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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 - collapse disease complications, e.g. device complication, trauma complication to complication

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] 3065    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] 2194

3 Disturbances to senses

disturb_senses_terms <- c("disturbances of sensation of smell and taste",
                          "abnormality of the sense of smell",
                          "ageusia")

4 Disease stage grouping

4.1 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"
         ))

5 Disease cause grouping

5.1 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"
         ))

6 Disease complication

disease_complication_terms = c("device complication",
                             "trauma complication",
                             "adverse effect",
                             "aseptic loosening"
                             )

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

7 Disease subtype grouping (non-cancer)

7.1 Abornmal total eosinophil count

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0020064/descendants"

abnormal_total_eosinophil_count_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 4
[1] "\n Some example terms"
[1] "severely increased total eosinophil count"
[2] "decreased total eosinophil count"         
[3] "increased total eosinophil count"         
[4] "episodic eosinophilia"                    
[5] NA                                         
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(abnormal_total_eosinophil_count_terms, collapse = "(?=,|$)|\\b"),
                          "abnormal total eosinophil count"
         ))

7.2 Abortion

pregnancy_loss_terms <- c("habitual abortion",
                          "incomplete abortion",
                          "spontaneous abortion",
                          "abortion",
                          "spontaneous loss of pregnancy",
                          "incomplete loss of pregnancy"
                          )

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

7.3 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"
         ))

7.5 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"
         ))

7.6 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"
           ))

7.7 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"
           ))

7.8 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"
         ))

7.9 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"
         ))

7.10 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"
         ))

7.11 Aortic aneurysm

aortic_aneurysm_terms <- c("thoracic aortic aneurysm",
                          "abdominal aortic aneurysm"
                          )

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

7.12 Aplastic anemia

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0015909/descendants"

aplastic_anemia_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 62
[1] "\n Some example terms"
[1] "diamond-blackfan anemia 15 with mandibulofacial dysostosis"
[2] "diamond-blackfan anemia 14 with mandibulofacial dysostosis"
[3] "cellular phase chronic idiopathic myelofibrosis"           
[4] "autosomal dominant aplasia and myelodysplasia"             
[5] "pancytopenia-developmental delay syndrome"                 
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(aplastic_anemia_terms, collapse = "(?=,|$)|\\b"),
                          "aplastic anemia"
         ))

7.13 Astigmatism

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

7.14 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"
           ))

7.15 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"
           ))

7.16 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"
         ))

7.17 Bone fracture

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0003931/descendants"

bone_fracture_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 29
[1] "\n Some example terms"
[1] "atypical femoral fracture" "periprosthetic fractures" 
[3] "upper extremity fracture"  "lower extremity fracture" 
[5] "multiple bone fractures"  
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(bone_fracture_terms, collapse = "(?=,|$)|\\b"),
                          "bone fracture"
         ))

7.18 Bundle branch block

bundle_branch_block_terms <- c("left bundle branch block",
                             "right bundle branch block",
                             "complete right bundle branch block"
                             )

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(bundle_branch_block_terms, collapse = "(?=,|$)|\\b"),
                          "bundle branch block"
         )
  )

7.19 Cardiomyopathy

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0001638/descendants"

cardiomyopathy_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 14
[1] "\n Some example terms"
[1] "right ventricular noncompaction cardiomyopathy"
[2] "left ventricular noncompaction cardiomyopathy" 
[3] "biventricular noncompaction cardiomyopathy"    
[4] "concentric hypertrophic cardiomyopathy"        
[5] "apical hypertrophic cardiomyopathy"            
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(cardiomyopathy_terms, collapse = "(?=,|$)|\\b"),
                          "cardiomyopathy"
         ))

7.20 Carotid artery disease

carotid_artery_disease_terms <- c("carotid artery thrombosis",
                             "carotid atherosclerosis"
                             )

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

7.21 Cataract

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0005129/descendants"

cataract_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 80
[1] "\n Some example terms"
[1] "autosomal recessive nonsyndromic congenital nuclear cataract"
[2] "diabetes mellitus type 2 associated cataract"                
[3] "early-onset posterior subcapsular cataract"                  
[4] "autosomal dominant non-nuclear cataract"                     
[5] "kozlowski rafinski klicharska syndrome"                      
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(cataract_terms, collapse = "(?=,|$)|\\b"),
                          "cataract"
         ))

7.22 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"
                          )  
        )

7.23 Charcot-marie-tooth disease type 1a

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "charcot-marie-tooth disease type 1a, decreased fine motor function",
                          "charcot-marie-tooth disease type 1a"
         ))


gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "charcot-marie-tooth disease type 1a, decreased walking ability",
                          "charcot-marie-tooth disease type 1a"
         ))

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "charcot-marie-tooth disease type 1a, gait imbalance",
                          "charcot-marie-tooth disease type 1a, gait disturbance"
         ))

7.24 Chronic pain

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0012532/descendants"

chronic_pain_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 9
[1] "\n Some example terms"
[1] "chronic musculoskeletal pain" "female chronic pelvic pain"  
[3] "chronic widespread pain"      "multisite chronic pain"      
[5] "chronic shoulder pain"       
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(chronic_pain_terms, collapse = "(?=,|$)|\\b"),
                          "chronic pain"
         ))

7.25 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"
         ))

7.26 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"
         ))

7.27 Cholecystitis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "acute cholecystitis",
                          "cholecystitis"
         ))

7.28 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] "coronary artery disease, autosomal dominant 2"
[2] "non-obstructive coronary artery disease"      
[3] "spontaneous coronary artery dissection"       
[4] "postoperative ventricular dysfunction"        
[5] "intermediate coronary syndrome"               
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"
         ))

7.29 Communication disorder

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0002182/descendants"

communication_disorder_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 20
[1] "\n Some example terms"
[1] "mixed receptive-expressive language disorder"
[2] "stuttering, familial persistent, 3"          
[3] "stuttering, familial persistent, 4"          
[4] "stuttering, familial persistent, 2"          
[5] "stuttering, familial persistent, 1"          
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(communication_disorder_terms, collapse = "(?=,|$)|\\b"),
                          "communication disorder"
         ))

7.30 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"
         ))

7.31 Creutzfeldt jacob disease

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "sporadic creutzfeld jacob disease",
                          "creutzfeldt jacob disease"
         ))

7.32 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"
         )
)

7.33 Dermatitis

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_2723/descendants"

dermatitis_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 93
[1] "\n Some example terms"
[1] "epidermolysis bullosa with congenital localized absence of skin and deformity of nails"
[2] "diphenylmethane-4,4'-diisocyanate allergic contact dermatitis"                         
[3] "1-chloro-2,4-dinitrobenzene allergic contact dermatitis"                               
[4] "epidermolysis bullosa simplex with mottled pigmentation"                               
[5] "junctional epidermolysis bullosa with pyloric atresia"                                 
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(dermatitis_terms, collapse = "(?=,|$)|\\b"),
                          "dermatitis"
         ))

# see: http://www.ebi.ac.uk/efo/EFO_0000274
eczema_terms <- c("atopic eczema",
                 "hand eczema",
                 "eczematoid dermatitis", # see: http://purl.obolibrary.org/obo/HP_0000964
                 "recalcitrant dermatitis" # assuming same as recalcitrant atopic dermatitis http://www.ebi.ac.uk/efo/EFO_1000651
                 )

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

7.34 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"
         ))

7.35 Diabetic eye disease

diabetic_eye_terms <- c("diabetic maculopathy",
                        "diabetic macular edema",
                        "diabetic retinopathy",
                        "proliferative diabetic retinopathy",
                        "non-proliferative diabetic retinopathy",
                        "diabetes mellitus type 2 associated cataract")


gwas_study_info = 
  gwas_study_info |> 
  mutate(l1_all_disease_terms  = 
           stringr::str_replace_all(l1_all_disease_terms ,
                                    pattern = paste0(diabetic_eye_terms, collapse = "(?=,|$)|\\b"),
                                    "diabetic eye disease"
           )  
  )

7.36 Diabetic neuropathy

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "diabetic polyneuropathy",
                          "diabetic neuropathy"
         ))

7.37 Deficiency anemia

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "iron deficiency anemia",
                          "deficiency anemia"
         ))

7.38 Endocarditis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "bacterial endocarditis",
                          "endocarditis"
         ))

7.39 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"
         ))

7.40 Glaucoma

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0005041/descendants"

glaucoma_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 19
[1] "\n Some example terms"
[1] "cyp1b1-related glaucoma with or without anterior segment dysgenesis"
[2] "glaucoma secondary to spherophakia/ectopia lentis and megalocornea" 
[3] "hereditary glaucoma, primary closed-angle"                          
[4] "primary angle closure glaucoma"                                     
[5] "secondary dysgenetic glaucoma"                                      
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(glaucoma_terms, collapse = "(?=,|$)|\\b"),
                          "glaucoma"
         ))

7.41 Gout

# from: http://www.ebi.ac.uk/efo/EFO_0004274
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "renal overload-type gout",
                          "gout"
         ))

7.42 Heart block

heart_block_terms <- c("first degree atrioventricular block",
                      "second degree atrioventricular block",
                      "third-degree atrioventricular block",
                      "bundle branch block"
                      )

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

7.43 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] "dehydrated hereditary stomatocytosis with or without pseudohyperkalemia and/or perinatal edema"
[2] "anemia, nonspherocytic hemolytic, associated with abnormality of red cell membrane"            
[3] "anemia, nonspherocytic hemolytic, possibly due to defect in porphyrin metabolism"              
[4] "x-linked dyserythropoetic anemia with abnormal platelets and neutropenia"                      
[5] "hemolytic anemia due to erythrocyte adenosine deaminase overproduction"                        
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"
         ))

7.44 Hernia of the abdominal wall

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0004299/children"

hernia_abdominal_wall_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 6
[1] "\n Some example terms"
[1] "incisional hernia" "umbilical hernia"  "inguinal hernia"  
[4] "femoral hernia"    "ventral hernia"   
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(hernia_abdominal_wall_terms, collapse = "(?=,|$)|\\b"),
                          "hernia of the abdominal wall"
         ))

7.45 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"
                          )  
        )

7.46 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] "pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosis"
[2] "pulmonary arterial hypertension associated with connective tissue disease"   
[3] "pulmonary arterial hypertension associated with chronic hemolytic anemia"    
[4] "pulmonary arterial hypertension associated with congenital heart disease"    
[5] "hyperuricemia-pulmonary hypertension-renal failure-alkalosis syndrome"       
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"
         ))

7.47 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"
         ))

7.48 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"
         ))

7.49 Idiopathic generalized epilepsy

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F36803009/descendants"

idiopathic_generalized_epilepsy_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 4
[1] "\n Some example terms"
[1] "epilepsy with generalized tonic-clonic seizures alone (disorder)"
[2] "juvenile myoclonic epilepsy"                                     
[3] "childhood absence epilepsy"                                      
[4] "juvenile absence epilepsy"                                       
[5] NA                                                                
idiopathic_generalized_epilepsy_terms = stringr::str_remove_all(
                                        idiopathic_generalized_epilepsy_terms, 
                                        " \\(disorder\\)$"
                                        )


gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(idiopathic_generalized_epilepsy_terms, collapse = "(?=,|$)|\\b"),
                          "idiopathic generalized epilepsy"
         ))

7.50 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"
         ))

7.51 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"
         ))

7.52 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"
                          )  )

7.53 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"
         ))

7.54 Intestinal obstruction

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0004565/descendants"

intestinal_obstruction_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 21
[1] "\n Some example terms"
[1] "intestinal obstruction in the newborn due to guanylate cyclase 2c deficiency"
[2] "intestinal pseudoobstruction, neuronal, chronic idiopathic, x-linked"        
[3] "visceral neuropathy, familial, 1, autosomal recessive"                       
[4] "visceral neuropathy, familial, 3, autosomal dominant"                        
[5] "cystic fibrosis associated meconium ileus"                                   
# also add: http://purl.obolibrary.org/obo/DOID_8437

intestinal_obstruction_terms = c(intestinal_obstruction_terms,
                                 "intestinal impaction"
                                 )

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

7.55 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")
        )

7.56 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"
         ))

7.57 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"
         ))

7.58 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"
         ))

7.59 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"
         ))

7.60 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"
         ))

7.61 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] "subsequent st elevation (stemi) and non-st elevation (nstemi) myocardial infarction"
[2] "acute anterolateral myocardial infarction"                                          
[3] "non-st elevation myocardial infarction"                                             
[4] "anterolateral myocardial infarction"                                                
[5] "st elevation 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"
         ))

7.62 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")
        )

7.63 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] "panic disorder with agoraphobia" "blood-injection-injury phobia"  
[3] "social anxiety disorder"         "specific phobia"                
[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"
         ))

7.64 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"
         ))

7.65 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"
         ))

7.66 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"
         ))

7.67 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"
         ))

7.68 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"
         ))

7.69 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"
                          )  
        )

7.70 Obsessive-compulsive disorder

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "obsessive-compulsive trait",
                          "obsessive-compulsive disorder"
         ))

7.71 Osteoarthritis

osteoarthritis_terms <- c("knee osteoarthritis",
                         "hip osteoarthritis",
                         "hand osteoarthritis",
                         "spine osteoarthritis",
                         "toe osteoarthritis"
                         )

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

7.72 Osteonecrosis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "idiopathic osteonecrosis of the femoral head",
                          "osteonecrosis"
         ))

7.73 Pancreatitis

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000278/descendants"

pancreatitis_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 9
[1] "\n Some example terms"
[1] "thiopurine immunosuppressant-induced pancreatitis"
[2] "asparaginase-induced acute pancreatitis"          
[3] "hereditary chronic pancreatitis"                  
[4] "autoimmune pancreatitis type 1"                   
[5] "non-alcoholic pancreatitis"                       
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(pancreatitis_terms, collapse = "(?=,|$)|\\b"),
                          "pancreatitis"
         ))

7.74 Pericardium disorder

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

7.75 Peridontal disease

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_3388/descendants"

periodontal_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 19
[1] "\n Some example terms"
[1] "suppurative periapical periodontitis"
[2] "necrotizing ulcerative gingivitis"   
[3] "chronic apical periodontitis"        
[4] "acute apical periodontitis"          
[5] "periapical periodontitis"            
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(periodontal_terms, collapse = "(?=,|$)|\\b"),
                          "periodontal disease"
         ))

7.76 Poisoning

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "carbon monoxide poisoning",
                          "poisoning"
         ))

7.77 Polycythemia

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005804/descendants"

polycythemia_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 16
[1] "\n Some example terms"
[1] "autosomal recessive secondary polycythemia not associated with vhl gene"
[2] "primary familial polycythemia due to epo receptor mutation"             
[3] "autosomal dominant secondary polycythemia"                              
[4] "congenital secondary polycythemia"                                      
[5] "acquired secondary polycythemia"                                        
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(polycythemia_terms, collapse = "(?=,|$)|\\b"),
                          "polycythemia"
         ))

7.78 Pulmonary embolism

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "pulmonary embolism, pulmonary infarction",
                          "pulmonary embolism"
         ))

7.79 Pulmonary fibrosis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "idiopathic pulmonary fibrosis",
                          "pulmonary fibrosis"
         ))

7.80 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")
  )

7.81 Psychosis

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "psychosis predisposition",
                          "psychosis")
         )

7.82 Rheumatoid arthritis

ra_terms <- c("acpa-positive rheumatoid arthritis",
               "acpa-negative rheumatoid arthritis",
              "adult-onset stills disease")

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"
                          )  
        )

7.83 Schizoaffective disorder

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "schizoaffective disorder-bipolar type",
                          "schizoaffective disorder")
         )

7.84 Schizophrenia

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          "treatment refractory schizophrenia",
                          "schizophrenia")
         )

7.85 Sciatica

gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_remove_all(l1_all_disease_terms,
                          "^ldh-related sciatica, |, ldh-related sciatica$"
         )
  )

7.86 Scoliosis

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

7.87 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")
         )

7.88 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")
  )

7.89 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"
         ))

7.90 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")
  )

stroke_terms <- c("stroke outcome",
                  "large artery stroke",
                  "small vessel stroke",
                  "ischemic stroke",
                  "stroke disorder",
                  "cardioembolic stroke",
                  "hemorrhagic stroke",
                  "intracranial hemorrhage",
                  "subdural hemorrhage"
                  )

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

7.91 Tacycardia

tacycardia_terms <- c("paroxysmal tachycardia",
                     "ventricular tachycardia",
                     "supraventricular tachycardia",
                     "paroxysmal supraventricular tachycardia",
                     "paroxysmal ventricular tachycardia"
                     )


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

7.92 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] "anti-topoisomerase-i-antibody-positive systemic scleroderma"
[2] "anti-centromere-antibody-positive systemic scleroderma"     
[3] "limited cutaneous systemic sclerosis"                       
[4] "limited scleroderma"                                        
[5] "diffuse scleroderma"                                        
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"
         ))

7.93 Tenosynovitis

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

7.94 Tuberculosis

tb_terms <- c("mycobacterium tuberculosis infection",
              "\\bpulmonary tuberculosis",
              "extrapulmonary tuberculosis",
              "meningeal tuberculosis")

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

7.95 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"
         ))

7.96 Thrombocytopenia

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

7.97 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"
         ))

7.98 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"
         ))

7.99 Visual impairment

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0000505/descendants"

visual_impairment_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 12
[1] "\n Some example terms"
[1] "constriction of peripheral visual field"
[2] "severely reduced visual acuity"         
[3] "slow decrease in visual acuity"         
[4] "peripheral visual field loss"           
[5] "cerebral visual impairment"             
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(visual_impairment_terms, collapse = "(?=,|$)|\\b"),
                          "visual impairment"
         ))

8 Further grouping of terms

8.1 Abnormal refraction

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/upheno/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0000539/descendants"

abnormal_refraction_terms <- get_descendants(url)
[1] "Number of terms collected:"
[1] 22
[1] "\n Some example terms"
[1] "against the rule astigmatism" "with the rule astigmatism"   
[3] "moderate hypermetropia"       "lenticular astigmatism"      
[5] "irregular astigmatism"       
gwas_study_info = gwas_study_info |>
  mutate(l1_all_disease_terms  = 
         stringr::str_replace_all(l1_all_disease_terms,
                          pattern = paste0(abnormal_refraction_terms, collapse = "(?=,|$)|\\b"),
                          "abnormality of refraction"
         ))

9 Final summary - number of unique study terns

9.1 Deal with duplicate terms created during grouping

gwas_study_info = 
 gwas_study_info |>
  rowwise() |>
  mutate(l1_all_disease_terms = paste0(sort(unique(unlist(strsplit(l1_all_disease_terms, ", ")))),
                                      collapse = ", ")
         ) |>
  ungroup()
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                          134
3 alzheimers disease              124
4 breast cancer                   112
5 major depressive disorder       108
6 schizophrenia                   108
dim(n_studies_trait)
[1] 2720    2

9.1.1 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] 1907
# 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                      7089                       922 
  coronary artery disease major depressive disorder        alzheimers disease 
                      501                       471                       422 
            schizophrenia                    asthma                  covid-19 
                      368                       348                       305 
                   stroke 
                      303

9.1.2 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")
         )

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