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The design of Ruby RDF API for evolutionary informatics

NeXML is a data format for evolutionary informatics that allows for semantic annotation with RDF triples, thereby providing unparalleled flexibility and extensibility of evolutionary data on the Semantic Web. BioRuby is a fastgrowing toolkit for bioinformatics currently lacking NeXML I/O, and, more generally, an API for triples. In this paper, we design the Ruby API of a NeXML parser and writer for BioRuby, including designing a Ruby RDF API for dealing with RDF triples in BioRuby.