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

[Duarte Molha]

Thank you... but this is not the only one like this... almost all the mitochondrial genes fail in the same way:

Failed > Query:MT-TG
Failed > Query:MT-TH
Failed > Query:MT-TI
Failed > Query:MT-TK
Failed > Query:MT-TL1
Failed > Query:MT-TP
Failed > Query:MT-TQ
Failed > Query:MT-TS1
Failed > Query:MT-TS2

So this leads be to believe it is not a isolated case. In the list above most of these genes are present in the link you gave me ... so why were they not imported?

Cheers

Duarte

-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Andy Yates
Sent: 21 November 2012 16:16
To: Ensembl developers list
Subject: Re: [ensembl-dev] Question regarding the fetching if gene info using external names

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
>  
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: 
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/


_______________________________________________
Dev mailing list    Dev at ensembl.org
Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/