[ensembl-dev] HGMD snps in ensembl and its web display

[Fiona Cunningham]

hi Pablo,

I am glad you find the new layout of the gene variation table helpful.
It is always nice to get feedback from users.

As to your error, this functionality has not been disabled
intentionally. I cannot reproduce it. Can you send me specific links
that you are clicking on?

> Another  question about web usability in this variation table page:
> In the panel with the summary:
> http://www.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?align=474;db=core;g=ENSG00000139618;r=13:32889611-32973347
>
> But ... if I want to see any of the SNPs class table in another page/tab
> instead of adding a new panel, when clicking with the middle button in a
> show links I have an error:
>
> ---
> AJAX error - Runtime Error in component
> "EnsEMBL::Web::Component::Gene::GeneSNPTable [content]"
>
Fiona

------------------------------------------------------
Fiona Cunningham
Ensembl Variation Project Leader, EBI
www.ensembl.org
www.lrg-sequence.org
t: 01223 494612 || e: fiona at ebi.ac.uk



On 5 February 2011 21:12, Pablo Marin-Garcia <pg4 at sanger.ac.uk> wrote:
> hello,
>
> Looking at the report tables of HGMD SNPs:
> http://www.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?align=474;db=core;g=ENSG00000139618;r=13:32889611-32973347#HGMD_MUTATION
>
> I wonder why they don't have neither allele nor consequences.
>
> Is there any kind of restriction in the agreement for displaying this data?
> this is the public HGMD data but despite being the public set, registration
> is needed in order to access the data in their website so probably there are
> some restrictions for the redistribution as well. Is this the case?
>
>
> Being able to access programatically to the HGMD with the ensembl API is
> fantastic for medical geneticist but without allele or the SNP-class is not
> very helpful. I have not tried yet with the API but would the alleles
> returned be also 'HGMD_MUTATION'?
>
>
> This lack of allele is a bit of a inconvenient when opening The variation
> tab for a SNP because you get something like:
>
> GCCTATTGGATCCAAAGAG[HGMD_MUTATION]GGCCA
>
>
> Finally as there is no allele or consequences the web table has a lot of
> redundant rows, because does not matter which transcript you are when you
> are looking for SNPs in the gene (for the variation_gene table). It is true
> that you would be able to sort by transcript and see all the SNPs for a
> transcript but also is true that if you hide the transcript column a lot of
> rows get duplicated.
>
>
> Another  question about web usability in this variation table page:
> In the panel with the summary:
> http://www.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?align=474;db=core;g=ENSG00000139618;r=13:32889611-32973347
>
> This hide/show functionality and the sorting and choosing columns and the
> row-limit-display are great
> ---
> Summary of variations in ENSG00000139618 by consequence type
> 264      Hide   Intronic        In intron
> 76       Show   3 prime UTR     In 3 prime untranslated region
> ---
>
> But ... if I want to see any of the SNPs class table in another page/tab
> instead of adding a new panel, when clicking with the middle button in a
> show links I have an error:
>
> ---
> AJAX error - Runtime Error in component
> "EnsEMBL::Web::Component::Gene::GeneSNPTable [content]"
>
> Function EnsEMBL::Web::Component::Gene::GeneSNPTable fails to execute due to
> the following error:
>
>        Can't call method "render" on an undefined value at
>        ...
> /ensemblweb/www/www_61/modules/EnsEMBL/Web/Component/Gene/GeneSNPTable.pm
> line 75.
> ----
>
> has the ability of displaying the tables in another tab/window not being
> implemented by design or is it an error?
>
>
>
>
>
>  -----
>
>  Pablo Marin-Garcia
>  Vertebrate Genomics
>  Wellcome Trust Genome Campus
>
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