stem to observation

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

    subgraph CDM-OMOP-v5.4
        person_id
        observation_date
        observation_source_value
        observation_source_concept_id
        visit_occurrence_id
    end

    finngenid-->person_id
    approx_event_day-->observation_date
    code1-->observation_source_value
    omop_source_concept_id-->observation_source_concept_id
    source-->visit_occurrence_id
    index-->visit_occurrence_id

Destination Field	Source field	Logic	Comment field
observation_id		Incremental integer. Unique value per each row observation.	Generated
person_id	finngenid	person_id from person table where person_source_value equals finngenid	Calculated
observation_concept_id		concept_id_2 from concept_relationship table where concept_id_1 equals observation_source_concept_id and relationship_id equals “Maps to”	Calculated NOTE: IF a observation_source_concept_id has more than one standard mapping (concept_id_2), one row is added per each additional observation_concept_id
observation_date	approx_event_day	Copied from approx_event_day	Copied
observation_datetime		Calculated from observation_date with time 00:00:0000	Calculated
observation_type_concept_id		Set 32879 - ‘Registry’ for all	Calculated
value_as_number		Set NULL for all	Info not available
value_as_string		Set NULL for all	Info not available
value_as_concept_id		Set 0 for all	Info not available
qualifier_concept_id		Set 0 for all	Info not available
unit_concept_id		Set 0 for all	Info not available
provider_id		provider_id for mapped visit_occurrence_id from visit_occurrence table.	Calculated
visit_occurrence_id	source index	Link to correspondent visit_occurrence_id from visit_occurrence table where visit_source_value equals “SOURCE=source;INDEX=index”.	Calculated
visit_detail_id		Set NULL for all	Info not available
observation_source_value	code1	Copied code1 as it is	Copied
observation_source_concept_id	omop_source_concept_id	IF omop_source_concept_id is not null then omop_source_concept_id ELSE 0	Calculated
unit_source_value		Set NULL for all	Info not available
qualifier_source_value		Set NULL for all	Info not available
value_source_value		Set NULL for all	Info not available
observation_event_id		Set NULL for all	Info not available
obs_event_field_concept_id		Set 0 for all	Info not available