detailed drugs

Integration/MINERVA_access/get_drug_targets.R

@@ -35,6 +35,15 @@ upd <- sapply(refs, unique_drugs)
 ### Get the id of the default project
 map_project <- paste0(map,"projects/",get_default_project(map),"/")
 
+format_targeting_drugs <- function(falias, fproject) {
+  ddata <- fromJSON(ask_GET(paste0(fproject,"drugs:search?target=ALIAS:", falias)))
+  ret <- c()
+  for(i in 1:length(ddata$id)) {
+    ret <- rbind(ret, cbind(drug = ddata$id[i], ddata$references[[i]][,c("resource", "type")]))
+  }
+  return(ret)
+}
+
 ### Lengthy calculation, ask for drug targets of all unique UniProt ids in every pathway
 all_drugs <- c()
 ### For each pathway
@@ -45,11 +54,12 @@ for(u in 1:length(upd)) {
     for(p in 1:length(upd[[u]])) {
       ### Add a row to the global table with pathway name, UniProt id and the drugs 
       ### targeting the element alias associated with this UniProt
+      this_drugs <- format_targeting_drugs(upd[[u]][p], map_project)
+      if(is.null(this_drugs)) { next }
       all_drugs <- rbind(all_drugs,
-                         c(pathway_name = map_components$models$name[u],
-                           uniprot = names(upd[[u]])[p],
-                           drugs = paste(fromJSON(ask_GET(paste0(map_project,"drugs:search?target=ALIAS:", upd[[u]][p])))$name,
-                                         collapse = ";")))
+                         cbind(pathway_name = map_components$models$name[u],
+                               uniprot = names(upd[[u]])[p],
+                               this_drugs))
     }
   }
 }