We would like to share an update on our progress with the Smoking hierarchy: in this v20230531 release, we have remapped smoking-related SNOMED concepts to new OMOP Extension concepts. As a result of these changes, certain concepts from source vocabularies such as ICD9CM, Read, CIEL, etc., have lost their mappings.
Explanation and details
Each vocabulary has its own load_stage, meaning that to extend these missing mappings to new OMOP Extension concepts, we must execute the load_stage of each vocabulary. This process often exposes numerous pitfalls due to variations in vocabulary versions, interdependencies, relationships, and domain assignments. Consequently, running each vocabulary and achieving satisfactory results consumes a considerable amount of time. We will address this issue in future releases.
We identified some issues that need to be discussed with the community:
- In the OMOP Extension, we have various types of smokers, including Cigar smoker, Cigarette smoker, Electronic cigarette smoker, etc. However, we lack a common concept that encompasses all types of smokers. The parent concept for these types is Tobacco or its derivatives user, which have the concept Smokeless tobacco user in subsumes. Consequently, we are currently assuming that concepts such as Smoker, Smokes tobacco daily, and Smoker in home refer to cigarette smokers and mapping them accordingly to the concept of Cigarette smoker.
We believe it would be beneficial to have a new concept that serves as a parent for all types of smokers. This would provide a more comprehensive and inclusive representation of smoking behavior within the OMOP Extension.
What do you think about it? Do we really need a new concept that would encompass all smokers?
- Another question pertains to the concept Currently doesn’t use tobacco or its derivatives. Currently, we have mapped all “ex-smoker” concepts to this concept. However, it is important to note that a person can be an ex-cigarette smoker but still use other tobacco products such as smokeless tobacco. Mapping concepts like Ex-user of moist powdered tobacco to Currently doesn’t use tobacco or its derivatives is not only logically incorrect but also problematic because Currently doesn’t use tobacco or its derivatives has the synonym “Current non-smoker.”
Examples of current mapping
| concept_id_1 | concept_name_1 | relationship_id | concept_id_2 | concept_name_2 |
|---|---|---|---|---|
| 4052949 | Ex-cigar smoker | Maps to | 903651 | Currently doesn’t use tobacco or its derivative |
| 4052949 | Ex-cigar smoker | Maps to | 1340204 | History of event |
| 4052949 | Ex-cigar smoker | Maps to value | 903664 | Cigar smoker |
| 4092281 | Ex-cigarette smoker | Maps to | 903651 | Currently doesn’t use tobacco or its derivative |
| 4092281 | Ex-cigarette smoker | Maps to | 1340204 | History of event |
| 4092281 | Ex-cigarette smoker | Maps to value | 903657 | Cigarette smoker |
| 44811943 | Ex user of electronic cigarette | Maps to | 1340204 | History of event |
| 44811943 | Ex user of electronic cigarette | Maps to value | 903655 | Electronic cigarette smoker |
| 4052465 | Ex-pipe smoker | Maps to | 1340204 | History of event |
| 4052465 | Ex-pipe smoker | Maps to value | 903663 | Pipe smoker |
A similar situation arises with the concept Never used tobacco or its derivatives. This concept should not be equated with “Never smoked tobacco.” There may be individuals who have never smoked tobacco but have used other forms of tobacco or derivatives.
We need to establish clear rules for when this concept is appropriate and consider the possibility of adding new concepts or modifying the existing one.
- We had extensive discussions within the team regarding concepts such as Maternal tobacco use in pregnancy, Stopped smoking before pregnancy, Stopped smoking during pregnancy, and Smoked before confirmation of pregnancy. We remapped them to smoking status and saved pregnancy information only in one case.
Examples of current mapping
| concept_id_1 | concept_name_1 | relationship_id | concept_id_2 | concept_name_2 |
|---|---|---|---|---|
| 42534813 | Maternal tobacco use in pregnancy | Maps to | 4270154 | Pregnancy observable |
| 42534813 | Maternal tobacco use in pregnancy | Maps to | 903654 | Tobacco or its derivatives user |
| 40486722 | Stopped smoking before pregnancy | Maps to | 1340204 | History of event |
| 40486722 | Stopped smoking before pregnancy | Maps to value | 903654 | Tobacco or its derivatives use |
| 40486721 | Stopped smoking during pregnancy | Maps to | 1340204 | History of event |
| 40486721 | Stopped smoking during pregnancy | Maps to value | 903654 | Tobacco or its derivatives use |
| 40486696 | Smoked before confirmation of pregnancy | Maps to | 1340204 | History of event |
| 40486696 | Smoked before confirmation of pregnancy | Maps to value | 903654 | Tobacco or its derivatives use |
It is important to acknowledge that this mapping decision compromises the granularity and functionality of SNOMED. We would like to ensure that everyone agrees that this is a suitable decision.
- The earlier community decided to treat the concepts related to nicotine dependency as Standard. However, we encountered concepts that simultaneously indicate nicotine dependency and reflect smoking status. In such cases, we made them Non-Standard and remapped them.
Examples of current mapping
| concept_id_1 | concept_name_1 | relationship_id | concept_id_2 | concept_name_2 |
|---|---|---|---|---|
| 37109024 | Tobacco dependence caused by chewing tobacco | Maps to | 4209423 | Nicotine dependence |
| 37109024 | Tobacco dependence caused by chewing tobacco | Maps to | 903667 | Chewing tobacco user |
| 3655996 | Tobacco dependence with current use | Maps to | 4209423 | Nicotine dependence |
| 3655996 | Tobacco dependence with current use | Maps to | 903654 | Tobacco or its derivatives use |
| 602340 | Tobacco dependence caused by cigarettes in remission | Maps to | 602340 | Tobacco dependence in remission |
| 602340 | Tobacco dependence caused by cigarettes in remission | Maps to | 1340204 | History of event |
| 602340 | Tobacco dependence caused by cigarettes in remission | Maps to value | 903657 | Cigarette smoker |
| 37110445 | Nicotine dependence with current use | Maps to | 4209423 | Nicotine dependence |
| 37110445 | Nicotine dependence with current use | Maps to value | 903654 | Tobacco or its derivatives use |
What is your opinion on this matter?
- Within SNOMED, there are certain complex concepts that pose a challenge when it comes to deciding whether to maintain them as Standard or not. Furthermore, even though we concluded that certain concepts should be destandardized, we faced the question of whether a universal replacement link was necessary (Findings of tobacco or its derivatives use or exposure). To witness our implementation of this process, kindly follow the provided link. We highly appreciate your valuable insights and suggestions if you come across any opportunities for improvement.