Releases - OHDSI/Vocabulary-v5.0 GitHub Wiki

The OMOP Standardized Vocabularies change over time. To manage the change of content, but to allow users to use and refer to a defined set of vocabularies, the whole resource is issued in releases. Releases do not (yet) happen in a standard frequency, but usually within one or two months. Twice a year, a major release is issued, which differs from the rest by having a larger number of issues fixed and vocabularies updated. These happen usually in summer and winter.

Between any two releases the content is fixed. Releases define the content, not the structure. Therefore, they are independent of the versions of the OMOP CDM. Instead of their major.minor version scheme, the releases of the Standardized Vocabularies are tagged with the release date.

Release notes

Each release is accompanied by a standard release note, formatted as follows:

1. Domain changes

  • Provides the number of concepts that were reassigned to a different domain.
  • Changes of domain assignments are rare, and occur mostly due to corrections or changes in OMOP CDM conventions.
  • The output is stratifed by vocabulary_id, old domain_id and new domain_id.
  • The old domain_id stands for the concept's domain in the previous vocabulary release.
  • The new_domain_id stands for the concept's domain in the current vocabulary release.

2. Newly added concepts grouped by vocabulary_id and domain

  • Provides the number of concepts that were newly introduced.
  • They may be:
  1. New concept added to the existing vocabularies due to a new vocabulary version release.
  2. New concepts created for the OMOP-authored vocabularies.
  3. Service concepts introduced to support OMOP CDM functioning.
  • The output is stratified by vocabulary_id and domain_id.

3. Standard concept changes

  • Provides the number of the concepts that changed their status.
  • The status may be:
  1. Standard - the concept is Standard (standard_concept = 'S') and mapped to itself through a 'Maps to' link.
  2. Classification - the concept is Classification (standard_concept = 'C') and may or may not be mapped to another Standard concept(s) through the 'Maps to' link.
  3. Non-standard with mapping - the concept is non-Standard (standard_concept = NULL) and mapped to another Standard concept (or several concepts) through a 'Maps to' link(s).
  4. Non-standard without mapping - the concept is non-Standard (standard_concept = NULL), and not mapped to any Standard concept.
  • The output is stratified by vocabulary_id, old standard_concept and new standard_concept.
  • Old standard_concept stands for the concept's status in the previous vocabulary release.
  • New standard_concept stands for the concept's status in the current vocabulary release.

4. Newly added concepts and their standard concept status

  • Provides the number and the status of concepts that were newly introduced.
  • The status may be:
  1. Standard - the concept is Standard (standard_concept = 'S') and mapped to itself through a 'Maps to' link.
  2. Classification - the concept is Classification (standard_concept = 'C') and can be mapped (or not) to other Standard concept with a 'Maps to' link.
  3. Non-standard with mapping - the concept is non-Standard (standard_concept = NULL) and mapped to another Standard concept (or several concepts) through 'Maps to' links.
  4. Non-standard without mapping - the concept is non-Standard (standard_concept = NULL), and not mapped to any Standard concept.
  • The output is stratified by vocabulary_id and new standard_concept.
  • New standard_concept stands for the concept's status.

5. Changes of concept mapping status grouped by target domain

  • Provides the number of the concepts for which their mapping changed.
  • Mapping status may be:
  1. No mapping - the concept has NO mapping to Standard concept (no valid 'Maps to' link).
  2. New concept - the concept was just introduced within the current vocabulary release.
  3. Domain (e.g., Condition) or combination of domains (e.g., Condition/Observation) - reflects the domain of the concept(s) the current concept is mapped to.
  • The output is stratified by vocabulary_id, old target Domain/Status and new target Domain/Status.
  • Old target Domain/Status stands for the concept's mapping status in the previous vocabulary release.
  • New target Domain/Status stands for the concept's mapping status in the current vocabulary release.

F.A.Q.

Q1: Why do we have a high count of NDC codes with a "Non-standard without mapping"?

A1: NDC regularly publish a lot of concept, and for most of them mapping to RxNorm isn't provided. Fortunately, most of non-mapped concepts are NOT real drugs, but devices, vitamins, etc. OHDSI vocabulary team periodically improves NDC mappings on the request basis. Here is the related Github issue for posting the requests.

Q2: Why do we introduce non-standard concepts into RxNorm Extension vocabulary?

A2: Not all the concepts introduced to the RxNorm Extension vocabulary are the actual drug concepts, i.e. product/form/ingredient. RxNorm Extension also includes auxiliary concepts that support the Drug Domain. These concept classes are: Brand Name, Dose Form, Supplier.

Q3: Why would a standard concept_id change to non-standard without mapping?

A3: This usually happens because of the changes done by the authors of the external vocabularies we adopted in OMOP (e.g. RxNorm, SNOMED, LOINC). Each vocabulary has its scope in terms of coverage and performs content improvement activities. Over time, some concepts may become out of scope (drugs withdrawn from the market), or get deprecated because of wrong design and therefore can't be straightforwardly mapped to a replacing concept, or these activities may be considered out of scope by the authoring organizations.

Also, OHDSI vocabularies don't represent the source vocabularies as is. Depending on the design choices in OMOP, only the pool of concepts is considered Standard. Content improvement activities or changes in the design can lead to status modification of certain concepts.