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

Paul Flicek flicek at ebi.ac.uk
Sat Feb 5 21:18:51 GMT 2011


Hi Pablo,

The way that we display the HGMD data is indeed in accordance with the agreement with with them for data distribution.  What they have provided we are able to include in all of our release databases and use across the project as we see fit.

Obviously it would be better to have more complete information, but this is currently not possible and we feel that having existence data for HGMD in Ensembl is better than having no information.  


Paul


On 5 Feb 2011, at 21:12, Pablo Marin-Garcia 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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> Dev at ensembl.org
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