Updated scripts for conversion from PC to AF maps using CasQ Minerva and...

Updated scripts for conversion from PC to AF maps using CasQ Minerva and Hipathia producing sif and att files

Resources/Hipathia/sif_att_converter/README.md

+# Converter of COVID-19 CellDesigner diagrams "raw SIF" files obtained using CaSQ and MINERVA to HiPathia "SIF" and "ATT" file format.
+
+The present directory contains the code and files necessary to convert *Simple Interaction Files (SIF)*, generated with CaSQ python package, from curated COVID-19 related CellDesigner diagrams to HiPathia's *SIF* and *ATT (attribute)* files. The *ATT* files are generated using Minerva, as a proxy between CaSQ and CellDesigner, to retrieve details of each node. These *SIF* and *ATT* files are needed by the HiPathia mechanistic modelling metagraphinfo database in order to run the algorithm over the diagrams. After running the conversor, each diagram will count with a *"diagram.sif"* and a *"diagram.att"* file,moreover a *"names.pathways.txt"* file listing the names of the diagrams converted will be also generated.
+
+**The directory is structured into 2 folders and 2 scripts.**
+
+### Scripts
+
+** - functions_retrieve_sif_att_hipathia_from_CellDesigner.R**:
+
+The present script contains the functions needed for converting *raw SIF *files from CellDesigner to HiPathia *SIF* and *ATT* files. The script is autodescriptive and counts with 5 functions for the retrieval, preprocessing and formatting of the raw SIF files. The functions enable to handle API querys, retrieve detailed information of each node from a CellDesigner diagram and format the information into HiPathia's SIF and ATT files. Each function is fully describe in the script. DO NOT EDIT (only edit for coding purposes).
+
+
+
+
+** - example_sif_Hipathia.R**
+
+The present script contains the example code to run over the existing diagrams on the [https://git-r3lab.uni.lu/covid/models/-/tree/master/](https://git-r3lab.uni.lu/covid/models/-/tree/master/) repository, please in order to run the code correctly clone the repository on a local directory and recode the "base_dir" variable to that directory. The script will read the *Simple Interaction Files (SIF)* from the CellDesigner diagrams located in */models-master/Executable Modules/SBML_qual_build/sif* in the repository, generate HiPathia formatted *SIF* and *ATT* files for each diagram and a *"names.pathways.txt"* file listing the names of the diagrams converted. The files are by default stored in the **test folder**, this parameter can be change in the *outputfolder* parameter of the *hipathia.att.sif* function.
+
+<u>**CAUTION**:</u> Please when running the script make sure you recode the variable "base_dir" to the local directory where the repo *models-master* was cloned.
+
+
+
+### Resources folder
+Contains the *"exceptions.txt"* file, which contains for the nodes we desire to avoid, nodes that are not allowed in the metagraphinfo database such as viral gene nodes.
+
+### Test folder
+Empty folder that will store the results of running the *"example_sif_Hipathia.R"*
+
+
+### Contributors
+
+[Marek Ostaszewski](https://fairdomhub.org/people/665)
+
+[Marina Esteban-Medina](https://fairdomhub.org/people/1873)
+
+
+

Resources/Hipathia/sif_att_converter/example_sif_Hipathia.R

+      ###############################################################################
+##########   EXAMPLE CODE: From CellDseigner CaSQ "Raw sif" files  to         ############
+##############             Hipathia "sif" and "att" format using Minerva   #############
+     #############################################################################
+     
+###############################################################################################################     
+## IMPORTANT: CHANGE THE "base_dir" parameter to the local directory where the repository was cloned !!!!  ####
+      
+      base_dir <- "~/Desktop/models-master/"
+      
+#####################################################################################################      
+      
+#### 1. LOAD LIBRARIES  AND FUNCTIONS  #####
+
+             ## Load functions
+      source(file.path(paste0(base_dir, "/Resources/Hipathia/sif_att_converter/functions_retrieve_sif_att_hipathia_from_CellDesigner.R")), echo=TRUE) 
+
+      
+#### 2. LOAD FOLDER, CREATE LIST OF RAW_SIF_FILES; LOAD MINERVA MAPS AND INFO NEEDED ####
+      
+      ### Read the raw sif files from the corresponding folder in the repository
+  
+      sif_files_path <- file.path(paste0(base_dir,"/Executable Modules/SBML_qual_build/sif"))
+      
+      raw_sif_list <- list.files(path = sif_files_path , all.files = F) %>% .[grep("*_raw*", .)] 
+      
+      diagrams <- gsub("_stable_raw.sif", "", raw_sif_list) 
+      
+      ### Get MINERVA elements
+      
+      ### The address of the COVID-19 Disease Map in MINERVA
+      map <- "https://covid19map.elixir-luxembourg.org/minerva/api/"
+      
+      ### Get configuration of the COVID-19 Disease Map, to obtain the latest (default) version
+      cfg <- fromJSON(ask_GET(map, "configuration/"))
+      project_id <- cfg$options[cfg$options$type == "DEFAULT_MAP","value"]
+      
+      
+      ### The address of the latest (default) build 
+      mnv_base <- paste0(map,"projects/",project_id,"/")
+      
+      message(paste0("Asking for diagrams in: ", mnv_base, "models/"))
+      
+      ### Get diagrams
+      models <- ask_GET(mnv_base, "models/")
+      models <- fromJSON(models, flatten = F)
+      
+      ### Read the list of resources to be integrated, from the MINERVA build scripts
+      res <- read.csv(url("https://git-r3lab.uni.lu/covid/models/raw/master/Integration/MINERVA_build/resources.csv"),
+                      header = T, stringsAsFactors = F)
+      
+      
+#### 3. RETRIEVE TTRANSALTED SIF FILES WITH DETAILED INFORMATION OF THE NODES AND INTERACTIONS OF EACH GRAPH USING MINERVA #####
+      
+  ### The obtained translated_sif_files counts with: X-Y coords info, genesList in entrez Identifier and type of 
+  ###  node ( simple, complex or protein family). The info will be retrieved and stored as a data.frame for each diagram.                                                    
+      
+      translated_sif_files <- lapply(raw_sif_list[-c(6)],
+                                     function(x){extract_translatedSIF_Minerva(x)}) 
+      
+      
+#### 4. FORMAT TRANSALTED SIF FILES OBTAINED FOR HIPATHIA METAGRAPHINFO DATABASE ##### 
+      
+      
+      att_sif_Hformat <- mapply(hipathia.att.sif, minerva_translated_sif = translated_sif_files, diagram_name = diagrams[-6], 
+                                outputfolder = "~/Desktop/models-master/Resources/Hipathia/sif_att_converter/test")
+      
+      
\ No newline at end of file

Resources/Hipathia/sif_att_converter/functions_retrieve_sif_att_hipathia_from_CellDesigner.R

+##########################################################################################
+###############   FUNCTIONS CREATED TO RETRIEVE, EDIT AND EXPORT CaSQ      ###############
+###############   Simple Interaction Files (SIF) FROM CellDesigner TO      ###############
+###############   HiPathia "ATT" and "SIF" FORMAT USING Minerva AS PROXY   ###############
+##########################################################################################
+
+
+if (!require(pacman)) {
+  install.packages("pacman")
+}
+
+if (!require(BiocManager)) {
+  install.packages("BiocManager")
+}
+
+if (!requireNamespace("AnnotationDbi", quietly = TRUE)){
+  BiocManager::install("AnnotationDbi")
+}
+  
+if (!requireNamespace("hipathia", quietly = TRUE)){
+  BiocManager::install("hipathia", version = "3.10")
+}
+
+if (!requireNamespace("SummarizedExperiment", quietly = TRUE)){
+  BiocManager::install("SummarizedExperiment", version = "3.10")
+}
+
+if (!requireNamespace("org.Hs.eg.db", quietly = TRUE)){
+  BiocManager::install("org.Hs.eg.db", version = "3.10")
+}
+
+
+pacman::p_load("here","igraph","rentrez","reutils","hipathia", "biomaRt", "utils", "stringr", "SummarizedExperiment", "magrittr",
+               "AnnotationDbi","org.Hs.eg.db","dplyr","tidyr", "openxlsx", "data.table", "gdata", "httr", "jsonlite")
+
+
+##################################################
+## Project: COVID-19 Disease Map
+## Script purpose: Translate raw CellDesigner SIF obtained from CaSQ to Entrez identifiers using MINERVA 
+## Date: 11.06.2020
+## Author: Marek Ostaszewski
+##################################################
+
+## A convenience function to handle API queries
+ask_GET <- function(furl, fask) {
+  print(URLencode(paste0(furl, fask)))
+  resp <- httr::GET(url = URLencode(paste0(furl, fask)), write_memory(),
+                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"),
+                    ### Currently ignoring SSL!
+                    httr::set_config(config(ssl_verifypeer = 0L)))
+  if(httr::status_code(resp) == 200) {
+    ### when the content is sent as a zip file, it needs to be handled differently,
+    ### i.e. saved to a tmp file and unzipped
+    if(headers(resp)$`content-type` == "application/zip") {
+      tmp <- tempfile()
+      tmpc <- file(tmp, "wb")
+      writeBin(httr::content(resp, as = "raw"), con = tmpc)
+      close(tmpc)
+      unzipped <- unzip(tmp)
+      file.remove(tmp)
+      return(unzipped)
+    }
+    return(httr::content(resp, as = "text"))
+  }
+  return(NULL)
+}
+
+### An utility function to retrieve Entrez based on the species id
+### if the id is a complex, the function goes recursively and fetches the ids of elements in this complex
+group_elements <- function(feid, felements, fentrez) {
+  pos <- which(felements$elementId == feid)
+  ### Any elements that may be nested in the 'feid' (CellDesigner alias)
+  incs <- felements$elementId[felements$complexId %in% felements$id[pos]]
+  if(length(incs) > 0) {
+    ### If nested elements found, run the function recursively for the contained elements
+    return(paste(unlist(sapply(incs, group_elements, felements, fentrez)), collapse = ";"))
+  } else {
+    ### If no nested elements, return Entrez
+    rid <- fentrez[[feid]]
+    if(is.na(rid)) {
+      ### If Entrez not available, return name
+      rid <- felements$name[pos]
+    }
+    return(rid)
+  }
+}
+
+### A workaround function to get information about hypothetical complexes; 
+### currently MINERVA API does not support this, we need to get the entire CD file and parse it
+get_groups <- function(fname) {
+  message(paste0("Getting groups for ", fname, "..."))
+  library(xml2)
+  ## Currently comment out the MINERVA download, some content dlded as binary!
+  cd_map <- read_xml(ask_GET(mnv_base,
+                             paste0("models/",
+                                    models$idObject[models$name == fname],
+                                    ":downloadModel?handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser")))
+  ### CellDesigner namespace
+  ns_cd <- xml_ns_rename(xml_ns(read_xml("<root>
+                                            <sbml xmlns = \"http://www.sbml.org/sbml/level2/version4\"/>
+                                            <cd xmlns = \"http://www.sbml.org/2001/ns/celldesigner\"/>
+                                          </root>")), 
+                         d1 = "sbml", d2 = "cd")
+  ### Get complex ids
+  cids <- xml_attr(xml_find_all(cd_map, "//cd:complexSpeciesAlias", ns_cd), "species")
+  ### For each check, which is hypothetical
+  hypocs <- sapply(cids, 
+                   function(x) {
+                     tcid <- xml_find_first(cd_map, paste0("//sbml:species[@id='", x, "']"), ns_cd)
+                     ifelse(length(tcid) > 0, xml_text(xml_find_first(tcid, ".//cd:hypothetical", ns_cd)), NA)
+                   })
+  names(hypocs) <- gsub("s_id_", "",names(hypocs))
+  return(hypocs)
+}
+
+### A convenience function that makes use of the previous ones to retrieve the translated SIF file from CellDesigner
+### and CaSQ using Minerva. The function allows to apply the operation to all the diagrams listed in "sif_raw_gitLab" 
+#' @param sif_raw_gitLab list of raw sif files obtained from CaSQ.
+
+extract_translatedSIF_Minerva <- function(sif_raw_gitLab, 
+                                          base_url = "https://git-r3lab.uni.lu/covid/models/-/raw/master/Executable%20Modules/SBML_qual_build/sif/"){
+  
+  message(paste0("Translating..", sif_raw_gitLab))
+  
+  ### Read in the raw SIF version (here straight from the gitLab Covid19)
+  
+  raw_sif <- read.table(url(paste0(base_url, sif_raw_gitLab)),
+                        sep = " ", header = F, stringsAsFactors = F)
+  
+  diagram <- gsub(pattern = "_raw.sif", ".xml", sif_raw_gitLab)
+  
+  
+  diag_name <- res[str_detect(res$Resource, diagram), "Name"]
+  
+  ### Get elements of the chosen diagram
+  model_elements <- fromJSON(ask_GET(paste0(mnv_base,"models/",models$idObject[models$name == diag_name],"/"), 
+                                     "bioEntities/elements/?columns=id,name,type,references,elementId,complexId,bounds"),
+                             flatten = F)
+  
+  message("Fetching entrez ids...")
+  
+  
+  ### Get information about Entrez identifiers from MINERVA elements
+  entrez <- sapply(model_elements$references, function(x) ifelse(length(x) == 0, NA, x[x$type == "ENTREZ", "resource"]))
+  names(entrez) <- model_elements$elementId
+  
+  cgroups <- get_groups(diag_name)
+  
+  message("Translating...")
+  
+  
+  ### Create a copy
+  translated_sif <- raw_sif
+  
+  
+  ### Retrieve Entrez and type for the entire columns of sources and targets
+  s.entrez <- sapply(raw_sif[,1], group_elements, model_elements, entrez)
+  s.type <- sapply(raw_sif[,1], function(x) { ifelse(x %in% names(cgroups),
+                                                     ifelse(is.na(cgroups[x]), "complex", "group"),
+                                                     "node") })
+  t.entrez <- sapply(raw_sif[,3], group_elements, model_elements, entrez)
+  t.type <- sapply(raw_sif[,3], function(x) { ifelse(x %in% names(cgroups),
+                                                     ifelse(is.na(cgroups[x]), "complex", "group"),
+                                                     "node") })
+  ### Collect x.y information
+  s.xy <- t(sapply(raw_sif[,1], function(x) unlist(model_elements$bounds[model_elements$elementId == x, c(3,4)])))
+  colnames(s.xy) <- c("source.x", "source.y")
+  t.xy <- t(sapply(raw_sif[,3], function(x) unlist(model_elements[model_elements$elementId == x,1][,c(3,4)])))
+  colnames(t.xy) <- c("targets.x", "targets.y")
+  
+  ### Combine into a single data frame
+  translated_sif <- data.frame(source = s.entrez, source.type = s.type,
+                               sign = raw_sif[,2], 
+                               target = t.entrez, target.type = t.type,
+                               s.xy, t.xy, stringsAsFactors = F)
+  
+  ## In case export is desired
+  # write.table(translated_sif, file = paste0(diag_name,"_translated_sif.txt"),
+  #             sep = "\t", quote = F, col.names = T, row.names = F)
+  
+  return(translated_sif)
+  message("Done.")  
+  
+}
+
+
+#################################################
+## Project: COVID-19 Disease Map
+## Script purpose: Translate Entrez identifiers SIF  files from MINERVA to HIPATHIA SIF and ATT files for metagraphinfo compilation.
+## Date: 21.10.2020 
+## Author: Marina Esteban Medina
+##################################################
+
+
+###################################################################################################
+### Function to pass translatedSIF_Minerva sif files information to Hipathia att and sif files ####
+#' @param minerva_translated_sif the sif file from CaSQ with entrez identifiers from MINERVA
+#' @param diagram_name name of the diagram we are adding
+#' @param outputfolder the output file path, it will return the sif an att file in Hipathia format
+#' @param exceptions file of the nodes exceptions, such as viral genes with entrez ID, that Hipathia does not processes
+########################################################################################################################
+
+hipathia.att.sif <- function (minerva_translated_sif, diagram_name, outputfolder, 
+                              exceptions = file.path(paste0(base_dir, "/Resources/Hipathia/sif_att_converter/resources/exceptions.txt"))) {
+  
+  message(paste0("Working on...", diagram_name))
+
+  exceptions_2avoid <- read.table(exceptions, stringsAsFactors = F) %>% mutate_all(as.character) %>% .$V1
+    
+  ## Clean auto interaction of nodes
+  minerva_translated_sif <- mutate_all(minerva_translated_sif, as.character)
+  minerva_translated_sif <- minerva_translated_sif[!minerva_translated_sif$source == minerva_translated_sif$target, ]
+  
+  ## Clean nodes that are not genes with and entrez ID nor a Function node.
+  ## We clean the source and target columns to avoid non gene-gene interactions.
+  minerva_translated_sif  <- minerva_translated_sif[which(!grepl("[a-z];[0-9]+|[A-Z];[0-9]+|[0-9]+;[a-z]|[0-9]+;[A-Z]|[A-Z]+[a-z]+[0-9]+[[:punct:]];[0-9]+|Unfolded protein", minerva_translated_sif$source)),] %>% 
+    .[which(!grepl("[a-z];[0-9]+|[A-Z];[0-9]+|[0-9]+;[a-z]|[0-9]+;[A-Z]|[A-Z]+[a-z]+[0-9]+[[:punct:]];[0-9]+|Unfolded protein", .$target)),] 
+  
+  ## Replace space with "_" in the diagrams name
+  
+  diagram_name <- gsub(" ", "_", diagram_name)
+  
+  ## Start bulding the att data frame, cols = ID, LABEL, X, Y, COLOR, SHAPE, TYPE, LABEL.CEX, LABEL.COLOR, WIDTH, HEIGHT, genesList
+  nodes <- unique(c(minerva_translated_sif$source, minerva_translated_sif$target))
+  
+  ## Create a table with the type of nodes, complex or protein family
+  
+  nodes_gene_type <- data.frame(nodes = c(minerva_translated_sif$source, minerva_translated_sif$target),
+                                type = c(minerva_translated_sif$source.type, minerva_translated_sif$target.type))%>% 
+    .[!duplicated(.$nodes),] %>% mutate_all(as.character)
+  
+  
+  
+  id_num <- seq_along(nodes)
+  
+  ## Create empty vectors for the columns of the att data.frame that we will then export to ".att" file of each diagram
+  ID = sapply(id_num, function(x) {paste("N", paste0("hsaCovid19", diagram_name ), x , sep = "-")})
+  
+  sif <- data.frame(ID, nodes)
+  
+  label <- c()
+  shape <- c()
+  type <- c()
+  genesList <- c()
+  
+  for (i in seq_along(nodes)){
+    
+    ## In the case of human gene nodes with entrez identifiers
+    if (grepl ("[A-Z]|[a-z]", nodes[i]) == F && nodes[i] != "8673700" && !(nodes[i] %in% exceptions_2avoid) ){ ## those are new entrez ID of SARS-CoV2 which we want to avoid
+      
+      message(paste0("Translating...", nodes[i]))
+      
+      label[i] <- str_split(nodes[i], pattern = ";")  %>% sapply ( . , function(x) { 
+        mapIds(org.Hs.eg.db, keys = x, column = "SYMBOL", keytype = "ENTREZID")
+      }) %>% paste(., collapse = ";")
+      
+      shape[i] <- "ellipse"
+      
+      type[i] <- "gene"
+      
+      genesList[i] <- nodes[i]
+      
+      if(nodes_gene_type$type[nodes_gene_type$nodes %in% nodes[i]] == "complex"){
+        genesList[i] <- gsub( ";", ",/,", nodes [i]) ##  substitute group sign (;) by what Hipathia takes as complex sign (,/,)
+      }
+      
+      ## In the case of function nodes 
+      
+    }else if(grepl ("^[A-Z]+[aeiou]+[[:punct:]]*|^[a-z]+[aeiou]+[[:punct:]]*", nodes[i]) == T){ 
+      
+      label[i] <- nodes[i]
+      
+      shape[i] <- "rectangle" ## Hipathia symbol for "function" element in the graph
+      
+      type[i] <- "node"
+      
+      genesList[i] <- "NA"
+      
+      ID[i] <- paste0(ID[i],"_func")
+      
+      
+      
+    }else{
+      
+      message(paste0("Translating...", nodes[i]))
+      
+      ## We only use this if we want to keep the non gene nodes visually  
+      label[i] <- nodes[i]
+      
+      shape[i] <- "circle"
+      
+      type[i] <- "other"
+      
+      genesList[i] <- "NA"
+    }
+  }
+  
+  
+  
+  X <- c()
+  
+  Y <- c()
+  
+  for (i in seq_along(nodes)){
+    
+    if(nodes[i] %in% minerva_translated_sif$source){
+      
+      X[i] <- minerva_translated_sif$source.x[match(nodes[i], minerva_translated_sif$source)] 
+      
+      Y[i] <- minerva_translated_sif$source.y[match(nodes[i], minerva_translated_sif$source)] 
+      
+    }else{
+      
+      X[i] <- minerva_translated_sif$targets.x[match(nodes[i], minerva_translated_sif$target)] 
+      
+      Y[i] <- minerva_translated_sif$targets.y[match(nodes[i], minerva_translated_sif$target)] 
+      
+    }
+    
+  }
+  
+  if(length(id_num) == 0 ){
+    
+    message(paste0("No human genes founded in ", diagram_name, "...DELETED "))
+    
+  }else{
+    
+    ## Color, label.cex, label.color, width and height are constant for all the nodes
+    att_hipathia = data.frame ( ID, label, X, Y, color = "white", shape, type, label.cex = "0.62", label.color = "black", 
+                                width = "46", height = "17", genesList )
+    
+    
+    ## Edit the .sif file in Hipathia format, subsitute interactions for "activation" or "inhibition".
+    
+    interaction = gsub("POSITIVE", "activation", minerva_translated_sif$sign) %>% gsub("NEGATIVE", "inhibition", .)
+    
+    sif_hipathia <- data.frame(source = sif$ID [match(minerva_translated_sif$source, sif$nodes)], interaction,
+                               target = sif$ID [match(minerva_translated_sif$target, sif$nodes)])
+    
+    sif_hipathia <- sif_hipathia[sif_hipathia$source %in% att_hipathia$ID, ]
+    
+    ## Create the "name.pathways_hsa.txt" file. This file serves as list of the pathways included in the metaginfo (metagraph-database) Hipathia takes as pathways database.
+    
+    name.pathways_hsa_file <- data.frame(code = paste0("Covid19", diagram_name), name = diagram_name)
+    
+    
+    ## Export the "att", "sif" and  "name.pathways_hsa.txt"  to the output folder selected
+    
+    write.table(att_hipathia, file = paste(outputfolder, paste0(paste0("hsaCovid19", diagram_name ) ,".att"), sep = "/"), sep = "\t", quote = F, col.names = T, row.names = F )
+    
+    write.table(sif_hipathia, file = paste(outputfolder, paste0(paste0("hsaCovid19", diagram_name ) ,".sif"), sep = "/"), sep = "\t", quote = F, col.names = F, row.names = F )
+    
+    write.table(name.pathways_hsa_file, file = paste(outputfolder, "name.pathways_hsa.txt", sep = "/"),append = T, sep = "\t", col.names = F, row.names = F, quote = F )
+    
+    message(paste0(diagram_name, "... Done"))
+    
+    ## The function also returns the  "sif and "att" data.frames created in a list for downstream actions.
+    
+    return(list("att" = att_hipathia, "sif" = sif_hipathia))
+    
+    
+  }
+  
+  
+}
+

Resources/Hipathia/sif_att_converter/resources/exceptions.txt

+8673700
+43740575
+443740570
+43740570
+43740571
+4348

Resources/Hipathia/sif_att_converter/test/hsaCovid19Apoptosis.att

+ID	label	X	Y	color	shape	type	label.cex	label.color	width	height	genesList
+N-hsaCovid19Apoptosis-1	FAS;FASLG	360	79.75	white	ellipse	gene	0.62	black	46	17	355,/,356
+N-hsaCovid19Apoptosis-2	BCL2L11;BBC3;BAD	1149	615	white	ellipse	gene	0.62	black	46	17	10018,/,27113,/,572
+N-hsaCovid19Apoptosis-3	BCL2;MCL1;BCL2L1	1013	470.5	white	ellipse	gene	0.62	black	46	17	596,/,4170,/,598
+N-hsaCovid19Apoptosis-4	CYCS;APAF1;CASP9	486	693	white	ellipse	gene	0.62	black	46	17	54205,/,317,/,842
+N-hsaCovid19Apoptosis-5	CYCS	998	743	white	ellipse	gene	0.62	black	46	17	54205
+N-hsaCovid19Apoptosis-6	APAF1	975	682	white	ellipse	gene	0.62	black	46	17	317
+N-hsaCovid19Apoptosis-7	CASP9	880	683	white	ellipse	gene	0.62	black	46	17	842
+N-hsaCovid19Apoptosis-8	AKT1	775	595	white	ellipse	gene	0.62	black	46	17	207
+N-hsaCovid19Apoptosis-9	TNFRSF1A;TNF	710	83	white	ellipse	gene	0.62	black	46	17	7132,/,7124
+N-hsaCovid19Apoptosis-10	TRADD;FADD	822.125	234.375	white	ellipse	gene	0.62	black	46	17	8717,/,8772
+N-hsaCovid19Apoptosis-11	FADD	532	273	white	ellipse	gene	0.62	black	46	17	8772
+N-hsaCovid19Apoptosis-12	TRADD	649.125	226.375	white	ellipse	gene	0.62	black	46	17	8717
+N-hsaCovid19Apoptosis-13	Orf7a	904	358.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Apoptosis-14	E	904	409.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Apoptosis-15	BAD	904	464	white	ellipse	gene	0.62	black	46	17	572
+N-hsaCovid19Apoptosis-16	CASP8	321.125	421.375	white	ellipse	gene	0.62	black	46	17	841
+N-hsaCovid19Apoptosis-17	CASP3	321.125	631.375	white	ellipse	gene	0.62	black	46	17	836
+N-hsaCovid19Apoptosis-18	BID	809.125	409.5	white	ellipse	gene	0.62	black	46	17	637
+N-hsaCovid19Apoptosis-19	MAPK14	896.125	820.375	white	ellipse	gene	0.62	black	46	17	1432
+N-hsaCovid19Apoptosis-20	M	672	661.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Apoptosis-21	CASP7	367.125	751.375	white	ellipse	gene	0.62	black	46	17	840
+N-hsaCovid19Apoptosis-22	Orf3b	250	895	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Apoptosis-23	Orf8a	250	940	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Apoptosis-24	N	250	985	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Apoptosis-25	S	250	805	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Apoptosis-26	Orf9b	250	1030	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Apoptosis-27	Orf6	250	850	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Apoptosis-28	Orf3a	784	878.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Apoptosis-29	BAX	1140	958.75	white	ellipse	gene	0.62	black	46	17	581
+N-hsaCovid19Apoptosis-30	Apoptosis	600	1014.5	white	circle	other	0.62	black	46	17	NA

Resources/Hipathia/sif_att_converter/test/hsaCovid19Apoptosis.sif

+N-hsaCovid19Apoptosis-1	activation	N-hsaCovid19Apoptosis-11
+N-hsaCovid19Apoptosis-2	activation	N-hsaCovid19Apoptosis-29
+N-hsaCovid19Apoptosis-3	activation	N-hsaCovid19Apoptosis-2
+N-hsaCovid19Apoptosis-3	inhibition	N-hsaCovid19Apoptosis-29
+N-hsaCovid19Apoptosis-4	activation	N-hsaCovid19Apoptosis-7
+N-hsaCovid19Apoptosis-5	activation	N-hsaCovid19Apoptosis-4
+N-hsaCovid19Apoptosis-6	activation	N-hsaCovid19Apoptosis-4
+N-hsaCovid19Apoptosis-7	activation	N-hsaCovid19Apoptosis-4
+N-hsaCovid19Apoptosis-8	inhibition	N-hsaCovid19Apoptosis-4
+N-hsaCovid19Apoptosis-8	inhibition	N-hsaCovid19Apoptosis-7
+N-hsaCovid19Apoptosis-8	inhibition	N-hsaCovid19Apoptosis-15
+N-hsaCovid19Apoptosis-9	activation	N-hsaCovid19Apoptosis-10
+N-hsaCovid19Apoptosis-10	activation	N-hsaCovid19Apoptosis-16
+N-hsaCovid19Apoptosis-11	activation	N-hsaCovid19Apoptosis-10
+N-hsaCovid19Apoptosis-11	activation	N-hsaCovid19Apoptosis-16
+N-hsaCovid19Apoptosis-12	activation	N-hsaCovid19Apoptosis-10
+N-hsaCovid19Apoptosis-13	activation	N-hsaCovid19Apoptosis-3
+N-hsaCovid19Apoptosis-14	activation	N-hsaCovid19Apoptosis-3
+N-hsaCovid19Apoptosis-15	inhibition	N-hsaCovid19Apoptosis-3
+N-hsaCovid19Apoptosis-16	activation	N-hsaCovid19Apoptosis-17
+N-hsaCovid19Apoptosis-16	activation	N-hsaCovid19Apoptosis-18
+N-hsaCovid19Apoptosis-16	activation	N-hsaCovid19Apoptosis-21
+N-hsaCovid19Apoptosis-17	activation	N-hsaCovid19Apoptosis-30
+N-hsaCovid19Apoptosis-7	activation	N-hsaCovid19Apoptosis-17
+N-hsaCovid19Apoptosis-7	activation	N-hsaCovid19Apoptosis-21
+N-hsaCovid19Apoptosis-18	activation	N-hsaCovid19Apoptosis-29
+N-hsaCovid19Apoptosis-19	activation	N-hsaCovid19Apoptosis-5
+N-hsaCovid19Apoptosis-20	inhibition	N-hsaCovid19Apoptosis-8
+N-hsaCovid19Apoptosis-21	activation	N-hsaCovid19Apoptosis-30
+N-hsaCovid19Apoptosis-22	activation	N-hsaCovid19Apoptosis-30
+N-hsaCovid19Apoptosis-23	activation	N-hsaCovid19Apoptosis-30
+N-hsaCovid19Apoptosis-24	activation	N-hsaCovid19Apoptosis-30
+N-hsaCovid19Apoptosis-25	activation	N-hsaCovid19Apoptosis-30
+N-hsaCovid19Apoptosis-26	activation	N-hsaCovid19Apoptosis-30
+N-hsaCovid19Apoptosis-27	activation	N-hsaCovid19Apoptosis-30
+N-hsaCovid19Apoptosis-28	activation	N-hsaCovid19Apoptosis-19

Resources/Hipathia/sif_att_converter/test/hsaCovid19Coagulation-pathway.att

+ID	label	X	Y	color	shape	type	label.cex	label.color	width	height	genesList
+N-hsaCovid19Coagulation-pathway-1	KLKB1;KNG1	119.3	921.455882352941	white	ellipse	gene	0.62	black	46	17	3818,/,3827
+N-hsaCovid19Coagulation-pathway-2	KLKB1	256	1148	white	ellipse	gene	0.62	black	46	17	3818
+N-hsaCovid19Coagulation-pathway-3	KNG1	118	1109	white	ellipse	gene	0.62	black	46	17	3827
+N-hsaCovid19Coagulation-pathway-4	F10;F5	435	1871.97058823529	white	ellipse	gene	0.62	black	46	17	2159,/,2153
+N-hsaCovid19Coagulation-pathway-5	F10	190	1789	white	ellipse	gene	0.62	black	46	17	2159
+N-hsaCovid19Coagulation-pathway-6	F9	241	1491	white	ellipse	gene	0.62	black	46	17	2158
+N-hsaCovid19Coagulation-pathway-7	SERPINC1	571	1997	white	ellipse	gene	0.62	black	46	17	462
+N-hsaCovid19Coagulation-pathway-8	F3	575	1677	white	ellipse	gene	0.62	black	46	17	2152
+N-hsaCovid19Coagulation-pathway-9	F2;THBD	756	2241	white	ellipse	gene	0.62	black	46	17	2147,/,7056
+N-hsaCovid19Coagulation-pathway-10	PROC	430	1628	white	ellipse	gene	0.62	black	46	17	5624
+N-hsaCovid19Coagulation-pathway-11	F8	430	1491	white	ellipse	gene	0.62	black	46	17	2157
+N-hsaCovid19Coagulation-pathway-12	SERPINE1	1049	2461	white	ellipse	gene	0.62	black	46	17	5054
+N-hsaCovid19Coagulation-pathway-13	PLAT	1084	2589	white	ellipse	gene	0.62	black	46	17	5327
+N-hsaCovid19Coagulation-pathway-14	SARS-CoV-2 infection	1610	2008.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-15	FGA;FGB;FGG	1826.25	2095	white	ellipse	gene	0.62	black	46	17	2243,/,2244,/,2266
+N-hsaCovid19Coagulation-pathway-16	F2	691	2085	white	ellipse	gene	0.62	black	46	17	2147
+N-hsaCovid19Coagulation-pathway-17	THBD	906	2926	white	ellipse	gene	0.62	black	46	17	7056
+N-hsaCovid19Coagulation-pathway-18	C3;C3;CFB	2066	1083.75	white	ellipse	gene	0.62	black	46	17	718,/,718,/,629
+N-hsaCovid19Coagulation-pathway-19	C3	1898	1188	white	ellipse	gene	0.62	black	46	17	718
+N-hsaCovid19Coagulation-pathway-20	C3;CFB	1888	1050.5	white	ellipse	gene	0.62	black	46	17	718,/,629
+N-hsaCovid19Coagulation-pathway-21	C7;C8A;C8G;C8B;C6;C5;C9	2741	679	white	ellipse	gene	0.62	black	46	17	730,/,731,/,733,/,732,/,729,/,727,/,735
+N-hsaCovid19Coagulation-pathway-22	C5	1713	1437	white	ellipse	gene	0.62	black	46	17	727
+N-hsaCovid19Coagulation-pathway-23	C4B;C2	1537	1328	white	ellipse	gene	0.62	black	46	17	721,/,717
+N-hsaCovid19Coagulation-pathway-24	C4B	1405	1190	white	ellipse	gene	0.62	black	46	17	721
+N-hsaCovid19Coagulation-pathway-25	C2	1545	1160	white	ellipse	gene	0.62	black	46	17	717
+N-hsaCovid19Coagulation-pathway-26	S	1167.5	527.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-27	PLG	555	2422	white	ellipse	gene	0.62	black	46	17	5340
+N-hsaCovid19Coagulation-pathway-28	SERPINF2	420	2535	white	ellipse	gene	0.62	black	46	17	5345
+N-hsaCovid19Coagulation-pathway-29	FGA;FGB;FGG;GP6	2172.5	2399.5	white	ellipse	gene	0.62	black	46	17	2243,/,2244,/,2266,/,51206
+N-hsaCovid19Coagulation-pathway-30	GP6	2070	2415	white	ellipse	gene	0.62	black	46	17	51206
+N-hsaCovid19Coagulation-pathway-31	GP6;VWF;ITGA2;ITGB1	1748.4375	2545.125	white	ellipse	gene	0.62	black	46	17	51206,/,7450,/,3673,/,3688
+N-hsaCovid19Coagulation-pathway-32	ITGA2;ITGB1;GP6	1805	2367.5	white	ellipse	gene	0.62	black	46	17	3673,/,3688,/,51206
+N-hsaCovid19Coagulation-pathway-33	VWF	1220	2249	white	ellipse	gene	0.62	black	46	17	7450
+N-hsaCovid19Coagulation-pathway-34	ITGA2;ITGB1	1945.5	2336.25	white	ellipse	gene	0.62	black	46	17	3673,/,3688
+N-hsaCovid19Coagulation-pathway-35	F12	425	1167	white	ellipse	gene	0.62	black	46	17	2161
+N-hsaCovid19Coagulation-pathway-36	F11	300	1312	white	ellipse	gene	0.62	black	46	17	2160
+N-hsaCovid19Coagulation-pathway-37	RPS3AP29	241	1392	white	ellipse	gene	0.62	black	46	17	730861
+N-hsaCovid19Coagulation-pathway-38_func	Heparin	632	2042.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-39_func	angiotensin II	945.25	1292.75	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-40_func	angiotensin I	943.25	1044.75	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-41	ACE	598	891	white	ellipse	gene	0.62	black	46	17	1636
+N-hsaCovid19Coagulation-pathway-42	AGT	934	567	white	ellipse	gene	0.62	black	46	17	183
+N-hsaCovid19Coagulation-pathway-43	REN	819	567	white	ellipse	gene	0.62	black	46	17	5972
+N-hsaCovid19Coagulation-pathway-44_func	aldosterone	707.4	1207.6	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-45_func	Fibrin polymer	1405	2155	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-46	SERPINH1	630	2372	white	ellipse	gene	0.62	black	46	17	871
+N-hsaCovid19Coagulation-pathway-47	PLAU	830	2638	white	ellipse	gene	0.62	black	46	17	5328
+N-hsaCovid19Coagulation-pathway-48	Bradykinin	390	950	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-49_func	angiotensin I-7	1210.5	1286.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-50	IL6	1477	1786.5625	white	ellipse	gene	0.62	black	46	17	3569
+N-hsaCovid19Coagulation-pathway-51	AGTR1	617.5	820	white	ellipse	gene	0.62	black	46	17	185
+N-hsaCovid19Coagulation-pathway-52	TNF	1430	1882.41666666667	white	ellipse	gene	0.62	black	46	17	7124
+N-hsaCovid19Coagulation-pathway-53_func	cytokine storm	1783	1918.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-54	IL1B	1487	1728.70833333333	white	ellipse	gene	0.62	black	46	17	3553
+N-hsaCovid19Coagulation-pathway-55	CRP	1278	1679	white	ellipse	gene	0.62	black	46	17	1401
+N-hsaCovid19Coagulation-pathway-56	IL2RA	1507	1613	white	ellipse	gene	0.62	black	46	17	3559
+N-hsaCovid19Coagulation-pathway-57	CXCL8	1497	1670.85416666667	white	ellipse	gene	0.62	black	46	17	3576
+N-hsaCovid19Coagulation-pathway-58	MASP1	1664	1030	white	ellipse	gene	0.62	black	46	17	5648
+N-hsaCovid19Coagulation-pathway-59	MASP2	1765	950	white	ellipse	gene	0.62	black	46	17	10747
+N-hsaCovid19Coagulation-pathway-60	C4	1465	1025	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-61	CFD	1354	1082	white	ellipse	gene	0.62	black	46	17	1675
+N-hsaCovid19Coagulation-pathway-62	C4d deposition	1437.85714285714	595.928571428571	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-63	C5b-9 deposition	2877.85714285714	561.928571428571	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-64	ACE2	1074	820	white	ellipse	gene	0.62	black	46	17	59272
+N-hsaCovid19Coagulation-pathway-65_func	Fibrin monomer	1573	2156	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-66	F13a	1535	2095	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-67_func	platelet activation	2050	2619.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-68	MAS1	2732	2581	white	ellipse	gene	0.62	black	46	17	4142
+N-hsaCovid19Coagulation-pathway-69	K+	776.5	1279.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-70	ACTH	825	1185.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-71	NR3C2	350.5	636	white	ellipse	gene	0.62	black	46	17	4306
+N-hsaCovid19Coagulation-pathway-72	Hypokalemia	593	1154	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-73	Small peptide	315	1245	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-74	F8;F9	318	1574	white	ellipse	gene	0.62	black	46	17	2157,/,2158
+N-hsaCovid19Coagulation-pathway-75	SERPINC1;F2	274	2158.5	white	ellipse	gene	0.62	black	46	17	462,/,2147
+N-hsaCovid19Coagulation-pathway-76	SERPINE1;PLAT	1271	2473	white	ellipse	gene	0.62	black	46	17	5054,/,5327
+N-hsaCovid19Coagulation-pathway-77	D-dimer	1238	2156	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-78	SERPINF2;PLG	280	2433	white	ellipse	gene	0.62	black	46	17	5345,/,5340
+N-hsaCovid19Coagulation-pathway-79	Thrombosis	1067.5	1752.25	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-80	Bradykinin(1-5)	590	950	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-81	C4A	1545	1115	white	ellipse	gene	0.62	black	46	17	720
+N-hsaCovid19Coagulation-pathway-82	MASP2 deposition	1590	599.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-83_func	septal capillary necrosis	1437.85714285714	500.928571428571	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-84_func	apoptosis	2967.85714285714	476.928571428571	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-85_func	platelet aggregation	2787.85714285714	476.928571428571	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-86_func	thrombus formation	2295	2618.75	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-87_func	vascular remodeling	197	750	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19Coagulation-pathway-88_func	vascular inflammation	170.5	695	white	rectangle	node	0.62	black	46	17	NA

Resources/Hipathia/sif_att_converter/test/hsaCovid19Coagulation-pathway.sif

+N-hsaCovid19Coagulation-pathway-1	activation	N-hsaCovid19Coagulation-pathway-3
+N-hsaCovid19Coagulation-pathway-1	activation	N-hsaCovid19Coagulation-pathway-2
+N-hsaCovid19Coagulation-pathway-1	activation	N-hsaCovid19Coagulation-pathway-48
+N-hsaCovid19Coagulation-pathway-2	activation	N-hsaCovid19Coagulation-pathway-1
+N-hsaCovid19Coagulation-pathway-2	activation	N-hsaCovid19Coagulation-pathway-35
+N-hsaCovid19Coagulation-pathway-2	activation	N-hsaCovid19Coagulation-pathway-73
+N-hsaCovid19Coagulation-pathway-2	activation	N-hsaCovid19Coagulation-pathway-27
+N-hsaCovid19Coagulation-pathway-3	activation	N-hsaCovid19Coagulation-pathway-1
+N-hsaCovid19Coagulation-pathway-4	activation	N-hsaCovid19Coagulation-pathway-16
+N-hsaCovid19Coagulation-pathway-5	activation	N-hsaCovid19Coagulation-pathway-4
+N-hsaCovid19Coagulation-pathway-5	activation	N-hsaCovid19Coagulation-pathway-73
+N-hsaCovid19Coagulation-pathway-6	activation	N-hsaCovid19Coagulation-pathway-4
+N-hsaCovid19Coagulation-pathway-6	activation	N-hsaCovid19Coagulation-pathway-74
+N-hsaCovid19Coagulation-pathway-6	activation	N-hsaCovid19Coagulation-pathway-73
+N-hsaCovid19Coagulation-pathway-7	inhibition	N-hsaCovid19Coagulation-pathway-4
+N-hsaCovid19Coagulation-pathway-7	activation	N-hsaCovid19Coagulation-pathway-75
+N-hsaCovid19Coagulation-pathway-7	inhibition	N-hsaCovid19Coagulation-pathway-73
+N-hsaCovid19Coagulation-pathway-7	inhibition	N-hsaCovid19Coagulation-pathway-16
+N-hsaCovid19Coagulation-pathway-8	activation	N-hsaCovid19Coagulation-pathway-4
+N-hsaCovid19Coagulation-pathway-9	inhibition	N-hsaCovid19Coagulation-pathway-4
+N-hsaCovid19Coagulation-pathway-9	inhibition	N-hsaCovid19Coagulation-pathway-65
+N-hsaCovid19Coagulation-pathway-10	inhibition	N-hsaCovid19Coagulation-pathway-4
+N-hsaCovid19Coagulation-pathway-10	inhibition	N-hsaCovid19Coagulation-pathway-11
+N-hsaCovid19Coagulation-pathway-10	inhibition	N-hsaCovid19Coagulation-pathway-73
+N-hsaCovid19Coagulation-pathway-10	inhibition	N-hsaCovid19Coagulation-pathway-13
+N-hsaCovid19Coagulation-pathway-11	activation	N-hsaCovid19Coagulation-pathway-74
+N-hsaCovid19Coagulation-pathway-12	activation	N-hsaCovid19Coagulation-pathway-76
+N-hsaCovid19Coagulation-pathway-12	inhibition	N-hsaCovid19Coagulation-pathway-13
+N-hsaCovid19Coagulation-pathway-12	inhibition	N-hsaCovid19Coagulation-pathway-47
+N-hsaCovid19Coagulation-pathway-13	activation	N-hsaCovid19Coagulation-pathway-76
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-76
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-15
+N-hsaCovid19Coagulation-pathway-14	inhibition	N-hsaCovid19Coagulation-pathway-7
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-77
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-17
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-65
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-33
+N-hsaCovid19Coagulation-pathway-15	activation	N-hsaCovid19Coagulation-pathway-29
+N-hsaCovid19Coagulation-pathway-15	activation	N-hsaCovid19Coagulation-pathway-65
+N-hsaCovid19Coagulation-pathway-16	activation	N-hsaCovid19Coagulation-pathway-75
+N-hsaCovid19Coagulation-pathway-16	activation	N-hsaCovid19Coagulation-pathway-9
+N-hsaCovid19Coagulation-pathway-16	activation	N-hsaCovid19Coagulation-pathway-36
+N-hsaCovid19Coagulation-pathway-16	activation	N-hsaCovid19Coagulation-pathway-36
+N-hsaCovid19Coagulation-pathway-16	activation	N-hsaCovid19Coagulation-pathway-11
+N-hsaCovid19Coagulation-pathway-16	activation	N-hsaCovid19Coagulation-pathway-73
+N-hsaCovid19Coagulation-pathway-16	activation	N-hsaCovid19Coagulation-pathway-46
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-75
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-78
+N-hsaCovid19Coagulation-pathway-17	activation	N-hsaCovid19Coagulation-pathway-9
+N-hsaCovid19Coagulation-pathway-18	activation	N-hsaCovid19Coagulation-pathway-21
+N-hsaCovid19Coagulation-pathway-18	activation	N-hsaCovid19Coagulation-pathway-22
+N-hsaCovid19Coagulation-pathway-19	activation	N-hsaCovid19Coagulation-pathway-18
+N-hsaCovid19Coagulation-pathway-20	activation	N-hsaCovid19Coagulation-pathway-18
+N-hsaCovid19Coagulation-pathway-20	activation	N-hsaCovid19Coagulation-pathway-19
+N-hsaCovid19Coagulation-pathway-20	activation	N-hsaCovid19Coagulation-pathway-19
+N-hsaCovid19Coagulation-pathway-21	activation	N-hsaCovid19Coagulation-pathway-27
+N-hsaCovid19Coagulation-pathway-21	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-21	activation	N-hsaCovid19Coagulation-pathway-63
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-21
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-11
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-10
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-52
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-50
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-54
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-22
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-57
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-56
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-55
+N-hsaCovid19Coagulation-pathway-22	activation	N-hsaCovid19Coagulation-pathway-21
+N-hsaCovid19Coagulation-pathway-23	activation	N-hsaCovid19Coagulation-pathway-21
+N-hsaCovid19Coagulation-pathway-23	activation	N-hsaCovid19Coagulation-pathway-22
+N-hsaCovid19Coagulation-pathway-23	activation	N-hsaCovid19Coagulation-pathway-19
+N-hsaCovid19Coagulation-pathway-23	activation	N-hsaCovid19Coagulation-pathway-19
+N-hsaCovid19Coagulation-pathway-24	activation	N-hsaCovid19Coagulation-pathway-23
+N-hsaCovid19Coagulation-pathway-25	activation	N-hsaCovid19Coagulation-pathway-23
+N-hsaCovid19Coagulation-pathway-26	activation	N-hsaCovid19Coagulation-pathway-24
+N-hsaCovid19Coagulation-pathway-27	activation	N-hsaCovid19Coagulation-pathway-78
+N-hsaCovid19Coagulation-pathway-27	activation	N-hsaCovid19Coagulation-pathway-77
+N-hsaCovid19Coagulation-pathway-28	activation	N-hsaCovid19Coagulation-pathway-78
+N-hsaCovid19Coagulation-pathway-29	activation	N-hsaCovid19Coagulation-pathway-67
+N-hsaCovid19Coagulation-pathway-30	activation	N-hsaCovid19Coagulation-pathway-29
+N-hsaCovid19Coagulation-pathway-30	activation	N-hsaCovid19Coagulation-pathway-32
+N-hsaCovid19Coagulation-pathway-31	activation	N-hsaCovid19Coagulation-pathway-67
+N-hsaCovid19Coagulation-pathway-32	activation	N-hsaCovid19Coagulation-pathway-31
+N-hsaCovid19Coagulation-pathway-33	activation	N-hsaCovid19Coagulation-pathway-31
+N-hsaCovid19Coagulation-pathway-33	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-34	activation	N-hsaCovid19Coagulation-pathway-32
+N-hsaCovid19Coagulation-pathway-35	activation	N-hsaCovid19Coagulation-pathway-36
+N-hsaCovid19Coagulation-pathway-35	activation	N-hsaCovid19Coagulation-pathway-36
+N-hsaCovid19Coagulation-pathway-35	activation	N-hsaCovid19Coagulation-pathway-2
+N-hsaCovid19Coagulation-pathway-35	activation	N-hsaCovid19Coagulation-pathway-73
+N-hsaCovid19Coagulation-pathway-36	activation	N-hsaCovid19Coagulation-pathway-6
+N-hsaCovid19Coagulation-pathway-36	activation	N-hsaCovid19Coagulation-pathway-27
+N-hsaCovid19Coagulation-pathway-37	activation	N-hsaCovid19Coagulation-pathway-6
+N-hsaCovid19Coagulation-pathway-11	activation	N-hsaCovid19Coagulation-pathway-73
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-39
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-24
+N-hsaCovid19Coagulation-pathway-14	inhibition	N-hsaCovid19Coagulation-pathway-64
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-59
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-44
+N-hsaCovid19Coagulation-pathway-14	activation	N-hsaCovid19Coagulation-pathway-72
+N-hsaCovid19Coagulation-pathway-41	activation	N-hsaCovid19Coagulation-pathway-39
+N-hsaCovid19Coagulation-pathway-41	activation	N-hsaCovid19Coagulation-pathway-73
+N-hsaCovid19Coagulation-pathway-41	activation	N-hsaCovid19Coagulation-pathway-80
+N-hsaCovid19Coagulation-pathway-42	activation	N-hsaCovid19Coagulation-pathway-40
+N-hsaCovid19Coagulation-pathway-43	activation	N-hsaCovid19Coagulation-pathway-40
+N-hsaCovid19Coagulation-pathway-2	activation	N-hsaCovid19Coagulation-pathway-43
+N-hsaCovid19Coagulation-pathway-46	activation	N-hsaCovid19Coagulation-pathway-77
+N-hsaCovid19Coagulation-pathway-13	activation	N-hsaCovid19Coagulation-pathway-27
+N-hsaCovid19Coagulation-pathway-47	activation	N-hsaCovid19Coagulation-pathway-27
+N-hsaCovid19Coagulation-pathway-48	activation	N-hsaCovid19Coagulation-pathway-13
+N-hsaCovid19Coagulation-pathway-48	activation	N-hsaCovid19Coagulation-pathway-73
+N-hsaCovid19Coagulation-pathway-48	activation	N-hsaCovid19Coagulation-pathway-80
+N-hsaCovid19Coagulation-pathway-50	activation	N-hsaCovid19Coagulation-pathway-12
+N-hsaCovid19Coagulation-pathway-50	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-51	activation	N-hsaCovid19Coagulation-pathway-12
+N-hsaCovid19Coagulation-pathway-51	activation	N-hsaCovid19Coagulation-pathway-44
+N-hsaCovid19Coagulation-pathway-51	activation	N-hsaCovid19Coagulation-pathway-71
+N-hsaCovid19Coagulation-pathway-51	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-52	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-54	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-27	activation	N-hsaCovid19Coagulation-pathway-22
+N-hsaCovid19Coagulation-pathway-24	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-24	activation	N-hsaCovid19Coagulation-pathway-62
+N-hsaCovid19Coagulation-pathway-55	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-56	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-57	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-58	activation	N-hsaCovid19Coagulation-pathway-25
+N-hsaCovid19Coagulation-pathway-58	activation	N-hsaCovid19Coagulation-pathway-25
+N-hsaCovid19Coagulation-pathway-59	activation	N-hsaCovid19Coagulation-pathway-58
+N-hsaCovid19Coagulation-pathway-60	activation	N-hsaCovid19Coagulation-pathway-81
+N-hsaCovid19Coagulation-pathway-60	activation	N-hsaCovid19Coagulation-pathway-24
+N-hsaCovid19Coagulation-pathway-59	activation	N-hsaCovid19Coagulation-pathway-81
+N-hsaCovid19Coagulation-pathway-59	activation	N-hsaCovid19Coagulation-pathway-24
+N-hsaCovid19Coagulation-pathway-59	activation	N-hsaCovid19Coagulation-pathway-82
+N-hsaCovid19Coagulation-pathway-61	activation	N-hsaCovid19Coagulation-pathway-24
+N-hsaCovid19Coagulation-pathway-62	activation	N-hsaCovid19Coagulation-pathway-83
+N-hsaCovid19Coagulation-pathway-63	activation	N-hsaCovid19Coagulation-pathway-84
+N-hsaCovid19Coagulation-pathway-63	activation	N-hsaCovid19Coagulation-pathway-85
+N-hsaCovid19Coagulation-pathway-64	activation	N-hsaCovid19Coagulation-pathway-49
+N-hsaCovid19Coagulation-pathway-16	activation	N-hsaCovid19Coagulation-pathway-65
+N-hsaCovid19Coagulation-pathway-66	activation	N-hsaCovid19Coagulation-pathway-45
+N-hsaCovid19Coagulation-pathway-51	activation	N-hsaCovid19Coagulation-pathway-86
+N-hsaCovid19Coagulation-pathway-68	activation	N-hsaCovid19Coagulation-pathway-86
+N-hsaCovid19Coagulation-pathway-69	activation	N-hsaCovid19Coagulation-pathway-44
+N-hsaCovid19Coagulation-pathway-70	activation	N-hsaCovid19Coagulation-pathway-44
+N-hsaCovid19Coagulation-pathway-71	activation	N-hsaCovid19Coagulation-pathway-79
+N-hsaCovid19Coagulation-pathway-72	inhibition	N-hsaCovid19Coagulation-pathway-69

Resources/Hipathia/sif_att_converter/test/hsaCovid19ER_Stress.att

+ID	label	X	Y	color	shape	type	label.cex	label.color	width	height	genesList
+N-hsaCovid19ER_Stress-1_func	Persistant ER Stress	3803	1124.625	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-2	SIGMAR1;ITPR3	1668.5	1432	white	ellipse	gene	0.62	black	46	17	10280,/,3710
+N-hsaCovid19ER_Stress-3	SIGMAR1	2041	1447	white	ellipse	gene	0.62	black	46	17	10280
+N-hsaCovid19ER_Stress-4	ITPR3	1891	1447	white	ellipse	gene	0.62	black	46	17	3710
+N-hsaCovid19ER_Stress-5	ER stress	1243.25	1134.75	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-6_func	Ca2+ ER depletion	1795	1357.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-7	GDP	4000	705.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-8	MAP1LC3A;ATG5;FADD;CASP8	3996.25	1956.625	white	ellipse	gene	0.62	black	46	17	84557,/,9474,/,8772,/,841
+N-hsaCovid19ER_Stress-9	CASP8;FADD	3711.78571428571	1919.41071428571	white	ellipse	gene	0.62	black	46	17	841,/,8772
+N-hsaCovid19ER_Stress-10	SQSTM1	3970	1759.125	white	ellipse	gene	0.62	black	46	17	8878
+N-hsaCovid19ER_Stress-11	MAP1LC3A	3955	1809.125	white	ellipse	gene	0.62	black	46	17	84557
+N-hsaCovid19ER_Stress-12	ATG5	3950	1859.125	white	ellipse	gene	0.62	black	46	17	9474
+N-hsaCovid19ER_Stress-13	TRIM13	3895	2045	white	ellipse	gene	0.62	black	46	17	10206
+N-hsaCovid19ER_Stress-14	SIGMAR1;HSPA5	2176	1397	white	ellipse	gene	0.62	black	46	17	10280,/,3309
+N-hsaCovid19ER_Stress-15	HSPA5	2030	1185	white	ellipse	gene	0.62	black	46	17	3309
+N-hsaCovid19ER_Stress-16	VAPB;RMDN3	499	1451.875	white	ellipse	gene	0.62	black	46	17	9217,/,55177
+N-hsaCovid19ER_Stress-17	VAPB	710	1363.875	white	ellipse	gene	0.62	black	46	17	9217
+N-hsaCovid19ER_Stress-18	RMDN3	689.03125	1666.15625	white	ellipse	gene	0.62	black	46	17	55177
+N-hsaCovid19ER_Stress-19	GTP	3893	564.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-20	EIF2B3;EIF2B4;EIF2B1;EIF2B2;EIF2B5	4275	502.5	white	ellipse	gene	0.62	black	46	17	8891,/,8890,/,1967,/,8892,/,8893
+N-hsaCovid19ER_Stress-21	PACS2;ADAM17	501	330.375	white	ellipse	gene	0.62	black	46	17	23241,/,6868
+N-hsaCovid19ER_Stress-22	PACS2	292	381.375	white	ellipse	gene	0.62	black	46	17	23241
+N-hsaCovid19ER_Stress-23	ADAM17	273	448.375	white	ellipse	gene	0.62	black	46	17	6868
+N-hsaCovid19ER_Stress-24	FIS1;BCAP31	1000	1446.875	white	ellipse	gene	0.62	black	46	17	51024,/,10134
+N-hsaCovid19ER_Stress-25	BCAP31	1195	1365	white	ellipse	gene	0.62	black	46	17	10134
+N-hsaCovid19ER_Stress-26	FIS1	1198.03125	1661.15625	white	ellipse	gene	0.62	black	46	17	51024
+N-hsaCovid19ER_Stress-27	MFN2;MFN2	374.5	1449.53125	white	ellipse	gene	0.62	black	46	17	9927,/,9927
+N-hsaCovid19ER_Stress-28	MFN2	640	915	white	ellipse	gene	0.62	black	46	17	9927
+N-hsaCovid19ER_Stress-29	BBC3;ERN1	1588	909.5	white	ellipse	gene	0.62	black	46	17	27113,/,2081
+N-hsaCovid19ER_Stress-30	ERN1	1602	1066	white	ellipse	gene	0.62	black	46	17	2081
+N-hsaCovid19ER_Stress-31	BBC3	1717	1061	white	ellipse	gene	0.62	black	46	17	27113
+N-hsaCovid19ER_Stress-32	CEACAMP4;MFN2	189.5	1449.53125	white	ellipse	gene	0.62	black	46	17	1093,/,9927
+N-hsaCovid19ER_Stress-33	CEACAMP4	114.03125	1666.15625	white	ellipse	gene	0.62	black	46	17	1093
+N-hsaCovid19ER_Stress-34	SMDT1;MCU;MICU1;MICU2	1782.390625	2146.765625	white	ellipse	gene	0.62	black	46	17	91689,/,90550,/,10367,/,221154
+N-hsaCovid19ER_Stress-35	MCU	1549.96875	2162.53125	white	ellipse	gene	0.62	black	46	17	90550
+N-hsaCovid19ER_Stress-36	SMDT1	1649.96875	2202.53125	white	ellipse	gene	0.62	black	46	17	91689
+N-hsaCovid19ER_Stress-37	MICU2	2025.53125	2251.40625	white	ellipse	gene	0.62	black	46	17	221154
+N-hsaCovid19ER_Stress-38	MICU1	2140.53125	2226.40625	white	ellipse	gene	0.62	black	46	17	10367
+N-hsaCovid19ER_Stress-39	BCL2L11;ERN1	1363	924.5	white	ellipse	gene	0.62	black	46	17	10018,/,2081
+N-hsaCovid19ER_Stress-40	BCL2L11	1477	1061	white	ellipse	gene	0.62	black	46	17	10018
+N-hsaCovid19ER_Stress-41_func	Ca2+	3073.75	868.75	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-42	EIF2AK3	4105	1315	white	ellipse	gene	0.62	black	46	17	9451
+N-hsaCovid19ER_Stress-43	MICU1;SMDT1;MCU;SMDT1;MICU2;MICU2;MCUB;MICU1	1733.53125	1811.71875	white	ellipse	gene	0.62	black	46	17	10367,/,91689,/,90550,/,91689,/,221154,/,221154,/,55013,/,10367
+N-hsaCovid19ER_Stress-44	ACE2	755	215	white	ellipse	gene	0.62	black	46	17	59272
+N-hsaCovid19ER_Stress-45	S	340	117	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-46	ATF4	1675	776	white	ellipse	gene	0.62	black	46	17	468
+N-hsaCovid19ER_Stress-47	DDIT3	1445	711	white	ellipse	gene	0.62	black	46	17	1649
+N-hsaCovid19ER_Stress-48_func	release of ER Ca2+	3596	813.375	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-49	BAX	3155	1889.125	white	ellipse	gene	0.62	black	46	17	581
+N-hsaCovid19ER_Stress-50	ATF6	4265	1380	white	ellipse	gene	0.62	black	46	17	22926
+N-hsaCovid19ER_Stress-51	ER Stress	3843	1056.875	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-52_func	retrograde transport from ER to cytosol	4116	1163.625	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-53	MAPK14	2760	2004.125	white	ellipse	gene	0.62	black	46	17	1432
+N-hsaCovid19ER_Stress-54	HSPA5;ATF6	4527	1328.125	white	ellipse	gene	0.62	black	46	17	3309,/,22926
+N-hsaCovid19ER_Stress-55	TMBIM6	2959.09375	941.125	white	ellipse	gene	0.62	black	46	17	7009
+N-hsaCovid19ER_Stress-56	ERO1A	3293.77777777778	1019.23611111111	white	ellipse	gene	0.62	black	46	17	30001
+N-hsaCovid19ER_Stress-57	XBP1	3970	2199.125	white	ellipse	gene	0.62	black	46	17	7494
+N-hsaCovid19ER_Stress-58_func	accumulation of misfolded protein in ER	3759	970.625	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-59_func	mitochondrial fission	1253.53125	1724.90625	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-60	TRAF2	2600	1874.125	white	ellipse	gene	0.62	black	46	17	7186
+N-hsaCovid19ER_Stress-61	PPP2CA	3220	2189.125	white	ellipse	gene	0.62	black	46	17	5515
+N-hsaCovid19ER_Stress-62	ITPR3;VDAC1;HSPA9	1338.5	1446.875	white	ellipse	gene	0.62	black	46	17	3710,/,7416,/,3313
+N-hsaCovid19ER_Stress-63	PPP1R15A	2235	716	white	ellipse	gene	0.62	black	46	17	23645
+N-hsaCovid19ER_Stress-64	EIF2AK1	3390	540	white	ellipse	gene	0.62	black	46	17	27102
+N-hsaCovid19ER_Stress-65	CASP9	2507	872	white	ellipse	gene	0.62	black	46	17	842
+N-hsaCovid19ER_Stress-66	CASP4	2629	820	white	ellipse	gene	0.62	black	46	17	837
+N-hsaCovid19ER_Stress-67_func	mitochondrion-endoplasmic reticulum membrane tethering 	415	1187.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-68	ERAD	3868	864.125	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-69	MAP3K5	2683.5	1949.125	white	ellipse	gene	0.62	black	46	17	4217
+N-hsaCovid19ER_Stress-70_func	Cell survival	3576.5	1926.125	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-71	Apoptosis	3530	2069.125	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-72	EIF2AK2	3240	375	white	ellipse	gene	0.62	black	46	17	5610
+N-hsaCovid19ER_Stress-73_func	presence of dsRNA	3180	327.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-74	DNAJC3	3090	320	white	ellipse	gene	0.62	black	46	17	5611
+N-hsaCovid19ER_Stress-75	MAPK8	2955	2084.125	white	ellipse	gene	0.62	black	46	17	5599
+N-hsaCovid19ER_Stress-76	MAP3K4	2725	2184.125	white	ellipse	gene	0.62	black	46	17	4216
+N-hsaCovid19ER_Stress-77	BID	3150	1950	white	ellipse	gene	0.62	black	46	17	637
+N-hsaCovid19ER_Stress-78	MBTPS2	4471.75	2033.125	white	ellipse	gene	0.62	black	46	17	51360
+N-hsaCovid19ER_Stress-79	CDK5	2653	2109.125	white	ellipse	gene	0.62	black	46	17	1020
+N-hsaCovid19ER_Stress-80	CASP3	2477	751	white	ellipse	gene	0.62	black	46	17	836
+N-hsaCovid19ER_Stress-81	RYR1	3365.09375	941.125	white	ellipse	gene	0.62	black	46	17	6261
+N-hsaCovid19ER_Stress-82	MBTPS1	4469.25	1933.125	white	ellipse	gene	0.62	black	46	17	8720
+N-hsaCovid19ER_Stress-83	TRIB3	3595	2160	white	ellipse	gene	0.62	black	46	17	57761
+N-hsaCovid19ER_Stress-84_func	viral entry into host cell	137	339	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-85	SARS-CoV infection	145	61	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-86_func	autophagy	820	1322.1875	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-87_func	unfolded protein response (UPR)	816.5	1076.75	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-88_func	endoplasmic reticulum calcium ion homeostasis	1100	1188.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-89_func	Ca2+ mitochondrial concentration	885.46875	2006.21875	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-90_func	Ca2+ cytosolic concentration	734.75	1596.375	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-91_func	mitochondrial outer membrane depolarization	1078.96875	1904.03125	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-92_func	endoplasmic reticulum organization	207	968.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-93_func	high Ca2+ cytosolic concentration	3327.5	769.875	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-94	UPR	3840	2174.125	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-95	EIF2S1	3210	490	white	ellipse	gene	0.62	black	46	17	1965
+N-hsaCovid19ER_Stress-96_func	mitochondrial calcium ion transmembrane transport	1395.96875	2075.28125	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-97_func	pulmonary fibrosis	893	134	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-98_func	viral RNA genome replication	1001	264	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-99_func	protein ubiquitination and destruction	4106	878.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-100	JUN	3090	2174.125	white	ellipse	gene	0.62	black	46	17	3725
+N-hsaCovid19ER_Stress-101	BCL2	1312	567.5	white	ellipse	gene	0.62	black	46	17	596
+N-hsaCovid19ER_Stress-102_func	mitochondria fragmentation	1241.03125	1794.90625	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ER_Stress-103	HYOU1	2082	567.5	white	ellipse	gene	0.62	black	46	17	10525
+N-hsaCovid19ER_Stress-104_func	hyperoxidation	1917	1033.5	white	rectangle	node	0.62	black	46	17	NA

Resources/Hipathia/sif_att_converter/test/hsaCovid19ER_Stress.sif

+N-hsaCovid19ER_Stress-2	activation	N-hsaCovid19ER_Stress-41
+N-hsaCovid19ER_Stress-3	activation	N-hsaCovid19ER_Stress-2
+N-hsaCovid19ER_Stress-3	inhibition	N-hsaCovid19ER_Stress-5
+N-hsaCovid19ER_Stress-3	inhibition	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-4	activation	N-hsaCovid19ER_Stress-2
+N-hsaCovid19ER_Stress-4	inhibition	N-hsaCovid19ER_Stress-86
+N-hsaCovid19ER_Stress-5	activation	N-hsaCovid19ER_Stress-2
+N-hsaCovid19ER_Stress-5	activation	N-hsaCovid19ER_Stress-15
+N-hsaCovid19ER_Stress-5	activation	N-hsaCovid19ER_Stress-3
+N-hsaCovid19ER_Stress-5	activation	N-hsaCovid19ER_Stress-87
+N-hsaCovid19ER_Stress-5	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-5	activation	N-hsaCovid19ER_Stress-28
+N-hsaCovid19ER_Stress-7	activation	N-hsaCovid19ER_Stress-19
+N-hsaCovid19ER_Stress-8	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-9	activation	N-hsaCovid19ER_Stress-8
+N-hsaCovid19ER_Stress-10	activation	N-hsaCovid19ER_Stress-8
+N-hsaCovid19ER_Stress-11	activation	N-hsaCovid19ER_Stress-8
+N-hsaCovid19ER_Stress-12	activation	N-hsaCovid19ER_Stress-8
+N-hsaCovid19ER_Stress-13	activation	N-hsaCovid19ER_Stress-8
+N-hsaCovid19ER_Stress-14	activation	N-hsaCovid19ER_Stress-15
+N-hsaCovid19ER_Stress-14	activation	N-hsaCovid19ER_Stress-3
+N-hsaCovid19ER_Stress-15	activation	N-hsaCovid19ER_Stress-14
+N-hsaCovid19ER_Stress-15	activation	N-hsaCovid19ER_Stress-88
+N-hsaCovid19ER_Stress-3	activation	N-hsaCovid19ER_Stress-14
+N-hsaCovid19ER_Stress-16	activation	N-hsaCovid19ER_Stress-67
+N-hsaCovid19ER_Stress-17	activation	N-hsaCovid19ER_Stress-16
+N-hsaCovid19ER_Stress-17	activation	N-hsaCovid19ER_Stress-89
+N-hsaCovid19ER_Stress-17	inhibition	N-hsaCovid19ER_Stress-86
+N-hsaCovid19ER_Stress-17	inhibition	N-hsaCovid19ER_Stress-90
+N-hsaCovid19ER_Stress-18	activation	N-hsaCovid19ER_Stress-16
+N-hsaCovid19ER_Stress-18	activation	N-hsaCovid19ER_Stress-89
+N-hsaCovid19ER_Stress-18	inhibition	N-hsaCovid19ER_Stress-86
+N-hsaCovid19ER_Stress-18	inhibition	N-hsaCovid19ER_Stress-90
+N-hsaCovid19ER_Stress-19	activation	N-hsaCovid19ER_Stress-7
+N-hsaCovid19ER_Stress-20	activation	N-hsaCovid19ER_Stress-7
+N-hsaCovid19ER_Stress-21	activation	N-hsaCovid19ER_Stress-23
+N-hsaCovid19ER_Stress-22	activation	N-hsaCovid19ER_Stress-21
+N-hsaCovid19ER_Stress-23	activation	N-hsaCovid19ER_Stress-21
+N-hsaCovid19ER_Stress-24	activation	N-hsaCovid19ER_Stress-67
+N-hsaCovid19ER_Stress-25	activation	N-hsaCovid19ER_Stress-24
+N-hsaCovid19ER_Stress-26	activation	N-hsaCovid19ER_Stress-24
+N-hsaCovid19ER_Stress-26	activation	N-hsaCovid19ER_Stress-89
+N-hsaCovid19ER_Stress-26	activation	N-hsaCovid19ER_Stress-91
+N-hsaCovid19ER_Stress-27	activation	N-hsaCovid19ER_Stress-67
+N-hsaCovid19ER_Stress-28	activation	N-hsaCovid19ER_Stress-27
+N-hsaCovid19ER_Stress-28	activation	N-hsaCovid19ER_Stress-32
+N-hsaCovid19ER_Stress-28	activation	N-hsaCovid19ER_Stress-92
+N-hsaCovid19ER_Stress-28	activation	N-hsaCovid19ER_Stress-87
+N-hsaCovid19ER_Stress-28	activation	N-hsaCovid19ER_Stress-5
+N-hsaCovid19ER_Stress-28	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-28	activation	N-hsaCovid19ER_Stress-88
+N-hsaCovid19ER_Stress-28	activation	N-hsaCovid19ER_Stress-27
+N-hsaCovid19ER_Stress-29	activation	N-hsaCovid19ER_Stress-57
+N-hsaCovid19ER_Stress-30	activation	N-hsaCovid19ER_Stress-29
+N-hsaCovid19ER_Stress-30	activation	N-hsaCovid19ER_Stress-39
+N-hsaCovid19ER_Stress-31	activation	N-hsaCovid19ER_Stress-29
+N-hsaCovid19ER_Stress-32	activation	N-hsaCovid19ER_Stress-67
+N-hsaCovid19ER_Stress-33	activation	N-hsaCovid19ER_Stress-32
+N-hsaCovid19ER_Stress-34	activation	N-hsaCovid19ER_Stress-43
+N-hsaCovid19ER_Stress-35	activation	N-hsaCovid19ER_Stress-34
+N-hsaCovid19ER_Stress-36	activation	N-hsaCovid19ER_Stress-34
+N-hsaCovid19ER_Stress-37	activation	N-hsaCovid19ER_Stress-34
+N-hsaCovid19ER_Stress-38	activation	N-hsaCovid19ER_Stress-34
+N-hsaCovid19ER_Stress-39	activation	N-hsaCovid19ER_Stress-57
+N-hsaCovid19ER_Stress-40	activation	N-hsaCovid19ER_Stress-39
+N-hsaCovid19ER_Stress-42	activation	N-hsaCovid19ER_Stress-94
+N-hsaCovid19ER_Stress-42	activation	N-hsaCovid19ER_Stress-52
+N-hsaCovid19ER_Stress-42	activation	N-hsaCovid19ER_Stress-95
+N-hsaCovid19ER_Stress-43	activation	N-hsaCovid19ER_Stress-41
+N-hsaCovid19ER_Stress-43	activation	N-hsaCovid19ER_Stress-96
+N-hsaCovid19ER_Stress-44	inhibition	N-hsaCovid19ER_Stress-15
+N-hsaCovid19ER_Stress-44	inhibition	N-hsaCovid19ER_Stress-15
+N-hsaCovid19ER_Stress-44	inhibition	N-hsaCovid19ER_Stress-5
+N-hsaCovid19ER_Stress-44	inhibition	N-hsaCovid19ER_Stress-97
+N-hsaCovid19ER_Stress-44	activation	N-hsaCovid19ER_Stress-98
+N-hsaCovid19ER_Stress-45	activation	N-hsaCovid19ER_Stress-15
+N-hsaCovid19ER_Stress-44	inhibition	N-hsaCovid19ER_Stress-84
+N-hsaCovid19ER_Stress-46	activation	N-hsaCovid19ER_Stress-63
+N-hsaCovid19ER_Stress-46	activation	N-hsaCovid19ER_Stress-47
+N-hsaCovid19ER_Stress-47	activation	N-hsaCovid19ER_Stress-63
+N-hsaCovid19ER_Stress-47	activation	N-hsaCovid19ER_Stress-83
+N-hsaCovid19ER_Stress-47	activation	N-hsaCovid19ER_Stress-56
+N-hsaCovid19ER_Stress-49	activation	N-hsaCovid19ER_Stress-48
+N-hsaCovid19ER_Stress-49	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-50	activation	N-hsaCovid19ER_Stress-52
+N-hsaCovid19ER_Stress-51	activation	N-hsaCovid19ER_Stress-50
+N-hsaCovid19ER_Stress-51	activation	N-hsaCovid19ER_Stress-79
+N-hsaCovid19ER_Stress-51	activation	N-hsaCovid19ER_Stress-1
+N-hsaCovid19ER_Stress-47	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-47	activation	N-hsaCovid19ER_Stress-100
+N-hsaCovid19ER_Stress-53	activation	N-hsaCovid19ER_Stress-47
+N-hsaCovid19ER_Stress-53	activation	N-hsaCovid19ER_Stress-49
+N-hsaCovid19ER_Stress-53	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-54	activation	N-hsaCovid19ER_Stress-15
+N-hsaCovid19ER_Stress-54	activation	N-hsaCovid19ER_Stress-50
+N-hsaCovid19ER_Stress-4	activation	N-hsaCovid19ER_Stress-41
+N-hsaCovid19ER_Stress-55	activation	N-hsaCovid19ER_Stress-4
+N-hsaCovid19ER_Stress-55	activation	N-hsaCovid19ER_Stress-41
+N-hsaCovid19ER_Stress-56	activation	N-hsaCovid19ER_Stress-4
+N-hsaCovid19ER_Stress-47	inhibition	N-hsaCovid19ER_Stress-101
+N-hsaCovid19ER_Stress-53	activation	N-hsaCovid19ER_Stress-47
+N-hsaCovid19ER_Stress-57	activation	N-hsaCovid19ER_Stress-94
+N-hsaCovid19ER_Stress-50	activation	N-hsaCovid19ER_Stress-94
+N-hsaCovid19ER_Stress-22	inhibition	N-hsaCovid19ER_Stress-59
+N-hsaCovid19ER_Stress-22	activation	N-hsaCovid19ER_Stress-67
+N-hsaCovid19ER_Stress-22	inhibition	N-hsaCovid19ER_Stress-25
+N-hsaCovid19ER_Stress-60	activation	N-hsaCovid19ER_Stress-69
+N-hsaCovid19ER_Stress-50	activation	N-hsaCovid19ER_Stress-47
+N-hsaCovid19ER_Stress-50	activation	N-hsaCovid19ER_Stress-57
+N-hsaCovid19ER_Stress-50	activation	N-hsaCovid19ER_Stress-74
+N-hsaCovid19ER_Stress-50	activation	N-hsaCovid19ER_Stress-103
+N-hsaCovid19ER_Stress-50	activation	N-hsaCovid19ER_Stress-56
+N-hsaCovid19ER_Stress-57	activation	N-hsaCovid19ER_Stress-47
+N-hsaCovid19ER_Stress-40	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-61	activation	N-hsaCovid19ER_Stress-40
+N-hsaCovid19ER_Stress-62	activation	N-hsaCovid19ER_Stress-41
+N-hsaCovid19ER_Stress-63	activation	N-hsaCovid19ER_Stress-95
+N-hsaCovid19ER_Stress-64	activation	N-hsaCovid19ER_Stress-95
+N-hsaCovid19ER_Stress-65	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-66	activation	N-hsaCovid19ER_Stress-65
+N-hsaCovid19ER_Stress-66	activation	N-hsaCovid19ER_Stress-80
+N-hsaCovid19ER_Stress-56	activation	N-hsaCovid19ER_Stress-104
+N-hsaCovid19ER_Stress-68	activation	N-hsaCovid19ER_Stress-58
+N-hsaCovid19ER_Stress-69	activation	N-hsaCovid19ER_Stress-53
+N-hsaCovid19ER_Stress-69	activation	N-hsaCovid19ER_Stress-75
+N-hsaCovid19ER_Stress-71	activation	N-hsaCovid19ER_Stress-70
+N-hsaCovid19ER_Stress-25	activation	N-hsaCovid19ER_Stress-87
+N-hsaCovid19ER_Stress-72	activation	N-hsaCovid19ER_Stress-95
+N-hsaCovid19ER_Stress-74	inhibition	N-hsaCovid19ER_Stress-72
+N-hsaCovid19ER_Stress-75	activation	N-hsaCovid19ER_Stress-49
+N-hsaCovid19ER_Stress-75	activation	N-hsaCovid19ER_Stress-77
+N-hsaCovid19ER_Stress-75	activation	N-hsaCovid19ER_Stress-100
+N-hsaCovid19ER_Stress-75	activation	N-hsaCovid19ER_Stress-40
+N-hsaCovid19ER_Stress-76	activation	N-hsaCovid19ER_Stress-75
+N-hsaCovid19ER_Stress-77	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-78	activation	N-hsaCovid19ER_Stress-50
+N-hsaCovid19ER_Stress-79	activation	N-hsaCovid19ER_Stress-76
+N-hsaCovid19ER_Stress-74	inhibition	N-hsaCovid19ER_Stress-95
+N-hsaCovid19ER_Stress-80	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-81	activation	N-hsaCovid19ER_Stress-41
+N-hsaCovid19ER_Stress-71	activation	N-hsaCovid19ER_Stress-25
+N-hsaCovid19ER_Stress-82	activation	N-hsaCovid19ER_Stress-50
+N-hsaCovid19ER_Stress-23	activation	N-hsaCovid19ER_Stress-44
+N-hsaCovid19ER_Stress-23	activation	N-hsaCovid19ER_Stress-44
+N-hsaCovid19ER_Stress-57	activation	N-hsaCovid19ER_Stress-68
+N-hsaCovid19ER_Stress-83	activation	N-hsaCovid19ER_Stress-71
+N-hsaCovid19ER_Stress-85	activation	N-hsaCovid19ER_Stress-84

Resources/Hipathia/sif_att_converter/test/hsaCovid19ETC.att

+ID	label	X	Y	color	shape	type	label.cex	label.color	width	height	genesList
+N-hsaCovid19ETC-1	NADH	308.5	566.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-2	mt mRNA	2020	1212.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-3	TUFM;TSFM;GFM1;C12orf65;TWNK	2108.5	1433.5	white	ellipse	gene	0.62	black	46	17	7284;10102;85476;91574;56652
+N-hsaCovid19ETC-4	MRPL3;MRPS16;MRPS22	1905	1321.5	white	ellipse	gene	0.62	black	46	17	11222;51021;56945
+N-hsaCovid19ETC-5	MRPS5;MRPS27;MRPS2;MRPS25	1904	1440	white	ellipse	gene	0.62	black	46	17	64969;23107;51116;64432
+N-hsaCovid19ETC-6	ACAD9	1040	862	white	ellipse	gene	0.62	black	46	17	28976
+N-hsaCovid19ETC-7	ECSIT	1040	890	white	ellipse	gene	0.62	black	46	17	51295
+N-hsaCovid19ETC-8	NDUFAF7	1040	919	white	ellipse	gene	0.62	black	46	17	55471
+N-hsaCovid19ETC-9	Q	1112	209	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-10_func	paraquat;H+	218	1289	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-11_func	paraquat	204.5	1434.375	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-12	O_sub_2_endsub_	356.5	1432.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-13	mt DNA	1903.5	866	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-14	TRMT1	1860	1051	white	ellipse	gene	0.62	black	46	17	55621
+N-hsaCovid19ETC-15	Nsp8	1470	1400	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-16	NSP4	865	1731	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-17	TIMM9;TIMM10	730	1885	white	ellipse	gene	0.62	black	46	17	26520,/,26519
+N-hsaCovid19ETC-18	Cyt C	1661.5	191.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-19	H+	1620	240	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-20	QH_sub_2_endsub_	1604.5	198.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-21	ADP	2052.5	437.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-22_func	Pi	2082.5	478	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-23_func	superoxide	762	1017.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-24	H_sub_2_endsub_O_sub_2_endsub_	762	1252.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-25_func	hydroxide	462	1137.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-26	SOD1	920	1128	white	ellipse	gene	0.62	black	46	17	6647
+N-hsaCovid19ETC-27	SOD2	482	1330	white	ellipse	gene	0.62	black	46	17	6648
+N-hsaCovid19ETC-28	TXN2	952	1240	white	ellipse	gene	0.62	black	46	17	25828
+N-hsaCovid19ETC-29	PRDX1;PRDX2;PRDX5;PRDX6;PRDX3	855	1326	white	ellipse	gene	0.62	black	46	17	5052;7001;25824;9588;10935
+N-hsaCovid19ETC-30_func	glutathione	572	1342.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-31	GPX4	652	1407	white	ellipse	gene	0.62	black	46	17	2879
+N-hsaCovid19ETC-32	GPX1	652	1360	white	ellipse	gene	0.62	black	46	17	2876
+N-hsaCovid19ETC-33	CAT	705	1307.5	white	ellipse	gene	0.62	black	46	17	847
+N-hsaCovid19ETC-34	SIRT3	417	1395	white	ellipse	gene	0.62	black	46	17	23410
+N-hsaCovid19ETC-35_func	Fe2+	730	1213.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-36_func	Fe3+	844	997.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-37_func	glutathione disulfide	572	1597.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-38	NADPH	645	1533.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-39	GSR	480	1510	white	ellipse	gene	0.62	black	46	17	2936
+N-hsaCovid19ETC-40	TXNRD2	1032	1360	white	ellipse	gene	0.62	black	46	17	10587
+N-hsaCovid19ETC-41	TFAM	2015	940	white	ellipse	gene	0.62	black	46	17	7019
+N-hsaCovid19ETC-42	TFB1M;TFB2M;POLRMT	2065.5	1071	white	ellipse	gene	0.62	black	46	17	51106;64216;5442
+N-hsaCovid19ETC-43_func	damaged mt DNA	1903.5	681	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-44	mt DNA replication	1795	945.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-45	POLG1;11232;55149;123263	1609	903	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-46	DGUOK;TK2;RRM2B;SUCLA2;SUCLG1	1601.5	676.5	white	ellipse	gene	0.62	black	46	17	1716;7084;50484;8803;8802
+N-hsaCovid19ETC-47	mt DNA damage	1800	771	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-48	ERCC6;ERCC8;POLG	2069.5	715	white	ellipse	gene	0.62	black	46	17	2074;1161;5428
+N-hsaCovid19ETC-49	Orf9c	680	765	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-50	Nsp7	954	968	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-51	ORF9b	515	2095	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-52	NAD+	435.5	567	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-53	ND1;ND2;ND3;ND4L;ND6;ND5;ND4;COX3;COX2;COX1;ATP8;ATP6;CYTB	1922.75	1630.5	white	ellipse	gene	0.62	black	46	17	4535;4536;4537;4539;4541;4540;4538;4514;4513;4512;4509;4508;4519
+N-hsaCovid19ETC-54	BCS1L;HCCS;COX7A2;CHCHD7;CMC1;COA1;COA3;COA4;COA5;COA6;COA7;COA8;COX10;COX11;COX14;COX15;COX16;COX17;COX18;COX19;COX20;HIGD1A;HIGD2A;NDUFAF5;NDUFAF3;NDUFAF4;NDUFAF1;ECSIT;NDUFAF2;NUBPL;ACAD9;FOXRED1;DMAC2;COA1;COA7;DMAC1;NDUFAF6;NDUFAF7;NDUFAF8;NUBPL;FDXR;FDX2;LYRM7;SDHAF1;SDHAF2	1051.125	473.5	white	ellipse	gene	0.62	black	46	17	617;3052;1347;79145;152100;55744;28958;51287;493753;388753;65260;84334;1352;1353;84987;1355;51241;10063;285521;90639;116228;25994;192286;79133;25915;29078;51103;51295;91942;80224;28976;55572;55101;55744;65260;90871;137682;55471;284184;80224;2232;112812;90624;644096;54949
+N-hsaCovid19ETC-55	MTRNR1;4511;4556;4558;4564;4565;4566;4567;4568;4570;4571;4572;4573;4574;4575;4576;4577;4578	1647.5	1143	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-56_func	precursor protein N-terminus binding	629	1824	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19ETC-57	O_super_2-_endsuper_	1760	277	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-58	ATP	2169	437.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-59	ROS	367	1022.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-60	H_sub_2_endsub_O	762	1487.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-61	HO	601.5	1183.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-62	NADP(+)	645	1497.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19ETC-63	NDUFB9	320	675	white	ellipse	gene	0.62	black	46	17	4715
+N-hsaCovid19ETC-64	NDUFA1	320	705	white	ellipse	gene	0.62	black	46	17	4694

Resources/Hipathia/sif_att_converter/test/hsaCovid19ETC.sif

+N-hsaCovid19ETC-1	activation	N-hsaCovid19ETC-52
+N-hsaCovid19ETC-1	activation	N-hsaCovid19ETC-19
+N-hsaCovid19ETC-2	activation	N-hsaCovid19ETC-53
+N-hsaCovid19ETC-3	activation	N-hsaCovid19ETC-53
+N-hsaCovid19ETC-4	activation	N-hsaCovid19ETC-53
+N-hsaCovid19ETC-5	activation	N-hsaCovid19ETC-53
+N-hsaCovid19ETC-6	activation	N-hsaCovid19ETC-54
+N-hsaCovid19ETC-7	activation	N-hsaCovid19ETC-54
+N-hsaCovid19ETC-8	activation	N-hsaCovid19ETC-54
+N-hsaCovid19ETC-9	activation	N-hsaCovid19ETC-20
+N-hsaCovid19ETC-12	activation	N-hsaCovid19ETC-10
+N-hsaCovid19ETC-12	activation	N-hsaCovid19ETC-23
+N-hsaCovid19ETC-13	activation	N-hsaCovid19ETC-55
+N-hsaCovid19ETC-13	activation	N-hsaCovid19ETC-2
+N-hsaCovid19ETC-13	activation	N-hsaCovid19ETC-43
+N-hsaCovid19ETC-14	activation	N-hsaCovid19ETC-55
+N-hsaCovid19ETC-15	inhibition	N-hsaCovid19ETC-5
+N-hsaCovid19ETC-16	inhibition	N-hsaCovid19ETC-17
+N-hsaCovid19ETC-17	activation	N-hsaCovid19ETC-56
+N-hsaCovid19ETC-12	activation	N-hsaCovid19ETC-9
+N-hsaCovid19ETC-12	activation	N-hsaCovid19ETC-19
+N-hsaCovid19ETC-12	activation	N-hsaCovid19ETC-57
+N-hsaCovid19ETC-12	activation	N-hsaCovid19ETC-18
+N-hsaCovid19ETC-18	activation	N-hsaCovid19ETC-9
+N-hsaCovid19ETC-18	activation	N-hsaCovid19ETC-19
+N-hsaCovid19ETC-18	activation	N-hsaCovid19ETC-57
+N-hsaCovid19ETC-19	activation	N-hsaCovid19ETC-9
+N-hsaCovid19ETC-19	activation	N-hsaCovid19ETC-57
+N-hsaCovid19ETC-19	activation	N-hsaCovid19ETC-18
+N-hsaCovid19ETC-20	activation	N-hsaCovid19ETC-9
+N-hsaCovid19ETC-20	activation	N-hsaCovid19ETC-19
+N-hsaCovid19ETC-20	activation	N-hsaCovid19ETC-57
+N-hsaCovid19ETC-20	activation	N-hsaCovid19ETC-18
+N-hsaCovid19ETC-21	activation	N-hsaCovid19ETC-58
+N-hsaCovid19ETC-19	activation	N-hsaCovid19ETC-58
+N-hsaCovid19ETC-24	activation	N-hsaCovid19ETC-23
+N-hsaCovid19ETC-24	activation	N-hsaCovid19ETC-60
+N-hsaCovid19ETC-24	activation	N-hsaCovid19ETC-59
+N-hsaCovid19ETC-24	activation	N-hsaCovid19ETC-61
+N-hsaCovid19ETC-24	activation	N-hsaCovid19ETC-25
+N-hsaCovid19ETC-24	activation	N-hsaCovid19ETC-36
+N-hsaCovid19ETC-24	activation	N-hsaCovid19ETC-60
+N-hsaCovid19ETC-24	activation	N-hsaCovid19ETC-19
+N-hsaCovid19ETC-24	activation	N-hsaCovid19ETC-37
+N-hsaCovid19ETC-24	activation	N-hsaCovid19ETC-28
+N-hsaCovid19ETC-12	activation	N-hsaCovid19ETC-23
+N-hsaCovid19ETC-19	activation	N-hsaCovid19ETC-24
+N-hsaCovid19ETC-26	activation	N-hsaCovid19ETC-24
+N-hsaCovid19ETC-19	activation	N-hsaCovid19ETC-24
+N-hsaCovid19ETC-27	activation	N-hsaCovid19ETC-24
+N-hsaCovid19ETC-28	activation	N-hsaCovid19ETC-60
+N-hsaCovid19ETC-29	activation	N-hsaCovid19ETC-60
+N-hsaCovid19ETC-29	activation	N-hsaCovid19ETC-28
+N-hsaCovid19ETC-31	activation	N-hsaCovid19ETC-60
+N-hsaCovid19ETC-31	activation	N-hsaCovid19ETC-37
+N-hsaCovid19ETC-32	activation	N-hsaCovid19ETC-60
+N-hsaCovid19ETC-32	activation	N-hsaCovid19ETC-37
+N-hsaCovid19ETC-33	activation	N-hsaCovid19ETC-60
+N-hsaCovid19ETC-34	activation	N-hsaCovid19ETC-27
+N-hsaCovid19ETC-38	activation	N-hsaCovid19ETC-30
+N-hsaCovid19ETC-38	activation	N-hsaCovid19ETC-62
+N-hsaCovid19ETC-39	activation	N-hsaCovid19ETC-30
+N-hsaCovid19ETC-39	activation	N-hsaCovid19ETC-62
+N-hsaCovid19ETC-28	activation	N-hsaCovid19ETC-62
+N-hsaCovid19ETC-38	activation	N-hsaCovid19ETC-28
+N-hsaCovid19ETC-38	activation	N-hsaCovid19ETC-62
+N-hsaCovid19ETC-40	activation	N-hsaCovid19ETC-28
+N-hsaCovid19ETC-40	activation	N-hsaCovid19ETC-62
+N-hsaCovid19ETC-41	activation	N-hsaCovid19ETC-2
+N-hsaCovid19ETC-41	activation	N-hsaCovid19ETC-44
+N-hsaCovid19ETC-41	activation	N-hsaCovid19ETC-13
+N-hsaCovid19ETC-42	activation	N-hsaCovid19ETC-2
+N-hsaCovid19ETC-44	activation	N-hsaCovid19ETC-13
+N-hsaCovid19ETC-45	activation	N-hsaCovid19ETC-44
+N-hsaCovid19ETC-46	activation	N-hsaCovid19ETC-44
+N-hsaCovid19ETC-46	activation	N-hsaCovid19ETC-13
+N-hsaCovid19ETC-47	inhibition	N-hsaCovid19ETC-13
+N-hsaCovid19ETC-47	activation	N-hsaCovid19ETC-43
+N-hsaCovid19ETC-48	activation	N-hsaCovid19ETC-13
+N-hsaCovid19ETC-49	inhibition	N-hsaCovid19ETC-63
+N-hsaCovid19ETC-49	inhibition	N-hsaCovid19ETC-64
+N-hsaCovid19ETC-49	inhibition	N-hsaCovid19ETC-7
+N-hsaCovid19ETC-49	inhibition	N-hsaCovid19ETC-6
+N-hsaCovid19ETC-50	inhibition	N-hsaCovid19ETC-8
+N-hsaCovid19ETC-51	inhibition	N-hsaCovid19ETC-56

Resources/Hipathia/sif_att_converter/test/hsaCovid19E_protein.att

+ID	label	X	Y	color	shape	type	label.cex	label.color	width	height	genesList
+N-hsaCovid19E_protein-1	BRD4	1370.02597402597	234.142857142857	white	ellipse	gene	0.62	black	46	17	23476
+N-hsaCovid19E_protein-2	BRD2	1370.52597402597	717.142857142857	white	ellipse	gene	0.62	black	46	17	6046
+N-hsaCovid19E_protein-3	STOML3;ASIC1	2129.52597402597	1187.14285714286	white	ellipse	gene	0.62	black	46	17	161003,/,41
+N-hsaCovid19E_protein-4	ASIC1	1858.07142857143	1234.32467532468	white	ellipse	gene	0.62	black	46	17	41
+N-hsaCovid19E_protein-5	STOML3	1982.52597402597	1234.14285714286	white	ellipse	gene	0.62	black	46	17	161003
+N-hsaCovid19E_protein-6	E	2397.5	1077.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19E_protein-7	ATP1A;ATP1B;FXYDs	2915.5	1195	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19E_protein-8	E;PALS1	567.5	1032.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19E_protein-9	PALS1	280.071428571429	1234.96103896104	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19E_protein-10	CCNT1;CDK9	1799.47402597403	283.357142857143	white	ellipse	gene	0.62	black	46	17	904,/,1025
+N-hsaCovid19E_protein-11	CDK9	1450	300	white	ellipse	gene	0.62	black	46	17	1025
+N-hsaCovid19E_protein-12	CCNT1	1461	351	white	ellipse	gene	0.62	black	46	17	904
+N-hsaCovid19E_protein-13	JQ1	1235	667	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19E_protein-14	H+	1710.02597402597	1302.64285714286	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19E_protein-15	TBP	1590	775	white	ellipse	gene	0.62	black	46	17	6908
+N-hsaCovid19E_protein-16	Activity of sodium channels	2322.5	1432.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19E_protein-17	K+	3230	1110	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19E_protein-18_func	Na+	3113	1468	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19E_protein-19_func	Maintenance of tight junction	703.5	1399.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19E_protein-20	RNA Polymerase II-dependent Transcription 	1780	455	white	circle	other	0.62	black	46	17	NA

Resources/Hipathia/sif_att_converter/test/hsaCovid19E_protein.sif

+N-hsaCovid19E_protein-1	activation	N-hsaCovid19E_protein-10
+N-hsaCovid19E_protein-2	activation	N-hsaCovid19E_protein-15
+N-hsaCovid19E_protein-3	activation	N-hsaCovid19E_protein-16
+N-hsaCovid19E_protein-4	activation	N-hsaCovid19E_protein-3
+N-hsaCovid19E_protein-5	activation	N-hsaCovid19E_protein-3
+N-hsaCovid19E_protein-5	inhibition	N-hsaCovid19E_protein-16
+N-hsaCovid19E_protein-6	inhibition	N-hsaCovid19E_protein-3
+N-hsaCovid19E_protein-6	inhibition	N-hsaCovid19E_protein-7
+N-hsaCovid19E_protein-7	activation	N-hsaCovid19E_protein-17
+N-hsaCovid19E_protein-7	activation	N-hsaCovid19E_protein-18
+N-hsaCovid19E_protein-7	activation	N-hsaCovid19E_protein-16
+N-hsaCovid19E_protein-8	activation	N-hsaCovid19E_protein-19
+N-hsaCovid19E_protein-6	activation	N-hsaCovid19E_protein-8
+N-hsaCovid19E_protein-9	activation	N-hsaCovid19E_protein-8
+N-hsaCovid19E_protein-10	activation	N-hsaCovid19E_protein-20
+N-hsaCovid19E_protein-11	activation	N-hsaCovid19E_protein-10
+N-hsaCovid19E_protein-12	activation	N-hsaCovid19E_protein-10
+N-hsaCovid19E_protein-6	inhibition	N-hsaCovid19E_protein-1
+N-hsaCovid19E_protein-6	inhibition	N-hsaCovid19E_protein-2
+N-hsaCovid19E_protein-13	inhibition	N-hsaCovid19E_protein-2
+N-hsaCovid19E_protein-14	activation	N-hsaCovid19E_protein-4

Resources/Hipathia/sif_att_converter/test/hsaCovid19IFN-lambda.att

+ID	label	X	Y	color	shape	type	label.cex	label.color	width	height	genesList
+N-hsaCovid19IFN-lambda-1	STAT1;STAT2;IRF9	951	2408.25	white	ellipse	gene	0.62	black	46	17	6772,/,6773,/,10379
+N-hsaCovid19IFN-lambda-2	STAT1;STAT2	808	2007.25	white	ellipse	gene	0.62	black	46	17	6772,/,6773
+N-hsaCovid19IFN-lambda-3	IRF9	1063	2088	white	ellipse	gene	0.62	black	46	17	10379
+N-hsaCovid19IFN-lambda-4	STAT3	693	2098	white	ellipse	gene	0.62	black	46	17	6774
+N-hsaCovid19IFN-lambda-5_func	ribosomal 40S subunit	1807	2105	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-6_func	viral nsp1	1813	2298	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-7_func	ribosomal 40S subunit;ribosomal 60S subunit	1608	2196.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-8	STAT1	658	1892.25	white	ellipse	gene	0.62	black	46	17	6772
+N-hsaCovid19IFN-lambda-9	STAT2	1083	1892.25	white	ellipse	gene	0.62	black	46	17	6773
+N-hsaCovid19IFN-lambda-10	RIG-I;pexMAVS;dsRNA	1793	409	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-11	dsRNA	1948	356.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-12_func	ribosomal 60S subunit	1699.5	2062	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-13	M-protein, membrane-bound	203	274	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-14	RIG-I	343	346.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-15	IFN-III	662	1220	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-16	ISGs	1480.5	2306	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-17	IFN-sensitive-response-element	1285.5	2511	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-18_func	viral RNA+N-methyl-Guanine	1907.5	202.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-19_func	viral RNA	1741.5	203.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-20	nsp14	1835.5	124	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-21	nsp16	2003.5	120	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-22	dsRNA_vesicle	248	176.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-23	RNA	416	86.5	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-24	PLPro	623	224	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-25	IRF1	1693	1039	white	ellipse	gene	0.62	black	46	17	3659
+N-hsaCovid19IFN-lambda-26_func	Riplet / TRIM25	523	234	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-27	STAT1;STAT2;STAT3	678	2207.25	white	ellipse	gene	0.62	black	46	17	6772,/,6773,/,6774
+N-hsaCovid19IFN-lambda-28_func	ribosomal 40S subunit;viral nsp1	1932	2184	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-29_func	ribosomal 40S subunit;ribosomal 60S subunit;viral nsp1	1663.5	2446.5	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-30	IFNs	2094	1628	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-31_func	antiviral proteins	1974	1627	white	rectangle	node	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-32	RIG-I;M-protein, membrane-bound	190	407	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-33	IFNL	662	1444	white	circle	other	0.62	black	46	17	NA
+N-hsaCovid19IFN-lambda-34	5'cap-viral-RNA	2089.5	200.5	white	circle	other	0.62	black	46	17	NA

Resources/Hipathia/sif_att_converter/test/hsaCovid19IFN-lambda.sif

+N-hsaCovid19IFN-lambda-1	activation	N-hsaCovid19IFN-lambda-16
+N-hsaCovid19IFN-lambda-2	activation	N-hsaCovid19IFN-lambda-1
+N-hsaCovid19IFN-lambda-2	activation	N-hsaCovid19IFN-lambda-27
+N-hsaCovid19IFN-lambda-3	activation	N-hsaCovid19IFN-lambda-1
+N-hsaCovid19IFN-lambda-4	activation	N-hsaCovid19IFN-lambda-27
+N-hsaCovid19IFN-lambda-8	activation	N-hsaCovid19IFN-lambda-2
+N-hsaCovid19IFN-lambda-9	activation	N-hsaCovid19IFN-lambda-2
+N-hsaCovid19IFN-lambda-10	activation	N-hsaCovid19IFN-lambda-25
+N-hsaCovid19IFN-lambda-11	activation	N-hsaCovid19IFN-lambda-10
+N-hsaCovid19IFN-lambda-13	activation	N-hsaCovid19IFN-lambda-32
+N-hsaCovid19IFN-lambda-14	activation	N-hsaCovid19IFN-lambda-32
+N-hsaCovid19IFN-lambda-15	activation	N-hsaCovid19IFN-lambda-33
+N-hsaCovid19IFN-lambda-16	activation	N-hsaCovid19IFN-lambda-30
+N-hsaCovid19IFN-lambda-16	activation	N-hsaCovid19IFN-lambda-31
+N-hsaCovid19IFN-lambda-17	activation	N-hsaCovid19IFN-lambda-16
+N-hsaCovid19IFN-lambda-20	activation	N-hsaCovid19IFN-lambda-18
+N-hsaCovid19IFN-lambda-21	activation	N-hsaCovid19IFN-lambda-34
+N-hsaCovid19IFN-lambda-11	activation	N-hsaCovid19IFN-lambda-14
+N-hsaCovid19IFN-lambda-11	activation	N-hsaCovid19IFN-lambda-22
+N-hsaCovid19IFN-lambda-22	activation	N-hsaCovid19IFN-lambda-11
+N-hsaCovid19IFN-lambda-23	activation	N-hsaCovid19IFN-lambda-11
+N-hsaCovid19IFN-lambda-24	activation	N-hsaCovid19IFN-lambda-14
+N-hsaCovid19IFN-lambda-25	activation	N-hsaCovid19IFN-lambda-15