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

[Andy Yates]

Hi Duarte,

Sorry I meant to say our human xrefs where done for 70 not 71. Apologies for any confusion

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 21 Nov 2012, at 16:39, Andy Yates wrote:

> It would suggest there is an issue when processing mitochondrial HGNC links in our xref pipeline. That narrows the problem set down at least from our perspective. As with most things I'm more worried when things *are* an isolated case. We will investigate & will be back in touch in the future. Human xrefs have been finished for release 71 but human is rerun every release so the data bug won't be around for long.
> 
> Andy
> 
> Andrew Yates                   Ensembl Core Software Project Leader
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensembl.org/
> 
> On 21 Nov 2012, at 16:28, Duarte Molha wrote:
> 
>> 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
>>> 
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>> 
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> 
> 
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