- Intro
- Formating source vocabulary to OMOP
- Mapping the source vocabulary to the standard vocabularies
- Assessing coverage of databases
TODO: intro icd9fi
The icd9fi codes have been …
TODO: i got it from aki now in the gitlab repo
The concept names are a mixed of Latin, Finnish, and English !!. These are not translated to English !!. The English name were append by matching the ICD9fi code to the ICD9 code dowloaded from Wolfbane.com (1.6.2020).
There are 5 tipes of maching :
TODO
ICD9fi codes ranked by frequency calculated from FinnGen-DF5.
Mapping was carried in USAGI by medical student @kalleaseppala.
From 9 115 codes 656 have been approved.
This makes 7% of codes approved.
How many codes labeled as ICD9fi in finngen are not in the atc standard?
There are 10 codes not found in the standard
Top10 sorted by freq:
| concept_code | freq | freq_per |
|---|---|---|
| 6341A | 264 | 0.066% |
| 2959X | 21 | 0.005% |
| 7181F | 15 | 0.004% |
| 6420A | 14 | 0.004% |
| 6500A | 10 | 0.003% |
| 7150F | 10 | 0.003% |
| 7890X | 9 | 0.002% |
| 4610B | 6 | 0.002% |
| 5409A | 6 | 0.002% |
| 6530C | 6 | 0.002% |
The full list can be found in ./3_freq_of_source_codes/finngen_not_in_ICD9fi.csv
Status of the ICD9fi codes infinngen
| status | n_codes | per_codes | n_events | per_events |
|---|---|---|---|---|
| mapped | 656 | 22.652% | 282739 | 70.736% |
| not_mapped | 2230 | 77.003% | 116612 | 29.174% |
| not_found | 10 | 0.345% | 361 | 0.090% |