Hi

The BiomaRT can only access Ensemble which have the old version from Xenopus tropicalis. But the updated version(X. tropicalis v9.0 genome assembly)  is available in Xenbase. 

Is there any possibility to update BiomaRT so that we can use files from other data bases also???

Best

Ann

Hi Anne,

I'm afraid biomaRt (the package) doesn't really work like that.  It is designed to provide a way to connect to data stores that are running BioMart (the service) as a way to query their databases.  Ensembl is by far the most widely used of these data stores, but there are many other smaller project also running BioMart instances that you can query using biomaRt e.g. Pancreatic Expression Database or Phytozome.

Unfortunately it doesn't look like Xenbase provide a BioMart service (or any other query API that I can see).  For now I think you will have to either work with the older annotation in Ensembl, or download their data from the FTP site and work with it offline.