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As with many other aspects of the modern world, in healthcare, the explosion of data and resources opens new opportunities for the development of added-value services. Still, a number of specific conditions on this domain greatly hinders these developments, including ethical and legal issues, fragmentation of the relevant data in different locations, and a level of (meta)data complexity that requires great expertise across technical, clinical, and biological domains. We propose the Patient Dossier paradigm as a way to organize new innovative healthcare services that sorts the current limitations. The Patient Dossier conceptual framework identifies the different issues and suggests how they can be tackled in a safe, efficient, and responsible way while opening options for independent development for different players in the healthcare sector. An initial implementation of the Patient Dossier concepts in the Rbbt framework is available as open-source at https://github.com/mikisvaz and https://github.com/Rbbt-Workflows. This work has received funding from the Elixir-Excelerate project, from the European Union's Horizon 2020 Research and Innovation Programme, under grant agreement N. 676559, and from Plataforma de Recursos Biomoleculares y Bioinformáticos PT13/0001/0030. Additional support came from the Lenovo - BSC Master Collaboration Agreement (2015) and from the IBM-BSC Deep Learning Centre (2016). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.