BioMart version 0.5 released

From an email sent to the gmod-announce mailing list by Arek Kasprzyk:

BioMart 0.5, a new version of the query-oriented data management system
has been released. The new release comes with a number of new features


BioMart web code has been re-implemented in order to make it easier to
up and run queries. Filters and attributes now come in collapsible
considerably improving the scalability of the interface. The handling of
two dataset queries has been much improved. It is now possible to
attributes as well as filters in such queries which makes it possible to
fully annotate a local dataset with a remote one. Customization of
including colour schemes, result file handling, logging options etc is
much easier to manage in the new code. Finally it is now possible to use
the webcode with apache 2 as well as apache 1.


The first version of a new tool for creating BioMart compatible schemas
from existing relational data sources has been included in this release.
It makes the task of designing, creating and managing the schema
transformation straightforward. MartBuilder allows you to select the
central table of interest in a database and automatically design
based around that central table. It follows the BioMart transformation
guidelines and naming conventions and will generate SQL statements that
you can execute to perform the actual transformation.


The Web service and Perl APIs have been considerably simplified in terms
of user friendliness. The Perl API and Web service follow exactly the
simple query building pattern used by MartView. In addition it is now
possible to find all the necessary attribute and filter internal names
building a query with one click of the MartView XML button.


MartShell now comes with auto-completion and command line history on
linux, mac and windows.

All the code and documentation is freely available and can be downloaded
from and the new web interface is accessible at

On behalf of the BioMart team,
Arek Kasprzyk

Posted by Scott Cain 2006-11-29

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