AGAVE - Introduction

AGAVE is an XML format designed to offer the life sciences community a comprehensive, extensible and open format for sharing genomic annotations. It also is the underlying data exchange medium for the DoubleTwist Annotated Human Genome Database, which is available through www.doubletwist.com and through DoubleTwist's Prophecy product suite. AGAVE is provided to the bioinformatics community as open standard. If you are interested in its development, send feedback to info-agave@agavexml.org.

Scope
AGAVE describes the relationship between a contig and its component sequence fragments, the orientation and order of the fragments and the features associated with each sequence fragment. You can visualize data that conform to the AGAVE format using the available DoubleTwist Genomic Viewer.

Goals
The design goals of AGAVE are to provide a comprehensive, extensible, open and readable markup language for genomic annotation. AGAVE is comprehensive because it can represent all the relevant biological data in public databases such as NCBI's GenBank, including the full sequence location format. It is extensible because it uses generic elements for computational results that can easily be used to capture results from new sequence annotation algorithms. Because AGAVE is XML-based, it is easy to use as an open standard for data storage and exchange. You can write programs to manipulate and extract genomic data using standard XML libraries, and you can easily transform data in the AGAVE format from and to other XML-based formats using tools such as XSLT (eXtensible Style Language Transformation). For example, you can easily transform data in GAME format to AGAVE format using XSLT templates. To aid readability, AGAVE focuses on biological data and uses standard biological terminology with a minimum of abbreviation.

Summary of AGAVE Tags
During the development of AGAVE, we placed emphasis on good object-oriented design. The driving criteria were the accurate modeling of the biological concepts for the annotation and visualization of genomic data.

Outline of AGAVE Tags

<sciobj>
    <contig>
       <fragment_order>
          <fragment_orientation>
             <bio_sequence>
                 <sequence_map>
                     <annotations>
                        <seq_feature>
                        </seq_feature>
                        <comp_result> 
                        </comp_result>
                     </annotations>
                  </sequence_map>

Tag	Description
<sciobj>	Top-level container for genomic data
<contig>	Container for ordered and un-ordered fragments
<bio_sequence>	DNA sequence, identifiers, descriptive elements, and annotations
<sequence_map>	A set of annotations on a <bio_sequence>
<annotations>	Collection of annotations on a <bio_sequence>
<seq_feature>	GenBank feature table compliant annotation, predicted genes
<comp_result>	Computational annotation, algorithm results

DoubleTwist Genomic Viewer
The provided DoubleTwist Genomic Viewer is a highly sophisticated data mining and visualization tool with point-and-click functionality for analyzing and visualizing genomic annotations. The Viewer facilitates rapid, interactive discovery and pattern recognition through graphical representation of genomic sequences and related information. This powerful Java-based application allows you to quickly search for items of interest, easily identify splice variations, align your sequences against the genome, integrate feature maps and alignments, and view multiple datasets together.

| |