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library(dplyr)
library(data.table)
library(stringr)source(here::here("code/get_term_descendants.R"))gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_disease_trait_simplified.csv"))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
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms = collected_all_disease_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 103dim(n_studies_trait)[1] 3043 2diseases <- 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] 2194disturb_senses_terms <- c("disturbances of sensation of smell and taste",
"abnormality of the sense of smell",
"ageusia")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"
))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"
))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 = "(?=,|$)|\\b"),
"complication"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001361/descendants"
pulmonary_arterial_hypertension_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 19
[1] "\n Some example terms"
[1] "pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosis"
[2] "pulmonary arterial hypertension associated with connective tissue disease"
[3] "pulmonary arterial hypertension associated with chronic hemolytic anemia"
[4] "pulmonary arterial hypertension associated with congenital heart disease"
[5] "pulmonary arterial hypertension associated with portal hypertension" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(pulmonary_arterial_hypertension_terms, collapse = "(?=,|$)|\\b"),
"pulmonary arterial hypertension"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"post-operative atrial fibrillation",
"atrial fibrillation, post-operative"
))
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F49436004/descendants"
atrial_fibrillation_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 17
[1] "\n Some example terms"
[1] "paroxysmal atrial fibrillation with rapid ventricular response"
[2] "persistent atrial fibrillation due to heart valve disorder"
[3] "paroxysmal atrial fibrillation due to heart valve disorder"
[4] "permanent atrial fibrillation due to heart valve disorder"
[5] "atrial fibrillation with rapid ventricular response" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(atrial_fibrillation_terms, collapse = "(?=,|$)|\\b"),
"atrial fibrillation"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F5370000/descendants"
atrial_flutter_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 5
[1] "\n Some example terms"
[1] "idiopathic neonatal atrial flutter" "paroxysmal atrial flutter"
[3] "atypical atrial flutter" "typical atrial flutter"
[5] "chronic atrial flutter" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(atrial_flutter_terms, collapse = "(?=,|$)|\\b"),
"atrial flutter"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F64715009/descendants"
hypertensive_heart_disease_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 40
[1] "\n Some example terms"
[1] "pre-existing hypertensive heart and renal disease complicating pregnancy, childbirth and the puerperium"
[2] "pre-existing hypertensive heart disease complicating pregnancy, childbirth and the puerperium"
[3] "pre-existing hypertensive heart and chronic kidney disease in mother complicating childbirth"
[4] "hypertensive heart and renal disease with both (congestive) heart failure and renal failure"
[5] "pre-existing hypertensive heart and chronic kidney disease in mother complicating pregnancy" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(hypertensive_heart_disease_terms, collapse = "(?=,|$)|\\b"),
"hypertensive heart disease"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/cvdo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_3394/descendants"
ischemic_heart_disease_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 4
[1] "\n Some example terms"
[1] "atherosclerotic ischemic cardiomyopathy"
[2] "ischemic cardiomyopathy"
[3] "acute coronary syndrome"
[4] "coronary heart disease"
[5] NA url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F414545008/descendants"
ischemic_heart_disease_terms_snomed <- get_descendants(url)[1] "Number of terms collected:"
[1] 201
[1] "\n Some example terms"
[1] "acute st segment elevation myocardial infarction due to occlusion of proximal portion of anterior descending branch of left coronary artery (disorder)"
[2] "acute st segment elevation myocardial infarction due to occlusion of posterior lateral branch of circumflex branch of left coronary artery (disorder)"
[3] "acute st segment elevation myocardial infarction due to occlusion of proximal portion of circumflex branch of left coronary artery (disorder)"
[4] "acute st segment elevation myocardial infarction due to occlusion of diagonal branch of anterior descending branch of left coronary artery"
[5] "acute st segment elevation myocardial infarction due to occlusion of septal branch of anterior descending branch of left coronary artery" ischemic_heart_disease_terms = c(ischemic_heart_disease_terms,
ischemic_heart_disease_terms_snomed
) |>
str_length_sort()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(ischemic_heart_disease_terms, collapse = "(?=,|$)|\\b"),
"ischemic heart disease"
))Likely also add, as ICD10 I25.1, seems to be coronary artery disease And gbd includes this in ischemic heart 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 = "(?=,|$)|\\b"),
"coronary artery disease"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"coronary artery disease",
"ischemic heart disease"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000612/descendants"
myocardial_infarction_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 7
[1] "\n Some example terms"
[1] "subsequent st elevation (stemi) and non-st elevation (nstemi) myocardial infarction"
[2] "acute anterolateral myocardial infarction"
[3] "non-st elevation myocardial infarction"
[4] "anterolateral myocardial infarction"
[5] "st elevation myocardial infarction" myocardial_infarction_terms <- c("subsequent st elevation \\(stemi\\) and non-st elevation \\(nstemi\\) myocardial infarction",
myocardial_infarction_terms
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(myocardial_infarction_terms, collapse = "(?=,|$)|\\b"),
"myocardial infarction"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"post-operative myocardial infarction",
"myocardial infarction, post-operative"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"myocardial infarction",
"ischemic heart disease"
))to_fix <- c("non-st elevation ischemic heart disease",
"post-operative ischemic heart disease",
"st elevation ischemic heart disease",
"subsequent st elevation (stemi) and non-st elevation (nstemi) ischemic heart disease")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
paste0(to_fix, collapse = "(?=,|$)|\\b"),
"ischemic heart disease"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0009551/descendants"
heart_valve_disease_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 40
[1] "\n Some example terms"
[1] "congenital mitral valve insufficiency"
[2] "cardiac valvular dysplasia, x-linked"
[3] "myxomatous mitral valve degeneration"
[4] "mitral valve prolapse, myxomatous 3"
[5] "mitral valve prolapse, myxomatous 2" # make non-rheumatic
rheumatic_terms <- c("rheumatic pulmonary valve disease",
"rheumatic disease of mitral valve")
heart_valve_disease_terms <-
heart_valve_disease_terms[!heart_valve_disease_terms %in% rheumatic_terms]
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(heart_valve_disease_terms,
collapse = "(?=,|$)|\\b"),
"heart valve disease"
)
)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 = "(?=,|$)|\\b"),
"aortic aneurysm"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"bacterial endocarditis",
"endocarditis"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0001638/descendants"
cardiomyopathy_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 14
[1] "\n Some example terms"
[1] "right ventricular noncompaction cardiomyopathy"
[2] "left ventricular noncompaction cardiomyopathy"
[3] "biventricular noncompaction cardiomyopathy"
[4] "concentric hypertrophic cardiomyopathy"
[5] "apical hypertrophic cardiomyopathy" cardiomyopathy_terms <- c("chagas cardiomyopathy",
"ischemic cardiomyopathy",
"idiopathic cardiomyopathy",
"nonischemic cardiomyopathy",
"peripartum cardiomyopathy", #? maybe include in pregnancy
cardiomyopathy_terms
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(cardiomyopathy_terms, collapse = "(?=,|$)|\\b"),
"cardiomyopathy"
))
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = "\\bidiopathic cardiomyopathy\\b",
"cardiomyopathy"
)
)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")
)# studies in gwas catalog don't specify lower or upper extremity
# but most peripheral artery disease is in lower extremities
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"\\bperipheral artery disease|\\bperipheral arterial disease",
"lower extremity peripheral 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 = "(?=,|$)|\\b"),
"carotid artery disease"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000537/descendants"
hypertension_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 46
[1] "\n Some example terms"
[1] "pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosis"
[2] "pulmonary arterial hypertension associated with connective tissue disease"
[3] "pulmonary arterial hypertension associated with chronic hemolytic anemia"
[4] "pulmonary arterial hypertension associated with congenital heart disease"
[5] "hyperuricemia-pulmonary hypertension-renal failure-alkalosis syndrome" hypertension_terms = c("primary hypertension",
"chronic venous hypertension",
"portal hypertension",
hypertension_terms
)
hypertension_terms = hypertension_terms[!hypertension_terms %in%
c(pulmonary_arterial_hypertension_terms,
hypertensive_heart_disease_terms,
"pulmonary arterial hypertension",
"hypertensive heart disease"
)
]
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(hypertension_terms, collapse = "(?=,|$)|\\b"),
"hypertension"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(hypertension_terms, collapse = "(?=,|$)|\\b"),
"hypertension"
))heart_block_terms <- c("first degree atrioventricular block",
"second degree atrioventricular block",
"third-degree atrioventricular block",
"atrioventricular block",
"bundle branch block",
"complete right heart block",
"left heart block"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(heart_block_terms, collapse = "(?=,|$)|\\b"),
"heart block"
))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 = "(?=,|$)|\\b"),
"tachycardia"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"sudden cardiac arrest",
"cardiac arrest"
)
)other_cardiac_arrhythmia_terms <- c("ventricular fibrillation",
"ventricular arrhythmia",
"cardiac arrest",
"bradycardia",
"cardiac arrhythmia"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(other_cardiac_arrhythmia_terms, collapse = "(?=,|$)|\\b"),
"other cardiac arrhythmias"
)
)congenital_heart_disease_terms <- c(
"congenital anomaly of cardiovascular system",
"congenital anomaly of the great arteries",
"congenital heart malformation",
"congenital left-sided heart lesions",
"congenital right-sided heart lesions",
"heart septal defect",
"atrial heart septal defect",
"atrioventricular canal defect",
"conotruncal heart malformations",
"abnormal aortic morphology",
"abnormal cardiovascular system physiology",
"abnormal cardiovascular system morphology",
"abnormality of the vasculature",
"cerebral arteriovenous malformation"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(congenital_heart_disease_terms, collapse = "(?=,|$)|\\b"),
"congenital heart disease"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0000831/descendants"
thrombosis_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 13
[1] "\n Some example terms"
[1] "isolated mesenteric vein thrombosis" "isolated splenic vein thrombosis"
[3] "heparin-induced thrombocytopenia" "intracranial sinus thrombosis"
[5] "acquired purpura fulminans" thrombosis_terms <- c("abnormal thrombosis",
thrombosis_terms)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(thrombosis_terms, collapse = "(?=,|$)|\\b"),
"thrombotic disease"
)
)arterial_occlusion_terms <- c("cerebral artery occlusion",
"occlusion precerebral artery",
"small artery occlusion"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(arterial_occlusion_terms, collapse = "(?=,|$)|\\b"),
"arterial occlusion"
)
)other_vascular_disorder_terms <- c("skin vascular disease",
"peripheral vascular disease",
"vascular disease",
"vasculitis",
"arteritis")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(other_vascular_disorder_terms, collapse = "(?=,|$)|\\b"),
"other vascular disorders"
)
)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 = "(?=,|$)|\\b"),
"congestive heart failure"
))brain_infarction_terms <- c("cerebral infarction",
"mri defined brain infarct",
"small cerebral infarction"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(brain_infarction_terms, collapse = "(?=,|$)|\\b"),
"brain infarction"
))vascular_insufficiency_terms <- c("vascular insufficiency disorder",
"chronic venous insufficiency",
"chronic intestinal vascular insufficiency"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(vascular_insufficiency_terms, collapse = "(?=,|$)|\\b"),
"vascular insufficiency"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0020064/descendants"
abnormal_total_eosinophil_count_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 4
[1] "\n Some example terms"
[1] "severely increased total eosinophil count"
[2] "decreased total eosinophil count"
[3] "increased total eosinophil count"
[4] "episodic eosinophilia"
[5] NA gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(abnormal_total_eosinophil_count_terms, collapse = "(?=,|$)|\\b"),
"abnormal total eosinophil count"
))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 = "(?=,|$)|\\b"),
"loss of pregnancy"
))
# exact synonyms (to avoid partial matches
# https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_1001491?lang=engwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"asparaginase-induced acute pancreatitis",
"acute pancreatitis"
))alcohol_use_disorder_terms <- c("alcohol dependence",
"alcohol withdrawal",
"alcohol withdrawal delirium",
"alcohol abuse",
"alcohol-related disorders delirium",
"alcohol use disorder",
"addictive alcohol use"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
paste0(alcohol_use_disorder_terms, collapse = "(?=,|$)|\\b"),
"alcohol-related disorders"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
paste0(alcohol_use_disorder_terms, collapse = "(?=,|$)|\\b"),
"alcohol-related disorders"
))alcoholic_liver_disease_terms <- c("alcoholic liver cirrhosis",
"alcoholic fatty liver disease",
"alcoholic hepatitis"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
paste0(alcoholic_liver_disease_terms, collapse = "(?=,|$)|\\b"),
"alcoholic liver disease"
))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"
))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"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"seasonal allergic rhinitis",
"allergic rhinitis"
))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" aplastic_anemia_terms <- c("severe aplastic anemia",
aplastic_anemia_terms
)
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 = "(?=,|$)|\\b"),
"aplastic anemia"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"corneal astigmatism",
"astigmatism"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"atopic asthma|chronic obstructive asthma",
"asthma"
)) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"childhood onset asthma|adult onset asthma|aspirin-induced asthma",
"asthma"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"autoimmune pancreatitis type 1",
"autoimmune pancreatitis"
)) gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"bipolar ii disorder|bipolar i disorder",
"bipolar disorder"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0003931/descendants"
bone_fracture_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 29
[1] "\n Some example terms"
[1] "atypical femoral fracture" "periprosthetic fractures"
[3] "upper extremity fracture" "lower extremity fracture"
[5] "multiple bone fractures" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(bone_fracture_terms, collapse = "(?=,|$)|\\b"),
"bone fracture"
))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 = "(?=,|$)|\\b"),
"bundle branch block"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0005129/descendants"
cataract_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 80
[1] "\n Some example terms"
[1] "autosomal recessive nonsyndromic congenital nuclear cataract"
[2] "diabetes mellitus type 2 associated cataract"
[3] "early-onset posterior subcapsular cataract"
[4] "autosomal dominant non-nuclear cataract"
[5] "kozlowski rafinski klicharska syndrome" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(cataract_terms, collapse = "(?=,|$)|\\b"),
"cataract"
))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"
)
)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"
))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 = "(?=,|$)|\\b"),
"chronic pain"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"chronic rhinosinusitis with nasal polyps",
"chronic rhinosinusitis"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"acute cholecystitis",
"cholecystitis"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0002182/descendants"
communication_disorder_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 20
[1] "\n Some example terms"
[1] "mixed receptive-expressive language disorder"
[2] "stuttering, familial persistent, 3"
[3] "stuttering, familial persistent, 4"
[4] "stuttering, familial persistent, 2"
[5] "stuttering, familial persistent, 1" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(communication_disorder_terms, collapse = "(?=,|$)|\\b"),
"communication disorder"
))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"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"post-operative delirium",
"delirium, post-operative"
))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 = "(?=,|$)|\\b"),
"dental caries"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_2723/descendants"
dermatitis_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 93
[1] "\n Some example terms"
[1] "epidermolysis bullosa with congenital localized absence of skin and deformity of nails"
[2] "diphenylmethane-4,4'-diisocyanate allergic contact dermatitis"
[3] "1-chloro-2,4-dinitrobenzene allergic contact dermatitis"
[4] "epidermolysis bullosa simplex with mottled pigmentation"
[5] "junctional epidermolysis bullosa with pyloric atresia" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(dermatitis_terms, collapse = "(?=,|$)|\\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 = "(?=,|$)|\\b"),
"dermatitis"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"beta-lactam allergy",
"drug allergy"
))diabetic_eye_terms <- c("diabetic maculopathy",
"diabetic macular edema",
"diabetic retinopathy",
"proliferative diabetic retinopathy",
"non-proliferative diabetic retinopathy",
"diabetes mellitus type 2 associated cataract")
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(diabetic_eye_terms, collapse = "(?=,|$)|\\b"),
"diabetic eye disease"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"diabetic polyneuropathy",
"diabetic neuropathy"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"iron deficiency anemia",
"deficiency anemia"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"delayed encephalopathy after acute poisoning",
"encephalopathy, poisoning"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"encephalopathy acute infection-induced",
"encephalopathy"
))]
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"
))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 = "(?=,|$)|\\b"),
"glaucoma"
))# from: http://www.ebi.ac.uk/efo/EFO_0004274
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"renal overload-type gout",
"gout"
))graft_vs_host_terms <- c("chronic graft versus host disease",
"chronic graft vs. host disease",
"acute graft versus host disease",
"acute graft vs. host disease"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
paste0(graft_vs_host_terms, collapse = "(?=,|$)|\\b"),
"graft versus host disease"
))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 = "(?=,|$)|\\b"),
"hemolytic anemia"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0004299/children"
hernia_abdominal_wall_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 6
[1] "\n Some example terms"
[1] "incisional hernia" "umbilical hernia" "inguinal hernia"
[4] "femoral hernia" "ventral hernia" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(hernia_abdominal_wall_terms, collapse = "(?=,|$)|\\b"),
"hernia of the abdominal wall"
))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"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"hiv-1 infection",
"hiv infection"
))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 = "(?=,|$)|\\b"),
"hyperlipidemia"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F36803009/descendants"
idiopathic_generalized_epilepsy_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 4
[1] "\n Some example terms"
[1] "epilepsy with generalized tonic-clonic seizures alone (disorder)"
[2] "juvenile myoclonic epilepsy"
[3] "childhood absence epilepsy"
[4] "juvenile absence epilepsy"
[5] NA idiopathic_generalized_epilepsy_terms = stringr::str_remove_all(
idiopathic_generalized_epilepsy_terms,
" \\(disorder\\)$"
)
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 = "(?=,|$)|\\b"),
"idiopathic generalized epilepsy"
))inborn_error_metab <- c("inborn disorder of amino acid metabolism",
"inborn disorder of amino acid transport",
"inborn disorder of porphyrin metabolism",
"inborn carbohydrate metabolic disorder",
"familial lipoprotein lipase deficiency",
"lactose intolerance",
"hereditary hemochromatosis",
"alpha 1-antitrypsin deficiency",
"urea cycle disorder",
"gaucher disease",
"plasma protein metabolism disease",
"disorder of metabolite absorption and transport")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(inborn_error_metab, collapse = "(?=,|$)|\\b"),
"inborn errors of metabolism"
))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"
))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"
) )gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"influenza a \\(h1n1\\)",
"influenza"
))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 = "(?=,|$)|\\b"),
"intestinal obstruction"
))jia_terms <- c("systemic juvenile idiopathic arthritis",
"oligoarticular juvenile idiopathic arthritis",
"polyarticular juvenile idiopathic arthritis"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
paste0(jia_terms, collapse = "(?=,|$)|\\b"),
"juvenile idiopathic arthritis")
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_1074/descendants"
kidney_disease_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 7
[1] "\n Some example terms"
[1] "acute kidney tubular necrosis" "end stage renal disease"
[3] "chronic kidney disease" "acute kidney failure"
[5] "hepatorenal syndrome" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(kidney_disease_terms, collapse = "(?=,|$)|\\b"),
"kidney disease"
))laryngitis_terms <- c("acute laryngitis",
"chronic laryngitis"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(laryngitis_terms, collapse = "(?=,|$)|\\b"),
"laryngitis"
))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"
))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"
))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"
))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"
))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"
))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")
)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 = "(?=,|$)|\\b"),
"phobic disorder"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"hereditary hemochromatosis type 1",
"hereditary hemochromatosis"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"late-onset myasthenia gravis",
"myasthenia gravis"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"aqp4-igg-negative neuromyelitis optica|aqp4-igg-positive neuromyelitis optica",
"neuromyelitis optica"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"neurofibromatosis type 1|neurofibromatosis type 2",
"neurofibromatosis"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"non-alcoholic steatohepatitis|non-alcoholic liver disease",
"non-alcoholic fatty liver disease"
))gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = "morbid obesity|metabolically healthy obesity",
"obesity"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"obsessive-compulsive trait",
"obsessive-compulsive disorder"
))osteoarthritis_terms <- c("knee osteoarthritis",
"hip osteoarthritis",
"hand osteoarthritis",
"spine osteoarthritis",
"toe osteoarthritis"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(osteoarthritis_terms, collapse = "(?=,|$)|\\b"),
"osteoarthritis"
)
)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"
))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 = "(?=,|$)|\\b"),
"pancreatitis"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_3388/descendants"
periodontal_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 19
[1] "\n Some example terms"
[1] "suppurative periapical periodontitis"
[2] "necrotizing ulcerative gingivitis"
[3] "chronic apical periodontitis"
[4] "acute apical periodontitis"
[5] "periapical periodontitis" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(periodontal_terms, collapse = "(?=,|$)|\\b"),
"periodontal disease"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"carbon monoxide poisoning",
"poisoning"
))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 = "(?=,|$)|\\b"),
"polycythemia"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"pulmonary embolism, pulmonary infarction",
"pulmonary embolism"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"idiopathic pulmonary fibrosis",
"pulmonary fibrosis"
))psoriasis_terms <- c("psoriasis vulgaris",
"psoriasis area and severity index",
"cutaneous psoriasis",
"psoriatic arthritis",
"parapsoriasis")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(psoriasis_terms, collapse = "(?=,|$)|\\b"),
"psoriasis")
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"psychosis predisposition",
"psychosis")
)retinopathy_terms <- c("chronic central serous retinopathy",
"central serous retinopathy"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(retinopathy_terms, collapse = "(?=,|$)|\\b"),
"retinopathy")
)ra_terms <- c("acpa-positive rheumatoid arthritis",
"acpa-negative rheumatoid arthritis",
"adult-onset stills disease")
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(ra_terms, collapse = "(?=,|$)|\\b"),
"rheumatoid arthritis"
)
)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")
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"treatment refractory schizophrenia",
"schizophrenia")
)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$"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"adolescent idiopathic scoliosis",
"scoliosis")
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"sickle cell anemia",
"sickle cell disease and related diseases")
)sleep_apnea_terms <- c("sleep apnea measurement during non-rem sleep",
"sleep apnea measurement during rem sleep",
"obstructive sleep apnea")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(sleep_apnea_terms, collapse = "(?=,|$)|\\b"),
"sleep apnea")
)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"
))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 = "(?=,|$)|\\b"),
"systemic scleroderma"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"stenosing tenosynovitis",
"tenosynovitis")
)tb_terms <- c("mycobacterium tuberculosis infection",
"\\bpulmonary tuberculosis",
"extrapulmonary tuberculosis",
"meningeal tuberculosis")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(tb_terms, collapse = "(?=,|$)|\\b"),
"tuberculosis"
))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"
))thrombocytopenia_terms <- c("thrombocytopenia 4",
"acquired thrombocytopenia",
"primary thrombocytopenia"
)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 = "(?=,|$)|\\b"),
"tinea"
))uveitis_terms <- c("anterior uveitis"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(uveitis_terms, collapse = "(?=,|$)|\\b"),
"uveitis"
))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"
))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 = "(?=,|$)|\\b"),
"visual impairment"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/upheno/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0000539/descendants"
abnormal_refraction_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 22
[1] "\n Some example terms"
[1] "against the rule astigmatism" "with the rule astigmatism"
[3] "moderate hypermetropia" "lenticular astigmatism"
[5] "irregular astigmatism" gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(abnormal_refraction_terms, collapse = "(?=,|$)|\\b"),
"abnormality of refraction"
))gwas_study_info =
gwas_study_info |>
rowwise() |>
mutate(l1_all_disease_terms = paste0(sort(unique(unlist(strsplit(l1_all_disease_terms, ", ")))),
collapse = ", ")
) |>
ungroup()gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms = stringr::str_remove_all(l1_all_disease_terms, "^,|,$")
) |>
mutate(l1_all_disease_terms = stringr::str_trim(l1_all_disease_terms)
) n_studies_trait = gwas_study_info |>
dplyr::filter(DISEASE_STUDY == T) |>
dplyr::select(l1_all_disease_terms, PUBMED_ID) |>
dplyr::distinct() |>
dplyr::group_by(l1_all_disease_terms) |>
dplyr::summarise(n_studies = dplyr::n()) |>
dplyr::arrange(desc(n_studies))
head(n_studies_trait)# A tibble: 6 × 2
l1_all_disease_terms n_studies
<chr> <int>
1 type 2 diabetes mellitus 145
2 asthma 134
3 alzheimers disease 124
4 breast cancer 112
5 ischemic heart disease 110
6 major depressive disorder 108dim(n_studies_trait)[1] 2660 2diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$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] 1847# 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)
kidney disease hypertension type 2 diabetes mellitus
10915 7102 922
ischemic heart disease major depressive disorder alzheimers disease
577 471 422
schizophrenia asthma covid-19
368 348 305
stroke
303 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