Level 1 Disease Trait Grouping - Non-cancer

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Last updated: 2025-09-10

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Knit directory: genomics_ancest_disease_dispar/

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1 Set up

library(dplyr)
library(data.table)
library(stringr)

1.1 Ontology help - for getting disease subtypes

source(here::here("code/get_term_descendants.R"))

gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_disease_trait_simplified.csv"))

2 Initial summary

2.1 Objectives of this analysis:

Level 1 disease grouping: - collapse disease causes, e.g. contact dermatitis due to nickel to contact dermatitis - collapse disease subtypes, e.g. bipolar I and bipolar II to bipolar disorder - collapse disease onset times, e.g. early-onset alzheimers disease and late-onset alzheimers disease to alzheimers disease - collapse disease stages

2.2 Grouping - level 1 set up

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms = collected_all_disease_terms)

2.3 Initial summary - number of unique study terms

n_studies_trait = gwas_study_info |>
  dplyr::filter(DISEASE_STUDY == T) |>
  dplyr::select(collected_all_disease_terms, PUBMED_ID) |>
  dplyr::distinct() |>
  dplyr::group_by(collected_all_disease_terms) |>
  dplyr::summarise(n_studies = dplyr::n()) |>
  dplyr::arrange(desc(n_studies))

head(n_studies_trait)

# A tibble: 6 × 2
  collected_all_disease_terms n_studies
  <chr>                           <int>
1 type 2 diabetes mellitus          145
2 alzheimers disease                116
3 breast cancer                     112
4 asthma                            110
5 major depressive disorder         108
6 schizophrenia                     103

dim(n_studies_trait)

[1] 3083    2

2.3.1 When separate studies with multiple terms

diseases <- stringr::str_split(pattern = ", ", 
 gwas_study_info$collected_all_disease_terms[gwas_study_info$collected_all_disease_terms != ""])  |> 
            unlist() |>
            stringr::str_trim()

length(unique(diseases))

[1] 2196

3 Disease stage grouping

3.1 Chronic kidney disease (CKD)

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "chronic kidney disease stage 5|chronic kidney disease stage 4",
                          "chronic kidney disease"
         ))


gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "stage 5 chronic kidney disease",
                          "chronic kidney disease"
         ))

4 Disease cause grouping

4.1 Contact dermatitis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "contact dermatitis due to nickel",
                          "contact dermatitis"
         ))

5 Disease subtype grouping (non-cancer)

5.1 Abortion

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "habitual abortion|abortion|spontaneous loss of pregnancy|incomplete loss of pregnancy",
                          "loss of pregnancy"
         ))
# exact synonyms (to avoid partial matches
# https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_1001491?lang=en

5.2 Acute pancreatitis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "asparaginase-induced acute pancreatitis",
                          "acute pancreatitis"
         ))

5.3 Alopecia

url<-  "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0004907/descendants"

alopecia_terms <- get_descendants(url)

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(alopecia_terms, collapse = "(?=,|$)|\\b"),
                          "alopecia"
         ))

5.4 Alcohol-use disorders

alchol_use_disorder_terms <- c("alcohol dependence",
                             "alcohol withdrawal",
                             "alcohol withdrawal delirium",
                             "alcohol abuse",
                             "alcohol-related disorders delirium",
                             "alcohol use disorder",
                             "addictive alcohol use"
                             )

gwas_study_info = gwas_study_info |>
      mutate(l1_all_disease_terms = 
           stringr::str_replace_all(l1_all_disease_terms,
                            paste0(alchol_use_disorder_terms, collapse = "(?=,|$)|\\b"),
                            "alcohol-related disorders"
           ))

gwas_study_info = gwas_study_info |>
      mutate(l1_all_disease_terms = 
           stringr::str_replace_all(l1_all_disease_terms,
                            paste0(alchol_use_disorder_terms, collapse = "(?=,|$)|\\b"),
                            "alcohol-related disorders"
           ))

5.5 Alcoholic liver disease

alcoholic_liver_disease_terms <- c("alcoholic liver cirrhosis",
                                   "alcoholic fatty liver disease",
                                   "alcoholic hepatitis"
                                   )


gwas_study_info = gwas_study_info |>
      mutate(l1_all_disease_terms = 
           stringr::str_replace_all(l1_all_disease_terms,
                             paste0(alcoholic_liver_disease_terms, collapse = "(?=,|$)|\\b"),
                            "alcoholic liver disease"
           ))

5.6 Alzheimer’s disease

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "early-onset alzheimers disease|late-onset alzheimers disease",
                          "alzheimers disease"
         ))

5.7 Allergic contact dermatitis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "allergic contact dermatitis of eyelid",
                          "allergic contact dermatitis"
         ))

5.8 Allergic rhinitis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "seasonal allergic rhinitis",
                          "allergic rhinitis"
         ))

5.9 Astigmatism

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "corneal astigmatism",
                          "astigmatism"
         ))

5.10 Asthma

gwas_study_info = gwas_study_info |>
      mutate(l1_all_disease_terms  = 
           stringr::str_replace_all(l1_all_disease_terms,
                            "atopic asthma|chronic obstructive asthma",
                            "asthma"
           )) |>
    mutate(l1_all_disease_terms  = 
           stringr::str_replace_all(l1_all_disease_terms,
                            "childhood onset asthma|adult onset asthma|aspirin-induced asthma",
                            "asthma"
           ))

5.11 Autoimmune pancreatitis

gwas_study_info = gwas_study_info |>
      mutate(l1_all_disease_terms  = 
           stringr::str_replace_all(l1_all_disease_terms,
                            "autoimmune pancreatitis type 1",
                            "autoimmune pancreatitis"
           )) 

5.12 Back pain

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "low back pain",
                          "back pain"
         ))

5.13 Bipolar disorder

gwas_study_info = gwas_study_info |> 
    mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "bipolar ii disorder|bipolar i disorder",
                          "bipolar disorder"
         ))

5.14 Celiac disease

gwas_study_info = 
gwas_study_info |> 
 mutate(l1_all_disease_terms  = 
          stringr::str_replace_all(l1_all_disease_terms,
                                  pattern = "refractory celiac disease",
                                   "celiac disease"
                          )  
        )

5.15 Chronic pancreatitis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "thiopurine immunosuppressant-induced pancreatitis|non-alcoholic pancreatitis",
                          "chronic pancreatitis"
         ))

5.16 Chronic rhinosinusitis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "chronic rhinosinusitis with nasal polyps",
                          "chronic rhinosinusitis"
         ))

5.17 Coronary artery disease

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001645/descendants"

coronary_artery_disease_terms <- get_descendants(url)

[1] "Number of terms collected:"
[1] 16
[1] "\n Some example terms"
[1] "non-obstructive coronary artery disease"
[2] "myocardial ischemia"                    
[3] "intermediate coronary syndrome"         
[4] "coronary thrombosis"                    
[5] "coronary aneurysm"                      

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(coronary_artery_disease_terms, collapse = "(?=,|$)|\\b"),
                          "coronary artery disease"
         ))

5.18 Congestive heart failure

congestive_heart_failure_terms <- c("systolic heart failure",
                                 "diastolic heart failure",
                                 "cor pulmonale",
                                 "congenital heart disease",
                                 "chronic pulmonary heart disease"
                                 )


gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(congestive_heart_failure_terms, collapse = "(?=,|$)|\\b"),
                          "congestive heart failure"
         ))

5.19 Dental caries

dental_caries_terms <- c("pit and fissure surface dental caries",
                         "smooth surface dental caries",
                         "primary dental caries",
                         "enamel caries",
                         "permanent dental caries"
                         )

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(dental_caries_terms, collapse = "(?=,|$)|\\b"),
                          "dental caries"
         )
)

5.20 Drug allergy

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "beta-lactam allergy",
                          "drug allergy"
         ))

5.21 Food allergy

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "peanut allergy|milk allergy|egg allergy|wheat allergic reaction",
                          "food allergy"
         ))

5.22 Hemolytic anemia

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0003664/descendants"


hemolytic_anemia_terms <- get_descendants(url)

[1] "Number of terms collected:"
[1] 76
[1] "\n Some example terms"
[1] "paroxysmal nocturnal hemoglobinuria"        
[2] "non-autoimmune hemolytic anemia"            
[3] "6-phosphogluconate dehydrogenase deficiency"
[4] "hereditary stomatocytosis"                  
[5] "autoimmune hemolytic anemia"                

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(hemolytic_anemia_terms, collapse = "(?=,|$)|\\b"),
                          "hemolytic anemia"
         ))

5.23 Herpes

gwas_study_info = 
gwas_study_info |> 
 mutate(l1_all_disease_terms  = 
          stringr::str_replace_all(l1_all_disease_terms,
                                  pattern = "herpes simplex infection",
                                   "herpesviridae infectious disease"
                          )  
        )

5.24 Hypertension

url <-  "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000537/descendants"

hypertension_terms <- get_descendants(url)

[1] "Number of terms collected:"
[1] 46
[1] "\n Some example terms"
[1] "secondary hypertension"           "treatment-resistant hypertension"
[3] "ocular hypertension"              "malignant hypertension"          
[5] "intracranial hypertension"       

hypertension_terms = c("primary hypertension",
                      hypertension_terms
                      )

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(hypertension_terms, collapse = "(?=,|$)|\\b"),
                          "hypertension"
         ))

5.25 HIV

gwas_study_info = gwas_study_info |>
    mutate(l1_all_disease_terms = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "hiv-1 infection",
                          "hiv infection"
         ))

5.26 Hyperlipidemia

hyperlipidemia_terms <- c("hypercholesterolemia",
                         "familial hypercholesterolemia",
                         "familial hyperlipidemia"
                         )

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(hyperlipidemia_terms, collapse = "(?=,|$)|\\b"),
                          "hyperlipidemia"
         ))

5.27 Inborn errors of metabolism

inborn_error_metab <- c("inborn disorder of amino acid metabolism",
                        "inborn disorder of amino acid transport",
                        "inborn disorder of porphyrin metabolism",
                        "inborn carbohydrate metabolic disorder",
                        "familial lipoprotein lipase deficiency",
                        "lactose intolerance",
                        "hereditary hemochromatosis",
                        "alpha 1-antitrypsin deficiency",
                        "urea cycle disorder",
                        "gaucher disease",
                        "plasma protein metabolism disease",
                        "disorder of metabolite absorption and transport")

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(inborn_error_metab, collapse = "(?=,|$)|\\b"),
                          "inborn errors of metabolism"
         ))

5.28 Infectious meningitis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "bacterial meningitis|pneumococcal meningitis|viral meningitis",
                          "infectious meningitis"
         ))

5.29 Infertility (female & male)

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "tubal factor infertility",
                          "female infertility"
                          )) |>
  mutate(l1_all_disease_terms  = 
                  stringr::str_replace_all(l1_all_disease_terms,
                          "azoospermia",
                          "male infertility"
                          )  )

5.30 Influenza a (h1n1) (subset of influenza)

gwas_study_info = gwas_study_info |>
    mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "influenza a \\(h1n1\\)",
                          "influenza"
         ))

5.31 Juvenile idiopathic arthritis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
        stringr::str_replace_all(l1_all_disease_terms ,
                         "systemic juvenile idiopathic arthritis|oligoarticular juvenile idiopathic arthritis|
                         polyarticular juvenile idiopathic arthritis",
                         "juvenile idiopathic arthritis")
        )

5.32 Lewy body dementia

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "lewy body attribute",
                          "lewy body dementia"
         ))

5.33 Malaria

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "plasmodium falciparum malaria|plasmodium vivax malaria",
                          "malaria"
         ))

5.34 Methamphetamine use disorders

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "methamphetamine dependence|methamphetamine-induced psychosis",
                          "methamphetamine use disorders"
         ))

5.35 Migrane

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "migraine disorder|migraine with aura|migraine without aura",
                          "migraine"
         ))

5.36 Multiple sclerosis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "relapsing-remitting multiple sclerosis",
                          "multiple sclerosis"
         ))

5.37 Myocardial infarction

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000612/descendants"

myocardial_infarction_terms <- get_descendants(url)

[1] "Number of terms collected:"
[1] 7
[1] "\n Some example terms"
[1] "inferior myocardial infarction"                                                     
[2] "anterolateral myocardial infarction"                                                
[3] "subsequent st elevation (stemi) and non-st elevation (nstemi) myocardial infarction"
[4] "acute myocardial infarction"                                                        
[5] "acute anterolateral myocardial infarction"                                          

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(myocardial_infarction_terms, collapse = "(?=,|$)|\\b"),
                          "myocardial infarction"
         ))

5.38 Photosensitivity disease

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
        stringr::str_replace_all(l1_all_disease_terms,
                         "phototoxic dermatitis|skin sensitivity to sun",
                         "photosensitivity disease")
        )

5.39 Phobic disorder

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_1001908/descendants"

phobic_disorder_terms <- get_descendants(url)

[1] "Number of terms collected:"
[1] 11
[1] "\n Some example terms"
[1] "specific phobia"         "social anxiety disorder"
[3] "agoraphobia"             "nosophobia"             
[5] "flying phobia"          

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(phobic_disorder_terms, collapse = "(?=,|$)|\\b"),
                          "phobic disorder"
         ))

5.40 Hereditary heterochromatosis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "hereditary hemochromatosis type 1",
                          "hereditary hemochromatosis"
         ))

5.41 Myasthenia gravis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "late-onset myasthenia gravis",
                          "myasthenia gravis"
         ))

5.42 Neuromyelitis optica

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "aqp4-igg-negative neuromyelitis optica|aqp4-igg-positive neuromyelitis optica",
                          "neuromyelitis optica"
         ))

5.43 Neurofibromatosis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "neurofibromatosis type 1|neurofibromatosis type 2",
                          "neurofibromatosis"
         ))

5.44 Non-alcoholic fatty liver disease (NAFLD)

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "non-alcoholic steatohepatitis|non-alcoholic liver disease",
                          "non-alcoholic fatty liver disease"
         ))

5.45 Obesity

gwas_study_info = 
gwas_study_info |> 
 mutate(l1_all_disease_terms  = 
          stringr::str_replace_all(l1_all_disease_terms,
                                  pattern = "morbid obesity|metabolically healthy obesity",
                                   "obesity"
                          )  
        )

5.46 Pericardium disorder

pericardium_disorder_terms <- c("pericarditis",
                               "pericardial effusion"
                               )

5.47 Psoriasis

psoriasis_terms <- c("psoriasis vulgaris",
                      "psoriasis area and severity index",
                      "cutaneous psoriasis",
                      "psoriatic arthritis",
                     "parapsoriasis")


gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(psoriasis_terms, collapse = "(?=,|$)|\\b"),
                          "psoriasis")
  )

5.48 Rheumatoid arthritis

ra_terms <- c("acpa-positive rheumatoid arthritis",
               "acpa-negative rheumatoid arthritis")

gwas_study_info = 
gwas_study_info |> 
 mutate(l1_all_disease_terms  = 
          stringr::str_replace_all(l1_all_disease_terms,
                                  pattern = paste0(ra_terms, collapse = "(?=,|$)|\\b"),
                                   "rheumatoid arthritis"
                          )  
        )

5.49 Scoliosis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "adolescent idiopathic scoliosis",
                          "scoliosis")
         )

5.50 Sickle cell disease

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "sickle cell anemia",
                          "sickle cell disease and related diseases")
         )

5.51 Sleep apnea

sleep_apnea_terms <- c("sleep apnea measurement during non-rem sleep",
                      "sleep apnea measurement during rem sleep",
                      "obstructive sleep apnea")

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(sleep_apnea_terms, collapse = "(?=,|$)|\\b"),
                          "sleep apnea")
  )

5.52 Staphylococcus aureus infection

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "methicillin-resistant staphylococcus aureus infection",
                          "staphylococcus aureus infection"
         ))

5.53 Stroke

https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000712?lang=en

hemorrhage_terms <- c("intracerebral hemorrhage",
                      "non-lobar intracerebral hemorrhage",
                      "lobar intracerebral hemorrhage")

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(hemorrhage_terms, collapse = "(?=,|$)|\\b"),
                          "hemorrhagic stroke")
  )

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "stroke outcome|large artery stroke|small vessel stroke|ischemic stroke|stroke disorder|cardioembolic stroke",
                          "stroke")
  )


gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "post-operative stroke",
                          "post-operative, stroke")
  )

5.54 Systemic scleroderma

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000717/descendants"

scleroderma_terms <- get_descendants(url)

[1] "Number of terms collected:"
[1] 5
[1] "\n Some example terms"
[1] "limited scleroderma"                                        
[2] "anti-topoisomerase-i-antibody-positive systemic scleroderma"
[3] "anti-centromere-antibody-positive systemic scleroderma"     
[4] "diffuse scleroderma"                                        
[5] "limited cutaneous systemic sclerosis"                       

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(scleroderma_terms, collapse = "(?=,|$)|\\b"),
                          "systemic scleroderma"
         ))

5.55 Tenosynovitis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
        stringr::str_replace_all(l1_all_disease_terms,
                         "stenosing tenosynovitis",
                         "tenosynovitis")
        )

5.56 Type 1 diabetes

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "latent autoimmune diabetes in adults",
                          "type 1 diabetes mellitus"
         ))

5.57 Thrombocytopenia

thrombocytopenia_terms <- c("thrombocytopenia 4",
                           "acquired thrombocytopenia",
                           "primary thrombocytopenia"
                           )

5.58 Tinea

tinea_terms <- c("tinea pedis",
                 "tinea unguium",
                 "dermatophytosis"
                 )


gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(tinea_terms, collapse = "(?=,|$)|\\b"),
                          "tinea"
         ))

5.59 Vitamin b deficiency

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "vitamin b12 deficiency",
                          "vitamin b deficiency"
         ))

6 Final summary - number of unique study terns

n_studies_trait = gwas_study_info |>
  dplyr::filter(DISEASE_STUDY == T) |>
  dplyr::select(l1_all_disease_terms, PUBMED_ID) |>
  dplyr::distinct() |>
  dplyr::group_by(l1_all_disease_terms) |>
  dplyr::summarise(n_studies = dplyr::n()) |>
  dplyr::arrange(desc(n_studies))


head(n_studies_trait)

# A tibble: 6 × 2
  l1_all_disease_terms      n_studies
  <chr>                         <int>
1 type 2 diabetes mellitus        145
2 asthma                          131
3 alzheimers disease              124
4 breast cancer                   112
5 major depressive disorder       108
6 schizophrenia                   103

dim(n_studies_trait)

[1] 2925    2

6.0.1 When separate studies with multiple terms

diseases <- stringr::str_split(pattern = ", ", 
                               gwas_study_info$l1_all_disease_terms[gwas_study_info$l1_all_disease_terms != ""])  |> 
            unlist() |>
            stringr::str_trim()


test <- data.frame(trait = unique(diseases))

length(unique(diseases))

[1] 2052

# make frequency table
freq <- table(as.factor(diseases))

# sort in decreasing order
freq_sorted <- sort(freq, decreasing = TRUE)

# show top N, e.g. top 10
head(freq_sorted, 10)

   chronic kidney disease              hypertension  type 2 diabetes mellitus 
                    10835                      7093                       922 
  coronary artery disease major depressive disorder        alzheimers disease 
                      514                       471                       422 
                   asthma             schizophrenia                  covid-19 
                      357                       356                       305 
            breast cancer 
                      270 

6.0.2 Save the updated gwas_study_info with harmonized disease terms

fwrite(gwas_study_info,
        here::here("output/gwas_cat/gwas_study_info_group_l1.csv")
         )

Session information

sessionInfo()

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.6.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] jsonlite_2.0.0    httr_1.4.7        stringr_1.5.1     data.table_1.17.8
[5] dplyr_1.1.4       workflowr_1.7.1  

loaded via a namespace (and not attached):
 [1] compiler_4.3.1    renv_1.0.3        promises_1.3.3    tidyselect_1.2.1 
 [5] Rcpp_1.1.0        git2r_0.36.2      callr_3.7.6       later_1.4.2      
 [9] jquerylib_0.1.4   yaml_2.3.10       fastmap_1.2.0     here_1.0.1       
[13] R6_2.6.1          generics_0.1.4    curl_6.4.0        knitr_1.50       
[17] tibble_3.3.0      rprojroot_2.1.0   bslib_0.9.0       pillar_1.11.0    
[21] rlang_1.1.6       utf8_1.2.6        cachem_1.1.0      stringi_1.8.7    
[25] httpuv_1.6.16     xfun_0.52         getPass_0.2-4     fs_1.6.6         
[29] sass_0.4.10       cli_3.6.5         withr_3.0.2       magrittr_2.0.3   
[33] ps_1.9.1          digest_0.6.37     processx_3.8.6    rstudioapi_0.17.1
[37] lifecycle_1.0.4   vctrs_0.6.5       evaluate_1.0.4    glue_1.8.0       
[41] whisker_0.4.1     rmarkdown_2.29    tools_4.3.1       pkgconfig_2.0.3  
[45] htmltools_0.5.8.1