[ensembl-dev] getting the entrez gene id from an ensembl record

Oliver, Gavin gavin.oliver at almacgroup.com
Mon Feb 7 13:43:23 GMT 2011

I'm just wondering if any further thought was given to the issue below, whereby the API would pull the Entrez ID for pseudogenes via the Havana HGNC assignments?

Also, someone suggested a means of differentiating the primary Entrez ID returned from the other, secondary ones to enable users to pull the 'expected' Entrez ID for a gene.

Are either of these issues considered live?



-----Original Message-----
From: Ewan Birney [mailto:birney at ebi.ac.uk] 
Sent: 02 December 2010 13:30
To: Oliver, Gavin
Cc: Andreas Kahari; dev
Subject: Re: [ensembl-dev] getting the entrez gene id from an ensembl record

On 2 Dec 2010, at 12:20, Oliver, Gavin wrote:

> I would still assume the end goal should be almost the same.
> Over the past few weeks I have found Ensembl genes that don't map to  
> either or where the two don't correspond to one another as they do  
> in either Entrez or the HGNC.  Regardless of approach, I wouldn't  
> expect that this is the expected outcome.

Oliver - the examples you sent were very useful, but just to
repeat - the majority of these cases were pseudogenes (not genes)
which nevertheless did have HGNC and thus EntrezGene identifiers.

Our focus is first on protein coding genes, and we want to get all
those locked down first. Then probably RNA genes. Pseudogenes get
named in a far more haphazard way.

However, we should probably look into a dedicated HGNC and EntrezGene
ID transfer for pseudogenes - if I remember correctly, we had hte
right HGNC symbol in many cases (due to Havana annotation primarily) but
we had not inherieted the EntrezGene link.

Glenn and Ian - for HGNC Symbols flagged as pseudogenes, could we bring
across the link

    Havana HGNC Assignments -> HGNC internal ID -> EntrezGene?

I presume this at least a 62 thing.

> -----Original Message-----
> From: Andreas Kahari [mailto:ak at ebi.ac.uk]
> Sent: 02 December 2010 11:47
> To: Oliver, Gavin
> Cc: ian Longden; Andy Jenkinson; dev
> Subject: Re: [ensembl-dev] getting the entrez gene id from an  
> ensembl record
> On Thu, Dec 02, 2010 at 10:22:35AM -0000, Oliver, Gavin wrote:
>> Is it possible to have Entrez genes at a couple of levels?
>> i.e. a top-level Entrez ID linked via the gene and the others below  
>> this at the transcript or translation stage?
>> Most end users expect a single accurate Entrez gene ID that will  
>> tie to a single HGNC ID.  They don't want to be aware of the actual  
>> complexity of things.  It would be good to be able to cater for  
>> this somehow.
> Just to comment on the last part of this:  It is not our job to  
> provide
> a mapping between HGNC and EntrezGene.  We provide mappings from  
> Ensembl
> objects to HGNC, and to EntrezGene.  That's different.
> Andreas
> -- 
> Andreas Kähäri, Ensembl Software Developer
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD, United Kingdom
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