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Modules
 

-  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 - 12.7 ko
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.

 
In the same section
Documentation
Modules
Presentation of BOXml
 
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