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>]
purch[<a href='purch.html'>purch</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>]
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
purch --> visit_occurrence
purch --> drug_exposure
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
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 -->provider