Release notes v20240229

This guide can provide you more background on how to read the release notes.

What's New

1. CVX

• The vocabulary has been updated according to the 2023AB version of the UMLS source.
• New CVX vaccines have been added (codes 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317).

2. RxNorm

• The vocabulary has been updated to the January 2024 version.

3. RxNorm Extension

• The indeterminacy of the BuildRxE script, which is used for the construction of the RxNorm Extension concepts, has been fixed in this release. Previously, multiple runs of BuildRxE with the same input resulted in outputs with 1-2% differences between runs. It was one of the reasons for duplicates in the RxNorm Extension vocabulary.

4. NDC/SPL

• The vocabulary has been updated to the February 2024 version, effective from February 25th, 2024.
• Bug fixing of reported issues - NDC devices were mapped to drugs.

5. SNOMED package

• SNOMED has been updated according to the following versions of its modules:
  2023-07-31 SNOMED CT International;
  2023-09-01 SNOMED CT US Edition;
  2023-09-27 SNOMED CT UK Edition.
• 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 the dm+d vocabulary. Their concept codes and names have been replaced by placeholders to avoid misuse.
  On the other hand, dm+d concepts in the Device domain, previously mapped to the SNOMED UK Drug Extension Module, have become standard. Gemscript Devices, previously mapped to SNOMED, have been remapped to dm+d.
  UK Drug Extension concepts in the Route domain have been de-standardized and mapped to standard Routes that belong to other SNOMED Modules.
• Validity dates assignment for concepts has been improved and now fully corresponds to the source data.
• Concept class Clinical Finding has been split into Disorder and Clinical Finding. Thus, all Disorders are assigned with Condition domain (except allergies), and Clinical Findings accommodate concepts in the Condition, Observation, and Measurement domains.
• 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. Thus, concepts ‘Positive’, ‘Negative’, and ‘Malignant’ have been moved from Spec Disease Status to the Meas Value domain, and countries have been moved to the Geography domain.
• Previously, not all replacement relationships to standard concepts were followed by the respective ‘Maps to’ links due to incorrect algorithms. Now this problem is fixed.
• Cleanup of mapping following ‘Concept poss_eq to’ relationships has been performed and its accuracy has been improved.
• 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 were split and mapped to ‘Allergic disposition’ + 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 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 Race and Provider domains have been mapped to standard concepts in the respective domains.
• The load_stage has been significantly refactored, which results in a more straightforward and fast release process in future.

6. PPI

• New modules (Behavioral Health and Personality and Emotional Health History and Wellbeing) have been introduced.
• The Mental Health and Well-Being Module has been deprecated.

7. HCPCS

• HCPCS has been updated according to the version effective from January 2024.
• 39 concepts have been destandardised and mapped over to the concepts in the respective domains.
• 31 concepts have been destandardized as they present no information or contain negative information.
• Concepts that previously were assigned the Visit and Provider domains according to their mapping were moved to the Observation domain according to the Community’s request.
• Domain assignment according to the domains of the target concepts has been deleted. This logic led to imprecise domain assignment and non-compliance with the concept semantics. Now domains are assigned according to concept semantics exclusively.
  All HCPCS concepts in the Drug domain should be 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.
• 3 concepts that belong to the Device domain have been mapped to SNOMED lost their mappings and became standard.
• In the course of release one standard concept previously embedded into the hierarchy of SNOMED has lost its hierarchical relationships as it has been mapped over to the standard concept in the Procedure domain and destandardized.
  HCPCS code ‘J9321, Injection, pemetrexed (sandoz) not therapeutically equivalent to J9305, 10 mg’ was added on 2023-07-01 and subsequently deleted as a duplicate of code J9297. On 2024-01-01 this concept code was reused and assigned with another description: ‘‘J9321, Injection, epcoritamab-bysp, 0.16 mg’. As the previous concept code was initially added by mistake as duplicative and deleted by the source in the scope of the same source version, we assumed that it was not widely presented in the raw data and that the new brand-specific concept code would be more actively used. In this case, we do not preserve the old code description as an exception to our general logic.

8. ICD10PCS

• Vocabulary has been updated according to the source version effective from April 01, 2024.
• In the course of the update, 69 concepts were mapped to standard concepts in the Drug domain and de-standardized.
• ICD10PCS Hierarchy concepts that refer to the XW0 section, especially first-degree ancestors of drug administration procedures, demonstrate high variability of concept names. This behaviour depends both on the intrinsic vocabulary logic (X-codes are assigned to the new or experimental technologies and are refreshed often so that the same ancestor may have different descendants in each vocabulary release) and the UMLS logic of concept name compilation (names are assembled from distinct values of ICD10PCS source files with @ symbol as separators, and these values may vary). To avoid redundant variability and subsequent confusion we decided to replace the last variable part of XW0 hierarchical concepts that refer to drug administration procedures with a placeholder ‘@ Drug administration’.
• ICD10PCS - SNOMED hierarchy has been improved in its accuracy, 4340 erroneous ‘Is a’ relationships have been deprecated.

9. Read

• The mappings have been updated according to the new SNOMED version.
• The wrong domain assignments for some concepts have been fixed.

10. MedDRA

• MedDRA has been updated according to the source version 26.1, effective from September 2023.
• A total of 10,189 PT concepts and 2,874 LLTs have been mapped to concepts in standard vocabularies, primarily SNOMED. Currently, there are 15,161 PT and 11,255 LLT MedDRA concepts with mappings.
• A hierarchy between MedDRA and SNOMED / OMOPext has been established with 25,623 'Is a'/'Subsumes' links. In this hierarchy, different MedDRA concepts can be ancestors or descendants of SNOMED / OMOP Extension concepts, depending on the mappings of the concept. The model of the hierarchy is described here.

11. LOINC

• LOINC vocabulary has been updated with its 2.76 Sep 2023 version.
• The LOINC-SNOMED hierarchy was significantly expanded - more than 2300 ‘Is a’ relationships were added. 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.
• We also incorporated the SNOMED - LOINC deduplication mappings, provided by the Community.

12. CPT4, Co-connect, OMOP Invest drug, OPCS4, UK Biobank

• We have updated mappings for these vocabularies without changing vocabulary versions.
• Minor bug fixing: symbols such ...

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:

1. New vocabularies - NHS Ethnic category and NHS Place of Service (link)
2. Remapping of ICD10CM terms to SNOMED (link)
3. 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

• 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 w...

Release notes v20230531

This guide can provide you more background on how to read the release notes.

What's New

1. HCPCS

• The vocabulary was updated according to the version effective from July 2023.
• Visit, Provider and a number of Procedure and Observation concepts have been destandardized and mapped over to the concepts in the respective domains.
• Mapping of Drugs has been improved in its granularity and completeness.
• Domain assignment according to the domains of the target concepts has been added.
• 13 concepts that represent contrast media changed their domain from Drug to Device and became standard.
• In the course of the release 525 standard concepts previously embedded into the hierarchy of SNOMED and CPT4 have lost their hierarchical relationships as they have been mapped over to standard concepts in the respective domains and destandardized.

2. CPT4

• One CPT4 code 0174A for immunization against COVID-19 was added.
• Domain_id of two concepts was fixed as per community request.

3. CVX

• New CVX vaccines have been added (codes 518, 519, 520, 521, 231). Existing mappings were improved, which resulted in destandardization of some CVX codes that are currently mapped to corresponding vaccines in RxNorm or RxNorm Extension vocabulary.
• The Vaccine Group concept class has been introduced, showcasing how a set of related vaccines can be organized into a family for easy reference.
• New attributes were added, such as:
• ‘Has vaccine group’ relationships were added to help with vaccine grouping. Vaccines themself serve as groups, therefore there are no new concepts for vaccine groups.
• ‘Non-US’ was added to names of the vaccines in use outside of the United States

4. MeSH

• More than 300000 concepts were added during this release
• Changed of logic assignment has been changed. At the moment domains are assigned according to the following priorities:
  • Domain of target concept, if mapping is available
  • Domain of ancestor concept, if available
  • Domain assigned according to algorithm using semantic tags
  • Default domain has been set to Observation

5. NAACCR

The update brings a set of community-provided mappings for NAACCR Values to Cancer Modifer OMOP Vocabulary. The total amount of invalidated NAACCR Values is 1517. Compared to provided mappings we refactored and remapped only a minor portion (less than 200) of codes from generic Lymph node spread to Regional spread as it inherited from the Variable parent. Note, that NAACCR Variables related to those Values did not change their standardness and validity status. Please find more details on the upcoming changes page.

6. Smoking hierarchy (SNOMED, OMOP Extension)

• As was announced in upcoming changes, during this release we focused on remapping of SNOMED concepts: the smoking-related SNOMED terms were mapped to new OMOP Extension concepts. As a result of this changes, some concepts of source vocabularies (ICD9CM, Read, CIEL, etc.) lost their mapping - this will be addressed in future releases.

7. OMOP Extension

• Added concepts for ACC/AHA classification and Ross classification.
• Implemented the Critical Care Pain Observation Tool (CPOT) pain scale.

8. PPI

• The mapping of 2 concepts: sdoh_dms_1 and sdoh_dms_2 has been omitted and these concepts have been made standard as per community request. The reason for the change is imprecise mapping.
• Concept_class_id of 2 other concepts has been changed as per community request

9. RxNorm

• The vocabulary has been updated to May 2023 version

10. NDC/SPL

• The vocabulary has been updated to May 2023 version, effective from 14th of May

11. dm+d

• The vocabulary has been updated to May 2023 version, effective from 22nd of May
• Previous version of dm+d vocabulary dated back to June 2021. This gap between versions determines huge differences. Almost 18000 concepts were added during this release
• Domain detection was improved what resulted in minor changes in concepts’ domains

12. Сo-connect

• A new IQVIA proprietary vocabulary consisting of 3 parts was added.

13. Problems found during the release, but not yet fixed

• Within a recent release of HCPCS sources, code reuse appeared to happen for 36 codes. Unless the code reuse handling approach is implemented in OMOP, we preserve reused codes with old semantics.
• The idea about mapping of the concepts associated with death of a patient to the CDM table ‘Death’ is discussed in the Community and has not been addressed yet in the scope of the current release.
• In CPT4 concepts may migrate between categories and obtain new concept_codes. This results in creation of semantic duplicates within the vocabulary. As at the release v20230531 there are 71 such duplicative concepts that are to be mapped and destandardized.
• As a result of recent run of BuildRxE, more than 6000 duplicates have been created in RxNorm Extension vocabulary. They have not been used as mapping targets for dm+d vocabulary. This is a known problem, which exacerbated significantly during this release.
• We also identified inconsistencies in BuildRxE mapping algorithm that resulted in changes of drug form of target mapping concepts (Eg. concepts previously mapped to lidocaine Injectable solution changed their mapping to lidocaine injection). These changes were manually curated for dm+d vocabulary. However, the algorithm was not changed.

Domain changes

vocabulary_id	old_domain_id	new_domain_id	count
CPT4	Device	Procedure	1
CPT4	Measurement	Procedure	1
dm+d	Device	Drug	57
dm+d	Drug	Device	48
HCPCS	Device	Drug	6
HCPCS	Device	Measurement	1
HCPCS	Device	Observation	3
HCPCS	Device	Procedure	18
HCPCS	Drug	Device	13
HCPCS	Drug	Observation	1
HCPCS	Drug	Procedure	8
HCPCS	Measurement	Procedure	3
HCPCS	Observation	Condition	94
HCPCS	Observation	Device	1
HCPCS	Observation	Drug	3
HCPCS	Observation	Procedure	72
HCPCS	Observation	Provider	27
HCPCS	Observation	Visit	183
HCPCS	Procedure	Condition	7
HCPCS	Procedure	Device	2
HCPCS	Procedure	Drug	3
HCPCS	Procedure	Measurement	14
HCPCS	Procedure	Observation	166
HCPCS	Procedure	Provider	2
HCPCS	Procedure	Visit	31
HCPCS	Provider	Observation	3
HCPCS	Provider	Visit	2
HCPCS	Visit	Observation	1
MeSH	Condition	Device	1
MeSH	Condition	Measurement	6
MeSH	Condition	Observation	102
MeSH	Condition	Procedure	14
MeSH	Condition	Spec Anatomic Site	12
MeSH	Drug	Condition	152
MeSH	Drug	Device	9
MeSH	Drug	Measurement	10
MeSH	Drug	Observation	316
MeSH	Drug	Procedure	20
MeSH	Drug	Spec Anatomic Site	8
MeSH	Measurement	Condition	5
MeSH	Measurement	Observation	6
MeSH	Measurement	Procedure	8
MeSH	Observation	Condition	10
MeSH	Observation	Measurement	1
MeSH	Observation	Procedure	3
MeSH	Procedure	Condition	4
MeSH	Procedure	Drug	1
MeSH	Procedure	Measurement	2
MeSH	Procedure...

Release notes v20230123

This guide can provide you more background on how to read the release notes.

What's New

1. Four CPT4 concepts for the bivalent COVID vaccines were added on request (issue #747).
2. Nine CPT4 concepts valid from 01-Jan-2023 were added.
3. NDC/SPL regular update.

Domain changes

vocabulary_id	old_domain_id	new_domain_id	count
CPT4	Observation	Measurement	1

Newly added concepts grouped by Vocabulary_id and Domain

vocabulary_id	domain_id	count
CPT4	Drug	4
CPT4	Measurement	9
NDC	Drug	1026
SPL	Drug	1592

Standard concept changes

vocabulary_id	old_standard_concept	new_standard_concept	count
CPT4	Standard	Non-standard with mapping	3
SPL	Classification with mapping	Non-standard with mapping	2

Newly added concepts and their standard concept status

vocabulary_id	new_standard_concept	count
CPT4	Non-standard with mapping	5
CPT4	Standard	8
NDC	Non-standard with mapping	71
NDC	Non-standard without mapping	955
SPL	Classification without mapping	1592

Changes of concept mapping status grouped by target domain

vocabulary_id	Old target Domain/Status	New target Domain/Status	count
CPT4	New concept	Drug	2
CPT4	New concept	Drug/Procedure	2
CPT4	New concept	Measurement	9
CPT4	Observation	Measurement	1
NDC	New concept	Drug	71
NDC	No mapping	Drug	2

New vocabularies added

there were no changes here

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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

Release notes v20221031

This guide can provide you more background on how to read the release notes.

What's New

This release contains a number of urgent fixes and additions requested by N3C (issue #697 ) and FDA-BEST (issues #666 - #683 - #685 ) as well as some pending refreshes that were originally meant to be released a little later. This is not yet the planned "Indian Summer release".

• selected additions to the CPT4 vocabulary to cover recent new codes for Monkeypox and bivalent COVID-19 vaccines. The full CPT4-2022 release is still not available in UMLS and will have to wait for a release later this year.
• several mapping fixes and additions in the HCPCS vocabulary
• refresh of the CGI and CIViC genomic variant vocabularies
• RxNorm refresh
• NDC refresh

Domain changes

vocabulary_id	old_domain_id	new_domain_id	count
CPT4	Procedure	Drug	25
HCPCS	Procedure	Drug	1
HCPCS	Provider	Observation	1
HCPCS	Visit	Drug	1
HCPCS	Visit	Procedure	1
SNOMED	Observation	Language	863

Newly added concepts grouped by Vocabulary_id and Domain

vocabulary_id	domain_id	count
CGI	Measurement	5028
CIViC	Measurement	398
CPT4	Drug	16
CPT4	Measurement	1
CVX	Drug	4
HCPCS	Device	10
HCPCS	Drug	10
HCPCS	Provider	2
Language	Language	1
NDC	Device	67
NDC	Drug	7120
OMOP Extension	Measurement	1
OMOP Extension	Procedure	1
RxNorm	Drug	406
SPL	Drug	9177
SPL	Observation	2
Type Concept	Type Concept	1

Standard concept changes

vocabulary_id	old_standard_concept	new_standard_concept	count
CPT4	Standard	Non-standard with mapping	28
HCPCS	Standard	Non-standard with mapping	2
HCPCS	Non-standard with mapping	Standard	1
RxNorm	Standard	Non-standard without mapping	44
RxNorm	Classification without mapping	Non-standard without mapping	20
RxNorm	Standard	Non-standard with mapping	17
RxNorm Extension	Standard	Non-standard with mapping	25
SPL	Classification without mapping	Non-standard without mapping	3
SPL	Classification with mapping	Non-standard with mapping	2
SPL	Classification without mapping	Non-standard with mapping	1

Newly added concepts and their standard concept status

vocabulary_id	new_standard_concept	count
CGI	Non-standard without mapping	5028
CIViC	Non-standard without mapping	398
Concept Class	Non-standard without mapping	1
CPT4	Non-standard with mapping	17
CVX	Non-standard with mapping	1
CVX	Standard	3
Domain	Non-standard without mapping	1
HCPCS	Standard	10
HCPCS	Non-standard with mapping	12
Language	Standard	1
NDC	Standard	67
NDC	Non-standard with mapping	2023
NDC	Non-standard without mapping	5097
OMOP Extension	Standard	2
RxNorm	Non-standard with mapping	15
RxNorm	Non-standard without mapping	27
RxNorm	Classification without mapping	59
RxNorm	Standard	305
SPL	Classification without mapping	9179
Type Concept	Standard	1
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
AMIS	Drug	No mapping	2
AMT	Drug	No mapping	2
ATC	Drug	No mapping	1
BDPM	Drug	No mapping	2
CIEL	Drug	No mapping	1
CIEL	Observation	Language	1
CPT4	Drug	Drug/Procedure	19
CPT4	New concept	Drug	5
CPT4	New concept	Drug/Procedure	11
CPT4	New concept	Measurement	1
CPT4	Procedure	Drug	3
CPT4	Procedure	Drug/Procedure	22
CTD	Drug	No mapping	2
CVX	Drug	Drug/Procedure	1
CVX	New concept	Drug	3
CVX	New concept	Drug/Procedure	1
DA_France	Drug	No mapping	1
dm+d	Drug	No mapping	5
Gemscript	Drug	No mapping	12
GGR	Drug	No mapping	1
GRR	Drug	No mapping	2
HCPCS	Condition/Visit	Procedure/Visit	1
HCPCS	Measurement	Measurement/Procedure	1
HCPCS	Measurement	Measurement/Type Concept	1
HCPCS	New concept	Device	10
HCPCS	New concept	Drug	10
HCPCS	New concept	Provider	2
HCPCS	Visit	Procedure/Visit	4
JMDC	Drug	No mapping	1
KDC	Drug	No mapping	1
Language	New concept	Language	1
LPD_Australia	Drug	No mapping	1
MeSH	Measurement	Measurement/Procedure	1
Multilex	Drug	No mapping	1
NCCD	Drug	No mapping	9
NDC	Drug	No mapping	22
NDC	New concept	Device	67
NDC	New concept	Drug	2023
NDC	No mapping	Drug	3002
Nebraska Lexicon	Observation	Language	846
OMOP Extension	New concept	Measurement	1
OMOP Extension	New concept	Procedure	1
OMOP Invest Drug	Drug	No mapping	8
OXMIS	Observation	Language	6
Read	Observation	Language	12
RxNorm	Drug	No mapping	51
RxNorm	New concept	Drug	320
RxNorm Extension	Drug	No mapping	3
SNOMED	No mapping	Condition	1
SNOMED	No mapping	Drug	85
SNOMED	Observation	Language	876
SPL	Drug	No mapping	11
SPL	No mapping	Drug	1
Type Concept	New concept	Type Concept	1
VANDF	Drug	No mapping	1

New vocabularies added

vocabulary_id
Language

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Release notes v20220909

This guide can provide you more background on how to read the release notes.

What's New

This is mostly a technical release of a minor oncology package.

• Cancer modifier vocabulary was updated with the addition of a new concept for initial diagnosis that is needed to facilitate Cancer Registries ETLs. The update of the Staging/Grading concept class provides a set of classification concepts gathering different staging or grading systems in hierarchical logical groups. Minor typos were fixed in the naming of post-therapeutic stages. The very first step in the improvement of Node (i.e. lymph nodes) classification was performed: concepts are aligned in the appropriate axis according to their biological nature.
• NAACCR vocabulary was updated with the provided by the community mapping package to the Cancer Modifier vocabulary for a subset of NAACCR values.
• NDC/SPL regular weekly update.

Domain changes

there were no changes here

Newly added concepts grouped by Vocabulary_id and Domain

vocabulary_id	domain_id	count
Cancer Modifier	Measurement	48
NDC	Drug	805
SPL	Drug	991
SPL	Observation	1

Standard concept changes

vocabulary_id	old_standard_concept	new_standard_concept	count
NAACCR	Standard	Non-standard with mapping	1781

Newly added concepts and their standard concept status

vocabulary_id	new_standard_concept	count
Cancer Modifier	Standard	10
Cancer Modifier	Classification without mapping	38
NDC	Non-standard with mapping	43
NDC	Non-standard without mapping	762
SPL	Classification without mapping	992

Changes of concept mapping status grouped by target domain

vocabulary_id	Old target Domain/Status	New target Domain/Status	count
Cancer Modifier	New concept	Measurement	10
NAACCR	Meas Value	Measurement	1781
NAACCR	No mapping	Measurement	31
NDC	New concept	Drug	43
NDC	No mapping	Drug	12

New vocabularies added

there were no changes here

---

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Release notes v20220829_major

This guide can provide you more background on how to read the release notes.

What's New

1. SNOMED package.

• The vocabulary was updated with the respective versions of its components: SNOMED CT International 2021/07, US 2021/09, UK 2021/11.
• We continued (after the v20220510 release) a construction of axis of historical concepts. The "History of clinical finding in subject", "Past history of procedure", "History of" and many other SNOMED concepts (including their descendants) were deStandardised and split (mapped over to the appropriate OMOP Extension concept of the "History of event" hierarchy with a value of a respective condition or procedure within a combination of "Maps to" and "Maps to value" relationships). The mentioned hierarchy was recently introduced as a set of new OMOP Extension domain-agnostic concepts. They include: (i) an all-in-one bucket History of event concept that implies the semantics of a historical event, context, qualifier, or value; (ii) a hierarchy of enhanced historical concepts that bring additional time context (History of event within... and History of event longer than...).
• Historical concepts that imply the allergic dispositions are mapped over to the non-historical concepts, e.g. "History of intravenous iron allergy" Maps to "Allergy to iron compound". The rationale behind this is that allergic dispositions are mostly permanent conditions. This rule is not applied to the actual allergic reactions that follow the general mapping rules.
• We introduced new metadata relationships: (i) "Has Module" from each concept to its module ("SNOMED CT core", "US National Library of Medicine maintained module", "SNOMED CT United Kingdom clinical extension module", "SNOMED CT United Kingdom drug extension module", etc.); (ii) "Has status" from each concept to its definition status ("Defined" or "Primitive").
• We revoked the "Concept poss_eq to" (Inactive possibly equivalent to active) from the list of replacement relationships. It means that "Maps to" relationships will no longer be automatically constructed based on "Concept poss_eq to". This decision was taken based on multiple erroneous "Maps to" relationships, previously built from "Concept poss_eq to" (because in many cases one from many was chosen randomly). Also, we allowed 1-to-many linkage for the "Concept poss_eq to" relationship so that multiple relationships that are provided by the source will be included to the concept_relationship table, e.g. "Integument anomalies: [ichthyosis congenita] or [Darier's] or [keratosis follicularis] or [Meige's] or [Milroy's] or [Mongolian spots] or [pseudoxanthoma elasticum] or [congenital NOS]" concept has 7 such links. All historical "Maps to" relationships that were build based on "Concept poss_eq to" are preserved for now but will be tagged for removal in a later clean-up job.
• Procedures describing the administration of vaccines were deStandardized and mapped over to the Drug Domain concepts, e.g. "Administration of third dose of smallpox vaccine". Additionally, those concepts that imply the number of the dosage or the primary vs booster immunization were mapped to the respective concepts (e.g., "Primary immunisation - second dose", "Booster vaccination", etc.).
• Units from the SNOMED vocabulary were mapped to the respective Standard units in UCUM vocabulary.
• We reviewed and fixed the process of the concept class assignment - now we expect them more clean.
• Domains of the concepts were slightly cleaned-up, some wrong Domains were fixed, e.g. #488.
• We removed special symbols from the concept names (such as "Megaloblastic anemia due to vitamin B-12 deficiency") - previously known as "Megaloblastic anemia due to vitamin B>12< deficiency". Concept synonyms are to be improved further.
• COVID-19 concepts were aligned with the current COVID vocabulary/ETL convention.

2. ICD-like family and source vocabulary package.

• The following vocabularies were updated with the 2022 versions: CIM10, ICD10GM.
• 249 local codes from the Vision(tm) GP software were added to the Read vocabulary and mapped to Standard concepts.
• Mappings were adjusted according to the concept invalidation/deStandardization due to the SNOMED refresh as well as other changes in OMOP vocabularies described above.
• Mappings were added for the concepts previously not mapped (Read - 2347, ICD10CN - 89, ICD10CM - 1).

3. HCPCS package.

• We updated the HCPCS vocabulary with its July 2022 version.
• HCPCS codes coming from the outdated CDT (Dental Procedures and Nomenclature) vocabulary were mapped over to the respective CDT vocabulary concepts (licensed).
• Mapping of Drug concepts was improved in its granularity and completeness.
• Visit, Provider and some other concepts (207 in total) were deStandardized and mapped over to Standard concepts in respective Domains.
• Mappings were added for the 562 concepts previously not mapped.
• 454 new concepts were incorporated into the existing hierarchy of Standard concepts or created as non-Standard and mapped over to the respective Standard concepts.

4. Other changes.

• The RxNorm vocabulary was updated to its 2022 Aug version. Missing multiple ingredient concepts were added.
• RxNorm Extension received a technical synchronization run in order to accommodate the RxNorm refresh (new concepts in RxNorm replaced its duplicates from RxNorm Extension).
• NDC/SPL regular weekly/monthly update.
• MedDRA vocabulary mappings were adjusted according to the concept invalidation/deStandardization due to the SNOMED refresh as well as other changes in OMOP vocabularies described above. Currently, it contains 13596 "Maps to/Maps to value" relationships from MedDRA LLT/PT Classification concepts to Standard OMOP concepts. Also, MedDRA vaccine concepts were remapped to CVX vocabulary.
• We updated CXV vocabulary to the latest 17-Aug-2022 version. Some of the concepts (that have full duplicates in RxNorm/RxE vocabularies) were deStandardized and mapped over accordingly.
• OMOP Extension: some trauma/injury severity scores added.
• DA_France (proprietary IQVIA vocabulary) update.

5. Problems found during the release, but not yet fixed.

• The ICD10CM vocabulary has a wrong vocabulary version assigned to it (2023), while the content is from its 2022 version. We will use the 2023 content in one of the next refreshes, probably early 2023.
• Mapping reuse logic among different ICD family vocabularies is corrupted. It leads to occasional different mapping of the same codes among different vocabularies. This will be fixed with an implementation of the CDE (common data environment) for ICD vocabulary family.
• A substantial part of concepts with replacement relationships ("Concept replaced by", "Concept same_as to", "Concept alt_to to", "Concept was_a to") do not have valid "Maps to" relationships. A possible reason is a wrong location of the "AddFreshMapsTo" function in the load_stages or conflicting function vs load_stage logic.
• In deStandardization/mapping of historical and vaccine administration concepts we faced unexpected results and lots of different patterns of script behavior. This is due to a complex (and probably stale) logic of vocabulary machinery that does not cope well with adjustments and requires lots of manual curation. In the long run, the entire machinery has to be revised / refactored. At the moment it may result in inconsistent mapping in a small number of concepts, e.g. missing or excessive mapping to value, duplicative mapping to pre-coordinated and post-coordinated expressions.
• In deStandardization/mapping of historical and vaccine administration concepts (and probably some other groups) we've missed a small part of them. It mostly happens due to discrepancies in hierarchy (most of the concepts derive from a single ancestor within a group, but a small portion of them are floating in SNOMED without a good hierarchy and should be pulled out manually, which inevitably results in missing concepts).
• For a substantial part of SNOMED concepts the validi...

Release notes v20220622

This guide can provide you more background on how to read the release notes.

What's New?

In this release we feature a new vocabulary: The OMOP Investigational Drugs, a compilation of drug entries that contains ingredient level drug entries that besides already existing ingredients also features concepts that are not marketed drugs (or sometimes never got to market) but have been used in trials. To support ETL of those, we also added working manufacturer codes to the synonym table so that you can also now search for your Infliximab as "TA-650".
Besides that we include the most recent NDC / SPL additions, some additions to the MedDRA vocabulary and some adjusted PPI concepts.

Domain changes

vocabulary_id	old_domain_id	new_domain_id	count
OMOP Extension	Observation	Condition	6

Newly added concepts grouped by Vocabulary_id and Domain

vocabulary_id	domain_id	count
NDC	Device	5
NDC	Drug	4187
OMOP Extension	Measurement	248
OMOP Invest Drug	Drug	29727
RxNorm Extension	Drug	15366
SPL	Device	1
SPL	Drug	2952

Standard concept changes

vocabulary_id	old_standard_concept	new_standard_concept	count
SPL	Non-standard with mapping	Classification with mapping	1
SPL	Non-standard without mapping	Classification without mapping	1

Newly added concepts and their standard concept status

vocabulary_id	new_standard_concept	count
NDC	Standard	5
NDC	Non-standard with mapping	319
NDC	Non-standard without mapping	3868
OMOP Extension	Standard	248
OMOP Invest Drug	Non-standard with mapping	29727
RxNorm Extension	Standard	15366
SPL	Classification without mapping	2953

Changes of concept mapping status grouped by target domain

vocabulary_id	Old target Domain/Status	New target Domain/Status	count
MedDRA	No mapping	Condition	400
MedDRA	No mapping	Condition/Procedure	1
MedDRA	No mapping	Measurement	20
MedDRA	No mapping	Observation	16
MedDRA	No mapping	Procedure	18
NDC	New concept	Device	5
NDC	New concept	Drug	319
NDC	No mapping	Drug	1884
OMOP Extension	New concept	Measurement	248
OMOP Extension	Observation	Condition	6
OMOP Invest Drug	New concept	Drug	29727
RxNorm Extension	New concept	Drug	15366

New vocabularies added

vocabulary_id
OMOP Invest Drug

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Release notes v20220602

This guide can provide you more background on how to read the release notes.

What's New

This release is mostly a technical release to publish a recent version of the proprietary LPD_Australia vocabulary (IQVIA).
Other than that, automated refreshes are performed on MeSH, NDC and SPL. We have added a small number of new OMOP Extension codes and a UCUM unit.

Domain changes

vocabulary_id	old_domain_id	new_domain_id	count
MeSH	Condition	Measurement	2
MeSH	Measurement	Procedure	2
MeSH	Procedure	Measurement	1

Newly added concepts grouped by Vocabulary_id and Domain

vocabulary_id	domain_id	count
LPD_Australia	Device	11
LPD_Australia	Drug	382
MeSH	Condition	34
MeSH	Drug	120
MeSH	Procedure	1
NDC	Device	9
NDC	Drug	4183
OMOP Extension	Measurement	3
OMOP Extension	Procedure	1
SPL	Drug	3671
UCUM	Unit	1

Standard concept changes

vocabulary_id	old_standard_concept	new_standard_concept	count
SPL	Classification without mapping	Non-standard without mapping	3
SPL	Classification with mapping	Non-standard with mapping	1
UCUM	Standard	Non-standard with mapping	1

Newly added concepts and their standard concept status

vocabulary_id	new_standard_concept	count
LPD_Australia	Non-standard without mapping	4
LPD_Australia	Standard	11
LPD_Australia	Non-standard with mapping	378
MeSH	Non-standard with mapping	155
NDC	Standard	9
NDC	Non-standard with mapping	403
NDC	Non-standard without mapping	3780
OMOP Extension	Standard	4
SPL	Classification without mapping	3671
UCUM	Standard	1
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
LPD_Australia	New concept	Device	11
LPD_Australia	New concept	Drug	378
LPD_Australia	No mapping	Drug	322
MeSH	Condition	Measurement	1
MeSH	Measurement	Procedure	1
MeSH	New concept	Condition	34
MeSH	New concept	Drug	120
MeSH	New concept	Procedure	1
MeSH	Procedure	Measurement	3
NDC	New concept	Device	9
NDC	New concept	Drug	403
NDC	No mapping	Drug	1635
OMOP Extension	New concept	Measurement	3
OMOP Extension	New concept	Procedure	1
UCUM	New concept	Unit	1

New vocabularies added

there were no changes here

---

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