[ensembl-dev] Variation::OverlapConsequence::rank()
Laurent Gil
lgil at ebi.ac.uk
Fri May 30 11:52:40 BST 2014
Hi Genomeo,
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",
e.g:
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.
Thanks for spotting that. We built the table a long time ago and it
definitively need to be updated.
We will change the table in the next release to match the ranking of
each individual consequence term.
Best regards,
Laurent
On 30/05/2014 11:41, Will McLaren wrote:
> Seems nc_transcript_variant is out of order in that table, thanks for
> spotting that.
>
> 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.
>
> You can get the consequence types and their various attributes from
> the hash:
>
> %Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES
>
> e.g. to get a hash with the ranks in:
>
> my %ranks = map {$_->SO_term => $_->rank} values
> %Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES;
>
> print "$_\t$ranks{$_}\n" for sort {$ranks{$a} <=> $ranks{$b}} keys %ranks;
>
> Regards
>
> Will
>
>
> On 30 May 2014 10:21, Genomeo Dev <genomeodev at gmail.com
> <mailto:genomeodev at gmail.com>> wrote:
>
> Hi Will,
>
> I wonder if that is the latest table as seems not consistent with
> these ranks obtained from OverlapConsequence::rank()
>
> 21INTRONIC
> 22NMD_TRANSCRIPT
> 23WITHIN_NON_CODING_GENE
> 24UPSTREAM
> 25DOWNSTREAM
> 36REGULATORY_REGION
> 38INTERGENIC
>
> 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:
>
> our %CONSEQUENCE_DESCRIPTIONS = (
> 'ESSENTIAL_SPLICE_SITE' => 'In the first 2 or the last 2
> basepairs of an intron',
> 'STOP_GAINED' => 'In coding sequence, resulting in
> the gain of a stop codon',
> 'STOP_LOST' => 'In coding sequence, resulting in
> the loss of a stop codon',
> 'COMPLEX_INDEL' => 'Insertion or deletion that spans an
> exon/intron or coding sequence/UTR border',
> 'FRAMESHIFT_CODING' => 'In coding sequence, resulting in a
> frameshift',
> 'NON_SYNONYMOUS_CODING' => 'In coding sequence and results in
> an amino acid change in the encoded peptide sequence',
> 'SPLICE_SITE' => '1-3 bps into an exon or 3-8 bps
> into an intron',
> 'PARTIAL_CODON' => 'Located within the final,
> incomplete codon of a transcript whose end coordinate is unknown',
> 'SYNONYMOUS_CODING' => 'In coding sequence, not resulting
> in an amino acid change (silent mutation)',
> 'REGULATORY_REGION' => 'In regulatory region annotated by
> Ensembl',
> 'WITHIN_MATURE_miRNA' => 'Located within a microRNA',
> '5PRIME_UTR' => 'In 5 prime untranslated region',
> '3PRIME_UTR' => 'In 3 prime untranslated region',
> 'INTRONIC' => 'In intron',
> 'NMD_TRANSCRIPT' => 'Located within a transcript
> predicted to undergo nonsense-mediated decay',
> 'WITHIN_NON_CODING_GENE' => 'Located within a gene that does not
> code for a protein',
> 'UPSTREAM' => 'Within 5 kb upstream of the 5 prime
> end of a transcript',
> 'DOWNSTREAM' => 'Within 5 kb downstream of the 3
> prime end of a transcript',
> 'HGMD_MUTATION' => 'Mutation from the HGMD database -
> consequence unknown',
> 'INTERGENIC' => 'More than 5 kb either upstream or
> downstream of a transcript',
> );
>
> Regards,
>
> G.
>
>
> On 30 May 2014 09:50, Will McLaren <wm2 at ebi.ac.uk
> <mailto:wm2 at ebi.ac.uk>> wrote:
>
> Hello,
>
> The ranks are given in this table:
>
> http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences
>
> Regards
>
> Will
>
>
> On 29 May 2014 17:26, Genomeo Dev <genomeodev at gmail.com
> <mailto:genomeodev at gmail.com>> wrote:
>
> Hi,
>
> 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".
>
> 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?
>
> LocationAlleleExisting_variationSYMBOLSYMBOL_SOURCEGeneENSPFeatureFeature_typeBIOTYPESTRANDCANONICALEXONINTRONDISTANCETSSDistanceFeatureDistanceConsequenceEffectRank
> 2:208228309Trs17808606AC007879.5Clone_based_vega_geneENSG00000223725-ENST00000412387Transcriptantisense-1--3/4--0intron_variant,nc_transcript_variantINTRONIC,WITHIN_NON_CODING_GENE21,23
> 2:208231478Trs17808718AC007879.5Clone_based_vega_geneENSG00000223725-ENST00000412387Transcriptantisense-1--3/4--0intron_variant,nc_transcript_variantINTRONIC,WITHIN_NON_CODING_GENE21,23
> 2:208440836Crs17811997CREB1HGNCENSG00000118260ENSP00000412016ENST00000418081Transcriptnonsense_mediated_decay1--5/8--0intron_variant,NMD_transcript_variantINTRONIC,NMD_TRANSCRIPT21,22
>
> Thanks,
>
> --
> G.
>
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> --
> G.
>
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