R/chspider.batch.annotation.child.R

In yufree/xMSannotator: xMSannotator: R package for network based annotation of metabolomics data.

#' Human Metabolome Database', 'ChEMBL', 'ChEBI', 'NIAID','Pesticide Common
#' Names','SMPDB Small Molecule Pathway Database',
#' MeSH','LipidMAPS','ChemBank','BioCyc'),token=tokenstr)
#' 
#' Human Metabolome Database', 'ChEMBL', 'ChEBI', 'NIAID','Pesticide Common
#' Names','SMPDB Small Molecule Pathway Database',
#' MeSH','LipidMAPS','ChemBank','BioCyc'),token=tokenstr)
#' 
#' 
chspider.batch.annotation.child <- function(mz.val, max.mz.diff, 
    adductname, datasources = c("KEGG"), tokenstr, maxhits = 30, 
    syssleep = 10, adduct_table) {
    
    # data(adduct_table)
    annot_res = {
    }
    
    Sys.sleep(syssleep)
    
    cs <- processWSDL("http://www.chemspider.com/MassSpecAPI.asmx?WSDL")
    o <- genSOAPClientInterface(, cs)
    
    cs2 <- processWSDL("http://www.chemspider.com/Search.asmx?WSDL")
    o2 <- genSOAPClientInterface(, cs2)
    
    # adduct_table<-read.table('/Users/karanuppal/Documents/Emory/JonesLab/Projects/xMSannotator/adduct_table.txt',sep='\t',header=TRUE)
    # adduct_table<-adduct_table[c(which(adduct_table[,6]=='S'),which(adduct_table[,6]=='Acetonitrile')),]
    
    adduct_names <- as.character(adduct_table[, 1])
    adductlist <- adduct_table[, 4]
    mult_charge <- adduct_table[, 3]
    num_mol <- adduct_table[, 2]
    names(adductlist) <- as.character(adduct_names)
    names(mult_charge) <- as.character(adduct_names)
    names(num_mol) <- as.character(adduct_names)
    alladducts <- adduct_names
    
    
    # print(mz.val) convert to neutral mass
    # mz=mz.val-adductmass
    
    adductmass = adductlist[as.character(adductname)]
    adduct_charge = mult_charge[as.character(adductname)]
    adductnmol = num_mol[as.character(adductname)]
    # mz=(mz.val-adductmass)*adductcharge
    # mz=(exact_mass/adductcharge)+adductmass
    
    # mz=(mz.val*adductcharge)-(adductmass)
    # mz=#((nmol*M)/charge)+adductMass
    
    # mz=((nmol*M)+adductMass)/charge
    # M=((mz*charge)-adductMass)/nmol
    
    
    # M=((mz.val-adductmass)*adductcharge)/(adductnmol)
    
    # reverse
    # mono_mass=((mz.val-adductmass)*adduct_charge)/(adductnmol)
    
    mono_mass = ((mz.val * adduct_charge) - (adductmass))/(adductnmol)
    
    mz = mono_mass
    
    # mz=(exact_mass/adductcharge)+adductmass
    delta_ppm = (max.mz.diff) * (mz/1e+06)
    min_mz = round((mz - delta_ppm), 5)
    max_mz = round((mz + delta_ppm), 5)
    
    
    
    # csids<-o@functions$SearchByMass2(mass=mz,range=delta_ppm)
    
    # csids<-o@functions$SearchByMassAsync(mass=mz,range=delta_ppm,dbs='KEGG',token=tokenstr)
    # csids<-o@functions$SearchByMassAsync(mass=mz,range=delta_ppm,dbs=c('PubChem','MassBank',
    # 'EPA DSSTox','EPA Toxcast','NIST Chemistry
    # WebBook','KEGG',
    #'Human Metabolome Database', 'ChEMBL', 'ChEBI', 'NIAID','Pesticide Common Names','SMPDB Small Molecule Pathway Database',
    #'MeSH','LipidMAPS','ChemBank','BioCyc'),token=tokenstr)
    # ttest_res=try(t.test(x,y,paired=TRUE),silent=TRUE)
    csids <- try(o@functions$SearchByMassAsync(mass = mz, 
        range = delta_ppm, dbs = datasources, token = tokenstr), 
        silent = TRUE)
    
    if (is(csids, "try-error")) {
        
        annotres <- c(mz.val, rep("NC", 50))
        write.table(mz.val, file = "chemspider_bad_mzs.txt", 
            sep = "\t", append = TRUE, row.names = FALSE)
        
    } else {
        csids <- try(o2@functions$GetAsyncSearchResult(rid = csids, 
            token = tokenstr), silent = TRUE)
        
        
        if (is(csids, "try-error")) {
            
            annotres <- c(mz.val, rep("NC", 50))
            
            write.table(mz.val, file = "chemspider_bad_mzs.txt", 
                sep = "\t", append = TRUE, row.names = FALSE)
            
        } else {
            
            # WikiPathways, DrugBank, Comparative Toxicogenomics
            # Database, ACToR: Aggregated Computational Toxicology
            # Resource
            
            external_sources <- c("PubChem", "MassBank", 
                "EPA DSSTox", "EPA Toxcast", "NIST Chemistry WebBook", 
                "KEGG", "Human Metabolome Database", "ChEMBL", 
                "ChEBI", "NIAID", "Pesticide Common Names", 
                "SMPDB Small Molecule Pathway Database", 
                "MeSH", "LipidMAPS", "ChemBank", "BioCyc", 
                "WikiPathways", "DrugBank", "Comparative Toxicogenomics Database", 
                "ACToR: Aggregated Computational Toxicology Resource")
            
            write.table(mz.val, file = "mzval.txt", sep = "\t", 
                row.names = FALSE)
            
            if (length(csids) > 0) {
                
                
                countid <- 0
                
                if (length(csids) < maxhits) {
                  maxhits = length(csids)
                }
                for (id_ind in 1:maxhits) {
                  Sys.sleep(syssleep)
                  csid <- csids[id_ind]
                  csid1 <- o2@functions$CSID2ExtRefs(CSID = as.integer(csid), 
                    datasources = external_sources, token = tokenstr)
                  info <- o@functions$GetExtendedCompoundInfo(CSID = csid, 
                    token = tokenstr)
                  urllink1 <- paste("www.chemspider.com/Chemical-Structure.", 
                    csid, ".html", sep = "")
                  urllink2 <- paste("<a href=http://www.chemspider.com/Chemical-Structure.", 
                    csid, ".html>", csid, "</a>", sep = "")
                  CommonName = "-"
                  MF = "-"
                  SMILES = "-"
                  InChI = "-"
                  InChIKey = "-"
                  AverageMass = "-"
                  MolecularWeight = "-"
                  MonoisotopicMass = "-"
                  NominalMass = "-"
                  ALogP = "-"
                  XLogP = "-"
                  
                  slotnames <- slotNames(class(info))
                  
                  for (i in slotnames) {
                    if (i == "CommonName") {
                      if (length(info@CommonName) > 0) {
                        CommonName = info@CommonName
                      }
                    } else {
                      if (i == "MF") {
                        if (length(info@MF) > 0) {
                          MF = info@MF
                        }
                      } else {
                        if (i == "SMILES") {
                          if (length(info@SMILES) > 0) {
                            SMILES = info@SMILES
                          }
                        } else {
                          if (i == "InChI") {
                            if (length(info@InChI) > 0) {
                              InChI = info@InChI
                            }
                          } else {
                            if (i == "InChIKey") {
                              if (length(info@InChIKey) > 
                                0) {
                                InChIKey = info@InChIKey
                              }
                            } else {
                              if (i == "AverageMass") {
                                if (length(info@AverageMass) > 
                                  0) {
                                  AverageMass = info@AverageMass
                                }
                              } else {
                                if (i == "MolecularWeight") {
                                  if (length(info@MolecularWeight) > 
                                    0) {
                                    MolecularWeight = info@MolecularWeight
                                  }
                                } else {
                                  if (i == "MonoisotopicMass") {
                                    if (length(info@MonoisotopicMass) > 
                                      0) {
                                      MonoisotopicMass = info@MonoisotopicMass
                                    }
                                  } else {
                                    if (i == "NominalMass") {
                                      if (length(info@NominalMass) > 
                                        0) {
                                        NominalMass = info@NominalMass
                                      }
                                    } else {
                                      if (i == "ALogP") {
                                        if (length(info@ALogP) > 
                                          0) {
                                          ALogP = info@ALogP
                                        }
                                      } else {
                                        if (i == "XLogP") {
                                          if (length(info@XLogP) > 
                                            0) {
                                            XLogP = info@XLogP
                                          }
                                        }
                                        
                                      }
                                      
                                    }
                                    
                                  }
                                }
                              }
                            }
                          }
                        }
                      }
                    }
                  }
                  
                  
                  csid1NAME <- o2@functions$GetCompoundThumbnail(id = csid, 
                    token = tokenstr)
                  
                  dec <- base64Decode(csid1NAME, "raw")
                  pngoutloc <- "pngfiles"
                  dir.create(pngoutloc)
                  png_image <- readPNG(dec)
                  fname <- paste(pngoutloc, "/", csid, ".png", 
                    sep = "")
                  
                  
                  writePNG(png_image, target = fname)
                  
                  # img_url<-paste('<img src=',fname,' alt=', csid,'
                  # width=100 height=100>',sep='')
                  img_url <- paste("<img src=\"", fname, 
                    "\" alt=", csid, " width=100 height=100>", 
                    sep = "")
                  
                  # if(FALSE)
                  {
                    
                    
                    ID.PubChem = "-"
                    ID.MassBank = "-"
                    ID.EPA.DSSTox = "-"
                    ID.EPA.Toxcast = "-"
                    ID.NIST.Chem.WebBook = "-"
                    ID.KEGG = "-"
                    ID.HMDB = "-"
                    ID.ChEMBL = "-"
                    ID.ChEBI = "-"
                    ID.Pesticide.Common.Names = "-"
                    ID.SMPDB = "-"
                    ID.MeSH = "-"
                    ID.LipidMAPS = "-"
                    ID.ChemBank = "-"
                    ID.BioCyc = "-"
                    ID.WikiPathways = "-"
                    ID.DrugBank = "-"
                    ID.CTD = "-"
                    ID.ACToR = "-"
                    
                    
                    URL.PubChem = "-"
                    URL.MassBank = "-"
                    URL.EPA.DSSTox = "-"
                    URL.EPA.Toxcast = "-"
                    URL.NIST.Chem.WebBook = "-"
                    URL.KEGG = "-"
                    URL.HMDB = "-"
                    URL.ChEMBL = "-"
                    URL.ChEBI = "-"
                    URL.Pesticide.Common.Names = "-"
                    URL.SMPDB = "-"
                    URL.MeSH = "-"
                    URL.LipidMAPS = "-"
                    URL.ChemBank = "-"
                    URL.BioCyc = "-"
                    URL.WikiPathways = "-"
                    URL.DrugBank = "-"
                    URL.CTD = "-"
                    URL.ACToR = "-"
                    
                    if (length(csid1) > 0) {
                      for (dbindex in 1:length(csid1)) {
                        if (length(csid1[dbindex]$ExtRef@ext_id) > 
                          0 && length(csid1[dbindex]$ExtRef@ds_name) > 
                          0) {
                          if (csid1[dbindex]$ExtRef@ds_name == 
                            "PubChem") {
                            ID.PubChem = csid1[dbindex]$ExtRef@ext_id
                            URL.PubChem <- paste("<a href=", 
                              csid1[dbindex]$ExtRef@ext_url, 
                              ">", ID.PubChem, "</a>", sep = "")
                          } else {
                            
                            if (csid1[dbindex]$ExtRef@ds_name == 
                              "MassBank") {
                              
                              ID.MassBank = csid1[dbindex]$ExtRef@ext_id
                              # URL.MassBank<-paste('<a
                              # href=',csid1[dbindex]$ExtRef@ext_url,'>',ID.MassBank,'</a>',sep='')
                              # http://massbank.normandata.eu/MassBank/jsp/Dispatcher.jsp?type=disp&id=PB000410&site=25
                              URL.MassBank <- csid1[dbindex]$ExtRef@ext_id
                              # paste('<a
                              # href=http://massbank.normandata.eu/MassBank/jsp/Dispatcher.jsp?type=disp&id=',ID.MassBank,'&site=25>',ID.MassBank,'</a>',sep='')
                              
                            } else {
                              
                              if (csid1[dbindex]$ExtRef@ds_name == 
                                "EPA DSSTox") {
                                ID.EPA.DSSTox = csid1[dbindex]$ExtRef@ext_id
                                URL.EPA.DSSTox <- paste("<a href=", 
                                  csid1[dbindex]$ExtRef@ext_url, 
                                  ">", ID.EPA.DSSTox, "</a>", 
                                  sep = "")
                              } else {
                                
                                if (csid1[dbindex]$ExtRef@ds_name == 
                                  "EPA Toxcast") {
                                  ID.EPA.Toxcast = csid1[dbindex]$ExtRef@ext_id
                                  URL.EPA.Toxcast <- paste("<a href=", 
                                    csid1[dbindex]$ExtRef@ext_url, 
                                    ">", ID.EPA.Toxcast, 
                                    "</a>", sep = "")
                                } else {
                                  
                                  if (csid1[dbindex]$ExtRef@ds_name == 
                                    "NIST Chemistry WebBook") {
                                    ID.NIST.Chem.WebBook = csid1[dbindex]$ExtRef@ext_id
                                    URL.NIST.Chem.WebBook <- paste("<a href=", 
                                      csid1[dbindex]$ExtRef@ext_url, 
                                      ">", ID.NIST.Chem.WebBook, 
                                      "</a>", sep = "")
                                  } else {
                                    
                                    if (csid1[dbindex]$ExtRef@ds_name == 
                                      "KEGG") {
                                      ID.KEGG = csid1[dbindex]$ExtRef@ext_id
                                      # URL.KEGG=csid1[dbindex]$ExtRef@ext_url
                                      URL.KEGG <- paste("<a href=", 
                                        csid1[dbindex]$ExtRef@ext_url, 
                                        ">", ID.KEGG, "</a>", 
                                        sep = "")
                                      
                                    } else {
                                      
                                      if (csid1[dbindex]$ExtRef@ds_name == 
                                        "Human Metabolome Database") {
                                        ID.HMDB = csid1[dbindex]$ExtRef@ext_id
                                        URL.HMDB <- paste("<a href=", 
                                          csid1[dbindex]$ExtRef@ext_url, 
                                          ">", ID.HMDB, "</a>", 
                                          sep = "")
                                      } else {
                                        
                                        if (csid1[dbindex]$ExtRef@ds_name == 
                                          "ChEMBL") {
                                          ID.ChEMBL = csid1[dbindex]$ExtRef@ext_id
                                          URL.ChEMBL <- paste("<a href=", 
                                            csid1[dbindex]$ExtRef@ext_url, 
                                            ">", ID.ChEMBL, 
                                            "</a>", sep = "")
                                        } else {
                                          
                                          if (csid1[dbindex]$ExtRef@ds_name == 
                                            "ChEBI") {
                                            ID.ChEBI = csid1[dbindex]$ExtRef@ext_id
                                            URL.ChEBI <- paste("<a href=", 
                                              csid1[dbindex]$ExtRef@ext_url, 
                                              ">", ID.ChEBI, 
                                              "</a>", sep = "")
                                          } else {
                                            
                                            if (csid1[dbindex]$ExtRef@ds_name == 
                                              "Pesticide Common Names") {
                                              ID.Pesticide.Common.Names = csid1[dbindex]$ExtRef@ext_id
                                              URL.Pesticide.Common.Names <- paste("<a href=", 
                                                csid1[dbindex]$ExtRef@ext_url, 
                                                ">", ID.Pesticide.Common.Names, 
                                                "</a>", sep = "")
                                            } else {
                                              
                                              if (csid1[dbindex]$ExtRef@ds_name == 
                                                "SMPDB Small Molecule Pathway Database") {
                                                ID.SMPDB = csid1[dbindex]$ExtRef@ext_id
                                                URL.SMPDB <- paste("<a href=", 
                                                  csid1[dbindex]$ExtRef@ext_url, 
                                                  ">", ID.SMPDB, 
                                                  "</a>", 
                                                  sep = "")
                                              } else {
                                                
                                                if (csid1[dbindex]$ExtRef@ds_name == 
                                                  "MeSH") {
                                                  ID.MeSH = csid1[dbindex]$ExtRef@ext_id
                                                  URL.MeSH <- paste("<a href=", 
                                                    csid1[dbindex]$ExtRef@ext_url, 
                                                    ">", 
                                                    ID.MeSH, 
                                                    "</a>", 
                                                    sep = "")
                                                } else {
                                                  
                                                  if (csid1[dbindex]$ExtRef@ds_name == 
                                                    "LipidMAPS") {
                                                    ID.LipidMAPS = csid1[dbindex]$ExtRef@ext_id
                                                    URL.LipidMAPS <- paste("<a href=", 
                                                      csid1[dbindex]$ExtRef@ext_url, 
                                                      ">", 
                                                      ID.LipidMAPS, 
                                                      "</a>", 
                                                      sep = "")
                                                  } else {
                                                    
                                                    if (csid1[dbindex]$ExtRef@ds_name == 
                                                      "ChemBank") {
                                                      ID.ChemBank = csid1[dbindex]$ExtRef@ext_id
                                                      URL.ChemBank <- paste("<a href=", 
                                                        csid1[dbindex]$ExtRef@ext_url, 
                                                        ">", 
                                                        ID.ChemBank, 
                                                        "</a>", 
                                                        sep = "")
                                                    } else {
                                                      
                                                      if (csid1[dbindex]$ExtRef@ds_name == 
                                                        "BioCyc") {
                                                        ID.BioCyc = csid1[dbindex]$ExtRef@ext_id
                                                        URL.BioCyc <- paste("<a href=", 
                                                          csid1[dbindex]$ExtRef@ext_url, 
                                                          ">", 
                                                          ID.BioCyc, 
                                                          "</a>", 
                                                          sep = "")
                                                      } else {
                                                        
                                                        if (csid1[dbindex]$ExtRef@ds_name == 
                                                          "WikiPathways") {
                                                          ID.WikiPathways = csid1[dbindex]$ExtRef@ext_id
                                                          URL.WikiPathways <- paste("<a href=", 
                                                            csid1[dbindex]$ExtRef@ext_url, 
                                                            ">", 
                                                            ID.WikiPathways, 
                                                            "</a>", 
                                                            sep = "")
                                                        } else {
                                                          
                                                          if (csid1[dbindex]$ExtRef@ds_name == 
                                                            "DrugBank") {
                                                            ID.DrugBank = csid1[dbindex]$ExtRef@ext_id
                                                            # URL.DrugBank<-paste('<a
                                                            # href=',csid1[dbindex]$ExtRef@ext_url,'>',ID.DrugBank,'</a>',sep='')
                                                            URL.DrugBank <- paste("<a href=http://www.drugbank.ca/drugs/", 
                                                              ID.DrugBank, 
                                                              ">", 
                                                              ID.DrugBank, 
                                                              "</a>", 
                                                              sep = "")
                                                          } else {
                                                            
                                                            if (csid1[dbindex]$ExtRef@ds_name == 
                                                              "Comparative Toxicogenomics Database") {
                                                              ID.CTD = csid1[dbindex]$ExtRef@ext_id
                                                              URL.CTD <- paste("<a href=", 
                                                                csid1[dbindex]$ExtRef@ext_url, 
                                                                ">", 
                                                                ID.CTD, 
                                                                "</a>", 
                                                                sep = "")
                                                            } else {
                                                              
                                                              if (csid1[dbindex]$ExtRef@ds_name == 
                                                                "ACToR: Aggregated Computational Toxicology Resource") {
                                                                if (length(csid1[dbindex]$ExtRef@ext_url) > 
                                                                  0) {
                                                                  ID.ACToR = csid1[dbindex]$ExtRef@ext_id
                                                                  # print(ID.ACToR) print(csid1[dbindex]$ExtRef)
                                                                  URL.ACToR <- paste("<a href=", 
                                                                    csid1[dbindex]$ExtRef@ext_url, 
                                                                    ">", 
                                                                    ID.ACToR, 
                                                                    "</a>", 
                                                                    sep = "")
                                                                }
                                                              }
                                                            }
                                                          }
                                                        }
                                                      }
                                                    }
                                                  }
                                                }
                                              }
                                            }
                                          }
                                        }
                                      }
                                    }
                                  }
                                }
                              }
                            }
                          }
                        }
                      }
                    }
                    annot_res <- rbind(annot_res, c(mz.val, 
                      delta_ppm, info@CSID, urllink1, urllink2, 
                      CommonName, MF, SMILES, InChI, InChIKey, 
                      AverageMass, MolecularWeight, MonoisotopicMass, 
                      NominalMass, ALogP, XLogP, img_url, 
                      ID.KEGG, URL.KEGG, ID.HMDB, URL.HMDB, 
                      ID.LipidMAPS, URL.LipidMAPS, ID.PubChem, 
                      URL.PubChem, ID.MassBank, URL.MassBank, 
                      ID.BioCyc, URL.BioCyc, ID.SMPDB, URL.SMPDB, 
                      ID.EPA.DSSTox, URL.EPA.DSSTox, ID.EPA.Toxcast, 
                      URL.EPA.Toxcast, ID.Pesticide.Common.Names, 
                      URL.Pesticide.Common.Names, ID.ChEMBL, 
                      URL.ChEMBL, ID.ChEBI, URL.ChEBI, ID.NIST.Chem.WebBook, 
                      URL.NIST.Chem.WebBook, ID.WikiPathways, 
                      URL.WikiPathways, ID.DrugBank, URL.DrugBank, 
                      ID.CTD, URL.CTD, ID.ACToR, URL.ACToR))
                    countid <- countid + 1
                    if (countid%%50 > 0) {
                      Sys.sleep(syssleep)
                    }
                  }
                }
                
            }
            
            
            write.table(annot_res, file = "chspider_annot_res.txt", 
                sep = "\t", row.names = FALSE, append = TRUE)
        }  #else{
        # annot_res<-c(mz.val,rep('-',50))
        # #'-','-','-','-','-','-','-','-','-','-','-','-','-','-','-')
        
    }
    Sys.sleep(syssleep * 2)
    
    
    return(annot_res)
    
}