[ensembl-dev] EntrezGene Synonyms missing since version 88

mag mr6 at ebi.ac.uk
Tue Aug 29 09:04:23 BST 2017

Hi Thomas,

Although we can have symbols from multiple sources associated to the 
same gene, we rank them by order of confidence to select the main symbol 
to use for a gene.
For human, most symbols will be from HGNC and only if no HGNC symbol is 
available will the EntrezGene association be used.

Synonyms should only be available for this primary symbol and not for 
alternate links.
This was not the case before and has been fixed in release 88.
Albeit few, there are cases where HGNC and EntrezGene disagree in the 
gene name, so we believe that having synonyms from EntrezGene that refer 
to a different gene than what the HGNC symbol refers to can be misleading.

This will mostly change the synonyms you can retrieve for human, mouse 
and zebrafish, where an official naming consortium exists.
For other species, EntrezGene is usually the main source for naming 
gene, so synonyms will still be available.

I hope this helps,

On 28/08/2017 17:17, Thomas Danhorn wrote:
> Hi,
> I noticed the the EntrezGene gene name synonyms for mouse, human, and 
> probably other species are missing (empty) since verion 88 (they were 
> present in verion 87; I looked using the REST and Perl APIs).  There 
> are some synonyms in other DBs (MGI, HGNC), but EntrezGene always had 
> the most comprehensive list.  Is there a reason why they are no longer 
> linked to the Ensembl database?
> Thanks,
> Thomas
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