[ensembl-dev] About the rank of "Coding unknown" in the VEP consequence output

[Sarah Hunt]

Hi Yen-Hua,

The consequences terms we are now using are arranged in a tree with
child branches providing increased levels of detail. The miso
documentation illustrates this:

http://www.sequenceontology.org/miso/current_release/term/SO:0001580

If we can call a detailed consequence, we use a child term of
SO:0001580/'coding_sequence_variation', such as 'synonymous variant' .
Where we cannot - either because the alleles are unknown or are longer
insertions/deletions not handled by our current analysis - we use the
parent term.

I can see how this looks odd, but as a variant would not have both
'unknown' consequence and 'known' consequence, we find it more useful
to list the child term where possible.

Best wishes,

Sarah
On Fri, Aug 10, 2012 at 5:05 PM, Huang Yen-Hua <yenhuahuang1 at gmail.com> wrote:
> Hi Ensembl dev.,
>
> I am using VEP to list the possible consequences of SNPs and just notice
> that the rank of "coding unknown" (16) is higher than that of "Synonymous
> coding" (15), as indicated in Bio::EnsEMBL::Variation::Utils::Constants as
> well as on
> http://www.ensembl.org/info/docs/variation/predicted_data.html#consequences.
>
> This looks a bit strange to me. I cannot clearly get the reason about why a
> synonymous change may cause a more severe consequence than a coding
> unknown case that is now also referred to as "coding_sequence_variant"
> in the SO-term system.
>
> Best,
> Yen-Hua
>
> ======================
> Yen-Hua Huang, PhD
> Institute of Biomedical Informatics
> National Yang-Ming University
> Taipei, Taiwan
> ======================
>
>
>
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