R/add_symbols_entrezids2biopax.R

In grishagin/RIGbiopax: Extract and Compare Genes and Pathways from BioPAX

add_symbols_entrezids2biopax<-
  function(biopax){
    #' @export
    #' @title 
    #' Annotate a BioPAX Object with Gene ID and Gene Symbol
    #' @description 
    #' Adds Gene IDs and Symbols to all physical entities, where possible.
    #' @param biopax A BioPAX object.
    #' 
    #' @author 
    #' Ivan Grishagin
    
    #find all current dbid pairs 
    dbid_df<-
      biopax$dt[property %in% c("db"
                                ,"id")
                ,.(dbid_db=property_value[property=="db"]
                   ,dbid_id=property_value[property=="id"])
                ,by=id] %>% 
      unique
    
    #find xrefs referencing these ids
    xref_df<-
      biopax$dt[property_attr_value %in% dbid_df$id
                ,.(xref_id=id
                   ,pav=property_attr_value)] %>% 
      unique
    
    #match them up and add to main df
    dbid_df<-
      dbid_df[match(xref_df$pav
                    ,id)] %>% 
      cbind(xref_df[,.(xref_id)]
            ,.)
    
    #find physent referencing these xrefs
    physent_df<-
      biopax$dt[property_attr_value %in% dbid_df$xref_id
                ,.(physent_id=id
                   ,physent_class=class
                   ,xref_pav=property_attr_value)] %>% 
      unique
    
    #match them up and add to main df
    dbid_df<-
      dbid_df[match(physent_df$xref_pav
                    ,xref_id)] %>% 
      cbind(physent_df[,.(physent_id
                          ,physent_class)]
            ,.)
    
    #annotate the data table with entrez ids and symbols
    dbid_df<-
      dbid_df %>% 
      add_symbols_entrezids_mult_keytypes(col_names=
                                            c(id_col = "dbid_id"
                                              ,type_col = "dbid_db"
                                              ,entrez_col = "entrezgene"
                                              ,symbol_col = "symbol"))
    
    #prepare all actual data tables that connect
    #physical entities to the entrez ids and symbols
    dTable_list<-list()
    dTable_list$entref<-
      dbid_df[,.(class=physent_class
                 ,id=physent_id
                 ,property="entityReference"
                 ,property_attr="rdf:resource"
                 ,property_attr_value=
                   paste0(xref_id
                          ,"entrez")
                 ,property_value="")]
    
    dTable_list$symbol<-
      dbid_df[,.(class=
                   paste0(physent_class
                          ,"Reference")
                 ,id=
                   paste0(xref_id
                          ,"entrez")
                 ,property="name"
                 ,property_attr="rdf:datatype"
                 ,property_attr_value="http://www.w3.org/2001/XMLSchema#string"
                 ,property_value=symbol)]
    
    if(nrow(dbid_df[dbid_id!=entrezgene])>0){
      dTable_list$xref<-
        dbid_df[,.(class=
                     paste0(physent_class[dbid_id!=entrezgene]
                            ,"Reference")
                   ,id=
                     paste0(xref_id[dbid_id!=entrezgene]
                            ,"entrez")
                   ,property="xref"
                   ,property_attr="rdf:resource"
                   ,property_attr_value=
                     paste0(id[dbid_id!=entrezgene]
                            ,"entrez")
                   ,property_value="")]
      dTable_list$db<-
        #do not take those values, where dbid_id==entrezid
        dbid_df[,.(class="RelationshipXref"
                   ,id=
                     paste0(id[dbid_id!=entrezgene]
                            ,"entrez")
                   ,property="db"
                   ,property_attr="rdf:datatype"
                   ,property_attr_value="http://www.w3.org/2001/XMLSchema#string"
                   ,property_value="entrezgene")]
      
      dTable_list$id<-
        #do not take those values, where dbid_id==entrezid
        dbid_df[,.(class="RelationshipXref"
                   ,id=
                     paste0(id[dbid_id!=entrezgene]
                            ,"entrez")
                   ,property="id"
                   ,property_attr="rdf:datatype"
                   ,property_attr_value="http://www.w3.org/2001/XMLSchema#string"
                   ,property_value=entrezgene[dbid_id!=entrezgene])]
    }
    
    
    #merge them and add them to biopax$dt
    biopax$dt<-
      dTable_list %>% 
      do.call(rbind
              ,.) %>% 
      unique %>% 
      rbind(biopax$dt)
    
    #fix the classes
    class(biopax$dt)<-
      c("biopax_df"
        ,class(biopax$dt))
    
    
    return(biopax)
  }