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

Mon Feb 7 17:56:40 GMT 2011

On Mon, 7 Feb 2011, Fiona Cunningham wrote:

> 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?

I just discover that is a browser problem (at least for me). In my firefox works 
but not in my safari or chrome.

[link tested]
http://www.ensembl.org/Homo_sapiens/Component/Gene/Web/GeneSNPTable?_rmd=0e38;_rmd=e16b;align=474;db=core;g=ENSG00000139618;r=13:32889611-32973347;time=1297100188869.869;sub_table=3PRIME_UTR;update_panel=1

Also in the firefox still there is a glitch. The page generated when asking for 
display the link in another page, got the <head> void, so not CSS and JS, 
therefore not sorting facility..

  -Pablo

>
>> 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
>>
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
>>
>

-----

   Pablo Marin-Garcia