example, take one

Resources/OmniPath/MINERVA_OmniPath_example.R

+##################################################
+## Project: COVID-19 Disease Map
+## Script purpose: Integrate OmniPathDB with COVID-19 Disease Map on MINERVA 
+## Date: 28.05.2020
+## Author: Marek Ostaszewski
+##################################################
+
+### A convenience function to handle API queries
+ask_GET <- function(furl, fask) {
+  resp <- httr::GET(url = paste0(furl, fask),
+                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"))
+  if(httr::status_code(resp) == 200) {
+    return(httr::content(resp, as = "text"))
+  }
+  return(NULL)
+}
+
+### Load OmniPath
+if(!'OmnipathR' %in% installed.packages()[,"Package"]){
+  require(devtools)
+  install_github('saezlab/OmnipathR')
+}
+
+require(OmnipathR)
+require(dplyr)
+
+message(paste0("Asking for OmniPath interactions"))
+
+### Get OmniPath interactions
+ia_omnipath <- import_Omnipath_Interactions() %>% as_tibble()
+
+### Get MINERVA elements
+### The address of the COVID-19 Disease Map in MINERVA
+map <- "https://covid19map.elixir-luxembourg.org/minerva/api/"
+### Get configuration of the COVID-19 Disease Map, to obtain the latest (default) version
+cfg <- fromJSON(ask_GET(map, "configuration/"))
+project_id <- cfg$options[cfg$options$type == "DEFAULT_MAP","value"]
+### The address of the latest (default) build 
+mnv_base <- paste0(map,"projects/",project_id,"/")
+
+message(paste0("Asking for diagrams in: ", mnv_base, "models/"))
+
+### Get diagrams
+models <- fromJSON(ask_GET(mnv_base, "models/"), flatten = F)
+### Get elements of diagrams
+model_elements <- lapply(models$idObject, 
+                         function(x) fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/"), 
+                                                      "bioEntities/elements/?columns=id,name,type,references"), 
+                                              flatten = F))
+names(model_elements) <- models$name
+
+### A convenience function to parse the annotations
+extract_hgnc <- function(model) {
+  ### For erroneous response, return NULL
+  if(is.null(model)) { return(NULL) }
+  ### Only elements that have annotations
+  these_refs <- model$references[sapply(model$references, length) > 0]
+  ### For empty list, return NULL
+  if(length(these_refs) == 0) { return(NULL) }
+  ### Get HGNC symbols, for elements that have annotations
+  hgncs <- sapply(these_refs, function(x) x[x$type == "HGNC_SYMBOL", "resource"])
+  hgncs <- hgncs[sapply(hgncs, function(x) ifelse(is.character(x) & length(x) > 0, TRUE, FALSE))]
+  return(unique(unlist(hgncs)))
+}
+
+hgncs_of_models <- sapply(model_elements, extract_hgnc)
+
+### Parse HGNCs list and compare to the interactions from the OmniPathDB
+for(hmi in 1:length(hgncs_of_models)) {
+  hmis <- hgncs_of_models[[hmi]]
+  
+  message(paste0("At least one interactor in ", names(hgncs_of_models)[hmi]))
+  ia_omnipath %>% filter(source_genesymbol %in% hmis | target_genesymbol %in% hmis) -> op_oneint
+  print(op_oneint)
+  
+  message(paste0("Both interactors in ", names(hgncs_of_models)[hmi]))
+  ia_omnipath %>% filter(source_genesymbol %in% hmis & target_genesymbol %in% hmis) -> op_twoint
+  print(op_twoint)
+}
+
+columns <- "id,reactionId,type,products,reactants,modifiers"
+model_reactions <- lapply(models$idObject, 
+                          function(x) fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/"), 
+                                                       paste0("bioEntities/reactions/?columns=", columns)),
+                                               flatten = F))
+for(mr in 1:length(model_reactions)) {
+  
+}
+