BOX version 1.0 contains 15 core modules. Here is a brief description of each of them, followed by a figure showing their dependencies.

Module Content

name	description
BoxCore	BOX core types and elements
BoxChemical	types and elements representing chemical compounds and reactions
BoxChemicalKb	root element representing a KB of chemical compounds and reactions
BoxExtChemicalKb	extension of BoxChemicalKb with additional external chemical references
BoxKeggKb	extension of BoxExtChemicalKb for representing KEGG entries (sample)
BoxOrganism	types and elements for representing organisms and taxonomies
BoxOrganismKb	root element for representing a KB of organisms
BoxPathway	types and elements for representing biochemical pathways
BoxPathwayKb	types and elements for representing biochemical pathways
BoxReplicon	types and elements representing replicons (e.g. chromosomes)
BoxLocation	types and elements representing sequence feature locations
BoxFeature	types and elements representing sequence features
BoxSequence	types and elements representing sequence data
BoxBioSequence	types and elements representing biosequences (i.e. sequence data + related biological information)
BoxBioSequenceKb	types and elements representing a KB of biosequences (i.e. sequence data + related biological information + features)

Module dependencies

BOX modules dependencies

Module validation

 All BOX modules (and samples) have been validated using Xerces (version 2.0.2) XSD/XML default parser from Apache software foundation and Java 1.4 on linux and MacOSX.

 UML notations and XML design guidelines are provided in a separate section.