The observational medical outcomes partnership (OMOP) common data model (CDM) is gaining interest in Finland. The most laborious task will be mapping and curating the medical vocabularies specific from Finland to the standard codes in the OMOP CDM but once done these mapping can be used in the hole country and some Nordic neighbors.
This folder contains the codes to create the mapping tables between the
Finnish vocabulary used in the FinnGen project and the standard
vocabularies used in the OMOP CDM.
This will benefit not only FinnGen but other projects in Finland. For
this reason, a similar project was started in a public GitHub
repo,
but now it is here as many vocabularies are private.
Background Rather than create a completely new vocabulary the OMOP
CDM proposes to use existing vocabularies, these are named standard
vocabularies. The OMOP CDM also includes many other vocabularies which
are mapped to the standard vocabularies. All the vocabularies used by
the OMOP CDM and their connexons are available in
Athena.
In short, mapping means to connecting the codes from a non-standard
vocabulary to the corresponding codes in the standard vocabulary.
Details of the process can be found
here
Vocabularies are organized into in medical domains. One vocabulary may cover more than one domain (see here).
Following picture shows the vocabularies and domains relevant to the FinnGen longitudinal data.
Aim The aim of this project is to convert the
not an OMOP vocabulary to a OMOP non-standard vocabulary mapped to
the corresponding OMOP standard vocabulary.
The resulting mapping tables will be included in the OMOP CDM, as suggested in this forum question, and the process published as done for other vocabularies (e.g. ICD10).
Tools USAGI is a java tool provide by OHDSI that helps in mapping process of new vocabularies here
| vocabulary | n_codes | mapped | mapping_method | FinnGen_DF5 | TAYS_oncology |
|---|---|---|---|---|---|
| FHL | 264 | 0% | TODO:USAGI | 100.0% | |
| HPN | 264 | 0% | TODO:USAGI | 100.0% | |
| ICD10fi | 68482 | 83% | ICD10who + USAGI | 98.8% 0.9% 0.2% | 96.3% 1.6% 2.0% |
| ICD9fi | 2855 | 23% | USAGI | 74.7% 23.4% 1.7% | |
| ICPC | 1443 | 77% | ICD10who | 87.2% 12.1% 0.5% | |
| NOMESCOfi | 11275 | 16% | USAGI | 89.0% 10.3% 0.5% | 96.7% 3.2% 0.0% |
| REIMB | 264 | 0% | TODO:USAGI | 100.0% | |
| ICD8fi | 6907 | 0% | TODO:USAGI | 98.0% 1.9% | |
| SPAT | 415 | 0% | TODO:USAGI | 99.9% 0.0% | |
| Dental codes (NIHW) | TODO |
Table: Percentage in sources as: percent of events mapped to standard vocabulary; not mapped to standard vocabulary ; not found in vocabulary