Why won't the RDF-XML file parse using RDF parsers?

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The GO RDF-XML format was originally developed some time ago, before the advent of OWL. It has a few unusual features that render it more of a pseudo-rdf format. The actual RDF is embedded within a xml element - this should be stripped out before handing to RDF parsers. Note that the GO RDF-XML conforms to a DTD, something that is not normally a requirement of RDF. This is because most people parse the file using conventional XML parsers rather than XML tools. We are working on a more up to date RDF representation of GO.