[Biojava-l] (no subject)

[David Huen]

On Sun, 17 Feb 2002, Gabriel lu wrote:

> I am wondering whether there is an open source for
> retrieving data from public sequence banks (such as
> GenBank) and storing the data into a relational
> database such as an Ms Access. If any, can the binary
> query such as human and Golgi and proteins be
> accepted? If none, I am interested in the development

We don't have software as such to do the task exactly as you describe but
we do have components with which you could construct such a program.

For example, we do have file format readers of various formats that you
could use to read in the release you have downloaded.  In BioSQL you would
have a schema and some basic methods to set up a database (though not
Access specifically - it is more likely to be mySQL, Postgres and poosibly
Oracle.  It is not difficult to extend it to other SQL databases.).

> of such a program. But I am new to biojava. Could you
> please make some suggestion for me to start? Any idea
> concerning this will be appropriated.
> 
If you already know SQL, I would suggest familiarising yourself with the
sequence model in BioJava and also with the SeqIO parts. I haven't used
BioSQL myself yet but I should expect it will be very nice indeed when the
developers are through with it.

You could also attend the bootcamp at the EBI next month if you want a
quick start.  I found this route much less effort myself.

Regards,
David Huen