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Commit ecd699d5 authored by cylon-x's avatar cylon-x 🤖
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Merge branch 'repo_update' of https://git-r3lab.uni.lu/covid/models into repo_update

parents 13467c79 0c51d734
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Curation/SARS-CoV-2 proteins/Orf3b/Orf3b_0620_2020.xml
View file @ ecd699d5
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......@@ -1253,11 +1261,7 @@
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......@@ -1322,9 +1326,16 @@
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......@@ -1806,6 +1772,19 @@
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......
Integration/MINERVA_access/get_drug_targets.R
View file @ ecd699d5
......@@ -6,7 +6,7 @@
##################################################
### Helper functions to access and retrieve content from MINERVA-hosted diagrams
source("minerva_access_functions.R")
source("https://git-r3lab.uni.lu/covid/models/-/raw/master/Integration/MINERVA_access/minerva_access_functions.R")
### The address of the COVID-19 Disease Map in MINERVA
map <- "https://covid19map.elixir-luxembourg.org/minerva/api/"
......@@ -18,5 +18,44 @@ refs <- lapply(map_components$map_elements, function(x) data.frame(id = x$id,
uniprot = get_annotation(x$references, "UNIPROT")))
names(refs) <- map_components$models$name
### A helper function to retrieve one (first) element alias for all unique UniProts.
### The drug search API call is based on the alias of an element in the MINERVA project,
### while the drug targets are HGNC/UniProt based. Multiple aliases can point to the
### same HGNC/UniProt. To optimise drug requests, we take only one alias for
### each unique UniProt in a given diagram.
unique_drugs <- function(funiprot_references) {
frefs <- funiprot_references[!is.na(funiprot_references[,"uniprot"]),]
if(nrow(frefs) == 0) { return(NULL) }
sapply(unique(frefs[,"uniprot"]), function(x) frefs[x == frefs[,"uniprot"],1][1])
}
### Get the UniProt-alias mappings using the helper function
upd <- sapply(refs, unique_drugs)
### Get the id of the default project
map_project <- paste0(map,"projects/",get_default_project(map),"/")
### Lengthy calculation, ask for drug targets of all unique UniProt ids in every pathway
all_drugs <- c()
### For each pathway
for(u in 1:length(upd)) {
if(!is.null(upd[[u]])) {
message(paste0("Processing diagram: ", map_components$models$name[u]))
### For each UniProt id
for(p in 1:length(upd[[u]])) {
### Add a row to the global table with pathway name, UniProt id and the drugs
### targeting the element alias associated with this UniProt
all_drugs <- rbind(all_drugs,
c(pathway_name = map_components$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 = ";")))
}
}
}
### Write down the table
write.table(all_drugs, file = "MINERVA_C19DM_drugs.tsv", sep = "\t", quote = F, col.names = T, row.names = F)
message("Done.")
Integration/MINERVA_access/get_formats.R 0 → 100644
View file @ ecd699d5
##################################################
## Project: COVID-19 Disease Map
## Script purpose: Get different formats of the MINERVA diagrams
## Date: 25.01.2021
## Author: Marek Ostaszewski
##################################################
### Helper functions to access and retrieve content from MINERVA-hosted diagrams
source("https://git-r3lab.uni.lu/covid/models/-/raw/master/Integration/MINERVA_access/minerva_access_functions.R")
### The address of the COVID-19 Disease Map in MINERVA
map <- "https://covid19map.elixir-luxembourg.org/minerva/api/"
library(jsonlite)
### Get config to obtain the default map and different format handlers
cfg <- fromJSON(ask_GET(paste0(map, "configuration/")))
### Get the default (most recent) project id
project_id <- cfg$options[cfg$options$type == "DEFAULT_MAP","value"]
### The address of the latest (default) build
mnv_base <- paste0(map, "projects/",project_id,"/")
### Get model information
models <- fromJSON(ask_GET(paste0(mnv_base, "models/")))
### Format handler;
### see cfg$modelFormats for available handlers, we will use the SBGNML handler
this_handler <- with(cfg$modelFormats, handler[name == "SBGN-ML"])
this_extension <- with(cfg$modelFormats, extension[name == "SBGN-ML"])
### Iterate over all model ids, get them in the format defined by the handler and add the handler-associated extension
for(i in 1:nrow(models)) {
lines <- ask_GET(paste0(mnv_base, "models/", models$idObject[i],":downloadModel?handlerClass=",this_handler))
cat(lines, file = paste0(models$name[i], ".", this_extension))
}
message("Done.")
\ No newline at end of file
Integration/MINERVA_access/minerva_access_functions.R
View file @ ecd699d5
......@@ -21,12 +21,17 @@ ask_GET <- function(fask_url, verbose = F) {
return(NULL)
}
### Get the id of the default project for this MINERVA instance
get_default_project <- function(map_api) {
cfg <- fromJSON(ask_GET(paste0(map_api, "configuration/")))
return(cfg$options[cfg$options$type == "DEFAULT_MAP","value"])
}
### Get the components of a given map/project on the MINERVA Platform
get_map_components <- function(map_api, project_id = NULL) {
if(is.null(project_id)) {
### If project id not given, get configuration of the map, to obtain the latest (default) version
cfg <- fromJSON(ask_GET(paste0(map_api, "configuration/")))
project_id <- cfg$options[cfg$options$type == "DEFAULT_MAP","value"]
project_id <- get_default_project(map_api)
}
### The address of the latest (default) build
mnv_base <- paste0(map_api, "projects/",project_id,"/")
......
Resources/Crosstalks/find_crosstalks.R
View file @ ecd699d5
......@@ -6,7 +6,7 @@
##################################################
### Helper functions to access and retrieve content from MINERVA-hosted diagrams
source("minerva_access.R")
source("https://git-r3lab.uni.lu/covid/models/-/raw/master/Integration/MINERVA_access/minerva_access_functions.R")
### For handling WikiPathway queries
library(rWikiPathways)
......
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