title: The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.
abstract: Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome.
authors.affiliation: Auckland Bioengineering Institute , The University of Auckland , Auckland , New Zealand.
authors.forename: David
authors.identifier: 0000-0003-4667-9779
authors.initials: D
authors.lastname: Nickerson
authors.affiliation: Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand; National Institute for Health Innovation (NIHI), The University of Auckland, Auckland, New Zealand.
authors.forename: Koray
authors.identifier: 0000-0003-0517-4803
authors.initials: K
authors.lastname: Atalag
authors.affiliation: Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand; Institute of Health Informatics, University College London, London NW1 2DA, UK.
authors.forename: Bernard
authors.identifier: 0000-0003-0638-5274
authors.initials: B
authors.lastname: de Bono
authors.affiliation: Interdisciplinary Bank of Biomaterials and Data , University Hospital Würzburg , Würzburg , Germany.
authors.forename: Jörg
authors.identifier: 0000-0002-7689-531X
authors.initials: J
authors.lastname: Geiger
authors.affiliation: School of Computer Science , University of Manchester , Manchester , UK.
authors.forename: Carole
authors.identifier: 0000-0003-1219-2137
authors.initials: C
authors.lastname: Goble
authors.affiliation: Research Center Plant Genomics and Systems Biology, Universitat Potsdam , Potsdam , Germany.
authors.forename: Susanne
authors.identifier: 0000-0001-9032-2035
authors.initials: S
authors.lastname: Hollmann
authors.affiliation: German Institute for Standardization , Berlin , Germany.
authors.forename: Joachim
authors.identifier: 0000-0002-1048-6943
authors.initials: J
authors.lastname: Lonien
authors.affiliation: Heidelberg Institute for Theoretical Studies (HITS gGmbH) , Heidelberg , Germany.
authors.forename: Wolfgang
authors.identifier: 0000-0002-4980-3512
authors.initials: W
authors.lastname: Müller
authors.affiliation: LifeGlimmer GmbH , Berlin , Germany.
authors.forename: Babette
authors.identifier: 0000-0002-5263-4553
authors.initials: B
authors.lastname: Regierer
authors.affiliation: School of Computer Science , University of Manchester , Manchester , UK.
authors.forename: Natalie J
authors.identifier: 0000-0003-4958-0184
authors.initials: NJ
authors.lastname: Stanford
authors.affiliation: Heidelberg Institute for Theoretical Studies (HITS gGmbH) , Heidelberg , Germany.
authors.forename: Martin
authors.identifier: 0000-0002-8683-7084
authors.initials: M
authors.lastname: Golebiewski
authors.affiliation: Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
authors.forename: Peter
authors.identifier: 0000-0001-9665-4145
authors.initials: P
authors.lastname: Hunter
keywords: Human Physiome; managing big data; repositories; reproducible science; service infrastructure; standards