Fix invalid ChEMBL-RDF files. Put the script in the ChEMBL-RDF directory, then exec. You get fixed files as "*.ttl.new"

gistfile1.rb

files =  ["chembl_16_biocmpt.ttl", "chembl_16_target.ttl", "chembl_16_targetcmpt.ttl"]

def iotax(arg)
  "<http://identifiers.org/taxonomy/#{arg}>"
end

def ncbitax(arg)
  "<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=#{arg}>"
end

files.each do |file|
  fin = File.new(file, "r")
  out = File.new(file + ".new", "w")

  fin.each("\n") do |line|
    if line =~ /iotax:(\d+)/
      num = $1
      line.sub!(/iotax:\d+/, iotax(num))
    end
    if line =~ /ncbitax:(\d+)/
      num = $1
      line.sub!(/ncbitax:\d+/, ncbitax(num))
    end
    out.print(line)
  end

  fin.close
  out.close   
end