As the Biomart check only allows one source to map to one type of ensembl...

As the Biomart check only allows one source to map to one type of ensembl entity, there is no point in mapping the Genes and Transcripts as one is moved to the other. So the Gene mapping has been removed

misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm

@@ -65,7 +65,11 @@ sub run {
       $added++;
     }
     $self->add_direct_xref($xref_id, $transcript_id, "Transcript", "") if (defined($transcript_id));    
-    $self->add_direct_xref($xref_id, $gene_id, "Gene", "")             if (defined($gene_id)); 
+
+    #just add to the transcript ONLY as the check at the end will move all
+    #the those mapped to the transcript to the genes anyway due to the
+    #biomart check
+    #    $self->add_direct_xref($xref_id, $gene_id, "Gene", "")             if (defined($gene_id)); 
   }
   close FILE;