There currently exists no community standardization approach to organize and represent genomic structural variation data with the essential attributes in an interchangeable manner. As transcriptome studies have been widely used for gene fusion discoveries, the current non-standard mode of data representation could potentially impede data accessibility, critical analyses, and further discoveries in the near future.
Now, researchers at the University of Michigan Medical School propose a prototype, Gene Fusion Markup Language (GFML) as an initiative to provide a standard format for organizing and representing the significant features of gene fusion data. GFML will offer the advantage of representing the data in a machine-readable format to enable data exchange, automated analysis interpretation, and independent verification. As this database-independent exchange initiative evolves it will further facilitate the formation of related databases, repositories, and analysis tools.
Availability: The GFML prototype is made available at http://code.google.com/p/gfml-prototype/
- Kalyana-Sundaram S, Shanmugam A, Chinnaiyan AM. (2012) Gene Fusion Markup Language: a prototype for exchanging gene fusion data. BMC Bioinformatics 13(1), 269. [article]