[ensembl-dev] Getting >1 stable IDs from HGNC symbols

[Christian Cole (Staff)]

Perfect! Thanks.

From: <dev-bounces at ensembl.org<mailto:dev-bounces at ensembl.org>> on behalf of mag
Reply-To: Ensembl developers list
Date: Tuesday, 4 August 2015 13:15
To: Ensembl developers list
Subject: Re: [ensembl-dev] Getting >1 stable IDs from HGNC symbols

Hi Christian,

The method 'fetch_by_display_label' will return the gene matching a particular gene symbol, excluding any gene symbols.


Regards,
Magali

On 04/08/2015 12:06, Christian Cole (Staff) wrote:

When using the $geneAdaptor->fetch_all_by_external_name($name,'HGNC') method I'm getting all synonym matches as well so it's returning several ensembl stable IDs for unrelated genes. E.g. searching FLG (Filaggrin, ENSG00000143631) also returns FGFR1 (ENSG00000077782). The order they are returned also varies with different versions of the API.

How can I avoid hitting synonyms or is there a more reliable way to get the correct ensembl stable ID given an HGNC gene name?

The University of Dundee is a registered Scottish Charity, No: SC015096


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The University of Dundee is a registered Scottish Charity, No: SC015096
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