[Biojava-l] persistence - and the problems with it

Mark Schreiber mark_s@sanger.otago.ac.nz
Thu, 4 May 2000 09:18:26 +1200 (NZST)

On Wed, 3 May 2000, Gerald Loeffler wrote:

> Thomas Down wrote:
> Regardless of all the niceties of XML, DTDs and handling DOMs from Java,
> we have to face the fact that XML is in essence just another way of
> defining flat file formats - fancy, easy-to-use file formats, granted,
> but flat files nevertheless. As such, an XML representation of an object
> graph suffers from many of the same drawbacks that other flat file
> representations suffer from (especially in contrast to a database
> representation of the same object graph): no datatypes (everything is a
> string); no transaction safety (isolation of access); no query
> capabilities against the data; ...
> Additionally, XML representations tend to be verbous - so you need to
> compress on the fly.
> All this makes XML IMHO a very nice vehicle for the transient, portable,
> platform-neutral representation of data (e.g. for database
> import/export) but makes the idea of building a datastore of objects in
> XML not really much more attractive than it would be in any other flat
> file format.

Along the 'ML lines has anyone ever used UML to make a object database?
I've only ever heard vague things about it and I would like to know what
others experiences are, ie is it worth looking into at all?


Mark Schreiber			Ph: 64 3 4797875
Rm 218				email mark_s@sanger.otago.ac.nz
Department of Biochemistry	email m.schreiber@clear.net.nz
University of Otago		
PO Box 56
New Zealand