FinnGen to OMOP CDM v5.4

In addition to genotype data, FinnGen includes the phenotype data from several national registers. This site details how the most relevant registers have been converted to the OMOP CDM v5.4.

In addition to the international vocabularies provided by OMOP, we use national vocabularies build by the FinOMOP group, and few custom vocabularies build by FinnGen [Appendix:Vocabularies]. As a result, most of the events in the clinical data tables have a source_concept_id that link to the source non-standard code. This makes the local codes searchable in Atlas and usable in local analysis 1.

Provided register data has been collected and preprocessed by the Finnish Institute for Health and Welfare (THL). Some of the original columns have been split and some have been merged together. To ease the code mapping, rather than reshape the large provided tables we use a mapping table fg_codes_info.

Moreover, an intermediate stem table is used to collects all the medical events. Events are then placed in the different OMOP domain tables based on the domain of the medical code.

%%{init: {'theme': 'base' } }%%
flowchart LR
    subgraph FinnGen Registers
        finngenid_info[<a href='finngenid_info.html'>finngenid_info</a>]
        drug_events[<a href='drug_events.html'>drug_events</a>]
        hilmo[<a href='hilmo.html'>hilmo</a>]
        prim_out[<a href='prim_out.html'>prim_out</a>]
        reimb[<a href='reimb.html'>reimb</a>]
        canc[<a href='canc.html'>canc</a>]
        death_register[<a href='death_register.html'>death_register</a>]
        birth_mother[<a href='birth_mother.html'>birth_mother</a>]
        vision[<a href='vision.html'>vision</a>]
        kidney[<a href='kidney.html'>kidney</a>]
        kanta[<a href='kanta.html'>kanta</a>]
    end

    stem[<a href='stem.html'>stem</a>]

    subgraph CDM OMOP v5.4
        person
        observation_period
        visit_occurrence
        drug_exposure
        conndition_occurrence
        procedure_occurrence
        device_exposure
        measurement
        observation
        death
        provider
    end


    finngenid_info --> person
    finngenid_info --> observation_period
    finngenid_info --> measurement
    finngenid_info --> observation

    hilmo --> visit_occurrence
    hilmo --> stem

    prim_out --> visit_occurrence
    prim_out --> stem

    reimb --> visit_occurrence
    reimb --> stem

    canc --> visit_occurrence
    canc --> stem

    death_register --> visit_occurrence
    death_register --> stem

    birth_mother --> visit_occurrence
    birth_mother --> stem

    vision --> visit_occurrence
    vision --> stem
    vision --> measurement

    drug_events --> visit_occurrence
    drug_events --> drug_exposure

    kidney --> visit_occurrence
    kidney --> stem
    kidney --> measurement
    kidney --> observation

    kanta --> visit_occurrence
    kanta --> measurement
    kanta --> provider
    
    stem --> conndition_occurrence 
    stem --> procedure_occurrence
    stem --> device_exposure
    stem --> observation
    stem --> measurement
    stem --> death

    fg_codes_info -.-> stem 
    fg_codes_info -.-> visit_occurrence 
    fg_codes_info -.-> measurement
    fg_codes_info --> provider

Registers

finngenid_info

Also know as minimum_extended is a file created by THL to collect participant details.

drug_events

Drug Events table is a combination of events from three registeries.

hilmo

Hilmo register gather the secondary health care diagnose and operations from the country [FinnGen Handbook].

prim_out

Avohilmo register gather the primary health care diagnose and operations from the country. [FinnGen Handbook]

reimb

Reimbursement register gathers [FinnGen Handbook].

canc

Cancer register [FinnGen Handbook].

death_register

Death register [FinnGen Handbook].

birth_mother

Birth Mother [FinnGen Handbook].

vision

Vision [FinnGen Handbook].

Kidney

Kidney [FinnGen Handbook].

Kanta

Kanta [FinnGen Handbook].

stem

Fg_codes_info

  1. M.Philofsky 2019 ↩