[Genome] : how is knowntoEnsembl generated?

[Jean Chang]

> Hi,
>
> I'm not able to find anywhere how knowntoEnsembl is generated...
>
> I found this:
>> The hg18 (March 2006/NCBI Build 36.1) knownToEnsembl table was  
>> built in May, 2006 using data downloaded from Ensembl BioMart at  
>> that time.  The hg17 (May 2004/NCBI Build 35.1) knownToEnsembl was  
>> built in May, 2005. We did not log specific Ensembl versions.
>
> But what I'd really like to know is how you create the mapping of  
> genes using the Ensembl BioMart - or if you could point me to how  
> Ensembl says they do it. I took a look at the Biomart and couldn't  
> figure out where you would get those mappings but what I'm looking  
> for is the methods to those mappings.

I tried contacting Biomart about my question above and got the  
following response:

> Apologies, but you will have to ask UCSC that question.  BioMart is a
> tool that extracts data from databases such as Ensembl.  With it, you
> could convert Ensembl gene IDs to IDs in UniProt, Refseq, etc.   
> However
> we don't have a UCSC 'known gene' set.  I would guess they convert
> Ensembl IDs to something else, such as UniProt IDs, then convert those
> to UCSC known genes, but you would have to ask them to be sure.  We  
> are
> not doing the mapping on this end.

Our group is very interested in mirroring the UCSC browser as an  
internal reference source but we need to know more about the mapping  
of knowntoEnsembl and the mapping methodology of a few of the other  
cross-mapped data sets (Affy probe sets, in particular)

Thanks,

Jean