To add a custom vocabulary to the OMOP Vocabulary table, you can follow these general steps:
Prepare your custom vocabulary: Define the concepts, codes, and relationships for your custom vocabulary. Make sure you have the necessary information, such as concept IDs, concept names, domain IDs, relationships, and any additional metadata.
Create a concept table: The concept table is the main table in the OMOP Vocabulary database. It contains information about all the concepts, including your custom ones. You’ll need to insert your custom concepts into this table. Ensure that you have the required columns, such as concept_id, concept_name, domain_id, vocabulary_id, etc.
Define relationships: If your custom vocabulary has relationships with existing concepts in the OMOP Vocabulary, you’ll need to establish those relationships. Determine which existing concepts your custom concepts are related to (e.g., is-a relationship, maps-to relationship), and insert the appropriate rows into the relationship tables (e.g., concept_relationship table).
Load the data: Once you have prepared the concept and relationship information, you need to load the data into the OMOP Vocabulary table. This can be done using SQL statements or by importing data from a file, depending on the method you prefer.
Validate and test: After loading the data, it’s essential to validate the entries and ensure they align with the OMOP Vocabulary specifications. Perform checks for consistency, accuracy, and adherence to the OMOP conventions.
Update the metadata: Update the metadata of your custom vocabulary in the metadata tables, such as the vocabulary table, to provide additional details about your custom vocabulary.
Hope this helps.