R/bp2.get.uniprot.ids.R

In microbiome/biopax2: BioPAX level 2 S4 object model

## Copyright (c) 2010 Ossi Koivistoinen

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# Input: List of objects of class bp2.protein
# Output: data.frame with two columns.
#   Column 1: numeric rdf.id of protein
#   Column 2: Uniprot id string
#   rownames: symbolic rdf.id
bp2.get.uniprot.ids <- function(proteins)
{
  uniprot.key = match("\"UniProt^^<http://www.w3.org/2001/XMLSchema#string>\"", .bp2[["symbol.names"]])
  uniprot.ids <- c()
  index <- 0
  for(p in proteins)
    {
      index <- index + 1
      xrefs = slot(p, 'xref')
      for(j in .bp2[["all.objects"]][xrefs])
        {
          if (is(j, 'bp2.unificationXref'))
            {
              if(slot(j,'db') == uniprot.key)
                {
                  uniprot.value.key <- slot(j,'id')
                  uniprot.value <- .bp2[["symbol.names"]][uniprot.value.key]
                  uniprot.ids[index] <- bp2.simplifyString(uniprot.value)
                }
            }
          else
            {
               uniprot.ids[index] <- NA
            }
        }
    }
  mapping <- data.frame(protein=bp2.objects2ids(proteins), uniprot.id=uniprot.ids)
  mapping
}