The paper presents a brief overview of the challenges facing institutions with the XML-ization of academic journals and the steps being taken in Japan to meet both those challenges with the new J-STAGE3 implementation and a solution for automatically analyzing and converting PDF into XML for JATS metadata and bibliographic information. J-STAGE3 has fully adopted the metadata and bibliographic JATS format. The automated solution is currently achieving more than a 90% accuracy rate and future plans are to expand it to be able to produce full-text XML from PDF.