Data merging logic

When OMOP records are recorded some records must be merged. An example of this would be if we detected patient is more than one data source.

In some cases we may partially record a record with the hope of detecting the missing information in later transformations. For example if we have a person data source that does not define the patient’s gender.

If all data is transformed and incomplete records still exist, use the prune command.

Person

Column	Merging rule
gender_concept_id	If new value is not null, set it
year_of_birth	If new value is not null, set it
month_of_birth	If new value is not null, set it
day_of_birth	If new value is not null, set it
birth_datetime	If new value is not null, set it
race_concept_id	If new value is not null, set it
ethnicity_concept_id	If new value is not null, set it
location_id	If new value is not null, set it
provider_id	If new value is not null, set it
care_site_id	If new value is not null, set it
person_source_value	If new value is not null, set it
gender_source_value	If new value is not null, set it
gender_source_concept_id	If new value is not null, set it
race_source_value	If new value is not null, set it
race_source_concept_id	If new value is not null, set it
ethnicity_source_value	If new value is not null, set it
ethnicity_source_concept_id	If new value is not null, set it

Remarks

• If two records are related to the same person, the fields related to that person such as gender are populated based on last record wins. For example if one record says gender is Male and the next record says gender is Female, we overwrite the gender to be Female.
• However if the second value says gender is null, we would not overwrite the gender.
• The order in which data is loaded will define what the ‘final’ value of fields like gender.

Location

Merging logic is not needed as we only record unique locations. If the location already exists in the location table, do not record it. We never update records in this table.

Condition Occurrence

Merging logic depends upon the data source.

Data source	Logic
CDS	Record the record if it does not already exist using the following columns as keys person_id, RecordConnectionIdentifier and condition_concept_id.
COSD	Record the record if it does not already exist using the following columns as keys person_id, condition_concept_id and condition_start_date.

Death

Merging logic is not needed. If a patient was recorded to have died then no futher records will be recorded.

Drug Exposure

Merging logic depends upon the data source.

Data source	Logic
CDS	Record the record if it does not already exist using the following columns as keys RecordConnectionIdentifier and drug_concept_id.

Observation

Merging logic depends upon the data source.

Data source	Logic
CDS	Record the record if it does not already exist using the following columns as keys RecordConnectionIdentifier, HospitalProviderSpellNumber, observation_date and observation_concept_id.

Procedure Occurrence

Merging logic depends upon the data source.

Data source	Logic
CDS	Record the record if it does not already exist using the following columns as keys RecordConnectionIdentifier, procedure_date and procedure_concept_id.
COSD	Record the record if it does not already exist using the following columns as keys procedure_date and procedure_concept_id.

Visit Occurrrence

Merging logic depends upon the data source.

Data source	Logic
CDS	Record the record if it does not already exist using the following columns as keys RecordConnectionIdentifier, HospitalProviderSpellNumber and person_id.

Visit Detail

Merging logic depends upon the data source.

Data source	Logic
CDS	Record the record if it does not already exist using the following columns as keys RecordConnectionIdentifier, HospitalProviderSpellNumber and person_id.

Measurements

Merging logic depends upon the data source.

Data source	Logic
COSD	Record the record if it does not already exist using the following columns as keys measurement_date, measurement_concept_id, measurement_source_concept_id and person_id.