The rapid increase of scientific digital assets in the last years has made clear that digital identifiers are crucial for effectively publishing, accessing and managing digital information in e-science contexts. From persistent keys for access to digital objects in network environments, the concept of persistent identifiers has been more recently extended to identify also physical objects like people, institutions and any type of relevant entity in the e-Science domain, opening the way to the creation of an integrated information space where a network of resources can be resolved, linked, navigated and analyzed, as the Linked Open Data approach envisions for the Web. However, the creation and full exploitation of this valuable network of connections is currently hindered by the fragmentation and lack of coordination of the digital identifier ecosystem. The aim of this paper is to propose an open, distributed and scalable infrastructure for interoperating existing Persistent Identifiers and other digital identifier systems (like Cool URIs) in e-science, overcoming geographical, disciplinary and organizational boundaries. The Digital Identifier interoperability infrastructure is presented as a crosscutting solution of core services enabling interoperability at three different levels: identifier, co-reference and semantic.