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

[Pablo Marin-Garcia]

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?





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   Pablo Marin-Garcia
   Vertebrate Genomics
   Wellcome Trust Genome Campus