Upload API retrieve example

R/API_retrieve.R

+##################################################
+## Script purpose: An example of MINERVA API call to retrieve elements with a 
+##                 given uniprot id and their interactions
+## Date: 17/03/2019
+## Author: Marek Ostaszewski (marek.ostaszewski@uni.lu)
+## MINERVA API version: 14.0
+##################################################
+
+### A convenience function to handle GET and POST requests to MINERVA API
+library(httr)
+library(jsonlite)
+
+### Utility function using httr:GET to send queries to a given MINERVA Platform instance
+ask_GET <- function(mnv_base, query) {
+  resp <- httr::GET(url = paste0(mnv_base, query),
+                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"))
+  if(httr::status_code(resp) == 200) {
+    return(httr::content(resp, as = "text"))
+  }
+  return(NULL)
+}
+
+### Base URL of the map, we use Parkinson's disease map
+base_url <- "https://pdmap.uni.lu/minerva/api/projects/pd_map_autumn_19/"
+
+### Request identifiers of models for a given project (main map and submaps)
+models <- ask_GET(base_url, "models/")
+models <- fromJSON(models, flatten = F)
+
+### For each model, retrieve elements with columns including references
+model_elements <- lapply(models$idObject, 
+                         function(x) fromJSON(ask_GET(paste0(base_url,"models/",x,"/"), 
+                                                      "bioEntities/elements/?columns=id,name,type,references"), 
+                                              flatten = F))
+#Define UniProt identifiers to be matched in model elements
+uniprot_examples <- c("O43521", "P63167")
+
+### For each model, retrieve reactions
+model_reactions <- lapply(models$idObject, 
+                          function(x) fromJSON(ask_GET(paste0(base_url,"models/",x,"/"), 
+                                                       "bioEntities/reactions/?columns=id,type,reactionId,products,reactants,modifiers"), 
+                                               flatten = F))
+
+### For results in each model, find element identifiers that have the selected uniprot id
+### then find reactions having at least one of these elements, and append them to the output vector
+reaction_identifiers <- c()
+
+for (m in 1:length(model_elements)) {
+  ### In "resources" of each element, find those which have requested UniProt identifiers 
+  hits <- sapply(model_elements[[m]]$references,
+                 function(x) any(uniprot_examples %in% x$resource[x$type == "UNIPROT"]))
+  
+  ### Identifiers of the elements matching the search criteria
+  identifiers <- model_elements[[m]]$id[hits]
+  
+  ### Look for reaction identifiers only for non-zero results and models with existing reactions 
+  if(length(identifiers) > 0 && length(model_reactions[[m]]) > 0) {
+    
+    ### Which reactions have at least one modifier, product and reactant matching the list
+    hits <- which(sapply(model_reactions[[m]]$modifiers, 
+                      function(x) ifelse(length(x) == 0, F, any(x$aliasId %in% identifiers))))
+    hits <- c(hits, which(sapply(model_reactions[[m]]$products, 
+                      function(x) ifelse(length(x) == 0, F, any(x$aliasId %in% identifiers)))))
+    hits <- c(hits, which(sapply(model_reactions[[m]]$reactants, 
+                      function(x) ifelse(length(x) == 0, F, any(x$aliasId %in% identifiers)))))
+    
+    ### Append the data frame by these reaction identifiers
+    reaction_identifiers <- rbind(reaction_identifiers,
+                                  data.frame(reaction_id = model_reactions[[m]]$reactionId[unique(hits)],
+                                             model_id = models$idObject[m], stringsAsFactors = F))
+  }
+}
+
+### Create a validation URL for the disease map these identifiers come from
+visualize_reactions <- "https://pdmap.uni.lu/minerva/?search="
+
+### Get searchable reaction identifiers from the search results
+searchable_identifiers <- paste(paste0("reaction:", reaction_identifiers$reaction_id), collapse = ";")
+
+### Create the final link
+print(paste0(visualize_reactions, searchable_identifiers))