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06/12/2005 Archived Entry: "Unlocking the genome with perl, XML and SQL by Chris Mungall"

Perpetual Entertainment is proud to host the SF Perl Users' Group.

This month, Chris Mungall, author of such modules as Data-Stag, will give a talk on XML <-> SQL Mapping Tools.

Chris Mungall works for the Howard Hughes Medical Institute at UC Berkeley as a bioinformatics researcher
specializing in databases and bio-ontologies. Chris is from Scotland, where he attended theUniversity of Edinburgh
and subsequently worked at the Roslin Institute alongside the world-famous Dolly the Sheep.

If you plan to attend, RSVP ASAP to dfetter@perpetual.com because

1. Security will need your name in order to let you in.
2. I need to know how much pizza to order.
3. It's nice to be considerate and help with capacity planning.

Date: Tuesday, June 28th

Details below.

Time: 8:00pm

Place: Perpetual Entertainment
149 New Montgomery Street
5th Floor
San Francisco

Parking in downtown San Francisco around 8:00pm is doable, but leave yourself some time. You're probably best off arriving via BART to Montgomery station. Caltrain is not recommended, as they have two trains running south between 10:00 and midnight.

More on the talk:

Within the many trillions of cells making up our bodies sits a
molecule known as DNA, encoding the blueprint for life itself. The
quest to understand this blueprint has generated vast quantities of
complex and diverse data, much of it in the public domain. The
discipline of analysing and integrating this data is known as
bioinformatics, and encompasses a wide arsenal of techniques. Amongst
these is the use of perl, SQL databases and XML, the workhorses of
bioinformatics data management.

Perl object models, relational database schemas and XML
representations are popular choices for modeling complex data in
bioinformatics (and in information technology as a whole). It is rare
for the three to be integrated in any formal way; hacks and kludges
abound. The two perl modules, Data::Stag and DBIx::DBStag, attempt to
address this situation.

Data::Stag is a module for manipulating data modeled using
hierarchical formalisms such as XML, and provides a convenient
object-oriented syntax for such XML and XML-like data. It also
provides searches using a powerful functional query composition
method. Data::Stag can be used independently of any database.

DBIx::DBStag is a module for mapping back and forth between SQL data
and either Stag objects or XML. Unlike many object-relational mapping
tools, it does not attempt to shield the module user from the
complexity of the underlying relational database and SQL queries;
rather it seeks to enhance SQL. This makes it ideal for sophisticated
data mining queries. DBIx::DBStag also has a templating system to
facilitate reuse of common query patterns.

Together, these tools have benefited our group in Berkeley, in
particular, our research on the evolution of gene structure in insects
and in our work building production databases for the biological
community.