NEW YORK, Sept. 27 – DoubleTwist said Thursday that the European Bioinformatics Institute, an outstation of the European Molecular Biology Laboratory, now supports DoubleTwist's genomic annotation XML format, AGAVE.
DoubleTwist made AGAVE (Architecture for Genomic Annotation, Visualization and Exchange) freely available to the life science community in July. Sun Microsystems, the Weizmann Institute of Science, and BioTools have also adopted the standard.
DoubleTwist, based in Oakland, Calif., also released several new data transformation tools and an AGAVE Java library at www.agavexml.org . The AGAVE Java library is a Java object model corresponding to the AGAVE document type definition with methods for parsing and manipulating AGAVE XML.
The EBI is supporting the standard as part of its XEMBL project, an effort to make EMBL nucleotide sequence data available to users in a variety of alternative formats. The project also supports the BSML XML standard developed by LabBook.
Researchers can use the data transformation tools to convert data from publicly available genomics databases such as GenBank, EMBL, and Swiss-Prot into AGAVE format. Converted data can then be used in viewers and programs that support the format.
"We are delighted that organizations such as the EBI have joined the AGAVE community,” said Edward Kiruluta, chief technology officer of DoubleTwist, in a statement. “These partnerships help to make AGAVE an even more robust platform that can enhance collaboration throughout the life sciences community.”
DoubleTwist originally developed AGAVE to build its annotated human genome database and its Prophecy product suite, which includes the database, a query system, and a graphical annotation viewer.