BioMart workshop

BioMart is a generic data management system developed jointly by the European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory (CSHL). It arose out of the EnsMart project designed to provide data-mining access to the Ensembl databases. The system can be used with any type of data and it comes with a range of query interfaces and administration tools, including an 'out of the box' website that can be installed, configured and customised according to requirements. The system simplifies the task of creation and maintenance of advanced query interfaces backed by a relational database and it is particularly suited for providing the 'data mining' like searches of complex descriptive (e.g. biological) data. BioMart can work with existing data repositories by converting them to a required BioMart format as well as newly created databases.

This workshop is ideally suited those with a basic computing (command line) background. In the morning there will be a brief introduction to the system followed by worked examples of the MartView website, MartExplorer GUI and MartShell command-line user interfaces. Practical demonstration of the administration tools, MartBuilder and MartEditor will follow. MartBuilder provides a graphical environment for the transformation of any normalised schema into the BioMart denormalised, query-optimised data model. MartEditor is then used to generate the XML configuration which describes the attributes and filters available for these newly created BioMart datasets and how these datasets can be linked with other BioMart datasets for distributed querying. In the afternoon participants will carry out a practical exercise to demonstrate the main aspects of the installing the BioMart system.

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