocabulary team and Oncology/Genomic WG supervisors designed the logic of concepts retrieval, naming strategies and worked on reducing the amount of relevant terms to be ingested in the OHDSI standardized vocabularies environment. However, this vocabulary is currently designated as “currently not available”, but will be used in the development of OMOP Genomic vocabulary.
3. ICD10CM
ICD10CM vocabulary has been updated with its FY2023 version. New content mapping has been introduced.
4. PPI
The ‘Life Functioning Survey’ Module was introduced.
5. OPS
The OPS vocabulary was updated with its 2021 and 2022 versions. 1858 new concepts were added. 741 additional concepts were mapped over to Standard concepts.
6. LOINC
- LOINC vocabulary has been updated with its 2.73 Aug 2022 version.
- LOINC Document Ontology-related concepts changed their domains from Observation to the new domain Note.
- LOINC Group names were normalized: instead of names like "Selenium|SCnc|Pt|ANYBldSerPl" we have "Selenium|Substance Concentration|Moment in time|Blood, Serum or Plasma".
- LOINC-SNOMED hierarchy was improved.
- COVID-2019-related lab tests were rolled up to the respective parent concept.
- SARS-CoV-2 antibody hierarchy was enhanced and became much granular due to OMOP Extension concepts separated by class of immunoglobulin.
- Deprecated concepts (not replaced by the source with a new concept) are mapped over to the respective Standard concepts in SNOMED and other vocabularies.
7. RxNorm
The vocabulary was updated with the January 2023 RxNorm release.
8. NDC / SPL
- The vocabulary was updated with the latest set of NDC and SPL concepts from January 2023.
- Fixed a bug when mappings to RxNorm were assigned randomly in case of multiple mappings with the same valid_date provided by source. Concept_class_id is added to the sorting of potential RxNorm targets to prevent undetermined choice.
9. OMOP Extension
9.1. Smoking hierarchy
We introduced a set of tobacco or its derivatives-related concepts to accompany the ETL Smoking conventions in a few axes. The top concepts 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). Cigarettes pack-years smoked during life is intended to capture the cumulative consumption of cigarettes.
Newly created concepts are Standard and should be used during ETL processes and mapping. We are going to destandardize concepts from other vocabularies during further releases.
9.2. Regular update
Besides that, two SARS-CoV-2 measurement concepts (Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in exhaled gas and Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in exhaled gas using gas chromatography-mass spectrometry) and a few lupus assessment concepts were created.
10. Other Changes
In this release we also implemented two manual checks:
- A check for 1-to many mapping to both a child concept and its ancestor,
- A check that helps to reveal Visit concepts in the source vocabulary and allows to review their mapping.
- Logic of the AddFreshMapsTO function has been slightly adjusted. Previously, only links present in concept_relationship_stage were extended. That led to the neglection of old relationships, that were no longer present in _stage tables. Now AddFreshMapsTO extends also relationships from both concept_relationship_stage and basic (concept_relationship) tables, if at least one of the affected vocabularies has been refreshed.
Domain changes
| vocabulary_id | old_domain_id | new_domain_id | count |
|---|---|---|---|
| CPT4 | Measurement | Observation | 2 |
| CPT4 | Measurement | Procedure | 11 |
| CPT4 | Measurement | Provider | 2 |
| CPT4 | Measurement | Visit | 1 |
| CPT4 | Observation | Measurement | 59 |
| CPT4 | Observation | Procedure | 9 |
| CPT4 | Observation | Provider | 1 |
| CPT4 | Observation | Visit | 53 |
| CPT4 | Procedure | Drug | 2 |
| CPT4 | Procedure | Measurement | 416 |
| CPT4 | Procedure | Observation | 96 |
| CPT4 | Procedure | Provider | 6 |
| CPT4 | Procedure | Visit | 127 |
| HemOnc | Drug | Regimen | 1 |
| ICD10CM | Condition | Observation | 3 |
| LOINC | Measurement | Note | 1 |
| LOINC | Observation | Note | 3714 |
| MeSH | Drug | Condition | 2 |
| MeSH | Drug | Measurement | 1 |
| MeSH | Measurement | Condition | 1 |
| MeSH | Measurement | Procedure | 1 |
| MeSH | Procedure | Condition | 1 |
| MeSH | Procedure | Measurement | 2 |
| OMOP Extension | Observation | Measurement | 30 |
Newly added concepts grouped by Vocabulary_id and Domain
| vocabulary_id | domain_id | count |
|---|---|---|
| COSMIC | Measurement | 273604 |
| CPT4 | Drug | 4 |
| CPT4 | Measurement | 80 |
| CPT4 | Observation | 18 |
| CPT4 | Procedure | 170 |
| CPT4 | Visit | 5 |
| HemOnc | Condition | 20 |
| HemOnc | Drug | 167 |
| HemOnc | Procedure | 3 |
| HemOnc | Regimen | 209 |
| ICD10CM | Condition | 1407 |
| ICD10CM | Observation | 62 |
| LOINC | Measurement | 440 |
| LOINC | Meas Value | 132 |
| LOINC | Note | 241 |
| LOINC | Observation | 792 |
| LOINC | Procedure | 19 |
| MeSH | Condition | 255 |
| MeSH | Drug | 56 |
| MeSH | Measurement | 2 |
| MeSH | Procedure | 14 |
| NDC | Device | 81 |
| NDC | Drug | 11387 |
| OMOP Extension | Measurement | 10 |
| OMOP Extension | Observation | 19 |
| OPS | Procedure | 1858 |
| PPI | Observation | 2 |
| RxNorm | Drug | 608 |
| SPL | Drug | 20294 |
Standard concept changes
| vocabulary_id | old_standard_concept | new_standard_concept | count |
|---|---|---|---|
| CPT4 | Standard | Non-standard with mapping | 1164 |
| HemOnc | Standard | Non-standard with mapping | 31 |
| HemOnc | Standard | Non-standard without mapping | 10 |
| HemOnc | Classification without mapping | Non-standard without mapping | 3 |
| HemOnc | Classification without mapping | Standard | 1 |
| LOINC | Standard | Non-standard without mapping | 75 |
| LOINC | Standard | Non-standard with mapping | 24 |
| LOINC | Classification without mapping | Non-standard without mapping | 6 |
| LOINC | Non-standard without mapping | Standard | 1 |
| NDC | Standard | Non-standard without mapping | 4 |
| RxNorm | Standard | Non-standard without mapping | 149 |
| RxNorm | Classification without mapping | Non-standard without mapping | 55 |
| RxNorm | Standard | Non-standard with mapping | 16 |
| RxNorm Extension | Standard | Non-standard with mapping | 27 |
| SPL | Classification without mapping | Non-standard without mapping | 6 |
| SPL | Classification with mapping | Non-standard with mapping | 2 |
| SPL | Classification without mapping | Non-standard with mapping | 2 |
Newly added concepts and their standard concept status
| vocabulary_id | new_standard_concept | count |
|---|---|---|
| COSMIC | Non-standard without mapping | 273604 |
| CPT4 | Non-standard with mapping | 36 |
| CPT4 | Classification without mapping | 67 |
| CPT4 | Standard | 174 |
| HemOnc | Classification without mapping | 15 |
| HemOnc | Non-standard with mapping | 48 |
| HemOnc | Non-standard without mapping | 126 |
| HemOnc | Standard | 210 |
| ICD10CM | Non-standard with mapping | 1469 |
| LOINC | Classification without mapping | 140 |
| LOINC | Non-standard without mapping | 521 |
| LOINC | Standard | 963 |
| MeSH | Non-standard with mapping | 327 |
| NDC | Standard | 81 |
| NDC | Non-standard with mapping | 4602 |
| NDC | Non-standard without mapping | 6785 |
| OMOP Extension | Standard | 29 |
| OPS | Non-standard without mapping | 1858 |
| PPI | Standard | 2 |
| Relationship | Non-standard without mapping | 18 |
| RxNorm | Non-standard with mapping | 28 |
| RxNorm | Non-standard without mapping | 30 |
| RxNorm | Classification without mapping | 80 |
| RxNorm | Standard | 470 |
| SPL | Classification without mapping | 20294 |
| Vocabulary | Non-standard without mapping | 1 |
Changes of concept mapping status grouped by target domain
| vocabulary_id | Old target Domain/Status | New target Domain/Status | count |
|---|---|---|---|
| AMT | Drug | No mapping | 5 |
| ATC | Drug | No mapping | 1 |
| CIEL | Device | Device/Drug | 2 |
| CIEL | Drug | No mapping | 7 |
| CIEL | Observation | Drug/Observation | 7 |
| CPT4 | Measurement | Procedure | 11 |
| CPT4 | Measurement | Provider | 2 |
| CPT4 | Measurement | Visit | 1 |
| CPT4 | New concept | Drug | 4 |
| CPT4 | New concept | Measurement | 74 |
| CPT4 | New concept | Observation | 7 |
| CPT4 | New concept | Procedure | 113 |
| CPT4 | New concept | Procedure/Visit | 7 |
| CPT4 | New concept | Visit | 5 |
| CPT4 | No mapping | Visit | 48 |
| CPT4 | Observation | Condition/Measurement | 10 |
| CPT4 | Observation | Condition/Visit | 2 |
| CPT4 | Observation | Measurement | 47 |
| CPT4 | Observation | Procedure | 3 |
| CPT4 | Observation | Procedure/Visit | 6 |
| CPT4 | Observation | Provider | 1 |
| CPT4 | Observation | Visit | 51 |
| CPT4 | Procedure | Drug/Visit | 2 |
| CPT4 | Procedure | Measurement | 385 |
| CPT4 | Procedure | Observation | 54 |
| CPT4 | Procedure | Observation/Visit | 3 |
| CPT4 | Procedure | Procedure/Provider | 6 |
| CPT4 | Procedure | Procedure/Visit | 51 |
| CPT4 | Procedure | Provider | 6 |
| CPT4 | Procedure | Visit | 124 |
| CTD | Drug | No mapping | 1 |
| DA_France | Drug | No mapping | 1 |
| dm+d | Drug | No mapping | 2 |
| GCN_SEQNO | Drug | No mapping | 6 |
| Gemscript | Drug | No mapping | 4 |
| GPI | Drug | No mapping | 2 |
| GRR | Drug | No mapping | 9 |
| HCPCS | Device | Device/Drug | 1 |
| HCPCS | Drug | No mapping | 1 |
| HCPCS | Measurement | No mapping | 1 |
| HCPCS | Measurement/Procedure | Measurement | 1 |
| HCPCS | Observation | No mapping | 5 |
| HCPCS | Procedure | No mapping | 27 |
| HCPCS | Procedure | Observation | 3 |
| HCPCS | Procedure/Visit | Visit | 4 |
| HemOnc | New concept | Condition | 19 |
| HemOnc | New concept | Condition/Measurement | 1 |
| HemOnc | New concept | Drug | 28 |
| HemOnc | New concept | Procedure | 1 |
| HemOnc | New concept | Regimen | 209 |
| HemOnc | No mapping | Condition | 2 |
| HemOnc | No mapping | Drug | 94 |
| HemOnc | No mapping | Regimen | 1 |
| HemOnc | Regimen | No mapping | 10 |
| ICD10CM | New concept | Condition | 1375 |
| ICD10CM | New concept | Condition/Observation | 32 |
| ICD10CM | New concept | Drug/Observation | 1 |
| ICD10CM | New concept | Observation | 61 |
| ICD10CM | No mapping | Condition | 52 |
| JMDC | Drug | No mapping | 2 |
| KDC | Drug | No mapping | 2 |
| LOINC | Measurement | No mapping | 1 |
| LOINC | Meas Value | No mapping | 1 |
| LOINC | New concept | Measurement | 318 |
| LOINC | New concept | Meas Value | 132 |
| LOINC | New concept | Note | 233 |
| LOINC | New concept | Observation | 266 |
| LOINC | New concept | Procedure | 14 |
| LOINC | No mapping | Measurement | 1 |
| LOINC | No mapping | Meas Value | 1 |
| LOINC | Observation | No mapping | 73 |
| LOINC | Observation | Note | 3307 |
| LPD_Australia | Drug | No mapping | 1 |
| LPD_Belgium | Drug | No mapping | 8 |
| MeSH | Condition | Measurement | 1 |
| MeSH | Drug | No mapping | 5 |
| MeSH | Measurement | Condition | 1 |
| MeSH | Measurement | No mapping | 3 |
| MeSH | Measurement | Procedure | 1 |
| MeSH | Measurement/Procedure | Measurement | 1 |
| MeSH | Meas Value | No mapping | 1 |
| MeSH | New concept | Condition | 255 |
| MeSH | New concept | Drug | 56 |
| MeSH | New concept | Measurement | 2 |
| MeSH | New concept | Procedure | 14 |
| MeSH | No mapping | Condition | 8 |
| MeSH | Observation | Condition | 2 |
| MeSH | Observation/Procedure | Observation | 3 |
| MeSH | Observation/Procedure | Procedure | 1 |
| MeSH | Procedure | Condition | 1 |
| MeSH | Procedure | Measurement | 1 |
| MeSH | Procedure | No mapping | 7 |
| NCCD | Drug | No mapping | 7 |
| NDC | Device | No mapping | 4 |
| NDC | Drug | No mapping | 23 |
| NDC | New concept | Device | 81 |
| NDC | New concept | Drug | 4602 |
| NDC | No mapping | Drug | 2347 |
| NDFRT | Drug | No mapping | 1 |
| Nebraska Lexicon | Device | Device/Drug | 16 |
| Nebraska Lexicon | Drug | No mapping | 10 |
| Nebraska Lexicon | Observation | Drug/Observation | 46 |
| OMOP Extension | New concept | Measurement | 10 |
| OMOP Extension | New concept | Observation | 19 |
| OMOP Extension | Observation | Measurement | 30 |
| OMOP Invest Drug | Drug | No mapping | 19 |
| OPS | Device | No mapping | 24 |
| OPS | Device | Procedure | 2 |
| OPS | No mapping | Drug | 37 |
| OPS | No mapping | Measurement | 1 |
| OPS | No mapping | Observation | 29 |
| OPS | No mapping | Procedure | 642 |
| OPS | Observation | Procedure | 1 |
| OPS | Observation/Procedure | Procedure | 1 |
| PPI | New concept | Observation | 2 |
| Read | Drug/Procedure | Procedure | 1 |
| RxNorm | Drug | No mapping | 155 |
| RxNorm | New concept | Drug | 498 |
| RxNorm Extension | Drug | No mapping | 8 |
| SNOMED | Device | Device/Drug | 28 |
| SNOMED | Drug | No mapping | 7 |
| SNOMED | No mapping | Drug | 6 |
| SNOMED | Observation | Drug/Observation | 116 |
| SPL | Drug | No mapping | 7 |
| SPL | No mapping | Drug | 2 |
| SUS | Measurement | No mapping | 6 |
| SUS | Observation | Note | 6 |
| SUS | Procedure | No mapping | 27 |
| VANDF | Drug | No mapping | 2 |
New vocabularies added
| vocabulary_id |
|---|
| COSMIC |
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