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Hello!
I am writing to ask why do some concept_ids on the concept_relationship table map to more than one valid value. Please find an example in the screenshot below.
I thought each concept_id maps to exactly one standard and valid concept_id. Please correct me if I am wrong. For the record, last time I updated my concept_relationship table from Athena was the 2nd of July 2018.
I would deeply appreciate your assistance!
You could have 1 non-standard map to multiple standard concepts, that is fair game. This is usually found in cases where one code is associated to multiple conditions, so the concept_relationship will map the single code to each specific condition that is packaged in it.
I think the rule you are thinking is that thereâs exactly one standard concept for a âmedical ideaâ, meaning you wonât find multiple concepts for Stillâs disease.
In the case you brought up, it looks like the ICD10 code M06.14 is mapping over to 2 concepts, one for Stillâs Disease, the other for RA of hand joint. From what I read, Stillâs shares many characteristics with RA so perhaps that is why there is the dual mapping. But, I checked the vocab and it doesnât look like Stillâs rolls up to anything under RA, so the mapping isnât redundant.
I canât give you the actual reason why this particular concept got mapped to two conditions. Most likely the vocabulary team got that mapping from some source, or you did find a mapping error. But, to your original question, it is valid to have a non-standard concept map to multiple standard concepts.
In ontology, it is possible to desribe info like that if the relation between two concepts is one-to-many relationship.
Hello!
Unfortunately, you have found real bug.
As you see, concept â42616600 M06.14 Adult-onset Still disease, handâ from ICD10 is non-standard. And it simultaneously MAPS TO standard concepts: â4344166 239920006 Adult onset Stillâs diseaseâ and â4115161 287007001 Rheumatoid arthritis - hand jointâ. And those are the main conclusions from vocabulary team:
firstly, this case contradicts our rules of data representation. Concepts can have more than one âMaps toâ relationship_id only when they are pre-coordinated concepts listing two or more semantic components through AND or OR (if there is no an equivalent combination concept that is also hierarchically well connected).
Evidently, your case is not about it. âRead moreâ link: http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:mapping
Secondly, mapping to the second SNOMED concept in this list (4115161) is incorrect, because Stillâs disease and rheumatoid arthritis are different diseases from the big category of autoimmune pathology.
Review and bug fix of âICD10â vocabulary is already in our backlog. We apologize for inconvenience caused.
@Chris_Knoll thank you for your reply. I see that it is valid for a non-standard concept to map to multiple standard concepts. However, how do I treat these double mappings in my ETL? 0.3% of my conditions (nearly 1000) map to two concept_ids. Is there an efficient way to map each of them to the most correct concept_id? Do I have to go over these conditions one by one and pick the most correct concept_id?
Youâll insert 2 records in your target CDM table, one for each mapping.
You donât need to pick, you map them both. The topic of this thread was pointing out an error in a map (where Stillâs disease ICD10 was mapping to 2 standard concepts: Stillâs disease and RA of joint). That wasnât a correct mapping, but there are legitimate cases where a source code can map to multiple concepts (which could possibly be to different domains, ie drug_exposure and procedure_occurrence). For example, it might be reasonable if thereâs a specific source code for âchemotherapy using Paclitaxelâ, you might get a procedure record for âchemotherapyâ and a drug exposure of âPaclitaxelâ.
1000 sounds like a lot, but perhaps you could go to your source system, group byâŚcount() those concepts and let us know the top 10 conditions (by occurrence count) in your data which map to multiple concepts? Perhaps youâve uncovered additional errors in the vocabulary mapping.
I see! It is all clear now. Thank you for the example
Here are the first few concept_ids that map to more than one concept_id in the concept_relationship table.
If you could (next time) add the concept name so that we can see quickly what the concept in question is, and also it would be helpful to understand the frequency of these multi-mapping concepts that appear in your data (ie: it wouldnât make sense to tackle a concept with 3 mapping_destination_counts when it appears once in your data).
Just for kicks, the first concept in there with the multi map is:
Closed fracture of base of skull with subarachnoid, subdural, and extradural hemorrhage, with prolonged [more than 24 hours] loss of consciousness, without return to pre-existing conscious level
Fun! This does look like a combo of things happening together (facture, hemorrhage, loss of consciousness) so this is an interesting case. Itâs very specific tho, I wonder how many times this appears in data.
