stem to death

%%{init: {'theme': 'base' } }%%
%%{init: {'theme': 'base' } }%%
flowchart LR
    subgraph Source
        finngenid
        approx_event_day
        code1
        omop_source_concept_id
        category
    end

    subgraph CDM-OMOP-v5.4
        person_id
        cause_concept_id
        death_date
        cause_source_value
        cause_source_concept_id
    end

    finngenid-->person_id
    category-->cause_concept_id
    approx_event_day-->death_date
    code1-->cause_source_value
    omop_source_concept_id-->cause_source_concept_id

Destination Field	Source field	Logic	Comment field
person_id	finngenid	person_id from person table where person_source_value equals finngenid	Calculated
death_date	approx_event_day	Copied from approx_event_day	Copied
death_datetime		Calculated from death_date with time 00:00:0000	Calculated
death_type_concept_id		Set 32879 - ‘Registry’ for all	Calculated
cause_concept_id	category	Add priority for cause of death using category and select the top priority. The priority for cause of death is as follows: I > U > c1 > c2 > c3 > c4. concept_id_2 from concept_relationship table where concept_id_1 equals cause_source_concept_id and relationship_id equals “Maps to”	Calculated NOTE: IF a cause_source_concept_id has more than one standard mapping (concept_id_2), one row is added per each additional cause_concept_id
cause_source_value	code1	Copied code1 as it is	Copied
cause_source_concept_id	omop_source_concept_id	IF omop_source_concept_id is not null then omop_source_concept_id ELSE 0	Calculated