R/lookups_and_mappings.R
build_all_lkps_maps.RdDownloads the lookup and mapping tables from UK Biobank resource 592 as well as the NHSBSA BNF-SNOMED mapping table (available here) and OPCS4, self-reported medical conditions/medications/operations from the UK Biobank codings file (available here).
build_all_lkps_maps(
all_lkps_maps = read_all_lkps_maps(),
ukb_codings = ukbwranglr::get_ukb_codings(),
bnf_dmd = get_nhsbsa_snomed_bnf(),
self_report_med_to_atc_map = get_ukb_self_report_med_to_atc_map(),
ctv3sctmap2 = NULL,
phecode_1_2_lkp = get_phecode_definitions(),
icd10_phecode_1_2 = get_phecode_icd10_map(),
icd9_phecode_1_2 = get_phecode_icd9_map()
)UK Biobank resource 592, as returned by
get_ukb_all_lkps_maps.
The UK Biobank codings file, as returned by
get_ukb_codings.
Optional: path to the NHSBSA BNF-SNOMED mapping table (see
get_nhsbsa_snomed_bnf()).
Optional: path to a UK Biobank
self-reported medication to ATC map (see
get_ukb_self_report_med_to_atc_map()).
Optional: path to the NHS TRUD mapping file for Read 3 to SNOMEDCT ("ctv3sctmap2_uk_20200401000001.txt").
Optional: path to the phecode v1.2 lookup file
(see get_phecode_definitions()).
Optional: path to the phecode v1.2 to ICD10 mapping
file (see get_phecode_icd10_map()).
Optional: path to the phecode v1.2 to ICD10 mapping
file (see get_phecode_icd9_map()).
Returns a named list of data frames.
# build dummy all_lkps_maps using just UKB resource 592 and UKB codings file
build_all_lkps_maps(
all_lkps_maps = read_all_lkps_maps_dummy(),
ukb_codings = read_ukb_codings_dummy(),
bnf_dmd = NULL,
self_report_med_to_atc_map = NULL,
ctv3sctmap2 = NULL,
phecode_1_2_lkp = NULL,
icd10_phecode_1_2 = NULL,
icd9_phecode_1_2 = NULL
)
#> Extending tables in UKB resource 592
#> Reformatting ICD9-Phecode map
#> Success!
#> $bnf_lkp
#> # A tibble: 25 × 10
#> BNF_Code BNF_Code_Level BNF_Chapter BNF_Section BNF_Paragraph
#> <chr> <chr> <chr> <chr> <chr>
#> 1 1106000ABAAAAAA full Eye Treatment Of Gl… Treatment Of…
#> 2 11 chapter Eye NA NA
#> 3 1106 section Eye Treatment Of Gl… NA
#> 4 110600 paragraph Eye Treatment Of Gl… Treatment Of…
#> 5 1106000 subparagraph Eye Treatment Of Gl… Treatment Of…
#> 6 1106000AB chemical_substance Eye Treatment Of Gl… Treatment Of…
#> 7 1106000ABAA product_name Eye Treatment Of Gl… Treatment Of…
#> 8 1106000ABAAAA further_info Eye Treatment Of Gl… Treatment Of…
#> 9 1106000ABAAABAB full Eye Treatment Of Gl… Treatment Of…
#> 10 1106000ABAAAB further_info Eye Treatment Of Gl… Treatment Of…
#> # … with 15 more rows, and 5 more variables: BNF_Subparagraph <chr>,
#> # BNF_Chemical_Substance <chr>, BNF_Product <chr>, BNF_Presentation <chr>,
#> # Description <chr>
#>
#> $dmd_lkp
#> # A tibble: 33 × 3
#> .rowid concept_id term
#> <int> <chr> <chr>
#> 1 1 9248101000001107 Cosopt (product)
#> 2 2 13283401000001102 Cosopt (qualifier value)
#> 3 3 3479501000001107 Cosopt (qualifier value)
#> 4 4 3479301000001100 Cosopt 2%/0.5% eye drops
#> 5 5 3479401000001108 Cosopt 2%/0.5% eye drops 5mL
#> 6 6 9007501000001101 COSOPT 2%/0.5% single-use eye drops 0.2mL (product)
#> 7 7 19873411000001103 Cosopt eye drops (Doncaster Pharmaceuticals Ltd) (p…
#> 8 8 19873511000001104 Cosopt eye drops (Doncaster Pharmaceuticals Ltd) 5 …
#> 9 9 19869611000001107 Cosopt eye drops (Lexon (UK) Ltd) (product)
#> 10 10 19869711000001103 Cosopt eye drops (Lexon (UK) Ltd) 5 ml (product)
#> # … with 23 more rows
#>
#> $icd9_lkp
#> # A tibble: 24 × 3
#> .rowid ICD9 DESCRIPTION_ICD9
#> <int> <chr> <chr>
#> 1 1 0020 TYPHOID FEVER
#> 2 2 0341 SCARLATINA
#> 3 3 250 DIABETES MELLITUS
#> 4 4 2500 DIABETES MELLITUS WITHOUT MENTION OF COMPLICATION
#> 5 5 2501 DIABETES WITH KETOACIDOSIS
#> 6 6 2502 DIABETES WITH COMA
#> 7 7 2503 DIABETES WITH RENAL MANIFESTATIONS
#> 8 8 2504 DIABETES WITH OPHTHALMIC MANIFESTATIONS
#> 9 9 2505 DIABETES WITH NEUROLOGICAL MANIFESTATIONS
#> 10 10 2506 DIABETES WITH PERIPHERAL CIRCULATORY DISORDERS
#> # … with 14 more rows
#>
#> $icd10_lkp
#> # A tibble: 197 × 13
#> .rowid ICD10_CODE ALT_CODE USAGE USAGE_UK DESCRIPTION MODIFIER_4 MODIFIER_5
#> <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 1 A00 A00 DEFAULT 3 Cholera NA NA
#> 2 2 A00.0 A000 DEFAULT 3 Cholera du… NA NA
#> 3 3 A00.1 A001 DEFAULT 3 Cholera du… NA NA
#> 4 4 A00.9 A009 DEFAULT 3 Cholera, u… NA NA
#> 5 5 A01.0 A010 DEFAULT 3 Typhoid fe… NA NA
#> 6 6 A02 A02 DEFAULT 3 Other salm… NA NA
#> 7 7 A02.0 A020 DEFAULT 3 Salmonella… NA NA
#> 8 8 A02.1 A021 DEFAULT 3 Salmonella… NA NA
#> 9 9 A02.2 A022 DEFAULT 3 Localized … NA NA
#> 10 10 A02.8 A028 DEFAULT 3 Other spec… NA NA
#> # … with 187 more rows, and 5 more variables: QUALIFIERS <chr>,
#> # GENDER_MASK <chr>, MIN_AGE <chr>, MAX_AGE <chr>, TREE_DESCRIPTION <chr>
#>
#> $icd9_icd10
#> # A tibble: 47 × 5
#> .rowid ICD9 DESCRIPTION_ICD9 ICD10 DESCRIPTION_ICD10
#> <int> <chr> <chr> <chr> <chr>
#> 1 1 0020 TYPHOID FEVER A010 Typhoid fever
#> 2 2 0341 SCARLATINA A38X Scarlet fever
#> 3 3 218 UTERINE LEIOMYOMA D250 Submucous leiomyoma of uterus
#> 4 4 218 UTERINE LEIOMYOMA D251 Intramural leiomyoma of uterus
#> 5 5 218 UTERINE LEIOMYOMA D252 Subserosal leiomyoma of uterus
#> 6 6 218 UTERINE LEIOMYOMA D259 Leiomyoma of uterus, unspecified
#> 7 7 2890 SECONDARY POLYCYTHAEMIA D751 Secondary polycythaemia
#> 8 8 NA NA E100 Insulin-dependent diabetes mellit…
#> 9 9 NA NA E101 Insulin-dependent diabetes mellit…
#> 10 10 NA NA E102 Insulin-dependent diabetes mellit…
#> # … with 37 more rows
#>
#> $read_v2_lkp
#> # A tibble: 23 × 4
#> .rowid read_code term_code term_description
#> <int> <chr> <chr> <chr>
#> 1 1 65V7. 00 Notification of scarlet fever
#> 2 2 A341. 00 Scarlet fever - scarlatina
#> 3 3 A341. 11 Scarlet fever
#> 4 4 B78.. 00 Uterine leiomyoma - fibroids
#> 5 5 B78.. 11 Fibroids
#> 6 6 B780. 00 Submucous uterine leiomyoma
#> 7 7 B781. 00 Intramural uterine leiomyoma
#> 8 8 B781. 11 Mural fibroids
#> 9 9 B782. 00 Subserous uterine leiomyoma
#> 10 10 B78z. 00 Uterine leiomyoma NOS
#> # … with 13 more rows
#>
#> $read_v2_drugs_lkp
#> # A tibble: 5 × 4
#> .rowid read_code term_description status_flag
#> <int> <chr> <chr> <chr>
#> 1 1 k8k.. DORZOLAMIDE+TIMOLOL 0
#> 2 2 k8k1. DORZOLAMIDE+TIMOLOL 2%/0.5% eye drops 0
#> 3 3 k8k2. COSOPT 2%/0.5% eye drops 5mL 0
#> 4 4 k8k3. COSOPT 2%/0.5% single-use eye drops 0.2mL 0
#> 5 5 k8k4. DORZOLAMIDE+TIMOLOL 2%/0.5% single-use eye drops 0
#>
#> $read_v2_drugs_bnf
#> # A tibble: 3 × 14
#> .rowid.x read_code bnf_code .rowid.y term_description status_flag
#> <int> <chr> <chr> <int> <chr> <chr>
#> 1 1 k8k.. 11.06.00.00 1 DORZOLAMIDE+TIMOLOL 0
#> 2 2 k8k1. 11.06.00.00 2 DORZOLAMIDE+TIMOLOL 2%/0.… 0
#> 3 3 k8k2. 11.06.00.00 3 COSOPT 2%/0.5% eye drops … 0
#> # … with 8 more variables: bnf_chapter_code <chr>, bnf_section_code <chr>,
#> # bnf_paragraph_code <chr>, bnf_subparagraph_code <chr>, BNF_Chapter <chr>,
#> # BNF_Section <chr>, BNF_Paragraph <chr>, BNF_Subparagraph <chr>
#>
#> $read_v2_icd9
#> # A tibble: 118 × 4
#> .rowid read_code icd9_code icd9_code_def
#> <int> <chr> <chr> <chr>
#> 1 1 A341. 0341 1
#> 2 2 B78.. 218 1
#> 3 3 B780. 218 1
#> 4 4 B781. 218 1
#> 5 5 B782. 218 1
#> 6 6 B78z. 218 1
#> 7 7 B79.. 219 1
#> 8 8 C1... 250-259 2
#> 9 9 C10.. 250 1
#> 10 10 C100. 2500 1
#> # … with 108 more rows
#>
#> $read_v2_icd10
#> # A tibble: 342 × 5
#> .rowid read_code icd10_code icd10_code_def icd10_dagger_asterisk
#> <int> <chr> <chr> <chr> <chr>
#> 1 1 A153. A180 7 D
#> 2 1 A153. M900 7 A
#> 3 2 A15x. A180 7 D
#> 4 2 A15x. M900 7 A
#> 5 3 A34.. J020 3 NA
#> 6 3 A34.. A38X 3 NA
#> 7 4 A341. A38X 1 NA
#> 8 5 B78.. D259 1 NA
#> 9 6 B780. D250 1 NA
#> 10 7 B781. D251 1 NA
#> # … with 332 more rows
#>
#> $read_v2_opcs4
#> # A tibble: 4 × 4
#> .rowid read_code opcs_4.2_code opcs_code_def
#> <int> <chr> <chr> <chr>
#> 1 1 77010 H021 1
#> 2 2 77011 H023 1
#> 3 3 77012 H024 1
#> 4 4 77013 H022 1
#>
#> $read_v2_read_ctv3
#> # A tibble: 26 × 12
#> .rowid CHAPTER READV2_CODE READV2_DESC TERMV2_DESC TERMV2_ORDER TERMV2_TYPE
#> <int> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 1 C C106. Diabetes mel… Diabetes m… 00 P
#> 2 2 C C106. Diabetes mel… Diabetes m… 12 S
#> 3 3 C C106. Diabetes mel… Diabetes m… 13 S
#> 4 4 C C106. Diabetes mel… Diabetic a… 11 S
#> 5 5 C C106. Diabetes mel… Diabetic a… 11 S
#> 6 6 C C108. Insulin depe… Insulin de… 00 P
#> 7 7 C C108. Insulin depe… Insulin de… 00 P
#> 8 8 C C108. Insulin depe… IDDM-Insul… 11 S
#> 9 9 C C108. Insulin depe… IDDM-Insul… 11 S
#> 10 10 C C108. Insulin depe… Type 1 dia… 12 S
#> # … with 16 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: 31 × 5
#> .rowid read_code term_description description_type status
#> <int> <chr> <chr> <chr> <chr>
#> 1 1 C10.. Diabetes mellitus P C
#> 2 2 C10.. DM - Diabetes mellitus S C
#> 3 3 X40J4 Type I diabetes mellitus P C
#> 4 4 X40J4 Type 1 diabetes mellitus S C
#> 5 5 X40J4 IDDM - Insulin-dependent diabetes m… S C
#> 6 6 X40J4 Juvenile onset diabetes mellitus S C
#> 7 7 X40J4 Insulin-dependent diabetes mellitus S C
#> 8 8 X30J0 End stage renal failure P C
#> 9 9 X30J0 ESRF - End stage renal failure S C
#> 10 10 X30J0 End stage renal disease S C
#> # … with 21 more rows
#>
#> $read_ctv3_icd9
#> # A tibble: 4 × 8
#> .rowid read_code icd9_code mapping_status refine_flag add_code_flag
#> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 1 X40J4 2500 D P C
#> 2 2 X40J4 250 A M P
#> 3 3 X40J4 6480 R C C
#> 4 4 X40J4 7902 R C C
#> # … with 2 more variables: element_num <chr>, block_num <chr>
#>
#> $read_ctv3_icd10
#> # A tibble: 36 × 9
#> .rowid read_code icd10_code mapping_status refine_flag add_code_flag
#> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 1 X40J4 E109 D C P
#> 2 2 X40J4 E10 A M P
#> 3 3 X40J4 O240 R C C
#> 4 4 C10.. E149 D C C
#> 5 5 C10.. E14 A M P
#> 6 6 C10.. E109 R C C
#> 7 7 C10.. E119 R C C
#> 8 8 C10.. E129 R C C
#> 9 9 C10.. E139 R C C
#> 10 10 C10.. O249 R C C
#> # … with 26 more rows, and 3 more variables: element_num <chr>,
#> # block_num <chr>, icd10_dagger_asterisk <chr>
#>
#> $read_ctv3_opcs4
#> # A tibble: 5 × 8
#> .rowid read_code opcs4_code mapping_status refine_flag add_code_flag
#> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 1 77010 H021 G C P
#> 2 2 77011 H023 G C P
#> 3 3 77012 H024 G C P
#> 4 4 77013 H022 G C P
#> 5 5 XaBAT H021 D C P
#> # … with 2 more variables: element_num <chr>, block_num <chr>
#>
#> $read_ctv3_read_v2
#> # A tibble: 10 × 11
#> .rowid READV3_CODE TERMV3_CODE TERMV3_TYPE TERMV3_DESC READV2_CODE
#> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 1 X40J4 Y41PV S Type 1 diabetes melli… C10E.
#> 2 2 X40J4 Y41PW S IDDM - Insulin-depend… C108.
#> 3 3 X40J4 Y41PW S IDDM - Insulin-depend… C10E.
#> 4 4 X40J4 Y41PW S IDDM - Insulin-depend… C10E.
#> 5 5 X40J4 Y41PX S Juvenile onset diabet… C108.
#> 6 6 X40J4 Y41PX S Juvenile onset diabet… C10E.
#> 7 7 X40J4 Y41PX S Juvenile onset diabet… C10E.
#> 8 8 X40J4 Yadjz S Insulin-dependent dia… C10E.
#> 9 9 X40J4 Yadjz S Insulin-dependent dia… C10E.
#> 10 10 X40J4 Yagv5 P Type I diabetes melli… C10E.
#> # … with 5 more variables: READV2_DESC <chr>, TERMV2_ORDER <chr>,
#> # TERMV2_TYPE <chr>, TERMV2_DESC <chr>, IS_ASSURED <chr>
#>
#> $opcs4_lkp
#> # A tibble: 6 × 2
#> opcs4_code description
#> <chr> <chr>
#> 1 H01 H01 Emergency excision of appendix
#> 2 H011 H01.1 Emergency excision of abnormal appendix and drainage HFQ
#> 3 H012 H01.2 Emergency excision of abnormal appendix NEC
#> 4 H013 H01.3 Emergency excision of normal appendix
#> 5 H018 H01.8 Other specified emergency excision of appendix
#> 6 H019 H01.9 Unspecified emergency excision of appendix
#>
#> $self_report_cancer
#> # A tibble: 0 × 2
#> # … with 2 variables: data_coding_3 <chr>, description <chr>
#>
#> $self_report_medication
#> # A tibble: 0 × 2
#> # … with 2 variables: data_coding_4 <chr>, description <chr>
#>
#> $self_report_operation
#> # A tibble: 0 × 2
#> # … with 2 variables: data_coding_5 <chr>, description <chr>
#>
#> $self_report_non_cancer
#> # A tibble: 0 × 2
#> # … with 2 variables: data_coding_6 <chr>, description <chr>
#>