How to add a custom vocabulary to the OMOP vocabulary table?

[zhuk (Oleg Zhuk)]

Hello, Tim @quinnt

@quinnt

Let’s say I propose to add my own custom concept to the ICD10CM vocabulary. I imagine there would be an outcry from the OHDSI community because I am not the authoring organization for the ICD10CM vocabulary. (Or would there be an outcry if its concept_id were over 2 billion?)

Yes, there still would be an outcry, not mainly because you are not an authoring organization for the ICD10CM vocabulary, but because the OHDSI goal is to maintain vocabulary consistency and uniformity across the globe. ICD10CM should be the same in the USA, China, all over Europe, etc. Thanks to this uniformity, you can easily expand your researches and collaborate with the community.

What you want to do: you want to create your own vocabulary, map it’s terms to Standard concepts (preferred way), or create them as standard concepts (still possible) to create cohorts later. To build your own vocabulary, you need to populate

• vocabulary: all the information on your custom vocabulary, done similar to other records, according to CDM specifications
• concept: try to see everything as a concept in CDM as we do in object-oriented programming
  *concept_relationship: put your relationships from your concepts to standard using ‘Maps to’ relationship. Remember, if you can’t find a corresponding concept in Standard vocabulary and create your concept as standard, you still need to create ‘Maps to’ relationship from concept to itself.

@quinnt

For your custom vocabulary called “social_hx”, how did you populate the column vocabulary.vocabulary_concept_id ?

2 bil something, the concept_id of concept you would create for your vocabulary ‘social_hx’

To illustrate what I’m talking about, try to check concepts of other vocabularies (ICD10CM is perfect example)

SELECT * FROM vocabulary WHERE vocabulary_id = 'ICD10CM';
SELECT * FROM concept WHERE concept_id = 44819098;

The book of OHDSI, Standardized Vocabularies chapter may be very helpful