title: Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework.
abstract: In neurosciences or psychiatry, the emergence of large multi-center population imaging studies raises numerous technological challenges. From distributed data collection, across different institutions and countries, to final data publication service, one must handle the massive, heterogeneous, and complex data from genetics, imaging, demographics, or clinical scores. These data must be both efficiently obtained and downloadable. We present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories. In addition, we focus on the tools developed around this framework to overcome the challenges associated with data sharing and collaborative requirements. We describe a set of three highly adaptive web services that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities. Two major European projects, IMAGEN and EU-AIMS, are currently supported by the described framework. We also present a Python package that enables end users to remotely query neuroimaging, genetics, and clinical data from scripts.
authors.affiliation: UNATI, Neurospin, CEA, Université Paris-Saclay , Gif-sur-Yvette , France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Grigis
authors.affiliation: UNATI, Neurospin, CEA, Université Paris-Saclay , Gif-sur-Yvette , France.
authors.forename: David
authors.initials: D
authors.lastname: Goyard
authors.affiliation: UNATI, Neurospin, CEA, Université Paris-Saclay , Gif-sur-Yvette , France.
authors.forename: Robin
authors.initials: R
authors.lastname: Cherbonnier
authors.affiliation: UNATI, Neurospin, CEA, Université Paris-Saclay , Gif-sur-Yvette , France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Gareau
authors.affiliation: UNATI, Neurospin, CEA, Université Paris-Saclay , Gif-sur-Yvette , France.
authors.forename: Dimitri
authors.initials: D
authors.lastname: Papadopoulos Orfanos
authors.affiliation: Logilab , Paris , France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Chauvat
authors.affiliation: Logilab , Paris , France.
authors.forename: Adrien
authors.initials: A
authors.lastname: Di Mascio
authors.affiliation: Medical Research Council, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London , London , UK.
authors.forename: Gunter
authors.initials: G
authors.lastname: Schumann
authors.affiliation: F. Hoffmann-La Roche Pharmaceuticals , Basel , Switzerland.
authors.forename: Will
authors.initials: W
authors.lastname: Spooren
authors.affiliation: King's College London , London , UK.
authors.forename: Declan
authors.initials: D
authors.lastname: Murphy
authors.affiliation: UNATI, Neurospin, CEA, Université Paris-Saclay , Gif-sur-Yvette , France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Frouin
keywords: Python; data sharing; database; genetics; medical informatics; neuroimaging; web service