I am performing an OMOP ETL and have run into a bit of a conundrum. While I have mapped out the source data table called ConsultationNotes to the OMOP CDM Note table (v5.4), the problem is that there exists multiple instances of a column named ‘AdditionalNotes’ in a number of other tables in my source data. For example, the source tables ‘PatientSensitivities’, ‘PatientImmunisations’, and ‘LabResults’ all have this column ‘AdditionalNotes’, which contains additional information about the sensitivity, immunisation, or lab result in question.
Should these notes also be mapped in the Note table as well? I’m just confused as to how I should map them in order to indicate their provenance. These ‘AdditionalNotes’ column are all derived from tables in the same EHR database, so I cannot use different values in the note_type_concept_id column.
I believe the intent is that each clinical note (each row in your ConsultationNotes table) will produce one row in the OMOP Note table. If you split a single clinical note into multiple Note rows how would you later associate them? I think you just want to append the “Additional Notes” column content onto the unstructured text you are writing to the note_text column. That column should contain the complete textual content of the clinical note.
Hello @jmethot, as you rightly pointed out, I currently have each row in the OMOP Note table set up so that it correlates to each row in the source ConsultationNotes table (since each row in the source represents one clinical note).
However, my confusion mainly stems from how I should format the contents of the AdditionalNotes columns. Each row in this column directly corresponds to providing additional information in text format an “event” that has occurred (e.g. in the PatientImmunisations table, each row represents one particular immunisation that has taken place). For example, the text in AdditionalNotes in the PatientImmunisations table might mention the patient getting a rash after getting the immunisation, or feeling nauseous. I want to include this information in my Notes table even though they were not part of the ConsultationNotes table (where the conventional notes made by a healthcare provider about a patient are typically stored).
I want to include the texts from the column AdditionalNotes in all the different tables mentioned previously, but I also want to maintain their provenance so that I show that the note ‘patient gets a rash after immunisation’ is derived from the PatientImmunisations table. How best can I do this?