group_non_cancer_diseases

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Last updated: 2025-09-28

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Knit directory: genomics_ancest_disease_dispar/

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rproj.user/
    Ignored:    data/.DS_Store
    Ignored:    data/gbd/.DS_Store
    Ignored:    data/gbd/IHME-GBD_2021_DATA-d8cf695e-1.csv
    Ignored:    data/gbd/ihme_gbd_2019_global_disease_burden_rate_all_ages.csv
    Ignored:    data/gbd/ihme_gbd_2019_global_paf_rate_percent_all_ages.csv
    Ignored:    data/gbd/ihme_gbd_2021_global_disease_burden_rate_all_ages.csv
    Ignored:    data/gbd/ihme_gbd_2021_global_paf_rate_percent_all_ages.csv
    Ignored:    data/gwas_catalog/
    Ignored:    data/icd/.DS_Store
    Ignored:    data/icd/IHME_GBD_2019_COD_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX
    Ignored:    data/icd/IHME_GBD_2019_NONFATAL_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX
    Ignored:    data/icd/IHME_GBD_2021_COD_CAUSE_ICD_CODE_MAP_Y2024M05D16.XLSX
    Ignored:    data/icd/IHME_GBD_2021_NONFATAL_CAUSE_ICD_CODE_MAP_Y2024M05D16.XLSX
    Ignored:    data/icd/UK_Biobank_master_file.tsv
    Ignored:    data/icd/cdc_valid_icd10_Sep_23_2025.xlsx
    Ignored:    data/icd/cdc_valid_icd9_Sep_23_2025.xlsx
    Ignored:    data/icd/phecode_international_version_unrolled.csv
    Ignored:    data/icd/semiautomatic_ICD-pheno.txt
    Ignored:    data/icd/~$IHME_GBD_2021_COD_CAUSE_ICD_CODE_MAP_Y2024M05D16.XLSX
    Ignored:    data/icd/~$IHME_GBD_2021_NONFATAL_CAUSE_ICD_CODE_MAP_Y2024M05D16.XLSX
    Ignored:    data/who/
    Ignored:    diseases.txt
    Ignored:    not_found_diseases.txt
    Ignored:    orig_phecode_map.csv
    Ignored:    original_phecodes_pheinfo.csv
    Ignored:    output/gwas_cat/
    Ignored:    output/gwas_study_info_cohort_corrected.csv
    Ignored:    output/gwas_study_info_trait_corrected.csv
    Ignored:    output/gwas_study_info_trait_ontology_info.csv
    Ignored:    output/gwas_study_info_trait_ontology_info_l1.csv
    Ignored:    output/gwas_study_info_trait_ontology_info_l2.csv
    Ignored:    output/trait_ontology/
    Ignored:    renv/
    Ignored:    sup_table.xlsx
    Ignored:    zooma.tsv
    Ignored:    zooma_res.tsv

Untracked files:
    Untracked:  analysis/garbage_icd_codes.Rmd
    Untracked:  analysis/map_trait_to_icd10.Rmd
    Untracked:  disease_mapping.R

Unstaged changes:
    Modified:   analysis/disease_inves_by_ancest.Rmd
    Modified:   analysis/exclude_infectious_diseases.Rmd
    Modified:   analysis/gbd_data_plots.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/level_1_disease_group_non_cancer.Rmd
    Modified:   analysis/level_2_disease_group.Rmd
    Modified:   analysis/trait_ontology_categorization.Rmd
    Modified:   data/icd/README.md

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File	Version	Author	Date	Message
Rmd	e777ee8	IJbeasley	2025-09-28	workflowr::wflow_publish("analysis/group_non_cancer_diseases.Rmd")
html	3640ce0	IJbeasley	2025-09-28	Build site.
Rmd	d8f04de	IJbeasley	2025-09-28	Using ICD / PheCode mapping

---

Set up

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

Ontology help - for getting disease subtypes

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

Load Data

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

How many unique traits are there now?

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

diseases <- unique(diseases)

print(length(diseases))

[1] 1718

Filtering some traits

Abnormality of skin pigmentation

gwas_study_info |> 
  filter(grepl("abnormality of skin pigmentation", collected_all_disease_terms)) |>
  pull(`DISEASE/TRAIT`) |>
  unique()

character(0)

# as can see, most of these traits are not about true skin pigmentation abnormalities
# just about skin pigmentation in general

# if `DISEASE/TRAIT` contains "UKB data field 1717" (which is just a skin colour measurment field)
# then remove "abnormality of skin pigmentation" from collected_all_disease_terms
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("UKB data field 1717", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_remove_all(collected_all_disease_terms,
                          pattern = "abnormality of skin pigmentation"
         ),
         collected_all_disease_terms
         )
  )

# also remove if `DISEASE/TRAIT` contains "Tatto pigmentation"
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("tatto pigmentation", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_remove_all(collected_all_disease_terms,
                          pattern = "abnormality of skin pigmentation"
         ),
         collected_all_disease_terms
         )
  )

# also remove if `DISEASE/TRAIT` is any of the following:
# - Perceived skin darkness 
# - Skin red/green component
# - Skin yellow/blue component
# - Skin pigmentation traits
# - Skin pigmentation 
# - Skin luminance

remove_terms <- c("Perceived skin darkness",
                  "Skin red/green component",
                  "Skin yellow/blue component",
                  "Skin pigmentation traits",
                  "Skin pigmentation",
                  "Skin luminance",
                  "Skin colour saturation"
                  )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(`DISEASE/TRAIT` %in% remove_terms,
                stringr::str_remove_all(collected_all_disease_terms,
                          pattern = "abnormality of skin pigmentation"
         ),
         collected_all_disease_terms
         )
  )

# this leaves PUBMED_ID 23548203, which according to suplementary table 1
# is `Number of non-melanoma skin cancer (5+)` 
# so change to "non-melanoma skin cancer"

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(PUBMED_ID == "23548203",
                stringr::str_replace_all(collected_all_disease_terms,
                          pattern = "abnormality of skin pigmentation",
                          replacement = "non-melanoma skin cancer"
         ),
         collected_all_disease_terms
         )
  )

Handedness

gwas_study_info |> 
  filter(grepl("handedness", collected_all_disease_terms)) |>
  pull(`DISEASE/TRAIT`) |>
  unique()

character(0)

# remove handedness
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_remove_all(collected_all_disease_terms,
                          pattern = "handedness"
         ))

# also remove functional laterality if Handedness chirality laterality is in DISEASE/TRAIT
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("Handedness", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_remove_all(collected_all_disease_terms,
                          pattern = "functional laterality"
         ),
         collected_all_disease_terms
         )
  )

# also remove functional laterality if Usual side of head for mobile phone use is in DISEASE/TRAIT
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("Usual side of head for mobile phone use", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_remove_all(collected_all_disease_terms,
                          pattern = "functional laterality"
         ),
         collected_all_disease_terms
         )
  )

# also remove functional laterality if PUBMED_ID=20585627
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(PUBMED_ID == "20585627",
                stringr::str_remove_all(collected_all_disease_terms,
                          pattern = "functional laterality"
         ),
         collected_all_disease_terms
         )
  ) 

Attached earlobe

gwas_study_info |> 
  filter(grepl("attached earlobe", collected_all_disease_terms)) |>
  pull(`DISEASE/TRAIT`) |>
  unique()

character(0)

# remove attached earlobe
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_remove_all(collected_all_disease_terms,
                          pattern = "attached earlobe"
         ))

Facial wrinkling

gwas_study_info |> 
  filter(grepl("facial wrinkling", collected_all_disease_terms)) |>
  pull(`DISEASE/TRAIT`) |>
  unique()

character(0)

# remove facial wrinkling
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_remove_all(collected_all_disease_terms,
                          pattern = "facial wrinkling"
         ))

Sneezing in response to bright light (autosomal dominant compelling helio-ophthalmic outburst syndrome)

gwas_study_info |> 
  filter(grepl("autosomal dominant compelling helio-ophthalmic outburst syndrome", collected_all_disease_terms)) |>
  pull(`DISEASE/TRAIT`) |>
  unique()

character(0)

# remove autosomal dominant compelling helio-ophthalmic outburst syndrome
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_remove_all(collected_all_disease_terms,
                          pattern = "autosomal dominant compelling helio-ophthalmic outburst syndrome"
         ))

Skin sensitivity to sun

gwas_study_info |> 
  filter(grepl("skin sensitivity to sun", collected_all_disease_terms)) |>
  pull(`DISEASE/TRAIT`) |>
  unique()

 [1] "Skin sensitivity to sun"                                                                           
 [2] "Ease of sunburn"                                                                                   
 [3] "Ease of skin tanning"                                                                              
 [4] "Ease of skin tanning - Get mildly or occasionally tanned (UKB data field 1727)"                    
 [5] "Ease of skin tanning - Get moderately tanned (UKB data field 1727)"                                
 [6] "Ease of skin tanning - Get very tanned (UKB data field 1727)"                                      
 [7] "Ease of skin tanning - Never tan only burn (UKB data field 1727)"                                  
 [8] "Ease of skin tanning - Get mildly or occasionally tanned (UKB data field 1727) (Gene-based burden)"
 [9] "Ease of skin tanning - Get moderately tanned (UKB data field 1727) (Gene-based burden)"            
[10] "Ease of skin tanning - Never tan only burn (UKB data field 1727) (Gene-based burden)"              
[11] "Ease of skin tanning - Get very tanned (UKB data field 1727) (Gene-based burden)"                  

# remove skin sensitivity to sun
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_remove_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern("skin sensitivity to sun")
         ))

# also remove suntan
gwas_study_info |> 
  filter(grepl("suntan", collected_all_disease_terms)) |>
  pull(`DISEASE/TRAIT`) |>
  unique()

[1] "Tanning"          "Low tan response"

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_remove_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern("suntan"
                          )
         ))

Group some non-cancer diseases together

Abnormal brain morphology

# if DISEASE/TRAIT contains Unidentified bright object on brain MRI, 
# then replace abnormal brain morphology with Other abnormal findings on diagnostic imaging of central nervous system 
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("Unidentified bright object on brain MRI", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("abnormal brain morphology"),
                          "other abnormal findings on diagnostic imaging of central nervous system"
         ),
         collected_all_disease_terms
         )
  )

Abnormality of gait

gwas_study_info = 
  gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                            "gait imbalance",
                            "decreased walking ability")
                            ),
                          "abnormality of gait"
         ))

Abdominal abscess

gwas_study_info |>
  filter(grepl(vec_to_grep_pattern("abdominal abscess"), 
               collected_all_disease_terms, perl = T)) 

Empty data.table (0 rows and 32 cols): DATE_ADDED_TO_CATALOG,PUBMED_ID,FIRST_AUTHOR,DATE,JOURNAL,LINK...

# just one study - 35173190, has abdominal abscess
# they define unusually as: D73.3, K35-37, K57, K61, K63.0, K65, K75.0, K81, K83.0
# 'Abdominal infections'

gwas_study_info = 
  gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(PUBMED_ID == "35173190",
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("abdominal abscess"),
                          "abdominal infections code"
         ),
         collected_all_disease_terms
         )
  )

Abnormal mammogram

# if DISEASE/TRAIT contains Abnormal mammogram, then change Abnormality of the breast to abnormal mammogram

gwas_study_info = 
  gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("Abnormal findings on mammogram or breast exam", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("abnormality of the breast"),
                          "abnormal mammogram"
         ),
         collected_all_disease_terms
         )
  )

Achalasia of cardia

gwas_study_info = 
  gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("achalasia"),
                          "achalasia of cardia"
         ))

Acute pancreatitis

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

Altitude sickness

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("chronic mountain sickness"),
                          "altitude sickness"
         ))

Alopecia

alopecia_terms <- c("frontal fibrosing alopecia" 
                   )


gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(alopecia_terms),
                          "alopecia"
         )
  )
         
         
drug_induced_alopecia_terms <- c(
                               "chemotherapy-induced alopecia"
                               )


gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(drug_induced_alopecia_terms),
                          "drug-induced androgenic alopecia"
         )
  )

Alcohol and nicotine codependence

# alcohol and nicotine codependence -> alcohol dependence, nicotine dependence

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("alcohol and nicotine codependence"),
                          "alcohol dependence, nicotine dependence"
         )) 

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("alcohol dependence"),
                          "alcohol-related disorders"
         ))

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("nicotine dependence"),
                          "tobacco use disorder"
         ))

Amyloidosis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("al amyloidosis"),
                          "amyloidosis"
         ))

Anxiety disorder

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("anxiety"),
                          "anxiety disorder"
         )) 

Aplastic anemia

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern("severe aplastic anemia"),
                          "aplastic anemia"
         ))

Androgenic alopecia

gwas_study_info = 
  gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern("androgenetic alopecia"),
                          "androgenic alopecia"
         ))  

angioedema -> Angioneurotic oedema

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("angioedema"),
                          "angioneurotic oedema"
         ))

Astigmatism

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

Asthma

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

Atrial fibrillation and flutter

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("atrial flutter"),
                          "atrial fibrillation and flutter"
         ))

Atopic dermatitis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("recalcitrant atopic dermatitis"),
                          "atopic dermatitis"
         ))

Eczema

# if DISEASE/STUDY contains eczema, change eczematoid dermatitis to eczema
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("eczema", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("eczematoid dermatitis"),
                          "eczema"
         ),
         collected_all_disease_terms
         )
  )


gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("hand eczema"),
                          "eczema"
         )
  )

Post-operative

gwas_study_info = gwas_study_info |> 
    mutate(collected_all_disease_terms  = 
         stringr::str_remove_all(collected_all_disease_terms,
                         pattern = "^post-operative |^postoperative"
         ))

Bipolar disorder

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

Bacterial infection

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                             "bacterial infection"
                             )
                             ),
                          "bacterial infection nos"
         ))

Benign mammary dysplasia

# if `DISEASE/TRAIT contains Benign mammary dysplasia`, then change abnormality of the breast to benign mammary dysplasia
gwas_study_info = 
  gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("Benign mammary dysplasia", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("abnormality of the breast"),
                          "benign mammary dysplasia"
         ),
         collected_all_disease_terms
         )
  )

Blindness and low vision

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                             "blindness",
                             "progressive visual loss",
                             "visual loss"
                             )
                             ),
                          "blindness and low vision"
         ))

# Disorders of optic nerve and visual pathways
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                             "visual pathway disorder",
                             "optic nerve disorder"
                             )
                             ),
                          "disorders of optic nerve and visual pathways"
         ))

# visuospatial impairment
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                             "visuospatial impairment"
                             )
                             ),
                          "other and unspecified symptoms and signs involving cognitive functions and awareness"
         ))

Cafe-au-lait spot

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("cafe-au-lait spot"),
                          "café au lait spots"
         ))

Cancer of eye

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                             "ocular melanoma")
                             ),
                          "cancer of eye"
         ))

Candidiasis of vulva and vagina

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                             "vaginal yeast infection")
                             ),
                          "candidiasis of vulva and vagina"
         ))

Carbuncle and furuncle

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                             "carbuncle", "furuncle")
                             ),
                          "carbuncle and furuncle"
         ))

Cardiac arrhythmia

arrhythmia_terms <-
c("ventricular arrhythmia",
  "torsades de pointes"
  )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(arrhythmia_terms),
                          "cardiac arrhythmia"
         ))

Cardiomyopathy

cardiomyopathy_terms <- c("nonischemic cardiomyopathy")

gwas_study_info =
gwas_study_info |> 
 mutate(collected_all_disease_terms  = 
          stringr::str_replace_all(collected_all_disease_terms,
                                  pattern = vec_to_grep_pattern(cardiomyopathy_terms),
                                   "cardiomyopathy"
                          )  
        )

Celiac disease

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

Central and perpheral ertigo

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("central nervous system origin vertigo"),
                          "central origin vertigo"
         ))


gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("peripheral vertigo"),
                          "peripheral or central vertigo"
         ))

Cerebral atherosclerosis

# if Brain vascular atherosclerosis in DISEASE/TRAIT, then change vascular brain injury to  cerebral atherosclerosis 

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("Brain vascular atherosclerosis", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("vascular brain injury"),
                          "cerebral atherosclerosis"
         ),
         collected_all_disease_terms
         )
  )

Cerebrovascular disease

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
        ifelse(grepl("Vascular brain injury", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                             "vascular brain injury"
                             )
                             ),
                          "cerebrovascular disease"
         ),
         collected_all_disease_terms)
  )

Occlusion of cerebral arteries

# if Brain vascular stenosis in DISEASE/TRAIT, then change vascular brain injury to  occlusion of cerebral arteries

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("Brain vascular stenosis", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("vascular brain injury"),
                          "occlusion of cerebral arteries"
         ),
         collected_all_disease_terms
         )
  )

Cerebral infarction

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                             "mri defined brain infarct",
                             "cardioembolic stroke")
                             ),
                          "cerebral infarction"
         ))

Chronic kidney disease

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

Chronic non-alcoholic pancreatitis

# if Non-alcoholic chronic pancreatitis  in `DISEASE/TRAIT`,
# then non-alcoholic pancreatitis to chronic pancreatitis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("Non-alcoholic chronic pancreatitis", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("non-alcoholic pancreatitis"),
                          "chronic pancreatitis"
         ),
         collected_all_disease_terms
         )
  )

Chronic rhinosinusitis

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

Chronic sinusitis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("chronic sinus infection"),
                          "chronic sinusitis"
         ))

Crohn’s Disease

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("perianal crohns disease"),
                          "crohns disease"
         ))

Cholangitis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("sclerosing cholangitis"),
                          "cholangitis"
         ))

Cluster headache syndrome

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("cluster headache"),
                          "cluster headache syndrome"
         ))

Circumscribed brain atrophy

brain_atropy <- c("frontotemporal dementia",
                  "grn-related frontotemporal lobar degeneration with tdp43 inclusions",
                  "pick disease")

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(brain_atropy),
                          "circumscribed brain atrophy"
         ))

Contact dermatitis

pattern <- vec_to_grep_pattern("contact dermatitis due to nickel")


gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = pattern,
                          "contact dermatitis"
         ))

Congenital heart disease/s

congenital_heart_disease_terms <- c(
  "heart septal defect",  
  "atrial heart septal defect",
  
  "congenital left-sided heart lesions",
  "congenital right-sided heart lesions",
  
  "congenital anomaly of the great arteries", # equiv = "Congenital malformation of great arteries, unspecified"
  
  # malformation of cardiac septum, 
    "abnormal cardiac septum morphology",
    "atrioventricular canal defect"
)
  

url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005207/descendants"

congenital_heart_disease_terms <- c(congenital_heart_disease_terms,
                                  get_descendants(url)
                                  ) |>
  unique()

[1] "Number of terms collected:"
[1] 102
[1] "\n Some example terms"
[1] "double outlet right ventricle with subaortic or doubly committed ventricular septal defect with pulmonary stenosis"
[2] "gata6-related congenital heart disease with or without pancreatic agenesis or neonatal diabetes"                   
[3] "double outlet right ventricle with non-committed subpulmonary ventricular septal defect"                           
[4] "congenitally uncorrected transposition of the great arteries with cardiac malformation"                            
[5] "congenitally uncorrected transposition of the great arteries with coarctation"                                     

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(congenital_heart_disease_terms),
                          "congenital heart disease"
         )
  )


url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0024239/descendants"

more_congenital_heart_disease_terms <- get_descendants(url)

[1] "Number of terms collected:"
[1] 229
[1] "\n Some example terms"
[1] "double outlet right ventricle with subaortic or doubly committed ventricular septal defect with pulmonary stenosis"
[2] "double outlet right ventricle with atrioventricular septal defect, pulmonary stenosis, heterotaxy"                 
[3] "gata6-related congenital heart disease with or without pancreatic agenesis or neonatal diabetes"                   
[4] "double outlet right ventricle with subaortic or doubly committed ventricular septal defect"                        
[5] "pulmonary valve agenesis-ventricular septal defect-persistent ductus arteriosus syndrome"                          

congenital_heart_disease_terms <- c(congenital_heart_disease_terms,
                                  more_congenital_heart_disease_terms
                                  ) |>
  unique() |>
  str_length_sort()


gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(congenital_heart_disease_terms),
                          "congenital anomaly of cardiovascular system"
         )
  )

Cardiac congenital anomalies

cardiac_congenital_anomalies_terms <- c(
  "bicuspid aortic valve"
)

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(cardiac_congenital_anomalies_terms),
                          "cardiac congenital anomalies"
         )
  )

Congenital hypertrophic pyloric stenosis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("infantile hypertrophic pyloric stenosis"),
                          "congenital hypertrophic pyloric stenosis"
         ))

Congenital hypothyroidism

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("congenital hypothyroidism due to developmental anomaly"),
                          "congenital hypothyroidism"
         ))

Congestive heart failure (CHF) NOS

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                            "diastolic heart failure",
                            "systolic heart failure")
                            ),
                          "congestive heart failure \\(chf\\) nos"
         ))

Coronary artery aneurysm and dissection

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                            "coronary aneurysm",
                            "coronary artery dissection")
                            ),
                          "coronary artery aneurysm and dissection"
         ))

# Aortic aneurysm

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                            "thoracic aortic aneurysm")
                            ),
                          "aortic aneurysm"
         ))

Creutzfeldt jacob disease

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(
                          c("sporadic creutzfeld jacob disease",
                            "creutzfeldt jacob disease",
                            "creutzfeldt-jacob disease")
                          ),
                          "creutzfeldt-jakob disease"
         ))

Cryoglobulinemia

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("cryoglobulinemia"),
                          "cryoglobulinaemia"
         ))

Chronic pain

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                            "chronic widespread pain",
                            "multisite chronic pain",
                            "chronic musculoskeletal pain",
                            "chronic pain syndrome")
                            ),
                          "chronic pain"
         ))

Cystic fibrosis with intestinal manifestations

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("cystic fibrosis associated meconium ileus"),
                          "cystic fibrosis with intestinal manifestations"
         ))

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(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(dental_caries_terms),
                          "dental caries"
         )
)

Dermatomyositis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("clinically amyopathic dermatomyositis"),
                          "dermatomyositis"
         ))

Dilated cardiomyopathy

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("idiopathic dilated cardiomyopathy"),
                          "dilated cardiomyopathy"
         ))

Disorders of tooth development

tooth_dev_terms <- c("dental enamel hypoplasia",
                     "tooth agenesis",
                     "molar-incisor hypomineralization"
                     )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(tooth_dev_terms),
                          "disorders of tooth development"
         )
  )

Depressive episode

depress_epi <- c("depressive",
                 "depression",
                 "depressive disorder"
                 )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(depress_epi),
                          "depressive episode"
         ))

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(depress_epi),
                          "depressive episode"
         ))

Disorders of purine and pyrimidine metabolism

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("hyperuricemia"),
                          "disorders of purine and pyrimidine metabolism"
         ))

Disorders of refraction and accommodation

refractive_terms <- c("hyperopia",
                      "refractive error"
                      )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(refractive_terms),
                          "disorders of refraction and accommodation"
         )
  )

Diseases of white blood cells

wbc_terms <- c("leukopenia")

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(wbc_terms),
                          "diseases of white blood cells"
         )
  )

Disorders of amino-acid metabolism

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("amino acid metabolism disease"),
                          "disorders of amino-acid metabolism"
         ))

Drug allergy

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

Degeneration of macula and posterior pole

macular <- c("macular degeneration",
             "atrophic macular degeneration",
             "retinal drusen"
             )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(macular),
                          "degeneration of macula and posterior pole"
         ))

Essential hypertension

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(
                            c(
                              "early onset hypertension",
                              "treatment-resistant hypertension")),
                          "essential hypertension"
         ))

Exstrophy of urinary bladder

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("bladder exstrophy"),
                          "exstrophy of urinary bladder"
         ))

Febrile seizures

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                                                "mmr-related febrile seizures",
                                                "febrile seizure")
                                              ),
                          "febrile convulsions"
         ))

Food allergy

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

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(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(glaucoma_terms),
                          "glaucoma"
         ))

Hordeolum and other deep inflammation of eyelid

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("hordeolum"),
                          "hordeolum and other deep inflammation of eyelid"
         ))

Graft vs host disease

graft_vs_host_terms <- c("chronic graft versus host disease",
                         "chronic graft vs. host disease",
                         "acute graft versus host disease",
                         "acute graft vs. host disease"
                         )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(graft_vs_host_terms),
                          "graft versus host disease"
         ))

Gingival and periodontal diseases

ginival_and_periodontal_terms <- c("periodontal pocket",
                                   "periodontal disorder",
                                   "gingival disease",
                                   "gingival bleeding"
                               )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(ginival_and_periodontal_terms),
                          "gingival and periodontal diseases"
         )
  )

Hemiplegia

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("hemiparesis")),
                          "hemiplegia"
         ))

Hearing loss

gwas_study_info  = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("age-related hearing impairment"),
                          "presbycusis"
         ))

gwas_study_info  = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                            "deafness",
                            "noise-induced hearing loss")
                            ),
                          "hearing loss"
         ))

Hereditary hemochromatosis

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

Hypercholesterolemia

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                            "familial hypercholesterolemia"
                            )),
                          "hypercholesterolemia"
         ))

Hyperlipidemia

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                            "familial hypercholesterolemia"
                            )),
                          "hyperlipidemia"
         ))

HIV disease resulting in encephalopathy

gwas_study_info = 
  gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                                               "aids dementia",
                                               "hiv-associated neurocognitive disorder")
                                              ),
                          "hiv disease resulting in encephalopathy"
         ))

Inherited retinal dystrophy

url <-  "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0019118/descendants"

inherited_retinal_dystrophy_terms <- get_descendants(url)

[1] "Number of terms collected:"
[1] 341
[1] "\n Some example terms"
[1] "spondyloepiphyseal dysplasia, sensorineural hearing loss, impaired intellectual development, and leber congenital amaurosis"
[2] "x-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome"                             
[3] "microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability"                                     
[4] "retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations"                                         
[5] "retinal dystrophy with inner retinal dysfunction and ganglion cell anomalies"                                               

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(inherited_retinal_dystrophy_terms),
                          "hereditary retinal dystrophy"
         ))

Intentional self-harm by unspecified means

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("self-injurious behavior",
                                                "self-injurious ideation")),
                          "intentional self-harm by unspecified means"
         ))

Infertility (male)

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
                  stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(
                            c("azoospermia",
                              "sertoli cell-only syndrome")
                            ),
                          "male infertility"
                          )  )

Induratio penis plastica

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
                  stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(
                            c("peyronie disease")
                            ),
                          "induratio penis plastica"
                          )  )

Intracerebral hemorrhage

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
                  stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(
                            c("non-lobar intracerebral hemorrhage",
                              "lobar intracerebral hemorrhage")
                            ),
                          "intracerebral hemorrhage"
                          )  )

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\\)$"
                                        )

idiopathic_generalized_epilepsy_terms = c("epilepsy with generalized tonic-clonic seizures",
                                          idiopathic_generalized_epilepsy_terms
                                         )


gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(idiopathic_generalized_epilepsy_terms),
                          "generalized idiopathic epilepsy and epileptic syndromes"
         ))

Idiopathic thrombocytopenic purpura

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("autoimmune thrombocytopenic purpura"),
                          "idiopathic thrombocytopenic purpura"
         ))

Juvenile idiopathic arthritis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("rheumatoid factor-negative juvenile idiopathic arthritis"),
                          "juvenile idiopathic arthritis"
         ))

Keratoconjunctivitis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("keratoconjunctivitis sicca"),
                          "keratoconjunctivitis"
         ))

Learning disorder

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("dyslexia",
                                                "mathematics disorder",
                                                "disorder of written expression"
                                                )
                                              ),
                          "learning disorder"
         ))

Lewy body dementia

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

Rheumatoid arthritis

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

gwas_study_info = 
gwas_study_info |> 
 mutate(collected_all_disease_terms  = 
          stringr::str_replace_all(collected_all_disease_terms,
                                  pattern = vec_to_grep_pattern(ra_terms),
                                   "rheumatoid arthritis"
                          )  
        )

Migraine

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

Multiple sclerosis

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

Myasthenia gravis

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

narcolepsy-cataplexy syndrome -> Narcolepsy and cataplexy

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("narcolepsy-cataplexy syndrom"),
                          "narcolepsy and cataplexy"
         ))

Nephrolithiasis

nephro_terms <- c("uric acid nephrolithiasis",
                   "calcium phosphate nephrolithiasis",
                    "calcium oxalate nephrolithiasis",
                   "struvite nephrolithiasis")


gwas_study_info =
gwas_study_info |> 
 mutate(collected_all_disease_terms  = 
          stringr::str_replace_all(collected_all_disease_terms,
                                  pattern = vec_to_grep_pattern(nephro_terms),
                                   "nephrolithiasis"
                          )  
        )

Nephritis and nephropathy with pathological lesion

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("acute tubulointerstitial nephritis",
                                              "iga glomerulonephritis",
                                              "membranous glomerulonephritis",
                                              "lupus nephritis")
                                              ),
                          "nephritis and nephropathy with pathological lesion"
         ))

Neurofibromatosis

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

Neuromyelitis optica

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(
                            c("aquaporin-4 antibody positive neuromyelitis optica",
                              "aquaporin-4 antibody negative neuromyelitis optica",
                              "aqp4-igg-positive neuromyelitis optica",
                              "aqp4-igg-negative neuromyelitis optica"
                            )
                          ),
                          "neuromyelitis optica"
         ))

Noninflammatory disorders of vagina

non_inflam_terms <- c("abnormal vaginal discharge itching",
                      "abnormal vaginal discharge smell",
                      "vaginal discharge")

gwas_study_info = 
  gwas_study_info |>
   mutate(collected_all_disease_terms  = 
          stringr::str_replace_all(collected_all_disease_terms,
                                  pattern = 
                                    vec_to_grep_pattern(
                                      non_inflam_terms
                                      ),
                                   "noninflammatory disorders of vagina"
                          )  
        )

Obesity

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

Obsessive-compulsive disorder

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

Osteonecrosis

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

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("osteoradionecrosis"),
                          "osteonecrosis"
         ))

Other epilepsy

gwas_study_info =
  gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(
                            c("mesial temporal lobe epilepsy with hippocampal sclerosis",
                              "rolandic epilepsy")
                            ),
                          "epilepsy"
         )) 

Chromosomal anomalies

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c(
                            "22q11.2 deletion syndrome",
                            "fragile x syndrome")
                            ),
                          "chromosomal anomalies"
         ))

Opiod dependence

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("heroin dependence",
                                              "opioid use disorder")),
                          "opioid dependence"
         ))

Other and unspecified cirrhosis of liver

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("hepatitis c induced liver cirrhosis",
                                                "biliary liver cirrhosis")
                                              ),
                          "other and unspecified cirrhosis of liver"
         ))

Other cardiac conduction disorders

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("familial long qt syndrome")
                                              ),
                          "other cardiac conduction disorders"
         ))

Other cerebral degenerations

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("brain atrophy"
                                                )
                                              ),
                          "other cerebral degenerations"
         ))

Other specified degenerative diseases of nervous system

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("corticobasal degeneration disorder"
                                                )
                                              ),
                          "other specified degenerative diseases of nervous system"
         ))

# progressive supranuclear palsy -> Dementia with cerebral degenerations

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("progressive supranuclear palsy"),
                          "dementia with cerebral degenerations"
         ))

Other chronic nonalcoholic liver disease

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("non-alcoholic fatty liver disease"
                                                )),
                          "other chronic nonalcoholic liver disease"
         ))

Other disorders of bone and cartilage

other_bone_cartilage_terms <- c("tietze syndrome"
                               )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(other_bone_cartilage_terms),
                          "other disorders of bone and cartilage"
         )
  )

Other eating disorders

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("binge eating")
                                              ),
                          "other eating disorders"
         ))

Other specified inflammatory liver diseases

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("primary biliary cholangitis",
                                                "primary sclerosing cholangitis"
                                                )
                                              ),
                          "non-alcoholic steatohepatitis"
         ))

Other haemoglobinopathies

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("hemoglobin e disease"),
                          "other haemoglobinopathies"
         ))

Other paralytic syndromes

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(
                            c("paraplegia",
                              "quadriplegia")
                            ),
                          "other paralytic syndromes"
         ))

Parkinsons disease

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("young adult-onset parkinsonism"),
                          "parkinsons disease"
         ))

Perinatal jaundice

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("neonatal jaundice"),
                          "perinatal jaundice"
         ))

Periodontitis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("aggressive periodontitis"),
                          "periodontitis"
         ))

Phlebitis and thrombophlebitis

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("thrombophlebitis")),
                          "phlebitis and thrombophlebitis"
         ))

Phobias

# social anxiety disorder -> social phobias
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("social anxiety disorder"),
                          "social phobias"
         ))

# specific phobia -> Specific \\(isolated\\) phobias

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("specific phobia"),
                          "specific \\(isolated\\) phobias"
         ))

Primary ovarian failure

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("primary ovarian insufficiency"),
                          "primary ovarian failure"
         ))

Premature menopause and other ovarian failure

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("premature menopause"),
                          "premature menopause and other ovarian failure"
         ))

Primary hyperaldosteronism

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("primary aldosteronism"),
                          "primary hyperaldosteronism"
         ))

Proteinuria

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("albuminuria",
                                                "moderate albuminuria")
                                              ),
                          "proteinuria"
         ))

Prurigo

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("prurigo"),
                          "other prurigo"
         ))

Precocious puberty

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("central precocious puberty"),
                          "precocious puberty"
         ))

Psoriasis

psoriasis_terms <- c("cutaneous psoriasis")


gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(psoriasis_terms),
                          "psoriasis")
  )

Psychosis (pyschotic, pyschotic symptoms)

psychosis_terms <- c("psychotic",
                     "psychotic symptoms"
                     )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(psychosis_terms),
                          "psychosis")
  )

Pulmonary fibrosis

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

Retinoschisis and retinoschisis and retinal cysts

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("retinoschisis"),
                          "retinoschisis and retinal cysts"
         ))

Separation of retinal layers

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("central serous retinopathy",
                                              "chronic central serous retinopathy")
                                              ),
                          "separation of retinal layers"
         ))

Rash and other nonspecific skin eruption

rash_terms <- c(
                "maculopapular eruption"
                )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(rash_terms),
                          "rash and other nonspecific skin eruption"
         )
  )

Rhinitis

rhinitis_terms <- c("non-allergic rhinitis")

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(rhinitis_terms),
                          "rhinitis"
         )
  )

Sciatica

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("ldh-related sciatica")
                                              ),
                          "sciatica"
         )) 

Schizoaffective disorder

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

Schizophrenia

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

Scoliosis

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

Sickle cell disease and related diseases

# if DISEASE/TRAIT contains sickle cell disease, change sickle cell disease and related diseases to sickle cell anemia
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(grepl("sickle cell disease", 
                     `DISEASE/TRAIT`,
                     ignore.case = TRUE),
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("sickle cell disease and related diseases"),
                          "sickle cell anemia"
         ),
         collected_all_disease_terms
         )
  )

Sleep apnea

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

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(sleep_apnea_terms),
                          "sleep apnea")
  )

Sleep disorders

sleep_disorder_terms <- c("sleepiness",
                          "somnambulism",
                          "rem sleep behavior disorder"
                         )


gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(sleep_disorder_terms),
                          "sleep disorders"
         )
  )

Speech and language disorder

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("specific language impairment"
                                                )
                                              ),
                          "speech and language disorder"
         ))

Staphylococcus infections

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(
                            c("staphylococcus aureus infection",
                              "skin and soft tissue staphylococcus aureus infection",
                              "methicillin-resistant staphylococcus aureus infection")),
                          "staphylococcus infections"
         ))

Strabismus

url <-  "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_540/descendants"

strabismus_terms <- get_descendants(url)

[1] "Number of terms collected:"
[1] 26
[1] "\n Some example terms"
[1] "abnormal retinal correspondence" "brown's tendon sheath syndrome" 
[3] "internuclear ophthalmoplegia"    "duane retraction syndrome 3"    
[5] "duane retraction syndrome 2"    

strabismus_terms = c("non-accomodative esotropia",
                     strabismus_terms)

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(strabismus_terms),
                          "strabismus"
         ))

Stroke

other_nonspec_stroke <- c("large artery stroke",
                         "small vessel stroke",
                         "stroke outcome",
                         "stroke disorder"
                         )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(other_nonspec_stroke),
                          "stroke"
         ))

Thyrotoxicosis with or without goiter

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("hyperthyroidism"),
                          "thyrotoxicosis with or without goiter"
         ))

Type 1 diabetes

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

Type 2 diabetes with a ophthalmic manifestations

type_2_eye_terms <- c("diabetes mellitus type 2 associated cataract",
                      "diabetic maculopathy, type 2 diabetes mellitus",
                      "diabetic macular edema, type 2 diabetes mellitus",
                      "proliferative diabetic retinopathy, type 2 diabetes mellitus"
                     )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(type_2_eye_terms),
                          "type 2 diabetes with ophthalmic manifestations"
         ))

# for 30487263, all discovery samples are type 2 diabetes - so 
# replace proliferative diabetic retinopathy with type 2 diabetes with ophthalmic manifestations
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(PUBMED_ID == 30487263,
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("proliferative diabetic retinopathy"),
                          "type 2 diabetes with ophthalmic manifestations"
         ),
         collected_all_disease_terms
         )
  )

# for pubmed id: 31482010
# all samples are type 2 diabetes
# so replace diabetic retinopathy with type 2 diabetes with ophthalmic manifestations
gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         ifelse(PUBMED_ID == 31482010,
                stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern("proliferative diabetic retinopathy"),
                          "type 2 diabetes with ophthalmic manifestations"
         ),
         collected_all_disease_terms
         )
)

Treatment resistant

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_remove_all(collected_all_disease_terms,
                       "^treatment-resistant |^treatment resistant |^treatment-resistant "
         ))

Unspecified condition associated with female genital organs and menstrual cycle

gwas_study_info = 
  gwas_study_info |>
  mutate(collected_all_disease_terms = 
    ifelse(grepl("Menstruation", 
                `DISEASE/TRAIT`,
                 ignore.case = TRUE),
           str_replace_all(collected_all_disease_terms,
                           pattern = vec_to_grep_pattern("decreased attention"),
                           "unspecified condition associated with female genital organs and menstrual cycle"),
           collected_all_disease_terms
    )
    )

Uveitis

uveitis_terms <- c("anterior uveitis",
                   "iritis",
                   "vogt-koyanagi-harada disease",
                   "birdshot chorioretinopathy",
                   "multifocal choroiditis"
                   )

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          pattern = vec_to_grep_pattern(uveitis_terms),
                          "uveitis"
         ))

Other specified retinal disorders

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("retinal edema"
                                              )),
                          "other specified retinal disorders"
         ))

Other disorders of eyelids

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("dermatochalasis",
                                                "filarial elephantiasis"
                                                )
                                              ),
                          "other disorders of eyelids"
         ))

Other disorders of iris and ciliary body

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("iris disorder"
                                                )
                                              ),
                          "other disorders of iris and ciliary body"
         ))

Background retinopathy and retinal vascular changes

gwas_study_info = gwas_study_info |>
  mutate(collected_all_disease_terms  = 
         stringr::str_replace_all(collected_all_disease_terms,
                          vec_to_grep_pattern(c("macular telangiectasia type 2"
                                                )
                                              ),
                          "background retinopathy and retinal vascular changes"
         ))

Save

How many unique traits are there now?

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

diseases <- unique(diseases)

print(length(diseases))

[1] 1708

fwrite(
  gwas_study_info,
  here::here("output/gwas_cat/gwas_study_info_group.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        data.table_1.17.8 stringr_1.5.1    
[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       cachem_1.1.0      stringi_1.8.7     httpuv_1.6.16    
[25] xfun_0.52         getPass_0.2-4     fs_1.6.6          sass_0.4.10      
[29] cli_3.6.5         withr_3.0.2       magrittr_2.0.3    ps_1.9.1         
[33] digest_0.6.37     processx_3.8.6    rstudioapi_0.17.1 lifecycle_1.0.4  
[37] vctrs_0.6.5       evaluate_1.0.4    glue_1.8.0        whisker_0.4.1    
[41] rmarkdown_2.29    tools_4.3.1       pkgconfig_2.0.3   htmltools_0.5.8.1