Skip to content
GitLab
Commit ecd699d5 authored by cylon-x's avatar cylon-x 🤖
Browse files

Merge branch 'repo_update' of https://git-r3lab.uni.lu/covid/models into repo_update

parents 13467c79 0c51d734
Hide whitespace changes
Inline Side-by-side
Curation/SARS-CoV-2 proteins/Orf3b/Orf3b_0620_2020.xml
View file @ ecd699d5
......@@ -399,6 +399,14 @@
<celldesigner:paint color="ffcccc00" scheme="Color"/>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:compartmentAlias>
<celldesigner:compartmentAlias id="ca5" compartment="c5">
<celldesigner:class>SQUARE</celldesigner:class>
<celldesigner:bounds x="235.0" y="485.0" w="240.0" h="255.0"/>
<celldesigner:namePoint x="407.5" y="698.5"/>
<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
<celldesigner:paint color="ffcccc00" scheme="Color"/>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:compartmentAlias>
</celldesigner:listOfCompartmentAliases>
<celldesigner:listOfComplexSpeciesAliases>
<celldesigner:complexSpeciesAlias id="csa4" species="s23" compartmentAlias="ca4">
......@@ -451,6 +459,7 @@
<celldesigner:backupSize w="0.0" h="0.0"/>
<celldesigner:backupView state="none"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="126.0" height="120.0"/>
<celldesigner:singleLine width="2.0"/>
<celldesigner:paint color="fff7f7f7" scheme="Color"/>
......@@ -528,13 +537,13 @@
</celldesigner:complexSpeciesAlias>
</celldesigner:listOfComplexSpeciesAliases>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:speciesAlias id="sa1" species="s1" compartmentAlias="ca5">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="314.83333333333326" y="510.58333333333326" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:innerPosition x="79.83333333333326" y="25.583333333333258"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffffcccc" scheme="Color"/>
......@@ -547,14 +556,14 @@
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa4" species="s7">
<celldesigner:speciesAlias id="sa4" species="s7" compartmentAlias="ca5">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="301.83333333333326" y="687.0833333333333" w="244.0" h="29.0"/>
<celldesigner:bounds x="380.0" y="635.0" w="80.0" h="30.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="244.0" height="29.0"/>
<celldesigner:innerPosition x="145.0" y="150.0"/>
<celldesigner:boxSize width="80.0" height="30.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffffff66" scheme="Color"/>
</celldesigner:usualView>
......@@ -587,11 +596,10 @@
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa7" species="s12">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="116.83333333333331" y="690.0833333333333" w="90.0" h="25.0"/>
<celldesigner:bounds x="115.0" y="637.5" w="90.0" h="25.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="90.0" height="25.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ff66ff66" scheme="Color"/>
......@@ -853,11 +861,11 @@
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa48" species="s43" complexSpeciesAlias="csa8">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="1022.3333333333333" y="438.66666666666663" w="80.0" h="40.0"/>
<celldesigner:bounds x="1025.0" y="445.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="9.333333333333258" y="53.66666666666663"/>
<celldesigner:innerPosition x="12.0" y="60.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
......@@ -1055,7 +1063,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1074,7 +1082,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1093,7 +1101,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1207,7 +1215,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1226,7 +1234,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1253,11 +1261,7 @@
<celldesigner:protein id="pr23" name="TCRβ" type="GENERIC"/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes>
<celldesigner:gene id="gn1" name="IFNB1" type="GENE">
<celldesigner:listOfRegions>
<celldesigner:region id="tr2" name="Promoter" size="0.24" pos="0.15647058823529414" type="RegulatoryRegion" active="false"/>
</celldesigner:listOfRegions>
</celldesigner:gene>
<celldesigner:gene id="gn1" name="IFNB1" type="GENE"/>
</celldesigner:listOfGenes>
<celldesigner:listOfRNAs>
<celldesigner:RNA id="rn1" name="IFNB1" type="RNA"/>
......@@ -1322,9 +1326,16 @@
</celldesigner:extension>
</annotation>
</compartment>
<compartment metaid="c5" id="c5" name="nucleus" size="1" units="volume" outside="default">
<annotation>
<celldesigner:extension>
<celldesigner:name>nucleus</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species metaid="s1" id="s1" name="Orf3b" compartment="default" initialAmount="0" charge="0">
<species metaid="s1" id="s1" name="Orf3b" compartment="c5" initialAmount="0" charge="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
......@@ -1332,10 +1343,13 @@
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re5"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s7" id="s7" name="IFNB1" compartment="default" initialAmount="0" charge="0">
<species metaid="s7" id="s7" name="IFNB1" compartment="c5" initialAmount="0" charge="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
......@@ -1742,54 +1756,6 @@
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="re11" id="re4" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>NEGATIVE_INFLUENCE</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s1" alias="sa1"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s7" alias="sa4">
<celldesigner:linkAnchor position="NNW"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#re11">
<bqmodel:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:doi:10.1101%2F2020.05.11.088179"/>
</rdf:Bag>
</bqmodel:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00005" species="s1">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00006" species="s7">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa4</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
</reaction>
<reaction metaid="re12" id="re5" reversible="false">
<annotation>
<celldesigner:extension>
......@@ -1806,6 +1772,19 @@
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="INHIBITION" modifiers="s1" aliases="sa1" targetLineIndex="-1,3">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s1" alias="sa1">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
......@@ -1826,6 +1805,15 @@
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00001" species="s1">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
<reaction metaid="re13" id="re6" reversible="false">
<annotation>
......@@ -2321,14 +2309,10 @@
<celldesigner:extension>
<celldesigner:reactionType>POSITIVE_INFLUENCE</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s22" alias="sa38">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseReactant>
<celldesigner:baseReactant species="s22" alias="sa38"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s73" alias="sa78">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseProduct>
<celldesigner:baseProduct species="s73" alias="sa78"/>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
......@@ -2339,7 +2323,7 @@
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00001" species="s22">
<speciesReference metaid="CDMT00002" species="s22">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa38</celldesigner:alias>
......@@ -2348,7 +2332,7 @@
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00002" species="s73">
<speciesReference metaid="CDMT00003" species="s73">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa78</celldesigner:alias>
......@@ -2362,9 +2346,7 @@
<celldesigner:extension>
<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s72" alias="sa34">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseReactant>
<celldesigner:baseReactant species="s72" alias="sa34"/>
<celldesigner:baseReactant species="s55" alias="csa11">
<celldesigner:linkAnchor position="ENE"/>
</celldesigner:baseReactant>
......@@ -2395,14 +2377,14 @@
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00003" species="s72">
<speciesReference metaid="CDMT00004" species="s72">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa34</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
<speciesReference metaid="CDMT00004" species="s55">
<speciesReference metaid="CDMT00005" species="s55">
<annotation>
<celldesigner:extension>
<celldesigner:alias>csa11</celldesigner:alias>
......
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)
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment