new SO terms for new biotype groupings

modules/t/sequenceOntologyMapper.t

@@ -70,12 +70,12 @@ my $mappings =
    # test various genes with/without biotypes
    { obj => Bio::EnsEMBL::Gene->new(-biotype => 'dummy'), accession => 'SO:0000704', name => 'gene' }, # if we don't pass a non empty biotype it will default to protein_coding hence it will fail
    { obj => Bio::EnsEMBL::Gene->new(-biotype => 'protein_coding'), accession => 'SO:0001217', name => 'protein_coding_gene' },
-   { obj => Bio::EnsEMBL::Gene->new(-biotype => 'tRNA'), accession => 'SO:0001272', name => 'tRNA_gene' },
+   { obj => Bio::EnsEMBL::Gene->new(-biotype => 'tRNA'), accession => 'SO:0001263', name => 'ncRNA_gene' },
    # test various transcripts with/without biotypes
    { obj => Bio::EnsEMBL::Transcript->new(-biotype => 'dummy'), accession => 'SO:0000673', name => 'transcript' },
    { obj => Bio::EnsEMBL::Transcript->new(), accession => 'SO:0000234', name => 'mRNA' },
-   { obj => Bio::EnsEMBL::Transcript->new(-biotype => 'processed_transcript'), accession => 'SO:0001503', name => 'processed_transcript' },
-   { obj => Bio::EnsEMBL::Transcript->new(-biotype => 'retrotransposed'), accession => 'SO:0000569', name => 'retrotransposed' },
+   { obj => Bio::EnsEMBL::Transcript->new(-biotype => 'processed_transcript'), accession => 'SO:0001877', name => 'lnc_RNA' },
+   { obj => Bio::EnsEMBL::Transcript->new(-biotype => 'tRNA'), accession => 'SO:0000253', name => 'tRNA' },
    # exons
    { obj => Bio::EnsEMBL::Exon->new, accession => 'SO:0000147', name => 'exon' },
    # slices

modules/t/test-genome-DBs/ontology/ontology/term.txt

@@ -163,3 +163,7 @@
 41072	5	NULL	SO:0001503	processed_transcript	"""A transcript for which no open reading frame has been identified and for which no other function has been determined."" [MGI:hdeen]"	0	0
 41494	5	SOFA	SO:0000340	chromosome	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	0	0
 44355	5	N	SO:0000234	mRNA	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	0	0
+43394	5	SOFA	SO:0000253	tRNA	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	0	0
+44395	5	NULL	SO:0001263	ncRNA_gene	"" []	0	0
+45000	5	NULL	SO:0001877	lnc_RNA	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	0	0
+43375	5	SOFA	SO:0000234	mRNA	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	0	0