minerva utils

Integration/MINERVA_access/get_drug_targets.R

+##################################################
+## Project: COVID-19 Disease Map
+## Script purpose: Get drug targets for unique UniProt identifiers
+## Date: 22.01.2021
+## Author: Marek Ostaszewski
+##################################################
+
+### Helper functions to access and retrieve content from MINERVA-hosted diagrams
+source("minerva_access_functions.R")
+
+### The address of the COVID-19 Disease Map in MINERVA
+map <- "https://covid19map.elixir-luxembourg.org/minerva/api/"
+### Get the components of MINERVA and WikiPathways (see minerva_access.R)
+map_components <- get_map_components(map)
+
+message("Retrieving MINERVA Uniprot collection")
+refs <- lapply(map_components$map_elements, function(x) data.frame(id = x$id,
+                                                                   uniprot = get_annotation(x$references, "UNIPROT")))
+names(refs) <- map_components$models$name
+
+message("Done.")
+

Integration/MINERVA_access/minerva_access_functions.R

+##################################################
+## Project: COVID-19 Disease Map
+## Script purpose: Convenience functions for accessing the MINERVA Platform
+## Date: 24.12.2020
+## Author: Marek Ostaszewski
+##################################################
+
+library(httr)
+library(jsonlite)
+
+### A convenience function to handle API queries
+ask_GET <- function(fask_url, verbose = F) {
+  if(verbose) {
+    message(URLencode(fask_url))
+  }
+  resp <- httr::GET(url = URLencode(fask_url),
+                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"))
+  if(httr::status_code(resp) == 200) {
+    return(httr::content(resp, as = "text"))
+  }
+  return(NULL)
+}
+
+### Get the components of a given map/project on the MINERVA Platform
+get_map_components <- function(map_api, project_id = NULL) {
+  if(is.null(project_id)) {
+    ### If project id not given, get configuration of the map, to obtain the latest (default) version
+    cfg <- fromJSON(ask_GET(paste0(map_api, "configuration/")))
+    project_id <- cfg$options[cfg$options$type == "DEFAULT_MAP","value"]
+  }
+  ### The address of the latest (default) build 
+  mnv_base <- paste0(map_api, "projects/",project_id,"/")
+  
+  message(paste0("Asking for diagrams in: ", mnv_base, "models/"))
+  
+  ### Get diagrams
+  models <- fromJSON(ask_GET(paste0(mnv_base, "models/")))
+  
+  ### Get elements of the chosen diagram
+  model_elements <- lapply(models$idObject, 
+                           function(x)
+                             fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/",
+                                                     "bioEntities/elements/?columns=id,name,type,references,elementId,complexId")),
+                                      flatten = F))
+  
+  ### Request for reactions that have at least one top 10 element as participant
+  model_reactions <- lapply(models$idObject,
+                            function(x)
+                              fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/",
+                                                      "bioEntities/reactions/?columns=modifiers,products,reactants")),
+                                       flatten = F))
+  ### Pack all into a list and return
+  return(list(models = models, map_elements = model_elements, map_reactions = model_reactions))
+}
+
+### Get annotation of a given type, from element/reaction references
+get_annotation <- function(freferences, ftype) {
+  sapply(freferences, 
+         function(x) {
+           ifelse(any(x$type == ftype), x$resource[x$type == ftype], NA)
+         })
+}
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