R/lookups_and_mappings.R
read_all_lkps_maps.RdReads the UK Biobank code mappings file (all_lkps_maps_v3.xlsx,
resource 592) into
a named list of data frames.
read_all_lkps_maps(path = get_ukb_all_lkps_maps())Path to all_lkps_maps_v3.xlsx. By default, this is downloaded
from the UK Biobank website using get_ukb_all_lkps_maps().
A named list of data frames.
Note: This is a large object (>450 MB)
read_all_lkps_maps(dummy_all_lkps_maps_path())
#> $bnf_lkp
#> # A tibble: 10 × 8
#> BNF_Presentation_Code BNF_Presentation BNF_Product BNF_Chemical_Su…
#> <chr> <chr> <chr> <chr>
#> 1 1106000ABAAAAAA Dorzolamide/Tim… Dorzolamid… Dorzolamide & T…
#> 2 1106000ABAAABAB Dorzolamide/Tim… Dorzolamid… Dorzolamide & T…
#> 3 1106000ABAAACAC Dorzolamide/Tim… Dorzolamid… Dorzolamide & T…
#> 4 1106000ABBBAAAA Cosopt_Eye Dps … Cosopt Dorzolamide & T…
#> 5 1106000ABBBABAB Cosopt_Eye Dps … Cosopt Dorzolamide & T…
#> 6 1106000ABBBACAC Cosopt iMulti_E… Cosopt Dorzolamide & T…
#> 7 1106000ABBCAAAA Tidomat_Eye Dps… Tidomat Dorzolamide & T…
#> 8 1106000ABBDAAAC Eylamdo_Eye Dps… Eylamdo Dorzolamide & T…
#> 9 NA NA NA NA
#> 10 BNF Code Information, NHSBSA C… NA NA NA
#> # … with 4 more variables: BNF_Subparagraph <chr>, BNF_Paragraph <chr>,
#> # BNF_Section <chr>, BNF_Chapter <chr>
#>
#> $dmd_lkp
#> # A tibble: 35 × 2
#> concept_id term
#> <chr> <chr>
#> 1 9248101000001107 Cosopt (product)
#> 2 13283401000001102 Cosopt (qualifier value)
#> 3 3479501000001107 Cosopt (qualifier value)
#> 4 3479301000001100 Cosopt 2%/0.5% eye drops
#> 5 3479401000001108 Cosopt 2%/0.5% eye drops 5mL
#> 6 9007501000001101 COSOPT 2%/0.5% single-use eye drops 0.2mL (product)
#> 7 19873411000001103 Cosopt eye drops (Doncaster Pharmaceuticals Ltd) (product)
#> 8 19873511000001104 Cosopt eye drops (Doncaster Pharmaceuticals Ltd) 5 ml (pro…
#> 9 19869611000001107 Cosopt eye drops (Lexon (UK) Ltd) (product)
#> 10 19869711000001103 Cosopt eye drops (Lexon (UK) Ltd) 5 ml (product)
#> # … with 25 more rows
#>
#> $icd9_lkp
#> # A tibble: 26 × 2
#> ICD9 DESCRIPTION_ICD9
#> <chr> <chr>
#> 1 0020 TYPHOID FEVER
#> 2 0341 SCARLATINA
#> 3 250 DIABETES MELLITUS
#> 4 2500 DIABETES MELLITUS WITHOUT MENTION OF COMPLICATION
#> 5 2501 DIABETES WITH KETOACIDOSIS
#> 6 2502 DIABETES WITH COMA
#> 7 2503 DIABETES WITH RENAL MANIFESTATIONS
#> 8 2504 DIABETES WITH OPHTHALMIC MANIFESTATIONS
#> 9 2505 DIABETES WITH NEUROLOGICAL MANIFESTATIONS
#> 10 2506 DIABETES WITH PERIPHERAL CIRCULATORY DISORDERS
#> # … with 16 more rows
#>
#> $icd10_lkp
#> # A tibble: 199 × 12
#> ICD10_CODE ALT_CODE USAGE USAGE_UK DESCRIPTION MODIFIER_4 MODIFIER_5
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 A00 A00 DEFAULT 3 Cholera NA NA
#> 2 A00.0 A000 DEFAULT 3 Cholera due to Vi… NA NA
#> 3 A00.1 A001 DEFAULT 3 Cholera due to Vi… NA NA
#> 4 A00.9 A009 DEFAULT 3 Cholera, unspecif… NA NA
#> 5 A01.0 A010 DEFAULT 3 Typhoid fever NA NA
#> 6 A02 A02 DEFAULT 3 Other salmonella … NA NA
#> 7 A02.0 A020 DEFAULT 3 Salmonella enteri… NA NA
#> 8 A02.1 A021 DEFAULT 3 Salmonella sepsis NA NA
#> 9 A02.2 A022 DEFAULT 3 Localized salmone… NA NA
#> 10 A02.8 A028 DEFAULT 3 Other specified s… NA NA
#> # … with 189 more rows, and 5 more variables: QUALIFIERS <chr>,
#> # GENDER_MASK <chr>, MIN_AGE <chr>, MAX_AGE <chr>, TREE_DESCRIPTION <chr>
#>
#> $icd9_icd10
#> # A tibble: 50 × 4
#> ICD9 DESCRIPTION_ICD9 ICD10 DESCRIPTION_ICD10
#> <chr> <chr> <chr> <chr>
#> 1 0020 TYPHOID FEVER A010 Typhoid fever
#> 2 0341 SCARLATINA A38X Scarlet fever
#> 3 218 UTERINE LEIOMYOMA D250 Submucous leiomyoma of uterus
#> 4 218 UTERINE LEIOMYOMA D251 Intramural leiomyoma of uterus
#> 5 218 UTERINE LEIOMYOMA D252 Subserosal leiomyoma of uterus
#> 6 218 UTERINE LEIOMYOMA D259 Leiomyoma of uterus, unspecified
#> 7 2890 SECONDARY POLYCYTHAEMIA D751 Secondary polycythaemia
#> 8 UNDEF NA E100 Insulin-dependent diabetes mellitus with…
#> 9 UNDEF NA E101 Insulin-dependent diabetes mellitus with…
#> 10 UNDEF NA E102 Insulin-dependent diabetes mellitus with…
#> # … with 40 more rows
#>
#> $read_v2_lkp
#> # A tibble: 25 × 3
#> read_code term_code term_description
#> <chr> <chr> <chr>
#> 1 65V7. 00 Notification of scarlet fever
#> 2 A341. 00 Scarlet fever - scarlatina
#> 3 A341. 11 Scarlet fever
#> 4 B78.. 00 Uterine leiomyoma - fibroids
#> 5 B78.. 11 Fibroids
#> 6 B780. 00 Submucous uterine leiomyoma
#> 7 B781. 00 Intramural uterine leiomyoma
#> 8 B781. 11 Mural fibroids
#> 9 B782. 00 Subserous uterine leiomyoma
#> 10 B78z. 00 Uterine leiomyoma NOS
#> # … with 15 more rows
#>
#> $read_v2_drugs_lkp
#> # A tibble: 7 × 3
#> read_code term_description status_flag
#> <chr> <chr> <chr>
#> 1 k8k.. DORZOLAMIDE+TIM… 0
#> 2 k8k1. DORZOLAMIDE+TIM… 0
#> 3 k8k2. COSOPT 2%/0.5% … 0
#> 4 k8k3. COSOPT 2%/0.5% … 0
#> 5 k8k4. DORZOLAMIDE+TIM… 0
#> 6 NA NA NA
#> 7 Contains information from NHS Digital, licenced … NA NA
#>
#> $read_v2_drugs_bnf
#> # A tibble: 6 × 2
#> read_code bnf_code
#> <chr> <chr>
#> 1 k8k.. 11.06.0…
#> 2 k8k1. 11.06.0…
#> 3 k8k2. 11.06.0…
#> 4 NA NA
#> 5 Contains information from NHS Digital, licenced under the current ve… NA
#> 6 BNF Code Information, NHSBSA Copyright 2019. This information is lic… NA
#>
#> $read_v2_icd9
#> # A tibble: 121 × 3
#> read_code icd9_code icd9_code_def
#> <chr> <chr> <chr>
#> 1 A341. 0341 1
#> 2 B78.. 218 1
#> 3 B780. 218 1
#> 4 B781. 218 1
#> 5 B782. 218 1
#> 6 B78z. 218 1
#> 7 B79.. 219 1
#> 8 C1... 250-259 2
#> 9 C10.. 250 1
#> 10 C100. 2500 1
#> # … with 111 more rows
#>
#> $read_v2_icd10
#> # A tibble: 107 × 3
#> read_code icd10_code icd10_code_def
#> <chr> <chr> <chr>
#> 1 A153. A180D M900A 7
#> 2 A15x. A180D M900A 7
#> 3 A34.. J020,A38X 3
#> 4 A341. A38X 1
#> 5 B78.. D259 1
#> 6 B780. D250 1
#> 7 B781. D251 1
#> 8 B782. D252 1
#> 9 B78z. D259 1
#> 10 C10.. E10-E14 2
#> # … with 97 more rows
#>
#> $read_v2_opcs4
#> # A tibble: 7 × 3
#> read_code opcs_4.2_code opcs_code_def
#> <chr> <chr> <chr>
#> 1 77010 H021 1
#> 2 77011 H023 1
#> 3 77012 H024 1
#> 4 77013 H022 1
#> 5 NA NA NA
#> 6 Contains information from NHS Digital, licenced u… NA NA
#> 7 The OPCS Classification of Interventions and Proc… NA NA
#>
#> $read_v2_read_ctv3
#> # A tibble: 28 × 11
#> CHAPTER READV2_CODE READV2_DESC TERMV2_DESC TERMV2_ORDER TERMV2_TYPE
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 C C106. Diabetes mellitus w… Diabetes m… 00 P
#> 2 C C106. Diabetes mellitus w… Diabetes m… 12 S
#> 3 C C106. Diabetes mellitus w… Diabetes m… 13 S
#> 4 C C106. Diabetes mellitus w… Diabetic a… 11 S
#> 5 C C106. Diabetes mellitus w… Diabetic a… 11 S
#> 6 C C108. Insulin dependent d… Insulin de… 00 P
#> 7 C C108. Insulin dependent d… Insulin de… 00 P
#> 8 C C108. Insulin dependent d… IDDM-Insul… 11 S
#> 9 C C108. Insulin dependent d… IDDM-Insul… 11 S
#> 10 C C108. Insulin dependent d… Type 1 dia… 12 S
#> # … with 18 more rows, and 5 more variables: READV3_CODE <chr>,
#> # TERMV3_CODE <chr>, TERMV3_TYPE <chr>, TERMV3_DESC <chr>, IS_ASSURED <chr>
#>
#> $read_ctv3_lkp
#> # A tibble: 33 × 4
#> read_code term_description description_type status
#> <chr> <chr> <chr> <chr>
#> 1 C10.. Diabetes mellitus P C
#> 2 C10.. DM - Diabetes mellitus S C
#> 3 X40J4 Type I diabetes mellitus P C
#> 4 X40J4 Type 1 diabetes mellitus S C
#> 5 X40J4 IDDM - Insulin-dependent diabetes mellitus S C
#> 6 X40J4 Juvenile onset diabetes mellitus S C
#> 7 X40J4 Insulin-dependent diabetes mellitus S C
#> 8 X30J0 End stage renal failure P C
#> 9 X30J0 ESRF - End stage renal failure S C
#> 10 X30J0 End stage renal disease S C
#> # … with 23 more rows
#>
#> $read_ctv3_icd9
#> # A tibble: 7 × 7
#> read_code icd9_code mapping_status refine_flag add_code_flag element_num
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 X40J4 2500 D P C 0
#> 2 X40J4 250 A M P 0
#> 3 X40J4 6480 R C C 0
#> 4 X40J4 7902 R C C 0
#> 5 NA NA NA NA NA NA
#> 6 Contains infor… NA NA NA NA NA
#> 7 ICD-9 is in th… NA NA NA NA NA
#> # … with 1 more variable: block_num <chr>
#>
#> $read_ctv3_icd10
#> # A tibble: 39 × 7
#> read_code icd10_code mapping_status refine_flag add_code_flag element_num
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 X40J4 E109 D C P 0
#> 2 X40J4 E10 A M P 0
#> 3 X40J4 O240 R C C 0
#> 4 C10.. E149 D C C 0
#> 5 C10.. E14 A M P 0
#> 6 C10.. E109 R C C 0
#> 7 C10.. E119 R C C 0
#> 8 C10.. E129 R C C 0
#> 9 C10.. E139 R C C 0
#> 10 C10.. O249 R C C 0
#> # … with 29 more rows, and 1 more variable: block_num <chr>
#>
#> $read_ctv3_opcs4
#> # A tibble: 8 × 7
#> read_code opcs4_code mapping_status refine_flag add_code_flag element_num
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 77010 H021 G C P 0
#> 2 77011 H023 G C P 0
#> 3 77012 H024 G C P 0
#> 4 77013 H022 G C P 0
#> 5 XaBAT H021 D C P 0
#> 6 NA NA NA NA NA NA
#> 7 Contains info… NA NA NA NA NA
#> 8 The OPCS Clas… NA NA NA NA NA
#> # … with 1 more variable: block_num <chr>
#>
#> $read_ctv3_read_v2
#> # A tibble: 12 × 10
#> READV3_CODE TERMV3_CODE TERMV3_TYPE TERMV3_DESC READV2_CODE READV2_DESC
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 X40J4 Y41PV S Type 1 dia… C10E. Type 1 dia…
#> 2 X40J4 Y41PW S IDDM - Ins… C108. Insulin de…
#> 3 X40J4 Y41PW S IDDM - Ins… C10E. NA
#> 4 X40J4 Y41PW S IDDM - Ins… C10E. Type 1 dia…
#> 5 X40J4 Y41PX S Juvenile o… C108. Insulin de…
#> 6 X40J4 Y41PX S Juvenile o… C10E. NA
#> 7 X40J4 Y41PX S Juvenile o… C10E. Type 1 dia…
#> 8 X40J4 Yadjz S Insulin-de… C10E. NA
#> 9 X40J4 Yadjz S Insulin-de… C10E. Type 1 dia…
#> 10 X40J4 Yagv5 P Type I dia… C10E. Type 1 dia…
#> 11 NA NA NA NA NA NA
#> 12 Contains informa… NA NA NA NA NA
#> # … with 4 more variables: TERMV2_ORDER <chr>, TERMV2_TYPE <chr>,
#> # TERMV2_DESC <chr>, IS_ASSURED <chr>
#>