- Intro
- Formating source vocabulary to OMOP
- Mapping the source vocabulary to the standard vocabularies
- Assessing coverage of databases
The procedure classification is based on the NCSP Nordic Classification of Surgical Procedures, first published in 1996. The NCSP classification is maintained by the Nordic Classification Center (NCC) and is copyrighted by NOMESKO ref
The NOMESCO codes have been downloaded from kodistopalvelu(7.5.2020).
The concept names were translated to English as translator by [email protected]
Details in ./1_source_vocabulary/README.md
NOMESCO codes ranked by frequency calculated from FinnGen-DF5 and TAYS-oncology.
Mapping was carried in USAGI by medical student @kalleaseppala and reviewed by @helmisuominen.
From 11 290 codes 1 804 have been approved.
This makes 16% of codes approved.
How many codes labeled as NOMESCOfi in finngen are not in the atc standard?
There are 260 codes not found in the standard
Top10 sorted by freq:
| concept_code | freq | freq_per |
|---|---|---|
| XLA10 | 7408 | 0.127% |
| RD211 | 3200 | 0.055% |
| XF640 | 2477 | 0.043% |
| 1LA05 | 1632 | 0.028% |
| 1XC03 | 1619 | 0.028% |
| WQ066 | 1300 | 0.022% |
| 4AA12 | 1102 | 0.019% |
| 6BA02 | 993 | 0.017% |
| 1XC02 | 830 | 0.014% |
| 1XC07 | 774 | 0.013% |
The full list can be found in ./3_freq_of_source_codes/finngen_not_in_NOMESCOfi.csv
Status of the NOMESCOfi codes infinngen
| status | n_codes | per_codes | n_events | per_events |
|---|---|---|---|---|
| mapped | 1397 | 26.044% | 4947275 | 85.045% |
| not_mapped | 3707 | 69.109% | 827930 | 14.232% |
| not_found | 260 | 4.847% | 42010 | 0.722% |
How many codes labeled as NOMESCOfi in tays are not in the atc standard?
There are 0 codes not found in the standard
Top10 sorted by freq:
| concept_code | freq | freq_per |
|---|
The full list can be found in ./3_freq_of_source_codes/tays_not_in_NOMESCOfi.csv
Status of the NOMESCOfi codes intays
| status | n_codes | per_codes | n_events | per_events |
|---|---|---|---|---|
| mapped | 1463 | 26.475% | 3454182 | 95.550% |
| not_mapped | 4063 | 73.525% | 160869 | 4.450% |