We present the ABLE document collection, which consists of a set of annotated volumes of the Bulletin of the British Museum (Natural History). These were developed during our ongoing work on automating the markup of scanned copies of the biodiversity literature. Such automation is required if historic literature is to be used to inform contemporary issues in biodiversity research. We consider an enhanced TEI XML markup language, which is used as an intermediate stage in translating from the initial XML obtained from Optical Character Recognition to taXMLit, the target annotation schema. The intermediate representation allows additional information from external sources such as a taxonomic thesaurus to be incorporated before the final translation into taXMLit. We give an overview of the project workflow in automating the markup process, and consider what extensions to existing markup schema will be required to best support working taxonomists. Finally, we discuss some of the particular issues which were encountered in converting between different XML formats.