Reads 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())

Arguments

path

Path to all_lkps_maps_v3.xlsx. By default, this is downloaded from the UK Biobank website using get_ukb_all_lkps_maps().

Value

A named list of data frames.

Details

Note: This is a large object (>450 MB)

Examples

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>
#>