6.9 years ago by
I looked into this myself before I resigned myself to using the Perl APIs. I wouldn't be too down on them as they have a lot of functionality (but still depend on BioPerl1.5 !).
You can access the Ensembl database directly through their MySQL server, but building the queries for the very complex schema is very time consuming. I can see them coming under increasing pressure to provide support for other languages (Python certainly would be very popular) but they have a lot of work to do as it is and I think an initiative like that would probably require extra funding.
You can access the MySQL server using the details here http://www.ensembl.org/info/data/mysql.html