Commit d4879445 authored by Marek Ostaszewski's avatar Marek Ostaszewski
Browse files

diagram harmonisation, UniProt identifiers

parent c8c5b579
Pipeline #50372 passed with stages
in 43 seconds
......@@ -3939,6 +3939,11 @@ RefSeq_ID: NM_197966
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......@@ -3960,21 +3965,11 @@ RefSeq_ID: NM_197966
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......@@ -5359,7 +5354,7 @@ RefSeq_ID: NM_004346
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......@@ -5372,7 +5367,7 @@ RefSeq_ID: NM_004346
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......@@ -6414,7 +6409,7 @@ RefSeq_ID: NM_004346
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......@@ -6852,7 +6847,7 @@ RefSeq_ID: NM_004346
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......@@ -6945,7 +6940,7 @@ RefSeq_ID: NM_004346
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......@@ -6958,7 +6953,7 @@ RefSeq_ID: NM_004346
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......@@ -6912,6 +6912,11 @@ SIGNOR-SCISOVG
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......@@ -7696,6 +7701,16 @@ SIGNOR-SCISOVG
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......@@ -8454,6 +8469,11 @@ SIGNOR-SCISOVG
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......@@ -9174,6 +9194,11 @@ SIGNOR-SCISOVG
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......@@ -11193,7 +11218,7 @@ SIGNOR-SCISOVG
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......@@ -5816,11 +5816,16 @@ cytoplasmic pattern recognition receptor (PRR)
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......@@ -9704,7 +9709,7 @@ Infection of macrophages with N15m1, which expresses an unstable nsp15, or N15m3
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......
......@@ -3035,11 +3035,16 @@ SARS-CoV-2 E protein
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<rdf:li rdf:resource="urn:miriam:ncbiprotein:BCD58755"/>
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<rdf:li rdf:resource="urn:miriam:uniprot:P0DTC4"/>
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......@@ -3643,7 +3648,7 @@ SARS-CoV-2 E protein
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......
URL Type Name
https://reactome.org/ContentService/exporter/event/R-HSA-9678108.sbml Reactome R-HSA-9678108
https://reactome.org/ContentService/exporter/event/R-HSA-9694516.sbml Reactome R-HSA-9694516
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4846.gpml WikiPathways WP4846
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4799.gpml WikiPathways WP4799
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4861.gpml WikiPathways WP4861
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP5027.gpml WikiPathways WP5027
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4860.gpml WikiPathways WP4860
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4936.gpml WikiPathways WP4936
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4863.gpml WikiPathways WP4863
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4864.gpml WikiPathways WP4864
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4877.gpml WikiPathways WP4877
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP5038.gpml WikiPathways WP5038
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4883.gpml WikiPathways WP4883
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4965.gpml WikiPathways WP4965
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4969.gpml WikiPathways WP4969
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4927.gpml WikiPathways WP4927
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4912.gpml WikiPathways WP4912
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4868.gpml WikiPathways WP4868
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4880.gpml WikiPathways WP4880
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4876.gpml WikiPathways WP4876
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4884.gpml WikiPathways WP4884
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4961.gpml WikiPathways WP4961
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP5039.gpml WikiPathways WP5039
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4853.gpml WikiPathways WP4853
https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/WP4904.gpml WikiPathways WP4904
https://covid19map.elixir-luxembourg.org/minerva/ MINERVA C19DMap
##################################################
## Project: COVID-19 Disease Map
## Script purpose: Expand COVID-19 Disease Map diagrams by TM interactions
## Date: 30.11.2021
## Author: Marek Ostaszewski
##################################################
library(xml2)
library(httr)
library(jsonlite)
library(dplyr)
### An 'xml2' namespace structure for parsing CellDesigner xml
ns_cd <- xml2::xml_ns_rename(
xml2::xml_ns(
xml2::read_xml("<root>
<sbml xmlns = 'http://www.sbml.org/sbml/level2/version4'/>
<cd xmlns = 'http://www.sbml.org/2001/ns/celldesigner'/>
<html xmlns = 'http://www.w3.org/1999/xhtml'/>
<rdf xmlns = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'/>
<bq xmlns = 'http://biomodels.net/biology-qualifiers/'/>
</root>")),
d1 = "sbml", d2 = "cd", d3 = "html", d4 = "rdf", d5 = "bq")
### Helper function to extract aliases from a given CellDesigner xml node
extract_aliases <- function(cd_node) {
sapply(xml2::xml_find_all(cd_node, ".//cd:alias", ns = ns_cd), xml2::xml_text)
}
### Helper function to find species for aliases from a given CellDesigner xml file
alias_to_species <- function(cd_alias, cd_xml) {
xml2::xml_attr(xml2::xml_find_first(cd_xml, paste0("//*[@id='",cd_alias,"']"), ns = ns_cd),
attr = "species")
}
### Helper function to split reaction nodes by reactants, products and modifiers
split_elements <- function(reaction_node) {
ins <- extract_aliases(xml2::xml_find_first(reaction_node, ".//sbml:listOfReactants", ns = ns_cd))
outs <- extract_aliases(xml2::xml_find_first(reaction_node, ".//sbml:listOfProducts", ns = ns_cd))
mods <- lapply(xml2::xml_find_all(reaction_node, ".//cd:modification", ns = ns_cd),
function(m) xml2::xml_attrs(m)[c("type","aliases")])
### Corner case possible (BOOLEAN_LOGIC_GATE_), where multiple aliases per modifier possible
if(any(sapply(mods, function(m) grepl(",", m["aliases"])))) {
mods <- lapply(mods, function(margs) {
lapply(strsplit(margs["aliases"], ",")[[1]], function(mal) c(margs["type"], aliases = mal))
})
mods <- unlist(mods, recursive = F)
}
return(list(reactants = ins,
products = outs,
modifiers = mods))
}
### Helper function to extract annotations from the species' nodes
species_annotation <- function(species_node, cd_xml) {
retlist <- list()
retlist[[ xml2::xml_attr(species_node, "name") ]] <-
sapply(xml2::xml_find_all(species_node, ".//rdf:li", ns = ns_cd), xml2::xml_attr, "resource")
if(xml2::xml_text(
xml2::xml_find_first(species_node,
".//cd:speciesIdentity/cd:class",
ns = ns_cd)) == "COMPLEX") {
species_in <- xml2::xml_find_all(cd_xml,
paste0("//cd:species[.//cd:complexSpecies[text() = '",
xml2::xml_attr(species_node, "id"),"']]"),
ns = ns_cd)
sp_in_ann <- sapply(species_in,
function(sp)
xml2::xml_attr(xml2::xml_find_all(sp, ".//rdf:li", ns = ns_cd), "resource"))
names(sp_in_ann) <- sapply(species_in, xml2::xml_attr, "name")
retlist <- c(retlist, sp_in_ann)
}
return(retlist)
}
get_annotations_by_miriam <- function(annotations_list, miriam, replace_miriam = NULL) {
ret <- paste(grep(miriam, unlist(annotations_list), value = T),
collapse = ";")
if(!is.null(replace_miriam) & ret != "") {
ret <- gsub(miriam, replace_miriam, ret)
}
return(ret)
}
alias_parameters <- function(alias, cd_xml, role) {
species_id <- alias_to_species(alias, cd_xml)
species_node <- xml2::xml_find_first(cd_xml,
paste0("//sbml:species[@id='",species_id,"']"),
ns = ns_cd)
### If included species is a part of a reaction
if(is.na(species_node)) {
species_node <- xml2::xml_find_first(cd_xml,
paste0("//cd:species[@id='",species_id,"']"),
ns = ns_cd)
}
if(is.na(species_node)) {
message("Species not found for alias '",alias,"'")
}
al_ann <- species_annotation(species_node, cd_xml)
ret <- data.frame(
id = alias,
name = names(al_ann)[1],
up = get_annotations_by_miriam(al_ann,
miriam = "urn:miriam:uniprot:",
replace_miriam = "UNIPROT:"),
hgnc = get_annotations_by_miriam(al_ann,
miriam = "urn:miriam:hgnc.symbol:",
replace_miriam = "HGNC_SYMBOL:"),
type = xml2::xml_text(xml2::xml_find_first(species_node,
".//cd:speciesIdentity/cd:class",
ns = ns_cd))
)
colnames(ret) <- paste0(role, colnames(ret))
return(ret)
}
reaction_parameters <- function(reaction_node, role) {
ret <- data.frame(
id = xml2::xml_attr(reaction_node, attr = "id"),
name = xml2::xml_attr(reaction_node, attr = "name"),
up = "", hgnc = "",
type = xml2::xml_text(xml2::xml_find_first(reaction_node, ".//cd:reactionType", ns = ns_cd))
)
colnames(ret) <- paste0(role, colnames(ret))
return(ret)
}
### For a given reaction, get aliases
### For each alias, get species
### For each species, get annotations
### if complex
### get included species and their annotations
### Append an entry of alias-reaction relation
### Return the table
reaction_to_bp <- function(reaction_node, cd_xml) {
### Get element aliases
elements <- split_elements(reaction_node)
### Create reactant-reaction interactions
rix <- lapply(elements$reactants, function(ral) {
cbind(alias_parameters(alias = ral, cd_xml, role = "source_"),
interaction_type = "CONSPUMPTION",
reaction_parameters(reaction_node,"target_"))
})
### Create modifier-reaction interactions
mix <- lapply(elements$modifiers, function(mal) {
cbind(alias_parameters(alias = mal["aliases"], cd_xml, role = "source_"),
interaction_type = mal["type"],
reaction_parameters(reaction_node,"target_"))
})
### Create reaction-product interactions
pix <- lapply(elements$products, function(pal) {
cbind(reaction_parameters(reaction_node,"source_"),
interaction_type = "PRODUCTION",
alias_parameters(alias = pal, cd_xml, role = "target_"))
})
### Collect the interaction components
bp_tab <- rbind(do.call(rbind,rix), #Collating reactant rows
do.call(rbind,mix), #Collating modifier rows
do.call(rbind,pix)) #Collating product rows
rownames(bp_tab) <- NULL
rann <- sapply(xml2::xml_find_all(reaction_node, ".//rdf:li", ns = ns_cd), xml2::xml_attr, "resource")
selected_rann <- c(get_annotations_by_miriam(rann, "urn:miriam:reactome:", "REACTOME:"),
get_annotations_by_miriam(rann, "urn:miriam:pubmed:", "PUBMED:"))
cbind(bp_tab, reaction_annotation = paste(selected_rann, collapse = ";"))
}
### CellDesigner to bipartite format
### Unconnected species are dropped
cd_to_bp <- function(cd_xml) {
reactions <- xml2::xml_find_all(cd_xml, "//sbml:reaction", ns = ns_cd)
bp_reactions <- lapply(reactions, reaction_to_bp, cd_xml)
return(do.call(rbind, bp_reactions))
}
harmonise_identifiers <- function(diagram_tab, prefix, keep_original_ids = F) {
id_space <- sort(unique(c(diagram_tab$source_id, diagram_tab$target_id)))
mapping <- data.frame(org_id = id_space, new_id = paste0(prefix,"_",seq_along(id_space)))
if(keep_original_ids) {
diagram_tab <- cbind(diagram_tab, org_source_id = diagram_tab$source_id)
diagram_tab <- cbind(diagram_tab, org_target_id = diagram_tab$target_id)
}
for(id in 1:nrow(mapping)) {
diagram_tab$source_id[diagram_tab$source_id == mapping$org_id[id]] <- mapping$new_id[id]
diagram_tab$target_id[diagram_tab$target_id == mapping$org_id[id]] <- mapping$new_id[id]
}
return(diagram_tab)
}
local_converter <- function(furl, type) {
message("'",furl,"'")
rls <- paste(readLines(furl), collapse = "\n")
message("API translation request")