- Intro
- Formating source vocabulary to OMOP
- Mapping the source vocabulary to the standard vocabularies
- Assessing coverage of databases
TODO:
ICPC2_merged_and__ICPC1_from_DF6_UTF8.txt Contains the ICPC codes with
English and Finnish names.
This table comes from several sources. Created by [email protected].
| concept_class_id | n |
|---|---|
| ICPC2 | 1383 |
| ICPC2proc | 40 |
| ICPC1 | 20 |
Details in ./1_source_vocabulary/README.md
In short, the source table already includes a column with the equivalent
ICD10 codes. This was mapped to the OMOP’s ICD10who concept_id.
From 1 443 codes 678 have been approved.
This makes 47% of codes approved.
How many codes labeled as ICPC in finngen are not in the atc standard?
There are 3 codes not found in the standard
Top10 sorted by freq:
| concept_code | freq | freq_per |
|---|---|---|
| -1 | 37669 | 0.498% |
| -2 | 4283 | 0.057% |
| F21 | 891 | 0.012% |
The full list can be found in ./3_freq_of_source_codes/finngen_not_in_ICPC.csv
Status of the ICPC codes infinngen
| status | n_codes | per_codes | n_events | per_events |
|---|---|---|---|---|
| mapped | 646 | 63.897% | 7230393 | 95.552% |
| not_mapped | 362 | 35.806% | 293731 | 3.882% |
| not_found | 3 | 0.297% | 42843 | 0.566% |