[Biodevelopers] xml database for bioinformatics

[Joseph Landman]

On Sun, 2003-02-23 at 14:59, John Merrells wrote:

> Does your scheme map XML onto a generic or specific relational
> schema? By which I mean does the user have to define a relational
> schema for their XML and then provide a mapping between the
> two... or do you have a generic schema... like a table where each
> row is a node like this...

The idea that I use is that you can generally define your XML structure
in a "schema-like" form (not currently the XML schema, but a simpler
form), or use the first store to define the database structure (not
generally recommended).  Then a parser builds the mapping between simple
data types and columns and nested structures as indexes into other
tables.  Tables are initialized.  Last, it builds the accessors,
queries, and mutators for the data object.  These are auto-loaded to
enable immediate use of the object.

The "schema-like" form is not an XML-Schema (yet).  I am refactoring it
to work with Class::DBI as well as with XML-Schema.

> Where might I find some a sample data, and even better a sample
> set of queries?

Depends upon what you want to do.  Look at the NCBI site, or the BioXML
site.

Joe

-- 
Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman at scalableinformatics.com
  web: http://scalableinformatics.com
phone: +1 734 612 4615