[ensembl-dev] Question regarding the fetching if gene info using external names

[Andy Yates]

Hi Duarte,

This is not possible to do since we have not imported this symbol into Ensembl which looks to be a bug in our xref pipeline. Our major source of HGNC mappings comes from the following URL:

http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=gd_pub_ensembl_id&col=md_prot_id&col=gd_lsdb_links&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr

The association you have highlighted is also in this file. It seems that for some reason we have not recorded this link. We will register a bug about this and will be able to feed back once it is fixed.

For the moment you can use HGNC's biomart to provide the symbol -> ENSG lookup as we look into what has gone wrong

Andy

On 21 Nov 2012, at 15:49, Duarte Molha wrote:

> Dear developers
>  
> I have a question regarding the use of the methods “fetch_all_by_display_label” and “fetch_all_by_external_name”
>  
> Consider this snippet of code:
>  
> my $query_gene = “MT-TG”;
> my @fetched_genes = @{$gene_adaptor->fetch_all_by_display_label($query_gene)};
> unless (@fetched_genes){
> @fetched_genes =  @{ $gene_adaptor->fetch_all_by_external_name($query_gene) };
> }
> foreach my $a (@fetched_genes) {
>                                 [do something]...
> }
>  
> Although, MT-TG is the approved HGNC symbol for this gene ( http://www.genenames.org/data/hgnc_data.php?hgnc_id=7486 ), I am unable to retrieve data for it from the ensemble database.
> In ensembl this gene is called J01415.16 with the ENSGID: ENSG00000210164 (http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000210164;r=MT:9991-10058;t=ENST00000387429 )
> Can you tell me what I am doing wrong and how to change my code so I can retrieve is particular gene of interest?
> Best regards
>  
> Duarte Molha
>  
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