All Of Us Data Quality Check on MU OMOP CDM

[vasanthi014]

@shossain-mizzou Did you work on this? Do you need anything to move forward?

[shossain-mizzou]

We need OMOP data first. I have tested with the test dataset

[vasanthi014]

OMOP views are accessible by you. You can download it to a SWB and run the DQ program on it.

[shossain-mizzou]

@vasanthi014 , columns needs to be modified in visit_occurrence:

• ADMITTED_FROM_CONCEPT_ID as admitting_source_concept_id
• ADMITTED_FROM_SOURCE_VALUE as admitting_source_value
• DISCHARGED_TO_CONCEPT_ID as discharge_to_concept_id
• DISCHARGED_TO_SOURCE_VALUE as discharge_to_source_value

[shossain-mizzou]

• [x] care_site.csv
• [x] cdm_source.csv
• [ ] condition_era
• [x] condition_occurrence
• [x] death
• [ ] device_exposure
• [ ] dose_era
• [ ] drug_era
• [x] drug_exposure
• [ ] fact_relationship
• [x] location
• [x] measurement
• [ ] note
• [x] observation_period
• [ ] observation
• [ ] participant_match
• [x] person
• [x] procedure_occurrence
• [ ] provider
• [ ] relationship
• [ ] source_concept_map
• [ ] specimen
• [ ] visit_detail
• [x] visit_occurrence

[shossain-mizzou]

[vasanthi014]

All these issues should be fixed now. I would expect NULL's in other columns, I will be revising the ETL to make sure the not NULL columns are addressed but please go ahead and run a report again.

[shossain-mizzou]

Ran on 1000 records per csv. Running on large dataset was talking longer time. We should deal with all the null values first.

[shossain-mizzou]

closing the ticket, we have to check null values though