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ICD10fi mappings

NOTES

Several codes cover the same concept. They have the same LongName and ShortName.

This is can be due to two reasons: - A concept exists on the table as to be append to others “C55”, and to be used as diagnosis “c55&”. - Same concept described as ”Oirekoodi” and ”Syykoodi”, e.g. J17.3*B77.8 (Pneumonia in ascariasis) and B77.8+J17.3 (ascariasis caused by Pneumonia)

Distribution

tmp_code_class n
1 code 13346
2 code 1037
2 code generated 54099

1. Mapping type : ICD10who + USAGUI

First, we map codes to ICD10who by code and name

Second, codes that didn’t find a map to ICD10who are mapped to standard-OMOP using USAGI

1.1 Matchind codes to ICD10who

Try to match icd10fi’s “1 code” codes to icd10who by code and name.

Also try to match icd10fi’s “2 code” to icd10who by name.

How many “1 code” are a direct match to ICD10who??

If matching directly to ICD10fi code

## [1] 9587

If matching to ICD10fi code without any union-marks

## [1] 10716
How well these agree in the definition ??

Count the differences in characters (string distance) between the English names of icd10fi and icd10who full matches

English_name_match_level n
0 8982
1 95
2 180
3 225
4 130
5 18
6 9
7 33
8 8
9 5
10 34
11 23
12 9
13 7
14 15
15 16
16 13
17 145
18 12
19 58

Most (8993) match the name exactly!!,

Expert checked almost matches

These almost matching are saved in icd10fi_almost_match_icd10who.csv.

Name matching was confirmed or rejected by had by Helmi and save as icd10fi_almost_match_icd10who_CHECKED.csv.

## [1] TRUE
How many concepts are in ICD10who but have a different code?

Some concepts are repeated with a different ICD10fi code. Find these in “2 code” and ICD10fi_1code_no_match by having the same tmp_name_fi(icd10fi)

concept_code concept_code_who tmp_name_fi concept_name
G46.3*I67.9 G46.3* Aivorungon halvausoireyhtymä Brain stem stroke syndrome (I60-I67+)
I67.9+G46.3 G46.3* Aivorungon halvausoireyhtymä Brain stem stroke syndrome (I60-I67+)
I00+L54.0 L54.0* Akuutti kuumereuma ja erythema marginatum Erythema marginatum in acute rheumatic fever
L54.0*I00 L54.0* Akuutti kuumereuma ja erythema marginatum Erythema marginatum in acute rheumatic fever
L40.5+M07.1 M07.1* Arthritis mutilans Arthritis mutilans
M07.1*L40.5 M07.1* Arthritis mutilans Arthritis mutilans
B57.3+K93.1 K93.1* Chagasin tauti ja jättikoolon Megacolon in Chagas’ disease
K93.1*B57.3 K93.1* Chagasin tauti ja jättikoolon Megacolon in Chagas’ disease
B57.3+K23.1 K23.1* Chagasin tautiin liittyvä jättiruokatorvi Megaoesophagus in Chagas’ disease
K23.1*B57.3 K23.1* Chagasin tautiin liittyvä jättiruokatorvi Megaoesophagus in Chagas’ disease

Create CONCEPT_RELATIONSHIP for ICD10who matcc

concept_id_1 concept_id_who tmp_mapping_type tmp_code_class tmp_domain_id_2 concept_id_2 relationship_id valid_start_date valid_end_date invalid_reason
7 45537706 ICD10who code and name_en 1 code Condition 198677 Maps to 2014-07-01 2099-12-31 NA
8 45537707 ICD10who code and name_en 1 code Condition 4344638 Maps to 2018-11-28 2099-12-31 NA
9 45552149 ICD10who code and name_en 1 code Condition 200629 Maps to 1970-01-01 2099-12-31 NA
10 45590788 ICD10who code and name_en 1 code Condition 198677 Maps to 1970-01-01 2099-12-31 NA
11 45576225 ICD10who code and name_en 1 code Condition 192819 Maps to 2016-12-01 2099-12-31 NA
12 45537708 ICD10who code and name_en 1 code Condition 192819 Maps to 2014-07-01 2099-12-31 NA
16 45566486 ICD10who code and name_en 1 code Condition 195460 Maps to 1970-01-01 2099-12-31 NA
17 45571411 ICD10who code and name_en 1 code Condition 193953 Maps to 1970-01-01 2099-12-31 NA
18 45600393 ICD10who code and name_en 1 code Condition 442291 Maps to 1970-01-01 2099-12-31 NA
19 45566487 ICD10who code and name_en 1 code Condition 195177 Maps to 1970-01-01 2099-12-31 NA

1.2 Matchind unmatched “1 code” and “2 code” fwith USAGUI

Prepare for USAGI
## [1] TRUE
After USAGI
Create CONCEPT_RELATIONSHIP wfrom USAGI
concept_id_1 concept_id_2 relationship_id valid_start_date valid_end_date invalid_reason tmp_mapping_type tmp_code_class tmp_domain_id_2
3808 4218017 Maps to 1970-01-01 2020-12-31 NA USAGI 2 code Condition
3816 4220313 Maps to 1970-01-01 2020-12-31 NA USAGI 2 code Condition
3824 43021816 Maps to 2013-01-31 2020-12-31 NA USAGI 2 code Condition
3888 44782422 Maps to 2014-01-31 2020-12-31 NA USAGI 2 code Condition
3916 44784474 Maps to 2014-01-31 2020-12-31 NA USAGI 2 code Condition
4762 438338 Maps to 1970-01-01 2020-12-31 NA USAGI 2 code Condition
5076 4102481 Maps to 2010-01-01 2020-12-31 NA USAGI 2 code Condition
5077 4102481 Maps to 1970-01-01 2020-12-31 NA USAGI 2 code Condition
5079 4105009 Maps to 1970-01-01 2020-12-31 NA USAGI 2 code Condition
5140 37017431 Maps to 2016-01-31 2020-12-31 NA USAGI 2 code Condition

2 Create CONCEPT_RELATIONSHIP for 2 code generated

concept_id_1 tmp_domain_id_2 concept_id_2 relationship_id valid_start_date valid_end_date tmp_mapping_type tmp_code_class
7 Condition 198677 Maps to 2014-07-01 2099-12-31 ICD10who code and name_en 1 code
8 Condition 4344638 Maps to 2018-11-28 2099-12-31 ICD10who code and name_en 1 code
9 Condition 200629 Maps to 1970-01-01 2099-12-31 ICD10who code and name_en 1 code
10 Condition 198677 Maps to 1970-01-01 2099-12-31 ICD10who code and name_en 1 code
11 Condition 192819 Maps to 2016-12-01 2099-12-31 ICD10who code and name_en 1 code
12 Condition 192819 Maps to 2014-07-01 2099-12-31 ICD10who code and name_en 1 code
16 Condition 195460 Maps to 1970-01-01 2099-12-31 ICD10who code and name_en 1 code
17 Condition 193953 Maps to 1970-01-01 2099-12-31 ICD10who code and name_en 1 code
18 Condition 442291 Maps to 1970-01-01 2099-12-31 ICD10who code and name_en 1 code
19 Condition 195177 Maps to 1970-01-01 2099-12-31 ICD10who code and name_en 1 code

Recalculate domain

domain_id n
Condition 67159
Observation 765
Condition/Obs 318
Procedure 198
Measurement 38
Metadata 5
Condition/Procedure 4