I wanted the concept_name of “Metastasis to bone” to just show “bone”. How can I do this? I thought this is what the synonym table is for. However, it doesn’t appear to work that way. Should I repurpose the synonym table for my use case?
Hello @Nsingleton1
You should never repurpose a table or field in the OMOP CDM. No one, except for you and maybe a few people on your team, will know the table has been redefined and the original data have been removed. If you like the structure of the Concept Synonym table, you are free to utilize it however you want since the data model is covered under the Apache 2 license.
I would like to help you and answer how you should change
But in order to give you an answer, I need to know why you want to do this? What is the use case to change words which represent a condition/diagnosis/disease process to a word which represents a physical structure?
Because the field I’m trying to populate is the anatomic location. In other words, ‘metastatic to bone’ has the anatomic location of ‘bone’. However, that is not captured in the Measurement table
It will help if you give more context about the source data element you are trying to represent in OMOP. You want to record bone as the site of what?
I’m trying to populate a custom data model from OMOP. A row might have the metastatic diagnosis code column along with the column for anatomic location which would need to be “bone” for this example.
In that case, why not parse the term into two parts on the way from OMOP to the custom model? Since you’re manipulating data on the way out of the OMOP CDM, you can do anything you want to it. Beware, it won’t be interoperable with other OMOP CDMs, so use wisely!