version updates, improved reaction query

R/API_find_drug_targets.R

 ##################################################
 ## Script purpose: An example of MINERVA API call to retrieve 
-##                 HGNC symbols of elements targetted by a given drug,
-##                 and to retrieve drugs targetting elements with a given UniProt
-## Date: 17/03/2020
+##                 HGNC symbols of elements targeted by a given drug,
+##                 and to retrieve drugs targeting elements with a given UniProt
+## Date: 17/03/2020 (updated 02.05.2022)
 ## Author: Marek Ostaszewski (marek.ostaszewski@uni.lu)
-## MINERVA API version: 14.0
+## MINERVA API version: 15.0
 ##################################################
 
 ### A convenience function to handle GET and POST requests to MINERVA API

R/API_retrieve.R

 ##################################################
 ## Script purpose: An example of MINERVA API call to retrieve elements with a 
-##                 given uniprot id and their interactions
-## Date: 17/03/2020
+##                 given UniProt id and their interactions
+## Date: 17/03/2020 (updated 02.05.2022)
 ## Author: Marek Ostaszewski (marek.ostaszewski@uni.lu)
-## MINERVA API version: 14.0
+## MINERVA API version: 15.0
 ##################################################
 
 ### A convenience function to handle GET and POST requests to MINERVA API
@@ -47,13 +47,14 @@ identifiers <- model_elements$id[hits]
 model_reactions <- fromJSON(ask_GET(base_url, 
                                     paste0("models/*/bioEntities/reactions/?participantId=", 
                                            paste(identifiers, collapse = ","), 
-                                           "&columns=reactionId")))
+                                           "&columns=id")))
 
 ### Create a validation URL for the disease map these identifiers come from
-visualize_reactions <- "https://pdmap.uni.lu/minerva/?search="
+### "search.perfect=true" is needed if we use MINERVA internal identifiers
+visualize_reactions <- "https://pdmap.uni.lu/minerva/?search.perfect=true&search="
 
 ### Get searchable reaction identifiers from the search results
-searchable_identifiers <- paste(paste0("reaction:", model_reactions$reactionId), collapse = ";")
+searchable_identifiers <- paste(paste0("reaction:", model_reactions$id), collapse = ";")
 
 ### Create the final link
 print(paste0(visualize_reactions, searchable_identifiers))