<div dir="ltr">The VEP can still report these Ensembl consequence terms, using "--terms ensembl"<div><br></div><div><a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_terms">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_terms</a><br>
</div><div><br></div><div>You can also retrieve the terms from the OverlapConsequence objects in %Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES using the display_term() method; you could use this in a plugin if you wished to display both SO (in the main Consequence column) and Ensembl (in the plugin's own field) terms.</div>
<div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 2 June 2014 13:03, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks. Actually the terms in <font face="arial, sans-serif">ConsequenceType.pm are quite a useful grouping for a broad classification. I would love to see them at least in the API in future releases as it would make a good common ground for those reporting broad variant consequences.</font><span class="HOEnZb"><font color="#888888"><div>
<font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">G.</font></div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On 30 May 2014 11:52, Laurent Gil <span dir="ltr"><<a href="mailto:lgil@ebi.ac.uk" target="_blank">lgil@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Genomeo,<br>
<br>
Actually it's because the terms are grouped by the Old Ensembl
term, using the highest rank of the terms which belong to this
"group",<br>
e.g:<br>
The Old Ensembl term "
Within non coding gene" should be ranked 23 but the term "
non_coding_exon_variant" is ranked 20, so we displayed it in the
table at the rank 20.<br>
<br>
Thanks for spotting that. We built the table a long time ago and
it definitively need to be updated.<br>
We will change the table in the next release to match the ranking
of each individual consequence term.<br>
<br>
Best regards,<br>
<pre cols="72">Laurent</pre><div><div>
On 30/05/2014 11:41, Will McLaren wrote:<br>
</div></div></div><div><div>
<blockquote type="cite">
<div dir="ltr">Seems nc_transcript_variant is out of order in that
table, thanks for spotting that.
<div><br>
</div>
<div>ConsequenceType.pm is not used by the current API code and
will be deprecated. The Ensembl terms are no longer the
preferred terms to use; the SO equivalents are what we
recommend for use now.</div>
<div><br>
</div>
<div>You can get the consequence types and their various
attributes from the hash:</div>
<div><br>
</div>
<div>%Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES<br>
</div>
<div><br>
</div>
<div>e.g. to get a hash with the ranks in:</div>
<div><br>
</div>
<div>my %ranks = map {$_->SO_term => $_->rank} values
%Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES;</div>
<div><br>
</div>
<div>print "$_\t$ranks{$_}\n" for sort {$ranks{$a} <=>
$ranks{$b}} keys %ranks;<br>
</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 30 May 2014 10:21, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Will,
<div><br>
</div>
<div>I wonder if that is the latest table as seems not
consistent with these ranks obtained from
OverlapConsequence::rank()
<div>
<br>
</div>
<div>
<div>21<span style="white-space:pre-wrap"> </span>INTRONIC</div>
<div>22<span style="white-space:pre-wrap"> </span>NMD_TRANSCRIPT</div>
<div>23<span style="white-space:pre-wrap"> </span>WITHIN_NON_CODING_GENE</div>
<div>24<span style="white-space:pre-wrap"> </span>UPSTREAM</div>
<div>25<span style="white-space:pre-wrap"> </span>DOWNSTREAM</div>
<div>36<span style="white-space:pre-wrap"> </span>REGULATORY_REGION</div>
<div>38<span style="white-space:pre-wrap"> </span>INTERGENIC</div>
</div>
<div><br>
</div>
<div>In particular ranks 36 and 38 go beyond the number
of entries in that table. Also note that in
ConsequenceType.pm, there are fewer ensembl display
terms compared to those shown under 'old Ensembl
terms' in the table, in case those are meant to be the
same:</div>
<div><br>
</div>
<div>
<div>our %CONSEQUENCE_DESCRIPTIONS = (</div>
<div> 'ESSENTIAL_SPLICE_SITE' => 'In the first 2
or the last 2 basepairs of an intron',</div>
<div> 'STOP_GAINED' => 'In coding
sequence, resulting in the gain of a stop codon',</div>
<div> 'STOP_LOST' => 'In coding
sequence, resulting in the loss of a stop codon',</div>
<div> 'COMPLEX_INDEL' => 'Insertion or
deletion that spans an exon/intron or coding
sequence/UTR border',</div>
<div> 'FRAMESHIFT_CODING' => 'In coding
sequence, resulting in a frameshift',</div>
<div> 'NON_SYNONYMOUS_CODING' => 'In coding
sequence and results in an amino acid change in the
encoded peptide sequence',</div>
<div> 'SPLICE_SITE' => '1-3 bps into an
exon or 3-8 bps into an intron',</div>
<div> 'PARTIAL_CODON' => 'Located within
the final, incomplete codon of a transcript whose
end coordinate is unknown',</div>
<div> 'SYNONYMOUS_CODING' => 'In coding
sequence, not resulting in an amino acid change
(silent mutation)',</div>
<div> 'REGULATORY_REGION' => 'In regulatory
region annotated by Ensembl',</div>
<div> 'WITHIN_MATURE_miRNA' => 'Located within
a microRNA',</div>
<div> '5PRIME_UTR' => 'In 5 prime
untranslated region',</div>
<div> '3PRIME_UTR' => 'In 3 prime
untranslated region',</div>
<div> 'INTRONIC' => 'In intron',</div>
<div> 'NMD_TRANSCRIPT' => 'Located within
a transcript predicted to undergo nonsense-mediated
decay',</div>
<div> 'WITHIN_NON_CODING_GENE' => 'Located within
a gene that does not code for a protein',</div>
<div> 'UPSTREAM' => 'Within 5 kb
upstream of the 5 prime end of a transcript',</div>
<div> 'DOWNSTREAM' => 'Within 5 kb
downstream of the 3 prime end of a transcript',</div>
<div> 'HGMD_MUTATION' => 'Mutation from
the HGMD database - consequence unknown',</div>
<div> 'INTERGENIC' => 'More than 5 kb
either upstream or downstream of a transcript',</div>
<div>);</div>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Regards,</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">G.
<div>
<div><br>
<br>
<div class="gmail_quote">On 30 May 2014 09:50,
Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">Hello,
<div><br>
</div>
<div>The ranks are given in this table:</div>
<div><br>
</div>
<div><a href="http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences" target="_blank">http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences</a><br>
</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">
<div>
<div>On 29 May 2014 17:26, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span>
wrote:<br>
</div>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div>
<div dir="ltr">
<div>Hi,</div>
<div><br>
</div>
<div>The method
Bio::EnsEMBL::Variation::OverlapConsequence::rank()
seems to return 'the relative
rank of this OverlapConsequence
when compared to other
OverlapConsequence objects. This
is used, for example, to
determine the most severe
consequence of a
VariationFeature".</div>
<div><br>
</div>
<div>As shown in this example each
consequence term appears to have
a unique rank independently of
the collective consequence terms
for the input variant. Is there
a dictionary somewhere of ranks
and corresponding terms?</div>
<div><br>
</div>
<div>
<div>Location<span style="white-space:pre-wrap">
</span>Allele<span style="white-space:pre-wrap">
</span>Existing_variation<span style="white-space:pre-wrap">
</span>SYMBOL<span style="white-space:pre-wrap">
</span>SYMBOL_SOURCE<span style="white-space:pre-wrap">
</span>Gene<span style="white-space:pre-wrap">
</span>ENSP<span style="white-space:pre-wrap">
</span>Feature<span style="white-space:pre-wrap">
</span>Feature_type<span style="white-space:pre-wrap">
</span>BIOTYPE<span style="white-space:pre-wrap">
</span>STRAND<span style="white-space:pre-wrap">
</span>CANONICAL<span style="white-space:pre-wrap">
</span>EXON<span style="white-space:pre-wrap">
</span>INTRON<span style="white-space:pre-wrap">
</span>DISTANCE<span style="white-space:pre-wrap">
</span>TSSDistance<span style="white-space:pre-wrap">
</span>FeatureDistance<span style="white-space:pre-wrap">
</span>Consequence<span style="white-space:pre-wrap">
</span>Effect<span style="white-space:pre-wrap">
</span>Rank</div>
<div>2:208228309<span style="white-space:pre-wrap">
</span>T<span style="white-space:pre-wrap">
</span>rs17808606<span style="white-space:pre-wrap">
</span>AC007879.5<span style="white-space:pre-wrap">
</span>Clone_based_vega_gene<span style="white-space:pre-wrap">
</span>ENSG00000223725<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>ENST00000412387<span style="white-space:pre-wrap">
</span>Transcript<span style="white-space:pre-wrap">
</span>antisense<span style="white-space:pre-wrap">
</span>-1<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>3/4<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>0<span style="white-space:pre-wrap">
</span>intron_variant,nc_transcript_variant<span style="white-space:pre-wrap">
</span>INTRONIC,WITHIN_NON_CODING_GENE<span style="white-space:pre-wrap">
</span>21,23</div>
<div>2:208231478<span style="white-space:pre-wrap">
</span>T<span style="white-space:pre-wrap">
</span>rs17808718<span style="white-space:pre-wrap">
</span>AC007879.5<span style="white-space:pre-wrap">
</span>Clone_based_vega_gene<span style="white-space:pre-wrap">
</span>ENSG00000223725<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>ENST00000412387<span style="white-space:pre-wrap">
</span>Transcript<span style="white-space:pre-wrap">
</span>antisense<span style="white-space:pre-wrap">
</span>-1<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>3/4<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>0<span style="white-space:pre-wrap">
</span>intron_variant,nc_transcript_variant<span style="white-space:pre-wrap">
</span>INTRONIC,WITHIN_NON_CODING_GENE<span style="white-space:pre-wrap">
</span>21,23</div>
<div>2:208440836<span style="white-space:pre-wrap">
</span>C<span style="white-space:pre-wrap">
</span>rs17811997<span style="white-space:pre-wrap">
</span>CREB1<span style="white-space:pre-wrap">
</span>HGNC<span style="white-space:pre-wrap">
</span>ENSG00000118260<span style="white-space:pre-wrap">
</span>ENSP00000412016<span style="white-space:pre-wrap">
</span>ENST00000418081<span style="white-space:pre-wrap">
</span>Transcript<span style="white-space:pre-wrap">
</span>nonsense_mediated_decay<span style="white-space:pre-wrap">
</span>1<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>5/8<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>-<span style="white-space:pre-wrap">
</span>0<span style="white-space:pre-wrap">
</span>intron_variant,NMD_transcript_variant<span style="white-space:pre-wrap">
</span>INTRONIC,NMD_TRANSCRIPT<span style="white-space:pre-wrap">
</span>21,22</div>
</div>
<div><br>
</div>
Thanks,<span><font color="#888888"><br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">G.</div>
</font></span></div>
<br>
</div>
</div>
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<br>
</blockquote>
</div>
<br>
</div>
<br>
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<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
</div>
</div>
<span><font color="#888888">-- <br>
<div dir="ltr">G.</div>
</font></span></div>
</div>
</div>
<br>
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<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
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</pre>
</blockquote>
<br>
</div></div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
</div>
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<br></blockquote></div><br></div>