[ensembl-dev] mapping between ensembl and other databases

Ewan Birney birney at ebi.ac.uk
Sun Dec 5 21:57:53 GMT 2010


You are taking the Xrefs from NCBI right here, not Ensembl.


These are both NCBI's Xref system, not Ensembl's, and some have them
have been created relatively recently:


CPE carboxypeptidase E [ Bos taurus ]Gene ID: 280753, updated on 26- 
Aug-2010



Ensembl cycles it's Xref code far faster for Human and Mouse (often  
every
release), and the lock down via the CCDS process means that the majority
of genes are consistent both release to release and consistent with NCBI
processes. Still, because of release cycles and processes, there is
always a chance of database skew due to when things are updated.



Outside of Human and Mouse, things are at a lower priority for updates,
so one will see more update/version skew. Unsurprisingly staying inside
of one database system (Ensembl, Entrez, etc) gives far less skew that  
between
database systems.


So - stick within Entrez or stick within Ensembl for maximum  
consistency.




On 5 Dec 2010, at 20:44, Andrea Edwards wrote:

> Hello
>
> I am confused as to why sometimes i can retrieve records from  
> ensembl via an entrezgene id and other times not.
>
> Take this entrezgene id: 441521
> The entry for this record says it is related to 2 ensembl genes
> =========================================== taken from entrezgene  
> record ===========================================
> See related Ensembl:ENSG00000228836; Ensembl:ENSG00000242284; HPRD: 
> 17573; MIM:300796 ==========================================
>
> but this code returns nothing
>
> my @genes = @{$gene_adaptor->fetch_all_by_external_name(441521,  
> "EntrezGene")};
> foreach my $gene  (@genes){
>     print "gene name: ", $gene->stable_id(), "\n";
> }
>
>
> the same code for another gene, 280753, with related ensembl records
> =========================================== taken from entrezgene  
> record ===========================================
> See related Ensembl:ENSBTAG00000016514  
> ===========================================
>
> does return the ensembl gene. I don't know the mappings which  
> determine the whether i can get a gene from ensembl by its entrez  
> gene id
>
> thanks a lot
>
>
>
>
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> Dev at ensembl.org
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